bluuebunny/crossref_metadata_2025 huggingface dataset:
Mechanisms for the far-infrared absorption in liquid methane
Authors: Lozano N. B. Huamán , Stassen H.
Published: March 2009

The time correlation function for the induced dipole moment in liquid methane was computed from molecular dynamics computer simulations for a thermodynamic state at a temperature of 122.2 K and density of 25.34 mol/l. We included first-order induction mechanisms from the electric fields emanated by octupole and hexadecapole moments, their field gradients, as well as electronic superposition. The octupole-induced dipole represents the most important contribution to the far-infrared absorption spectrum. However, additional mechanisms are important for absorption in liquid methane. By comparing the computed absorption line shape with the experimental spectrum, we found a very satisfactory agreement between the two if we account for detailed balancing.
Electrostatic correlations in colloidal suspensions: Density profiles and effective charges beyond the Poisson–Boltzmann theory
Authors: dos Santos Alexandre P. , Diehl Alexandre , Levin Yan
Published: March 2009

A theory is proposed which allows us to calculate the distribution of the multivalent counterions around a colloidal particle using the cell model. The results are compared with the Monte Carlo simulations and are found to be very accurate in the two asymptotic regimes, close to the colloidal particle and far from it. The theory allows to accurately calculate the osmotic pressure and the effective charge of colloidal particles with multivalent counterions.
Osmotic pressure and virial coefficients of star and comb polymer solutions: Dissipative particle dynamics
Authors: Wang Tzu-Yu , Fang Che-Ming , Sheng Yu-Jane , Tsao Heng-Kwong
Published: March 2009

The effects of macromolecular architecture on the osmotic pressure π and virial coefficients (B2 and B3) of star and comb polymers in good solvents are studied by dissipative particle dynamics simulations for both dilute and semiconcentrated regimes. The dependence of the osmotic pressure on polymer concentration is directly calculated by considering two reservoirs separated by a semipermeable, fictitious membrane. Our simulation results show that the ratios An+1≡Bn+1/R̂g3n are essentially constant and A2 and A3 are arm number (f) dependent, where R̂g is zero-density radius of gyration. The value of dimensionless virial ratio g=A3/A22 increases with arm number of stars whereas it is essentially arm number independent for comb polymers. In semiconcentrated regime the scaling relation between osmotic pressure and volume fraction, π∝φλ, still holds for both star and comb polymers. For comb polymers, the exponent λ is close to λ∗ (≈2.73 for linear chains) and is independent of the arm number. However, for star polymers, the exponent λ deviates from λ∗ and actually grows with increasing the arm number. This may be attributed to the significant ternary interactions near the star core in the many-arm systems.
Structural change of ionic association in ionic liquid/water mixtures: A high-pressure infrared spectroscopic study
Authors: Umebayashi Yasuhiro , Jiang Jyh-Chiang , Shan Yu-Lun , Lin Kuan-Hung , Fujii Kenta , Seki Shiro , Ishiguro Shin-Ichi , Lin Sheng Hsien , Chang Hai-Chou
Published: March 2009

High-pressure infrared measurements were carried out to observe the microscopic structures of two imidazolium-based ionic liquids, i.e., 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)amide [EMI+(CF3SO2)2N−, EMI+TFSA−] and 1-ethyl-3-methylimidazolium bis(fluorosulfonyl)amide [EMI+(FSO2)2N−, EMI+FSA−]. The results obtained at ambient pressure indicate that the imidazolium C–H may exist in two different forms, i.e., isolated and network structures. As the sample of pure EMI+FSA− was compressed, the network configuration is favored with increasing pressure by debiting the isolated form. For EMI+TFSA−/H2O mixtures, the imidazolium C–H peaks split into four bands at high pressures. The new spectral features at approximately 3117 and 3190 cm−1, being concentration sensitive, can be attributed to the interactions between the imidazolium C–H and water molecules. The alkyl C–H absorption exhibits a new band at approximately 3025 cm−1 under high pressures. This observation suggests the formation of a certain water structure around the alkyl C–H groups. The O–H stretching absorption reveals two types of O–H species, i.e., free O–H and bonded O–H. For EMI+TFSA−/H2O mixtures, the compression leads to a loss of the free O–H band intensities, and pressure somehow stabilizes the bonded O–H configurations. The results also suggest the non-negligible roles of weak hydrogen bonds in the structure of ionic liquids.
Metal-semiconductor-metal TiO2 ultraviolet detectors with Ni electrodes
Authors: Kong Xiangzi , Liu Caixia , Dong Wei , Zhang Xindong , Tao Chen , Shen Liang , Zhou Jingran , Fei Yongfeng , Ruan Shengping
Published: March 2009

In this letter, metal-semiconductor-metal (MSM) TiO2 ultraviolet (UV) detectors with Ni electrodes have been fabricated. TiO2 thin films were prepared by sol-gel method. At 5 V bias, the dark current of the detector with Ni electrode was 1.83 nA. High photoresponse of 889.6 A/W was found under irradiation of 260 nm UV light, which was much higher than those of other wide bandgap UV detectors with MSM structure. The high photoresponse was due to the great internal gain caused by the hole trapping at interface. The rise time of the device was 13.34 ms and the fall time was 11.43 s.
Temperature- and field-dependent leakage current of epitaxial YMnO3/GaN heterostructure
Authors: Wu H. , Yuan J. , Peng T. , Pan Y. , Han T. , Liu C.
Published: March 2009

Epitaxial ferroelectric YMnO3 (YMO) thin films were fabricated on (0001) GaN substrates by pulsed laser deposition followed by rapid thermal annealing. The temperature and field dependence of the leakage current of YMO/GaN interface was studied in a temperature range from 150 to 300 K and for an applied voltage up to 10 V. In a low temperature region from 180 to 220 K, the YMO/GaN interface acted as a Schottky barrier with a height of 0.27 eV for a field below 1.4 MV/cm, while the leakage mechanism was governed by the Fowler–Nordheim tunneling for a field above 1.4 MV/cm. Moreover, a space-charge-limited-current behavior was observed in a high field for a temperature above 270 K, while an Ohmic behavior was observed in a low field. In comparison, the dominant leakage mechanism of In/YMO interface was an Ohmic behavior in the whole measured voltage and temperature ranges.
High-speed switching of spin polarization for proposed spin-photon memory
Authors: Zayets V. , Ando K.
Published: March 2009

Nonvolatile high-speed optical memory is proposed, which utilizes the magnetization reversal of nanomagnet by spin-polarized photoexcited electrons. It was demonstrated experimentally that one selected pulse from the train of two optical data pulses with interval of 450 fs can solely excite the spin-polarized electrons without a disturbance from the unselected optical data pulse. That proves feasibility for operation of the memory with speed of 2.2 Tbits/s.
Europe as Borderland
Authors: Balibar Etienne
Published: March 2009

The discussion in this paper moves through three stages. In the first the relation of political spaces and borders to citizenship is interrogated; in the second, notions of deterritorialization and reterritorialization are examined in relation to ideas of the material constitution of Europe; and, in the third section it returns to the issue of citizenship and its relation to cosmopolitanism. Rather than being a solution or a prospect, Europe currently exists as a ‘borderland’, and this raises a number of issues that need to be confronted.
Geographies of Geborgenheit: Beyond Feelings of Safety and the Fear of Crime
Authors: Hutta J Simon
Published: March 2009

This paper critically engages with the concepts of ‘feelings of safety’ and ‘fear of crime’ as they have been deployed in recent politics of community safety. While the first part of the paper discusses the staging of what is referred to as a dispositif of safety, which discursively frames subjective–spatial relations in powerful ways, the second part moves towards an understanding of lived experiences of spaces and places that unfold within, but also beyond, the dispositif of safety. For this purpose, the German concept of Geborgenheit is introduced. For a theoretical elaboration of this concept, Walter Benjamin's work around experience and temporality is referred to and articulated with Deleuzian theory. An analysis of Geborgenheit, it is argued, displaces hegemonic notions of ‘safety’ by addressing the dynamics that enable subjects to open up to and nest within a place. The paper concludes with a discussion of vignettes from a qualitative study in Berlin in order to exemplify the constitution of geographies of Geborgenheit in the context of recent safety politics.
Justice and the Geographies of Moral Protest: Reflections from Mexico
Authors: Wright Melissa W
Published: March 2009

Protest movements offer a rich vernacular for investigating how the connections between social justice and creating political subjects always involve spatial transformations. In this paper, I put Jacques Derrida's contemplations regarding justice as incalculable in conversation with critiques of public witnessing and the role of empathy for catalyzing political action, and I do so to present some speculations over why a social justice movement in northern Mexico has weakened domestically as it has gained steam internationally. The movement has grown since 1993 in response to the violence against women and girls and the surrounding impunity that has made northern Mexico famous as a place of ‘femicide’. By examining these events in relation to the debates on calculating justice and on the politics of witnessing, I hope to add to the growing literature within and beyond geography on the interplay of emotion and social justice politics while illustrating what is at stake in these dynamics for Mexico's democracy and for women's participation in it.
Refugee Registration as Foreclosure of the Freedom to Move: The Virtualisation of Refugees' Rights within Maps of International Protection
Authors: Franke Mark F N
Published: March 2009

The lack of solid footing in political space is what makes the human rights claims of refugees most vulnerable in the contemporary international order. However, modern international human rights law and protection are predicated on a spatialised sense of the subject of rights that is formed in opposition to and in exclusion of the refugee. The United Nations High Commissioner for Refugees (UNHCR) seeks to locate refugees as part of the universe of human rights through refugee registration exercises; it attempts to map their displacement within the geography of emplaced citizenry. Its conventional efforts in this regard fail, though, and, rather, serve to illustrate how the informal international movement of refugees still exceeds and, thus, undermines the universalism of the UN vision of human rights and freedoms. Consequently, the UNHCR has recently resorted to the highly sophisticated computerised registration technology, called proGres, under its Project Profile system. While the detail and complexity of Project Profile allow for a mapping no more capable of accurately tracing the movements of refugees within the global geography of universal human rights, the complex of digitalised mapping systems brought together within Project Profile permit the production and performance of an international space in which humanitarians may expect refugees to fit. The force of the UNHCR's new registration system is to produce a manner of spatialising refugees that can legitimate and moralise their constraint within orders of international politics and security which allow little room for response to the rights claims of refugees. Rather, their claims to human rights become foreclosed within a virtual understanding of human displacement with respect to emplacement in the state.
Gonadal morphology of the weedy seadragon, Phyllopteryx taeniolatus (Lacépède): characterisation of ovarian and testicular maturation
Authors: Forsgren K. L. , Young K. A.
Published: March 2009

Because little is known about the reproductive biology of the weedy seadragon, Phyllopteryx taeniolatus, we sought to characterise for the first time the morphology and histology of the gonads of female and male weedy seadragons. Each seadragon ovary consisted of a pair of cylindrical tubes with a total of four tubes per female with follicles arranged with less mature oocytes originating from the germinal ridge and progressively more advanced oocytes occurring in a spiral fashion around the periphery of less-developed oocytes. Seadragon testes had a system of interconnecting seminiferous tubules with spermatocyte development occurring within the tubule. Spermatocytes were observed along the testis wall and appeared to emerge into the lumen where further development of spermatocytes occurred. This study represents the first examination of the gonadal structures of the weedy seadragon, a species currently classified by the International Union for Conservation of Nature (IUCN) as ‘Near Threatened’. The descriptions of morphological development of the gonads may be useful in the histological identification of the stages of gametogenesis and reproductive status of other syngnathids. In addition, this information may also provide useful information in elucidating the phylogeny of this family of fishes.
Age structure, mortality and breeding in a population of agile wallabies (Macropus agilis)
Authors: Stirrat Simon C.
Published: March 2009

Aspects of the demography of the agile wallaby (Macropus agilis) were investigated in an overabundant population in East Point Reserve, Darwin. The maximum wet-season population size was relatively stable for several years before, and during, this study. Data suggest that the population fluctuated in size seasonally. Life table analysis indicated that mortality of animals up to 18 months old (including pouch young and young-at-foot) was high compared with adult mortality rates. After 18 months of age, mortality rates of males increased throughout life whereas those of females declined slightly and were relatively stable in older age classes. Females reproduced throughout the year, but more large pouch young were observed in the wet season than at other times of the year. The sex ratio of the population was female-biased, probably a result of higher mortality of males in the dry season. Predation by dogs was documented but contributed a relatively small fraction of total annual mortality.
Clutch parameters and reproductive success of a translocated population of red-crowned parakeet (Cyanoramphus novaezelandiae)
Authors: Ortiz-Catedral Luis , H. Brunton Dianne
Published: March 2009

At least four populations of the red-crowned parakeet (Cyanoramphus novaezelandiae) have been established via translocation within New Zealand over the last 40 years, but reproductive parameters of these populations have not been documented. We quantified differences in clutch parameters and reproductive success for a translocated population of this species on Tiritiri Matangi Island over two breeding seasons. Overall clutch parameters and estimates of reproductive success were consistent with reported values from natural populations. However, we found previously unreported differences in clutch size, hatching success and brood size between breeding seasons. The number of fledglings produced per breeding pair increased significantly from 1.4 to 3.4 fledglings during our two-year study. In contrast, egg volume and fertility per clutch did not vary during the same period. Overall, 7 eggs were laid per breeding pair but only 2.22 nestlings fledged, representing a 63.8% loss of initial reproductive potential. Losses during the incubation stage were caused by partial and total hatching failure, whereas starvation of nestlings caused all losses during the brood-rearing stage. Hatching success during our study was lower than that reported for wild populations of this and other parrot species, and remained lower even during the most productive breeding season. We found no cases of predation on eggs or nestlings during our study despite the presence of native and exotic avian predators on Tiritiri Matangi Island. We show that clutch size, brood size and changes in loss between breeding seasons are determinants of reproductive output in translocated red-crowned parakeet and also that reproductive output can vary greatly between breeding seasons. Finally, if reduced hatching success is the result of small founder size, management of parakeets should consider the movement of larger and more genetically diverse flocks.
Early modern human diversity suggests subdivided population structure and a complex out-of-Africa scenario
Authors: Gunz Philipp , Bookstein Fred L. , Mitteroecker Philipp , Stadlmayr Andrea , Seidler Horst , Weber Gerhard W.
Published: March 2009

The interpretation of genetic evidence regarding modern human origins depends, among other things, on assessments of the structure and the variation of ancient populations. Because we lack genetic data from the time when the first anatomically modern humans appeared, between 200,000 and 60,000 years ago, instead we exploit the phenotype of neurocranial geometry to compare the variation in early modern human fossils with that in other groups of fossil
Homo
and recent modern humans. Variation is assessed as the mean-squared Procrustes distance from the group average shape in a representation based on several hundred neurocranial landmarks and semilandmarks. We find that the early modern group has more shape variation than any other group in our sample, which covers 1.8 million years, and that they are morphologically similar to recent modern humans of diverse geographically dispersed populations but not to archaic groups. Of the currently competing models of modern human origins, some are inconsistent with these findings. Rather than a single out-of-Africa dispersal scenario, we suggest that early modern humans were already divided into different populations in Pleistocene Africa, after which there followed a complex migration pattern. Our conclusions bear implications for the inference of ancient human demography from genetic models and emphasize the importance of focusing research on those early modern humans, in particular, in Africa.
Agricultural origins and the isotopic identity of domestication in northern China
Authors: Barton Loukas , Newsome Seth D. , Chen Fa-Hu , Wang Hui , Guilderson Thomas P. , Bettinger Robert L.
Published: March 2009

Stable isotope biochemistry (δ
13
C and δ
15
N) and radiocarbon dating of ancient human and animal bone document 2 distinct phases of plant and animal domestication at the Dadiwan site in northwest China. The first was brief and nonintensive: at various times between 7900 and 7200 calendar years before present (calBP) people harvested and stored enough broomcorn millet (
Panicum miliaceum
) to provision themselves and their hunting dogs (
Canis
sp.) throughout the year. The second, much more intensive phase was in place by 5900 calBP: during this time both broomcorn and foxtail (
Setaria viridis
spp
. italica
) millets were cultivated and made significant contributions to the diets of people, dogs, and pigs (
Sus
sp.). The systems represented in both phases developed elsewhere: the earlier, low-intensity domestic relationship emerged with hunter–gatherers in the arid north, while the more intensive, later one evolved further east and arrived at Dadiwan with the Yangshao Neolithic. The stable isotope methodology used here is probably the best means of detecting the symbiotic human–plant–animal linkages that develop during the very earliest phases of domestication and is thus applicable to the areas where these connections first emerged and are critical to explaining how and why agriculture began in East Asia.
Binding of an octylglucoside detergent molecule in the second substrate (S2) site of LeuT establishes an inhibitor-bound conformation
Authors: Quick Matthias , Winther Anne-Marie Lund , Shi Lei , Nissen Poul , Weinstein Harel , Javitch Jonathan A.
Published: March 2009

The first crystal structure of the neurotransmitter/sodium symporter homolog LeuT revealed an occluded binding pocket containing leucine and 2 Na
+
; later structures showed tricyclic antidepressants (TCAs) in an extracellular vestibule ≈11 Å above the bound leucine and 2 Na
+
. We recently found this region to be a second binding (S2) site and that binding of substrate to this site triggers Na
+
-coupled substrate symport. Here, we show a profound inhibitory effect of
n
-octyl-β-
d
-glucopyranoside (OG), the detergent used for LeuT crystallization, on substrate binding to the S2 site. In parallel, we determined at 2.8 Å the structure of LeuT-E290S, a mutant that, like LeuT-WT, binds 2 substrate molecules. This structure was similar to that of WT and clearly revealed an OG molecule in the S2 site. We also observed electron density at the S2 site in LeuT-WT crystals, and this also was accounted for by an OG molecule in that site. Computational analyses, based on the available crystal structures of LeuT, indicated the nature of structural arrangements in the extracellular region of LeuT that differentiate the actions of substrates from inhibitors bound in the S2 site. We conclude that the current LeuT crystal structures, all of which have been solved in OG, represent functionally blocked forms of the transporter, whereas a substrate bound in the S2 site will promote a different state that is essential for Na
+
-coupled symport.
Pleasant music overcomes the loss of awareness in patients with visual neglect
Authors: Soto David , Funes María J. , Guzmán-García Azucena , Warbrick Tracy , Rotshtein Pia , Humphreys Glyn W.
Published: March 2009

During the past 20 years there has been much research into the factors that modulate awareness of contralesional information in neurological patients with visual neglect or extinction. However, the potential role of the individual's emotional state in modulating awareness has been largely overlooked. In the current study, we induced a pleasant and positive affective response in patients with chronic visual neglect by allowing them to listen to their pleasant preferred music. We report that the patients showed enhanced visual awareness when tasks were performed under preferred music conditions relative to when tasks were performed either with unpreferred music or in silence. These results were also replicated when positive affect was induced before neglect was tested. Functional MRI data showed enhanced activity in the orbitofrontal cortex and the cingulate gyrus associated with emotional responses when tasks were performed with preferred music relative to unpreferred music. Improved awareness of contralesional (left) targets with preferred music was also associated with a strong functional coupling between emotional areas and attentional brain regions in spared areas of the parietal cortex and early visual areas of the right hemisphere. These findings suggest that positive affect, generated by preferred music, can decrease visual neglect by increasing attentional resources. We discuss the possible roles of arousal and mood in generating these effects.
Auditory recognition memory is inferior to visual recognition memory
Authors: Cohen Michael A. , Horowitz Todd S. , Wolfe Jeremy M.
Published: March 2009

Visual memory for scenes is surprisingly robust. We wished to examine whether an analogous ability exists in the auditory domain. Participants listened to a variety of sound clips and were tested on their ability to distinguish old from new clips. Stimuli ranged from complex auditory scenes (e.g., talking in a pool hall) to isolated auditory objects (e.g., a dog barking) to music. In some conditions, additional information was provided to help participants with encoding. In every situation, however, auditory memory proved to be systematically inferior to visual memory. This suggests that there exists either a fundamental difference between auditory and visual stimuli, or, more plausibly, an asymmetry between auditory and visual processing.
An intertidal snail shows a dramatic size increase over the past century
Authors: Fisher Jonathan A. D. , Rhile Erika C. , Liu Harrison , Petraitis Peter S.
Published: March 2009

Changes in the shell architecture of marine snails enhance defenses and greatly improve survival against predators. In the northwest Atlantic Ocean, shorter and thicker shells have been reported for several species following the introduction of predatoryCarcinus maenascrabs early in the 20th century. But we report that the shell lengths ofNucella lapillusactually increased by an average of 22.6% over the past century, with no evidence of shell thickening after correcting for shell length. The increases in shell length were greatest on sheltered shores, highlighting the interaction between wave exposure and the sampling period. Comparisons were based on archived shells collected in 1915–1922 from sites that were resampled in 2007.N. lapillusis an important member of North Atlantic marine ecosystems, and our results suggest that the impacts of historical changes in species' key morphological traits on marine ecosystems remain underappreciated.
The cultural and chronological context of early Holocene maize and squash domestication in the Central Balsas River Valley, Mexico
Authors: Ranere Anthony J. , Piperno Dolores R. , Holst Irene , Dickau Ruth , Iriarte José
Published: March 2009

Molecular evidence indicates that the wild ancestor of maize is presently native to the seasonally dry tropical forest of the Central Balsas watershed in southwestern Mexico. We report here on archaeological investigations in a region of the Central Balsas located near the Iguala Valley in Guerrero state that show for the first time a long sequence of human occupation and plant exploitation reaching back to the early Holocene. One of the sites excavated, the Xihuatoxtla Shelter, contains well-stratified deposits and a stone tool assemblage of bifacially flaked points, simple flake tools, and numerous handstones and milling stone bases radiocarbon dated to at least 8700 calendrical years B.P. As reported in a companion paper (Piperno DR, et al., in this issue of PNAS), starch grain and phytolith residues from the ground and chipped stone tools, plus phytoliths from directly associated sediments, provide evidence for maize (
Zea mays
L.) and domesticated squash (
Cucurbita
spp.) in contexts contemporaneous with and stratigraphically below the 8700 calendrical years B.P. date. The radiocarbon determinations, stratigraphic integrity of Xihuatoxtla's deposits, and characteristics of the stone tool assemblages associated with the maize and squash remains all indicate that these plants were early Holocene domesticates. Early agriculture in this region of Mexico appears to have involved small groups of cultivators who were shifting their settlements seasonally and engaging in a variety of subsistence pursuits.
The role of symmetry in the mass independent isotope effect in ozone
Authors: Michalski Greg , Bhattacharya S. K.
Published: March 2009

Understanding the internal distribution of “anomalous” isotope enrichments has important implications for validating theoretical postulates on the origin of these enrichments in molecules such as ozone and for understanding the transfer of these enrichments to other compounds in the atmosphere via mass transfer. Here, we present an approach, using the reaction NO
2
−
+ O
3
, for assessing the internal distribution of the Δ
17
O anomaly and the δ
18
O enrichment in ozone produced by electric discharge. The Δ
17
O results strongly support the symmetry mechanism for generating mass independent fractionations, and the δ
18
O results are consistent with published data. Positional Δ
17
O and δ
18
O enrichments in ozone can now be more effectively used in photochemical models that use mass balance oxygen atom transfer mechanisms to infer atmospheric oxidation chemistry.
Longitudinal trajectories of non-rapid eye movement delta and theta EEG as indicators of adolescent brain maturation
Authors: Campbell Ian G. , Feinberg Irwin
Published: March 2009

It is now recognized that extensive maturational changes take place in the human brain during adolescence, and that the trajectories of these changes are best studied longitudinally. We report the first longitudinal study of the adolescent decline in non-rapid eye movement (NREM) delta (1–4 Hz) and theta (4–8 Hz) EEG. Delta and theta are the homeostatic frequencies of human sleep. We recorded sleep EEG in 9- and 12-year-old cohorts twice yearly over a 5-year period. Delta power density (PD) was unchanged between age 9 and 11 years and then fell precipitously, decreasing by 66% between age 11 and 16.5 years (
P
< .000001). The decline in theta PD began significantly earlier than that in delta PD and also was very steep (by 60%) between age 11 and 16.5 years (
P
< .000001). These data suggest that age 11–16.5 years is a critically important maturational period for the brain processes that underlie homeostatic NREM EEG, a finding not suggested in previous cross-sectional data. We hypothesize that these EEG changes reflect synaptic pruning. Comparing our data with published longitudinal declines in MRI-estimated cortical thickness suggests the theta age curve parallels the earlier maturational thinning in 3-layer cortex, whereas the delta curve tracks the later changes in 5-layer cortex. This comparison also reveals that adolescent declines in NREM delta and theta are substantially larger than decreases in cortical thickness (>60% vs. <20%). The magnitude, interindividual difference, and tight link to age of these EEG changes indicate that they provide excellent noninvasive tools for investigating neurobehavioral correlates of adolescent brain maturation.
A family of thermostable fungal cellulases created by structure-guided recombination
Authors: Heinzelman Pete , Snow Christopher D. , Wu Indira , Nguyen Catherine , Villalobos Alan , Govindarajan Sridhar , Minshull Jeremy , Arnold Frances H.
Published: March 2009

SCHEMA structure-guided recombination of 3 fungal class II cellobiohydrolases (CBH II cellulases) has yielded a collection of highly thermostable CBH II chimeras. Twenty-three of 48 genes sampled from the 6,561 possible chimeric sequences were secreted by the
Saccharomyces cerevisiae
heterologous host in catalytically active form. Five of these chimeras have half-lives of thermal inactivation at 63 °C that are greater than the most stable parent, CBH II enzyme from the thermophilic fungus
Humicola insolen
s, which suggests that this chimera collection contains hundreds of highly stable cellulases. Twenty-five new sequences were designed based on mathematical modeling of the thermostabilities for the first set of chimeras. Ten of these sequences were expressed in active form; all 10 retained more activity than
H. insolens
CBH II after incubation at 63 °C. The total of 15 validated thermostable CBH II enzymes have high sequence diversity, differing from their closest natural homologs at up to 63 amino acid positions. Selected purified thermostable chimeras hydrolyzed phosphoric acid swollen cellulose at temperatures 7 to 15 °C higher than the parent enzymes. These chimeras also hydrolyzed as much or more cellulose than the parent CBH II enzymes in long-time cellulose hydrolysis assays and had pH/activity profiles as broad, or broader than, the parent enzymes. Generating this group of diverse, thermostable fungal CBH II chimeras is the first step in building an inventory of stable cellulases from which optimized enzyme mixtures for biomass conversion can be formulated.
Nanotechnology approach for drug addiction therapy: Gene silencing using delivery of gold nanorod-siRNA nanoplex in dopaminergic neurons
Authors: Bonoiu Adela C. , Mahajan Supriya D. , Ding Hong , Roy Indrajit , Yong Ken-Tye , Kumar Rajiv , Hu Rui , Bergey Earl J. , Schwartz Stanley A. , Prasad Paras N.
Published: March 2009

Drug abuse is a worldwide health concern in which addiction involves activation of the dopaminergic signaling pathway in the brain. Here, we introduce a nanotechnology approach that utilizes gold nanorod-DARPP-32 siRNA complexes (nanoplexes) that target this dopaminergic signaling pathway in the brain. The shift in the localized longitudinal plasmon resonance peak of gold nanorods (GNRs) was used to show their interaction with siRNA. Plasmonic enhanced dark field imaging was used to visualize the uptake of these nanoplexes in dopaminergic neurons in vitro. Gene silencing of the nanoplexes in these cells was evidenced by the reduction in the expression of key proteins (DARPP-32, ERK, and PP-1) belonging to this pathway, with no observed cytotoxicity. Moreover, these nanoplexes were shown to transmigrate across an in vitro model of the blood–brain barrier (BBB). Therefore, these nanoplexes appear to be suited for brain-specific delivery of appropriate siRNA for therapy of drug addiction and other brain diseases.
Oxidative stress but not endothelial dysfunction exists in non‐obese, young group of patients with polycystic ovary syndrome
Authors: KUŞÇU NACI KEMAL , VAR AHMET
Published: March 2009

Objective. To determine if oxidative stress and endothelial dysfunction exist at the same time in a young, non‐obese group of patients with polycystic ovary syndrome (PCOS). Design. Cross‐sectional study. Setting. Celal Bayar University, School of Medicine, Manisa, Turkey. Sample. Thirty‐one young, non‐obese patients with PCOS and 23 age‐ and body mass index‐matched controls. Methods. Following clinical and biochemical diagnosis, malonyldialdehyde (MDA), superoxide dismutase (SOD), von Willebrand Factor (vWF), and nitric oxide (NO) levels of patients and controls were measured and compared. Main outcome measures. To find out oxidative stress and endothelial dysfunction parameters. Results. MDA (0.12±0.03 vs 0.10±0.03, p = 0.01) and SOD (8.0±0.7 vs 7.28±0.8, p = 0.001) levels were significantly higher in PCOS group while there was no difference in vWF (527.2±280.1 vs 568.1±276.8, p>0.05) and NO levels (169.9±47.4 vs 168.9±80, p>0.05). When the results of the PCOS patients were divided into two subgroups in terms of insulin resistance (IR– and IR +), the IR– subgroup had significantly higher MDA levels compared to the control (0.125±0.03 vs 0.101±0.03, p = 0.03). Though IR+ group also had higher MDA than the control group, it did not reach to a significant level (0.117±0.05 vs 0.101±0.03, p>0.05). Both IR– and IR+ groups had significantly higher SOD levels compared with control group (7.99±0.7 vs 7.28±0.8, p = 0.009 and 8.22±0.8 vs 7.28±0.8, p = 0.03, respectively). vWF and NO levels were not different among these three groups (p>0.05). Conclusions. Oxidative stress is prominent while endothelial dysfunction does not exist in young, non‐obese patients with PCOS.
Towards a Methodical Approach to Implement Biomimetic Paradigms in the Design of Robotic Systems for Space Applications
Authors: Menon C. , Lan N. , Sameoto D.
Published: March 2009

Biomimetic design is considered a promising source of novel solutions to problems in space engineering and robotics in particular. With the maturing of this discipline, however, a need is identified: a more systematic approach to its application to reduce the element of chance in the design of biomimetic systems. A methodology is proposed to address this concern and provide a basis for further development of biomimetic design procedures. The application of this process is illustrated through case studies of ongoing biomimetics research with relevance to space robotics in the form of climbing robots utilising synthetic dry adhesives.
The Wiskott-Aldrich syndrome protein is required for iNKT cell maturation and function
Authors: Locci Michela , Draghici Elena , Marangoni Francesco , Bosticardo Marita , Catucci Marco , Aiuti Alessandro , Cancrini Caterina , Marodi Laszlo , Espanol Teresa , Bredius Robbert G.M. , Thrasher Adrian J. , Schulz Ansgar , Litzman Jiri , Roncarolo Maria Grazia , Casorati Giulia , Dellabona Paolo , Villa Anna
Published: March 2009

The Wiskott-Aldrich syndrome (WAS) protein (WASp) is a regulator of actin cytoskeleton in hematopoietic cells. Mutations of the WASp gene cause WAS. Although WASp is involved in various immune cell functions, its role in invariant natural killer T (iNKT) cells has never been investigated. Defects of iNKT cells could indeed contribute to several WAS features, such as recurrent infections and high tumor incidence. We found a profound reduction of circulating iNKT cells in WAS patients, directly correlating with the severity of clinical phenotype. To better characterize iNKT cell defect in the absence of WASp, we analyzed was−/− mice. iNKT cell numbers were significantly reduced in the thymus and periphery of was−/− mice as compared with wild-type controls. Moreover analysis of was−/− iNKT cell maturation revealed a complete arrest at the CD44+ NK1.1− intermediate stage. Notably, generation of BM chimeras demonstrated a was−/− iNKT cell-autonomous developmental defect. was−/− iNKT cells were also functionally impaired, as suggested by the reduced secretion of interleukin 4 and interferon γ upon in vivo activation. Altogether, these results demonstrate the relevance of WASp in integrating signals critical for development and functional differentiation of iNKT cells and suggest that defects in these cells may play a role in WAS pathology.
Evolution of HLA-B*5703 HIV-1 escape mutations in HLA-B*5703–positive individuals and their transmission recipients
Authors: Crawford Hayley , Lumm Wendy , Leslie Alasdair , Schaefer Malinda , Boeras Debrah , Prado Julia G. , Tang Jianming , Farmer Paul , Ndung'u Thumbi , Lakhi Shabir , Gilmour Jill , Goepfert Paul , Walker Bruce D. , Kaslow Richard , Mulenga Joseph , Allen Susan , Goulder Philip J.R. , Hunter Eric
Published: March 2009

HLA-B*57 is the class I allele most consistently associated with control of human immunodeficiency virus (HIV) replication, which may be linked to the specific HIV peptides that this allele presents to cytotoxic T lymphocytes (CTLs), and the resulting efficacy of these cellular immune responses. In two HIV C clade–infected populations in South Africa and Zambia, we sought to elucidate the role of HLA-B*5703 in HIV disease outcome. HLA-B*5703–restricted CTL responses select for escape mutations in three Gag p24 epitopes, in a predictable order. We show that the accumulation of these mutations sequentially reduces viral replicative capacity in vitro. Despite this, in vivo data demonstrate that there is ultimately an increase in viral load concomitant with evasion of all three HLA-B*5703–restricted CTL responses. In HLA-B*5703–mismatched recipients, the previously described early benefit of transmitted HLA-B*5703–associated escape mutations is abrogated by the increase in viral load coincident with reversion. Rapid disease progression is observed in HLA-matched recipients to whom mutated virus is transmitted. These data demonstrate that, although costly escape from CTL responses can progressively attenuate the virus, high viral loads develop in the absence of adequate, continued CTL responses. These data underline the need for a CTL vaccine against multiple conserved epitopes.
Infernal 1.0: inference of RNA alignments
Authors: Nawrocki Eric P. , Kolbe Diana L. , Eddy Sean R.
Published: March 2009

Summary:  infernal builds consensus RNA secondary structure profiles called covariance models (CMs), and uses them to search nucleic acid sequence databases for homologous RNAs, or to create new sequence- and structure-based multiple sequence alignments.

Availability: Source code, documentation and benchmark downloadable from http://infernal.janelia.org. infernal is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X.

Contact: nawrockie,kolbed,eddys@janelia.hhmi.org
A study of the relationship between tag-signal characteristics and achievable performances in acoustic fish-tag studies
Authors: Ehrenberg John E. , Steig Tracey W.
Published: March 2009

Ehrenberg, J. E., and Steig, T. W. 2009. A study of the relationship between tag-signal characteristics and achievable performances in acoustic fish-tag studies. – ICES Journal of Marine Science, 66: 1278–1283. Acoustic tags have been used in fish-behaviour studies in a variety of marine and freshwater environments. The intended objectives of these studies vary widely. In some cases, they require accurate three-dimensional tracking of the individual fish locations. In other cases, tags are used for estimating fish survival along a migration route. There are varieties of schemes that have been proposed and used for implementing tag systems. The purpose of this paper is to explain the relationship between the various characteristics of acoustic signals transmitted by the tags and the tag-system performance that can be achieved. In particular, the ranges at which the tags can be detected and uniquely identified, the positional accuracy, and the number of unique codes that can be assigned to individual fish are all functions of the signal type. This paper demonstrates that when the pulse-repetition period is used to encode the tag identification, the range performance for the tag is superior to that achieved using a scheme that has binary-encoded bits as part of the transmitter signal. The parametric results presented will assist investigators in their selection of the type of acoustic tags or tag parameters needed to achieve the objectives of acoustic fish-tag studies.
Independent component analysis: Jacobi-like diagonalization of optimized composite-order cumulants
Authors: Abrar Shafayat , Nandi Asoke Kumar
Published: March 2009

In the field of blind source separation, Jacobi-like diagonalization-based approaches constitute an important tool for independent component analysis (ICA). Recently, simultaneous diagonalization of cumulant matrices of third- and fourth-order has been studied by a number of authors. In this work, we present an optimal parametrized composition of these cumulants that puts two classical contrasts, namely, the cumulant-based ICA and the weighted fourth-order contrast in a common framework. It is shown that the optimal weight parameter depends on the
a priori
statistical knowledge of the original mixing sources. Following the same spirit of the ICA algorithm, we derive the analytical solution for the case of two sources. Finally, a number of computer simulations have been performed to illustrate the behaviour of the Jacobi-like iterations for the maximization of the proposed parametrized contrast.
Computational complexity with experiments as oracles. II. Upper bounds
Authors: Beggs Edwin , Costa José Félix , Loff Bruno , Tucker J.V.
Published: March 2009

Earlier, to explore the idea of combining physical experiments with algorithms, we introduced a new form of analogue–digital (AD) Turing machine. We examined in detail a case study where an experimental procedure, based on Newtonian kinematics, is used as an oracle with classes of Turing machines. The physical cost of oracle calls was counted and three forms of AD queries were studied, in which physical parameters can be set exactly and approximately. Here, in this sequel, we complete the classification of the computational power of these AD Turing machines and determine precisely what they can compute, using non-uniform complexity classes and probabilities.
Temporally unstructured quantum computation
Authors: Shepherd Dan , Bremner Michael J.
Published: March 2009

We examine theoretic architectures and an abstract model for a restricted class of quantum computation, called heretemporally unstructured(‘instantaneous’)quantum computationbecause it allows for essentially no temporal structure within the quantum dynamics. Using the theory of binary matroids, we argue that the paradigm is rich enough to enable sampling from probability distributions that cannot, classically, be sampled efficiently and accurately. This paradigm also admits simple interactive proof games that may convince a sceptic of the existence of truly quantum effects. Furthermore, these effects can be created using significantly fewer qubits than are required for running Shor's algorithm.
Dynamo action in the presence of an imposed magnetic field
Authors: Hughes D.W. , Proctor M.R.E.
Published: March 2009

We consider the linear stability to three-dimensional perturbations of two-dimensional nonlinear magnetohydrodynamic basic states obtained from a specified forcing function in the presence of an imposed initially uniform magnetic field of strength
B
0
. The forcing is chosen such that it drives the ‘circularly polarized’ (CP) flow of Galloway & Proctor (
Galloway & Proctor 1992
Nature
356
, 691–693) when
B
0
=0. We first examine the properties of these basic states and their dependence on
B
0
and the magnetic Reynolds number
Rm
. The linear stability of these states is then investigated. It is found that, at a given
Rm
, the presence of a background field is stabilizing. The results also allow us to speculate that, at a fixed value of
B
0
, the growth of the unstable perturbations is ‘fast’, in the sense that the growth rate becomes independent of
Rm
as
Rm
→∞.
A pseudo-dynamical systems approach to a class of inverse problems in engineering
Authors: Banerjee B. , Roy D. , Vasu R.M.
Published: March 2009

A pseudo-dynamical approach for a class of inverse problems involving static measurements is proposed and explored. Following linearization of the minimizing functional associated with the underlying optimization problem, the new strategy results in a system of linearized ordinary differential equations (ODEs) whose steady-state solutions yield the desired reconstruction. We consider some explicit and implicit schemes for integrating the ODEs and thus establish a deterministic reconstruction strategy without an explicit use of regularization. A stochastic reconstruction strategy is then developed making use of an ensemble Kalman filter wherein these ODEs serve as the measurement model. Finally, we assess the numerical efficacy of the developed tools against a few linear and nonlinear inverse problems of engineering interest.