Structural connectivity in schizophrenia and its impact on the dynamics of spontaneous functional networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cabral, Joana; Department of Psychiatry, University of Oxford, Oxford OX3 7JX; Fernandes, Henrique M.

The neuropathology of schizophrenia remains unclear. Some insight has come from modern neuroimaging techniques, which offer an unparalleled opportunity to explore in vivo the structure and function of the brain. Using functional magnetic resonance imaging, it has been found that the large-scale resting-state functional connectivity (rsFC) in schizophrenia — measured as the temporal correlations of the blood-oxygen-level-dependent (BOLD) signal — exhibit altered network topology, with lower small-world index. The origin of these rsFC alterations and link with the underlying structural connectivity remain unclear. In this work, we used a computational model of spontaneous large-scale brain activity to explore the rolemore » of the structural connectivity in the large-scale dynamics of the brain in health and schizophrenia. The structural connectomes from 15 adolescent patients with early-onset schizophrenia and 15 age- and gender-matched controls were built from diffusion tensor imaging data to detect the white matter tracts between 90 brain areas. Brain areas, simulated using a reduced dynamic mean-field model, receive excitatory input from other areas in proportion to the number of fibre tracts between them. The simulated mean field activity was transformed into BOLD signal, and the properties of the simulated functional networks were analyzed. Our results suggest that the functional alterations observed in schizophrenia are not directly linked to alterations in the structural topology. Instead, subtly randomized and less small-world functional networks appear when the brain operates with lower global coupling, which shifts the dynamics from the optimal healthy regime.« less

Structural connectivity in schizophrenia and its impact on the dynamics of spontaneous functional networks

NASA Astrophysics Data System (ADS)

Cabral, Joana; Fernandes, Henrique M.; Van Hartevelt, Tim J.; James, Anthony C.; Kringelbach, Morten L.; Deco, Gustavo

2013-12-01

The neuropathology of schizophrenia remains unclear. Some insight has come from modern neuroimaging techniques, which offer an unparalleled opportunity to explore in vivo the structure and function of the brain. Using functional magnetic resonance imaging, it has been found that the large-scale resting-state functional connectivity (rsFC) in schizophrenia — measured as the temporal correlations of the blood-oxygen-level-dependent (BOLD) signal — exhibit altered network topology, with lower small-world index. The origin of these rsFC alterations and link with the underlying structural connectivity remain unclear. In this work, we used a computational model of spontaneous large-scale brain activity to explore the role of the structural connectivity in the large-scale dynamics of the brain in health and schizophrenia. The structural connectomes from 15 adolescent patients with early-onset schizophrenia and 15 age- and gender-matched controls were built from diffusion tensor imaging data to detect the white matter tracts between 90 brain areas. Brain areas, simulated using a reduced dynamic mean-field model, receive excitatory input from other areas in proportion to the number of fibre tracts between them. The simulated mean field activity was transformed into BOLD signal, and the properties of the simulated functional networks were analyzed. Our results suggest that the functional alterations observed in schizophrenia are not directly linked to alterations in the structural topology. Instead, subtly randomized and less small-world functional networks appear when the brain operates with lower global coupling, which shifts the dynamics from the optimal healthy regime.

1997 Technology Applications Report,

DTIC Science & Technology

1997-01-01

handle high -power loads at microwave radio frequencies , microwave vacuum tubes remain the chosen technology to amplify high power. Aria Microwave...structure called the active RF cavity amplifier (ARFCA). With this design , the amplifier handles high -power loads at radio and microwave frequencies ...developed this technology using BMDO-funded modeling methods designed to simulate the dynamics of large space-based structures. Because it increases

Primer on Condition Curves for Water Mains

EPA Science Inventory

ABSTRACT The development of economical tools to prioritize pipe renewal based upon structural condition and remaining asset life is essential to effectively manage water infrastructure assets for both large and small diameter pipes. One tool that may facilitate asset management...

The caprine abomasal microbiome

USDA-ARS?s Scientific Manuscript database

Parasitism is considered the number one health problem in small ruminants. The barber's pole worm Haemonchus contortus infection in goats elicits a strong host immune response. However, the effect of the parasitic infection on the structure and function of the gut microbiome remains largely unknown....

The future of large old trees in urban landscapes.

PubMed

Le Roux, Darren S; Ikin, Karen; Lindenmayer, David B; Manning, Adrian D; Gibbons, Philip

2014-01-01

Large old trees are disproportionate providers of structural elements (e.g. hollows, coarse woody debris), which are crucial habitat resources for many species. The decline of large old trees in modified landscapes is of global conservation concern. Once large old trees are removed, they are difficult to replace in the short term due to typically prolonged time periods needed for trees to mature (i.e. centuries). Few studies have investigated the decline of large old trees in urban landscapes. Using a simulation model, we predicted the future availability of native hollow-bearing trees (a surrogate for large old trees) in an expanding city in southeastern Australia. In urban greenspace, we predicted that the number of hollow-bearing trees is likely to decline by 87% over 300 years under existing management practices. Under a worst case scenario, hollow-bearing trees may be completely lost within 115 years. Conversely, we predicted that the number of hollow-bearing trees will likely remain stable in semi-natural nature reserves. Sensitivity analysis revealed that the number of hollow-bearing trees perpetuated in urban greenspace over the long term is most sensitive to the: (1) maximum standing life of trees; (2) number of regenerating seedlings ha(-1); and (3) rate of hollow formation. We tested the efficacy of alternative urban management strategies and found that the only way to arrest the decline of large old trees requires a collective management strategy that ensures: (1) trees remain standing for at least 40% longer than currently tolerated lifespans; (2) the number of seedlings established is increased by at least 60%; and (3) the formation of habitat structures provided by large old trees is accelerated by at least 30% (e.g. artificial structures) to compensate for short term deficits in habitat resources. Immediate implementation of these recommendations is needed to avert long term risk to urban biodiversity.

The Future of Large Old Trees in Urban Landscapes

PubMed Central

Le Roux, Darren S.; Ikin, Karen; Lindenmayer, David B.; Manning, Adrian D.; Gibbons, Philip

2014-01-01

Large old trees are disproportionate providers of structural elements (e.g. hollows, coarse woody debris), which are crucial habitat resources for many species. The decline of large old trees in modified landscapes is of global conservation concern. Once large old trees are removed, they are difficult to replace in the short term due to typically prolonged time periods needed for trees to mature (i.e. centuries). Few studies have investigated the decline of large old trees in urban landscapes. Using a simulation model, we predicted the future availability of native hollow-bearing trees (a surrogate for large old trees) in an expanding city in southeastern Australia. In urban greenspace, we predicted that the number of hollow-bearing trees is likely to decline by 87% over 300 years under existing management practices. Under a worst case scenario, hollow-bearing trees may be completely lost within 115 years. Conversely, we predicted that the number of hollow-bearing trees will likely remain stable in semi-natural nature reserves. Sensitivity analysis revealed that the number of hollow-bearing trees perpetuated in urban greenspace over the long term is most sensitive to the: (1) maximum standing life of trees; (2) number of regenerating seedlings ha−1; and (3) rate of hollow formation. We tested the efficacy of alternative urban management strategies and found that the only way to arrest the decline of large old trees requires a collective management strategy that ensures: (1) trees remain standing for at least 40% longer than currently tolerated lifespans; (2) the number of seedlings established is increased by at least 60%; and (3) the formation of habitat structures provided by large old trees is accelerated by at least 30% (e.g. artificial structures) to compensate for short term deficits in habitat resources. Immediate implementation of these recommendations is needed to avert long term risk to urban biodiversity. PMID:24941258

Large-scale transport across narrow gaps in rod bundles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guellouz, M.S.; Tavoularis, S.

1995-09-01

Flow visualization and how-wire anemometry were used to investigate the velocity field in a rectangular channel containing a single cylindrical rod, which could be traversed on the centreplane to form gaps of different widths with the plane wall. The presence of large-scale, quasi-periodic structures in the vicinity of the gap has been demonstrated through flow visualization, spectral analysis and space-time correlation measurements. These structures are seen to exist even for relatively large gaps, at least up to W/D=1.350 (W is the sum of the rod diameter, D, and the gap width). The above measurements appear to compatible with the fieldmore » of a street of three-dimensional, counter-rotating vortices, whose detailed structure, however, remains to be determined. The convection speed and the streamwise spacing of these vortices have been determined as functions of the gap size.« less

Read count-based method for high-throughput allelic genotyping of transposable elements and structural variants.

PubMed

Kuhn, Alexandre; Ong, Yao Min; Quake, Stephen R; Burkholder, William F

2015-07-08

Like other structural variants, transposable element insertions can be highly polymorphic across individuals. Their functional impact, however, remains poorly understood. Current genome-wide approaches for genotyping insertion-site polymorphisms based on targeted or whole-genome sequencing remain very expensive and can lack accuracy, hence new large-scale genotyping methods are needed. We describe a high-throughput method for genotyping transposable element insertions and other types of structural variants that can be assayed by breakpoint PCR. The method relies on next-generation sequencing of multiplex, site-specific PCR amplification products and read count-based genotype calls. We show that this method is flexible, efficient (it does not require rounds of optimization), cost-effective and highly accurate. This method can benefit a wide range of applications from the routine genotyping of animal and plant populations to the functional study of structural variants in humans.

Examination of the Reelfoot Rift Petroleum System, south-central United States, and the elements that remain for potential exploration and development

USGS Publications Warehouse

Coleman, James; Pratt, Thomas L.

2016-01-01

No production has been established in the Reel-foot rift. However, at least nine of 22 exploratory wells have reported petroleum shows, mainly gas shows with some asphalt or solid hydrocarbon residue. Regional seismic profiling shows the presence of two large inversion structures (Blytheville arch and Pascola arch). The Blytheville arch is marked by a core of structurally thickened Elvins Shale, whereas the Pascola arch reflects the structural uplift of a portion of the entire rift basin. Structural uplift and faulting within the Reelfoot rift since the late Paleozoic appear to have disrupted older conventional hydrocarbon traps and likely spilled any potential conventional petroleum accumulations. The remaining potential resources within the Reelfoot rift are likely shale gas accumulations within the Elvins Shale; however, reservoir continuity and porosity as well as pervasive faulting appear to be significant future challenges for explorers and drillers.

Chemical and structural order in silicon oxynitrides by methods of surface physics

NASA Astrophysics Data System (ADS)

Finster, J.; Heeg, J.; Klinkenberg, E.-D.

A large number of thin amorphous layers of SiO xN y and several (crystalline) reference compounds (SiO 2, Si 3N 4, Si 2N 2O) are studied. Although XANES and SEXAFS are well sulted to derive structural and chemical order, for these compounds many problems remain to be solved. We show how core level spectra (XPS, AES) can be used to gain such information (e.g. random bonding structure, N coordination, oxidation behaviour).

Changes in bacterial community of anthracene bioremediation in municipal solid waste composting soil*

PubMed Central

Zhang, Shu-ying; Wang, Qing-feng; Wan, Rui; Xie, Shu-guang

2011-01-01

Polycyclic aromatic hydrocarbons (PAHs) are common contaminants in a municipal solid waste (MSW) composting site. Knowledge of changes in microbial structure is useful to identify particular PAH degraders. However, the microbial community in the MSW composting soil and its change associated with prolonged exposure to PAHs and subsequent biodegradation remain largely unknown. In this study, anthracene was selected as a model compound. The bacterial community structure was investigated using terminal restriction fragment length polymorphism (TRFLP) and 16S rRNA gene clone library analysis. The two bimolecular tools revealed a large shift of bacterial community structure after anthracene amendment and subsequent biodegradation. Genera Methylophilus, Mesorhizobium, and Terrimonas had potential links to anthracene biodegradation, suggesting a consortium playing an active role. PMID:21887852

Fate of Large-Scale Structure in Modified Gravity After GW170817 and GRB170817A

NASA Astrophysics Data System (ADS)

Amendola, Luca; Kunz, Martin; Saltas, Ippocratis D.; Sawicki, Ignacy

2018-03-01

The coincident detection of gravitational waves (GW) and a gamma-ray burst from a merger of neutron stars has placed an extremely stringent bound on the speed of GWs. We showed previously that the presence of gravitational slip (η ) in cosmology is intimately tied to modifications of GW propagation. This new constraint implies that the only remaining viable source of gravitational slip is a conformal coupling to gravity in scalar-tensor theories, while viable vector-tensor theories cannot now generate gravitational slip at all. We discuss structure formation in the remaining viable models, demonstrating that (i) the dark-matter growth rate must now be at least as fast as in general relativity (GR), with the possible exception of that beyond the Horndeski model, and (ii) if there is any scale dependence at all in the slip parameter, it is such that it takes the GR value at large scales. We show a consistency relation that must be violated if gravity is modified.

Internal structure of normal maize starch granules revealed by chemical surface gelatinization.

PubMed

Pan, D D; Jane, J I

2000-01-01

Normal maize starch was fractionated into two sizes: large granules with diameters more than 5 microns and small granules with diameters less than 5 microns. The large granules were surface gelatinized by treating them with an aqueous LiCl solution (13 M) at 22-23 degrees C. Surface-gelatinized remaining granules were obtained by mechanical blending, and gelatinized surface starch was obtained by grinding with a mortar and a pestle. Starches of different granular sizes and radial locations, obtained after different degrees of surface gelatinization, were subjected to scanning electron microscopy, iodine potentiometric titration, gel-permeation chromatography, and amylopectin branch chain length analysis. Results showed that the remaining granules had a rough surface with a lamella structure. Amylose was more concentrated at the periphery than at the core of the granule. Amylopectin had longer long B-chains at the core than at the periphery of the granule. Greater proportions of the long B-chains were present at the core than at the periphery of the granule.

Passage of American shad: paradigms and realities

USGS Publications Warehouse

Haro, Alex; Castro-Santos, Theodore

2012-01-01

Despite more than 250 years of development, the passage of American shad Alosa sapidissima at dams and other barriers frequently remains problematic. Few improvements in design based on knowledge of the swimming, schooling, and migratory behaviors of American shad have been incorporated into passage structures. Large-scale technical fishways designed for the passage of adult salmonids on the Columbia River have been presumed to have good performance for American shad but have never been rigorously evaluated for this species. Similar but smaller fishway designs on the East Coast frequently have poor performance. Provision of effective downstream passage for both juvenile and postspawning adult American shad has been given little consideration in most passage projects. Ways to attract and guide American shad to both fishway entrances and downstream bypasses remain marginally understood. The historical development of passage structures for American shad has resulted in assumptions and paradigms about American shad behavior and passage that are frequently unsubstantiated by supporting data or appropriate experimentation. We propose that many of these assumptions and paradigms are either unfounded or invalid and that significant improvements to American shad upstream and downstream passage can be made via a sequential program of behavioral experimentation, application of experimental results to the physical and hydraulic design of new structures, and controlled tests of large-scale prototype structures in the laboratory and field.

Crystal Structure of a UDP-glucose-specific Glycosyltransferase from a Mycobacterium Species

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fulton, Zara; McAlister, Adrian; Wilce, Matthew C.J.

2008-10-24

Glycosyltransferases (GTs) are a large and ubiquitous family of enzymes that specifically transfer sugar moieties to a range of substrates. Mycobacterium tuberculosis contains a large number of GTs, many of which are implicated in cell wall synthesis, yet the majority of these GTs remain poorly characterized. Here, we report the high resolution crystal structures of an essential GT (MAP2569c) from Mycobacterium avium subsp. paratuberculosis (a close homologue of Rv1208 from M. tuberculosis) in its apo- and ligand-bound forms. The structure adopted the GT-A fold and possessed the characteristic DXD motif that coordinated an Mn{sup 2+} ion. Atypical of most GTsmore » characterized to date, MAP2569c exhibited specificity toward the donor substrate, UDP-glucose. The structure of this ligated complex revealed an induced fit binding mechanism and provided a basis for this unique specificity. Collectively, the structural features suggested that MAP2569c may adopt a 'retaining' enzymatic mechanism, which has implications for the classification of other GTs in this large superfamily.« less

The endoplasmic reticulum: structure, function and response to cellular signaling.

PubMed

Schwarz, Dianne S; Blower, Michael D

2016-01-01

The endoplasmic reticulum (ER) is a large, dynamic structure that serves many roles in the cell including calcium storage, protein synthesis and lipid metabolism. The diverse functions of the ER are performed by distinct domains; consisting of tubules, sheets and the nuclear envelope. Several proteins that contribute to the overall architecture and dynamics of the ER have been identified, but many questions remain as to how the ER changes shape in response to cellular cues, cell type, cell cycle state and during development of the organism. Here we discuss what is known about the dynamics of the ER, what questions remain, and how coordinated responses add to the layers of regulation in this dynamic organelle.

Life in the Outer Limits: Insight into Hierarchical Merging from the Outermost Structure of the Andromeda Stellar Halo

NASA Astrophysics Data System (ADS)

Beaton, Rachael; Majewski, S. R.; Patterson, R. J.; Guhathakurta, P.; Gilbert, K.; Kalirai, J. S.; Tollerud, E. J.; SPLASH Team

2014-01-01

Owing to their large dynamical timescales, the stellar haloes of Milky Way (MW) sized galaxies represent ideal environments to test modern theories of galaxy formation in the Lambda-CDM paradigm. Only in stellar haloes can the remnants of hierarchical accretion be preserved over long timescales as in-tact dwarf satellites or as tidal debris and can be easily distinguished from the underlying smooth structure. Stellar haloes, however, remain some of the most difficult galactic structures to constrain due to their large angular extent and extremely low surface brightness. Thus, the basic properties of stellar haloes -- the overall stellar distribution, substructure fraction, global kinematics and detailed stellar content -- remained relatively unconstrained. In this thesis, we present several projects designed to understand the current structure and the the formation of the Andromeda (M31) stellar halo, the only stellar halo -- besides our own -- that is within reach of current ground based facilities on the large scale required to constrain the basic properties of stellar haloes. First, we describe a seven season imaging campaign comprising the backbone of the Spectroscopic and Photometric Landscape of the Andromeda Stellar Halo (SPLASH) program. This survey is unique in its application of the Washington + DDO51 filter system to select individual M31 RGB stars without spectroscopic follow up. Second, we use the SPLASH photometric survey to identify sample of halo stars at projected radii of 120 kpc, for which we have obtained spectroscopic follow-up. Third, we add this large radius sample to the existing spectroscopic results from SPLASH, and use this unique sample to explore the stellar kinematics of the halo at large radii with full azimuthal coverage. Lastly, we preview on-going work to constrain the formation of the Andromeda stellar halo, using both in-tact satellites and resolved M31 halo members as tracers of its accretion history.

Effects of Large-Scale Releases on the Genetic Structure of Red Sea Bream (Pagrus major, Temminck et Schlegel) Populations in Japan.

PubMed

Blanco Gonzalez, Enrique; Aritaki, Masato; Knutsen, Halvor; Taniguchi, Nobuhiko

2015-01-01

Large-scale hatchery releases are carried out for many marine fish species worldwide; nevertheless, the long-term effects of this practice on the genetic structure of natural populations remains unclear. The lack of knowledge is especially evident when independent stock enhancement programs are conducted simultaneously on the same species at different geographical locations, as occurs with red sea bream (Pagrus major, Temminck et Schlegel) in Japan. In this study, we examined the putative effects of intensive offspring releases on the genetic structure of red sea bream populations along the Japanese archipelago by genotyping 848 fish at fifteen microsatellite loci. Our results suggests weak but consistent patterns of genetic divergence (F(ST) = 0.002, p < 0.001). Red sea bream in Japan appeared spatially structured with several patches of distinct allelic composition, which corresponded to areas receiving an important influx of fish of hatchery origin, either released intentionally or from unintentional escapees from aquaculture operations. In addition to impacts upon local populations inhabiting semi-enclosed embayments, large-scale releases (either intentionally or from unintentional escapes) appeared also to have perturbed genetic structure in open areas. Hence, results of the present study suggest that independent large-scale marine stock enhancement programs conducted simultaneously on one species at different geographical locations may compromise native genetic structure and lead to patchy patterns in population genetic structure.

From Theory to Action: Learning Shifts into High Gear with Structured Supports

ERIC Educational Resources Information Center

Anderson, Andrea; Steffen, Beth; Wiese, Chad; King, M. Bruce

2014-01-01

While teachers face new expectations for student learning and more equitable educational outcomes, instruction and assessment remain rooted in traditional approaches that are largely inequitable, culturally irrelevant, and intellectually disengaging, contributing to gaps in academic achievement across student groups (Darling-Hammond, 2010; King…

The State of the Summer: a Review of Child Summer Weight Gain and Efforts to Prevent It.

PubMed

Tanskey, Lindsay A; Goldberg, Jeanne; Chui, Kenneth; Must, Aviva; Sacheck, Jennifer

2018-06-01

Accumulating evidence shows that children in the USA gain weight more rapidly during the summer, when school is not in session. This narrative review spanning 2007 to 2017 summarizes efforts to characterize the problem, identify key determinants, and intervene to prevent excess summer weight gain. Summer weight gain remains a concern for elementary-age youth. Few studies have examined its determinants, but unfavorable summertime shifts in diet, physical activity, sedentary time, screen media use, and sleep have been reported. Increased structure is thought to protect against summer weight gain. Interventions to support physical activity and nutrition during the summer show promise, though large-scale impact on weight outcomes remains to be seen. Supporting health behaviors during the summer remains a priority for obesity prevention researchers, practitioners, and policymakers. Strategies to expand access to structured programs and reach beyond such programs to improve behaviors at home are of particular importance.

Clapeyron slope reversal in the melting curve of AuGa2 at 5.5 GPa.

PubMed

Geballe, Z M; Raju, S V; Godwal, B K; Jeanloz, R

2013-10-16

We use x-ray diffraction in a resistively heated diamond anvil cell to extend the melting curve of AuGa2 beyond its minimum at 5.5 GPa and 720 K, and to constrain the high-temperature phase boundaries between cubic (fluorite structure), orthorhombic (cottunite structure) and monoclinic phases. We document a large change in Clapeyron slope that coincides with the transitions from cubic to lower symmetry phases, showing that a structural transition is the direct cause of the change in slope. In addition, moderate (~30 K) to large (90 K) hysteresis is detected between melting and freezing, from which we infer that at high pressures, AuGa2 crystals can remain in a metastable state at more than 5% above the thermodynamic melting temperature.

Network cosmology.

PubMed

Krioukov, Dmitri; Kitsak, Maksim; Sinkovits, Robert S; Rideout, David; Meyer, David; Boguñá, Marián

2012-01-01

Prediction and control of the dynamics of complex networks is a central problem in network science. Structural and dynamical similarities of different real networks suggest that some universal laws might accurately describe the dynamics of these networks, albeit the nature and common origin of such laws remain elusive. Here we show that the causal network representing the large-scale structure of spacetime in our accelerating universe is a power-law graph with strong clustering, similar to many complex networks such as the Internet, social, or biological networks. We prove that this structural similarity is a consequence of the asymptotic equivalence between the large-scale growth dynamics of complex networks and causal networks. This equivalence suggests that unexpectedly similar laws govern the dynamics of complex networks and spacetime in the universe, with implications to network science and cosmology.

Network Cosmology

PubMed Central

Krioukov, Dmitri; Kitsak, Maksim; Sinkovits, Robert S.; Rideout, David; Meyer, David; Boguñá, Marián

2012-01-01

Prediction and control of the dynamics of complex networks is a central problem in network science. Structural and dynamical similarities of different real networks suggest that some universal laws might accurately describe the dynamics of these networks, albeit the nature and common origin of such laws remain elusive. Here we show that the causal network representing the large-scale structure of spacetime in our accelerating universe is a power-law graph with strong clustering, similar to many complex networks such as the Internet, social, or biological networks. We prove that this structural similarity is a consequence of the asymptotic equivalence between the large-scale growth dynamics of complex networks and causal networks. This equivalence suggests that unexpectedly similar laws govern the dynamics of complex networks and spacetime in the universe, with implications to network science and cosmology. PMID:23162688

Avoiding Aging? Social Psychology's Treatment of Age

ERIC Educational Resources Information Center

Barrett, Anne E.; Redmond, Rebecca; von Rohr, Carmen

2012-01-01

Population aging, in conjunction with social and cultural transformations of the life course, has profound implications for social systems--from large-scale structures to micro-level processes. However, much of sociology remains fairly quiet on issues of age and aging, including the subfield of social psychology that could illuminate the impact of…

Economic Structure and Change in Persistently Low-Income Nonmetro Counties.

ERIC Educational Resources Information Center

Hoppe, Robert A.

Some nonmetropolitan counties, largely in the southern United States, remained severely economically depressed during the 1970's despite nonmetro America's economic gains during the period; other severely economically depressed counties improved their incomes in the 1970's. This report builds on an earlier study which identified 298 persistently…

Effect of von Karman Vortex Shedding on Regular and Open-slit V-gutter Stabilized Turbulent Premixed Flames

DTIC Science & Technology

2012-04-01

Both flame lengths shrink and large scale disruptions occur downstream with vortex shedding carrying reaction zones. Flames in both flameholders...9) the flame structure changes dramatically for both regular and open-slit V-gutter. Both flame lengths shrink and large scale disruptions occur...reduces the flame length . However, qualitatively the open-slit V-gutter appears to be more sensitive than the regular V-gutter. Both flames remain

TRPC Channel Structure and Properties.

PubMed

Feng, Shengjie

2017-01-01

TRPC channels are the first identified members in the TRP family. They function as either homo- or heterotetramers regulating intracellular Ca 2+ concentration in response to numerous physiological or pathological stimuli. TRPC channels are nonselective cation channels permeable to Ca 2+ . The properties and the functional domains of TRPC channels have been identified by electrophysiological and biochemical methods. However, due to the large size, instability, and flexibility of their complexes, the structures of the members in TRPC family remain unrevealed. More efforts should be made on structure analysis and generating good tools, including specific antibodies, agonist, and antagonist.

Atomic view of the histidine environment stabilizing higher-pH conformations of pH-dependent proteins

PubMed Central

Valéry, Céline; Deville-Foillard, Stéphanie; Lefebvre, Christelle; Taberner, Nuria; Legrand, Pierre; Meneau, Florian; Meriadec, Cristelle; Delvaux, Camille; Bizien, Thomas; Kasotakis, Emmanouil; Lopez-Iglesias, Carmen; Gall, Andrew; Bressanelli, Stéphane; Le Du, Marie-Hélène; Paternostre, Maïté; Artzner, Franck

2015-01-01

External stimuli are powerful tools that naturally control protein assemblies and functions. For example, during viral entry and exit changes in pH are known to trigger large protein conformational changes. However, the molecular features stabilizing the higher pH structures remain unclear. Here we elucidate the conformational change of a self-assembling peptide that forms either small or large nanotubes dependent on the pH. The sub-angstrom high-pH peptide structure reveals a globular conformation stabilized through a strong histidine-serine H-bond and a tight histidine-aromatic packing. Lowering the pH induces histidine protonation, disrupts these interactions and triggers a large change to an extended β-sheet-based conformation. Re-visiting available structures of proteins with pH-dependent conformations reveals both histidine-containing aromatic pockets and histidine-serine proximity as key motifs in higher pH structures. The mechanism discovered in this study may thus be generally used by pH-dependent proteins and opens new prospects in the field of nanomaterials. PMID:26190377

Examining gray matter structure associated with academic performance in a large sample of Chinese high school students.

PubMed

Wang, Song; Zhou, Ming; Chen, Taolin; Yang, Xun; Chen, Guangxiang; Wang, Meiyun; Gong, Qiyong

2017-04-18

Achievement in school is crucial for students to be able to pursue successful careers and lead happy lives in the future. Although many psychological attributes have been found to be associated with academic performance, the neural substrates of academic performance remain largely unknown. Here, we investigated the relationship between brain structure and academic performance in a large sample of high school students via structural magnetic resonance imaging (S-MRI) using voxel-based morphometry (VBM) approach. The whole-brain regression analyses showed that higher academic performance was related to greater regional gray matter density (rGMD) of the left dorsolateral prefrontal cortex (DLPFC), which is considered a neural center at the intersection of cognitive and non-cognitive functions. Furthermore, mediation analyses suggested that general intelligence partially mediated the impact of the left DLPFC density on academic performance. These results persisted even after adjusting for the effect of family socioeconomic status (SES). In short, our findings reveal a potential neuroanatomical marker for academic performance and highlight the role of general intelligence in explaining the relationship between brain structure and academic performance.

Type II Heat-labile Enterotoxins: Structure, Function, and Immunomofdulatory Properties

PubMed Central

Hajishengallis, George; Connell, Terry D.

2012-01-01

The heat-labile enterotoxins (HLTs) of Escherichia coli and Vibrio cholerae are classified into two major types on the basis of genetic, biochemical, and immunological properties. Type I and Type II HLT have been intensively studied for their exceptionally strong adjuvant activities. Despite general structural similarities, these molecules, in intact or derivative (non-toxic) forms, display notable differences in their mode of immunomodulatory action. The molecular basis of these differences has remained largely uncharacterized until recently. This review focuses on the Type II HLTs and their immunomodulatory properties which depend largely on interactions with unique gangliosides and Toll-like receptors that are not utilized by the Type I HLTs. PMID:23137790

Original size of the Vredefort structure, South Africa

NASA Technical Reports Server (NTRS)

Therriault, A. M.; Reid, A. M.; Reimold, W. U.

1993-01-01

The Vredefort structure is located approximately 120 km southwest of Johannesburg, South Africa, and is deeply eroded. Controversies remain on the origin of this structure with the most popular hypotheses being: (1) by impact cratering about 2.0 Ga; (2) as a cryptoexplosion structure about 2.0 Ga; and (3) by purely tectonic processes starting at about 3.0 Ga and ending with the Vredefort event at 2.0 Ga. In view of recent work in which the granophyre dikes are interpreted as the erosional remants of a more extensive impact melt sheet, injected downward into the underlying country rocks, the impact origin hypothesis for Vredefort is adopted. In order to estimate the original dimensions of the Vredefort impact structure, it is assumed that the structure was initially circular, that its predeformation center corresponds to the center of the granitic core, and that the pre-Vredefort geology of the area prior to approximately 2.0 Ga ago is as suggested by Fletcher and Reimold. The spatial relationship between shock metamorphic effects, the shock pressures they record, and the morphological features of the crater were established for a number of large terrestrial craters. The principles of crater formation at large complex impact structures comparable in size to Vredefort were also established, although many details remain unresolved. An important conclusion is that the transient crater, which is formed directly by excavation and displacement by the shock-induced cratering flow-field (i.e., the particle velocity flow field existing in the region of the transient crater but behind the initial outgoing shock front), is highly modified during the late stage processes. The original transient crater diameter lies well within the final rim of the crater, which is established by structural movements during late-stage cavity modification.

Microgravity protein crystallization

PubMed Central

McPherson, Alexander; DeLucas, Lawrence James

2015-01-01

Over the past 20 years a variety of technological advances in X-ray crystallography have shortened the time required to determine the structures of large macromolecules (i.e., proteins and nucleic acids) from several years to several weeks or days. However, one of the remaining challenges is the ability to produce diffraction-quality crystals suitable for a detailed structural analysis. Although the development of automated crystallization systems combined with protein engineering (site-directed mutagenesis to enhance protein solubility and crystallization) have improved crystallization success rates, there remain hundreds of proteins that either cannot be crystallized or yield crystals of insufficient quality to support X-ray structure determination. In an attempt to address this bottleneck, an international group of scientists has explored use of a microgravity environment to crystallize macromolecules. This paper summarizes the history of this international initiative along with a description of some of the flight hardware systems and crystallization results. PMID:28725714

Do we understand what creates 150-km echoes and gives them their distinct structure?

NASA Astrophysics Data System (ADS)

Oppenheim, M. M.; Kudeki, E.; Salas Reyes, P.; Dimant, Y. S.

2017-12-01

Researchers first discovered 150-km echoes over 50 years ago using the first large VHF radars near the geomagnetic equator. However, the underlying mechanism that creates and modulates them remains largely a mystery. Despite this lack of understanding the aeronomy community uses them to monitor daytime vertical plasma drifts between 130 and 160 km altitude. In a 2016 paper, Oppenheim and Dimant used simulations to show that photoelectrons can generate the type of echoes seen by the radars but this theory doesn't explain any of the detailed structures. This paper will show the modern observations of 150 km echoes using simultaneous radar and ionosonde measurements. It will then describe the latest analysis to attempt to explain these features using large-scale kinetic simulations of photoelectrons interacting with the ambient ionospheric plasma under a range of conditions.

Bioinspired large-scale aligned porous materials assembled with dual temperature gradients

PubMed Central

Bai, Hao; Chen, Yuan; Delattre, Benjamin; Tomsia, Antoni P.; Ritchie, Robert O.

2015-01-01

Natural materials, such as bone, teeth, shells, and wood, exhibit outstanding properties despite being porous and made of weak constituents. Frequently, they represent a source of inspiration to design strong, tough, and lightweight materials. Although many techniques have been introduced to create such structures, a long-range order of the porosity as well as a precise control of the final architecture remain difficult to achieve. These limitations severely hinder the scale-up fabrication of layered structures aimed for larger applications. We report on a bidirectional freezing technique to successfully assemble ceramic particles into scaffolds with large-scale aligned, lamellar, porous, nacre-like structure and long-range order at the centimeter scale. This is achieved by modifying the cold finger with a polydimethylsiloxane (PDMS) wedge to control the nucleation and growth of ice crystals under dual temperature gradients. Our approach could provide an effective way of manufacturing novel bioinspired structural materials, in particular advanced materials such as composites, where a higher level of control over the structure is required. PMID:26824062

Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta.

PubMed

Wang, Ray Yu-Ruei; Song, Yifan; Barad, Benjamin A; Cheng, Yifan; Fraser, James S; DiMaio, Frank

2016-09-26

Cryo-EM has revealed the structures of many challenging yet exciting macromolecular assemblies at near-atomic resolution (3-4.5Å), providing biological phenomena with molecular descriptions. However, at these resolutions, accurately positioning individual atoms remains challenging and error-prone. Manually refining thousands of amino acids - typical in a macromolecular assembly - is tedious and time-consuming. We present an automated method that can improve the atomic details in models that are manually built in near-atomic-resolution cryo-EM maps. Applying the method to three systems recently solved by cryo-EM, we are able to improve model geometry while maintaining the fit-to-density. Backbone placement errors are automatically detected and corrected, and the refinement shows a large radius of convergence. The results demonstrate that the method is amenable to structures with symmetry, of very large size, and containing RNA as well as covalently bound ligands. The method should streamline the cryo-EM structure determination process, providing accurate and unbiased atomic structure interpretation of such maps.

Crystal structure of group II intron domain 1 reveals a template for RNA assembly

DOE PAGES

Zhao, Chen; Rajashankar, Kanagalaghatta R.; Marcia, Marco; ...

2015-10-26

Although the importance of large noncoding RNAs is increasingly appreciated, our understanding of their structures and architectural dynamics remains limited. In particular, we know little about RNA folding intermediates and how they facilitate the productive assembly of RNA tertiary structures. In this paper, we report the crystal structure of an obligate intermediate that is required during the earliest stages of group II intron folding. Composed of domain 1 from the Oceanobacillus iheyensis group II intron (266 nucleotides), this intermediate retains native-like features but adopts a compact conformation in which the active site cleft is closed. Transition between this closed andmore » the open (native) conformation is achieved through discrete rotations of hinge motifs in two regions of the molecule. Finally, the open state is then stabilized by sequential docking of downstream intron domains, suggesting a 'first come, first folded' strategy that may represent a generalizable pathway for assembly of large RNA and ribonucleoprotein structures.« less

Large-scale production and study of a synthetic G protein-coupled receptor: Human olfactory receptor 17-4

PubMed Central

Cook, Brian L.; Steuerwald, Dirk; Kaiser, Liselotte; Graveland-Bikker, Johanna; Vanberghem, Melanie; Berke, Allison P.; Herlihy, Kara; Pick, Horst; Vogel, Horst; Zhang, Shuguang

2009-01-01

Although understanding of the olfactory system has progressed at the level of downstream receptor signaling and the wiring of olfactory neurons, the system remains poorly understood at the molecular level of the receptors and their interaction with and recognition of odorant ligands. The structure and functional mechanisms of these receptors still remain a tantalizing enigma, because numerous previous attempts at the large-scale production of functional olfactory receptors (ORs) have not been successful to date. To investigate the elusive biochemistry and molecular mechanisms of olfaction, we have developed a mammalian expression system for the large-scale production and purification of a functional OR protein in milligram quantities. Here, we report the study of human OR17-4 (hOR17-4) purified from a HEK293S tetracycline-inducible system. Scale-up of production yield was achieved through suspension culture in a bioreactor, which enabled the preparation of >10 mg of monomeric hOR17-4 receptor after immunoaffinity and size exclusion chromatography, with expression yields reaching 3 mg/L of culture medium. Several key post-translational modifications were identified using MS, and CD spectroscopy showed the receptor to be ≈50% α-helix, similar to other recently determined G protein-coupled receptor structures. Detergent-solubilized hOR17-4 specifically bound its known activating odorants lilial and floralozone in vitro, as measured by surface plasmon resonance. The hOR17-4 also recognized specific odorants in heterologous cells as determined by calcium ion mobilization. Our system is feasible for the production of large quantities of OR necessary for structural and functional analyses and research into OR biosensor devices. PMID:19581598

Local Helioseismology of Emerging Active Regions: A Case Study

NASA Astrophysics Data System (ADS)

Kosovichev, Alexander G.; Zhao, Junwei; Ilonidis, Stathis

2018-04-01

Local helioseismology provides a unique opportunity to investigate the subsurface structure and dynamics of active regions and their effect on the large-scale flows and global circulation of the Sun. We use measurements of plasma flows in the upper convection zone, provided by the Time-Distance Helioseismology Pipeline developed for analysis of solar oscillation data obtained by Helioseismic and Magnetic Imager (HMI) on Solar Dynamics Observatory (SDO), to investigate the subsurface dynamics of emerging active region NOAA 11726. The active region emergence was detected in deep layers of the convection zone about 12 hours before the first bipolar magnetic structure appeared on the surface, and 2 days before the emergence of most of the magnetic flux. The speed of emergence determined by tracking the flow divergence with depth is about 1.4 km/s, very close to the emergence speed in the deep layers. As the emerging magnetic flux becomes concentrated in sunspots local converging flows are observed beneath the forming sunspots. These flows are most prominent in the depth range 1-3 Mm, and remain converging after the formation process is completed. On the larger scale converging flows around active region appear as a diversion of the zonal shearing flows towards the active region, accompanied by formation of a large-scale vortex structure. This process occurs when a substantial amount of the magnetic flux emerged on the surface, and the converging flow pattern remains stable during the following evolution of the active region. The Carrington synoptic flow maps show that the large-scale subsurface inflows are typical for active regions. In the deeper layers (10-13 Mm) the flows become diverging, and surprisingly strong beneath some active regions. In addition, the synoptic maps reveal a complex evolving pattern of large-scale flows on the scale much larger than supergranulation

Large-scale production and study of a synthetic G protein-coupled receptor: human olfactory receptor 17-4.

PubMed

Cook, Brian L; Steuerwald, Dirk; Kaiser, Liselotte; Graveland-Bikker, Johanna; Vanberghem, Melanie; Berke, Allison P; Herlihy, Kara; Pick, Horst; Vogel, Horst; Zhang, Shuguang

2009-07-21

Although understanding of the olfactory system has progressed at the level of downstream receptor signaling and the wiring of olfactory neurons, the system remains poorly understood at the molecular level of the receptors and their interaction with and recognition of odorant ligands. The structure and functional mechanisms of these receptors still remain a tantalizing enigma, because numerous previous attempts at the large-scale production of functional olfactory receptors (ORs) have not been successful to date. To investigate the elusive biochemistry and molecular mechanisms of olfaction, we have developed a mammalian expression system for the large-scale production and purification of a functional OR protein in milligram quantities. Here, we report the study of human OR17-4 (hOR17-4) purified from a HEK293S tetracycline-inducible system. Scale-up of production yield was achieved through suspension culture in a bioreactor, which enabled the preparation of >10 mg of monomeric hOR17-4 receptor after immunoaffinity and size exclusion chromatography, with expression yields reaching 3 mg/L of culture medium. Several key post-translational modifications were identified using MS, and CD spectroscopy showed the receptor to be approximately 50% alpha-helix, similar to other recently determined G protein-coupled receptor structures. Detergent-solubilized hOR17-4 specifically bound its known activating odorants lilial and floralozone in vitro, as measured by surface plasmon resonance. The hOR17-4 also recognized specific odorants in heterologous cells as determined by calcium ion mobilization. Our system is feasible for the production of large quantities of OR necessary for structural and functional analyses and research into OR biosensor devices.

Live Load Testing of Historic Covered Timber Bridges

Treesearch

Travis Hosteng; James Wacker; Brent Phares

2013-01-01

The National Historic Covered Bridge Preservation Program (NHCBP), sponsored by the Federal Highway Administration (FHWA), is intended to preserve covered timber bridge structures nationwide. Today, less than 700 covered timber bridges still exist in the United States and of those many are closed to vehicular traffic. Furthermore, a large percentage of the remaining...

Constraints on Statistical Computations at 10 Months of Age: The Use of Phonological Features

ERIC Educational Resources Information Center

Gonzalez-Gomez, Nayeli; Nazzi, Thierry

2015-01-01

Recently, several studies have argued that infants capitalize on the statistical properties of natural languages to acquire the linguistic structure of their native language, but the kinds of constraints which apply to statistical computations remain largely unknown. Here we explored French-learning infants' perceptual preference for…

Standardization of Selected Semantic Differential Scales with Secondary School Children.

ERIC Educational Resources Information Center

Evans, G. T.

A basic assumption of this study is that the meaning continuum registered by an adjective pair remains relatively constant over a large universe of concepts and over subjects within a relatively homogeneous population. An attempt was made to validate this assumption by showing the invariance of the factor structure across different types of…

The Road Barely Taken: Funerals, and People with Intellectual Disabilities

ERIC Educational Resources Information Center

Forrester-Jones, Rachel

2013-01-01

Background: The topic of funerals within the life cycle approach to care in the UK remains largely absent. This small exploratory study sought to investigate how practitioners deal with this sensitive issue and to capture the views of older people with and without intellectual disabilities about funerals. Methods: A semi-structured questionnaire…

Linguistic and Structural Analyses of Stand-Alone Literature Reviews: Seventy-Five Years of Change

ERIC Educational Resources Information Center

Wright, Heidi Rachel

2016-01-01

The purpose of this dissertation is to offer a multifaceted overview of stand-alone literature reviews. These texts, literature reviews published unattached to research articles, have existed for centuries but remained largely unstudied by linguists. Thus, the goal of this project is to present these reviews' situational, grammatical, and…

Practicing What We Teach? An Autobiographical Reflection on Navigating Academia as a Single Mother

ERIC Educational Resources Information Center

Schlehofer, Michele

2012-01-01

Despite the contributions of feminist theory and practice to improve workplace conditions in various sectors of business and industry, academic workplaces largely remain structured around a traditionally hierarchical, male workplace model and culture, which can inhibit women's career advancement. Using autobiographical narrative, I draw upon my…

Neurodevelopmental alterations of large-scale structural networks in children with new-onset epilepsy

PubMed Central

Bonilha, Leonardo; Tabesh, Ali; Dabbs, Kevin; Hsu, David A.; Stafstrom, Carl E.; Hermann, Bruce P.; Lin, Jack J.

2014-01-01

Recent neuroimaging and behavioral studies have revealed that children with new onset epilepsy already exhibit brain structural abnormalities and cognitive impairment. How the organization of large-scale brain structural networks is altered near the time of seizure onset and whether network changes are related to cognitive performances remain unclear. Recent studies also suggest that regional brain volume covariance reflects synchronized brain developmental changes. Here, we test the hypothesis that epilepsy during early-life is associated with abnormalities in brain network organization and cognition. We used graph theory to study structural brain networks based on regional volume covariance in 39 children with new-onset seizures and 28 healthy controls. Children with new-onset epilepsy showed a suboptimal topological structural organization with enhanced network segregation and reduced global integration compared to controls. At the regional level, structural reorganization was evident with redistributed nodes from the posterior to more anterior head regions. The epileptic brain network was more vulnerable to targeted but not random attacks. Finally, a subgroup of children with epilepsy, namely those with lower IQ and poorer executive function, had a reduced balance between network segregation and integration. Taken together, the findings suggest that the neurodevelopmental impact of new onset childhood epilepsies alters large-scale brain networks, resulting in greater vulnerability to network failure and cognitive impairment. PMID:24453089

Broca's area: a supramodal hierarchical processor?

PubMed

Tettamanti, Marco; Weniger, Dorothea

2006-05-01

Despite the presence of shared characteristics across the different domains modulating Broca's area activity (e.g., structural analogies, as between language and music, or representational homologies, as between action execution and action observation), the question of what exactly the common denominator of such diverse brain functions is, with respect to the function of Broca's area, remains largely a debated issue. Here, we suggest that an important computational role of Broca's area may be to process hierarchical structures in a wide range of functional domains.

Agonistic reciprocity is associated with reduced male reproductive success within haremic social networks

PubMed Central

Solomon-Lane, Tessa K.; Pradhan, Devaleena S.; Willis, Madelyne C.; Grober, Matthew S.

2015-01-01

While individual variation in social behaviour is ubiquitous and causes social groups to differ in structure, how these structural differences affect fitness remains largely unknown. We used social network analysis of replicate bluebanded goby (Lythrypnus dalli) harems to identify the reproductive correlates of social network structure. In stable groups, we quantified agonistic behaviour, reproduction and steroid hormones, which can both affect and respond to social/reproductive cues. We identified distinct, optimal social structures associated with different reproductive measures. Male hatching success (HS) was negatively associated with agonistic reciprocity, a network structure that describes whether subordinates ‘reciprocated’ agonism received from dominants. Egg laying was associated with the individual network positions of the male and dominant female. Thus, males face a trade-off between promoting structures that facilitate egg laying versus HS. Whether this reproductive conflict is avoidable remains to be determined. We also identified different social and/or reproductive roles for 11-ketotestosterone, 17β-oestradiol and cortisol, suggesting that specific neuroendocrine mechanisms may underlie connections between network structure and fitness. This is one of the first investigations of the reproductive and neuroendocrine correlates of social behaviour and network structure in replicate, naturalistic social groups and supports network structure as an important target for natural selection. PMID:26156769

Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity

PubMed Central

Pope, Welkin H; Bowman, Charles A; Russell, Daniel A; Jacobs-Sera, Deborah; Asai, David J; Cresawn, Steven G; Jacobs, William R; Hendrix, Roger W; Lawrence, Jeffrey G; Hatfull, Graham F; Abbazia, Patrick; Ababio, Amma; Adam, Naazneen

2015-01-01

The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery. DOI: http://dx.doi.org/10.7554/eLife.06416.001 PMID:25919952

Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity.

PubMed

Pope, Welkin H; Bowman, Charles A; Russell, Daniel A; Jacobs-Sera, Deborah; Asai, David J; Cresawn, Steven G; Jacobs, William R; Hendrix, Roger W; Lawrence, Jeffrey G; Hatfull, Graham F

2015-04-28

The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery.

Local order study of YFe 2D x (0⩽ x⩽3.5) compounds by X-ray absorption and Mössbauer spectroscopy

NASA Astrophysics Data System (ADS)

Paul-Boncour, V.; Wiesinger, G.; Reichl, Ch.; Latroche, M.; Percheron-Guégan, A.; Cortes, R.

2001-12-01

The local order in YFe 2D x deuterides has been characterized by EXAFS and 57Fe Mössbauer spectroscopy. For all the deuterides several Fe sites and a large distribution of Fe-Fe distances are observed. The Y-Fe and Y-Y distances are close to those calculated for a cubic C15 type structure, but with significant static disorder. These large distance distributions are related to the influence of hydrogen atoms which induce local distortions of the interstitial sites with a displacement of Y and Fe atoms. However, the bulk and mean local magnetic properties remain sensitive to the long range order structure of the deuterides.

A large iris-like expansion of a mechanosensitive channel protein induced by membrane tension

NASA Technical Reports Server (NTRS)

Betanzos, Monica; Chiang, Chien-Sung; Guy, H. Robert; Sukharev, Sergei

2002-01-01

MscL, a bacterial mechanosensitive channel of large conductance, is the first structurally characterized mechanosensor protein. Molecular models of its gating mechanisms are tested here. Disulfide crosslinking shows that M1 transmembrane alpha-helices in MscL of resting Escherichia coli are arranged similarly to those in the crystal structure of MscL from Mycobacterium tuberculosis. An expanded conformation was trapped in osmotically shocked cells by the specific bridging between Cys 20 and Cys 36 of adjacent M1 helices. These bridges stabilized the open channel. Disulfide bonds engineered between the M1 and M2 helices of adjacent subunits (Cys 32-Cys 81) do not prevent channel gating. These findings support gating models in which interactions between M1 and M2 of adjacent subunits remain unaltered while their tilts simultaneously increase. The MscL barrel, therefore, undergoes a large concerted iris-like expansion and flattening when perturbed by membrane tension.

Marriage and Suicide among Chinese Rural Young Women

ERIC Educational Resources Information Center

Zhang, Jie

2010-01-01

Suicides by young females in rural China contribute substantially to the high rate of suicide and the total number of suicides in China. Given the traditional familial structure that remains largely intact in rural China, this research focuses on whether being married is a risk or protective factor for suicide by young women. I examined 168 rural…

Thinning effects on tree mortality and snag recruitment in western Oregon

Treesearch

Erich Kyle Dodson; Klaus J. Puettmann; Adrian Ares

2013-01-01

Tree mortality shapes forest structural development and the resulting dead wood provides habitat for many species. However, the eff ects of thinning on mortality and large snag recruitment have been variable and remain poorly understood. We examined thinning eff ects on tree mortality at eleven Density Management Study (DMS) sites in western Oregon. Th inning reduced...

New Pay: Compensation as a Strategic Tool. Workforce Brief #5.

ERIC Educational Resources Information Center

Mitchell, Stephen

Although what the work companies do and how they do it have shifted significantly, companies' reward and salary structures have remained largely the same; however, a properly designed compensation and pay system can be a strategic tool to enhance a firm's competitiveness. New approaches tie pay more closely to performance, rather than to tenure…

Observational Learning in Mice Can Be Prevented by Medial Prefrontal Cortex Stimulation and Enhanced by Nucleus Accumbens Stimulation

ERIC Educational Resources Information Center

Jurado-Parras, M. Teresa; Gruart, Agnes; Delgado-Garcia, Jose M.

2012-01-01

The neural structures involved in ongoing appetitive and/or observational learning behaviors remain largely unknown. Operant conditioning and observational learning were evoked and recorded in a modified Skinner box provided with an on-line video recording system. Mice improved their acquisition of a simple operant conditioning task by…

Reintroducing fire in regenerated dry forests following stand-replacing wildfire.

Treesearch

David W. Peterson; Paul F. Hessburg; Brion Salter; Kevin M. James; Matthew C. Dahlgreen; John A. Barnes

2007-01-01

Prescribed fire use may be effective for increasing fire resilience in young coniferous forests by reducing surface fuels, modifying overstory stand structure, and promoting development of large trees of fire resistant species. Questions remain, however, about when and how to reintroduce fire in regenerated forests, and to what end. We studied the effects of spring...

ARC-1979-AC79-7095

NASA Image and Video Library

1979-07-11

Range : 312, 000 kilometers (195,000 miles) This photo of Ganymede (Ice Giant) was taken from Voyager 2 and shows features down to about 5 to 6 kilometers across. Different types of terrain common on Ganymede's surface are visible. The boundary of the largest region of dark ancient terrain on Ganymede can be seen to the east (right), revealing some of the light linear features which may be all that remains of a large ancient impact structure similar to the large ring structure on Callisto. The broad light regions running through the image are the typical grooved structures seen within another example of what might be evidence of large scale lateral motion in Ganymede's crust. The band of grooved terrain (about 100 kilometers wide) in this region appears to be offset by 50 kilometers or more on the left hand edge by a linear feature perpendicular to it. A feature similar to this one was previously discovered by Voyager 1. These are the first clear examples of strike-slip style faulting on any planet other than Earth. Many examples of craters of all ages can be seen in this image, ranging from fresh, bright ray craters to large, subdued circular markings thought to be the 'scars' of large ancient impacts that have been flatteded by glacier-like flows.

Ultrafast dynamics of self-assembled monolayers under shock compression: effects of molecular and substrate structure.

PubMed

Lagutchev, Alexei S; Patterson, James E; Huang, Wentao; Dlott, Dana D

2005-03-24

Laser-driven approximately 1 GPa shock waves are used to dynamically compress self-assembled monolayers (SAMs) consisting of octadecanethiol (ODT) on Au and Ag, and pentanedecanethiol (PDT) and benzyl mercaptan (BMT) on Au. The SAM response to <4 ps shock loading and approximately 25 ps shock unloading is monitored by vibrational sum-frequency generation spectroscopy (SFG), which is sensitive to the instantaneous tilt angle of the SAM terminal group relative to the surface normal. Arrival of the shock front causes SFG signal loss in all SAMs with a material time constant <3.5 ps. Thermal desorption and shock recovery experiments show that SAMs remain adsorbed on the substrate, so signal loss is attributed to shock tilting of the methyl or phenyl groups to angles near 90 degrees. When the shock unloads, PDT/Au returns elastically to its native structure whereas ODT/Au does not. ODT evidences a complicated viscoelastic response that arises from at least two conformers, one that remains kinetically trapped in a large-tilt-angle conformation for times >250 ps and one that relaxes in approximately 30 ps to a nearly upright conformation. Although the shock responses of PDT/Au, ODT/Ag, and BMT/Au are primarily elastic, a small portion of the molecules, 10-20%, evidence viscoelastic response, either becoming kinetically trapped in large-tilt states or by relaxing in approximately 30 ps back to the native structure. The implications of the observed large-amplitude monolayer dynamics for lubrication under extreme conditions of high strain rates are discussed briefly.

Satellite traces: An ionogram signature for large-scale wave structure and a precursor for equatorial spread F

NASA Astrophysics Data System (ADS)

Tsunoda, Roland T.

2008-10-01

Although the source that controls day-to-day variability in the occurrence of equatorial plasma structure (i.e., equatorial spread F, or ESF) remains to be identified, progress is being made. There is evidence that the appearance of large-scale wave structure (LSWS) in the bottomside F layer, around the time of its post-sunset rise (PSSR), is a more-direct precursor of ESF than the PSSR itself. The bulk of the evidence, however, is in the form of ``satellite'' F traces in ionograms, which may be viewed as less than convincing, because these signatures have not been shown to be causally related to LSWS. In this paper, incoherent-scatter radar and ionosonde data, both collected on 24 July 1979 from the Kwajalein atoll, Marshall Islands, are used to show that this is indeed the case.

Molecular Precision at Micrometer Length Scales: Hierarchical Assembly of DNA-Protein Nanostructures.

PubMed

Schiffels, Daniel; Szalai, Veronika A; Liddle, J Alexander

2017-07-25

Robust self-assembly across length scales is a ubiquitous feature of biological systems but remains challenging for synthetic structures. Taking a cue from biology-where disparate molecules work together to produce large, functional assemblies-we demonstrate how to engineer microscale structures with nanoscale features: Our self-assembly approach begins by using DNA polymerase to controllably create double-stranded DNA (dsDNA) sections on a single-stranded template. The single-stranded DNA (ssDNA) sections are then folded into a mechanically flexible skeleton by the origami method. This process simultaneously shapes the structure at the nanoscale and directs the large-scale geometry. The DNA skeleton guides the assembly of RecA protein filaments, which provides rigidity at the micrometer scale. We use our modular design strategy to assemble tetrahedral, rectangular, and linear shapes of defined dimensions. This method enables the robust construction of complex assemblies, greatly extending the range of DNA-based self-assembly methods.

Co-residence patterns in hunter-gatherer societies show unique human social structure.

PubMed

Hill, Kim R; Walker, Robert S; Bozicević, Miran; Eder, James; Headland, Thomas; Hewlett, Barry; Hurtado, A Magdalena; Marlowe, Frank; Wiessner, Polly; Wood, Brian

2011-03-11

Contemporary humans exhibit spectacular biological success derived from cumulative culture and cooperation. The origins of these traits may be related to our ancestral group structure. Because humans lived as foragers for 95% of our species' history, we analyzed co-residence patterns among 32 present-day foraging societies (total n = 5067 individuals, mean experienced band size = 28.2 adults). We found that hunter-gatherers display a unique social structure where (i) either sex may disperse or remain in their natal group, (ii) adult brothers and sisters often co-reside, and (iii) most individuals in residential groups are genetically unrelated. These patterns produce large interaction networks of unrelated adults and suggest that inclusive fitness cannot explain extensive cooperation in hunter-gatherer bands. However, large social networks may help to explain why humans evolved capacities for social learning that resulted in cumulative culture.

Altered contralateral sensorimotor system organization after experimental hemispherectomy: a structural and functional connectivity study.

PubMed

Otte, Willem M; van der Marel, Kajo; van Meer, Maurits P A; van Rijen, Peter C; Gosselaar, Peter H; Braun, Kees P J; Dijkhuizen, Rick M

2015-08-01

Hemispherectomy is often followed by remarkable recovery of cognitive and motor functions. This reflects plastic capacities of the remaining hemisphere, involving large-scale structural and functional adaptations. Better understanding of these adaptations may (1) provide new insights in the neuronal configuration and rewiring that underlies sensorimotor outcome restoration, and (2) guide development of rehabilitation strategies to enhance recovery after hemispheric lesioning. We assessed brain structure and function in a hemispherectomy model. With MRI we mapped changes in white matter structural integrity and gray matter functional connectivity in eight hemispherectomized rats, compared with 12 controls. Behavioral testing involved sensorimotor performance scoring. Diffusion tensor imaging and resting-state functional magnetic resonance imaging were acquired 7 and 49 days post surgery. Hemispherectomy caused significant sensorimotor deficits that largely recovered within 2 weeks. During the recovery period, fractional anisotropy was maintained and white matter volume and axial diffusivity increased in the contralateral cerebral peduncle, suggestive of preserved or improved white matter integrity despite overall reduced white matter volume. This was accompanied by functional adaptations in the contralateral sensorimotor network. The observed white matter modifications and reorganization of functional network regions may provide handles for rehabilitation strategies improving functional recovery following large lesions.

How mammalian predation contributes to tropical tree community structure.

PubMed

Paine, C E Timothy; Beck, Harald; Terborgh, John

2016-12-01

The recruitment of seedlings from seeds is the key demographic transition for rain forest trees. Though tropical forest mammals are known to consume many seeds, their effects on tree community structure remain little known. To evaluate their effects, we monitored 8,000 seeds of 24 tree species using exclosure cages that were selectively permeable to three size classes of mammals for up to 4.4 years. Small and medium-bodied mammals removed many more seeds than did large mammals, and they alone generated beta diversity and negative density dependence, whereas all mammals reduced diversity and shaped local species composition. Thus, small and medium-bodied mammals more strongly contributed to community structure and promoted species coexistence than did large mammals. Given that seedling recruitment is seed limited for most species, alterations to the composition of the community of mammalian seed predators is expected to have long-term consequences for tree community structure in tropical forests. © 2016 by the Ecological Society of America.

Structural morphology of zinc oxide structures with antibacterial application of calamine lotion

NASA Astrophysics Data System (ADS)

Ann, Ling Chuo; Mahmud, Shahrom; Bakhori, Siti Khadijah Mohd; Sirelkhatim, Amna; Mohamad, Dasmawati; Hasan, Habsah; Seeni, Azman; Rahman, Rosliza Abdul

2015-04-01

In this study, we report the structural morphology of a zinc oxide (ZnO) sample and antibacterial application of the ZnO structures in calamine lotion. Antibacterial activities of the calamine lotion towards Staphylococcus aureus and Pseudomonas aeruginosa were investigated. The structural morphology of ZnO sample was studied using a transmission electron microscope (TEM) and a field-emission scanning electron microscope (FESEM). The morphologies of the ZnO structure consisted of many rod and spherical structures. The particle sizes of the sample ranged from 40 nm to 150 nm. A calamine lotion was prepared through mixing the ZnO structures with other constituents in suitable proportion. The energy-dispersive x-ray spectroscopy (EDS) revealed the presence of large amount of ZnO structures whiles the X-ray diffraction (XRD) results showed a good crystalline property of ZnO in the calamine lotion mixture. The morphological structures of ZnO were found to remain unchanged in the calamine lotion mixture through FESEM imaging. In the antibacterial test, prepared calamine lotion exhibited a remarkable bacterial inhibition on Staphylococcus aureus and Pseudomonas aeruginosa after 24 h of treatment. The bactericidal capability of calamine lotion was largely due to the presence of ZnO structures which induce high toxicity and killing effect on the bacteria.

Global properties of the plasma in the outer heliosphere. I - Large-scale structure and evolution

NASA Technical Reports Server (NTRS)

Barnes, A.; Mihalov, J. D.; Gazis, P. R.; Lazarus, A. J.; Belcher, J. W.; Gordon, G. S., Jr.; Mcnutt, R. L., Jr.

1992-01-01

Pioneers 10 and 11, and Voyager 2, have active plasma analyzers as they proceed through heliocentric distances of the order of 30-50 AU, facilitating comparative studies of the global character of the outer solar wind and its variation over the solar cycle. Careful study of these data show that wind ion temperature remains constant beyond 15 AU, and that there may be large-scale variations of temperature with celestial longitude and heliographic latitude. There has thus far been no indication of a heliospheric terminal shock.

Why is hydrofluoric acid a weak acid?

PubMed

Ayotte, Patrick; Hébert, Martin; Marchand, Patrick

2005-11-08

The infrared vibrational spectra of amorphous solid water thin films doped with HF at 40 K reveal a strong continuous absorbance in the 1000-3275 cm(-1) range. This so-called Zundel continuum is the spectroscopic hallmark for aqueous protons. The extensive ionic dissociation of HF at such low temperature suggests that the reaction enthalpy remains negative down to 40 K. These observations support the interpretation that dilute HF aqueous solutions behave as weak acids largely due to the large positive reaction entropy resulting from the structure making character of the hydrated fluoride ion.

Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry.

PubMed

Rappoport, Dmitrij; Galvin, Cooper J; Zubarev, Dmitry Yu; Aspuru-Guzik, Alán

2014-03-11

While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for modeling complex structures and large-scale chemical systems. Here, we present a heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in cell metabolism and prebiotic chemistry. Chemical heuristics offer an expedient way of traversing high-dimensional reactive potential energy surfaces and are combined here with quantum chemical structure optimizations, which yield the structures and energies of the reaction intermediates and products. Application of heuristics-aided quantum chemical methodology to the formose reaction reproduces the experimentally observed reaction products, major reaction pathways, and autocatalytic cycles.

CELFE: Coupled Eulerian-Lagrangian Finite Element program for high velocity impact. Part 1: Theory and formulation. [hydroelasto-viscoplastic model

NASA Technical Reports Server (NTRS)

Lee, C. H.

1978-01-01

A 3-D finite element program capable of simulating the dynamic behavior in the vicinity of the impact point, together with predicting the dynamic response in the remaining part of the structural component subjected to high velocity impact is discussed. The finite algorithm is formulated in a general moving coordinate system. In the vicinity of the impact point contained by a moving failure front, the relative velocity of the coordinate system will approach the material particle velocity. The dynamic behavior inside the region is described by Eulerian formulation based on a hydroelasto-viscoplastic model. The failure front which can be regarded as the boundary of the impact zone is described by a transition layer. The layer changes the representation from the Eulerian mode to the Lagrangian mode outside the failure front by varying the relative velocity of the coordinate system to zero. The dynamic response in the remaining part of the structure described by the Lagrangian formulation is treated using advanced structural analysis. An interfacing algorithm for coupling CELFE with NASTRAN is constructed to provide computational capabilities for large structures.

Discrete-continuous duality of protein structure space.

PubMed

Sadreyev, Ruslan I; Kim, Bong-Hyun; Grishin, Nick V

2009-06-01

Recently, the nature of protein structure space has been widely discussed in the literature. The traditional discrete view of protein universe as a set of separate folds has been criticized in the light of growing evidence that almost any arrangement of secondary structures is possible and the whole protein space can be traversed through a path of similar structures. Here we argue that the discrete and continuous descriptions are not mutually exclusive, but complementary: the space is largely discrete in evolutionary sense, but continuous geometrically when purely structural similarities are quantified. Evolutionary connections are mainly confined to separate structural prototypes corresponding to folds as islands of structural stability, with few remaining traceable links between the islands. However, for a geometric similarity measure, it is usually possible to find a reasonable cutoff that yields paths connecting any two structures through intermediates.

The structure of mouse cytomegalovirus m04 protein obtained from sparse NMR data reveals a conserved fold of the m02-m06 viral immune modulator family.

PubMed

Sgourakis, Nikolaos G; Natarajan, Kannan; Ying, Jinfa; Vogeli, Beat; Boyd, Lisa F; Margulies, David H; Bax, Ad

2014-09-02

Immunoevasins are key proteins used by viruses to subvert host immune responses. Determining their high-resolution structures is key to understanding virus-host interactions toward the design of vaccines and other antiviral therapies. Mouse cytomegalovirus encodes a unique set of immunoevasins, the m02-m06 family, that modulates major histocompatibility complex class I (MHC-I) antigen presentation to CD8+ T cells and natural killer cells. Notwithstanding the large number of genetic and functional studies, the structural biology of immunoevasins remains incompletely understood, largely because of crystallization bottlenecks. Here we implement a technology using sparse nuclear magnetic resonance data and integrative Rosetta modeling to determine the structure of the m04/gp34 immunoevasin extracellular domain. The structure reveals a β fold that is representative of the m02-m06 family of viral proteins, several of which are known to bind MHC-I molecules and interfere with antigen presentation, suggesting its role as a diversified immune regulation module. Copyright © 2014 Elsevier Ltd. All rights reserved.

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures.

PubMed

McGreevy, Ryan; Singharoy, Abhishek; Li, Qufei; Zhang, Jingfen; Xu, Dong; Perozo, Eduardo; Schulten, Klaus

2014-09-01

X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of D-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

Survey of large protein complexes D. vulgaris reveals great structural diversity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, B.-G.; Dong, M.; Liu, H.

2009-08-15

An unbiased survey has been made of the stable, most abundant multi-protein complexes in Desulfovibrio vulgaris Hildenborough (DvH) that are larger than Mr {approx} 400 k. The quaternary structures for 8 of the 16 complexes purified during this work were determined by single-particle reconstruction of negatively stained specimens, a success rate {approx}10 times greater than that of previous 'proteomic' screens. In addition, the subunit compositions and stoichiometries of the remaining complexes were determined by biochemical methods. Our data show that the structures of only two of these large complexes, out of the 13 in this set that have recognizable functions,more » can be modeled with confidence based on the structures of known homologs. These results indicate that there is significantly greater variability in the way that homologous prokaryotic macromolecular complexes are assembled than has generally been appreciated. As a consequence, we suggest that relying solely on previously determined quaternary structures for homologous proteins may not be sufficient to properly understand their role in another cell of interest.« less

Neurodevelopmental alterations of large-scale structural networks in children with new-onset epilepsy.

PubMed

Bonilha, Leonardo; Tabesh, Ali; Dabbs, Kevin; Hsu, David A; Stafstrom, Carl E; Hermann, Bruce P; Lin, Jack J

2014-08-01

Recent neuroimaging and behavioral studies have revealed that children with new onset epilepsy already exhibit brain structural abnormalities and cognitive impairment. How the organization of large-scale brain structural networks is altered near the time of seizure onset and whether network changes are related to cognitive performances remain unclear. Recent studies also suggest that regional brain volume covariance reflects synchronized brain developmental changes. Here, we test the hypothesis that epilepsy during early-life is associated with abnormalities in brain network organization and cognition. We used graph theory to study structural brain networks based on regional volume covariance in 39 children with new-onset seizures and 28 healthy controls. Children with new-onset epilepsy showed a suboptimal topological structural organization with enhanced network segregation and reduced global integration compared with controls. At the regional level, structural reorganization was evident with redistributed nodes from the posterior to more anterior head regions. The epileptic brain network was more vulnerable to targeted but not random attacks. Finally, a subgroup of children with epilepsy, namely those with lower IQ and poorer executive function, had a reduced balance between network segregation and integration. Taken together, the findings suggest that the neurodevelopmental impact of new onset childhood epilepsies alters large-scale brain networks, resulting in greater vulnerability to network failure and cognitive impairment. Copyright © 2014 Wiley Periodicals, Inc.

Structural attributes of two old-growth Cross Timbers stands in western Arkansas

Treesearch

Don C. Bragg; David W. Stahle; K. Chris Cerny

2012-01-01

Comprised of largely non-commercial, xeric, oak-dominated forests, the Cross Timbers in Arkansas have been heavily altered over the last two centuries, and thus only scattered parcels of old-growth timber remain. We inventoried and mapped two such stands on Fort Chaffee Military Training Center in Sebastian County, Arkansas. The west-facing Christmas Knob site is...

Airborne lidar-based estimates of tropical forest structure in complex terrain: opportunities and trade-offs for REDD+

Treesearch

Veronika Leitold; Michael Keller; Douglas C Morton; Bruce D Cook; Yosio E Shimabukuro

2015-01-01

Background: Carbon stocks and fluxes in tropical forests remain large sources of uncertainty in the global carbon budget. Airborne lidar remote sensing is a powerful tool for estimating aboveground biomass, provided that lidar measurements penetrate dense forest vegetation to generate accurate estimates of surface topography and canopy heights. Tropical forest areas...

Structural insight into exosite binding and discovery of novel exosite inhibitors of botulinum neurotoxin serotype A through in silico screening

NASA Astrophysics Data System (ADS)

Hu, Xin; Legler, Patricia M.; Southall, Noel; Maloney, David J.; Simeonov, Anton; Jadhav, Ajit

2014-07-01

Botulinum neurotoxin serotype A (BoNT/A) is the most lethal toxin among the Tier 1 Select Agents. Development of potent and selective small molecule inhibitors against BoNT/A zinc metalloprotease remains a challenging problem due to its exceptionally large substrate binding surface and conformational plasticity. The exosites of the catalytic domain of BoNT/A are intriguing alternative sites for small molecule intervention, but their suitability for inhibitor design remains largely unexplored. In this study, we employed two recently identified exosite inhibitors, D-chicoric acid and lomofungin, to probe the structural features of the exosites and molecular mechanisms of synergistic inhibition. The results showed that D-chicoric acid favors binding at the α-exosite, whereas lomofungin preferentially binds at the β-exosite by mimicking the substrate β-sheet binding interaction. Molecular dynamics simulations and binding interaction analysis of the exosite inhibitors with BoNT/A revealed key elements and hotspots that likely contribute to the inhibitor binding and synergistic inhibition. Finally, we performed database virtual screening for novel inhibitors of BoNT/A targeting the exosites. Hits C1 and C2 showed non-competitive inhibition and likely target the α- and β-exosites, respectively. The identified exosite inhibitors may provide novel candidates for structure-based development of therapeutics against BoNT/A intoxication.

Structural insight into exosite binding and discovery of novel exosite inhibitors of botulinum neurotoxin serotype A through in silico screening.

PubMed

Hu, Xin; Legler, Patricia M; Southall, Noel; Maloney, David J; Simeonov, Anton; Jadhav, Ajit

2014-07-01

Botulinum neurotoxin serotype A (BoNT/A) is the most lethal toxin among the Tier 1 Select Agents. Development of potent and selective small molecule inhibitors against BoNT/A zinc metalloprotease remains a challenging problem due to its exceptionally large substrate binding surface and conformational plasticity. The exosites of the catalytic domain of BoNT/A are intriguing alternative sites for small molecule intervention, but their suitability for inhibitor design remains largely unexplored. In this study, we employed two recently identified exosite inhibitors, D-chicoric acid and lomofungin, to probe the structural features of the exosites and molecular mechanisms of synergistic inhibition. The results showed that D-chicoric acid favors binding at the α-exosite, whereas lomofungin preferentially binds at the β-exosite by mimicking the substrate β-sheet binding interaction. Molecular dynamics simulations and binding interaction analysis of the exosite inhibitors with BoNT/A revealed key elements and hotspots that likely contribute to the inhibitor binding and synergistic inhibition. Finally, we performed database virtual screening for novel inhibitors of BoNT/A targeting the exosites. Hits C1 and C2 showed non-competitive inhibition and likely target the α- and β-exosites, respectively. The identified exosite inhibitors may provide novel candidates for structure-based development of therapeutics against BoNT/A intoxication.

Long-term stability in the richness and structure of helminth communities in eels, Anguilla anguilla, in Lough Derg, River Shannon, Ireland.

PubMed

Kennedy, C R; Moriarty, C

2002-12-01

A data set on intestinal helminth parasites was collected in the course of an 18 year investigation into the biology of eels in Meelick Bay, Lough Derg, River Shannon. This was used to test two hypotheses relating to the composition and structure of intestinal helminth communities, namely that eels in large rivers do not harbour richer and more diverse communities than those in small rivers but that community composition and structure are more stable over time than in small rivers. The helminth community was species poor, with only six species comprising the component community and a maximum infracommunity richness of three species. The community was overwhelmingly dominated by the acanthocephalan Acanthocephalus lucii, reflecting the importance of its intermediate host Asellus aquaticus in the eels' diet. The remaining helminth species contributed to species richness but made very little contribution to community diversity. Population levels of Acanthocephalus lucii fell and remained low between 1992 and 2000, probably reflecting increased movement of eels from other parts of the lough into Meelick Bay. Diversity values were low, but similar to those reported from other rivers in Britain and Europe. The results provided support for both hypotheses and indicated that in respect of richness, diversity and dominance, the helminth communities of eels in the River Shannon were typical of, and comparable to, those of other large rivers throughout Europe.

The stable clustering ansatz, consistency relations and gravity dual of large-scale structure

NASA Astrophysics Data System (ADS)

Munshi, Dipak

2018-02-01

Gravitational clustering in the nonlinear regime remains poorly understood. Gravity dual of gravitational clustering has recently been proposed as a means to study the nonlinear regime. The stable clustering ansatz remains a key ingredient to our understanding of gravitational clustering in the highly nonlinear regime. We study certain aspects of violation of the stable clustering ansatz in the gravity dual of Large Scale Structure (LSS). We extend the recent studies of gravitational clustering using AdS gravity dual to take into account possible departure from the stable clustering ansatz and to arbitrary dimensions. Next, we extend the recently introduced consistency relations to arbitrary dimensions. We use the consistency relations to test the commonly used models of gravitational clustering including the halo models and hierarchical ansätze. In particular we establish a tower of consistency relations for the hierarchical amplitudes: Q, Ra, Rb, Sa,Sb,Sc etc. as a functions of the scaled peculiar velocity h. We also study the variants of popular halo models in this context. In contrast to recent claims, none of these models, in their simplest incarnation, seem to satisfy the consistency relations in the soft limit.

Fine structure of 25 extragalactic radio sources. [interferometric observations of quasars

NASA Technical Reports Server (NTRS)

Wittels, J. J.; Knight, C. A.; Shapiro, I. I.; Hinteregger, H. F.; Rogers, A. E. E.; Whitney, A. R.; Clark, T. A.; Hutton, L. K.; Marandino, G. E.; Niell, A. E.

1975-01-01

Interferometric observations taken at 7.8 GHz (gamma approximately = 3.8 cm) with five pairings of antennae of 25 extragalactic radio sources between April, 1972 and May, 1973 are reported. These sources exhibit a broad variety of fine structure from very simple to complex. The total flux and the correlated flux of some of the sources underwent large changes in a few weeks, while the structure and total power of others remained constant during the entire period of observation. Some aspects of the data processing and a discussion of errors are presented. Numerous figures are provided and explained. The individual radio sources are described in detail.

Structure of exoplanets

PubMed Central

Spiegel, David S.; Fortney, Jonathan J.; Sotin, Christophe

2014-01-01

The hundreds of exoplanets that have been discovered in the past two decades offer a new perspective on planetary structure. Instead of being the archetypal examples of planets, those of our solar system are merely possible outcomes of planetary system formation and evolution, and conceivably not even especially common outcomes (although this remains an open question). Here, we review the diverse range of interior structures that are both known and speculated to exist in exoplanetary systems—from mostly degenerate objects that are more than 10× as massive as Jupiter, to intermediate-mass Neptune-like objects with large cores and moderate hydrogen/helium envelopes, to rocky objects with roughly the mass of Earth. PMID:24379369

Structure of exoplanets.

PubMed

Spiegel, David S; Fortney, Jonathan J; Sotin, Christophe

2014-09-02

The hundreds of exoplanets that have been discovered in the past two decades offer a new perspective on planetary structure. Instead of being the archetypal examples of planets, those of our solar system are merely possible outcomes of planetary system formation and evolution, and conceivably not even especially common outcomes (although this remains an open question). Here, we review the diverse range of interior structures that are both known and speculated to exist in exoplanetary systems--from mostly degenerate objects that are more than 10× as massive as Jupiter, to intermediate-mass Neptune-like objects with large cores and moderate hydrogen/helium envelopes, to rocky objects with roughly the mass of Earth.

Structure, synthesis and biological properties of the pentacyclic guanidinium alkaloids.

PubMed

Shi, Yunlong; Moazami, Yasamin; Pierce, Joshua G

2017-06-01

The pentacyclic guanidinium alkaloids (PGAs) are a family of marine natural products that possess a polycyclic guanidine-containing core and a long alkyl chain tethered spermidine-derived tail that is rarely observed in other natural products. These natural products exhibit potent activities on a wide range of organisms and therefore have attracted the attention of many synthetic chemists; however, the structure-activity relationships and mechanisms of action of PGAs remain largely elusive. Herein we summarize the structure, synthesis, toxicity and mechanisms of action of PGAs and highlight their potential as chemical probes and/or therapeutic leads. Copyright © 2017 Elsevier Ltd. All rights reserved.

Where's the Beaverhead beef?. [meteorite impact structure

NASA Technical Reports Server (NTRS)

Hargraves, R. B.

1992-01-01

Only rare quartz grains with single-set planar (1013) deformation features (PDF's) are present in breccia dikes found in association with uniformly oriented shatter cones that occur over an area 8 x 25 km. This suggests that the Beaverhead shocked rocks come from only the outer part of the central uplift of what must have been a large (greater than 100 km diameter) complex impact structure. An impact event of this magnitude on continental crust (thought to have occurred in late Precambrian or ealy Paleozoic time) could be expected to punctuate local geologic history. Furthermore, although it may now be covered, its scar should remain despite all the considerable subsequent erosion/deposition and tectonism since the impact. The following are three large-scale singularities or anomalies that may reflect the event and mark its source. (1) The Lemhi Arch is a major structural uplift that occurred in late Proterozoic-early Paleozoic time in East Central Idaho and caused the erosion of at least 4 km of sedimentary cover. This may be directly related to the impact. (2) Of the many thrust sheets comprising the Cordilleran belt, the Cabin plate that carries the shocked rocks is unique in that it alone intersected the crystalline basement. It also now marks the apex of the Southwest Montana Recess in the Sevier front. The basement uplift remaining from the impact may have constituted a mechanical obstacle to the advancing thrust sheets in Cretaceous time, causing the recess. (3) What could be interpreted as a roughly circular aeromagnetic anomaly approx. 70 km in diameter can be discerned in the state aeromagnetic map centered about 20 km southeast of Challis, Idaho, in the Lost River range. It is in approximately the right place, and ignoring the possibility that the anomalies have diverse causes and the circular pattern is coincidental, it may mark what remains of the buried central uplift structure.

Magnetostructural Transition Kinetics in Shocked Iron

DOE PAGES

Surh, Michael P.; Benedict, Lorin X.; Sadigh, Babak

2016-08-15

Here, a generalized Heisenberg model is implemented to study the effect of thermal magnetic disorder on kinetics of the Fe α–ε transition. The barrier to bulk martensitic displacement remains large in α-Fe shocked well past the phase line but is much reduced in the [001] α–ε boundary. The first result is consistent with observed overdriving to metastable α, while the second suggests structural instability, as implied by observation of a [001] shock transformation front without plastic relaxation. Reconciling both behaviors may require concurrent treatment of magnetic and structural order.

The colibactin warhead crosslinks DNA

NASA Astrophysics Data System (ADS)

Vizcaino, Maria I.; Crawford, Jason M.

2015-05-01

Members of the human microbiota are increasingly being correlated to human health and disease states, but the majority of the underlying microbial metabolites that regulate host-microbe interactions remain largely unexplored. Select strains of Escherichia coli present in the human colon have been linked to the initiation of inflammation-induced colorectal cancer through an unknown small-molecule-mediated process. The responsible non-ribosomal peptide-polyketide hybrid pathway encodes ‘colibactin’, which belongs to a largely uncharacterized family of small molecules. Genotoxic small molecules from this pathway that are capable of initiating cancer formation have remained elusive due to their high instability. Guided by metabolomic analyses, here we employ a combination of NMR spectroscopy and bioinformatics-guided isotopic labelling studies to characterize the colibactin warhead, an unprecedented substituted spirobicyclic structure. The warhead crosslinks duplex DNA in vitro, providing direct experimental evidence for colibactin's DNA-damaging activity. The data support unexpected models for both colibactin biosynthesis and its mode of action.

Induction of Female-to-Male Sex Change in Adult Zebrafish by Aromatase Inhibitor Treatment

NASA Astrophysics Data System (ADS)

Takatsu, Kanae; Miyaoku, Kaori; Roy, Shimi Rani; Murono, Yuki; Sago, Tomohiro; Itagaki, Hideyuki; Nakamura, Masaru; Tokumoto, Toshinobu

2013-12-01

This study investigated whether undifferentiated germ and/or somatic stem cells remain in the differentiated ovary of a species that does not undergo sex changes under natural conditions and retain their sexual plasticity. The effect of aromatase inhibitor (AI)-treatment on sexually mature female zebrafish was examined. A 5-month AI treatment caused retraction of the ovaries after which testes-like organs appeared, and cyst structures filled with spermatozoa-like cells were observed in sections of these tissues. Electron microscopic observations revealed that these cells appeared as large sperm heads without tails. Sperm formation was re-examined after changing the diet to an AI-free food. A large number of normal sperm were obtained after eight weeks, and no formation of ovarian tissue was observed. Artificial fertilization using sperm from the sex-changed females was successful. These results demonstrated that sex plasticity remains in the mature ovaries of this species.

Protein Models Docking Benchmark 2

PubMed Central

Anishchenko, Ivan; Kundrotas, Petras J.; Tuzikov, Alexander V.; Vakser, Ilya A.

2015-01-01

Structural characterization of protein-protein interactions is essential for our ability to understand life processes. However, only a fraction of known proteins have experimentally determined structures. Such structures provide templates for modeling of a large part of the proteome, where individual proteins can be docked by template-free or template-based techniques. Still, the sensitivity of the docking methods to the inherent inaccuracies of protein models, as opposed to the experimentally determined high-resolution structures, remains largely untested, primarily due to the absence of appropriate benchmark set(s). Structures in such a set should have pre-defined inaccuracy levels and, at the same time, resemble actual protein models in terms of structural motifs/packing. The set should also be large enough to ensure statistical reliability of the benchmarking results. We present a major update of the previously developed benchmark set of protein models. For each interactor, six models were generated with the model-to-native Cα RMSD in the 1 to 6 Å range. The models in the set were generated by a new approach, which corresponds to the actual modeling of new protein structures in the “real case scenario,” as opposed to the previous set, where a significant number of structures were model-like only. In addition, the larger number of complexes (165 vs. 63 in the previous set) increases the statistical reliability of the benchmarking. We estimated the highest accuracy of the predicted complexes (according to CAPRI criteria), which can be attained using the benchmark structures. The set is available at http://dockground.bioinformatics.ku.edu. PMID:25712716

Changing structure and resources in a rheumatology combined unit during 1977-1999.

PubMed

Kvalvik, A G; Larsen, S; Aadland, H A; Høyeraal, H M

2007-01-01

The aim was to study the changing structure and resources in a rheumatism hospital during the period 1977-1999 when rheumatology care was decentralized and new treatment strategies were introduced. Data on hospital management and production were retrieved retrospectively. The number of beds was stepwise reduced from 133 to 44 and the average length of stay declined from 48 to 16 days. The combined unit and multidisciplinary team organization was kept, ensuring the combined effort of rheumatologists, rheumasurgeons, registered nurses, physiotherapists, occupational therapists, and social workers. One-third of the total staff was rheumateam members in 1977 compared to one-half in 1999. The proportions of physicians and registered nurses increased while the proportion of physiotherapists was stable. The number of discharges remained relatively unchanged and the number of outpatient consultations increased. Inflammatory rheumatic diseases remained the largest diagnostic group of in- and outpatients. Hospitalized care was received primarily by patients with arthritis and spondylitis. Patients with vasculitis and diffuse disorders of connective tissue accounted for an increasing proportion of the outpatient clinic production. Surgical procedures became more prevalent. Since 1995 approximately 50 large joint replacements have been performed annually. The length of stay declined and patient care was shifted towards the outpatient clinic. The multidisciplinary team was strengthened. More resources were dedicated to physician-led and nurse-dependent procedures, but physiotherapy and rehabilitation remained part of inpatient care throughout the period. The expertise concentrated on inflammatory rheumatic disorders. The modesty of the large joint replacement caseload may challenge decentralized care.

Nickel Ferrite Nanoparticles Anchored onto Silica Nanofibers for Designing Magnetic and Flexible Nanofibrous Membranes.

PubMed

Hong, Feifei; Yan, Chengcheng; Si, Yang; He, Jianxin; Yu, Jianyong; Ding, Bin

2015-09-16

Many applications proposed for magnetic silica nanofibers require their assembly into a cellular membrane structure. The feature to keep structure stable upon large deformation is crucial for a macroscopic porous material which functions reliably. However, it remains a key issue to realize robust flexibility in two-dimensional (2D) magnetic silica nanofibrous networks. Here, we report that the combination of electrospun silica nanofibers with zein dip-coating can lead to the formation of flexible, magnetic, and hierarchical porous silica nanofibrous membranes (SNM). The 290 nm diameter silica nanofibers act as templates for the uniform anchoring of nickel ferrite nanoparticles (size of 50 nm). Benefiting from the homogeneous and stable nanofiber-nanoparticle composite structure, the resulting magnetic SNM can maintain their structure integrity under repeated bending as high as 180° and can facilely recover. The unique hierarchical structure also provides this new class of silica membrane with integrated properties of ultralow density, high porosity, large surface area, good magnetic responsiveness, robust dye adsorption capacity, and effective emulsion separation performance. Significantly, the synthesis of such fascinating membranes may provide new insight for further application of silica in a self-supporting, structurally adaptive, and 2D membrane form.

Colorful Niches of Phytoplankton Shaped by the Spatial Connectivity in a Large River Ecosystem: A Riverscape Perspective

PubMed Central

Frenette, Jean-Jacques; Massicotte, Philippe; Lapierre, Jean-François

2012-01-01

Large rivers represent a significant component of inland waters and are considered sentinels and integrators of terrestrial and atmospheric processes. They represent hotspots for the transport and processing of organic and inorganic material from the surrounding landscape, which ultimately impacts the bio-optical properties and food webs of the rivers. In large rivers, hydraulic connectivity operates as a major forcing variable to structure the functioning of the riverscape, and–despite increasing interest in large-river studies–riverscape structural properties, such as the underwater spectral regime, and their impact on autotrophic ecological processes remain poorly studied. Here we used the St. Lawrence River to identify the mechanisms structuring the underwater spectral environment and their consequences on pico- and nanophytoplankton communities, which are good biological tracers of environmental changes. Our results, obtained from a 450 km sampling transect, demonstrate that tributaries exert a profound impact on the receiving river’s photosynthetic potential. This occurs mainly through injection of chromophoric dissolved organic matter (CDOM) and non-algal material (tripton). CDOM and tripton in the water column selectively absorbed wavelengths in a gradient from blue to red, and the resulting underwater light climate was in turn a strong driver of the phytoplankton community structure (prokaryote/eukaryote relative and absolute abundances) at scales of many kilometers from the tributary confluence. Our results conclusively demonstrate the proximal impact of watershed properties on underwater spectral composition in a highly dynamic river environment characterized by unique structuring properties such as high directional connectivity, numerous sources and forms of carbon, and a rapidly varying hydrodynamic regime. We surmise that the underwater spectral composition represents a key integrating and structural property of large, heterogeneous river ecosystems and a promising tool to study autotrophic functional properties. It confirms the usefulness of using the riverscape approach to study large-river ecosystems and initiate comparison along latitudinal gradients. PMID:22558259

Recent Advances and Future Challenges in Modified Mycotoxin Analysis: Why HRMS Has Become a Key Instrument in Food Contaminant Research

PubMed Central

Righetti, Laura; Paglia, Giuseppe; Galaverna, Gianni; Dall’Asta, Chiara

2016-01-01

Mycotoxins are secondary metabolites produced by pathogenic fungi in crops worldwide. These compounds can undergo modification in plants, leading to the formation of a large number of possible modified forms, whose toxicological relevance and occurrence in food and feed is still largely unexplored. The analysis of modified mycotoxins by liquid chromatography–mass spectrometry remains a challenge because of their chemical diversity, the large number of isomeric forms, and the lack of analytical standards. Here, the potential benefits of high-resolution and ion mobility mass spectrometry as a tool for separation and structure confirmation of modified mycotoxins have been investigated/reviewed. PMID:27918432

Photographer : JPL Range : 312, 000 kilometers (195,000 miles) This photo of Ganymede (Ice Giant)

NASA Technical Reports Server (NTRS)

1979-01-01

Photographer : JPL Range : 312, 000 kilometers (195,000 miles) This photo of Ganymede (Ice Giant) was taken from Voyager 2 and shows features down to about 5 to 6 kilometers across. Different types of terrain common on Ganymede's surface are visible. The boundary of the largest region of dark ancient terrain on Ganymede can be seen to the east (right), revealing some of the light linear features which may be all that remains of a large ancient impact structure similar to the large ring structure on Callisto. The broad light regions running through the image are the typical grooved structures seen within another example of what might be evidence of large scale lateral motion in Ganymede's crust. The band of grooved terrain (about 100 kilometers wide) in this region appears to be offset by 50 kilometers or more on the left hand edge by a linear feature perpendicular to it. A feature similar to this one was previously discovered by Voyager 1. These are the first clear examples of strike-slip style faulting on any planet other than Earth. Many examples of craters of all ages can be seen in this image, ranging from fresh, bright ray craters to large, subdued circular markings thought to be the 'scars' of large ancient impacts that have been flatteded by glacier-like flows.

Virtual interface substructure synthesis method for normal mode analysis of super-large molecular complexes at atomic resolution.

PubMed

Chen, Xuehui; Sun, Yunxiang; An, Xiongbo; Ming, Dengming

2011-10-14

Normal mode analysis of large biomolecular complexes at atomic resolution remains challenging in computational structure biology due to the requirement of large amount of memory space and central processing unit time. In this paper, we present a method called virtual interface substructure synthesis method or VISSM to calculate approximate normal modes of large biomolecular complexes at atomic resolution. VISSM introduces the subunit interfaces as independent substructures that join contacting molecules so as to keep the integrity of the system. Compared with other approximate methods, VISSM delivers atomic modes with no need of a coarse-graining-then-projection procedure. The method was examined for 54 protein-complexes with the conventional all-atom normal mode analysis using CHARMM simulation program and the overlap of the first 100 low-frequency modes is greater than 0.7 for 49 complexes, indicating its accuracy and reliability. We then applied VISSM to the satellite panicum mosaic virus (SPMV, 78,300 atoms) and to F-actin filament structures of up to 39-mer, 228,813 atoms and found that VISSM calculations capture functionally important conformational changes accessible to these structures at atomic resolution. Our results support the idea that the dynamics of a large biomolecular complex might be understood based on the motions of its component subunits and the way in which subunits bind one another. © 2011 American Institute of Physics

Design of structurally distinct proteins using strategies inspired by evolution

DOE PAGES

Jacobs, T. M.; Williams, B.; Williams, T.; ...

2016-05-06

Natural recombination combines pieces of preexisting proteins to create new tertiary structures and functions. In this paper, we describe a computational protocol, called SEWING, which is inspired by this process and builds new proteins from connected or disconnected pieces of existing structures. Helical proteins designed with SEWING contain structural features absent from other de novo designed proteins and, in some cases, remain folded at more than 100°C. High-resolution structures of the designed proteins CA01 and DA05R1 were solved by x-ray crystallography (2.2 angstrom resolution) and nuclear magnetic resonance, respectively, and there was excellent agreement with the design models. Finally, thismore » method provides a new strategy to rapidly create large numbers of diverse and designable protein scaffolds.« less

Numerical simulation of vehicle crashworthiness and occupant protection

NASA Astrophysics Data System (ADS)

Saha, Nripen K.

1993-08-01

Numerical simulation of vehicle crashworthiness and occupant protection are addressed. The vehicle crashworthiness design objectives are to design the vehicle structure for optimum impact energy absorption, and to design the restraint system (seatbelts, airbags, bolsters, etc.) for optimum occupant protection. The following approaches are taken; a major part of the impact energy is to be absorbed by the vehicle structure; the restraint components will provide protection against the remaining crash energy; certain vehicle components are designed to deform under specific types and speeds of impact in a desired mode for sound energy management; structural components such as front side rails, rear rails, door structure and pillars undergo large amounts of deformation; and with properly designed geometry and material these components assist in mitigating the effects of impact.

Numerical simulation of vehicle crashworthiness and occupant protection

NASA Technical Reports Server (NTRS)

Saha, Nripen K.

1993-01-01

Numerical simulation of vehicle crashworthiness and occupant protection are addressed. The vehicle crashworthiness design objectives are to design the vehicle structure for optimum impact energy absorption, and to design the restraint system (seatbelts, airbags, bolsters, etc.) for optimum occupant protection. The following approaches are taken; a major part of the impact energy is to be absorbed by the vehicle structure; the restraint components will provide protection against the remaining crash energy; certain vehicle components are designed to deform under specific types and speeds of impact in a desired mode for sound energy management; structural components such as front side rails, rear rails, door structure and pillars undergo large amounts of deformation; and with properly designed geometry and material these components assist in mitigating the effects of impact.

Chemical Structural Characteristics of HULIS and Other Fractionated Organic Matter in Urban Aerosols: Results from Mass Spectral and FT-IR Analysis.

PubMed

Chen, Qingcai; Ikemori, Fumikazu; Higo, Hayato; Asakawa, Daichi; Mochida, Michihiro

2016-02-16

The chemical characteristics of complex organic matter in atmospheric aerosols remain poorly understood. Water-insoluble organic matter (WISOM) and water-soluble organic matter (WSOM) in the total suspended particulates collected in the city of Nagoya in summer/early autumn and winter were extracted using multiple solvents. Two fractions of humic-like substances, showing neutral and acidic behavior (HULIS-n and HULIS-a, respectively), and the remaining highly polar part (HP-WSOM) were fractionated from WSOM using solid phase extraction. The chemical structural characteristics and concentrations of the organic matter were investigated using mass spectrometry and Fourier transform infrared (FT-IR) spectroscopy. WISOM and HULIS-n had low O/C ratios (0.1 and 0.4, respectively) and accounted for a large fraction of the organics in aerosols (70%). HULIS-a and HP-WSOM had higher O/C ratios (0.7 and 1.0, respectively), and their concentrations in summer and early autumn were on average ∼2 times higher than those in winter. The mass spectrum and FT-IR analyses suggest the following: (1) WISOM were high-molecular-weight aliphatics (primarily C27-C32) with small proportions of -CH3, -OH, and C═O groups; (2) HULIS-n was abundant in aliphatic structures and hydroxyl groups (primarily C9-C18) and by branched structures; (3) HULIS-a and HP-WSOM contained relatively large amounts of low-molecular-weight carboxylic acids and alcohols (primarily C4-C10); and (4) WISOM and HULIS-n were relatively abundant in amines and organic nitrates.

Structural morphology of zinc oxide structures with antibacterial application of calamine lotion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ann, Ling Chuo; Mahmud, Shahrom; Bakhori, Siti Khadijah Mohd

In this study, we report the structural morphology of a zinc oxide (ZnO) sample and antibacterial application of the ZnO structures in calamine lotion. Antibacterial activities of the calamine lotion towards Staphylococcus aureus and Pseudomonas aeruginosa were investigated. The structural morphology of ZnO sample was studied using a transmission electron microscope (TEM) and a field-emission scanning electron microscope (FESEM). The morphologies of the ZnO structure consisted of many rod and spherical structures. The particle sizes of the sample ranged from 40 nm to 150 nm. A calamine lotion was prepared through mixing the ZnO structures with other constituents in suitable proportion. Themore » energy-dispersive x-ray spectroscopy (EDS) revealed the presence of large amount of ZnO structures whiles the X-ray diffraction (XRD) results showed a good crystalline property of ZnO in the calamine lotion mixture. The morphological structures of ZnO were found to remain unchanged in the calamine lotion mixture through FESEM imaging. In the antibacterial test, prepared calamine lotion exhibited a remarkable bacterial inhibition on Staphylococcus aureus and Pseudomonas aeruginosa after 24 h of treatment. The bactericidal capability of calamine lotion was largely due to the presence of ZnO structures which induce high toxicity and killing effect on the bacteria.« less

Tornado Recovery Ongoing at NASA’s Michoud Assembly Facility, New Orleans LA

NASA Image and Video Library

2017-02-07

Teams at NASA’s Michoud Assembly Facility in New Orleans are continuing with recovery efforts following a tornado strike at the facility Tuesday, Feb. 7. Michoud remains closed to all but security and emergency operations crews. For more than half a century, Michoud has been the space agency’s premiere site for manufacturing and assembly of large-scale space structures and systems.

Satisfaction with College: Re-Examining Its Structure and Its Relationships with the Intent to Remain in College and Academic Performance

ERIC Educational Resources Information Center

Strahan, Sarah; Credé, Marcus

2015-01-01

Satisfaction with college is an important component of various theories of college student retention and academic performance but empirical support for the relationship of satisfaction with college with these two criteria has been mixed. Using data from two large datasets (N = 34,047 and N = 35,503) from 300 institutions we examine whether…

Ultrahigh-pressure polyamorphism in GeO2 glass with coordination number >6

NASA Astrophysics Data System (ADS)

Kono, Yoshio; Kenney-Benson, Curtis; Ikuta, Daijo; Shibazaki, Yuki; Wang, Yanbin; Shen, Guoyin

2016-03-01

Knowledge of pressure-induced structural changes in glasses is important in various scientific fields as well as in engineering and industry. However, polyamorphism in glasses under high pressure remains poorly understood because of experimental challenges. Here we report new experimental findings of ultrahigh-pressure polyamorphism in GeO2 glass, investigated using a newly developed double-stage large-volume cell. The Ge-O coordination number (CN) is found to remain constant at ∼6 between 22.6 and 37.9 GPa. At higher pressures, CN begins to increase rapidly and reaches 7.4 at 91.7 GPa. This transformation begins when the oxygen-packing fraction in GeO2 glass is close to the maximal dense-packing state (the Kepler conjecture = ∼0.74), which provides new insights into structural changes in network-forming glasses and liquids with CN higher than 6 at ultrahigh-pressure conditions.

Solvothermal transformation of a calcium oleate precursor into large-sized highly ordered arrays of ultralong hydroxyapatite microtubes.

PubMed

Lu, Bing-Qiang; Zhu, Ying-Jie; Chen, Feng; Qi, Chao; Zhao, Xin-Yu; Zhao, Jing

2014-06-02

Hydroxyapatite (HAP), a well-known member of the calcium phosphate family, is the major inorganic component of bones and teeth in vertebrates. The highly ordered arrays of HAP structures are of great significance for hard tissue repair and for understanding the formation mechanisms of bones and teeth. However, the synthesis of highly ordered HAP structure arrays remains a great challenge. In this work, inspired by the ordered structure of tooth enamel, we have successfully synthesized three-dimensional bulk materials with large sizes (millimeter scale) that are made of highly ordered arrays of ultralong HAP microtubes (HOAUHMs) by solvothermal transformation of calcium oleate precursor. The core-shell-structured oblate sphere consists of a core that is composed of HAP nanorods and a shell that consists of highly ordered HAP microtube arrays. The prepared HOAUHMs are large: 6.0 mm in diameter and up to 1.4 mm in thickness. With increasing solvothermal reaction time, the HOAUHMs grow larger; the microtubes become more uniform and more ordered. This work provides a new synthetic method for synthesizing highly ordered arrays of uniform HAP ultralong microtubes that are promising for biomedical applications. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Enabling Controlling Complex Networks with Local Topological Information.

PubMed

Li, Guoqi; Deng, Lei; Xiao, Gaoxi; Tang, Pei; Wen, Changyun; Hu, Wuhua; Pei, Jing; Shi, Luping; Stanley, H Eugene

2018-03-15

Complex networks characterize the nature of internal/external interactions in real-world systems including social, economic, biological, ecological, and technological networks. Two issues keep as obstacles to fulfilling control of large-scale networks: structural controllability which describes the ability to guide a dynamical system from any initial state to any desired final state in finite time, with a suitable choice of inputs; and optimal control, which is a typical control approach to minimize the cost for driving the network to a predefined state with a given number of control inputs. For large complex networks without global information of network topology, both problems remain essentially open. Here we combine graph theory and control theory for tackling the two problems in one go, using only local network topology information. For the structural controllability problem, a distributed local-game matching method is proposed, where every node plays a simple Bayesian game with local information and local interactions with adjacent nodes, ensuring a suboptimal solution at a linear complexity. Starring from any structural controllability solution, a minimizing longest control path method can efficiently reach a good solution for the optimal control in large networks. Our results provide solutions for distributed complex network control and demonstrate a way to link the structural controllability and optimal control together.

Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement.

PubMed

Jiang, Hanlun; Sheong, Fu Kit; Zhu, Lizhe; Gao, Xin; Bernauer, Julie; Huang, Xuhui

2015-07-01

Argonaute (Ago) proteins and microRNAs (miRNAs) are central components in RNA interference, which is a key cellular mechanism for sequence-specific gene silencing. Despite intensive studies, molecular mechanisms of how Ago recognizes miRNA remain largely elusive. In this study, we propose a two-step mechanism for this molecular recognition: selective binding followed by structural re-arrangement. Our model is based on the results of a combination of Markov State Models (MSMs), large-scale protein-RNA docking, and molecular dynamics (MD) simulations. Using MSMs, we identify an open state of apo human Ago-2 in fast equilibrium with partially open and closed states. Conformations in this open state are distinguished by their largely exposed binding grooves that can geometrically accommodate miRNA as indicated in our protein-RNA docking studies. miRNA may then selectively bind to these open conformations. Upon the initial binding, the complex may perform further structural re-arrangement as shown in our MD simulations and eventually reach the stable binary complex structure. Our results provide novel insights in Ago-miRNA recognition mechanisms and our methodology holds great potential to be widely applied in the studies of other important molecular recognition systems.

Structural biology computing: Lessons for the biomedical research sciences.

PubMed

Morin, Andrew; Sliz, Piotr

2013-11-01

The field of structural biology, whose aim is to elucidate the molecular and atomic structures of biological macromolecules, has long been at the forefront of biomedical sciences in adopting and developing computational research methods. Operating at the intersection between biophysics, biochemistry, and molecular biology, structural biology's growth into a foundational framework on which many concepts and findings of molecular biology are interpreted1 has depended largely on parallel advancements in computational tools and techniques. Without these computing advances, modern structural biology would likely have remained an exclusive pursuit practiced by few, and not become the widely practiced, foundational field it is today. As other areas of biomedical research increasingly embrace research computing techniques, the successes, failures and lessons of structural biology computing can serve as a useful guide to progress in other biomedically related research fields. Copyright © 2013 Wiley Periodicals, Inc.

Long-term effects of prescribed fire on mixed conifer forest structure in the Sierra Nevada, California

USGS Publications Warehouse

van Mantgem, Phillip J.; Stephenson, Nathan L.; Knapp, Eric; Keeley, Jon E.

2011-01-01

The capacity of prescribed fire to restore forest conditions is often judged by changes in forest structure within a few years following burning. However, prescribed fire might have longer-term effects on forest structure, potentially changing treatment assessments. We examined annual changes in forest structure in five 1 ha old-growth plots immediately before prescribed fire and up to eight years after fire at Sequoia National Park, California. Fire-induced declines in stem density (67% average decrease at eight years post-fire) were nonlinear, taking up to eight years to reach a presumed asymptote. Declines in live stem biomass were also nonlinear, but smaller in magnitude (32% average decrease at eight years post-fire) as most large trees survived the fires. The preferential survival of large trees following fire resulted in significant shifts in stem diameter distributions. Mortality rates remained significantly above background rates up to six years after the fires. Prescribed fire did not have a large influence on the representation of dominant species. Fire-caused mortality appeared to be spatially random, and therefore did not generally alter heterogeneous tree spatial patterns. Our results suggest that prescribed fire can bring about substantial changes to forest structure in old-growth mixed conifer forests in the Sierra Nevada, but that long-term observations are needed to fully describe some measures of fire effects.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schreck, S.; Sant, T.; Micallef, D.

Wind turbine structures and components suffer excessive loads and premature failures when key aerodynamic phenomena are not well characterized, fail to be understood, or are inaccurately predicted. Turbine blade rotational augmentation remains incompletely characterized and understood, thus limiting robust prediction for design. Pertinent rotational augmentation research including experimental, theoretical, and computational work has been pursued for some time, but large scale wind tunnel testing is a relatively recent development for investigating wind turbine blade aerodynamics. Because of their large scale and complementary nature, the MEXICO and UAE Phase VI wind tunnel experiments offer unprecedented synergies to better characterize and understandmore » rotational augmentation of blade aerodynamics.« less

Large protein as a potential target for use in rabies diagnostics.

PubMed

Santos Katz, I S; Dias, M H; Lima, I F; Chaves, L B; Ribeiro, O G; Scheffer, K C; Iwai, L K

Rabies is a zoonotic viral disease that remains a serious threat to public health worldwide. The rabies lyssavirus (RABV) genome encodes five structural proteins, multifunctional and significant for pathogenicity. The large protein (L) presents well-conserved genomic regions, which may be a good alternative to generate informative datasets for development of new methods for rabies diagnosis. This paper describes the development of a technique for the identification of L protein in several RABV strains from different hosts, demonstrating that MS-based proteomics is a potential method for antigen identification and a good alternative for rabies diagnosis.

The Synaptic Function of α-Synuclein

PubMed Central

Burré, Jacqueline

2015-01-01

α-Synuclein is an abundant neuronal protein which localizes predominantly to presynaptic terminals, and is strongly linked genetically and pathologically to Parkinson’s disease and other neurodegenerative diseases. While the accumulation of α-synuclein in the form of misfolded oligomers and large aggregates defines multiple neurodegenerative diseases called “synucleinopathies”, its cellular function has remained largely unclear, and is the subject of intense investigation. In this review, I focus on the structural characteristics of α-synuclein, its cellular and subcellular localization, and discuss how this relates to its function in neurons, in particular at the neuronal synapse. PMID:26407041

Electronic polarization stabilizes tertiary structure prediction of HP-36.

PubMed

Duan, Li L; Zhu, Tong; Zhang, Qing G; Tang, Bo; Zhang, John Z H

2014-04-01

Molecular dynamic (MD) simulations with both implicit and explicit solvent models have been carried out to study the folding dynamics of HP-36 protein. Starting from the extended conformation, the secondary structure of all three helices in HP-36 was formed in about 50 ns and remained stable in the remaining simulation. However, the formation of the tertiary structure was difficult. Although some intermediates were close to the native structure, the overall conformation was not stable. Further analysis revealed that the large structure fluctuation of loop and hydrophobic core regions was devoted mostly to the instability of the structure during MD simulation. The backbone root-mean-square deviation (RMSD) of the loop and hydrophobic core regions showed strong correlation with the backbone RMSD of the whole protein. The free energy landscape indicated that the distribution of main chain torsions in loop and turn regions was far away from the native state. Starting from an intermediate structure extracted from the initial AMBER simulation, HP-36 was found to generally fold to the native state under the dynamically adjusted polarized protein-specific charge (DPPC) simulation, while the peptide did not fold into the native structure when AMBER force filed was used. The two best folded structures were extracted and taken into further simulations in water employing AMBER03 charge and DPPC for 25 ns. Result showed that introducing polarization effect into interacting potential could stabilize the near-native protein structure.

Computational modeling of RNA 3D structures, with the aid of experimental restraints

PubMed Central

Magnus, Marcin; Matelska, Dorota; Łach, Grzegorz; Chojnowski, Grzegorz; Boniecki, Michal J; Purta, Elzbieta; Dawson, Wayne; Dunin-Horkawicz, Stanislaw; Bujnicki, Janusz M

2014-01-01

In addition to mRNAs whose primary function is transmission of genetic information from DNA to proteins, numerous other classes of RNA molecules exist, which are involved in a variety of functions, such as catalyzing biochemical reactions or performing regulatory roles. In analogy to proteins, the function of RNAs depends on their structure and dynamics, which are largely determined by the ribonucleotide sequence. Experimental determination of high-resolution RNA structures is both laborious and difficult, and therefore, the majority of known RNAs remain structurally uncharacterized. To address this problem, computational structure prediction methods were developed that simulate either the physical process of RNA structure formation (“Greek science” approach) or utilize information derived from known structures of other RNA molecules (“Babylonian science” approach). All computational methods suffer from various limitations that make them generally unreliable for structure prediction of long RNA sequences. However, in many cases, the limitations of computational and experimental methods can be overcome by combining these two complementary approaches with each other. In this work, we review computational approaches for RNA structure prediction, with emphasis on implementations (particular programs) that can utilize restraints derived from experimental analyses. We also list experimental approaches, whose results can be relatively easily used by computational methods. Finally, we describe case studies where computational and experimental analyses were successfully combined to determine RNA structures that would remain out of reach for each of these approaches applied separately. PMID:24785264

Laser Scanning Holographic Lithography for Flexible 3D Fabrication of Multi-Scale Integrated Nano-structures and Optical Biosensors

PubMed Central

Yuan, Liang (Leon); Herman, Peter R.

2016-01-01

Three-dimensional (3D) periodic nanostructures underpin a promising research direction on the frontiers of nanoscience and technology to generate advanced materials for exploiting novel photonic crystal (PC) and nanofluidic functionalities. However, formation of uniform and defect-free 3D periodic structures over large areas that can further integrate into multifunctional devices has remained a major challenge. Here, we introduce a laser scanning holographic method for 3D exposure in thick photoresist that combines the unique advantages of large area 3D holographic interference lithography (HIL) with the flexible patterning of laser direct writing to form both micro- and nano-structures in a single exposure step. Phase mask interference patterns accumulated over multiple overlapping scans are shown to stitch seamlessly and form uniform 3D nanostructure with beam size scaled to small 200 μm diameter. In this way, laser scanning is presented as a facile means to embed 3D PC structure within microfluidic channels for integration into an optofluidic lab-on-chip, demonstrating a new laser HIL writing approach for creating multi-scale integrated microsystems. PMID:26922872

Structure of a [NiFe] hydrogenase maturation protease HycI provides insights into its substrate selectivity.

PubMed

Kwon, Sunghark; Nishitani, Yuichi; Hirao, Yoshinori; Kanai, Tamotsu; Atomi, Haruyuki; Miki, Kunio

2018-04-15

The immature large subunit of [NiFe] hydrogenases undergoes C-terminal cleavage by a specific protease in the final step of the post-translational process before assembly with other subunits. It has been reported that the [NiFe] hydrogenase maturation protease HycI from Thermococcus kodakarensis (TkHycI) has the catalytic ability to target the membrane-bound hydrogenase large subunit MbhL from T. kodakarensis. However, the detailed mechanism of its substrate recognition remains elusive. We determined the crystal structure of TkHycI at 1.59 Å resolution to clarify how TkHycI recognizes its own substrate MbhL. Although the overall structure of TkHycI is similar to that of its homologous protease TkHybD, TkHycI adopts a larger loop than TkHybD, thereby creating a broad and deep cleft. We analyzed the structural properties of the TkHycI cleft probably involved in its substrate recognition. Our findings provide novel and profound insights into the substrate selectivity of TkHycI. Copyright © 2018 Elsevier Inc. All rights reserved.

The structure of SV40 large T hexameric helicase in complex with AT-rich origin DNA

PubMed Central

Gai, Dahai; Wang, Damian; Li, Shu-Xing; Chen, Xiaojiang S

2016-01-01

DNA replication is a fundamental biological process. The initial step in eukaryotic DNA replication is the assembly of the pre-initiation complex, including the formation of two head-to-head hexameric helicases around the replication origin. How these hexameric helicases interact with their origin dsDNA remains unknown. Here, we report the co-crystal structure of the SV40 Large-T Antigen (LT) hexameric helicase bound to its origin dsDNA. The structure shows that the six subunits form a near-planar ring that interacts with the origin, so that each subunit makes unique contacts with the DNA. The origin dsDNA inside the narrower AAA+ domain channel shows partial melting due to the compression of the two phosphate backbones, forcing Watson-Crick base-pairs within the duplex to flip outward. This structure provides the first snapshot of a hexameric helicase binding to origin dsDNA, and suggests a possible mechanism of origin melting by LT during SV40 replication in eukaryotic cells. DOI: http://dx.doi.org/10.7554/eLife.18129.001 PMID:27921994

The design of low cost structures for extensive ground arrays

NASA Technical Reports Server (NTRS)

Franklin, H. A.; Leonard, R. S.

1980-01-01

The development of conceptual designs of solar array support structures and their foundations including considerations of the use of concrete, steel, aluminum, or timber are reported. Some cost trends were examined by varying selected parameters to determine optimum configurations. Detailed civil/structural design criteria were developed. Using these criteria, eight detailed designs for support structures and foundations were developed and cost estimates were made. As a result of the study wind was identified as the major loading experienced by these low height structures, whose arrays are likely to extend over large tracts of land. Proper wind load estimating is considered essential to developing realistic structural designs and achieving minimum cost support structures. Wind tunnel testing of a conceptual array field was undertaken and some of the resulting wind design criteria are presented. The SPS rectenna system designs may be less sensitive to wind load estimates, but consistent design criteria remain important.

Controlling the intermediate structure of an ionic liquid for f-block element separations

DOE PAGES

Abney, Carter W.; Do, Changwoo; Luo, Huimin; ...

2017-04-19

Recent research has revealed molecular structure beyond the inner coordination sphere is essential in defining the performance of separations processes, but nevertheless remains largely unexplored. Here we apply small angle neutron scattering (SANS) and x-ray absorption fine structure (XAFS) spectroscopy to investigate the structure of an ionic liquid system studied for f-block element separations. SANS data reveal dramatic changes in the ionic liquid microstructure (~150 Å) which we demonstrate can be controlled by judicious selection of counter ion. Mesoscale structural features (> 500 Å) are also observed as a function of metal concentration. XAFS analysis supports formation of extended aggregatemore » structures, similar to those observed in traditional solvent extraction processes, and suggest additional parallels may be drawn from further study. As a result, achieving precise tunability over the intermediate features is an important development in controlling mesoscale structure and realizing advanced new forms of soft matter.« less

Structure of a designed protein cage that self-assembles into a highly porous cube

DOE PAGES

Lai, Yen-Ting; Reading, Eamonn; Hura, Greg L.; ...

2014-11-10

Natural proteins can be versatile building blocks for multimeric, self-assembling structures. Yet, creating protein-based assemblies with specific geometries and chemical properties remains challenging. Highly porous materials represent particularly interesting targets for designed assembly. Here we utilize a strategy of fusing two natural protein oligomers using a continuous alpha-helical linker to design a novel protein that self assembles into a 750 kDa, 225 Å diameter, cube-shaped cage with large openings into a 130 Å diameter inner cavity. A crystal structure of the cage showed atomic level agreement with the designed model, while electron microscopy, native mass spectrometry, and small angle x-raymore » scattering revealed alternate assembly forms in solution. These studies show that accurate design of large porous assemblies with specific shapes is feasible, while further specificity improvements will likely require limiting flexibility to select against alternative forms. Finally, these results provide a foundation for the design of advanced materials with applications in bionanotechnology, nanomedicine and material sciences.« less

A thorough experimental study of CH/π interactions in water: quantitative structure-stability relationships for carbohydrate/aromatic complexes.

PubMed

Jiménez-Moreno, Ester; Jiménez-Osés, Gonzalo; Gómez, Ana M; Santana, Andrés G; Corzana, Francisco; Bastida, Agatha; Jiménez-Barbero, Jesus; Asensio, Juan Luis

2015-11-13

CH/π interactions play a key role in a large variety of molecular recognition processes of biological relevance. However, their origins and structural determinants in water remain poorly understood. In order to improve our comprehension of these important interaction modes, we have performed a quantitative experimental analysis of a large data set comprising 117 chemically diverse carbohydrate/aromatic stacking complexes, prepared through a dynamic combinatorial approach recently developed by our group. The obtained free energies provide a detailed picture of the structure-stability relationships that govern the association process, opening the door to the rational design of improved carbohydrate-based ligands or carbohydrate receptors. Moreover, this experimental data set, supported by quantum mechanical calculations, has contributed to the understanding of the main driving forces that promote complex formation, underlining the key role played by coulombic and solvophobic forces on the stabilization of these complexes. This represents the most quantitative and extensive experimental study reported so far for CH/π complexes in water.

Temperature-driven topological transition in 1T'-MoTe2

NASA Astrophysics Data System (ADS)

Berger, Ayelet Notis; Andrade, Erick; Kerelsky, Alexander; Edelberg, Drew; Li, Jian; Wang, Zhijun; Zhang, Lunyong; Kim, Jaewook; Zaki, Nader; Avila, Jose; Chen, Chaoyu; Asensio, Maria C.; Cheong, Sang-Wook; Bernevig, Bogdan A.; Pasupathy, Abhay N.

2018-01-01

The topology of Weyl semimetals requires the existence of unique surface states. Surface states have been visualized in spectroscopy measurements, but their connection to the topological character of the material remains largely unexplored. 1T'-MoTe2, presents a unique opportunity to study this connection. This material undergoes a phase transition at 240 K that changes the structure from orthorhombic (putative Weyl semimetal) to monoclinic (trivial metal), while largely maintaining its bulk electronic structure. Here, we show from temperature-dependent quasiparticle interference measurements that this structural transition also acts as a topological switch for surface states in 1T'-MoTe2. At low temperature, we observe strong quasiparticle scattering, consistent with theoretical predictions and photoemission measurements for the surface states in this material. In contrast, measurements performed at room temperature show the complete absence of the scattering wavevectors associated with the trivial surface states. These distinct quasiparticle scattering behaviors show that 1T'-MoTe2 is ideal for separating topological and trivial electronic phenomena via temperature-dependent measurements.

Quantum-gravity predictions for the fine-structure constant

NASA Astrophysics Data System (ADS)

Eichhorn, Astrid; Held, Aaron; Wetterich, Christof

2018-07-01

Asymptotically safe quantum fluctuations of gravity can uniquely determine the value of the gauge coupling for a large class of grand unified models. In turn, this makes the electromagnetic fine-structure constant calculable. The balance of gravity and matter fluctuations results in a fixed point for the running of the gauge coupling. It is approached as the momentum scale is lowered in the transplanckian regime, leading to a uniquely predicted value of the gauge coupling at the Planck scale. The precise value of the predicted fine-structure constant depends on the matter content of the grand unified model. It is proportional to the gravitational fluctuation effects for which computational uncertainties remain to be settled.

Excitonic fine-structure splitting in telecom-wavelength InAs/GaAs quantum dots: Statistical distribution and height-dependence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goldmann, Elias, E-mail: goldmann@itp.uni-bremen.de; Barthel, Stefan; Florian, Matthias

The variation of the excitonic fine-structure splitting is studied for semiconductor quantum dots under the influence of a strain-reducing layer, utilized to shift the emission wavelength of the excitonic transition into the telecom-wavelength regime of 1.3–1.5 μm. By means of a sp{sup 3}s{sup *}-tight-binding model and configuration interaction, we calculate wavelength shifts and fine-structure splittings for various quantum dot geometries. We find the splittings remaining small and even decreasing with strain-reducing layer composition for quantum dots with large height. Combined with an observed increased emission efficiency, the applicability for generation of entanglement photons is persistent.

KSC-2010-4941

NASA Image and Video Library

2010-09-30

CAPE CANAVERAL, Fla. -- At NASA's Kennedy Space Center in Florida, the rotating service structure (RSS) on Launch Pad 39B is being dismantled. Sand, reinforcing steel and large wooden mats were put down under the RSS to protect the structure's concrete from falling debris during deconstruction. Starting in 2009, the structure at the pad was no longer needed for NASA's Space Shuttle Program, so it is being restructured for future use. The new design will feature a "clean pad" for rockets to come with their own launcher, making it more versatile for a number of vehicles. The new lightning protection system, consisting of three lightning towers and a wire catenary system will remain. Photo credit: NASA/Jim Grossmann

KSC-2010-4942

NASA Image and Video Library

2010-09-30

CAPE CANAVERAL, Fla. -- At NASA's Kennedy Space Center in Florida, crews are dismantling the rotating service structure (RSS) on Launch Pad 39B. Sand, reinforcing steel and large wooden mats were put down under the RSS to protect the structure's concrete from falling debris during deconstruction. Starting in 2009, the structure at the pad was no longer needed for NASA's Space Shuttle Program, so it is being restructured for future use. The new design will feature a "clean pad" for rockets to come with their own launcher, making it more versatile for a number of vehicles. The new lightning protection system, consisting of three lightning towers and a wire catenary system will remain. Photo credit: NASA/Jim Grossmann

KSC-2010-4946

NASA Image and Video Library

2010-09-30

CAPE CANAVERAL, Fla. -- At NASA's Kennedy Space Center in Florida, crews are dismantling the rotating service structure (RSS) on Launch Pad 39B. Sand, reinforcing steel and large wooden mats were put down under the RSS to protect the structure's concrete from falling debris during deconstruction. Starting in 2009, the structure at the pad was no longer needed for NASA's Space Shuttle Program, so it is being restructured for future use. The new design will feature a "clean pad" for rockets to come with their own launcher, making it more versatile for a number of vehicles. The new lightning protection system, consisting of three lightning towers and a wire catenary system will remain. Photo credit: NASA/Jim Grossmann

KSC-2010-4944

NASA Image and Video Library

2010-09-30

CAPE CANAVERAL, Fla. -- At NASA's Kennedy Space Center in Florida, crews are dismantling the rotating service structure (RSS) on Launch Pad 39B. Sand, reinforcing steel and large wooden mats were put down under the RSS to protect the structure's concrete from falling debris during deconstruction. Starting in 2009, the structure at the pad was no longer needed for NASA's Space Shuttle Program, so it is being restructured for future use. The new design will feature a "clean pad" for rockets to come with their own launcher, making it more versatile for a number of vehicles. The new lightning protection system, consisting of three lightning towers and a wire catenary system will remain. Photo credit: NASA/Jim Grossmann

KSC-2010-4943

NASA Image and Video Library

2010-09-30

CAPE CANAVERAL, Fla. -- At NASA's Kennedy Space Center in Florida, the rotating service structure (RSS) on Launch Pad 39B is being dismantled. Sand, reinforcing steel and large wooden mats were put down under the RSS to protect the structure's concrete from falling debris during deconstruction. Starting in 2009, the structure at the pad was no longer needed for NASA's Space Shuttle Program, so it is being restructured for future use. The new design will feature a "clean pad" for rockets to come with their own launcher, making it more versatile for a number of vehicles. The new lightning protection system, consisting of three lightning towers and a wire catenary system will remain. Photo credit: NASA/Jim Grossmann

KSC-2010-4945

NASA Image and Video Library

2010-09-30

CAPE CANAVERAL, Fla. -- At NASA's Kennedy Space Center in Florida, the rotating service structure (RSS) on Launch Pad 39B is being dismantled. Sand, reinforcing steel and large wooden mats were put down under the RSS to protect the structure's concrete from falling debris during deconstruction. Starting in 2009, the structure at the pad was no longer needed for NASA's Space Shuttle Program, so it is being restructured for future use. The new design will feature a "clean pad" for rockets to come with their own launcher, making it more versatile for a number of vehicles. The new lightning protection system, consisting of three lightning towers and a wire catenary system will remain. Photo credit: NASA/Jim Grossmann

KSC-2010-4987

NASA Image and Video Library

2010-10-04

CAPE CANAVERAL, Fla. -- At NASA's Kennedy Space Center in Florida, crews continue dismantling the rotating service structure (RSS) on Launch Pad 39B. Sand, reinforcing steel and large wooden mats were put down under the RSS to protect the structure's concrete from falling debris during deconstruction. Starting in 2009, the structure at the pad was no longer needed for NASA's Space Shuttle Program, so it is being restructured for future use. The new design will feature a "clean pad" for rockets to come with their own launcher, making it more versatile for a number of vehicles. The new lightning protection system, consisting of three lightning towers and a wire catenary system will remain. Photo credit: NASA/Jack Pfaller

ERUPTING FILAMENTS WITH LARGE ENCLOSING FLUX TUBES AS SOURCES OF HIGH-MASS THREE-PART CMEs, AND ERUPTING FILAMENTS IN THE ABSENCE OF ENCLOSING FLUX TUBES AS SOURCES OF LOW-MASS UNSTRUCTURED CMEs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hutton, Joe; Morgan, Huw, E-mail: joh9@aber.ac.uk

2015-11-01

The 3-part appearance of many coronal mass ejections (CMEs) arising from erupting filaments emerges from a large magnetic flux tube structure, consistent with the form of the erupting filament system. Other CMEs arising from erupting filaments lack a clear 3-part structure and reasons for this have not been researched in detail. This paper aims to further establish the link between CME structure and the structure of the erupting filament system and to investigate whether CMEs which lack a 3-part structure have different eruption characteristics. A survey is made of 221 near-limb filament eruptions observed from 2013 May 03 to 2014more » June 30 by Extreme UltraViolet (EUV) imagers and coronagraphs. Ninety-two filament eruptions are associated with 3-part structured CMEs, 41 eruptions are associated with unstructured CMEs. The remaining 88 are categorized as failed eruptions. For 34% of the 3-part CMEs, processing applied to EUV images reveals the erupting front edge is a pre-existing loop structure surrounding the filament, which subsequently erupts with the filament to form the leading bright front edge of the CME. This connection is confirmed by a flux-rope density model. Furthermore, the unstructured CMEs have a narrower distribution of mass compared to structured CMEs, with total mass comparable to the mass of 3-part CME cores. This study supports the interpretation of 3-part CME leading fronts as the outer boundaries of a large pre-existing flux tube. Unstructured (non 3-part) CMEs are a different family to structured CMEs, arising from the eruption of filaments which are compact flux tubes in the absence of a large system of enclosing closed field.« less

Weighing trees with lasers: advances, challenges and opportunities

PubMed Central

Boni Vicari, M.; Burt, A.; Calders, K.; Lewis, S. L.; Raumonen, P.; Wilkes, P.

2018-01-01

Terrestrial laser scanning (TLS) is providing exciting new ways to quantify tree and forest structure, particularly above-ground biomass (AGB). We show how TLS can address some of the key uncertainties and limitations of current approaches to estimating AGB based on empirical allometric scaling equations (ASEs) that underpin all large-scale estimates of AGB. TLS provides extremely detailed non-destructive measurements of tree form independent of tree size and shape. We show examples of three-dimensional (3D) TLS measurements from various tropical and temperate forests and describe how the resulting TLS point clouds can be used to produce quantitative 3D models of branch and trunk size, shape and distribution. These models can drastically improve estimates of AGB, provide new, improved large-scale ASEs, and deliver insights into a range of fundamental tree properties related to structure. Large quantities of detailed measurements of individual 3D tree structure also have the potential to open new and exciting avenues of research in areas where difficulties of measurement have until now prevented statistical approaches to detecting and understanding underlying patterns of scaling, form and function. We discuss these opportunities and some of the challenges that remain to be overcome to enable wider adoption of TLS methods. PMID:29503726

The structural stability of lunar lava tubes

NASA Astrophysics Data System (ADS)

Blair, David M.; Chappaz, Loic; Sood, Rohan; Milbury, Colleen; Bobet, Antonio; Melosh, H. Jay; Howell, Kathleen C.; Freed, Andrew M.

2017-01-01

Mounting evidence from the SELENE, LRO, and GRAIL spacecraft suggests the presence of vacant lava tubes under the surface of the Moon. GRAIL evidence, in particular, suggests that some may be more than a kilometer in width. Such large sublunarean structures would be of great benefit to future human exploration of the Moon, providing shelter from the harsh environment at the surface-but could empty lava tubes of this size be stable under lunar conditions? And what is the largest size at which they could remain structurally sound? We address these questions by creating elasto-plastic finite element models of lava tubes using the Abaqus modeling software and examining where there is local material failure in the tube's roof. We assess the strength of the rock body using the Geological Strength Index method with values appropriate to the Moon, assign it a basaltic density derived from a modern re-analysis of lunar samples, and assume a 3:1 width-to-height ratio for the lava tube. Our results show that the stability of a lava tube depends on its width, its roof thickness, and whether the rock comprising the structure begins in a lithostatic or Poisson stress state. With a roof 2 m thick, lava tubes a kilometer or more in width can remain stable, supporting inferences from GRAIL observations. The theoretical maximum size of a lunar lava tube depends on a variety of factors, but given sufficient burial depth (500 m) and an initial lithostatic stress state, our results show that lava tubes up to 5 km wide may be able to remain structurally stable.

Dynamics of Topological Excitations in a Model Quantum Spin Ice

NASA Astrophysics Data System (ADS)

Huang, Chun-Jiong; Deng, Youjin; Wan, Yuan; Meng, Zi Yang

2018-04-01

We study the quantum spin dynamics of a frustrated X X Z model on a pyrochlore lattice by using large-scale quantum Monte Carlo simulation and stochastic analytic continuation. In the low-temperature quantum spin ice regime, we observe signatures of coherent photon and spinon excitations in the dynamic spin structure factor. As the temperature rises to the classical spin ice regime, the photon disappears from the dynamic spin structure factor, whereas the dynamics of the spinon remain coherent in a broad temperature window. Our results provide experimentally relevant, quantitative information for the ongoing pursuit of quantum spin ice materials.

Confirmatory factor analytic structure and measurement invariance of quantitative autistic traits measured by the social responsiveness scale-2.

PubMed

Frazier, Thomas W; Ratliff, Kristin R; Gruber, Chris; Zhang, Yi; Law, Paul A; Constantino, John N

2014-01-01

Understanding the factor structure of autistic symptomatology is critical to the discovery and interpretation of causal mechanisms in autism spectrum disorder. We applied confirmatory factor analysis and assessment of measurement invariance to a large (N = 9635) accumulated collection of reports on quantitative autistic traits using the Social Responsiveness Scale, representing a broad diversity of age, severity, and reporter type. A two-factor structure (corresponding to social communication impairment and restricted, repetitive behavior) as elaborated in the updated Diagnostic and Statistical Manual of Mental Disorders (5th ed.; DSM-5) criteria for autism spectrum disorder exhibited acceptable model fit in confirmatory factor analysis. Measurement invariance was appreciable across age, sex, and reporter (self vs other), but somewhat less apparent between clinical and nonclinical populations in this sample comprised of both familial and sporadic autism spectrum disorders. The statistical power afforded by this large sample allowed relative differentiation of three factors among items encompassing social communication impairment (emotion recognition, social avoidance, and interpersonal relatedness) and two factors among items encompassing restricted, repetitive behavior (insistence on sameness and repetitive mannerisms). Cross-trait correlations remained extremely high, that is, on the order of 0.66-0.92. These data clarify domains of statistically significant factoral separation that may relate to partially-but not completely-overlapping biological mechanisms, contributing to variation in human social competency. Given such robust intercorrelations among symptom domains, understanding their co-emergence remains a high priority in conceptualizing common neural mechanisms underlying autistic syndromes.

Estimation of fatigue life using electromechanical impedance technique

NASA Astrophysics Data System (ADS)

Lim, Yee Yan; Soh, Chee Kiong

2010-04-01

Fatigue induced damage is often progressive and gradual in nature. Structures subjected to large number of fatigue load cycles will encounter the process of progressive crack initiation, propagation and finally fracture. Monitoring of structural health, especially for the critical components, is therefore essential for early detection of potential harmful crack. Recent advent of smart materials such as piezo-impedance transducer adopting the electromechanical impedance (EMI) technique and wave propagation technique are well proven to be effective in incipient damage detection and characterization. Exceptional advantages such as autonomous, real-time and online, remote monitoring may provide a cost-effective alternative to the conventional structural health monitoring (SHM) techniques. In this study, the main focus is to investigate the feasibility of characterizing a propagating fatigue crack in a structure using the EMI technique as well as estimating its remaining fatigue life using the linear elastic fracture mechanics (LEFM) approach. Uniaxial cyclic tensile load is applied on a lab-sized aluminum beam up to failure. Progressive shift in admittance signatures measured by the piezo-impedance transducer (PZT patch) corresponding to increase of loading cycles reflects effectiveness of the EMI technique in tracing the process of fatigue damage progression. With the use of LEFM, prediction of the remaining life of the structure at different cycles of loading is possible.

CONTINUITY AND CHANGE IN THE AMERICAN CLASS STRUCTURE: WORKPLACE OWNERSHIP AND AUTHORITY RELATIONS FROM 1972 TO 2010.

PubMed

Wodtke, Geoffrey T

2015-12-01

This study investigates changes in the American class structure-defined in terms of workplace ownership and authority relations-and trends in status group disparities in class attainment from 1972 to 2010. Although theory and prior research suggest a variety of appreciable changes in class structure and class attainment, data from the General Social Survey indicate that the sizes of different classes remained fairly stable during this time period and that status group disparities in access to ownership and authority persisted largely intact. The 1970s witnessed a decline in the proportion of workers and growth in the proportion of managers and proprietors, but these trends reversed in the 1980s. As a result, by the late 2000s, the ownership and authority structure of the U.S. economy closely resembled that of the early 1970s. Racial and gender disparities in class attainment also did not change significantly over time: blacks and women remained underrepresented (relative to whites and men) in positions of ownership and authority throughout this period. Even after controlling for an extensive set of human capital characteristics, family constraints, and structural economic factors, there is little evidence of status group integration across these key dimensions of economic power.

The metallization and superconductivity of dense hydrogen sulfide

NASA Astrophysics Data System (ADS)

Li, Yinwei; Hao, Jian; Liu, Hanyu; Li, Yanling; Ma, Yanming

2014-05-01

Hydrogen sulfide (H2S) is a prototype molecular system and a sister molecule of water (H2O). The phase diagram of solid H2S at high pressures remains largely unexplored arising from the challenges in dealing with the pressure-induced weakening of S-H bond and larger atomic core difference between H and S. Metallization is yet achieved for H2O, but it was observed for H2S above 96 GPa. However, the metallic structure of H2S remains elusive, greatly impeding the understanding of its metallicity and the potential superconductivity. We have performed an extensive structural study on solid H2S at pressure ranges of 10-200 GPa through an unbiased structure prediction method based on particle swarm optimization algorithm. Besides the findings of candidate structures for nonmetallic phases IV and V, we are able to establish stable metallic structures violating an earlier proposal of elemental decomposition into sulfur and hydrogen [R. Rousseau, M. Boero, M. Bernasconi, M. Parrinello, and K. Terakura, Phys. Rev. Lett. 85, 1254 (2000)]. Our study unravels a superconductive potential of metallic H2S with an estimated maximal transition temperature of ˜80 K at 160 GPa, higher than those predicted for most archetypal hydrogen-containing compounds (e.g., SiH4, GeH4, etc.).

Molecular Architecture of Full-length TRF1 Favors Its Interaction with DNA.

PubMed

Boskovic, Jasminka; Martinez-Gago, Jaime; Mendez-Pertuz, Marinela; Buscato, Alberto; Martinez-Torrecuadrada, Jorge Luis; Blasco, Maria A

2016-10-07

Telomeres are specific DNA-protein structures found at both ends of eukaryotic chromosomes that protect the genome from degradation and from being recognized as double-stranded breaks. In vertebrates, telomeres are composed of tandem repeats of the TTAGGG sequence that are bound by a six-subunit complex called shelterin. Molecular mechanisms of telomere functions remain unknown in large part due to lack of structural data on shelterins, shelterin complex, and its interaction with the telomeric DNA repeats. TRF1 is one of the best studied shelterin components; however, the molecular architecture of the full-length protein remains unknown. We have used single-particle electron microscopy to elucidate the structure of TRF1 and its interaction with telomeric DNA sequence. Our results demonstrate that full-length TRF1 presents a molecular architecture that assists its interaction with telometic DNA and at the same time makes TRFH domains accessible to other TRF1 binding partners. Furthermore, our studies suggest hypothetical models on how other proteins as TIN2 and tankyrase contribute to regulate TRF1 function. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Molecular Architecture of Full-length TRF1 Favors Its Interaction with DNA*

PubMed Central

Boskovic, Jasminka; Martinez-Gago, Jaime; Mendez-Pertuz, Marinela; Buscato, Alberto; Martinez-Torrecuadrada, Jorge Luis; Blasco, Maria A.

2016-01-01

Telomeres are specific DNA-protein structures found at both ends of eukaryotic chromosomes that protect the genome from degradation and from being recognized as double-stranded breaks. In vertebrates, telomeres are composed of tandem repeats of the TTAGGG sequence that are bound by a six-subunit complex called shelterin. Molecular mechanisms of telomere functions remain unknown in large part due to lack of structural data on shelterins, shelterin complex, and its interaction with the telomeric DNA repeats. TRF1 is one of the best studied shelterin components; however, the molecular architecture of the full-length protein remains unknown. We have used single-particle electron microscopy to elucidate the structure of TRF1 and its interaction with telomeric DNA sequence. Our results demonstrate that full-length TRF1 presents a molecular architecture that assists its interaction with telometic DNA and at the same time makes TRFH domains accessible to other TRF1 binding partners. Furthermore, our studies suggest hypothetical models on how other proteins as TIN2 and tankyrase contribute to regulate TRF1 function. PMID:27563064

[Computational chemistry in structure-based drug design].

PubMed

Cao, Ran; Li, Wei; Sun, Han-Zi; Zhou, Yu; Huang, Niu

2013-07-01

Today, the understanding of the sequence and structure of biologically relevant targets is growing rapidly and researchers from many disciplines, physics and computational science in particular, are making significant contributions to modern biology and drug discovery. However, it remains challenging to rationally design small molecular ligands with desired biological characteristics based on the structural information of the drug targets, which demands more accurate calculation of ligand binding free-energy. With the rapid advances in computer power and extensive efforts in algorithm development, physics-based computational chemistry approaches have played more important roles in structure-based drug design. Here we reviewed the newly developed computational chemistry methods in structure-based drug design as well as the elegant applications, including binding-site druggability assessment, large scale virtual screening of chemical database, and lead compound optimization. Importantly, here we address the current bottlenecks and propose practical solutions.

Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures.

PubMed

Yesselman, Joseph D; Horowitz, Scott; Brooks, Charles L; Trievel, Raymond C

2015-03-01

The propensity of backbone Cα atoms to engage in carbon-oxygen (CH · · · O) hydrogen bonding is well-appreciated in protein structure, but side chain CH · · · O hydrogen bonding remains largely uncharacterized. The extent to which side chain methyl groups in proteins participate in CH · · · O hydrogen bonding is examined through a survey of neutron crystal structures, quantum chemistry calculations, and molecular dynamics simulations. Using these approaches, methyl groups were observed to form stabilizing CH · · · O hydrogen bonds within protein structure that are maintained through protein dynamics and participate in correlated motion. Collectively, these findings illustrate that side chain methyl CH · · · O hydrogen bonding contributes to the energetics of protein structure and folding. © 2014 Wiley Periodicals, Inc.

Conformation of a Group 2 Late Embryogenesis Abundant Protein from Soybean. Evidence of Poly (l-Proline)-type II Structure1

PubMed Central

Soulages, Jose L.; Kim, Kangmin; Arrese, Estela L.; Walters, Christina; Cushman, John C.

2003-01-01

Late embryogenesis abundant (LEA) proteins are members of a large group of hydrophilic, glycine-rich proteins found in plants, algae, fungi, and bacteria known collectively as hydrophilins that are preferentially expressed in response to dehydration or hyperosmotic stress. Group 2 LEA (dehydrins or responsive to abscisic acid) proteins are postulated to stabilize macromolecules against damage by freezing, dehydration, ionic, or osmotic stress. However, the structural and physicochemical properties of group 2 LEA proteins that account for such functions remain unknown. We have analyzed the structural properties of a recombinant form of a soybean (Glycine max) group 2 LEA (rGmDHN1). Differential scanning calorimetry of purified rGmDHN1 demonstrated that the protein does not display a cooperative unfolding transition upon heating. Ultraviolet absorption and circular dichroism spectroscopy revealed that the protein is in a largely hydrated and unstructured conformation in solution. However, ultraviolet absorption and circular dichroism measurements collected at different temperatures showed that the protein exists in equilibrium between two extended conformational states: unordered and left-handed extended helical or poly (l-proline)-type II structures. It is estimated that 27% of the residues of rGmDHN1 adopt or poly (l-proline)-type II-like helical conformation at 12°C. The content of extended helix gradually decreases to 15% as the temperature is increased to 80°C. Studies of the conformation of the protein in solution in the presence of liposomes, trifluoroethanol, and sodium dodecyl sulfate indicated that rGmDHN1 has a very low intrinsic ability to adopt α-helical structure and to interact with phospholipid bilayers through amphipathic α-helices. The ability of the protein to remain in a highly extended conformation at low temperatures could constitute the basis of the functional role of GmDHN1 in the prevention of freezing, desiccation, ionic, or osmotic stress-related damage to macromolecular structures. PMID:12644649

Structure and dynamics of Ebola virus matrix protein VP40 by a coarse-grained Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Pandey, Ras; Farmer, Barry

Ebola virus matrix protein VP40 (consisting of 326 residues) plays a critical role in viral assembly and its functions such as regulation of viral transcription, packaging, and budding of mature virions into the plasma membrane of infected cells. How does the protein VP40 go through structural evolution during the viral life cycle remains an open question? Using a coarse-grained Monte Carlo simulation we investigate the structural evolution of VP40 as a function of temperature with the input of a knowledge-based residue-residue interaction. A number local and global physical quantities (e.g. mobility profile, contact map, radius of gyration, structure factor) are analyzed with our large-scale simulations. Our preliminary data show that the structure of the protein evolves through different state with well-defined morphologies which can be identified and quantified via a detailed analysis of structure factor.

Relating Structure and Function in the Human Brain: Relative Contributions of Anatomy, Stationary Dynamics, and Non-stationarities

PubMed Central

Messé, Arnaud; Rudrauf, David; Benali, Habib; Marrelec, Guillaume

2014-01-01

Investigating the relationship between brain structure and function is a central endeavor for neuroscience research. Yet, the mechanisms shaping this relationship largely remain to be elucidated and are highly debated. In particular, the existence and relative contributions of anatomical constraints and dynamical physiological mechanisms of different types remain to be established. We addressed this issue by systematically comparing functional connectivity (FC) from resting-state functional magnetic resonance imaging data with simulations from increasingly complex computational models, and by manipulating anatomical connectivity obtained from fiber tractography based on diffusion-weighted imaging. We hypothesized that FC reflects the interplay of at least three types of components: (i) a backbone of anatomical connectivity, (ii) a stationary dynamical regime directly driven by the underlying anatomy, and (iii) other stationary and non-stationary dynamics not directly related to the anatomy. We showed that anatomical connectivity alone accounts for up to 15% of FC variance; that there is a stationary regime accounting for up to an additional 20% of variance and that this regime can be associated to a stationary FC; that a simple stationary model of FC better explains FC than more complex models; and that there is a large remaining variance (around 65%), which must contain the non-stationarities of FC evidenced in the literature. We also show that homotopic connections across cerebral hemispheres, which are typically improperly estimated, play a strong role in shaping all aspects of FC, notably indirect connections and the topographic organization of brain networks. PMID:24651524

A Large-Scale Super-Structure at z=0.65 in the UKIDSS Ultra-Deep Survey Field

NASA Astrophysics Data System (ADS)

Galametz, Audrey; Candels Clustering Working Group

2017-07-01

In hierarchical structure formation scenarios, galaxies accrete along high density filaments. Superclusters represent the largest density enhancements in the cosmic web with scales of 100 to 200 Mpc. As they represent the largest components of LSS, they are very powerful tools to constrain cosmological models. Since they also offer a wide range of density, from infalling group to high density cluster core, they are also the perfect laboratory to study the influence of environment on galaxy evolution. I will present a newly discovered large scale structure at z=0.65 in the UKIDSS UDS field. Although statistically predicted, the presence of such structure in UKIDSS, one of the most extensively covered and studied extragalactic field, remains a serendipity. Our follow-up confirmed more than 15 group members including at least three galaxy clusters with M200 10^14Msol . Deep spectroscopy of the quiescent core galaxies reveals that the most massive structure knots are at very different formation stage with a range of red sequence properties. Statistics allow us to map formation age across the structure denser knots and identify where quenching is most probably occurring across the LSS. Spectral diagnostics analysis also reveals an interesting population of transition galaxies we suspect are transforming from star-forming to quiescent galaxies.

Extraordinary Structured Noncoding RNAs Revealed by Bacterial Metagenome Analysis

PubMed Central

Weinberg, Zasha; Perreault, Jonathan; Meyer, Michelle M.; Breaker, Ronald R.

2012-01-01

Estimates of the total number of bacterial species1-3 suggest that existing DNA sequence databases carry only a tiny fraction of the total amount of DNA sequence space represented by this division of life. Indeed, environmental DNA samples have been shown to encode many previously unknown classes of proteins4 and RNAs5. Bioinformatics searches6-10 of genomic DNA from bacteria commonly identify novel noncoding RNAs (ncRNAs)10-12 such as riboswitches13,14. In rare instances, RNAs that exhibit more extensive sequence and structural conservation across a wide range of bacteria are encountered15,16. Given that large structured RNAs are known to carry out complex biochemical functions such as protein synthesis and RNA processing reactions, identifying more RNAs of great size and intricate structure is likely to reveal additional biochemical functions that can be achieved by RNA. We applied an updated computational pipeline17 to discover ncRNAs that rival the known large ribozymes in size and structural complexity or that are among the most abundant RNAs in bacteria that encode them. These RNAs would have been difficult or impossible to detect without examining environmental DNA sequences, suggesting that numerous RNAs with extraordinary size, structural complexity, or other exceptional characteristics remain to be discovered in unexplored sequence space. PMID:19956260

The structure of plasmodesmata as revealed by plasmolysis, detergent extraction, and protease digestion

PubMed Central

1991-01-01

Plasmodesmata or intercellular bridges that connect plant cells are cylindrical channels approximately 40 nm in diameter. Running through the center of each is a dense rod, the desmotubule, that is connected to the endoplasmic reticulum of adjacent cells. Fern, Onoclea sensibilis, gametophytes were cut in half and the cut surfaces exposed to the detergent, Triton X 100, then fixed. Although the plasma membrane limiting the plasmodesma is solubilized partially or completely, the desmotubule remains intact. Alternatively, if the cut surface is exposed to papain, then fixed, the desmotubule disappears, but the plasma membrane limiting the plasmodesmata remains intact albeit swollen and irregular in profile. Gametophytes were plasmolyzed, and then fixed. As the cells retract from their cell walls they leave behind the plasmodesmata still inserted in the cell wall. They can break cleanly when the cell proper retracts or can pull away portions of the plasma membrane of the cell with them. Where the desmotubule remains intact, the plasmodesma retains its shape. These images and the results with detergents and proteases indicate that the desmotubule provides a cytoskeletal element for each plasmodesma, an element that not only stabilizes the whole structure, but also limits its size and porosity. It is likely to be composed in large part of protein. Suggestions are made as to why this structure has been selected for in evolution. PMID:1993740

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adamek, Julian; Daverio, David; Durrer, Ruth

We present a new N-body code, gevolution , for the evolution of large scale structure in the Universe. Our code is based on a weak field expansion of General Relativity and calculates all six metric degrees of freedom in Poisson gauge. N-body particles are evolved by solving the geodesic equation which we write in terms of a canonical momentum such that it remains valid also for relativistic particles. We validate the code by considering the Schwarzschild solution and, in the Newtonian limit, by comparing with the Newtonian N-body codes Gadget-2 and RAMSES . We then proceed with a simulation ofmore » large scale structure in a Universe with massive neutrinos where we study the gravitational slip induced by the neutrino shear stress. The code can be extended to include different kinds of dark energy or modified gravity models and going beyond the usually adopted quasi-static approximation. Our code is publicly available.« less

Protozoal Digestion of Coat-Defective Bacillus subtilis Spores Produces “Rinds” Composed of Insoluble Coat Protein▿

PubMed Central

Carroll, Alicia Monroe; Plomp, Marco; Malkin, Alexander J.; Setlow, Peter

2008-01-01

The Bacillus subtilis spore coat is a multilayer, proteinaceous structure that consists of more than 50 proteins. Located on the surface of the spore, the coat provides resistance to potentially toxic molecules as well as to predation by the protozoan Tetrahymena thermophila. When coat-defective spores are fed to Tetrahymena, the spores are readily digested. However, a residue termed a “rind” that looks like coat material remains. As observed with a phase-contrast microscope, the rinds are spherical or hemispherical structures that appear to be devoid of internal contents. Atomic force microscopy and chemical analyses showed that (i) the rinds are composed of insoluble protein largely derived from both outer and inner spore coat layers, (ii) the amorphous layer of the outer coat is largely responsible for providing spore resistance to protozoal digestion, and (iii) the rinds and intact spores do not contain significant levels of silicon. PMID:18689521

A network property necessary for concentration robustness

NASA Astrophysics Data System (ADS)

Eloundou-Mbebi, Jeanne M. O.; Küken, Anika; Omranian, Nooshin; Kleessen, Sabrina; Neigenfind, Jost; Basler, Georg; Nikoloski, Zoran

2016-10-01

Maintenance of functionality of complex cellular networks and entire organisms exposed to environmental perturbations often depends on concentration robustness of the underlying components. Yet, the reasons and consequences of concentration robustness in large-scale cellular networks remain largely unknown. Here, we derive a necessary condition for concentration robustness based only on the structure of networks endowed with mass action kinetics. The structural condition can be used to design targeted experiments to study concentration robustness. We show that metabolites satisfying the necessary condition are present in metabolic networks from diverse species, suggesting prevalence of this property across kingdoms of life. We also demonstrate that our predictions about concentration robustness of energy-related metabolites are in line with experimental evidence from Escherichia coli. The necessary condition is applicable to mass action biological systems of arbitrary size, and will enable understanding the implications of concentration robustness in genetic engineering strategies and medical applications.

The optimal density of cellular solids in axial tension.

PubMed

Mihai, L Angela; Alayyash, Khulud; Wyatt, Hayley

2017-05-01

For cellular bodies with uniform cell size, wall thickness, and shape, an important question is whether the same volume of material has the same effect when arranged as many small cells or as fewer large cells. To answer this question, for finite element models of periodic structures of Mooney-type material with different structural geometry and subject to large strain deformations, we identify a nonlinear elastic modulus as the ratio between the mean effective stress and the mean effective strain in the solid cell walls, and show that this modulus increases when the thickness of the walls increases, as well as when the number of cells increases while the volume of solid material remains fixed. Since, under the specified conditions, this nonlinear elastic modulus increases also as the corresponding mean stress increases, either the mean modulus or the mean stress can be employed as indicator when the optimum wall thickness or number of cells is sought.

The Explorer of Diffuse Galactic Emission (EDGE): Determination of Large-Scale Structure Evolution from Measurement of the Anisotropy of the Cosmic Infrared Background

NASA Technical Reports Server (NTRS)

Silverberg, R. F.; Cheng, E. S.; Cottingham, D. A.; Fixsen, D. J.; Meyer, S. S.; Wilson, G. W.

2004-01-01

The formation of the first objects, stars and galaxies and their subsequent evolution remain a cosmological unknown. Few observational probes of these processes exist. The Cosmic Infrared Background (CIB) originates from this era, and can provide information to test models of both galaxy evolution and the growth of primordial structure. The Explorer of Diffuse Galactic Emission (EDGE) is a proposed balloon-borne mission designed to measure the spatial fluctuations in the CIB from 200 micrometers to 1 millimeter on 6' to 3 degree scales with 2 microKelvin sensitivity/resolution element. Such measurements would provide a sensitive probe of the large-scale variation in protogalaxy density at redshifts approximately 0.5-3. In this paper, we present the scientific justification for the mission and show a concept for the instrument and observations.

A network property necessary for concentration robustness.

PubMed

Eloundou-Mbebi, Jeanne M O; Küken, Anika; Omranian, Nooshin; Kleessen, Sabrina; Neigenfind, Jost; Basler, Georg; Nikoloski, Zoran

2016-10-19

Maintenance of functionality of complex cellular networks and entire organisms exposed to environmental perturbations often depends on concentration robustness of the underlying components. Yet, the reasons and consequences of concentration robustness in large-scale cellular networks remain largely unknown. Here, we derive a necessary condition for concentration robustness based only on the structure of networks endowed with mass action kinetics. The structural condition can be used to design targeted experiments to study concentration robustness. We show that metabolites satisfying the necessary condition are present in metabolic networks from diverse species, suggesting prevalence of this property across kingdoms of life. We also demonstrate that our predictions about concentration robustness of energy-related metabolites are in line with experimental evidence from Escherichia coli. The necessary condition is applicable to mass action biological systems of arbitrary size, and will enable understanding the implications of concentration robustness in genetic engineering strategies and medical applications.

A network property necessary for concentration robustness

PubMed Central

Eloundou-Mbebi, Jeanne M. O.; Küken, Anika; Omranian, Nooshin; Kleessen, Sabrina; Neigenfind, Jost; Basler, Georg; Nikoloski, Zoran

2016-01-01

Maintenance of functionality of complex cellular networks and entire organisms exposed to environmental perturbations often depends on concentration robustness of the underlying components. Yet, the reasons and consequences of concentration robustness in large-scale cellular networks remain largely unknown. Here, we derive a necessary condition for concentration robustness based only on the structure of networks endowed with mass action kinetics. The structural condition can be used to design targeted experiments to study concentration robustness. We show that metabolites satisfying the necessary condition are present in metabolic networks from diverse species, suggesting prevalence of this property across kingdoms of life. We also demonstrate that our predictions about concentration robustness of energy-related metabolites are in line with experimental evidence from Escherichia coli. The necessary condition is applicable to mass action biological systems of arbitrary size, and will enable understanding the implications of concentration robustness in genetic engineering strategies and medical applications. PMID:27759015

A quantum spin-probe molecular microscope

NASA Astrophysics Data System (ADS)

Perunicic, V. S.; Hill, C. D.; Hall, L. T.; Hollenberg, L. C. L.

2016-10-01

Imaging the atomic structure of a single biomolecule is an important challenge in the physical biosciences. Whilst existing techniques all rely on averaging over large ensembles of molecules, the single-molecule realm remains unsolved. Here we present a protocol for 3D magnetic resonance imaging of a single molecule using a quantum spin probe acting simultaneously as the magnetic resonance sensor and source of magnetic field gradient. Signals corresponding to specific regions of the molecule's nuclear spin density are encoded on the quantum state of the probe, which is used to produce a 3D image of the molecular structure. Quantum simulations of the protocol applied to the rapamycin molecule (C51H79NO13) show that the hydrogen and carbon substructure can be imaged at the angstrom level using current spin-probe technology. With prospects for scaling to large molecules and/or fast dynamic conformation mapping using spin labels, this method provides a realistic pathway for single-molecule microscopy.

Where's the Beaverhead beef?

NASA Astrophysics Data System (ADS)

Hargraves, R. B.

Only rare quartz grains with single-set planar (1013) deformation features (PDF's) are present in breccia dikes found in association with uniformly oriented shatter cones that occur over an area 8 x 25 km. This suggests that the Beaverhead shocked rocks come from only the outer part of the central uplift of what must have been a large (greater than 100 km diameter) complex impact structure. An impact event of this magnitude on continental crust (thought to have occurred in late Precambrian or ealy Paleozoic time) could be expected to punctuate local geologic history. Furthermore, although it may now be covered, its scar should remain despite all the considerable subsequent erosion/deposition and tectonism since the impact. The following are three large-scale singularities or anomalies that may reflect the event and mark its source. (1) The Lemhi Arch is a major structural uplift that occurred in late Proterozoic-early Paleozoic time in East Central Idaho and caused the erosion of at least 4 km of sedimentary cover. This may be directly related to the impact. (2) Of the many thrust sheets comprising the Cordilleran belt, the Cabin plate that carries the shocked rocks is unique in that it alone intersected the crystalline basement. It also now marks the apex of the Southwest Montana Recess in the Sevier front. The basement uplift remaining from the impact may have constituted a mechanical obstacle to the advancing thrust sheets in Cretaceous time, causing the recess. (3) What could be interpreted as a roughly circular aeromagnetic anomaly approx. 70 km in diameter can be discerned in the state aeromagnetic map centered about 20 km southeast of Challis, Idaho, in the Lost River range. It is in approximately the right place, and ignoring the possibility that the anomalies have diverse causes and the circular pattern is coincidental, it may mark what remains of the buried central uplift structure.

Atomistic simulations of highly conductive molecular transport junctions under realistic conditions

NASA Astrophysics Data System (ADS)

French, William R.; Iacovella, Christopher R.; Rungger, Ivan; Souza, Amaury Melo; Sanvito, Stefano; Cummings, Peter T.

2013-04-01

We report state-of-the-art atomistic simulations combined with high-fidelity conductance calculations to probe structure-conductance relationships in Au-benzenedithiolate (BDT)-Au junctions under elongation. Our results demonstrate that large increases in conductance are associated with the formation of monatomic chains (MACs) of Au atoms directly connected to BDT. An analysis of the electronic structure of the simulated junctions reveals that enhancement in the s-like states in Au MACs causes the increases in conductance. Other structures also result in increased conductance but are too short-lived to be detected in experiment, while MACs remain stable for long simulation times. Examinations of thermally evolved junctions with and without MACs show negligible overlap between conductance histograms, indicating that the increase in conductance is related to this unique structural change and not thermal fluctuation. These results, which provide an excellent explanation for a recently observed anomalous experimental result [Bruot et al., Nat. Nanotechnol., 2012, 7, 35-40], should aid in the development of mechanically responsive molecular electronic devices.We report state-of-the-art atomistic simulations combined with high-fidelity conductance calculations to probe structure-conductance relationships in Au-benzenedithiolate (BDT)-Au junctions under elongation. Our results demonstrate that large increases in conductance are associated with the formation of monatomic chains (MACs) of Au atoms directly connected to BDT. An analysis of the electronic structure of the simulated junctions reveals that enhancement in the s-like states in Au MACs causes the increases in conductance. Other structures also result in increased conductance but are too short-lived to be detected in experiment, while MACs remain stable for long simulation times. Examinations of thermally evolved junctions with and without MACs show negligible overlap between conductance histograms, indicating that the increase in conductance is related to this unique structural change and not thermal fluctuation. These results, which provide an excellent explanation for a recently observed anomalous experimental result [Bruot et al., Nat. Nanotechnol., 2012, 7, 35-40], should aid in the development of mechanically responsive molecular electronic devices. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr00459g

Diversity of herbaceous plants and bacterial communities regulates soil resistome across forest biomes.

PubMed

Hu, Hang-Wei; Wang, Jun-Tao; Singh, Brajesh K; Liu, Yu-Rong; Chen, Yong-Liang; Zhang, Yu-Jing; He, Ji-Zheng

2018-04-24

Antibiotic resistance is ancient and prevalent in natural ecosystems and evolved long before the utilization of synthetic antibiotics started, but factors influencing the large-scale distribution patterns of natural antibiotic resistance genes (ARGs) remain largely unknown. Here, a large-scale investigation over 4000 km was performed to profile soil ARGs, plant communities and bacterial communities from 300 quadrats across five forest biomes with minimal human impact. We detected diverse and abundant ARGs in forests, including over 160 genes conferring resistance to eight major categories of antibiotics. The diversity of ARGs was strongly and positively correlated with the diversity of bacteria, herbaceous plants and mobile genetic elements (MGEs). The ARG composition was strongly correlated with the taxonomic structure of bacteria and herbs. Consistent with this strong correlation, structural equation modelling demonstrated that the positive effects of bacterial and herb communities on ARG patterns were maintained even when simultaneously accounting for multiple drivers (climate, spatial predictors and edaphic factors). These findings suggest a paradigm that the interactions between aboveground and belowground communities shape the large-scale distribution of soil resistomes, providing new knowledge for tackling the emerging environmental antibiotic resistance. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Mysticism and schizophrenia: A phenomenological exploration of the structure of consciousness in the schizophrenia spectrum disorders.

PubMed

Parnas, Josef; Henriksen, Mads Gram

2016-07-01

Mysticism and schizophrenia are different categories of human existence and experience. Nonetheless, they exhibit important phenomenological affinities, which, however, remain largely unaddressed. In this study, we explore structural analogies between key features of mysticism and major clinical-phenomenological aspects of the schizophrenia spectrum disorders-i.e. attitudes, the nature of experience, and the 'other', mystical or psychotic reality. Not only do these features gravitate around the issue of the basic dimensions of consciousness, they crucially seem to implicate and presuppose a specific alteration of the very structure of consciousness. This finding has bearings for the understanding of consciousness and its psychopathological distortions. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures.

PubMed

Kuriata, Aleksander; Gierut, Aleksandra Maria; Oleniecki, Tymoteusz; Ciemny, Maciej Pawel; Kolinski, Andrzej; Kurcinski, Mateusz; Kmiecik, Sebastian

2018-05-14

Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and applied in numerous studies of protein structure-function relationships. Here, we present a major update of the CABS-flex web server to version 2.0. The new features include: extension of the method to significantly larger and multimeric proteins, customizable distance restraints and simulation parameters, contact maps and a new, enhanced web server interface. CABS-flex 2.0 is freely available at http://biocomp.chem.uw.edu.pl/CABSflex2.

KSC-2010-4984

NASA Image and Video Library

2010-10-04

CAPE CANAVERAL, Fla. -- At NASA's Kennedy Space Center in Florida, this image shows the progress of the rotating service structure (RSS) on Launch Pad 39B as it is being dismantled. Sand, reinforcing steel and large wooden mats were put down under the RSS to protect the structure's concrete from falling debris during deconstruction. Starting in 2009, the structure at the pad was no longer needed for NASA's Space Shuttle Program, so it is being restructured for future use. The new design will feature a "clean pad" for rockets to come with their own launcher, making it more versatile for a number of vehicles. The new lightning protection system, consisting of three lightning towers and a wire catenary system will remain. Photo credit: NASA/Jack Pfaller

KSC-2010-4988

NASA Image and Video Library

2010-10-04

CAPE CANAVERAL, Fla. -- At NASA's Kennedy Space Center in Florida, this long range view shows the progress of the rotating service structure (RSS) on Launch Pad 39B as it is being dismantled. Sand, reinforcing steel and large wooden mats were put down under the RSS to protect the structure's concrete from falling debris during deconstruction. Starting in 2009, the structure at the pad was no longer needed for NASA's Space Shuttle Program, so it is being restructured for future use. The new design will feature a "clean pad" for rockets to come with their own launcher, making it more versatile for a number of vehicles. The new lightning protection system, consisting of three lightning towers and a wire catenary system will remain. Photo credit: NASA/Jack Pfaller

KSC-2010-4986

NASA Image and Video Library

2010-10-04

CAPE CANAVERAL, Fla. -- At NASA's Kennedy Space Center in Florida, this image shows the progress of the rotating service structure (RSS) on Launch Pad 39B as it is being dismantled. Sand, reinforcing steel and large wooden mats were put down under the RSS to protect the structure's concrete from falling debris during deconstruction. Starting in 2009, the structure at the pad was no longer needed for NASA's Space Shuttle Program, so it is being restructured for future use. The new design will feature a "clean pad" for rockets to come with their own launcher, making it more versatile for a number of vehicles. The new lightning protection system, consisting of three lightning towers and a wire catenary system will remain. Photo credit: NASA/Jack Pfaller

Carbon source in the future chemical industries

NASA Astrophysics Data System (ADS)

Hofmann, Peter; Heinrich Krauch, Carl

1982-11-01

Rising crude oil prices favour the exploitation of hitherto unutilised energy carriers and the realisation of new technologies in all sectors where carbon is used. These changed economic constraints necessitate both savings in conventional petrochemistry and a change to oil-independent carbon sources in the chemical industry. While, in coal chemistry, the synthesis and process principles of petrochemistry — fragmentation of the raw material and subsequent buildup of molecular structures — can be maintained, the raw material structure largely remains unchanged in the chemistry of renewable raw materials. This lecture is to demonstrate the structural as well as the technological and energy criteria of the chemistry of alternative carbon sources, to forecast the chances of commercial realization and to discuss some promising fields of research and development.

Stability of cavitation structures in a thin liquid layer.

PubMed

Wu, Pengfei; Bai, Lixin; Lin, Weijun; Yan, Jiuchun

2017-09-01

The inception and evolution of acoustic cavitation structures in thin liquid layers under different conditions and perturbations are investigated experimentally with high speed photography. The stability and characterization of cavitation structures are quantified by image analysis methods. It is found that cavitation structures (shape of bubble cloud and number of bubbles) are stable under unaltered experimental conditions, and the cavitation bubble cloud will return to the original structure and remain stable even in the face of large perturbations. When the experimental conditions are altered (for example, acoustic intensity, cavitation nuclei, boundary), the cavitation structures will vary correspondingly. Further analysis implies that the stability of cavitation structures is closely related to the number of bubbles in the cavitation bubble cloud. There are two mechanisms acting simultaneously in the cavitation bubble cloud evolution, one "bubble production" and the other "bubble disappearance". We propose that the two mechanisms acting together constitute the most likely explanation for the stability of cavitation structures and their transformation. Copyright © 2017 Elsevier B.V. All rights reserved.

Structure and Evoluton of the Large Scale Solar and Heliospheric Magnetic Fields.

DTIC Science & Technology

1984-04-01

symmetric about the equator and therefore reinforces the dipole field. This has the effect of pushing the current sheet toward the equator as shown in Figure...drift only slightly in longitude. The postive sector near 90’ remains strong through the year too. The positive sector near 2700 appears to grow in...sheet position determined from coronal polarization brightness measurements from the Mauna Loa coronameter. An immediate problem with using the

Eighty-five million years of Pacific Ocean gyre ecosystem structure: long-term stability marked by punctuated change.

PubMed

Sibert, Elizabeth; Norris, Richard; Cuevas, Jose; Graves, Lana

2016-05-25

While the history of taxonomic diversification in open ocean lineages of ray-finned fish and elasmobranchs is increasingly known, the evolution of their roles within the open ocean ecosystem remains poorly understood. To assess the relative importance of these groups through time, we measured the accumulation rate of microfossil fish teeth and elasmobranch dermal denticles (ichthyoliths) in deep-sea sediment cores from the North and South Pacific gyres over the past 85 million years (Myr). We find three distinct and stable open ocean ecosystem structures, each defined by the relative and absolute abundance of elasmobranch and ray-finned fish remains. The Cretaceous Ocean (pre-66 Ma) was characterized by abundant elasmobranch denticles, but low abundances of fish teeth. The Palaeogene Ocean (66-20 Ma), initiated by the Cretaceous/Palaeogene mass extinction, had nearly four times the abundance of fish teeth compared with elasmobranch denticles. This Palaeogene Ocean structure remained stable during the Eocene greenhouse (50 Ma) and the Eocene-Oligocene glaciation (34 Ma), despite large changes in the overall accumulation of both groups during those intervals, suggesting that climate change is not a primary driver of ecosystem structure. Dermal denticles virtually disappeared from open ocean ichthyolith assemblages approximately 20 Ma, while fish tooth accumulation increased dramatically in variability, marking the beginning of the Modern Ocean. Together, these results suggest that open ocean fish community structure is stable on long timescales, independent of total production and climate change. The timing of the abrupt transitions between these states suggests that the transitions may be due to interactions with other, non-preserved pelagic consumer groups. © 2016 The Author(s).

Eighty-five million years of Pacific Ocean gyre ecosystem structure: long-term stability marked by punctuated change

PubMed Central

Norris, Richard; Cuevas, Jose; Graves, Lana

2016-01-01

While the history of taxonomic diversification in open ocean lineages of ray-finned fish and elasmobranchs is increasingly known, the evolution of their roles within the open ocean ecosystem remains poorly understood. To assess the relative importance of these groups through time, we measured the accumulation rate of microfossil fish teeth and elasmobranch dermal denticles (ichthyoliths) in deep-sea sediment cores from the North and South Pacific gyres over the past 85 million years (Myr). We find three distinct and stable open ocean ecosystem structures, each defined by the relative and absolute abundance of elasmobranch and ray-finned fish remains. The Cretaceous Ocean (pre-66 Ma) was characterized by abundant elasmobranch denticles, but low abundances of fish teeth. The Palaeogene Ocean (66–20 Ma), initiated by the Cretaceous/Palaeogene mass extinction, had nearly four times the abundance of fish teeth compared with elasmobranch denticles. This Palaeogene Ocean structure remained stable during the Eocene greenhouse (50 Ma) and the Eocene–Oligocene glaciation (34 Ma), despite large changes in the overall accumulation of both groups during those intervals, suggesting that climate change is not a primary driver of ecosystem structure. Dermal denticles virtually disappeared from open ocean ichthyolith assemblages approximately 20 Ma, while fish tooth accumulation increased dramatically in variability, marking the beginning of the Modern Ocean. Together, these results suggest that open ocean fish community structure is stable on long timescales, independent of total production and climate change. The timing of the abrupt transitions between these states suggests that the transitions may be due to interactions with other, non-preserved pelagic consumer groups. PMID:27194702

Evolution of the Valley Position in Bulk Transition-Metal Chalcogenides and Their Monolayer Limit.

PubMed

Yuan, Hongtao; Liu, Zhongkai; Xu, Gang; Zhou, Bo; Wu, Sanfeng; Dumcenco, Dumitru; Yan, Kai; Zhang, Yi; Mo, Sung-Kwan; Dudin, Pavel; Kandyba, Victor; Yablonskikh, Mikhail; Barinov, Alexei; Shen, Zhixun; Zhang, Shoucheng; Huang, Yingsheng; Xu, Xiaodong; Hussain, Zahid; Hwang, Harold Y; Cui, Yi; Chen, Yulin

2016-08-10

Layered transition metal chalcogenides with large spin orbit coupling have recently sparked much interest due to their potential applications for electronic, optoelectronic, spintronics, and valleytronics. However, most current understanding of the electronic structure near band valleys in momentum space is based on either theoretical investigations or optical measurements, leaving the detailed band structure elusive. For example, the exact position of the conduction band valley of bulk MoS2 remains controversial. Here, using angle-resolved photoemission spectroscopy with submicron spatial resolution (micro-ARPES), we systematically imaged the conduction/valence band structure evolution across representative chalcogenides MoS2, WS2, and WSe2, as well as the thickness dependent electronic structure from bulk to the monolayer limit. These results establish a solid basis to understand the underlying valley physics of these materials, and also provide a link between chalcogenide electronic band structure and their physical properties for potential valleytronics applications.

Mounting structure

NASA Technical Reports Server (NTRS)

Ganssle, Eugene Robert (Inventor); Scott, Ralph Richard (Inventor); Williams, Richard Jean (Inventor)

1978-01-01

A mounting platform for heat producing instruments operated in a narrow equilibrium temperature range comprises a grid-like structure with relatively large openings therein. The instruments are secured to and thermally coupled with the grid surface facing the instruments. Excess heat from the instruments is selectively radiated to the ambient through openings in the grid, the grid surfaces at these openings exhibiting low thermal emissivity and adsorptivity. The remainder of the grid is maintained at the equilibrium temperature and is covered with a thermal insulating blanket. Thus, the entire system including the platform and instruments is maintained substantially isothermal, whereby the instruments remain in fixed physical relationship to one another.

International Conference: Milky Way Surveys: The Structure and Evolution of Our Galaxy

NASA Technical Reports Server (NTRS)

Clemens, Dan

2004-01-01

We were granted NASA support for partial sponsorship of an international conference on Galactic science, held June 15-17, 2003 and hosted by the Institute for Astrophysical Research at Boston University. This conference, entitled 'Milky Way Surveys: The Structure and Evolution of Our Galaxy' drew some 125 scientific experts, researchers, and graduate students to Boston to: (1) Present large area survey plans and findings; (2) Discuss important remaining questions and puzzles in Galactic science; and (3) To inform and excite students and researchers about the potential for using large area survey databases to address key Galactic science questions. An international Scientific Organizing Committee for this conference crafted a tightly packed two-day conference designed to highlight many recent and upcoming large area surveys (including 2MASS, SDSS, MSX, VLA-HI, GRS, and SIRTF/GLIMPSE) and current theoretical understandings and questions. By bringing together experts in the conduct of Galactic surveys and leading theorists, new ways of attacking long-standing scientific questions were encouraged. The titles of most of the talks and posters presented are attached to the end of this report.

Decoding the future from past experience: learning shapes predictions in early visual cortex.

PubMed

Luft, Caroline D B; Meeson, Alan; Welchman, Andrew E; Kourtzi, Zoe

2015-05-01

Learning the structure of the environment is critical for interpreting the current scene and predicting upcoming events. However, the brain mechanisms that support our ability to translate knowledge about scene statistics to sensory predictions remain largely unknown. Here we provide evidence that learning of temporal regularities shapes representations in early visual cortex that relate to our ability to predict sensory events. We tested the participants' ability to predict the orientation of a test stimulus after exposure to sequences of leftward- or rightward-oriented gratings. Using fMRI decoding, we identified brain patterns related to the observers' visual predictions rather than stimulus-driven activity. Decoding of predicted orientations following structured sequences was enhanced after training, while decoding of cued orientations following exposure to random sequences did not change. These predictive representations appear to be driven by the same large-scale neural populations that encode actual stimulus orientation and to be specific to the learned sequence structure. Thus our findings provide evidence that learning temporal structures supports our ability to predict future events by reactivating selective sensory representations as early as in primary visual cortex. Copyright © 2015 the American Physiological Society.

Examining gray matter structures associated with individual differences in global life satisfaction in a large sample of young adults

PubMed Central

Kong, Feng; Ding, Ke; Yang, Zetian; Dang, Xiaobin; Hu, Siyuan; Song, Yiying

2015-01-01

Although much attention has been directed towards life satisfaction that refers to an individual’s general cognitive evaluations of his or her life as a whole, little is known about the neural basis underlying global life satisfaction. In this study, we used voxel-based morphometry to investigate the structural neural correlates of life satisfaction in a large sample of young healthy adults (n = 299). We showed that individuals’ life satisfaction was positively correlated with the regional gray matter volume (rGMV) in the right parahippocampal gyrus (PHG), and negatively correlated with the rGMV in the left precuneus and left ventromedial prefrontal cortex. This pattern of results remained significant even after controlling for the effect of general positive and negative affect, suggesting a unique structural correlates of life satisfaction. Furthermore, we found that self-esteem partially mediated the association between the PHG volume and life satisfaction as well as that between the precuneus volume and global life satisfaction. Taken together, we provide the first evidence for the structural neural basis of life satisfaction, and highlight that self-esteem might play a crucial role in cultivating an individual’s life satisfaction. PMID:25406366

Geophysical survey of the proposed Tsenkher impact structure, Gobi Altai, Mongolia

NASA Astrophysics Data System (ADS)

Ormö, Jens; Gomez-Ortiz, David; Komatsu, Goro; Bayaraa, Togookhuu; Tserendug, Shoovdor

2010-03-01

We have performed forward magnetic and gravity modeling of data obtained during the 2007 expedition to the 3.7km in diameter, circular, Tsenkher structure, Mongolia, in order to evaluate the cause of its formation. Extensive occurrences of brecciated rocks, mainly in the form of an ejecta blanket outside the elevated rim of the structure, support an explosive origin (e.g., cosmic impact, explosive volcanism). The host rocks in the area are mainly weakly magnetic, silica-rich sandstones, and siltstones. A near absence of surface exposures of volcanic rocks makes any major volcanic structures (e.g., caldera) unlikely. Likewise, the magnetic models exclude any large, subsurface, intrusive body. This is supported by an 8mGal gravity low over the structure indicating a subsurface low density body. Instead, the best fit is achieved for a bowl-shaped structure with a slight central rise as expected for an impact crater of this size in mainly sedimentary target. The structure can be either root-less (i.e., impact crater) or rooted with a narrow feeder dyke with relatively higher magnetic susceptibility and density (i.e., volcanic maar crater). The geophysical signature, the solitary appearance, the predominantly sedimentary setting, and the comparably large size of the Tsenkher structure favor the impact crater alternative. However, until mineralogical/geochemical evidence for an impact is presented, the maar alternative remains plausible although exceptional as it would make the Tsenkher structure one of the largest in the world in an unusual setting for maar craters.

Heat resistive dielectric multi-layer micro-mirror array in epitaxial lateral overgrowth gallium nitride.

PubMed

Huang, Chen-Yang; Ku, Hao-Min; Liao, Wei-Tsai; Chao, Chu-Li; Tsay, Jenq-Dar; Chao, Shiuh

2009-03-30

Ta2O5 / SiO2 dielectric multi-layer micro-mirror array (MMA) with 3mm mirror size and 6mm array period was fabricated on c-plane sapphire substrate. The MMA was subjected to 1200 degrees C high temperature annealing and remained intact with high reflectance in contrast to the continuous multi-layer for which the layers have undergone severe damage by 1200 degrees C annealing. Epitaxial lateral overgrowth (ELO) of gallium nitride (GaN) was applied to the MMA that was deposited on both sapphire and sapphire with 2:56 mm GaN template. The MMA was fully embedded in the ELO GaN and remained intact. The result implies that our MMA is compatible to the high temperature growth environment of GaN and the MMA could be incorporated into the structure of the micro-LED array as a one to one micro backlight reflector, or as the patterned structure on the large area LED for controlling the output light.

Cytotoxic Helix-Rich Oligomer Formation by Melittin and Pancreatic Polypeptide

PubMed Central

Singh, Pradeep K.; Ghosh, Dhiman; Tewari, Debanjan; Mohite, Ganesh M.; Carvalho, Edmund; Jha, Narendra Nath; Jacob, Reeba S.; Sahay, Shruti; Banerjee, Rinti; Bera, Amal K.; Maji, Samir K.

2015-01-01

Conversion of amyloid fibrils by many peptides/proteins involves cytotoxic helix-rich oligomers. However, their toxicity and biophysical studies remain largely unknown due to their highly dynamic nature. To address this, we chose two helical peptides (melittin, Mel and pancreatic polypeptide, PP) and studied their aggregation and toxicity. Mel converted its random coil structure to oligomeric helical structure upon binding to heparin; however, PP remained as helix after oligomerization. Interestingly, similar to Parkinson’s associated α-synuclein (AS) oligomers, Mel and PP also showed tinctorial properties, higher hydrophobic surface exposure, cellular toxicity and membrane pore formation after oligomerization in the presence of heparin. We suggest that helix-rich oligomers with exposed hydrophobic surface are highly cytotoxic to cells irrespective of their disease association. Moreover as Mel and PP (in the presence of heparin) instantly self-assemble into stable helix-rich amyloidogenic oligomers; they could be represented as models for understanding the biophysical and cytotoxic properties of helix-rich intermediates in detail. PMID:25803428

A microscopic study investigating the structure of SnSe surfaces

NASA Astrophysics Data System (ADS)

Kim, Sang-ui; Duong, Anh-Tuan; Cho, Sunglae; Rhim, S. H.; Kim, Jungdae

2016-09-01

SnSe has been widely studied due to its many potential applications that take advantage of its excellent thermoelectric, photovoltaic, and optoelectronic properties. However, experimental investigations into the microscopic structure of SnSe remain largely unexplored. Herein, for the first time, the atomic and electronic structures of SnSe surfaces are studied by a home-built low temperature scanning tunneling microscope (STM) and density functional theory (DFT) calculations. The cleaved surface of SnSe is comprised of covalently bonded Se and Sn atoms in zigzag patterns. However, rectangular periodicity was observed in the atomic images of SnSe surfaces for filled and empty state probing. Detailed atomic structures are analyzed by DFT calculations, indicating that the bright extrusions of both filled and empty state images are mostly located at the positions of Sn atoms.

Building 3D structures of vanadium pentoxide nanosheets and application as electrodes in supercapacitors.

PubMed

Zhu, Jixin; Cao, Liujun; Wu, Yingsi; Gong, Yongji; Liu, Zheng; Hoster, Harry E; Zhang, Yunhuai; Zhang, Shengtao; Yang, Shubin; Yan, Qingyu; Ajayan, Pulickel M; Vajtai, Robert

2013-01-01

Various two-dimensional (2D) materials have recently attracted great attention owing to their unique properties and wide application potential in electronics, catalysis, energy storage, and conversion. However, large-scale production of ultrathin sheets and functional nanosheets remains a scientific and engineering challenge. Here we demonstrate an efficient approach for large-scale production of V2O5 nanosheets having a thickness of 4 nm and utilization as building blocks for constructing 3D architectures via a freeze-drying process. The resulting highly flexible V2O5 structures possess a surface area of 133 m(2) g(-1), ultrathin walls, and multilevel pores. Such unique features are favorable for providing easy access of the electrolyte to the structure when they are used as a supercapacitor electrode, and they also provide a large electroactive surface that advantageous in energy storage applications. As a consequence, a high specific capacitance of 451 F g(-1) is achieved in a neutral aqueous Na2SO4 electrolyte as the 3D architectures are utilized for energy storage. Remarkably, the capacitance retention after 4000 cycles is more than 90%, and the energy density is up to 107 W·h·kg(-1) at a high power density of 9.4 kW kg(-1).

A pomegranate-inspired nanoscale design for large-volume-change lithium battery anodes

NASA Astrophysics Data System (ADS)

Liu, Nian; Lu, Zhenda; Zhao, Jie; McDowell, Matthew T.; Lee, Hyun-Wook; Zhao, Wenting; Cui, Yi

2014-03-01

Silicon is an attractive material for anodes in energy storage devices, because it has ten times the theoretical capacity of its state-of-the-art carbonaceous counterpart. Silicon anodes can be used both in traditional lithium-ion batteries and in more recent Li-O2 and Li-S batteries as a replacement for the dendrite-forming lithium metal anodes. The main challenges associated with silicon anodes are structural degradation and instability of the solid-electrolyte interphase caused by the large volume change (~300%) during cycling, the occurrence of side reactions with the electrolyte, and the low volumetric capacity when the material size is reduced to a nanometre scale. Here, we propose a hierarchical structured silicon anode that tackles all three of these problems. Our design is inspired by the structure of a pomegranate, where single silicon nanoparticles are encapsulated by a conductive carbon layer that leaves enough room for expansion and contraction following lithiation and delithiation. An ensemble of these hybrid nanoparticles is then encapsulated by a thicker carbon layer in micrometre-size pouches to act as an electrolyte barrier. As a result of this hierarchical arrangement, the solid-electrolyte interphase remains stable and spatially confined, resulting in superior cyclability (97% capacity retention after 1,000 cycles). In addition, the microstructures lower the electrode-electrolyte contact area, resulting in high Coulombic efficiency (99.87%) and volumetric capacity (1,270 mAh cm-3), and the cycling remains stable even when the areal capacity is increased to the level of commercial lithium-ion batteries (3.7 mAh cm-2).

Grey matter density changes of structures involved in Posttraumatic Stress Disorder (PTSD) after recovery following Eye Movement Desensitization and Reprocessing (EMDR) therapy.

PubMed

Boukezzi, Sarah; El Khoury-Malhame, Myriam; Auzias, Guillaume; Reynaud, Emmanuelle; Rousseau, Pierre-François; Richard, Emmanuel; Zendjidjian, Xavier; Roques, Jacques; Castelli, Nathalie; Correard, Nadia; Guyon, Valérie; Gellato, Caroline; Samuelian, Jean-Claude; Cancel, Aida; Comte, Magali; Latinus, Marianne; Guedj, Eric; Khalfa, Stéphanie

2017-08-30

Recovery of stress-induced structural alterations in Posttraumatic Stress Disorder (PTSD) remains largely unexplored. This study aimed to determine whether symptoms improvement is associated with grey matter (GM) density changes of brain structures involved in PTSD. Two groups of PTSD patients were involved in this study. The first group was treated with Eye Movement Desensitization and Reprocessing (EMDR) therapy and recovered from their symptoms (recovery group) (n = 11); Patients were scanned prior to therapy (T1), one week (T2) and five months after the end of therapy (T3). The second group included patients which followed a supportive therapy and remained symptomatic (wait-list group) (n = 7). They were scanned at three time-steps mimicking the same inter-scan intervals. Voxel-based morphometry (VBM) was used to characterize GM density evolution. GM density values showed a significant group-by-time interaction effect between T1 and T3 in prefrontal cortex areas. These interaction effects were driven by a GM density increase in the recovery group with respect to the wait-list group. Symptoms removal goes hand-in-hand with GM density enhancement of structures involved in emotional regulation. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

CONTINUITY AND CHANGE IN THE AMERICAN CLASS STRUCTURE: WORKPLACE OWNERSHIP AND AUTHORITY RELATIONS FROM 1972 TO 2010

PubMed Central

Wodtke, Geoffrey T.

2016-01-01

This study investigates changes in the American class structure—defined in terms of workplace ownership and authority relations—and trends in status group disparities in class attainment from 1972 to 2010. Although theory and prior research suggest a variety of appreciable changes in class structure and class attainment, data from the General Social Survey indicate that the sizes of different classes remained fairly stable during this time period and that status group disparities in access to ownership and authority persisted largely intact. The 1970s witnessed a decline in the proportion of workers and growth in the proportion of managers and proprietors, but these trends reversed in the 1980s. As a result, by the late 2000s, the ownership and authority structure of the U.S. economy closely resembled that of the early 1970s. Racial and gender disparities in class attainment also did not change significantly over time: blacks and women remained underrepresented (relative to whites and men) in positions of ownership and authority throughout this period. Even after controlling for an extensive set of human capital characteristics, family constraints, and structural economic factors, there is little evidence of status group integration across these key dimensions of economic power. PMID:27134335

Local thermal energy as a structural indicator in glasses.

PubMed

Zylberg, Jacques; Lerner, Edan; Bar-Sinai, Yohai; Bouchbinder, Eran

2017-07-11

Identifying heterogeneous structures in glasses-such as localized soft spots-and understanding structure-dynamics relations in these systems remain major scientific challenges. Here, we derive an exact expression for the local thermal energy of interacting particles (the mean local potential energy change caused by thermal fluctuations) in glassy systems by a systematic low-temperature expansion. We show that the local thermal energy can attain anomalously large values, inversely related to the degree of softness of localized structures in a glass, determined by a coupling between internal stresses-an intrinsic signature of glassy frustration-anharmonicity and low-frequency vibrational modes. These anomalously large values follow a fat-tailed distribution, with a universal exponent related to the recently observed universal [Formula: see text] density of states of quasilocalized low-frequency vibrational modes. When the spatial thermal energy field-a "softness field"-is considered, this power law tail manifests itself by highly localized spots, which are significantly softer than their surroundings. These soft spots are shown to be susceptible to plastic rearrangements under external driving forces, having predictive powers that surpass those of the normal modes-based approach. These results offer a general, system/model-independent, physical/observable-based approach to identify structural properties of quiescent glasses and relate them to glassy dynamics.

Molecular structure of quinoa starch.

PubMed

Li, Guantian; Zhu, Fan

2017-02-20

Quinoa starch has very small granules with unique properties. However, the molecular structure of quinoa starch remains largely unknown. In this study, composition and amylopectin molecular structure of 9 quinoa starch samples were characterised by chromatographic techniques. In particular, the amylopectin internal molecular structure, represented by φ, β-limit dextrins (LDs), was explored. Great variations in the composition and molecular structures were recorded among samples. Compared with other amylopectins, quinoa amylopectin showed a high ratio of short chain to long chains (mean:14.6) and a high percentage of fingerprint A-chains (A fp ) (mean:10.4%). The average chain length, external chain length, and internal chain length of quinoa amylopectin were 16.6, 10.6, and 5.00 glucosyl residues, respectively. Pearson correlation and principal component analysis revealed some inherent correlations among structural parameters and a similarity of different samples. Overall, quinoa amylopectins are structurally similar to that from starches with A-type polymorph such as oat and amaranth starches. Copyright © 2016 Elsevier Ltd. All rights reserved.

Replica Exchange with Solute Tempering: Efficiency in Large Scale Systems

PubMed Central

Huang, Xuhui; Hagen, Morten; Kim, Byungchan; Friesner, Richard A.; Zhou, Ruhong; Berne, B. J.

2009-01-01

We apply the recently developed replica exchange with solute tempering (REST) to three large solvated peptide systems: an α-helix, a β-hairpin, and a TrpCage, with these peptides defined as the “central group”. We find that our original implementation of REST is not always more efficient than the replica exchange method (REM). Specifically, we find that exchanges between folded (F) and unfolded (U) conformations with vastly different structural energies are greatly reduced by the nonappearance of the water self-interaction energy in the replica exchange acceptance probabilities. REST, however, is expected to remain useful for a large class of systems for which the energy gap between the two states is not large, such as weakly bound protein–ligand complexes. Alternatively, a shell of water molecules can be incorporated into the central group, as discussed in the original paper. PMID:17439169

Challenges in Accommodating Volume Change of Si Anodes for Li-Ion Batteries

PubMed Central

Ko, Minseong; Chae, Sujong; Cho, Jaephil

2015-01-01

Si has been considered as a promising alternative anode for next-generation Li-ion batteries (LIBs) because of its high theoretical energy density, relatively low working potential, and abundance in nature. However, Si anodes exhibit rapid capacity decay and an increase in the internal resistance, which are caused by the large volume changes upon Li insertion and extraction. This unfortunately limits their practical applications. Therefore, managing the total volume change remains a critical challenge for effectively alleviating the mechanical fractures and instability of solid-electrolyte-interphase products. In this regard, we review the recent progress in volume-change-accommodating Si electrodes and investigate their ingenious structures with significant improvements in the battery performance, including size-controlled materials, patterned thin films, porous structures, shape-preserving shell designs, and graphene composites. These representative approaches potentially overcome the large morphologic changes in the volume of Si anodes by securing the strain relaxation and structural integrity in the entire electrode. Finally, we propose perspectives and future challenges to realize the practical application of Si anodes in LIB systems. PMID:27525208

Characterization of the transport properties of channel delta-doped structures by light-modulated Shubnikov-de Haas measurements

NASA Technical Reports Server (NTRS)

Mena, R. A.; Schacham, S. E.; Haugland, E. J.; Alterovitz, S. A.; Young, P. G.; Bibyk, S. B.; Ringel, S. A.

1995-01-01

The transport properties of channel delta-doped quantum well structures were characterized by conventional Hall effect and light-modulated Shubnikov-de Haas (SdH) effect measurements. The large number of carriers that become available due to the delta-doping of the channel, leads to an apparent degeneracy in the well. As a result of this degeneracy, the carrier mobility remains constant as a function of temperature from 300 K down to 1.4 K. The large amount of impurity scattering, associated with the overlap of the charge carriers and the dopants, resulted in low carrier mobilities and restricted the observation of the oscillatory magneto-resistance used to characterize the two-dimensional electron gas (2DEG) by conventional SdH measurements. By light-modulating the carriers, we were able to observe the SdH oscillation at low magnetic fields, below 1.4 tesla, and derive a value for the quantum scattering time. Our results for the ratio of the transport and quantum scattering times are lower than those previously measured for similar structures using much higher magnetic fields.

Genetically targeted 3D visualisation of Drosophila neurons under Electron Microscopy and X-Ray Microscopy using miniSOG

PubMed Central

Ng, Julian; Browning, Alyssa; Lechner, Lorenz; Terada, Masako; Howard, Gillian; Jefferis, Gregory S. X. E.

2016-01-01

Large dimension, high-resolution imaging is important for neural circuit visualisation as neurons have both long- and short-range patterns: from axons and dendrites to the numerous synapses at terminal endings. Electron Microscopy (EM) is the favoured approach for synaptic resolution imaging but how such structures can be segmented from high-density images within large volume datasets remains challenging. Fluorescent probes are widely used to localise synapses, identify cell-types and in tracing studies. The equivalent EM approach would benefit visualising such labelled structures from within sub-cellular, cellular, tissue and neuroanatomical contexts. Here we developed genetically-encoded, electron-dense markers using miniSOG. We demonstrate their ability in 1) labelling cellular sub-compartments of genetically-targeted neurons, 2) generating contrast under different EM modalities, and 3) segmenting labelled structures from EM volumes using computer-assisted strategies. We also tested non-destructive X-ray imaging on whole Drosophila brains to evaluate contrast staining. This enabled us to target specific regions for EM volume acquisition. PMID:27958322

Multidimensional Simulations of Filament Channel Structure and Evolution

NASA Astrophysics Data System (ADS)

Karpen, J. T.

2007-10-01

Over the past decade, the NRL Solar Theory group has made steady progress toward formulating a comprehensive model of filament-channel structure and evolution, combining the results of our sheared 3D arcade model for the magnetic field with our thermal nonequilibrium model for the cool, dense material suspended in the corona. We have also discovered that, when a sheared arcade is embedded within the global dipolar field, the resulting stressed filament channel can erupt through the mechanism of magnetic breakout. Our progress has been largely enabled by the development and implementation of state-of-the-art 1D hydrodynamic and 3D magnetohydrodynamic (MHD) codes to simulate the field-aligned plasma thermodynamics and large-scale magnetic-field evolution, respectively. Significant questions remain, however, which could be answered with the advanced observations anticipated from Solar-B. In this review, we summarize what we have learned from our simulations about the magnetic and plasma structure, evolution, and eruption of filament channels, and suggest key observational objectives for Solar-B that will test our filament-channel and CME-initiation models and augment our understanding of the underlying physical processes.

SETTER: web server for RNA structure comparison

PubMed Central

Čech, Petr; Svozil, Daniel; Hoksza, David

2012-01-01

The recent discoveries of regulatory non-coding RNAs changed our view of RNA as a simple information transfer molecule. Understanding the architecture and function of active RNA molecules requires methods for comparing and analyzing their 3D structures. While structural alignment of short RNAs is achievable in a reasonable amount of time, large structures represent much bigger challenge. Here, we present the SETTER web server for the RNA structure pairwise comparison utilizing the SETTER (SEcondary sTructure-based TERtiary Structure Similarity Algorithm) algorithm. The SETTER method divides an RNA structure into the set of non-overlapping structural elements called generalized secondary structure units (GSSUs). The SETTER algorithm scales as O(n2) with the size of a GSSUs and as O(n) with the number of GSSUs in the structure. This scaling gives SETTER its high speed as the average size of the GSSU remains constant irrespective of the size of the structure. However, the favorable speed of the algorithm does not compromise its accuracy. The SETTER web server together with the stand-alone implementation of the SETTER algorithm are freely accessible at http://siret.cz/setter. PMID:22693209

Experimental study designs to improve the evaluation of road mitigation measures for wildlife.

PubMed

Rytwinski, Trina; van der Ree, Rodney; Cunnington, Glenn M; Fahrig, Lenore; Findlay, C Scott; Houlahan, Jeff; Jaeger, Jochen A G; Soanes, Kylie; van der Grift, Edgar A

2015-05-01

An experimental approach to road mitigation that maximizes inferential power is essential to ensure that mitigation is both ecologically-effective and cost-effective. Here, we set out the need for and standards of using an experimental approach to road mitigation, in order to improve knowledge of the influence of mitigation measures on wildlife populations. We point out two key areas that need to be considered when conducting mitigation experiments. First, researchers need to get involved at the earliest stage of the road or mitigation project to ensure the necessary planning and funds are available for conducting a high quality experiment. Second, experimentation will generate new knowledge about the parameters that influence mitigation effectiveness, which ultimately allows better prediction for future road mitigation projects. We identify seven key questions about mitigation structures (i.e., wildlife crossing structures and fencing) that remain largely or entirely unanswered at the population-level: (1) Does a given crossing structure work? What type and size of crossing structures should we use? (2) How many crossing structures should we build? (3) Is it more effective to install a small number of large-sized crossing structures or a large number of small-sized crossing structures? (4) How much barrier fencing is needed for a given length of road? (5) Do we need funnel fencing to lead animals to crossing structures, and how long does such fencing have to be? (6) How should we manage/manipulate the environment in the area around the crossing structures and fencing? (7) Where should we place crossing structures and barrier fencing? We provide experimental approaches to answering each of them using example Before-After-Control-Impact (BACI) study designs for two stages in the road/mitigation project where researchers may become involved: (1) at the beginning of a road/mitigation project, and (2) after the mitigation has been constructed; highlighting real case studies when available. Copyright © 2015 Elsevier Ltd. All rights reserved.

Identification of both copy number variation-type and constant-type core elements in a large segmental duplication region of the mouse genome

PubMed Central

2013-01-01

Background Copy number variation (CNV), an important source of diversity in genomic structure, is frequently found in clusters called CNV regions (CNVRs). CNVRs are strongly associated with segmental duplications (SDs), but the composition of these complex repetitive structures remains unclear. Results We conducted self-comparative-plot analysis of all mouse chromosomes using the high-speed and large-scale-homology search algorithm SHEAP. For eight chromosomes, we identified various types of large SD as tartan-checked patterns within the self-comparative plots. A complex arrangement of diagonal split lines in the self-comparative-plots indicated the presence of large homologous repetitive sequences. We focused on one SD on chromosome 13 (SD13M), and developed SHEPHERD, a stepwise ab initio method, to extract longer repetitive elements and to characterize repetitive structures in this region. Analysis using SHEPHERD showed the existence of 60 core elements, which were expected to be the basic units that form SDs within the repetitive structure of SD13M. The demonstration that sequences homologous to the core elements (>70% homology) covered approximately 90% of the SD13M region indicated that our method can characterize the repetitive structure of SD13M effectively. Core elements were composed largely of fragmented repeats of a previously identified type, such as long interspersed nuclear elements (LINEs), together with partial genic regions. Comparative genome hybridization array analysis showed that whereas 42 core elements were components of CNVR that varied among mouse strains, 8 did not vary among strains (constant type), and the status of the others could not be determined. The CNV-type core elements contained significantly larger proportions of long terminal repeat (LTR) types of retrotransposon than the constant-type core elements, which had no CNV. The higher divergence rates observed in the CNV-type core elements than in the constant type indicate that the CNV-type core elements have a longer evolutionary history than constant-type core elements in SD13M. Conclusions Our methodology for the identification of repetitive core sequences simplifies characterization of the structures of large SDs and detailed analysis of CNV. The results of detailed structural and quantitative analyses in this study might help to elucidate the biological role of one of the SDs on chromosome 13. PMID:23834397

Large-scale coherent structures of suspended dust concentration in the neutral atmospheric surface layer: A large-eddy simulation study

NASA Astrophysics Data System (ADS)

Zhang, Yangyue; Hu, Ruifeng; Zheng, Xiaojing

2018-04-01

Dust particles can remain suspended in the atmospheric boundary layer, motions of which are primarily determined by turbulent diffusion and gravitational settling. Little is known about the spatial organizations of suspended dust concentration and how turbulent coherent motions contribute to the vertical transport of dust particles. Numerous studies in recent years have revealed that large- and very-large-scale motions in the logarithmic region of laboratory-scale turbulent boundary layers also exist in the high Reynolds number atmospheric boundary layer, but their influence on dust transport is still unclear. In this study, numerical simulations of dust transport in a neutral atmospheric boundary layer based on an Eulerian modeling approach and large-eddy simulation technique are performed to investigate the coherent structures of dust concentration. The instantaneous fields confirm the existence of very long meandering streaks of dust concentration, with alternating high- and low-concentration regions. A strong negative correlation between the streamwise velocity and concentration and a mild positive correlation between the vertical velocity and concentration are observed. The spatial length scales and inclination angles of concentration structures are determined, compared with their flow counterparts. The conditionally averaged fields vividly depict that high- and low-concentration events are accompanied by a pair of counter-rotating quasi-streamwise vortices, with a downwash inside the low-concentration region and an upwash inside the high-concentration region. Through the quadrant analysis, it is indicated that the vertical dust transport is closely related to the large-scale roll modes, and ejections in high-concentration regions are the major mechanisms for the upward motions of dust particles.

Assessing health plan ownership.

PubMed

Eyestone, Katherine M; Moore, Keith D; Coddington, Dean C

2014-01-01

In the emerging healthcare environment, providers will require many capabilities of traditional health plans simply to remain viable. Providers that are contemplating entering the health plan business should consider the likely strategic, structural, and cultural effects of such a strategy on their organizations. Providers that own health plans will need to determine how they will differentiate themselves in the markets to foster patient loyalty and which insurance lines of business they will pursue (e.g., individual, small group, large group, or other).

Novel pharmacological targets for the rhythm control management of atrial fibrillation.

PubMed

Burashnikov, Alexander; Antzelevitch, Charles

2011-12-01

Atrial fibrillation (AF) is a growing clinical problem associated with increased morbidity and mortality. Development of safe and effective pharmacological treatments for AF is one of the greatest unmet medical needs facing our society. In spite of significant progress in non-pharmacological AF treatments (largely due to the use of catheter ablation techniques), anti-arrhythmic agents (AADs) remain first line therapy for rhythm control management of AF for most AF patients. When considering efficacy, safety and tolerability, currently available AADs for rhythm control of AF are less than optimal. Ion channel inhibition remains the principal strategy for termination of AF and prevention of its recurrence. Practical clinical experience indicates that multi-ion channel blockers are generally more optimal for rhythm control of AF compared to ion channel-selective blockers. Recent studies suggest that atrial-selective sodium channel block can lead to safe and effective suppression of AF and that concurrent inhibition of potassium ion channels may potentiate this effect. An important limitation of the ion channel block approach for AF treatment is that non-electrical factors (largely structural remodeling) may importantly determine the generation of AF, so that "upstream therapy", aimed at preventing or reversing structural remodeling, may be required for effective rhythm control management. This review focuses on novel pharmacological targets for the rhythm control management of AF. Copyright © 2011 Elsevier Inc. All rights reserved.

The effect of plate motion history on the longevity of deep mantle heterogeneities

NASA Astrophysics Data System (ADS)

Bull, Abigail L.; Domeier, Mathew; Torsvik, Trond H.

2014-09-01

Understanding the first-order dynamical structure and evolution of Earth's mantle is a fundamental goal in solid-earth geophysics. Tomographic observations reveal a lower mantle characterised by higher-than-average shear-wave speeds beneath Asia and encircling the Pacific, consistent with cold slabs beneath regions of ancient subduction, and lower-than-average shear-wave speeds in broad regional areas beneath Africa and the Central Pacific (termed LLSVPs). The LLSVPs are not well understood from a dynamical perspective and their origin and evolution remain enigmatic. Some numerical studies propose that the LLSVP beneath Africa is post-Pangean in origin, formed as a result of return flow in the mantle due to circum-Pangean subduction, countered by an older Pacific LLSVP, suggested to have formed during the break up of Rodinia. This propounds that, prior to the formation of Pangea, the lower mantle was dominated by a degree-1 convection pattern with a major upwelling centred close to the present-day Pacific LLSVP and subduction concentrated mainly in the antipodal hemisphere. In contrast, palaeomagnetic observations which proffer a link between the reconstructed eruption sites of Phanerozoic kimberlites and Large Igneous Provinces with regions on the margins of the present-day LLSVPs suggest that the anomalies may have remained stationary for at least the last 540 Myr and further that the anomalies were largely insensitive to the formation and subsequent break-up of Pangea. Here we investigate the evolution and long-term stability of LLSVP-like structures in Earth's mantle by integrating plate tectonics and numerical models of global thermochemical mantle dynamics. We explore the possibility that either one or both LLSVPs existed prior to the formation of Pangea and improve upon previous studies by using a new, true polar wander-corrected global plate model to impose surface velocity boundary conditions for a time interval that spans the amalgamation and subsequent break-up of the supercontinent. We find that, were only the Pacific LLSVP to exist prior to the formation of Pangea, the African LLSVP would not have been created within the lifetime of the supercontinent. We also find that, were the mantle to be dominated by two antipodal LLSVP-like structures prior to the formation of Pangea, the structures would remain relatively unchanged to the present day and would be insensitive to the formation and break-up of the supercontinent. Our results suggest that both the African and Pacific LLSVPs have remained close to their present-day positions for at least the past 410 Myr.

Tetragonal bismuth bilayer: A stable and robust quantum spin hall insulator

DOE PAGES

Kou, Liangzhi; Tan, Xin; Ma, Yandong; ...

2015-11-23

In this study, topological insulators (TIs) exhibit novel physics with great promise for new devices, but considerable challenges remain to identify TIs with high structural stability and large nontrivial band gap suitable for practical applications. Here we predict by first-principles calculations a two-dimensional (2D) TI, also known as a quantum spin Hall (QSH) insulator, in a tetragonal bismuth bilayer (TB-Bi) structure that is dynamically and thermally stable based on phonon calculations and finite-temperature molecular dynamics simulations. Density functional theory and tight-binding calculations reveal a band inversion among the Bi-p orbits driven by the strong intrinsic spin–orbit coupling, producing a largemore » nontrivial band gap, which can be effectively tuned by moderate strains. The helical gapless edge states exhibit a linear dispersion with a high Fermi velocity comparable to that of graphene, and the QSH phase remains robust on a NaCl substrate. These remarkable properties place TB-Bi among the most promising 2D TIs for high-speed spintronic devices, and the present results provide insights into the intriguing QSH phenomenon in this new Bi structure and offer guidance for its implementation in potential applications.« less

Neurogenesis and Developmental Anesthetic Neurotoxicity

PubMed Central

Kang, Eunchai; Berg, Daniel A.; Furmanski, Orion; Jackson, William M.; Ryu, Yun Kyoung; Gray, Christy D.; Mintz, C. David

2017-01-01

The mechanism by which anesthetics might act on the developing brain in order to cause long term deficits remains incompletely understood. The hippocampus has been identified as a structure that is likely to be involved, as rodent models show numerous deficits in behavioral tasks of learning that are hippocampal-dependent. The hippocampus is an unusual structure in that it is the site of large amounts of neurogenesis postnatally, particularly in the first year of life in humans, and these newly generated neurons are critical to the function of this structure. Intriguingly, neurogenesis is a major developmental event that occurs during postulated windows of vulnerability to developmental anesthetic neurotoxicity across the different species in which it has been studied. In this review, we examine the evidence for anesthetic effects on neurogenesis in the early postnatal period and ask whether neurogenesis should be studied further as a putative mechanism of injury. Multiple anesthetics are considered, and both in vivo and in vitro work is presented. While there is abundant evidence that anesthetics act to suppress neurogenesis at several different phases, evidence of a causal link between these effects and any change in learning behavior remains elusive. PMID:27751818

Neurogenesis and developmental anesthetic neurotoxicity.

PubMed

Kang, Eunchai; Berg, Daniel A; Furmanski, Orion; Jackson, William M; Ryu, Yun Kyoung; Gray, Christy D; Mintz, C David

The mechanism by which anesthetics might act on the developing brain in order to cause long term deficits remains incompletely understood. The hippocampus has been identified as a structure that is likely to be involved, as rodent models show numerous deficits in behavioral tasks of learning that are hippocampal-dependent. The hippocampus is an unusual structure in that it is the site of large amounts of neurogenesis postnatally, particularly in the first year of life in humans, and these newly generated neurons are critical to the function of this structure. Intriguingly, neurogenesis is a major developmental event that occurs during postulated windows of vulnerability to developmental anesthetic neurotoxicity across the different species in which it has been studied. In this review, we examine the evidence for anesthetic effects on neurogenesis in the early postnatal period and ask whether neurogenesis should be studied further as a putative mechanism of injury. Multiple anesthetics are considered, and both in vivo and in vitro work is presented. While there is abundant evidence that anesthetics act to suppress neurogenesis at several different phases, evidence of a causal link between these effects and any change in learning behavior remains elusive. Copyright © 2016. Published by Elsevier Inc.

Nutritional Lipidomics: Molecular Metabolism, Analytics, and Diagnostics

PubMed Central

Smilowitz, Jennifer T.; Zivkovic, Angela M.; Wan, Yu-Jui Yvonne; Watkins, Steve M.; Nording, Malin L.; Hammock, Bruce D.; German, J. Bruce

2013-01-01

The field of lipidomics is providing nutritional science a more comprehensive view of lipid intermediates. Lipidomics research takes advantage of the increase in accuracy and sensitivity of mass detection of mass spectrometry with new bioinformatics toolsets to characterize the structures and abundances of complex lipids. Yet, translating lipidomics to practice via nutritional interventions is still in its infancy. No single instrumentation platform is able to solve the varying analytical challenges of the different molecular lipid species. Biochemical pathways of lipid metabolism remain incomplete and the tools to map lipid compositional data to pathways are still being assembled. Biology itself is dauntingly complex and simply separating biological structures remains a key challenge to lipidomics. Nonetheless, the strategy of combining tandem analytical methods to perform the sensitive, high-throughput, quantitative and comprehensive analysis of lipid metabolites of very large numbers of molecules is poised to drive the field forward rapidly. Among the next steps for nutrition to understand the changes in structures, compositions and function of lipid biomolecules in response to diet is to describe their distribution within discrete functional compartments-lipoproteins. Additionally, lipidomics must tackle the task of assigning the functions of lipids as signaling molecules, nutrient sensors, and intermediates of metabolic pathways. PMID:23818328

Technology development for cryogenic deployable telescope structures and mechanisms

NASA Astrophysics Data System (ADS)

Atkinson, Charles B.; Gilman, Larry; Reynolds, Paul

2003-12-01

At 6-7 meters in diameter, the James Webb Space Telescope (JWST) will require structures that remain stable to levels that are on the order of 10 nanometers under dynamic and thermal loading while operating at cryogenic temperatures. Moreover, the JWST will be the first telescope in space that is deployed, resulting in an aperture that is not only segmented, but has hinge-lines and the associated joining systems or latches in it. In order to understand the behavior and reduce the risk associated with very large, deployed structures and the stability of the associated structure and latches, we developed and tested the largest cryogenic structure ever built and then characterized its stability. This paper presents a description of the design of the Development Optical Telescope Assembly (DOTA), the testing performed, and the results of the testing performed on it. We discuss the material selection and characterization processes, give a description of the test configurations, describe the metrology equipment and the validation process for it, provide the test results, and summarize the conclusions drawn from the results. The testing and associated results include characterization of the thermal stability of the large-scale structure, characterization of the micro-dynamic stability of the latching system, and measurements of the deployment capability of the mechanisms. We also describe how the DOTA design relates to the JWST design and how the test results relate to the JWST requirements.

Adsorption structures and energetics of molecules on metal surfaces: Bridging experiment and theory

NASA Astrophysics Data System (ADS)

Maurer, Reinhard J.; Ruiz, Victor G.; Camarillo-Cisneros, Javier; Liu, Wei; Ferri, Nicola; Reuter, Karsten; Tkatchenko, Alexandre

2016-05-01

Adsorption geometry and stability of organic molecules on surfaces are key parameters that determine the observable properties and functions of hybrid inorganic/organic systems (HIOSs). Despite many recent advances in precise experimental characterization and improvements in first-principles electronic structure methods, reliable databases of structures and energetics for large adsorbed molecules are largely amiss. In this review, we present such a database for a range of molecules adsorbed on metal single-crystal surfaces. The systems we analyze include noble-gas atoms, conjugated aromatic molecules, carbon nanostructures, and heteroaromatic compounds adsorbed on five different metal surfaces. The overall objective is to establish a diverse benchmark dataset that enables an assessment of current and future electronic structure methods, and motivates further experimental studies that provide ever more reliable data. Specifically, the benchmark structures and energetics from experiment are here compared with the recently developed van der Waals (vdW) inclusive density-functional theory (DFT) method, DFT + vdWsurf. In comparison to 23 adsorption heights and 17 adsorption energies from experiment we find a mean average deviation of 0.06 Å and 0.16 eV, respectively. This confirms the DFT + vdWsurf method as an accurate and efficient approach to treat HIOSs. A detailed discussion identifies remaining challenges to be addressed in future development of electronic structure methods, for which the here presented benchmark database may serve as an important reference.

Structure and dynamics of human vimentin intermediate filament dimer and tetramer in explicit and implicit solvent models.

PubMed

Qin, Zhao; Buehler, Markus J

2011-01-01

Intermediate filaments, in addition to microtubules and microfilaments, are one of the three major components of the cytoskeleton in eukaryotic cells, and play an important role in mechanotransduction as well as in providing mechanical stability to cells at large stretch. The molecular structures, mechanical and dynamical properties of the intermediate filament basic building blocks, the dimer and the tetramer, however, have remained elusive due to persistent experimental challenges owing to the large size and fibrillar geometry of this protein. We have recently reported an atomistic-level model of the human vimentin dimer and tetramer, obtained through a bottom-up approach based on structural optimization via molecular simulation based on an implicit solvent model (Qin et al. in PLoS ONE 2009 4(10):e7294, 9). Here we present extensive simulations and structural analyses of the model based on ultra large-scale atomistic-level simulations in an explicit solvent model, with system sizes exceeding 500,000 atoms and simulations carried out at 20 ns time-scales. We report a detailed comparison of the structural and dynamical behavior of this large biomolecular model with implicit and explicit solvent models. Our simulations confirm the stability of the molecular model and provide insight into the dynamical properties of the dimer and tetramer. Specifically, our simulations reveal a heterogeneous distribution of the bending stiffness along the molecular axis with the formation of rather soft and highly flexible hinge-like regions defined by non-alpha-helical linker domains. We report a comparison of Ramachandran maps and the solvent accessible surface area between implicit and explicit solvent models, and compute the persistence length of the dimer and tetramer structure of vimentin intermediate filaments for various subdomains of the protein. Our simulations provide detailed insight into the dynamical properties of the vimentin dimer and tetramer intermediate filament building blocks, which may guide the development of novel coarse-grained models of intermediate filaments, and could also help in understanding assembly mechanisms.

[The dynamic nature of the nutrition of the population of 1 of the districts of Moscow over a 10-year period].

PubMed

Eganian, R A; Kalinina, A M; Izmaĭlova, O V; Shaternikova, I N

2000-01-01

On the basis of three-multiple research of character of a feed of the inhabitants of one of Moscow district by the standardized method of the 24-th hour interrogation reveals significant changes in structure of a feed of the population from 1986 to 1996. The shifts have appeared more dynamical in the second five-year from 1991 to 1996. Nevertheless, atherogenicity of ration of a researched population with superfluous consumption of the saturated fats and simple carbohydrates remains. Is established, in a feed of the women there were large shifts, than at the men. The structure of a feed of the inhabitants of Moscow differed from structure of a feed of the inhabitants of Russia.

50. The apartment building on the left (164166 West Granite) ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

50. The apartment building on the left (164-166 West Granite) was built about 1885-1886, and was used as a combination of residence and rooming house. It is one of the few remaining wood-frame structures dating from the beginning of Butte's economic and building development. Modifications, both interior and exterior, have been minimal, and the historic integrity of the structure has been retained. The Courthouse Grocery on the right (ca. 1887), is another early wood-frame building, and was also originally used as a residence and rooming house. It was modified in the early 20th century to accomodate commercial use on the ground floor, but the historic fabric of the structure is largely intact. - Butte Historic District, Bounded by Copper, Arizona, Mercury & Continental Streets, Butte, Silver Bow County, MT

Using natural language processing to analyze physician modifications to data entry templates.

PubMed Central

Wilcox, Adam B.; Narus, Scott P.; Bowes, Watson A.

2002-01-01

Efficient data entry by clinicians remains a significant challenge for electronic medical records. Current approaches have largely focused on either structured data entry, which can be limiting in expressive power, or free-text entry, which restricts the use of the data for automated decision support. Text-based templates are a semi-structured data entry method that has been used to assist physicians in manually entering clinical notes, by allowing them to edit predefined example notes. We analyzed changes made to 18,726 sentences from text templates, using a natural language processor. The most common changes were addition or deletion of normal observations, or changes in certainty. We identified common modifications that could be captured in structured form by a graphical user interface. PMID:12463955

Problems with small area surveys: lensing covariance of supernova distance measurements.

PubMed

Cooray, Asantha; Huterer, Dragan; Holz, Daniel E

2006-01-20

While luminosity distances from type Ia supernovae (SNe) are a powerful probe of cosmology, the accuracy with which these distances can be measured is limited by cosmic magnification due to gravitational lensing by the intervening large-scale structure. Spatial clustering of foreground mass leads to correlated errors in SNe distances. By including the full covariance matrix of SNe, we show that future wide-field surveys will remain largely unaffected by lensing correlations. However, "pencil beam" surveys, and those with narrow (but possibly long) fields of view, can be strongly affected. For a survey with 30 arcmin mean separation between SNe, lensing covariance leads to a approximately 45% increase in the expected errors in dark energy parameters.

Imaging the Chicxulub central crater zone from large scale seismic acoustic wave propagation and gravity modeling

NASA Astrophysics Data System (ADS)

Fucugauchi, J. U.; Ortiz-Aleman, C.; Martin, R.

2017-12-01

Large complex craters are characterized by central uplifts that represent large-scale differential movement of deep basement from the transient cavity. Here we investigate the central sector of the large multiring Chicxulub crater, which has been surveyed by an array of marine, aerial and land-borne geophysical methods. Despite high contrasts in physical properties,contrasting results for the central uplift have been obtained, with seismic reflection surveys showing lack of resolution in the central zone. We develop an integrated seismic and gravity model for the main structural elements, imaging the central basement uplift and melt and breccia units. The 3-D velocity model built from interpolation of seismic data is validated using perfectly matched layer seismic acoustic wave propagation modeling, optimized at grazing incidence using shift in the frequency domain. Modeling shows significant lack of illumination in the central sector, masking presence of the central uplift. Seismic energy remains trapped in an upper low velocity zone corresponding to the sedimentary infill, melt/breccias and surrounding faulted blocks. After conversion of seismic velocities into a volume of density values, we use massive parallel forward gravity modeling to constrain the size and shape of the central uplift that lies at 4.5 km depth, providing a high-resolution image of crater structure.The Bouguer anomaly and gravity response of modeled units show asymmetries, corresponding to the crater structure and distribution of post-impact carbonates, breccias, melt and target sediments

Graft Utilization in the Augmentation of Large-to-Massive Rotator Cuff Repairs: A Systematic Review.

PubMed

Ferguson, Devin P; Lewington, Matthew R; Smith, T Duncan; Wong, Ivan H

2016-11-01

Current treatment options for symptomatic large-to-massive rotator cuff tears can reduce pain, but failure rates remain high. Surgeons have incorporated synthetic and biologic grafts to augment these repairs, with promising results. Multiple reviews exist that summarize these products; however, no systematic review has investigated the grafts' ability to maintain structural integrity after augmentation of large-to-massive rotator cuff repairs. To systematically review and evaluate the effectiveness of grafts in the augmentation of large-to-massive rotator cuff repairs. Systematic review. A comprehensive search of 4 reputable databases was completed. Inclusion criteria were (1) large-to-massive rotator cuff tear, (2) graft augmentation of primary repairs ± primary repair control group, and (3) minimum clinical and radiologic follow-up of 12 months. Two reviewers screened the titles, abstracts, and full articles and extracted the data from eligible studies. Results were summarized into evidence tables stratified by graft origin and level of evidence. Ten studies fit the inclusion criteria. Allograft augmentation was functionally and structurally superior to primary repair controls, with intact repairs in 85% versus 40% of patients (P < .01). This was supported by observational study data. Xenograft augmentation failed to demonstrate superiority to primary repair controls, with worse structural healing rates (27% vs 60%; P =.11). Both comparative studies supported this finding. There have also been many reports of inflammatory reactions with xenograft use. Polypropylene patches are associated with improved structural (83% vs 59% and 49%; P < .01) and functional outcomes when compared with controls and xenograft augmentation; however, randomized data are lacking. Augmentation of large-to-massive rotator cuff repairs with human dermal allografts is associated with superior functional and structural outcome when compared with conventional primary repair. Xenograft augmentation failed to demonstrate a statistically significant difference and may be associated with worse rerupture rates and occasional severe inflammatory reactions. Polypropylene patches have initial promising results. Research in this field is limited; future researchers should continue to develop prospective, randomized controlled trials to establish clear recommendations. © 2016 The Author(s).

Structural Plasticity of Helical Nanotubes Based on Coiled-Coil Assemblies

DOE PAGES

Egelman, Edward H.; Xu, C.; DiMaio, F.; ...

2015-01-22

Numerous instances can be seen in evolution in which protein quaternary structures have diverged while the sequences of the building blocks have remained fairly conserved. However, the path through which such divergence has taken place is usually not known. We have designed two synthetic 29-residue α-helical peptides, based on the coiled-coil structural motif, that spontaneously self-assemble into helical nanotubes in vitro. Using electron cryomicroscopy with a newly available direct electron detection capability, we can achieve near-atomic resolution of these thin structures. We show how conservative changes of only one or two amino acids result in dramatic changes in quaternary structure,more » in which the assemblies can be switched between two very different forms. This system provides a framework for understanding how small sequence changes in evolution can translate into very large changes in supramolecular structure, a phenomenon that may have significant implications for the de novo design of synthetic peptide assemblies.« less

Babinet to the half: coupling of solid and inverse plasmonic structures.

PubMed

Hentschel, Mario; Weiss, Thomas; Bagheri, Shahin; Giessen, Harald

2013-09-11

We study the coupling between the plasmonic resonances of solid and inverse metallic nanostructures. While the coupling between solid-solid and inverse-inverse plasmonic structures is well-understood, mixed solid-inverse systems have not yet been studied in detail. In particular, it remains unclear whether or not an efficient coupling is even possible and which prerequisites have to be met. We find that an efficient coupling between inverse and solid resonances is indeed possible, identify the necessary geometrical prerequisites, and demonstrate a novel solid-inverse plasmonic electromagnetically induced transparency (EIT) structure as well as a mixed chiral system. We furthermore show that for the coupling of asymmetric rod-shaped inverse and solid structures symmetry breaking is crucial. In contrast, highly symmetric structures such as nanodisks and nanoholes are straightforward to couple. Our results constitute a significant extension of the plasmonic coupling toolkit, and we thus envision the emergence of a large number of intriguing novel plasmonic coupling phenomena in mixed solid-inverse structures.

Altered brain structural connectivity in post-traumatic stress disorder: a diffusion tensor imaging tractography study.

PubMed

Long, Zhiliang; Duan, Xujun; Xie, Bing; Du, Handan; Li, Rong; Xu, Qiang; Wei, Luqing; Zhang, Shao-xiang; Wu, Yi; Gao, Qing; Chen, Huafu

2013-09-25

Post-traumatic stress disorder (PTSD) is characterized by dysfunction of several discrete brain regions such as medial prefrontal gyrus with hypoactivation and amygdala with hyperactivation. However, alterations of large-scale whole brain topological organization of structural networks remain unclear. Seventeen patients with PTSD in motor vehicle accident survivors and 15 normal controls were enrolled in our study. Large-scale structural connectivity network (SCN) was constructed using diffusion tensor tractography, followed by thresholding the mean factional anisotropy matrix of 90 brain regions. Graph theory analysis was then employed to investigate their aberrant topological properties. Both patient and control group showed small-world topology in their SCNs. However, patients with PTSD exhibited abnormal global properties characterized by significantly decreased characteristic shortest path length and normalized characteristic shortest path length. Furthermore, the patient group showed enhanced nodal centralities predominately in salience network including bilateral anterior cingulate and pallidum, and hippocampus/parahippocamus gyrus, and decreased nodal centralities mainly in medial orbital part of superior frontal gyrus. The main limitation of this study is the small sample of PTSD patients, which may lead to decrease the statistic power. Consequently, this study should be considered an exploratory analysis. These results are consistent with the notion that PTSD can be understood by investigating the dysfunction of large-scale, spatially distributed neural networks, and also provide structural evidences for further exploration of neurocircuitry models in PTSD. © 2013 Elsevier B.V. All rights reserved.

The structure of turbulent flow around vertical plates containing holes and attached to a channel bed

NASA Astrophysics Data System (ADS)

Basnet, K.; Constantinescu, G.

2017-11-01

High-resolution, 3-D large eddy simulations are conducted to study the physics of flow past 2-D solid and porous vertical plates of height H mounted on a horizontal surface (no bottom gap) with a fully developed, turbulent incoming flow. The porous plate consists of an array of spanwise-oriented, identical solid cylinders of rectangular cross section. The height of the solid cylinders and the spacing between the solid cylinders, corresponding to the plate's "holes," are kept constant for any given configuration, as the present study considers only plates of uniform porosity. The paper discusses how the mean flow and turbulence structure around the vertical plate, the unsteady forces acting on the plate, the dynamics of the large-scale turbulent eddies, the spectral content of the wake, and the distribution of the bed friction velocity on the horizontal channel bed vary as a function of the plate porosity (0% < P < 36%), the relative spacing between the solid elements of the porous plate (d/H), and the roughness of the channel bed surface. Simulation results are used to explain how the bleeding flow affects the dynamics on the larger billow eddies advected in the separated shear layer (SSL) forming at the top of the plate and the wake structure. It is found that the main recirculation eddy in the wake remains attached to the plate for P < 30%. For larger porosities, the main recirculation eddy forms away from the porous plate. The energy of the billows advected in the SSL decays monotonically with increasing plate porosity. For cases when the recirculation eddy remains attached to the plate, the larger billows advected in the downstream part of the SSL are partially reinjected inside the main recirculation eddy as a result of their interaction with the channel bed. This creates a feedback mechanism that induces large-scale disturbances of the spanwise-oriented vortex tubes advected inside the upstream part of the SSL. Results also show that the mean drag coefficient and the root-mean-square of the drag coefficient fluctuations increase mildly with increasing d/H. Meanwhile, varying d/H has a negligible effect on the position and size of the main recirculation eddy. The presence of large-scale roughness elements (2-D ribs) at the bed results in the decrease of the mean drag coefficient of the plate and, in the case of a solid plate, in a large decrease of the frequency of the large-scale eddies advected in the SSL.

Polarization-independent actively tunable colour generation on imprinted plasmonic surfaces

PubMed Central

Franklin, Daniel; Chen, Yuan; Vazquez-Guardado, Abraham; Modak, Sushrut; Boroumand, Javaneh; Xu, Daming; Wu, Shin-Tson; Chanda, Debashis

2015-01-01

Structural colour arising from nanostructured metallic surfaces offers many benefits compared to conventional pigmentation based display technologies, such as increased resolution and scalability of their optical response with structure dimensions. However, once these structures are fabricated their optical characteristics remain static, limiting their potential application. Here, by using a specially designed nanostructured plasmonic surface in conjunction with high birefringence liquid crystals, we demonstrate a tunable polarization-independent reflective surface where the colour of the surface is changed as a function of applied voltage. A large range of colour tunability is achieved over previous reports by utilizing an engineered surface which allows full liquid crystal reorientation while maximizing the overlap between plasmonic fields and liquid crystal. In combination with imprinted structures of varying periods, a full range of colours spanning the entire visible spectrum is achieved, paving the way towards dynamic pixels for reflective displays. PMID:26066375

Structural basis of lipid-driven conformational transitions in the KvAP voltage-sensing domain.

PubMed

Li, Qufei; Wanderling, Sherry; Sompornpisut, Pornthep; Perozo, Eduardo

2014-02-01

Voltage-gated ion channels respond to transmembrane electric fields through reorientations of the positively charged S4 helix within the voltage-sensing domain (VSD). Despite a wealth of structural and functional data, the details of this conformational change remain controversial. Recent electrophysiological evidence showed that equilibrium between the resting ('down') and activated ('up') conformations of the KvAP VSD from Aeropyrum pernix can be biased through reconstitution in lipids with or without phosphate groups. We investigated the structural transition between these functional states, using site-directed spin-labeling and EPR spectroscopic methods. Solvent accessibility and interhelical distance determinations suggest that KvAP gates through S4 movements involving an ∼3-Å upward tilt and simultaneous ∼2-Å axial shift. This motion leads to large accessibly changes in the intracellular water-filled crevice and supports a new model of gating that combines structural rearrangements and electric-field remodeling.

Rapid encoding of relationships between spatially remote motion signals.

PubMed

Maruya, Kazushi; Holcombe, Alex O; Nishida, Shin'ya

2013-02-06

For visual processing, the temporal correlation of remote local motion signals is a strong cue to detect meaningful large-scale structures in the retinal image, because related points are likely to move together regardless of their spatial separation. While the processing of multi-element motion patterns involved in biological motion and optic flow has been studied intensively, the encoding of simpler pairwise relationships between remote motion signals remains poorly understood. We investigated this process by measuring the temporal rate limit for perceiving the relationship of two motion directions presented at the same time at different spatial locations. Compared to luminance or orientation, motion comparison was more rapid. Performance remained very high even when interstimulus separation was increased up to 100°. Motion comparison also remained rapid regardless of whether the two motion directions were similar to or different from each other. The exception was a dramatic slowing when the elements formed an orthogonal "T," in which two motions do not perceptually group together. Motion presented at task-irrelevant positions did not reduce performance, suggesting that the rapid motion comparison could not be ascribed to global optic flow processing. Our findings reveal the existence and unique nature of specialized processing that encodes long-range relationships between motion signals for quick appreciation of global dynamic scene structure.

Solution structure and backbone dynamics of an endopeptidase HycI from Escherichia coli: implications for mechanism of the [NiFe] hydrogenase maturation.

PubMed

Yang, Fan; Hu, Wei; Xu, Huimin; Li, Congmin; Xia, Bin; Jin, Changwen

2007-02-09

[NiFe] hydrogenases are metalloenzymes involved in many biological processes concerning the metabolism of hydrogen. The maturation of the large subunit of these hydrogenases requires the cleavage of a peptide at the C terminus by an endopeptidase before the final formation of the [NiFe] metallocenter. HycI is an endopeptidase of the M52 family and responsible for the C-terminal cleavage of the large subunit of hydrogenase 3 in Escherichia coli. Although extensive studies were performed, the molecular mechanism of recognition and cleavage of hydrogenase 3 remains elusive. Herein, we report the solution structure of E. coli HycI determined by high resolution nuclear magnetic resonance spectroscopy. This is the first solution structure of the apo form of endopeptidase of the M52 family reported thus far. The overall structure is similar to the crystal structure of holo-HybD in the same family. However, significant diversity was observed between the two structures. Especially, HycI shows an open conformation at the putative nickel-binding site, whereas HybD adopts a closed conformation. In addition, we performed backbone dynamic studies to probe the motional properties of the apo form of HycI. Furthermore, the metal ion titration experiments provide insightful information on the substrate recognition and cleavage processes. Taken together, our current structural, biochemical, and dynamic studies extend the knowledge of the M52 family proteins and provide novel insights into the biological function of HycI.

Protostar formation in the early universe.

PubMed

Yoshida, Naoki; Omukai, Kazuyuki; Hernquist, Lars

2008-08-01

The nature of the first generation of stars in the universe remains largely unknown. Observations imply the existence of massive primordial stars early in the history of the universe, and the standard theory for the growth of cosmic structure predicts that structures grow hierarchically through gravitational instability. We have developed an ab initio computer simulation of the formation of primordial stars that follows the relevant atomic and molecular processes in a primordial gas in an expanding universe. The results show that primeval density fluctuations left over from the Big Bang can drive the formation of a tiny protostar with a mass 1% that of the Sun. The protostar is a seed for the subsequent formation of a massive primordial star.

The genus curve of the Abell clusters

NASA Technical Reports Server (NTRS)

Rhoads, James E.; Gott, J. Richard, III; Postman, Marc

1994-01-01

We study the topology of large-scale structure through a genus curve measurement of the recent Abell catalog redshift survey of Postman, Huchra, and Geller (1992). The structure is found to be spongelike near median density and to exhibit isolated superclusters and voids at high and low densities, respectively. The genus curve shows a slight shift toward 'meatball' topology, but remains consistent with the hypothesis of Gaussian random phase initial conditions. The amplitude of the genus curve corresponds to a power-law spectrum with index n = 0.21(sub -0.47 sup +0.43) on scales of 48/h Mpc or to a cold dark matter power spectrum with omega h = 0.36(sub -0.17 sup +0.46).

The genus curve of the Abell clusters

NASA Astrophysics Data System (ADS)

Rhoads, James E.; Gott, J. Richard, III; Postman, Marc

1994-01-01

We study the topology of large-scale structure through a genus curve measurement of the recent Abell catalog redshift survey of Postman, Huchra, and Geller (1992). The structure is found to be spongelike near median density and to exhibit isolated superclusters and voids at high and low densities, respectively. The genus curve shows a slight shift toward 'meatball' topology, but remains consistent with the hypothesis of Gaussian random phase initial conditions. The amplitude of the genus curve corresponds to a power-law spectrum with index n = 0.21-0.47+0.43 on scales of 48/h Mpc or to a cold dark matter power spectrum with omega h = 0.36-0.17+0.46.

A Comparative Study of Airflow and Odorant Deposition in the Mammalian Nasal Cavity

NASA Astrophysics Data System (ADS)

Richter, Joseph; Rumple, Christopher; Ranslow, Allison; Quigley, Andrew; Pang, Benison; Neuberger, Thomas; Krane, Michael; van Valkenburgh, Blaire; Craven, Brent

2013-11-01

The complex structure of the mammalian nasal cavity provides a tortuous airflow path and a large surface area for respiratory air conditioning, filtering of inspired contaminants, and olfaction. Due to the small and contorted structure of the nasal turbinals, nasal anatomy and function remains poorly understood in most mammals. Here, we utilize high-resolution MRI scans to reconstruct anatomically-accurate models of the mammalian nasal cavity. These data are used to compare the form and function of the mammalian nose. High-fidelity computational fluid dynamics (CFD) simulations of nasal airflow and odorant deposition are presented and used to compare olfactory function across species (primate, rodent, canine, feline, ungulate).

Mixed Feelings: East Asia’s Debate about China’s Economic Growth and Regional Integration

DTIC Science & Technology

2003-12-01

to its large subscription and the weighted voting system. Instead of establishing an AMF, Japan and China took part in the multilateral Chiang Mai Initiative...and its damaging impact on trade. Therefore, it too has taken part in the Chiang Mai Initiative. Southeast Asia China remains a minor trade partner for...with the multilateral structure of the Chiang Mai Initiative to manage currency exchange rates than a Japan-dominated AMF. For this reason, they are

Electronic structure studies of La2CuO4

NASA Astrophysics Data System (ADS)

Wachs, A. L.; Turchi, P. E. A.; Jean, Y. C.; Wetzler, K. H.; Howell, R. H.; Fluss, M. J.; Harshman, D. R.; Remeika, J. P.; Cooper, A. S.; Fleming, R. M.

1988-07-01

We report results of positron-electron momentum-distribution measurements of single-crystal La2CuO4 using two-dimensional angular correlation of positron-annihilation-radiation techniques. The data contain two components: a large (~85%), isotropic corelike electron contribution and a remaining, anisotropic valence-electron contribution modeled using a linear combination of atomic orbitals-molecular orbital method and a localized ion scheme, within the independent-particle model approximation. This work suggests a ligand-field Hamiltonian to be justified for describing the electronic properties of perovskite materials.

Historical pesticide applications coincided with an altered diet of aerially foraging insectivorous chimney swifts

PubMed Central

Nocera, Joseph J.; Blais, Jules M.; Beresford, David V.; Finity, Leah K.; Grooms, Christopher; Kimpe, Lynda E.; Kyser, Kurt; Michelutti, Neal; Reudink, Matthew W.; Smol, John P.

2012-01-01

Numerous environmental pressures have precipitated long-term population reductions of many insect species. Population declines in aerially foraging insectivorous birds have also been detected, but the cause remains unknown partly because of a dearth of long-term monitoring data on avian diets. Chimney swifts (Chaetura pelagica) are a model aerial insectivore to fill such information gaps because their roosting behaviour makes them easy to sample in large numbers over long time periods. We report a 48-year-long (1944–1992) dietary record for the chimney swift, determined from a well-preserved deposit of guano and egested insect remains in Ontario (Canada). This unique archive of palaeo-environmental data reflecting past chimney swift diets revealed a steep rise in dichlorodiphenyltrichloroethane (DDT) and metabolites, which were correlated with a decrease in Coleoptera remains and an increase in Hemiptera remains, indicating a significant change in chimney swift prey. We argue that DDT applications decimated Coleoptera populations and dramatically altered insect community structure by the 1960s, triggering nutritional consequences for swifts and other aerial insectivores. PMID:22513860

Improved accuracy for finite element structural analysis via an integrated force method

NASA Technical Reports Server (NTRS)

Patnaik, S. N.; Hopkins, D. A.; Aiello, R. A.; Berke, L.

1992-01-01

A comparative study was carried out to determine the accuracy of finite element analyses based on the stiffness method, a mixed method, and the new integrated force and dual integrated force methods. The numerical results were obtained with the following software: MSC/NASTRAN and ASKA for the stiffness method; an MHOST implementation method for the mixed method; and GIFT for the integrated force methods. The results indicate that on an overall basis, the stiffness and mixed methods present some limitations. The stiffness method generally requires a large number of elements in the model to achieve acceptable accuracy. The MHOST method tends to achieve a higher degree of accuracy for course models than does the stiffness method implemented by MSC/NASTRAN and ASKA. The two integrated force methods, which bestow simultaneous emphasis on stress equilibrium and strain compatibility, yield accurate solutions with fewer elements in a model. The full potential of these new integrated force methods remains largely unexploited, and they hold the promise of spawning new finite element structural analysis tools.

Momentum-resolved hidden-order gap reveals symmetry breaking and origin of entropy loss in URu2Si2

NASA Astrophysics Data System (ADS)

Bareille, C.; Boariu, F. L.; Schwab, H.; Lejay, P.; Reinert, F.; Santander-Syro, A. F.

2014-07-01

Spontaneous symmetry breaking in physical systems leads to salient phenomena at all scales, from the Higgs mechanism and the emergence of the mass of the elementary particles, to superconductivity and magnetism in solids. The hidden-order state arising below 17.5 K in URu2Si2 is a puzzling example of one of such phase transitions: its associated broken symmetry and gap structure have remained longstanding riddles. Here we directly image how, across the hidden-order transition, the electronic structure of URu2Si2 abruptly reconstructs. We observe an energy gap of 7 meV opening over 70% of a large diamond-like heavy-fermion Fermi surface, resulting in the formation of four small Fermi petals, and a change in the electronic periodicity from body-centred tetragonal to simple tetragonal. Our results explain the large entropy loss in the hidden-order phase, and the similarity between this phase and the high-pressure antiferromagnetic phase found in quantum-oscillation experiments.

Development of an automated large-scale protein-crystallization and monitoring system for high-throughput protein-structure analyses.

PubMed

Hiraki, Masahiko; Kato, Ryuichi; Nagai, Minoru; Satoh, Tadashi; Hirano, Satoshi; Ihara, Kentaro; Kudo, Norio; Nagae, Masamichi; Kobayashi, Masanori; Inoue, Michio; Uejima, Tamami; Oda, Shunichiro; Chavas, Leonard M G; Akutsu, Masato; Yamada, Yusuke; Kawasaki, Masato; Matsugaki, Naohiro; Igarashi, Noriyuki; Suzuki, Mamoru; Wakatsuki, Soichi

2006-09-01

Protein crystallization remains one of the bottlenecks in crystallographic analysis of macromolecules. An automated large-scale protein-crystallization system named PXS has been developed consisting of the following subsystems, which proceed in parallel under unified control software: dispensing precipitants and protein solutions, sealing crystallization plates, carrying robot, incubators, observation system and image-storage server. A sitting-drop crystallization plate specialized for PXS has also been designed and developed. PXS can set up 7680 drops for vapour diffusion per hour, which includes time for replenishing supplies such as disposable tips and crystallization plates. Images of the crystallization drops are automatically recorded according to a preprogrammed schedule and can be viewed by users remotely using web-based browser software. A number of protein crystals were successfully produced and several protein structures could be determined directly from crystals grown by PXS. In other cases, X-ray quality crystals were obtained by further optimization by manual screening based on the conditions found by PXS.

The Syrtis Major volcano, Mars: A multidisciplinary approach to interpreting its magmatic evolution and structural development

NASA Astrophysics Data System (ADS)

Lillis, Robert J.; Dufek, Josef; Kiefer, Walter S.; Black, Benjamin A.; Manga, Michael; Richardson, Jacob A.; Bleacher, Jacob E.

2015-09-01

Very weak crustal magnetic fields over the Syrtis Major volcanic complex imply almost total thermal demagnetization via magmatic intrusions over a large area less than ~4 Ga. We fit a model of these intrusions and the resulting thermal demagnetization to maps of crustal magnetic field strength at 185 km altitude. The best fits are most consistent with a "dog bone"-shaped region of intrusive material, elongated approximately north-south, with an area of ~350,000 km2 and an inferred volume of ~4-19 × 106 km3. Such a large volume is best explained by a long-lived mantle plume beneath the Syrtis edifice. A free-air gravity anomaly high over the Syrtis Major caldera is consistent with dense mafic residue remaining at depth following crystal fractionation that produced the silicic magmas seen at the surface. The elongation of this region is consistent with ascent and north-south emplacement of magma enabled by structures parallel to and associated with the preexisting Isidis impact basin.

Beyond the Joint: The Role of Central Nervous System Reorganizations in Chronic Musculoskeletal Disorders.

PubMed

Roy, Jean-Sébastien; Bouyer, Laurent J; Langevin, Pierre; Mercier, Catherine

2017-11-01

To a large extent, management of musculoskeletal disorders has traditionally focused on structural dysfunctions found within the musculoskeletal system, mainly around the affected joint. While a structural-dysfunction approach may be effective for musculoskeletal conditions in some populations, especially in acute presentations, its effectiveness remains limited in patients with recurrent or chronic musculoskeletal pain. Numerous studies have shown that the human central nervous system can undergo plastic reorganizations following musculoskeletal disorders; however, they can be maladaptive and contribute to altered joint control and chronic pain. In this Viewpoint, the authors argue that to improve rehabilitation outcomes in patients with chronic musculoskeletal pain, a global view of the disorder that incorporates both central (neural) and peripheral (joint-level) changes is needed. The authors also discuss the challenge of evaluating and rehabilitating central changes and the need for large, high-level studies to evaluate approaches incorporating central and peripheral changes and emerging therapies. J Orthop Sports Phys Ther 2017;47(11):817-821. doi:10.2519/jospt.2017.0608.

The dynamic organization of fungal acetyl-CoA carboxylase

NASA Astrophysics Data System (ADS)

Hunkeler, Moritz; Stuttfeld, Edward; Hagmann, Anna; Imseng, Stefan; Maier, Timm

2016-04-01

Acetyl-CoA carboxylases (ACCs) catalyse the committed step in fatty-acid biosynthesis: the ATP-dependent carboxylation of acetyl-CoA to malonyl-CoA. They are important regulatory hubs for metabolic control and relevant drug targets for the treatment of the metabolic syndrome and cancer. Eukaryotic ACCs are single-chain multienzymes characterized by a large, non-catalytic central domain (CD), whose role in ACC regulation remains poorly characterized. Here we report the crystal structure of the yeast ACC CD, revealing a unique four-domain organization. A regulatory loop, which is phosphorylated at the key functional phosphorylation site of fungal ACC, wedges into a crevice between two domains of CD. Combining the yeast CD structure with intermediate and low-resolution data of larger fragments up to intact ACCs provides a comprehensive characterization of the dynamic fungal ACC architecture. In contrast to related carboxylases, large-scale conformational changes are required for substrate turnover, and are mediated by the CD under phosphorylation control.

Non-radial pulsations and large-scale structure in stellar winds

NASA Astrophysics Data System (ADS)

Blomme, R.

2009-07-01

Almost all early-type stars show Discrete Absorption Components (DACs) in their ultraviolet spectral lines. These can be attributed to Co-rotating Interaction Regions (CIRs): large-scale spiral-shaped structures that sweep through the stellar wind. We used the Zeus hydrodynamical code to model the CIRs. In the model, the CIRs are caused by ``spots" on the stellar surface. Through the radiative acceleration these spots create fast streams in the stellar wind material. Where the fast and slow streams collide, a CIR is formed. By varying the parameters of the spots, we quantitatively fit the observed DACs in HD~64760. An important result from our work is that the spots do not rotate with the same velocity as the stellar surface. The fact that the cause of the CIRs is not fixed on the surface eliminates many potential explanations. The only remaining explanation is that the CIRs are due to the interference pattern of a number of non-radial pulsations.

Vertical resonant tunneling transistors with molecular quantum dots for large-scale integration.

PubMed

Hayakawa, Ryoma; Chikyow, Toyohiro; Wakayama, Yutaka

2017-08-10

Quantum molecular devices have a potential for the construction of new data processing architectures that cannot be achieved using current complementary metal-oxide-semiconductor (CMOS) technology. The relevant basic quantum transport properties have been examined by specific methods such as scanning probe and break-junction techniques. However, these methodologies are not compatible with current CMOS applications, and the development of practical molecular devices remains a persistent challenge. Here, we demonstrate a new vertical resonant tunneling transistor for large-scale integration. The transistor channel is comprised of a MOS structure with C 60 molecules as quantum dots, and the structure behaves like a double tunnel junction. Notably, the transistors enabled the observation of stepwise drain currents, which originated from resonant tunneling via the discrete molecular orbitals. Applying side-gate voltages produced depletion layers in Si substrates, to achieve effective modulation of the drain currents and obvious peak shifts in the differential conductance curves. Our device configuration thus provides a promising means of integrating molecular functions into future CMOS applications.

GDP Release Preferentially Occurs on the Phosphate Side in Heterotrimeric G-proteins

PubMed Central

Louet, Maxime; Martinez, Jean; Floquet, Nicolas

2012-01-01

After extra-cellular stimulation of G-Protein Coupled Receptors (GPCRs), GDP/GTP exchange appears as the key, rate limiting step of the intracellular activation cycle of heterotrimeric G-proteins. Despite the availability of a large number of X-ray structures, the mechanism of GDP release out of heterotrimeric G-proteins still remains unknown at the molecular level. Starting from the available X-ray structure, extensive unconstrained/constrained molecular dynamics simulations were performed on the complete membrane-anchored Gi heterotrimer complexed to GDP, for a total simulation time overcoming 500 ns. By combining Targeted Molecular Dynamics (TMD) and free energy profiles reconstruction by umbrella sampling, our data suggest that the release of GDP was much more favored on its phosphate side. Interestingly, upon the forced extraction of GDP on this side, the whole protein encountered large, collective motions in perfect agreement with those we described previously including a domain to domain motion between the two ras-like and helical sub-domains of Gα. PMID:22829757

SPED light sheet microscopy: fast mapping of biological system structure and function

PubMed Central

Tomer, Raju; Lovett-Barron, Matthew; Kauvar, Isaac; Andalman, Aaron; Burns, Vanessa M.; Sankaran, Sethuraman; Grosenick, Logan; Broxton, Michael; Yang, Samuel; Deisseroth, Karl

2016-01-01

The goal of understanding living nervous systems has driven interest in high-speed and large field-of-view volumetric imaging at cellular resolution. Light-sheet microscopy approaches have emerged for cellular-resolution functional brain imaging in small organisms such as larval zebrafish, but remain fundamentally limited in speed. Here we have developed SPED light sheet microscopy, which combines large volumetric field-of-view via an extended depth of field with the optical sectioning of light sheet microscopy, thereby eliminating the need to physically scan detection objectives for volumetric imaging. SPED enables scanning of thousands of volumes-per-second, limited only by camera acquisition rate, through the harnessing of optical mechanisms that normally result in unwanted spherical aberrations. We demonstrate capabilities of SPED microscopy by performing fast sub-cellular resolution imaging of CLARITY mouse brains and cellular-resolution volumetric Ca2+ imaging of entire zebrafish nervous systems. Together, SPED light sheet methods enable high-speed cellular-resolution volumetric mapping of biological system structure and function. PMID:26687363

Evaluation of analysis techniques for low frequency interior noise and vibration of commercial aircraft

NASA Technical Reports Server (NTRS)

Landmann, A. E.; Tillema, H. F.; Marshall, S. E.

1989-01-01

The application of selected analysis techniques to low frequency cabin noise associated with advanced propeller engine installations is evaluated. Three design analysis techniques were chosen for evaluation including finite element analysis, statistical energy analysis (SEA), and a power flow method using element of SEA (computer program Propeller Aircraft Interior Noise). An overview of the three procedures is provided. Data from tests of a 727 airplane (modified to accept a propeller engine) were used to compare with predictions. Comparisons of predicted and measured levels at the end of the first year's effort showed reasonable agreement leading to the conclusion that each technique had value for propeller engine noise predictions on large commercial transports. However, variations in agreement were large enough to remain cautious and to lead to recommendations for further work with each technique. Assessment of the second year's results leads to the conclusion that the selected techniques can accurately predict trends and can be useful to a designer, but that absolute level predictions remain unreliable due to complexity of the aircraft structure and low modal densities.

The impact pseudotachylitic breccia controversy: Insights from first isotope analysis of Vredefort impact-generated melt rocks

NASA Astrophysics Data System (ADS)

Reimold, Wolf Uwe; Hauser, Natalia; Hansen, Bent T.; Thirlwall, Matthew; Hoffmann, Marie

2017-10-01

Besides impact melt rock, several large terrestrial impact structures, notably the Sudbury (Canada) and Vredefort (South Africa) structures, exhibit considerable occurrences of a second type of impact-generated melt rock, so-called pseudotachylitic breccia (previously often termed ;pseudotachylite; - the term today reserved in structural geology for friction melt in shear or fault zones). At the Vredefort Dome, the eroded central uplift of the largest and oldest known terrestrial impact structure, pseudotachylitic breccia is well-exposed, with many massive occurrences of tens of meters width and many hundreds of meters extent. Genesis of these breccias has been discussed variably in terms of melt formation due to friction melting, melting due to decompression after initial shock compression, decompression melting upon formation/collapse of a central uplift, or a combination of these processes. In addition, it was recently suggested that they could have formed by the infiltration of impact melt into the crater floor, coming off a coherent melt sheet and under assimilation of wall rock; even seismic shaking has been invoked. Field evidence for generation of such massive melt bodies by friction on large shear/fault zones is missing. Also, no evidence for the generation of massive pseudotachylitic breccias in rocks of low to moderate shock degree by melting upon pressure release after shock compression has been demonstrated. The efficacy of seismic shaking to achieve sufficient melting as a foundation for massive pseudotachylitic melt generation as typified by the breccias of the Sudbury and Vredefort structures has so far remained entirely speculative. The available petrographic and chemical evidence has, thus, been interpreted to favor either decompression melting (i.e., in situ generation of melt) upon central uplift collapse, or the impact melt infiltration hypothesis. Importantly, all the past clast population and chemical analyses have invariably supported an origin of these breccias from local lithologies only. Here, the first Rb-Sr, Sm-Nd, and U-Pb isotopic data for Vredefort pseudotachylitic breccias and their host rocks, in comparison to data for Vredefort Granophyre (impact melt rock), are presented. They strongly support that the pseudotachylitic breccias were exclusively formed from local precursor lithologies - in agreement with earlier isotopic results for Sudbury Breccia and chemical results for Vredefort pseudotachylitic breccias. A contribution from a Granophyre-like impact melt component to form Vredefort pseudotachylitic breccia is not indicated. The most likely process for the genesis of voluminous pseudotachylitic breccias in large impact structures remains decompression melting upon formation and collapse of the central uplift, during the modification stage of impact cratering.

Todorokite-type manganese oxide nanowires as an intercalation cathode for Li-ion and Na-ion batteries

DOE PAGES

Byles, B. W.; West, P.; Cullen, D. A.; ...

2015-12-03

Extended hydrothermal treatment at an elevated temperature of 220 °C allowed high yield synthesis of manganese oxide nanowires with a todorokite crystal structure suitable for ions intercalation. The flexible, high aspect ratio nanowires are 50–100 nm in diameter and up to several microns long, with 3 × 3 structural tunnels running parallel to the nanowire longitudinal axis. Moreover, the tunnels are occupied by magnesium ions and water molecules, with the chemical composition found to be Mg 0.2MnO 2·0.5H 2O. The todorokite nanowires were, for the first time, electrochemically tested in both Li-ion and Na-ion cells. A first discharge capacity ofmore » 158 mA h g -1 was achieved in a Na-ion system, which was found to be greater than the first discharge capacity in a Li-ion system (133 mA h g -1). In spite of the large structural tunnel dimensions, todorokite showed a significant first cycle capacity loss in a Na-ion battery. After 20 cycles, the capacity was found to stabilize around 50 mA h g -1 and remained at this level for 100 cycles. In a Li-ion system, todorokite nanowires showed significantly better capacity retention with 78% of its initial capacity remaining after 100 cycles. Rate capability tests also showed superior performance of todorokite nanowires in Li-ion cells compared to Na-ion cells at higher current rates. Finally, these results highlight the difference in electrochemical cycling behavior of Li-ion and Na-ion batteries for a host material with spacious 3 × 3 tunnels tailored for large Na + ion intercalation.« less

Effects of Variable Surface Temperatures on the Dynamics of Convection within Enceladus' Ice Shell

NASA Astrophysics Data System (ADS)

Weller, M. B.; Fuchs, L.; Becker, T. W.; Soderlund, K. M.

2017-12-01

Despite Enceladus' relatively small size, observations reveal it as one of the more geologically active bodies in the solar system. Its surface is heavily deformed, including ridges, grooves, grabens, rifts, and folds that cover a significant fraction of the planet. Perhaps most notably, there is evidence of a hemispheric dichotomy between the south (the South Polar Terrain - SPT), and the remainder of the satellite. While the origin of the SPT has spurred much debate, ranging from oceans and tides to impacts, its existence suggests some form of localization process. Here, we use the mantle convection code CitcomS with temperature-dependent viscosity to address the effects of latitudinally variable surface temperature (due to differences in solar heating) for a range of internal heating rates (as proxy for tidal heating)on the convective vigor and planform within Enceladus' ice shell. Heterogeneous surface temperatures can produce a large, degree-1 upwelling with the other hemisphere fully dominated by a slower, colder downwelling. As internal heating decreases, the degree-1 upwelling forms and localizes, resulting in larger strain rates that arerestricted to 5-20% of the satellite. The remaining 80-95% of the surface remains cold and relatively quiescent, in general agreement with observations of Enceladus and the SPT today. These results show the initial degree-1 structure forms at a polar latitude, the region of greatest radial temperature contrast. This configuration is unstable, however, with the plume structure migrating towards a stable orientation at equatorial latitudes, the region of the highest absolute surface temperature. While an equatorial configuration is currently not witnessed on Enceladus,such a large and persistent dynamic structure could lead to reorientation of the satellite.

Electrical characterization of organic thin film transistors and alternative device architectures

NASA Astrophysics Data System (ADS)

Newman, Christopher R.

In the last 10--15 years, organic semiconductors have evolved from experimental curiosities into viable alternatives for practical applications involving large-area and low-cost electronics such as display backplanes, electronic paper, radio frequency identification (RFID) tags, and solar cells. Many of the initially-stated goals in this field have been achieved; organic semconductors have demonstrated performance comparable to or greater than amorphous silicon (a-Si), the entrenched technology for most of the applications listed above. At present, the major obstacles remaining to commercialization of devices based on organic semiconductors involve material stability, processing considerations and optimization of the other device components (e.g. metal contacts and dielectric materials). Despite these technical achievements, significant gaps remain in our understanding of the underlying transport physics in these devices. This thesis summarizes experiments performed on organic field-effect transistors (OFETs) in an attempt to address some of these knowledge gaps. The FET, in addition to being a very useful device for practical applications (such as the driving elements in pixel backplanes), is also a very flexible architecture from an experimental standpoint. The presence of a capacitively-coupled gate electrode allows the investigation of transport physics as a function of carrier concentration. For devices in which non-idealities (i.e. carrier traps) largely dictate the observed characteristics, this is a very useful feature. Although practical OFETs are fabricated as conventional single-gate structures on an organic thin film (OTFTs), more exotic structures can often provide insights that standard OTFTs cannot. Specifically, single-crystal OFETs allow the investigation of carrier transport in the absence of grain boundaries, and double-gated OTFTs facilitate the investigation and comparison of properties across two discrete interfaces. One of the remaining challenges in terms of achieving stability inorganic semiconductors involves understanding, and hopefully minimizing, the bias stress effect of operating OTFTs. Largely ignored during the years in which research groups sought to optimize the standard device metrics of field-effect mobility, current on/off ratio, and threshold voltage, operational stability is emerging as a dominant consideration in these materials. Experiments performed with the goal of quantifying and understanding the bias-stress effect in organic semiconductors are described at the end of this thesis.

Role of passive deformation on propulsion through a lumped torsional flexibility model

NASA Astrophysics Data System (ADS)

Arora, Nipun; Gupta, Amit

2016-11-01

Scientists and biologists have been affianced in a deeper examination of insect flight to develop an improved understanding of the role of flexibility on aerodynamic performance. Here, we mimic a flapping wing through a fluid-structure interaction framework based upon a lumped torsional flexibility model. The developed fluid and structural solvers together determine the aerodynamic forces and wing deformation, respectively. An analytical solution to the simplified single-spring structural dynamics equation is established to substantiate simulations. It is revealed that the dynamics of structural deformation is governed by the balance between inertia, stiffness and aerodynamics, where the former two oscillate at the plunging frequency and the latter oscillates at twice the plunging frequency. We demonstrate that an induced phase difference between plunging and passive pitching is responsible for a higher thrust coefficient. This phase difference is also shown to be dependent on aerodynamics to inertia and natural to plunging frequency ratios. For inertia dominated flows, pitching and plunging always remain in phase. As the aerodynamics dominates, a large phase difference is induced which is accountable for a large passive deformation and higher thrust. Authors acknowledge the financial support received from the Aeronautics Research and Development Board (ARDB) under SIGMA Project No. 1705 and thank the IIT Delhi HPC facility for computational resources.

Reversible Self-Actuated Thermo-Responsive Pore Membrane

PubMed Central

Park, Younggeun; Gutierrez, Maria Paz; Lee, Luke P.

2016-01-01

Smart membranes, which can selectively control the transfer of light, air, humidity and temperature, are important to achieve indoor climate regulation. Even though reversible self-actuation of smart membranes is desirable in large-scale, reversible self-regulation remains challenging. Specifically, reversible 100% opening/closing of pore actuation showing accurate responsiveness, reproducibility and structural flexibility, including uniform structure assembly, is currently very difficult. Here, we report a reversible, thermo-responsive self-activated pore membrane that achieves opening and closing of pores. The reversible, self-actuated thermo-responsive pore membrane was fabricated with hybrid materials of poly (N-isopropylacrylamide), (PNIPAM) within polytetrafluoroethylene (PTFE) to form a multi-dimensional pore array. Using Multiphysics simulation of heat transfer and structural mechanics based on finite element analysis, we demonstrated that pore opening and closing dynamics can be self-activated at environmentally relevant temperatures. Temperature cycle characterizations of the pore structure revealed 100% opening ratio at T = 40 °C and 0% opening ratio at T = 20 °C. The flexibility of the membrane showed an accurate temperature-responsive function at a maximum bending angle of 45°. Addressing the importance of self-regulation, this reversible self-actuated thermo-responsive pore membrane will advance the development of future large-scale smart membranes needed for sustainable indoor climate control. PMID:27991563

Reversible Self-Actuated Thermo-Responsive Pore Membrane

NASA Astrophysics Data System (ADS)

Park, Younggeun; Gutierrez, Maria Paz; Lee, Luke P.

2016-12-01

Smart membranes, which can selectively control the transfer of light, air, humidity and temperature, are important to achieve indoor climate regulation. Even though reversible self-actuation of smart membranes is desirable in large-scale, reversible self-regulation remains challenging. Specifically, reversible 100% opening/closing of pore actuation showing accurate responsiveness, reproducibility and structural flexibility, including uniform structure assembly, is currently very difficult. Here, we report a reversible, thermo-responsive self-activated pore membrane that achieves opening and closing of pores. The reversible, self-actuated thermo-responsive pore membrane was fabricated with hybrid materials of poly (N-isopropylacrylamide), (PNIPAM) within polytetrafluoroethylene (PTFE) to form a multi-dimensional pore array. Using Multiphysics simulation of heat transfer and structural mechanics based on finite element analysis, we demonstrated that pore opening and closing dynamics can be self-activated at environmentally relevant temperatures. Temperature cycle characterizations of the pore structure revealed 100% opening ratio at T = 40 °C and 0% opening ratio at T = 20 °C. The flexibility of the membrane showed an accurate temperature-responsive function at a maximum bending angle of 45°. Addressing the importance of self-regulation, this reversible self-actuated thermo-responsive pore membrane will advance the development of future large-scale smart membranes needed for sustainable indoor climate control.

Progress with modeling activity landscapes in drug discovery.

PubMed

Vogt, Martin

2018-04-19

Activity landscapes (ALs) are representations and models of compound data sets annotated with a target-specific activity. In contrast to quantitative structure-activity relationship (QSAR) models, ALs aim at characterizing structure-activity relationships (SARs) on a large-scale level encompassing all active compounds for specific targets. The popularity of AL modeling has grown substantially with the public availability of large activity-annotated compound data sets. AL modeling crucially depends on molecular representations and similarity metrics used to assess structural similarity. Areas covered: The concepts of AL modeling are introduced and its basis in quantitatively assessing molecular similarity is discussed. The different types of AL modeling approaches are introduced. AL designs can broadly be divided into three categories: compound-pair based, dimensionality reduction, and network approaches. Recent developments for each of these categories are discussed focusing on the application of mathematical, statistical, and machine learning tools for AL modeling. AL modeling using chemical space networks is covered in more detail. Expert opinion: AL modeling has remained a largely descriptive approach for the analysis of SARs. Beyond mere visualization, the application of analytical tools from statistics, machine learning and network theory has aided in the sophistication of AL designs and provides a step forward in transforming ALs from descriptive to predictive tools. To this end, optimizing representations that encode activity relevant features of molecules might prove to be a crucial step.

Large Block Copolymer Self-Assembly for Fabrication of Subwavelength Nanostructures for Applications in Optics.

PubMed

Mokarian-Tabari, Parvaneh; Senthamaraikannan, Ramsankar; Glynn, Colm; Collins, Timothy W; Cummins, Cian; Nugent, David; O'Dwyer, Colm; Morris, Michael A

2017-05-10

Nanostructured surfaces are common in nature and exhibit properties such as antireflectivity (moth eyes), self-cleaning (lotus leaf), iridescent colors (butterfly wings), and water harvesting (desert beetles). We now understand such properties and can mimic some of these natural structures in the laboratory. However, these synthetic structures are limited since they are not easily mass produced over large areas due to the limited scalability of current technologies such as UV-lithography, the high cost of infrastructure, and the difficulty in nonplanar surfaces. Here, we report a solution process based on block copolymer (BCP) self-assembly to fabricate subwavelength structures on large areas of optical and curved surfaces with feature sizes and spacings designed to efficiently scatter visible light. Si nanopillars (SiNPs) with diameters of ∼115 ± 19 nm, periodicity of 180 ± 18 nm, and aspect ratio of 2-15 show a reduction in reflectivity by a factor of 100, <0.16% between 400 and 900 nm at an angle of incidence of 30°. Significantly, the reflectivity remains below 1.75% up to incident angles of 75°. Modeling the efficiency of a SiNP PV suggests a 24.6% increase in efficiency, representing a 3.52% (absolute) or 16.7% (relative) increase in electrical energy output from the PV system compared to AR-coated device.

Subduction History and the Evolution of Earth's Lower Mantle

NASA Astrophysics Data System (ADS)

Bull, Abigail; Shephard, Grace; Torsvik, Trond

2016-04-01

Understanding the complex structure, dynamics and evolution of the deep mantle is a fundamental goal in solid Earth geophysics. Close to the core-mantle boundary, seismic images reveal a mantle characterised by (1) higher than average shear wave speeds beneath Asia and encircling the Pacific, consistent with sub ducting lithosphere beneath regions of ancient subduction, and (2) large regions of anomalously low seismic wavespeeds beneath Africa and the Central Pacific. The anomalously slow areas are often referred to as Large Low Shear Velocity Provinces (LLSVPs) due to the reduced velocity of seismic waves passing through them. The origin, composition and long-term evolution of the LLSVPs remain enigmatic. Geochemical inferences of multiple chemical reservoirs at depth, strong seismic contrasts, increased density, and an anticorrelation of shear wave velocity to bulk sound velocity in the anomalous regions imply that heterogeneities in both temperature and composition may be required to explain the seismic observations. Consequently, heterogeneous mantle models place the anomalies into the context of thermochemical piles, characterised by an anomalous component whose intrinsic density is a few percent higher relative to that of the surrounding mantle. Several hypotheses have arisen to explain the LLSVPs in the context of large-scale mantle convection. One end member scenario suggests that the LLSVPs are relatively mobile features over short timescales and thus are strongly affected by supercontinent cycles and Earth's plate motion history. In this scenario, the African LLSVP formed as a result of return flow in the mantle due to circum-Pangean subduction (~240 Ma), contrasting a much older Pacific LLSVP, which may be linked to the Rodinia supercontinent and is implied to have remained largely unchanged since Rodinian breakup (~750-700 Ma). This propounds that Earth's plate motion history plays a controlling role in LLSVP development, suggesting that the location, geometry and morphology of lower mantle structures can be influenced by the movement of subducting slabs, and thus by the motions of tectonic plates at the surface. Alternatively, a long-term stability for both LLSVPs, which would suggest a first-order dissociation from the effects of surface plate motions, is hypothesised by recent studies which propose a geographic correlation between the reconstructed surface eruption sites of kimberlites and Large Igneous Provinces with the margins of the LLSVPs. If the surface volcanism was sourced from the lower mantle, such a link would suggest that the LLSVPs may have remained stationary for at least the age of the volcanic rocks (> 500 Myr) and further that the anomalies were largely insensitive to the formation and subsequent breakup of Pangea, and thus to Earth's plate motion history. Here we discuss the evolution of lower mantle structure, LLSVPs and surface volcanics in terms of subduction dynamics. We integrate high-resolution plate tectonic histories and numerical models of mantle convection and perform a series of 3D spherical calculations with Earth-like boundary conditions to investigate the role that subduction history plays in the development and evolution of lower mantle structures. To test whether such an interaction exists, and if so, to what degree over time, we apply varying shifts to the absolute reference frame of the plate reconstruction. We incorporate global shifts in both longitude and latitude, with the correction applied over timescales of 230-50 Myrs. With this method, the location of subduction at the surface and thus the global flow field can be altered. This in turn affects the time-dependent sinking of lithospheric slabs and may affect their interaction with the lower mantle and the LLSVPs at both their margins and top surfaces. We aim to understand how the subduction history has affected mantle structure on a global scale. We show that shifts to the surface history of subduction, even for extreme and unrealistic cases, lead to minimal changes in LLSVP geometry and position, suggesting that the LLSVPs may be long-lived features (> 250 Ma).

Local thermal energy as a structural indicator in glasses

NASA Astrophysics Data System (ADS)

Zylberg, Jacques; Lerner, Edan; Bar-Sinai, Yohai; Bouchbinder, Eran

2017-07-01

Identifying heterogeneous structures in glasses—such as localized soft spots—and understanding structure-dynamics relations in these systems remain major scientific challenges. Here, we derive an exact expression for the local thermal energy of interacting particles (the mean local potential energy change caused by thermal fluctuations) in glassy systems by a systematic low-temperature expansion. We show that the local thermal energy can attain anomalously large values, inversely related to the degree of softness of localized structures in a glass, determined by a coupling between internal stresses—an intrinsic signature of glassy frustration—anharmonicity and low-frequency vibrational modes. These anomalously large values follow a fat-tailed distribution, with a universal exponent related to the recently observed universal ω4ω4 density of states of quasilocalized low-frequency vibrational modes. When the spatial thermal energy field—a “softness field”—is considered, this power law tail manifests itself by highly localized spots, which are significantly softer than their surroundings. These soft spots are shown to be susceptible to plastic rearrangements under external driving forces, having predictive powers that surpass those of the normal modes-based approach. These results offer a general, system/model-independent, physical/observable-based approach to identify structural properties of quiescent glasses and relate them to glassy dynamics.

Seven challenges for metapopulation models of epidemics, including households models.

PubMed

Ball, Frank; Britton, Tom; House, Thomas; Isham, Valerie; Mollison, Denis; Pellis, Lorenzo; Scalia Tomba, Gianpaolo

2015-03-01

This paper considers metapopulation models in the general sense, i.e. where the population is partitioned into sub-populations (groups, patches,...), irrespective of the biological interpretation they have, e.g. spatially segregated large sub-populations, small households or hosts themselves modelled as populations of pathogens. This framework has traditionally provided an attractive approach to incorporating more realistic contact structure into epidemic models, since it often preserves analytic tractability (in stochastic as well as deterministic models) but also captures the most salient structural inhomogeneity in contact patterns in many applied contexts. Despite the progress that has been made in both the theory and application of such metapopulation models, we present here several major challenges that remain for future work, focusing on models that, in contrast to agent-based ones, are amenable to mathematical analysis. The challenges range from clarifying the usefulness of systems of weakly-coupled large sub-populations in modelling the spread of specific diseases to developing a theory for endemic models with household structure. They include also developing inferential methods for data on the emerging phase of epidemics, extending metapopulation models to more complex forms of human social structure, developing metapopulation models to reflect spatial population structure, developing computationally efficient methods for calculating key epidemiological model quantities, and integrating within- and between-host dynamics in models. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Structural and Biochemical Characterization of Acinetobacter spp. Aminoglycoside Acetyltransferases Highlights Functional and Evolutionary Variation among Antibiotic Resistance Enzymes.

PubMed

Stogios, Peter J; Kuhn, Misty L; Evdokimova, Elena; Law, Melissa; Courvalin, Patrice; Savchenko, Alexei

2017-02-10

Modification of aminoglycosides by N-acetyltransferases (AACs) is one of the major mechanisms of resistance to these antibiotics in human bacterial pathogens. More than 50 enzymes belonging to the AAC(6') subfamily have been identified in Gram-negative and Gram-positive clinical isolates. Our understanding of the molecular function and evolutionary origin of these resistance enzymes remains incomplete. Here we report the structural and enzymatic characterization of AAC(6')-Ig and AAC(6')-Ih from Acinetobacter spp. The crystal structure of AAC(6')-Ig in complex with tobramycin revealed a large substrate-binding cleft remaining partially unoccupied by the substrate, which is in stark contrast with the previously characterized AAC(6')-Ib enzyme. Enzymatic analysis indicated that AAC(6')-Ig and -Ih possess a broad specificity against aminoglycosides but with significantly lower turnover rates as compared to other AAC(6') enzymes. Structure- and function-informed phylogenetic analysis of AAC(6') enzymes led to identification of at least three distinct subfamilies varying in oligomeric state, active site composition, and drug recognition mode. Our data support the concept of AAC(6') functionality originating through convergent evolution from diverse Gcn5-related-N-acetyltransferase (GNAT) ancestral enzymes, with AAC(6')-Ig and -Ih representing enzymes that may still retain ancestral nonresistance functions in the cell as provided by their particular active site properties.

Spatial structure and distribution of small pelagic fish in the northwestern Mediterranean Sea.

PubMed

Saraux, Claire; Fromentin, Jean-Marc; Bigot, Jean-Louis; Bourdeix, Jean-Hervé; Morfin, Marie; Roos, David; Van Beveren, Elisabeth; Bez, Nicolas

2014-01-01

Understanding the ecological and anthropogenic drivers of population dynamics requires detailed studies on habitat selection and spatial distribution. Although small pelagic fish aggregate in large shoals and usually exhibit important spatial structure, their dynamics in time and space remain unpredictable and challenging. In the Gulf of Lions (north-western Mediterranean), sardine and anchovy biomasses have declined over the past 5 years causing an important fishery crisis while sprat abundance rose. Applying geostatistical tools on scientific acoustic surveys conducted in the Gulf of Lions, we investigated anchovy, sardine and sprat spatial distributions and structures over 10 years. Our results show that sardines and sprats were more coastal than anchovies. The spatial structure of the three species was fairly stable over time according to variogram outputs, while year-to-year variations in kriged maps highlighted substantial changes in their location. Support for the McCall's basin hypothesis (covariation of both population density and presence area with biomass) was found only in sprats, the most variable of the three species. An innovative method to investigate species collocation at different scales revealed that globally the three species strongly overlap. Although species often co-occurred in terms of presence/absence, their biomass density differed at local scale, suggesting potential interspecific avoidance or different sensitivity to local environmental characteristics. Persistent favourable areas were finally detected, but their environmental characteristics remain to be determined.

Compact groups in theory and practice - IV. The connection to large-scale structure

NASA Astrophysics Data System (ADS)

Mendel, J. Trevor; Ellison, Sara L.; Simard, Luc; Patton, David R.; McConnachie, Alan W.

2011-12-01

We investigate the properties of photometrically selected compact groups (CGs) in the Sloan Digital Sky Survey. In this paper, the fourth in a series, we focus on understanding the characteristics of our observed CG sample with particular attention paid to quantifying and removing contamination from projected foreground or background galaxies. Based on a simple comparison of pairwise redshift likelihoods, we find that approximately half of CGs in the parent sample contain one or more projected (interloping) members; our final clean sample contains 4566 galaxies in 1086 CGs. We show that half of the remaining CGs are associated with rich groups (or clusters), i.e. they are embedded sub-structure. The other half have spatial distributions and number-density profiles consistent with the interpretation that they are either independently distributed structures within the field (i.e. they are isolated) or associated with relatively poor structures. Comparisons of late-type and red-sequence fractions in radial annuli show that galaxies around apparently isolated CGs resemble the field population by 300 to 500 kpc from the group centre. In contrast, the galaxy population surrounding embedded CGs appears to remain distinct from the field out beyond 1 to 2 Mpc, consistent with results for rich groups. We take this as additional evidence that the observed distinction between CGs, i.e. isolated versus embedded, is a separation between different host environments.

Quasi-steady solar wind dynamics

NASA Technical Reports Server (NTRS)

Pizzo, V. J.

1983-01-01

Progress in understanding the large scale dynamics of quasisteady, corotating solar wind structure was reviewed. The nature of the solar wind at large heliocentric distances preliminary calculations from a 2-D MHD model are used to demonstrate theoretical expectations of corotating structure out to 30 AU. It is found that the forward and reverse shocks from adjacent CIR's begin to interact at about 10 AU, producing new shock pairs flanking secondary CIR's. These sawtooth secondary CIR's interact again at about 20 AU and survive as visible entities to 30 AU. The model predicts the velocity jumps at the leading edge of the secondary CIR's at 30 AU should be very small but there should still be sizable variations in the thermodynamic and magnetic parameters. The driving dynamic mechanism in the distant solar wind is the relaxation of pressure gradients. The second topic is the influence of weak, nonimpulsive time dependence in quasisteady dynamics. It is suggested that modest large scale variations in the coronal flow speed on periods of several hours to a day may be responsible for many of the remaining discrepancies between theory and observation. Effects offer a ready explanation for the apparent rounding of stream fronts between 0.3 and 1.0 AU discovered by Helios.

Out-of-the-groove transport of lipids by TMEM16 and GPCR scramblases.

PubMed

Malvezzi, Mattia; Andra, Kiran K; Pandey, Kalpana; Lee, Byoung-Cheol; Falzone, Maria E; Brown, Ashley; Iqbal, Rabia; Menon, Anant K; Accardi, Alessio

2018-06-20

Phospholipid scramblases externalize phosphatidylserine to facilitate numerous physiological processes. Several members of the structurally unrelated TMEM16 and G protein-coupled receptor (GPCR) protein families mediate phospholipid scrambling. The structure of a TMEM16 scramblase shows a membrane-exposed hydrophilic cavity, suggesting that scrambling occurs via the ‟credit-card" mechanism where lipid headgroups permeate through the cavity while their tails remain associated with the membrane core. Here we show that afTMEM16 and opsin, representatives of the TMEM16 and GCPR scramblase families, transport phospholipids with polyethylene glycol headgroups whose globular dimensions are much larger than the width of the cavity. This suggests that transport of these large headgroups occurs outside rather than within the cavity. These large lipids are scrambled at rates comparable to those of normal phospholipids and their presence in the reconstituted vesicles promotes scrambling of normal phospholipids. This suggests that both large and small phospholipids can move outside the cavity. We propose that the conformational rearrangements underlying TMEM16- and GPCR-mediated credit-card scrambling locally deform the membrane to allow transbilayer lipid translocation outside the cavity and that both mechanisms underlie transport of normal phospholipids.

Tetrahedrality and structural order for hydrophobic interactions in a coarse-grained water model

NASA Astrophysics Data System (ADS)

Chaimovich, Aviel; Shell, M. Scott

2014-02-01

The hydrophobic interaction manifests two separate regimes in terms of size: Small nonpolar bodies exhibit a weak oscillatory force (versus distance) while large nonpolar surfaces exhibit a strong monotonic one. This crossover in hydrophobic behavior is typically explained in terms of water's tetrahedral structure: Its tetrahedrality is enhanced near small solutes and diminished near large planar ones. Here, we demonstrate that water's tetrahedral correlations signal this switch even in a highly simplified, isotropic, "core-softened" water model. For this task, we introduce measures of tetrahedrality based on the angular distribution of water's nearest neighbors. On a quantitative basis, the coarse-grained model of course is only approximate: (1) While greater than simple Lennard-Jones liquids, its bulk tetrahedrality remains lower than that of fully atomic models; and (2) the decay length of the large-scale hydrophobic interaction is less than has been found in experiments. Even so, the qualitative behavior of the model is surprisingly rich and exhibits numerous waterlike hydrophobic behaviors, despite its simplicity. We offer several arguments for the manner in which it should be able to (at least partially) reproduce tetrahedral correlations underlying these effects.

Tetrahedrality and structural order for hydrophobic interactions in a coarse-grained water model.

PubMed

Chaimovich, Aviel; Shell, M Scott

2014-02-01

The hydrophobic interaction manifests two separate regimes in terms of size: Small nonpolar bodies exhibit a weak oscillatory force (versus distance) while large nonpolar surfaces exhibit a strong monotonic one. This crossover in hydrophobic behavior is typically explained in terms of water's tetrahedral structure: Its tetrahedrality is enhanced near small solutes and diminished near large planar ones. Here, we demonstrate that water's tetrahedral correlations signal this switch even in a highly simplified, isotropic, "core-softened" water model. For this task, we introduce measures of tetrahedrality based on the angular distribution of water's nearest neighbors. On a quantitative basis, the coarse-grained model of course is only approximate: (1) While greater than simple Lennard-Jones liquids, its bulk tetrahedrality remains lower than that of fully atomic models; and (2) the decay length of the large-scale hydrophobic interaction is less than has been found in experiments. Even so, the qualitative behavior of the model is surprisingly rich and exhibits numerous waterlike hydrophobic behaviors, despite its simplicity. We offer several arguments for the manner in which it should be able to (at least partially) reproduce tetrahedral correlations underlying these effects.

Detailed Quantitative Classifications of Galaxy Morphology

NASA Astrophysics Data System (ADS)

Nair, Preethi

2018-01-01

Understanding the physical processes responsible for the growth of galaxies is one of the key challenges in extragalactic astronomy. The assembly history of a galaxy is imprinted in a galaxy’s detailed morphology. The bulge-to-total ratio of galaxies, the presence or absence of bars, rings, spiral arms, tidal tails etc, all have implications for the past merger, star formation, and feedback history of a galaxy. However, current quantitative galaxy classification schemes are only useful for broad binning. They cannot classify or exploit the wide variety of galaxy structures seen in nature. Therefore, comparisons of observations with theoretical predictions of secular structure formation have only been conducted on small samples of visually classified galaxies. However large samples are needed to disentangle the complex physical processes of galaxy formation. With the advent of large surveys, like the Sloan Digital Sky Survey (SDSS) and the upcoming Large Synoptic Survey Telescope (LSST) and WFIRST, the problem of statistics will be resolved. However, the need for a robust quantitative classification scheme will still remain. Here I will present early results on promising machine learning algorithms that are providing detailed classifications, identifying bars, rings, multi-armed spiral galaxies, and Hubble type.

Effects of large pressure amplitude low frequency noise in the parotid gland perivasculo-ductal connective tissue.

PubMed

Oliveira, Pedro; Brito, José; Mendes, João; da Fonseca, Jorge; Águas, Artur; Martins dos Santos, José

2013-01-01

In tissues and organs exposed to large pressure amplitude low frequency noise fibrosis occurs in the absence of inflammatory signs, which is thought to be a protective response. In the parotid gland the perivasculo-ductal connective tissue surrounds arteries, veins and the ductal tree. Perivasculo-ductal connective tissue is believed to function as a mechanical stabilizer of the glandular tissue. In order to quantify the proliferation of perivasculo-ductal connective tissue in large pressure amplitude low frequency noise-exposed rats we used sixty Wistar rats which were equally divided into 6 groups. One group kept in silence, and the remaining five exposed to continuous large pressure amplitude low frequency noise: g1-168h (1 week); g2-504h (3 weeks); g3-840h (5 weeks); g4-1512h (9 weeks); and g5-2184h (13 weeks). After exposure, parotid glands were removed and the perivasculo-ductal connective tissue area was measured in all groups. We applied ANOVA statistical analysis, using SPSS 13.0. The global trend is an increase in the average perivasculo-ductal connective tissue areas, that develops linearly and significantly with large pressure amplitude low frequency noise exposure time (p < 0.001). It has been suggested that the biological response to large pressure amplitude low frequency noise exposure is associated with the need to maintain structural integrity. The structural reinforcement would be achieved by increased perivasculo-ductal connective tissue. Hence, these results show that in response to large pressure amplitude low frequency noise exposure, rat parotid glands increase their perivasculo-ductal connective tissue.

WE-E-18A-01: Large Area Avalanche Amorphous Selenium Sensors for Low Dose X-Ray Imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scheuermann, J; Goldan, A; Zhao, W

2014-06-15

Purpose: A large area indirect flat panel imager (FPI) with avalanche gain is being developed to achieve x-ray quantum noise limited low dose imaging. It uses a thin optical sensing layer of amorphous selenium (a-Se), known as High-Gain Avalanche Rushing Photoconductor (HARP), to detect optical photons generated from a high resolution x-ray scintillator. We will report initial results in the fabrication of a solid-state HARP structure suitable for a large area FPI. Our objective is to establish the blocking layer structures and defect suppression mechanisms that provide stable and uniform avalanche gain. Methods: Samples were fabricated as follows: (1) ITOmore » signal electrode. (2) Electron blocking layer. (3) A 15 micron layer of intrinsic a-Se. (4) Transparent hole blocking layer. (5) Multiple semitransparent bias electrodes to investigate avalanche gain uniformity over a large area. The sample was exposed to 50ps optical excitation pulses through the bias electrode. Transient time of flight (TOF) and integrated charge was measured. A charge transport simulation was developed to investigate the effects of varying blocking layer charge carrier mobility on defect suppression, avalanche gain and temporal performance. Results: Avalanche gain of ∼200 was achieved experimentally with our multi-layer HARP samples. Simulations using the experimental sensor structure produced the same magnitude of gain as a function of electric field. The simulation predicted that the high dark current at a point defect can be reduced by two orders of magnitude by blocking layer optimization which can prevent irreversible damage while normal operation remained unaffected. Conclusion: We presented the first solid state HARP structure directly scalable to a large area FPI. We have shown reproducible and uniform avalanche gain of 200. By reducing mobility of the blocking layers we can suppress defects and maintain stable avalanche. Future work will optimize the blocking layers to prevent lag and ghosting.« less

Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending

PubMed Central

Bebel, Aleksandra; Karaca, Ezgi; Kumar, Banushree; Stark, W Marshall; Barabas, Orsolya

2016-01-01

Bacterial Xer site-specific recombinases play an essential genome maintenance role by unlinking chromosome multimers, but their mechanism of action has remained structurally uncharacterized. Here, we present two high-resolution structures of Helicobacter pylori XerH with its recombination site DNA difH, representing pre-cleavage and post-cleavage synaptic intermediates in the recombination pathway. The structures reveal that activation of DNA strand cleavage and rejoining involves large conformational changes and DNA bending, suggesting how interaction with the cell division protein FtsK may license recombination at the septum. Together with biochemical and in vivo analysis, our structures also reveal how a small sequence asymmetry in difH defines protein conformation in the synaptic complex and orchestrates the order of DNA strand exchanges. Our results provide insights into the catalytic mechanism of Xer recombination and a model for regulation of recombination activity during cell division. DOI: http://dx.doi.org/10.7554/eLife.19706.001 PMID:28009253

Structure of p73 DNA-binding domain tetramer modulates p73 transactivation

PubMed Central

Ethayathulla, Abdul S.; Tse, Pui-Wah; Monti, Paola; Nguyen, Sonha; Inga, Alberto; Fronza, Gilberto; Viadiu, Hector

2012-01-01

The transcription factor p73 triggers developmental pathways and overlaps stress-induced p53 transcriptional pathways. How p53-family response elements determine and regulate transcriptional specificity remains an unsolved problem. In this work, we have determined the first crystal structures of p73 DNA-binding domain tetramer bound to response elements with spacers of different length. The structure and function of the adaptable tetramer are determined by the distance between two half-sites. The structures with zero and one base-pair spacers show compact p73 DNA-binding domain tetramers with large tetramerization interfaces; a two base-pair spacer results in DNA unwinding and a smaller tetramerization interface, whereas a four base-pair spacer hinders tetramerization. Functionally, p73 is more sensitive to spacer length than p53, with one base-pair spacer reducing 90% of transactivation activity and longer spacers reducing transactivation to basal levels. Our results establish the quaternary structure of the p73 DNA-binding domain required as a scaffold to promote transactivation. PMID:22474346

Emergence of structured communities through evolutionary dynamics.

PubMed

Shtilerman, Elad; Kessler, David A; Shnerb, Nadav M

2015-10-21

Species-rich communities, in which many competing species coexist in a single trophic level, are quite frequent in nature, but pose a formidable theoretical challenge. In particular, it is known that complex competitive systems become unstable and unfeasible when the number of species is large. Recently, many studies have attributed the stability of natural communities to the structure of the interspecific interaction network, yet the nature of such structures and the underlying mechanisms responsible for them remain open questions. Here we introduce an evolutionary model, based on the generic Lotka-Volterra competitive framework, from which a stable, structured, diverse community emerges spontaneously. The modular structure of the competition matrix reflects the phylogeny of the community, in agreement with the hierarchial taxonomic classification. Closely related species tend to have stronger niche overlap and weaker fitness differences, as opposed to pairs of species from different modules. The competitive-relatedness hypothesis and the idea of emergent neutrality are discussed in the context of this evolutionary model. Copyright © 2015 Elsevier Ltd. All rights reserved.

Activator Protein-1: redox switch controlling structure and DNA-binding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yin, Zhou; Machius, Mischa; Nestler, Eric J.

The transcription factor, activator protein-1 (AP-1), binds to cognate DNA under redox control; yet, the underlying mechanism has remained enigmatic. A series of crystal structures of the AP-1 FosB/JunD bZIP domains reveal ordered DNA-binding regions in both FosB and JunD even in absence DNA. However, while JunD is competent to bind DNA, the FosB bZIP domain must undergo a large conformational rearrangement that is controlled by a ‘redox switch’ centered on an inter-molecular disulfide bond. Solution studies confirm that FosB/JunD cannot undergo structural transition and bind DNA when the redox-switch is in the ‘OFF’ state, and show that the mid-pointmore » redox potential of the redox switch affords it sensitivity to cellular redox homeostasis. The molecular and structural studies presented here thus reveal the mechanism underlying redox-regulation of AP-1 Fos/Jun transcription factors and provide structural insight for therapeutic interventions targeting AP-1 proteins.« less

Surface-enhanced Raman spectroscopy of hexabenzobenzene, C24H12, an analogue of a graphene nanostructure

NASA Astrophysics Data System (ADS)

Owens, Frank J.

2018-05-01

While large scale fabrication of graphene nanoribbons remains a challenge, there exist materials which can be fabricated in quantities such as hexabenzobenzene,HBZB, (C24H12) and which have a two-dimensional (2D) carbon structure similar to graphene nanostructures. Using a 632 nm laser, no Raman spectra could be obtained from the solid material because of a strong luminescence produced by the laser. However, surface-enhanced Raman spectroscopy enabled the measurement of some of the Raman active modes. The G and D modes, which are characteristic fingerprints of a 2D graphene structure, were observed at 1331 and 1600 cm-1, respectively. Density functional theory at the B3LYP/6-31G* level was used to calculate the minimum energy structure and the Raman active vibrational frequencies of HBZB. The calculated minimum energy structure was 2D having D6h symmetry in agreement with the experimental structure in the liquid phase. The calculated frequencies were in good agreement with the measured values.

Laser surface treatment of porous ceramic substrate for application in solid oxide fuel cells

NASA Astrophysics Data System (ADS)

Mahmod, D. S. A.; Khan, A. A.; Munot, M. A.; Glandut, N.; Labbe, J. C.

2016-08-01

Laser has offered a large number of benefits for surface treatment of ceramics due to possibility of localized heating, very high heating/cooling rates and possibility of growth of structural configurations only produced under non-equilibrium high temperature conditions. The present work investigates oxidation of porous ZrB2-SiC sintered ceramic substrates through treatment by a 1072 ± 10 nm ytterbium fiber laser. A multi-layer structure is hence produced showing successively oxygen rich distinct layers. The porous bulk beneath these layers remained unaffected as this laser-formed oxide scale and protected the substrate from oxidation. A glassy SiO2 structure thus obtained on the surface of the substrate becomes subject of interest for further research, specifically for its utilization as solid protonic conductor in Solid Oxide Fuel Cells (SOFCs).

Maltose-neopentyl glycol (MNG) amphiphiles for solubilization, stabilization and crystallization of membrane proteins.

PubMed

Chae, Pil Seok; Rasmussen, Søren G F; Rana, Rohini R; Gotfryd, Kamil; Chandra, Richa; Goren, Michael A; Kruse, Andrew C; Nurva, Shailika; Loland, Claus J; Pierre, Yves; Drew, David; Popot, Jean-Luc; Picot, Daniel; Fox, Brian G; Guan, Lan; Gether, Ulrik; Byrne, Bernadette; Kobilka, Brian; Gellman, Samuel H

2010-12-01

The understanding of integral membrane protein (IMP) structure and function is hampered by the difficulty of handling these proteins. Aqueous solubilization, necessary for many types of biophysical analysis, generally requires a detergent to shield the large lipophilic surfaces of native IMPs. Many proteins remain difficult to study owing to a lack of suitable detergents. We introduce a class of amphiphiles, each built around a central quaternary carbon atom derived from neopentyl glycol, with hydrophilic groups derived from maltose. Representatives of this maltose-neopentyl glycol (MNG) amphiphile family show favorable behavior relative to conventional detergents, as manifested in multiple membrane protein systems, leading to enhanced structural stability and successful crystallization. MNG amphiphiles are promising tools for membrane protein science because of the ease with which they may be prepared and the facility with which their structures may be varied.

Discovering Network Structure Beyond Communities

NASA Astrophysics Data System (ADS)

Nishikawa, Takashi; Motter, Adilson E.

2011-11-01

To understand the formation, evolution, and function of complex systems, it is crucial to understand the internal organization of their interaction networks. Partly due to the impossibility of visualizing large complex networks, resolving network structure remains a challenging problem. Here we overcome this difficulty by combining the visual pattern recognition ability of humans with the high processing speed of computers to develop an exploratory method for discovering groups of nodes characterized by common network properties, including but not limited to communities of densely connected nodes. Without any prior information about the nature of the groups, the method simultaneously identifies the number of groups, the group assignment, and the properties that define these groups. The results of applying our method to real networks suggest the possibility that most group structures lurk undiscovered in the fast-growing inventory of social, biological, and technological networks of scientific interest.

Thermoelastic vibration test techniques

NASA Technical Reports Server (NTRS)

Kehoe, Michael W.; Snyder, H. Todd

1991-01-01

The structural integrity of proposed high speed aircraft can be seriously affected by the extremely high surface temperatures and large temperature gradients throughout the vehicle's structure. Variations in the structure's elastic characteristics as a result of thermal effects can be observed by changes in vibration frequency, damping, and mode shape. Analysis codes that predict these changes must be correlated and verified with experimental data. The experimental modal test techniques and procedures used to conduct uniform, nonuniform, and transient thermoelastic vibration tests are presented. Experimental setup and elevated temperature instrumentation considerations are also discussed. Modal data for a 12 by 50 inch aluminum plate heated to a temperature of 475 F are presented. These data show the effect of heat on the plate's modal characteristics. The results indicated that frequency decreased, damping increased, and mode shape remained unchanged as the temperature of the plate was increased.

Study of coherent structures of turbulence with large wall-normal gradients in thermophysical properties using direct numerical simulation

NASA Astrophysics Data System (ADS)

Reinink, Shawn K.; Yaras, Metin I.

2015-06-01

Forced-convection heat transfer in a heated working fluid at a thermodynamic state near its pseudocritical point is poorly predicted by correlations calibrated with data at subcritical temperatures and pressures. This is suggested to be primarily due to the influence of large wall-normal thermophysical property gradients that develop in proximity of the pseudocritical point on the concentration of coherent turbulence structures near the wall. The physical mechanisms dominating this influence remain poorly understood. In the present study, direct numerical simulation is used to study the development of coherent vortical structures within a turbulent spot under the influence of large wall-normal property gradients. A turbulent spot rather than a fully turbulent boundary layer is used for the study, for the coherent structures of turbulence in a spot tend to be in a more organized state which may allow for more effective identification of cause-and-effect relationships. Large wall-normal gradients in thermophysical properties are created by heating the working fluid which is near the pseudocritical thermodynamic state. It is found that during improved heat transfer, wall-normal gradients in density accelerate the growth of the Kelvin-Helmholtz instability mechanism in the shear layer enveloping low-speed streaks, causing it to roll up into hairpin vortices at a faster rate. It is suggested that this occurs by the baroclinic vorticity generation mechanism which accelerates the streamwise grouping of vorticity during shear layer roll-up. The increased roll-up frequency leads to reduced streamwise spacing between hairpin vortices in wave packets. The density gradients also promote the sinuous instability mode in low-speed streaks. The resulting oscillations in the streaks in the streamwise-spanwise plane lead to locally reduced spanwise spacing between hairpin vortices forming over adjacent low-speed streaks. The reduction in streamwise and spanwise spacing between hairpin vortices causes them to interact more frequently by merging together and by breaking apart into smaller turbulence structures.

Study of coherent structures of turbulence with large wall-normal gradients in thermophysical properties using direct numerical simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reinink, Shawn K.; Yaras, Metin I., E-mail: Metin.Yaras@carleton.ca

2015-06-15

Forced-convection heat transfer in a heated working fluid at a thermodynamic state near its pseudocritical point is poorly predicted by correlations calibrated with data at subcritical temperatures and pressures. This is suggested to be primarily due to the influence of large wall-normal thermophysical property gradients that develop in proximity of the pseudocritical point on the concentration of coherent turbulence structures near the wall. The physical mechanisms dominating this influence remain poorly understood. In the present study, direct numerical simulation is used to study the development of coherent vortical structures within a turbulent spot under the influence of large wall-normal propertymore » gradients. A turbulent spot rather than a fully turbulent boundary layer is used for the study, for the coherent structures of turbulence in a spot tend to be in a more organized state which may allow for more effective identification of cause-and-effect relationships. Large wall-normal gradients in thermophysical properties are created by heating the working fluid which is near the pseudocritical thermodynamic state. It is found that during improved heat transfer, wall-normal gradients in density accelerate the growth of the Kelvin-Helmholtz instability mechanism in the shear layer enveloping low-speed streaks, causing it to roll up into hairpin vortices at a faster rate. It is suggested that this occurs by the baroclinic vorticity generation mechanism which accelerates the streamwise grouping of vorticity during shear layer roll-up. The increased roll-up frequency leads to reduced streamwise spacing between hairpin vortices in wave packets. The density gradients also promote the sinuous instability mode in low-speed streaks. The resulting oscillations in the streaks in the streamwise-spanwise plane lead to locally reduced spanwise spacing between hairpin vortices forming over adjacent low-speed streaks. The reduction in streamwise and spanwise spacing between hairpin vortices causes them to interact more frequently by merging together and by breaking apart into smaller turbulence structures.« less

Microbial shaping of sedimentary wrinkle structures

NASA Astrophysics Data System (ADS)

Mariotti, G.; Pruss, S. B.; Perron, J. T.; Bosak, T.

2014-10-01

Wrinkle structures on sandy bed surfaces were present in some of the earliest sedimentary environments, but are rare in modern environments. These enigmatic millimetre- to centimetre-scale ridges or pits are particularly common in sediments that harbour trace fossils and imprints of early animals, and appeared in the aftermath of some large mass extinctions. Wrinkle structures have been interpreted as possible remnants of microbial mats, but the formation mechanism and associated palaeoenvironmental and palaeoecological implications of these structures remain debated. Here we show that microbial aggregates can form wrinkle structures on a bed of bare sand in wave tank experiments. Waves with a small orbital amplitude at the bed surface do not move sand grains directly. However, they move millimetre-size, light microbial fragments and thereby produce linear sand ridges and rounded scour pits at the wavelengths observed in nature within hours. We conclude that wrinkle structures are morphological biosignatures that form at the sediment-water interface in wave-dominated environments, and not beneath microbial mats as previously thought. During early animal evolution, grazing by eukaryotic organisms may have temporarily increased the abundance of microbial fragments and thus the production of wrinkle structures.

A voxel-based asymmetry study of the relationship between hemispheric asymmetry and language dominance in Wada tested patients.

PubMed

Keller, Simon S; Roberts, Neil; Baker, Gus; Sluming, Vanessa; Cezayirli, Enis; Mayes, Andrew; Eldridge, Paul; Marson, Anthony G; Wieshmann, Udo C

2018-03-23

Determining the anatomical basis of hemispheric language dominance (HLD) remains an important scientific endeavor. The Wada test remains the gold standard test for HLD and provides a unique opportunity to determine the relationship between HLD and hemispheric structural asymmetries on MRI. In this study, we applied a whole-brain voxel-based asymmetry (VBA) approach to determine the relationship between interhemispheric structural asymmetries and HLD in a large consecutive sample of Wada tested patients. Of 135 patients, 114 (84.4%) had left HLD, 10 (7.4%) right HLD, and 11 (8.2%) bilateral language representation. Fifty-four controls were also studied. Right-handed controls and right-handed patients with left HLD had comparable structural brain asymmetries in cortical, subcortical, and cerebellar regions that have previously been documented in healthy people. However, these patients and controls differed in structural asymmetry of the mesial temporal lobe and a circumscribed region in the superior temporal gyrus, suggesting that only asymmetries of these regions were due to brain alterations caused by epilepsy. Additional comparisons between patients with left and right HLD, matched for type and location of epilepsy, revealed that structural asymmetries of insula, pars triangularis, inferior temporal gyrus, orbitofrontal cortex, ventral temporo-occipital cortex, mesial somatosensory cortex, and mesial cerebellum were significantly associated with the side of HLD. Patients with right HLD and bilateral language representation were significantly less right-handed. These results suggest that structural asymmetries of an insular-fronto-temporal network may be related to HLD. © 2018 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

Human Gut Microbiome: Function Matters.

PubMed

Heintz-Buschart, Anna; Wilmes, Paul

2017-11-22

The human gut microbiome represents a complex ecosystem contributing essential functions to its host. Recent large-scale metagenomic studies have provided insights into its structure and functional potential. However, the functional repertoire which is actually contributed to human physiology remains largely unexplored. Here, by leveraging recent omics datasets, we challenge current assumptions regarding key attributes of the functional gut microbiome, in particular with respect to its variability. We further argue that the closing of existing gaps in functional knowledge should be addressed by a most-wanted gene list, the development and application of molecular and cellular high-throughput measurements, the development and sensible use of experimental models, as well as the direct study of observable molecular effects in the human host. Copyright © 2017 Elsevier Ltd. All rights reserved.

Interaction strength combinations and the overfishing of a marine food web.

PubMed

Bascompte, Jordi; Melián, Carlos J; Sala, Enric

2005-04-12

The stability of ecological communities largely depends on the strength of interactions between predators and their prey. Here we show that these interaction strengths are structured nonrandomly in a large Caribbean marine food web. Specifically, the cooccurrence of strong interactions on two consecutive levels of food chains occurs less frequently than expected by chance. Even when they occur, these strongly interacting chains are accompanied by strong omnivory more often than expected by chance. By using a food web model, we show that these interaction strength combinations reduce the likelihood of trophic cascades after the overfishing of top predators. However, fishing selectively removes predators that are overrepresented in strongly interacting chains. Hence, the potential for strong community-wide effects remains a threat.

Interaction strength combinations and the overfishing of a marine food web

PubMed Central

Bascompte, Jordi; Melián, Carlos J.; Sala, Enric

2005-01-01

The stability of ecological communities largely depends on the strength of interactions between predators and their prey. Here we show that these interaction strengths are structured nonrandomly in a large Caribbean marine food web. Specifically, the cooccurrence of strong interactions on two consecutive levels of food chains occurs less frequently than expected by chance. Even when they occur, these strongly interacting chains are accompanied by strong omnivory more often than expected by chance. By using a food web model, we show that these interaction strength combinations reduce the likelihood of trophic cascades after the overfishing of top predators. However, fishing selectively removes predators that are overrepresented in strongly interacting chains. Hence, the potential for strong community-wide effects remains a threat. PMID:15802468

Structural chemistry of Au(III)-substituted Ba2YCu3O(7-delta)

NASA Technical Reports Server (NTRS)

Hepp, A. F.; Gaier, J. R.; Pouch, J. J.; Hambourger, P. D.

1988-01-01

A series of gold-substituted perovskite superconductors Ba2Y(Cu/1-x/Aux)3O(7-delta)(x = 0-0.1) was synthesized. For x = 0.1, there was no change in the a and b lattice parameters (a = 3.826 A and b = 3.889 A), but a 0.06 A c-axis expansion to 11.75 A was observed. Substituted gold was found to be trivalent by X-ray photoelectron spectroscopy. Replacing Cu(1) in the copper oxide chain with a slight reordering of oxygen is consistent with c-axis expansion. The formal charge of the site remains trivalent, while remaining Cu in the chains is reduced to Cu(I), resulting in an oxygen stoichiometry of less than 7. Finally, no large effect on Tc is observed (Tc = 89 K for x = 0.10), in contrast to the effect of a number of other metal ion dopants. These results are discussed relative to the chemistry of Au(III) and to the use of the metal in structures containing gold and ceramic superconductors.

Stabilizing all geometric moduli in heterotic Calabi-Yau vacua

DOE PAGES

Anderson, Lara B.; Gray, James; Lukas, Andre; ...

2011-05-27

We propose a scenario to stabilize all geometric moduli - that is, the complex structure, Kähler moduli and the dilaton - in smooth heterotic Calabi-Yau compactifications without Neveu-Schwarz three-form flux. This is accomplished using the gauge bundle required in any heterotic compactification, whose perturbative effects on the moduli are combined with non-perturbative corrections. We argue that, for appropriate gauge bundles, all complex structure and a large number of other moduli can be perturbatively stabilized - in the most restrictive case, leaving only one combination of Kähler moduli and the dilaton as a flat direction. At this stage, the remaining modulimore » space consists of Minkowski vacua. That is, the perturbative superpotential vanishes in the vacuum without the necessity to fine-tune flux. Finally, we incorporate non-perturbative effects such as gaugino condensation and/or instantons. These are strongly constrained by the anomalous U(1) symmetries which arise from the required bundle constructions. We present a specific example, with a consistent choice of non-perturbative effects, where all remaining flat directions are stabilized in an AdS vacuum.« less

Multifunctional Co₀.₈₅Se/graphene hybrid nanosheets: controlled synthesis and enhanced performances for the oxygen reduction reaction and decomposition of hydrazine hydrate.

PubMed

Zhang, Lin-fei; Zhang, Chun-yang

2014-01-01

Ultrathin nanosheets possess novel electronic structures and physical properties as compared with their corresponding bulk samples. However, the controlled synthesis of ultrathin monolayer nanosheets still remains a great challenge due to the lack of an intrinsic driving force for anisotropic growth of two-dimensional (2D) structures. Here we demonstrate, for the first time to our knowledge, the in situ synthesis of large-scale ultrathin single-crystalline Co₀.₈₅Se nanosheets on graphene oxide (GO) sheets, with a thickness of 3 nm. Owing to the synergetic chemical coupling effects between GO and Co₀.₈₅Se, the Co₀.₈₅Se/graphene hybrid nanosheets exhibit the highest catalytic performance among the available cobalt chalcogenide-based catalysts for the oxygen reduction reaction (ORR). Moreover, Co₀.₈₅Se/graphene hybrid nanosheets can catalyze the decomposition of hydrazine hydrate rapidly, with 97% of hydrazine hydrate being degraded in 12 min and the degradation rate remaining constant over 10 consecutive cycles, thus having great potential as long-term catalysts in wastewater treatment.

Low-temperature thermal reduction of graphene oxide: In situ correlative structural, thermal desorption, and electrical transport measurements

NASA Astrophysics Data System (ADS)

Lipatov, Alexey; Guinel, Maxime J.-F.; Muratov, Dmitry S.; Vanyushin, Vladislav O.; Wilson, Peter M.; Kolmakov, Andrei; Sinitskii, Alexander

2018-01-01

Elucidation of the structural transformations in graphene oxide (GO) upon reduction remains an active and important area of research. We report the results of in situ heating experiments, during which electrical, mass spectrometry, X-ray photoelectron spectroscopy (XPS), Raman spectroscopy, and transmission electron microscopy (TEM) measurements were carried out correlatively. The simultaneous electrical and temperature programmed desorption measurements allowed us to correlate the onset of the increase in the electrical conductivity of GO by five orders of magnitude at about 150 °C with the maxima of the rates of desorption of H2O, CO, and CO2. Interestingly, this large conductivity change happens at an intermediate level of the reduction of GO, which likely corresponds to the point when the graphitic domains become large enough to enable percolative electronic transport. We demonstrate that the gas desorption is intimately related to (i) the changes in the chemical structure of GO detected by XPS and Raman spectroscopy and (ii) the formation of nanoscopic holes in GO sheets revealed by TEM. These in situ observations provide a better understanding of the mechanism of the GO thermal reduction.

Environmental Screening Effects in 2D Materials: Renormalization of the Bandgap, Electronic Structure, and Optical Spectra of Few-Layer Black Phosphorus.

PubMed

Qiu, Diana Y; da Jornada, Felipe H; Louie, Steven G

2017-08-09

Few-layer black phosphorus has recently emerged as a promising 2D semiconductor, notable for its widely tunable bandgap, highly anisotropic properties, and theoretically predicted large exciton binding energies. To avoid degradation, it has become common practice to encapsulate black phosphorus devices. It is generally assumed that this encapsulation does not qualitatively affect their optical properties. Here, we show that the contrary is true. We have performed ab initio GW and GW plus Bethe-Salpeter equation (GW-BSE) calculations to determine the quasiparticle (QP) band structure and optical spectrum of one-layer (1L) through four-layer (4L) black phosphorus, with and without encapsulation between hexagonal boron nitride and sapphire. We show that black phosphorus is exceptionally sensitive to environmental screening. Encapsulation reduces the exciton binding energy in 1L by as much as 70% and completely eliminates the presence of a bound exciton in the 4L structure. The reduction in the exciton binding energies is offset by a similarly large renormalization of the QP bandgap so that the optical gap remains nearly unchanged, but the nature of the excited states and the qualitative features of the absorption spectrum change dramatically.

Genetic structure of Culex erraticus populations across the Americas.

PubMed

Mendenhall, Ian H; Bahl, Justin; Blum, Michael J; Wesson, Dawn M

2012-05-01

Culex erraticus (Dyar & Knab) is a potential competent vector for several arboviruses such as Eastern and Venezuelan equine encephalitis viruses and West Nile virus. It therefore may play a role in the maintenance and spread of viral populations in areas of concern, including the United States where it occurs in >33 states. However, little information is available on potential barriers to movement across the species' distribution. Here, we analyze genetic variation among Cx. erraticus collected from Colombia, Guatemala, and nine locations in the United States to better understand population structure and connectivity. Comparative sequence analysis of the second internal transcribed spacer and mitochondrial NADH dehydrogenase genes identified two major lineages of sampled populations. One lineage represented the central and eastern United States, whereas the other corresponded to Central America, South America, and the western United States. Hierarchical analysis of genetic variation provided further evidence of regional population structure, although the majority of genetic variation was found to reside within populations, suggestive of large population sizes. Although significant physical barriers such as the Chihuahuan Desert probably constrain the spread of Cx. erraticus, large population sizes and connectivity within regions remain important risk factors that probably contribute to the movement of arboviruses within and between these regions.

FR-type radio sources in COSMOS: relation of radio structure to size, accretion modes and large-scale environment

NASA Astrophysics Data System (ADS)

Vardoulaki, Eleni; Faustino Jimenez Andrade, Eric; Delvecchio, Ivan; Karim, Alexander; Smolčić, Vernesa; Magnelli, Benjamin; Bertoldi, Frank; Schinnener, Eva; Sargent, Mark; Finoguenov, Alexis; VLA COSMOS Team

2018-01-01

The radio sources associated with active galactic nuclei (AGN) can exhibit a variety of radio structures, from simple to more complex, giving rise to a variety of classification schemes. The question which still remains open, given deeper surveys revealing new populations of radio sources, is whether this plethora of radio structures can be attributed to the physical properties of the host or to the environment. Here we present an analysis on the radio structure of radio-selected AGN from the VLA-COSMOS Large Project at 3 GHz (JVLA-COSMOS; Smolčić et al.) in relation to: 1) their linear projected size, 2) the Eddington ratio, and 3) the environment their hosts lie within. We classify these as FRI (jet-like) and FRII (lobe-like) based on the FR-type classification scheme, and compare them to a sample of jet-less radio AGN in JVLA-COSMOS. We measure their linear projected sizes using a semi-automatic machine learning technique. Their Eddington ratios are calculated from X-ray data available for COSMOS. As environmental probes we take the X-ray groups (hundreds kpc) and the density fields (~Mpc-scale) in COSMOS. We find that FRII radio sources are on average larger than FRIs, which agrees with literature. But contrary to past studies, we find no dichotomy in FR objects in JVLA-COSMOS given their Eddington ratios, as on average they exhibit similar values. Furthermore our results show that the large-scale environment does not explain the observed dichotomy in lobe- and jet-like FR-type objects as both types are found on similar environments, but it does affect the shape of the radio structure introducing bents for objects closer to the centre of an X-ray group.

Unbiased, scalable sampling of protein loop conformations from probabilistic priors.

PubMed

Zhang, Yajia; Hauser, Kris

2013-01-01

Protein loops are flexible structures that are intimately tied to function, but understanding loop motion and generating loop conformation ensembles remain significant computational challenges. Discrete search techniques scale poorly to large loops, optimization and molecular dynamics techniques are prone to local minima, and inverse kinematics techniques can only incorporate structural preferences in adhoc fashion. This paper presents Sub-Loop Inverse Kinematics Monte Carlo (SLIKMC), a new Markov chain Monte Carlo algorithm for generating conformations of closed loops according to experimentally available, heterogeneous structural preferences. Our simulation experiments demonstrate that the method computes high-scoring conformations of large loops (>10 residues) orders of magnitude faster than standard Monte Carlo and discrete search techniques. Two new developments contribute to the scalability of the new method. First, structural preferences are specified via a probabilistic graphical model (PGM) that links conformation variables, spatial variables (e.g., atom positions), constraints and prior information in a unified framework. The method uses a sparse PGM that exploits locality of interactions between atoms and residues. Second, a novel method for sampling sub-loops is developed to generate statistically unbiased samples of probability densities restricted by loop-closure constraints. Numerical experiments confirm that SLIKMC generates conformation ensembles that are statistically consistent with specified structural preferences. Protein conformations with 100+ residues are sampled on standard PC hardware in seconds. Application to proteins involved in ion-binding demonstrate its potential as a tool for loop ensemble generation and missing structure completion.

Unbiased, scalable sampling of protein loop conformations from probabilistic priors

PubMed Central

2013-01-01

Background Protein loops are flexible structures that are intimately tied to function, but understanding loop motion and generating loop conformation ensembles remain significant computational challenges. Discrete search techniques scale poorly to large loops, optimization and molecular dynamics techniques are prone to local minima, and inverse kinematics techniques can only incorporate structural preferences in adhoc fashion. This paper presents Sub-Loop Inverse Kinematics Monte Carlo (SLIKMC), a new Markov chain Monte Carlo algorithm for generating conformations of closed loops according to experimentally available, heterogeneous structural preferences. Results Our simulation experiments demonstrate that the method computes high-scoring conformations of large loops (>10 residues) orders of magnitude faster than standard Monte Carlo and discrete search techniques. Two new developments contribute to the scalability of the new method. First, structural preferences are specified via a probabilistic graphical model (PGM) that links conformation variables, spatial variables (e.g., atom positions), constraints and prior information in a unified framework. The method uses a sparse PGM that exploits locality of interactions between atoms and residues. Second, a novel method for sampling sub-loops is developed to generate statistically unbiased samples of probability densities restricted by loop-closure constraints. Conclusion Numerical experiments confirm that SLIKMC generates conformation ensembles that are statistically consistent with specified structural preferences. Protein conformations with 100+ residues are sampled on standard PC hardware in seconds. Application to proteins involved in ion-binding demonstrate its potential as a tool for loop ensemble generation and missing structure completion. PMID:24565175

Population Structure of Humpback Whales from Their Breeding Grounds in the South Atlantic and Indian Oceans

PubMed Central

Rosenbaum, Howard C.; Pomilla, Cristina; Mendez, Martin; Leslie, Matthew S.; Best, Peter B.; Findlay, Ken P.; Minton, Gianna; Ersts, Peter J.; Collins, Timothy; Engel, Marcia H.; Bonatto, Sandro L.; Kotze, Deon P. G. H.; Meÿer, Mike; Barendse, Jaco; Thornton, Meredith; Razafindrakoto, Yvette; Ngouessono, Solange; Vely, Michel; Kiszka, Jeremy

2009-01-01

Although humpback whales are among the best-studied of the large whales, population boundaries in the Southern Hemisphere (SH) have remained largely untested. We assess population structure of SH humpback whales using 1,527 samples collected from whales at fourteen sampling sites within the Southwestern and Southeastern Atlantic, the Southwestern Indian Ocean, and Northern Indian Ocean (Breeding Stocks A, B, C and X, respectively). Evaluation of mtDNA population structure and migration rates was carried out under different statistical frameworks. Using all genetic evidence, the results suggest significant degrees of population structure between all ocean basins, with the Southwestern and Northern Indian Ocean most differentiated from each other. Effective migration rates were highest between the Southeastern Atlantic and the Southwestern Indian Ocean, followed by rates within the Southeastern Atlantic, and the lowest between the Southwestern and Northern Indian Ocean. At finer scales, very low gene flow was detected between the two neighbouring sub-regions in the Southeastern Atlantic, compared to high gene flow for whales within the Southwestern Indian Ocean. Our genetic results support the current management designations proposed by the International Whaling Commission of Breeding Stocks A, B, C, and X as four strongly structured populations. The population structure patterns found in this study are likely to have been influenced by a combination of long-term maternally directed fidelity of migratory destinations, along with other ecological and oceanographic features in the region. PMID:19812698

Population structure of humpback whales from their breeding grounds in the South Atlantic and Indian Oceans.

PubMed

Rosenbaum, Howard C; Pomilla, Cristina; Mendez, Martin; Leslie, Matthew S; Best, Peter B; Findlay, Ken P; Minton, Gianna; Ersts, Peter J; Collins, Timothy; Engel, Marcia H; Bonatto, Sandro L; Kotze, Deon P G H; Meÿer, Mike; Barendse, Jaco; Thornton, Meredith; Razafindrakoto, Yvette; Ngouessono, Solange; Vely, Michel; Kiszka, Jeremy

2009-10-08

Although humpback whales are among the best-studied of the large whales, population boundaries in the Southern Hemisphere (SH) have remained largely untested. We assess population structure of SH humpback whales using 1,527 samples collected from whales at fourteen sampling sites within the Southwestern and Southeastern Atlantic, the Southwestern Indian Ocean, and Northern Indian Ocean (Breeding Stocks A, B, C and X, respectively). Evaluation of mtDNA population structure and migration rates was carried out under different statistical frameworks. Using all genetic evidence, the results suggest significant degrees of population structure between all ocean basins, with the Southwestern and Northern Indian Ocean most differentiated from each other. Effective migration rates were highest between the Southeastern Atlantic and the Southwestern Indian Ocean, followed by rates within the Southeastern Atlantic, and the lowest between the Southwestern and Northern Indian Ocean. At finer scales, very low gene flow was detected between the two neighbouring sub-regions in the Southeastern Atlantic, compared to high gene flow for whales within the Southwestern Indian Ocean. Our genetic results support the current management designations proposed by the International Whaling Commission of Breeding Stocks A, B, C, and X as four strongly structured populations. The population structure patterns found in this study are likely to have been influenced by a combination of long-term maternally directed fidelity of migratory destinations, along with other ecological and oceanographic features in the region.

Petroleum exploration and the Atlantic OCS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edson, G.; Adinolfi, F.; Gray, F.

1993-08-01

The largest Atlantic outer continental shelf (OCS) lease sale was the first one, Sale 40 in 1976. Ninety-three Baltimore Canyon Trough petroleum leases were issued, and industry's winning bids total $1.1 billion. The highest bonus bids were for leases overlying the Schlee Dome, then called Great Stone Dome, a large structure with a very large fetch area. By 1981, seven dry wells on the dome moderated this initial flush of optimism. However, subeconomic quantities of gas and light oil were discovered on the nearby Hudson Canyon Block 598-642 structure. Now after 9 lease sales, 410 lease awards, and 46 explorationmore » wells, United States Atlantic petroleum exploration activity is in a hiatus. Fifty-three leases remain active under suspensions of operation. Twenty-one lease blocks, about 50 mi offshore from Cape Hatteras, have been combined as the Manteo Exploration Unit. Mobil and partners submitted an exploration plant for the unit in 1989. The Atlantic OCS has petroleum potential, especially for gas. With only 46 exploration wells, entire basins and plays remain untested. During the present exploration inactivity, some petroleum evaluation of the Atlantic OCS continues by the Minerals Management Service and others. Similarities and differences are being documented between United States basins and the Canadian Scotian Basin, which contains oil and gas in commercial quantities. Other initiatives include geochemical, thermal history, seismic stratigraphic, and petroleum system modeling studies. The gas-prone Atlantic OCS eventually may make an energy contribution, especially to nearby East Coast markets.« less

(Finite) statistical size effects on compressive strength.

PubMed

Weiss, Jérôme; Girard, Lucas; Gimbert, Florent; Amitrano, David; Vandembroucq, Damien

2014-04-29

The larger structures are, the lower their mechanical strength. Already discussed by Leonardo da Vinci and Edmé Mariotte several centuries ago, size effects on strength remain of crucial importance in modern engineering for the elaboration of safety regulations in structural design or the extrapolation of laboratory results to geophysical field scales. Under tensile loading, statistical size effects are traditionally modeled with a weakest-link approach. One of its prominent results is a prediction of vanishing strength at large scales that can be quantified in the framework of extreme value statistics. Despite a frequent use outside its range of validity, this approach remains the dominant tool in the field of statistical size effects. Here we focus on compressive failure, which concerns a wide range of geophysical and geotechnical situations. We show on historical and recent experimental data that weakest-link predictions are not obeyed. In particular, the mechanical strength saturates at a nonzero value toward large scales. Accounting explicitly for the elastic interactions between defects during the damage process, we build a formal analogy of compressive failure with the depinning transition of an elastic manifold. This critical transition interpretation naturally entails finite-size scaling laws for the mean strength and its associated variability. Theoretical predictions are in remarkable agreement with measurements reported for various materials such as rocks, ice, coal, or concrete. This formalism, which can also be extended to the flowing instability of granular media under multiaxial compression, has important practical consequences for future design rules.

Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies.

PubMed

Furnham, Nicholas; Dawson, Natalie L; Rahman, Syed A; Thornton, Janet M; Orengo, Christine A

2016-01-29

Enzymes, as biological catalysts, form the basis of all forms of life. How these proteins have evolved their functions remains a fundamental question in biology. Over 100 years of detailed biochemistry studies, combined with the large volumes of sequence and protein structural data now available, means that we are able to perform large-scale analyses to address this question. Using a range of computational tools and resources, we have compiled information on all experimentally annotated changes in enzyme function within 379 structurally defined protein domain superfamilies, linking the changes observed in functions during evolution to changes in reaction chemistry. Many superfamilies show changes in function at some level, although one function often dominates one superfamily. We use quantitative measures of changes in reaction chemistry to reveal the various types of chemical changes occurring during evolution and to exemplify these by detailed examples. Additionally, we use structural information of the enzymes active site to examine how different superfamilies have changed their catalytic machinery during evolution. Some superfamilies have changed the reactions they perform without changing catalytic machinery. In others, large changes of enzyme function, in terms of both overall chemistry and substrate specificity, have been brought about by significant changes in catalytic machinery. Interestingly, in some superfamilies, relatives perform similar functions but with different catalytic machineries. This analysis highlights characteristics of functional evolution across a wide range of superfamilies, providing insights that will be useful in predicting the function of uncharacterised sequences and the design of new synthetic enzymes. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

A hierarchical architecture S/MWCNT nanomicrosphere with large pores for lithium sulfur batteries.

PubMed

Chen, Jia-jia; Zhang, Qian; Shi, Yi-ning; Qin, Lin-lin; Cao, Yong; Zheng, Ming-sen; Dong, Quan-feng

2012-04-28

A hierarchical S/MWCNT nanomicrosphere for lithium/sulfur batteries with a high power and energy density as well as an excellent cycle life is introduced. Sulfur was uniformly coated on the surface of functional MWCNTs, which serves as a carbon matrix, to form a typical nanoscale core-shell structure with a sulfur layer of thickness 10-20 nm. Then the nanoscale sulfur intermediate composite was ball-milled to form interwoven and porous sphere architecture with large pores (around 1 μm to 5 μm). Different from most sulfur/carbon materials with micropore and mesopore structure, the micrometre scale S/MWCNT nanomicrosphere with a large pore structure could also exhibit high sulfur utilization and cycle retention. It could maintain a reversible capacity of 1000 mA h g(-1) after 100 cycles at 0.3 A g(-1) current density. And it even remained 780 mA h g(-1) after 200 cycles at 0.5 A g(-1) and 650 mA h g(-1) after 200 cycles at 1 A g(-1), showing a significant cyclability enhancement. It is believed that under the collective effect of hierarchical architecture, as well as the existence of carboxyl functional groups, sulfur/carbon materials with large pores could also exhibit an excellent electrochemical performance. The synthesis process introduced here is simple and broadly applicable, which would not only be beneficial to design new materials for lithium sulfur batteries but can also be extended to many different electrode materials for lithium ion batteries. This journal is © the Owner Societies 2012

Giant actuation strain nearly 0.6% in a periodically orthogonal poled lead titanate zirconate ceramic via reversible domain switching

NASA Astrophysics Data System (ADS)

Li, Faxin; Wang, Qiangzhong; Miao, Hongchen

2017-08-01

The widely used ferroelectric ceramics based actuators always suffer from small output strains (typically ˜0.1%-0.15%). Non-180° domain switching can generate a large strain in ferroelectrics but it is usually irreversible. In this work, we tailored the domain structures in a soft lead titanate zirconate (PZT) ceramic by periodical orthogonal poling. The non-180° switching in this domain-engineered PZT ceramics turns to be reversible, resulting in a local giant actuation strain of nearly 0.6% under a field of 2 kV/mm at 0.1 Hz. The large interfacial stresses between regions with different poling directions during electric loading/unloading were thought to be responsible for the reversible non-180° domain switching. The switching strain drops quickly with the increasing frequency, and stabilized at about 0.2% at or above 1.0 Hz. The large actuation strain remains quite stable after 104 cycles of loading, which is very promising for low-frequency, large-strain actuators.

Fatigue life estimation of a 1D aluminum beam under mode-I loading using the electromechanical impedance technique

NASA Astrophysics Data System (ADS)

Lim, Yee Yan; Kiong Soh, Chee

2011-12-01

Structures in service are often subjected to fatigue loads. Cracks would develop and lead to failure if left unnoticed after a large number of cyclic loadings. Monitoring the process of fatigue crack propagation as well as estimating the remaining useful life of a structure is thus essential to prevent catastrophe while minimizing earlier-than-required replacement. The advent of smart materials such as piezo-impedance transducers (lead zirconate titanate, PZT) has ushered in a new era of structural health monitoring (SHM) based on non-destructive evaluation (NDE). This paper presents a series of investigative studies to evaluate the feasibility of fatigue crack monitoring and estimation of remaining useful life using the electromechanical impedance (EMI) technique employing a PZT transducer. Experimental tests were conducted to study the ability of the EMI technique in monitoring fatigue crack in 1D lab-sized aluminum beams. The experimental results prove that the EMI technique is very sensitive to fatigue crack propagation. A proof-of-concept semi-analytical damage model for fatigue life estimation has been developed by incorporating the linear elastic fracture mechanics (LEFM) theory into the finite element (FE) model. The prediction of the model matches closely with the experiment, suggesting the possibility of replacing costly experiments in future.

Release of Native-like Gaseous Proteins from Electrospray Droplets via the Charged Residue Mechanism: Insights from Molecular Dynamics Simulations.

PubMed

McAllister, Robert G; Metwally, Haidy; Sun, Yu; Konermann, Lars

2015-10-07

The mechanism whereby gaseous protein ions are released from charged solvent droplets during electrospray ionization (ESI) remains a matter of debate. Also, it is unclear to what extent electrosprayed proteins retain their solution structure. Molecular dynamics (MD) simulations offer insights into the temporal evolution of protein systems. Surprisingly, there have been no all-atom simulations of the protein ESI process to date. The current work closes this gap by investigating the behavior of protein-containing aqueous nanodroplets that carry excess positive charge. We focus on "native ESI", where proteins initially adopt their biologically active solution structures. ESI proceeds while the protein remains entrapped within the droplet. Protein release into the gas phase occurs upon solvent evaporation to dryness. Droplet shrinkage is accompanied by ejection of charge carriers (Na(+) for the conditions chosen here), keeping the droplet at ∼85% of the Rayleigh limit throughout its life cycle. Any remaining charge carriers bind to the protein as the final solvent molecules evaporate. The outcome of these events is largely independent of the initial protein charge and the mode of charge carrier binding. ESI charge states and collision cross sections of the MD structures agree with experimental data. Our results confirm the Rayleigh/charged residue model (CRM). Field emission of excess Na(+) plays an ancillary role by governing the net charge of the shrinking droplet. Models that envision protein ejection from the droplet are not supported. Most nascent CRM ions retain native-like conformations. For unfolded proteins ESI likely proceeds along routes that are different from the native state mechanism explored here.

A synoptic review of the Eocene (Ypresian) cartilaginous fishes (Chondrichthyes: Holocephali, Elasmobranchii) of the Bolca Konservat-Lagerstätte, Italy

PubMed Central

Marramà, Giuseppe; Carnevale, Giorgio; Engelbrecht, Andrea; Claeson, Kerin M.; Zorzin, Roberto; Fornasiero, Mariagabriella; Kriwet, Jürgen

2018-01-01

Here, we review and discuss the records and taxonomy of the Ypresian (Eocene) chondrichthyans from the famous Bolca Konservat-Lagerstätte in northeastern Italy. Despite the outstanding diversity and the numerous studies focusing on the actinopterygian faunas from Pesciara and Monte Postale, the current knowledge about the systematics, taxonomy and phylogenetic relationships of the cartilaginous fishes from these Eocene sites remains elusive and largely inadequate. The celebrated Eocene Bolca Lagerstätte has yielded several exquisitely preserved articulated remains of chondrichthyan fishes in which delicate structures and soft tissues are preserved, as well as isolated teeth. The cartilaginous fish assemblage of Bolca comprises at least 17 species-level taxa belonging to 10 families in 6 orders, including selachians (Carcharhiniformes, Lamniformes), batoids (Torpediniformes, Myliobatiformes, Rajiformes) and holocephalans (Chimaeriformes). The occurrence of holocephalans represented by an isolated fin-spine of the chimeroid Ischyodus in the Bolca assemblage is reported here for the first time and represents the first record of chimeroids in the Eocene of Italy and also southern Europe. The Bolca chondrichthyan assemblage is remarkably different from those of other contemporaneous Boreal or Tethyan deposits, suggesting that its taxonomic composition is largely influenced by the palaeoenvironmental context. However, this synoptic review also highlights the importance of detailed revisions of all chondrichthyan remains from the Bolca Konservat-Lagerstätten.

A synoptic review of the Eocene (Ypresian) cartilaginous fishes (Chondrichthyes: Holocephali, Elasmobranchii) of the Bolca Konservat-Lagerstätte, Italy.

PubMed

Marramà, Giuseppe; Carnevale, Giorgio; Engelbrecht, Andrea; Claeson, Kerin M; Zorzin, Roberto; Fornasiero, Mariagabriella; Kriwet, Jürgen

2018-01-01

Here, we review and discuss the records and taxonomy of the Ypresian (Eocene) chondrichthyans from the famous Bolca Konservat-Lagerstätte in northeastern Italy. Despite the outstanding diversity and the numerous studies focusing on the actinopterygian faunas from Pesciara and Monte Postale, the current knowledge about the systematics, taxonomy and phylogenetic relationships of the cartilaginous fishes from these Eocene sites remains elusive and largely inadequate. The celebrated Eocene Bolca Lagerstätte has yielded several exquisitely preserved articulated remains of chondrichthyan fishes in which delicate structures and soft tissues are preserved, as well as isolated teeth. The cartilaginous fish assemblage of Bolca comprises at least 17 species-level taxa belonging to 10 families in 6 orders, including selachians (Carcharhiniformes, Lamniformes), batoids (Torpediniformes, Myliobatiformes, Rajiformes) and holocephalans (Chimaeriformes). The occurrence of holocephalans represented by an isolated fin-spine of the chimeroid Ischyodus in the Bolca assemblage is reported here for the first time and represents the first record of chimeroids in the Eocene of Italy and also southern Europe. The Bolca chondrichthyan assemblage is remarkably different from those of other contemporaneous Boreal or Tethyan deposits, suggesting that its taxonomic composition is largely influenced by the palaeoenvironmental context. However, this synoptic review also highlights the importance of detailed revisions of all chondrichthyan remains from the Bolca Konservat-Lagerstätten.

An Analysis of Artificial Reef Fish Community Structure along the Northwestern Gulf of Mexico Shelf: Potential Impacts of “Rigs-to-Reefs” Programs

PubMed Central

Ajemian, Matthew J.; Wetz, Jennifer J.; Shipley-Lozano, Brooke; Shively, J. Dale; Stunz, Gregory W.

2015-01-01

Artificial structures are the dominant complex marine habitat type along the northwestern Gulf of Mexico (GOM) shelf. These habitats can consist of a variety of materials, but in this region are primarily comprised of active and reefed oil and gas platforms. Despite being established for several decades, the fish communities inhabiting these structures remain poorly investigated. Between 2012 and 2013 we assessed fish communities at 15 sites using remotely operated vehicles (ROVs). Fish assemblages were quantified from standing platforms and an array of artificial reef types (Liberty Ships and partially removed or toppled platforms) distributed over the Texas continental shelf. The depth gradient covered by the surveys (30–84 m) and variability in structure density and relief also permitted analyses of the effects of these characteristics on fish richness, diversity, and assemblage composition. ROVs captured a variety of species inhabiting these reefs from large transient piscivores to small herbivorous reef fishes. While structure type and relief were shown to influence species richness and community structure, major trends in species composition were largely explained by the bottom depth where these structures occurred. We observed a shift in fish communities and relatively high diversity at approximately 60 m bottom depth, confirming trends observed in previous studies of standing platforms. This depth was also correlated with some of the largest Red Snapper captured on supplementary vertical longline surveys. Our work indicates that managers of artificial reefing programs (e.g., Rigs-to-Reefs) in the GOM should carefully consider the ambient environmental conditions when designing reef sites. For the Texas continental shelf, reefing materials at a 50–60 m bottom depth can serve a dual purpose of enhancing diving experiences and providing the best potential habitat for relatively large Red Snapper. PMID:25954943

Surveying the CGM and IGM across 4 orders of magnitude in environmental density

NASA Astrophysics Data System (ADS)

Burchett, Joseph

2017-08-01

Environment matters when it comes to galaxy evolution, and the mechanisms driving this evolution are reflected in the diffuse gas residing within the large-scale structures enveloping the cosmic galaxy population. QSO absorption lines effectively probe the circumgalactic medium (CGM) and intragroup and intracluster media, and work thus far hints at profound environmental effects on the CGM. However, sample sizes remain small, and a unifying picture of the gas characteristics across diverse environments has yet to emerge. Within the Sloan Digital Sky Survey, we have identified a sample volume containing a remarkable diversity in large-scale environment with an array of voids, >10,000 groups, several filaments, and 5 clusters, including the Coma Supercluster and CfA Great Wall. Leveraging the Hubble Spectroscopic Legacy Archive (HSLA), we propose a study using >360 background QSOs probing this volume to study the effects of large-scale environment on CGM and intergalactic medium (IGM) gas. The z = 0.019-0.028 spectroscopic galaxy sample is uniformly complete to galaxies L > 0.03 L* and, with the HSLA, produces 200 galaxy/sightline pairs within 300-kpc impact parameters across a wide range of environmental densities and structures.Upon quantifying the galaxy environment and identifying/measuring the QSO absorption lines at z = 0.019-0.028, we will pursue the following primary science goals:1. Constrain the CGM/IGM physical conditions across four orders of magnitude in galaxy density2. Compare ionic abundances and ionization states in the CGM of galaxies in filaments vs. voids3. Statistically investigate the IGM/CGM gas properties from structure to structure

Phase-relationships between scales in the perturbed turbulent boundary layer

NASA Astrophysics Data System (ADS)

Jacobi, I.; McKeon, B. J.

2017-12-01

The phase-relationship between large-scale motions and small-scale fluctuations in a non-equilibrium turbulent boundary layer was investigated. A zero-pressure-gradient flat plate turbulent boundary layer was perturbed by a short array of two-dimensional roughness elements, both statically, and under dynamic actuation. Within the compound, dynamic perturbation, the forcing generated a synthetic very-large-scale motion (VLSM) within the flow. The flow was decomposed by phase-locking the flow measurements to the roughness forcing, and the phase-relationship between the synthetic VLSM and remaining fluctuating scales was explored by correlation techniques. The general relationship between large- and small-scale motions in the perturbed flow, without phase-locking, was also examined. The synthetic large scale cohered with smaller scales in the flow via a phase-relationship that is similar to that of natural large scales in an unperturbed flow, but with a much stronger organizing effect. Cospectral techniques were employed to describe the physical implications of the perturbation on the relative orientation of large- and small-scale structures in the flow. The correlation and cospectral techniques provide tools for designing more efficient control strategies that can indirectly control small-scale motions via the large scales.

Quenched Magnon excitations by oxygen sublattice reconstruction in (SrCuO2)n/(SrTiO3)2 superlattices.

PubMed

Dantz, M; Pelliciari, J; Samal, D; Bisogni, V; Huang, Y; Olalde-Velasco, P; Strocov, V N; Koster, G; Schmitt, T

2016-09-12

The recently discovered structural reconstruction in the cuprate superlattice (SrCuO2)n/(SrTiO3)2 has been investigated across the critical value of n = 5 using resonant inelastic x-ray scattering (RIXS). We find that at the critical value of n, the cuprate layer remains largely in the bulk-like two-dimensional structure with a minority of Cu plaquettes being reconstructed. The partial reconstruction leads to quenching of the magnons starting at the Γ-point due to the minority plaquettes acting as scattering points. Although comparable in relative abundance, the doped charge impurities in electron-doped cuprate superconductors do not show this quenching of magnetic excitations.

An analytical model of prominence dynamics

NASA Astrophysics Data System (ADS)

Routh, Swati; Saha, Snehanshu; Bhat, Atul; Sundar, M. N.

2018-01-01

Solar prominences are magnetic structures incarcerating cool and dense gas in an otherwise hot solar corona. Prominences can be categorized as quiescent and active. Their origin and the presence of cool gas (∼104 K) within the hot (∼106K) solar corona remains poorly understood. The structure and dynamics of solar prominences was investigated in a large number of observational and theoretical (both analytical and numerical) studies. In this paper, an analytic model of quiescent solar prominence is developed and used to demonstrate that the prominence velocity increases exponentially, which means that some gas falls downward towards the solar surface, and that Alfvén waves are naturally present in the solar prominences. These theoretical predictions are consistent with the current observational data of solar quiescent prominences.

Using Arabidopsis to understand centromere function: progress and prospects.

PubMed

Copenhaver, Gregory P

2003-01-01

Arabidopsis thaliana has emerged in recent years as a leading model for understanding the structure and function of higher eukaryotic centromeres. Arabidopsis centromeres, like those of virtually all higher eukaryotes, encompass large DNA domains consisting of a complex combination of unique, dispersed middle repetitive and highly repetitive DNA. For this reason, they have required creative analysis using molecular, genetic, cytological and genomic techniques. This synergy of approaches, reinforced by rapid progress in understanding how proteins interact with the centromere DNA to form a complete functional unit, has made Arabidopsis one the best understood centromere systems. Yet major problems remain to be solved: gaining a complete structural definition of the centromere has been surprisingly difficult, and developing synthetic mini-chromosomes in plants has been even more challenging.

Domain structure of the ribozyme from eubacterial ribonuclease P.

PubMed Central

Loria, A; Pan, T

1996-01-01

Large RNAs can be composed of discrete domains that fold independently. One such "folding domain" has been identified previously in the ribozyme from Bacillus subtilis ribonuclease P (denoted P RNA). This domain contains roughly one-third of all residues. Folding of an RNA construct consisting of the remaining two-thirds of B. subtilis P RNA was examined by Fe(II)-EDTA hydroxyl radical protection. This molecule folds into the proper higher-order structure under identical conditions as the full-length P RNA, suggesting the presence of a second folding domain in B. subtilis P RNA. Folding analysis of the Escherichia coli P RNA by hydroxyl radical protection shows that this P RNA is completely folded at 5-6 mM Mg2+. In order to analyze the structural organization of folding domains in E. coli P RNA, constructs were designed based on the domain structure of B. subtilis P RNA. Fe(II)-EDTA protection indicates that E. coli P RNA also contains two folding domains. Despite the significant differences at the secondary structure level, both P RNAs appear to converge structurally at the folding domain level. The pre-tRNA substrate, localized in previous studies, may bind across the folding domains with the acceptor stem/3'CCA contacting the domain including the active site and the T stem-loop contacting the other. Because all eubacterial P RNAs share considerable homology in secondary structure to either B. subtilis or E. coli P RNA, these results suggest that this domain structure may be applicable for most, if not all, eubacterial P RNAs. Identification of folding domains should be valuable in dissecting structure-function relationship of large RNAs. PMID:8718684

Integrating protein structural dynamics and evolutionary analysis with Bio3D.

PubMed

Skjærven, Lars; Yao, Xin-Qiu; Scarabelli, Guido; Grant, Barry J

2014-12-10

Popular bioinformatics approaches for studying protein functional dynamics include comparisons of crystallographic structures, molecular dynamics simulations and normal mode analysis. However, determining how observed displacements and predicted motions from these traditionally separate analyses relate to each other, as well as to the evolution of sequence, structure and function within large protein families, remains a considerable challenge. This is in part due to the general lack of tools that integrate information of molecular structure, dynamics and evolution. Here, we describe the integration of new methodologies for evolutionary sequence, structure and simulation analysis into the Bio3D package. This major update includes unique high-throughput normal mode analysis for examining and contrasting the dynamics of related proteins with non-identical sequences and structures, as well as new methods for quantifying dynamical couplings and their residue-wise dissection from correlation network analysis. These new methodologies are integrated with major biomolecular databases as well as established methods for evolutionary sequence and comparative structural analysis. New functionality for directly comparing results derived from normal modes, molecular dynamics and principal component analysis of heterogeneous experimental structure distributions is also included. We demonstrate these integrated capabilities with example applications to dihydrofolate reductase and heterotrimeric G-protein families along with a discussion of the mechanistic insight provided in each case. The integration of structural dynamics and evolutionary analysis in Bio3D enables researchers to go beyond a prediction of single protein dynamics to investigate dynamical features across large protein families. The Bio3D package is distributed with full source code and extensive documentation as a platform independent R package under a GPL2 license from http://thegrantlab.org/bio3d/ .

Anomalously low amplitude of S waves produced by the 3D structures in the lower mantle

NASA Astrophysics Data System (ADS)

To, Akiko; Capdeville, Yann; Romanowicz, Barbara

2016-07-01

Direct S and Sdiff phases with anomalously low amplitudes are recorded for the earthquakes in Papua New Guinea by seismographs in northern America. According to the prediction by a standard 1D model, the amplitudes are the lowest at stations in southern California, at a distance and azimuth of around 95° and 55°, respectively, from the earthquake. The amplitude anomaly is more prominent at frequencies higher than 0.03 Hz. We checked and ruled out the possibility of the anomalies appearing because of the errors in the focal mechanism used in the reference synthetic waveform calculations. The observed anomaly distribution changes drastically with a relatively small shift in the location of the earthquake. The observations indicate that the amplitude reduction is likely due to the 3D shear velocity (Vs) structure, which deflects the wave energy away from the original ray paths. Moreover, some previous studies suggested that some of the S and Sdiff phases in our dataset are followed by a prominent postcursor and show a large travel time delay, which was explained by placing a large ultra-low velocity zone (ULVZ) located on the core-mantle boundary southwest of Hawaii. In this study, we evaluated the extent of amplitude anomalies that can be explained by the lower mantle structures in the existing models, including the previously proposed ULVZ. In addition, we modified and tested some models and searched for the possible causes of low amplitudes. Full 3D synthetic waveforms were calculated and compared with the observations. Our results show that while the existing models explain the trends of the observed amplitude anomalies, the size of such anomalies remain under-predicted especially at large distances. Adding a low velocity zone, which is spatially larger and has less Vs reduction than ULVZ, on the southwest side of ULVZ, contributes to explain the low amplitudes observed at distances larger than 100° from the earthquake. The newly proposed low velocity zone mostly overlaps with the northern part of the Pacific large low shear velocity province (LLSVP) revealed in tomographic models. Although the very low amplitudes observed at a distance of about 95° remain unexplained, our results indicate that the boundary of the Pacific LLSVP is sharp, and the amplitude of S waves at these large distances is lowered by strong vertical and/or lateral deflection at the boundary toward the interior of the low velocity province.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Gang

Mid-latitude extreme weather events are responsible for a large part of climate-related damage. Yet large uncertainties remain in climate model projections of heat waves, droughts, and heavy rain/snow events on regional scales, limiting our ability to effectively use these projections for climate adaptation and mitigation. These uncertainties can be attributed to both the lack of spatial resolution in the models, and to the lack of a dynamical understanding of these extremes. The approach of this project is to relate the fine-scale features to the large scales in current climate simulations, seasonal re-forecasts, and climate change projections in a very widemore » range of models, including the atmospheric and coupled models of ECMWF over a range of horizontal resolutions (125 to 10 km), aqua-planet configuration of the Model for Prediction Across Scales and High Order Method Modeling Environments (resolutions ranging from 240 km – 7.5 km) with various physics suites, and selected CMIP5 model simulations. The large scale circulation will be quantified both on the basis of the well tested preferred circulation regime approach, and very recently developed measures, the finite amplitude Wave Activity (FAWA) and its spectrum. The fine scale structures related to extremes will be diagnosed following the latest approaches in the literature. The goal is to use the large scale measures as indicators of the probability of occurrence of the finer scale structures, and hence extreme events. These indicators will then be applied to the CMIP5 models and time-slice projections of a future climate.« less

Modular cell-internalizing aptamer nanostructure enables targeted delivery of large functional RNAs in cancer cell lines.

PubMed

Porciani, David; Cardwell, Leah N; Tawiah, Kwaku D; Alam, Khalid K; Lange, Margaret J; Daniels, Mark A; Burke, Donald H

2018-06-11

Large RNAs and ribonucleoprotein complexes have powerful therapeutic potential, but effective cell-targeted delivery tools are limited. Aptamers that internalize into target cells can deliver siRNAs (<15 kDa, 19-21 nt/strand). We demonstrate a modular nanostructure for cellular delivery of large, functional RNA payloads (50-80 kDa, 175-250 nt) by aptamers that recognize multiple human B cell cancer lines and transferrin receptor-expressing cells. Fluorogenic RNA reporter payloads enable accelerated testing of platform designs and rapid evaluation of assembly and internalization. Modularity is demonstrated by swapping in different targeting and payload aptamers. Both modules internalize into leukemic B cell lines and remained colocalized within endosomes. Fluorescence from internalized RNA persists for ≥2 h, suggesting a sizable window for aptamer payloads to exert influence upon targeted cells. This demonstration of aptamer-mediated, cell-internalizing delivery of large RNAs with retention of functional structure raises the possibility of manipulating endosomes and cells by delivering large aptamers and regulatory RNAs.

Non-reciprocal wave propagation in one-dimensional nonlinear periodic structures

NASA Astrophysics Data System (ADS)

Luo, Benbiao; Gao, Sha; Liu, Jiehui; Mao, Yiwei; Li, Yifeng; Liu, Xiaozhou

2018-01-01

We study a one-dimensional nonlinear periodic structure which contains two different spring stiffness and an identical mass in each period. The linear dispersion relationship we obtain indicates that our periodic structure has obvious advantages compared to other kinds of periodic structures (i.e. those with the same spring stiffness but two different mass), including its increased flexibility for manipulating the band gap. Theoretically, the optical cutoff frequency remains unchanged while the acoustic cutoff frequency shifts to a lower or higher frequency. A numerical simulation verifies the dispersion relationship and the effect of the amplitude-dependent signal filter. Based upon this, we design a device which contains both a linear periodic structure and a nonlinear periodic structure. When incident waves with the same, large amplitude pass through it from opposite directions, the output amplitude of the forward input is one order magnitude larger than that of the reverse input. Our devised, non-reciprocal device can potentially act as an acoustic diode (AD) without an electrical circuit and frequency shifting. Our result represents a significant step forwards in the research of non-reciprocal wave manipulation.

Blood-brain barrier permeability is increased after acute adult stroke but not neonatal stroke in the rat

PubMed Central

Lopez, David Fernandez; Faustino, Joel; Daneman, Richard; Zhou, Lu; Lee, Sarah; Derugin, Nikita; Wendland, Michael F.; Vexler, Zinaida S

2012-01-01

The immaturity of the CNS at birth greatly affects injury after stroke but the contribution of the blood-brain barrier (BBB) to the differential response to stroke in adults and neonates is poorly understood. We asked if the structure and function of the BBB is disrupted differently in neonatal and adult rats by transient middle cerebral artery occlusion. In adult rats, albumin leakage into injured regions was markedly increased during 2–24 h reperfusion but leakage remained low in the neonates. Functional assays employing intravascular tracers in the neonates showed that BBB permeability to both large (70-kDa dextran) and small (3-kDa dextran, Gd-DTPA) tracers remained largely undisturbed 24h after reperfusion. The profoundly different functional integrity of the BBB was associated with the largely nonoverlapping patterns of regulated genes in endothelial cells purified from injured and uninjured adult and neonatal brain at 24h (endothelial transcriptome, 31,042 total probe sets). Within significantly regulated 1,266 probe sets in injured adults and 361 probe sets in neonates, changes in the gene expression of the basal lamina components, adhesion molecules, the tight junction protein occludin, and MMP-9 were among the key differences. The protein expression of collagen-IV, laminin, claudin-5, occludin and ZO-1 was also better preserved in neonatal rats. Neutrophil infiltration remained low in acutely injured neonates but neutralization of CINC-1 in the systemic circulation enhanced neutrophil infiltration, BBB permeability and injury. The markedly more integrant BBB in neonatal brain than in adult brain after acute stroke may have major implications for the treatment of neonatal stroke. PMID:22787045

Toxicology in Addiction Medicine.

PubMed

Schwarz, Daniel A; George, M P; Bluth, Martin H

2016-12-01

Toxicology testing in addiction medicine varies across the spectrum, yet remains a powerful tool in monitoring addictive patients. There are many reference laboratories offering toxicology testing, and physicians should have some understanding of laboratory, methodology, testing portfolio, and customer support structure to aid them in selecting the best toxicology laboratory for their patients. Consultation with a clinical pathologist/toxicologist in conjunction with the consideration of monitoring large numbers of illicit and psychoactive drugs in the addictive patient may provide important clinical information for their treatment. Copyright © 2016 Elsevier Inc. All rights reserved.

Long-term stability of microcrystalline silicon p-i-n solar cells exposed to sun light

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanguino, P.; Koynov, S.; Schwarz, R.

1999-07-01

The performance of an entirely microcrystalline p-i-n solar cell was monitored during a long-term outdoor test in Lisbon starting in September 1998. A small decrease of the short circuit current was observed after 5 months of operation. The open-circuit voltage remained stable around 400 mV. From the analysis of the I-V characteristic in dark and under illumination they could identify the weak points of the test structure, like large series resistance, high recombination rate, and intensity-dependent collection efficiency.

Determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hong, Liang; Jain, Nitin; Cheng, Xiaolin

Protein function often depends on global, collective internal motions. However, the simultaneous quantitative experimental determination of the forms, amplitudes, and time scales of these motions has remained elusive. We demonstrate that a complete description of these large-scale dynamic modes can be obtained using coherent neutron-scattering experiments on perdeuterated samples. With this approach, a microscopic relationship between the structure, dynamics, and function in a protein, cytochrome P450cam, is established. The approach developed here should be of general applicability to protein systems.

Determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering

DOE PAGES

Hong, Liang; Jain, Nitin; Cheng, Xiaolin; ...

2016-10-14

Protein function often depends on global, collective internal motions. However, the simultaneous quantitative experimental determination of the forms, amplitudes, and time scales of these motions has remained elusive. We demonstrate that a complete description of these large-scale dynamic modes can be obtained using coherent neutron-scattering experiments on perdeuterated samples. With this approach, a microscopic relationship between the structure, dynamics, and function in a protein, cytochrome P450cam, is established. The approach developed here should be of general applicability to protein systems.

Boron Nitride Nanotubes: Recent Advances in Their Synthesis, Functionalization, and Applications.

PubMed

Lee, Chee Huei; Bhandari, Shiva; Tiwari, Bishnu; Yapici, Nazmiye; Zhang, Dongyan; Yap, Yoke Khin

2016-07-15

A comprehensive overview of current research progress on boron nitride nanotubes (BNNTs) is presented in this article. Particularly, recent advancements in controlled synthesis and large-scale production of BNNTs will first be summarized. While recent success in mass production of BNNTs has opened up new opportunities to implement the appealing properties in various applications, concerns about product purity and quality still remain. Secondly, we will summarize the progress in functionalization of BNNTs, which is the necessary step for their applications. Additionally, selected potential applications in structural composites and biomedicine will be highlighted.

GNE-886: A Potent and Selective Inhibitor of the Cat Eye Syndrome Chromosome Region Candidate 2 Bromodomain (CECR2).

PubMed

Crawford, Terry D; Audia, James E; Bellon, Steve; Burdick, Daniel J; Bommi-Reddy, Archana; Côté, Alexandre; Cummings, Richard T; Duplessis, Martin; Flynn, E Megan; Hewitt, Michael; Huang, Hon-Ren; Jayaram, Hariharan; Jiang, Ying; Joshi, Shivangi; Kiefer, James R; Murray, Jeremy; Nasveschuk, Christopher G; Neiss, Arianne; Pardo, Eneida; Romero, F Anthony; Sandy, Peter; Sims, Robert J; Tang, Yong; Taylor, Alexander M; Tsui, Vickie; Wang, Jian; Wang, Shumei; Wang, Yongyun; Xu, Zhaowu; Zawadzke, Laura; Zhu, Xiaoqin; Albrecht, Brian K; Magnuson, Steven R; Cochran, Andrea G

2017-07-13

The biological function of bromodomains, epigenetic readers of acetylated lysine residues, remains largely unknown. Herein we report our efforts to discover a potent and selective inhibitor of the bromodomain of cat eye syndrome chromosome region candidate 2 (CECR2). Screening of our internal medicinal chemistry collection led to the identification of a pyrrolopyridone chemical lead, and subsequent structure-based drug design led to a potent and selective CECR2 bromodomain inhibitor (GNE-886) suitable for use as an in vitro tool compound.

Architecture of the sperm whale forehead facilitates ramming combat.

PubMed

Panagiotopoulou, Olga; Spyridis, Panagiotis; Mehari Abraha, Hyab; Carrier, David R; Pataky, Todd C

2016-01-01

Herman Melville's novel Moby Dick was inspired by historical instances in which large sperm whales (Physeter macrocephalus L.) sank 19th century whaling ships by ramming them with their foreheads. The immense forehead of sperm whales is possibly the largest, and one of the strangest, anatomical structures in the animal kingdom. It contains two large oil-filled compartments, known as the "spermaceti organ" and "junk," that constitute up to one-quarter of body mass and extend one-third of the total length of the whale. Recognized as playing an important role in echolocation, previous studies have also attributed the complex structural configuration of the spermaceti organ and junk to acoustic sexual selection, acoustic prey debilitation, buoyancy control, and aggressive ramming. Of these additional suggested functions, ramming remains the most controversial, and the potential mechanical roles of the structural components of the spermaceti organ and junk in ramming remain untested. Here we explore the aggressive ramming hypothesis using a novel combination of structural engineering principles and probabilistic simulation to determine if the unique structure of the junk significantly reduces stress in the skull during quasi-static impact. Our analyses indicate that the connective tissue partitions in the junk reduce von Mises stresses across the skull and that the load-redistribution functionality of the former is insensitive to moderate variation in tissue material parameters, the thickness of the partitions, and variations in the location and angle of the applied load. Absence of the connective tissue partitions increases skull stresses, particularly in the rostral aspect of the upper jaw, further hinting of the important role the architecture of the junk may play in ramming events. Our study also found that impact loads on the spermaceti organ generate lower skull stresses than an impact on the junk. Nevertheless, whilst an impact on the spermaceti organ would reduce skull stresses, it would also cause high compressive stresses on the anterior aspect of the organ and the connective tissue case, possibly making these structures more prone to failure. This outcome, coupled with the facts that the spermaceti organ houses sensitive and essential sonar producing structures and the rostral portion of junk, rather than the spermaceti organ, is frequently a site of significant scarring in mature males suggest that whales avoid impact with the spermaceti organ. Although the unique structure of the junk certainly serves multiple functions, our results are consistent with the hypothesis that the structure also evolved to function as a massive battering ram during male-male competition.

Determinants of Mammalian Nucleolar Architecture

PubMed Central

Farley, Katherine I.; Surovtseva, Yulia; Merkel, Janie; Baserga, Susan J.

2015-01-01

The nucleolus is responsible for the production of ribosomes, essential machines which synthesize all proteins needed by the cell. The structure of human nucleoli is highly dynamic and is directly related to its functions in ribosome biogenesis. Despite the importance of this organelle, the intricate relationship between nucleolar structure and function remains largely unexplored. How do cells control nucleolar formation and function? What are the minimal requirements for making a functional nucleolus? Here we review what is currently known regarding mammalian nucleolar formation at nucleolar organizer regions (NORs), which can be studied by observing the dissolution and reformation of the nucleolus during each cell division. Additionally, the nucleolus can be examined by analyzing how alterations in nucleolar function manifest in differences in nucleolar architecture. Furthermore, changes in nucleolar structure and function are correlated with cancer, highlighting the importance of studying the determinants of nucleolar formation. PMID:25670395

Maltose-neopentyl glycol (MNG) amphiphiles for solubilization, stabilization and crystallization of membrane proteins

PubMed Central

Chae, Pil Seok; Rasmussen, Søren G. F.; Rana, Rohini; Gotfryd, Kamil; Chandra, Richa; Goren, Michael A.; Kruse, Andrew C.; Nurva, Shailika; Loland, Claus J.; Pierre, Yves; Drew, David; Popot, Jean-Luc; Picot, Daniel; Fox, Brian G.; Guan, Lan; Gether, Ulrik; Byrne, Bernadette; Kobilka, Brian; Gellman, Samuel H.

2011-01-01

The understanding of integral membrane protein (IMP) structure and function is hampered by the difficulty of handling these proteins. Aqueous solubilization, necessary for many types of biophysical analysis, generally requires a detergent to shield the large lipophilic surfaces displayed by native IMPs. Many proteins remain difficult to study owing to a lack of suitable detergents. We introduce a class of amphiphiles, each of which is built around a central quaternary carbon atom derived from neopentyl glycol, with hydrophilic groups derived from maltose. Representatives of this maltose-neopentyl glycol (MNG) amphiphile family display favorable behavior relative to conventional detergents, as tested on multiple membrane protein systems, leading to enhanced structural stability and successful crystallization. MNG amphiphiles are promising tools for membrane protein science because of the ease with which they may be prepared and the facility with which their structures may be varied. PMID:21037590

Complex and oriented ZnO nanostructures.

PubMed

Tian, Zhengrong R; Voigt, James A; Liu, Jun; McKenzie, Bonnie; McDermott, Matthew J; Rodriguez, Mark A; Konishi, Hiromi; Xu, Huifang

2003-12-01

Extended and oriented nanostructures are desirable for many applications, but direct fabrication of complex nanostructures with controlled crystalline morphology, orientation and surface architectures remains a significant challenge. Here we report a low-temperature, environmentally benign, solution-based approach for the preparation of complex and oriented ZnO nanostructures, and the systematic modification of their crystal morphology. Using controlled seeded growth and citrate anions that selectively adsorb on ZnO basal planes as the structure-directing agent, we prepared large arrays of oriented ZnO nanorods with controlled aspect ratios, complex film morphologies made of oriented nanocolumns and nanoplates (remarkably similar to biomineral structures in red abalone shells) and complex bilayers showing in situ column-to-rod morphological transitions. The advantages of some of these ZnO structures for photocatalytic decompositions of volatile organic compounds were demonstrated. The novel ZnO nanostructures are expected to have great potential for sensing, catalysis, optical emission, piezoelectric transduction, and actuations.

Self-organization of cosmic radiation pressure instability

NASA Technical Reports Server (NTRS)

Hogan, Craig J.

1991-01-01

Under some circumstances the absorption of radiation momentum by an absorbing medium opens the possibility of a dynamical instability, sometimes called 'mock gravity'. Here, a simplified abstract model is studied in which the radiation source is assumed to remain spatially uniform, there is no reabsorption or reradiated light, and no forces other than radiative pressure act on the absorbing medium. It is shown that this model displays the unique feature of being not only unstable, but also self-organizing. The structure approaches a statistical dynamical steady state which is almost independent of initial conditions. In this saturated state the absorbers are concentrated in thin walls around empty bubbles; as the instability develops the big bubbles get bigger and the small ones get crushed and disappear. A linear analysis shows that to first order the thin walls are indeed stable structures. It is speculated that this instability may play a role in forming cosmic large-scale structure.

The network of concepts in written texts

NASA Astrophysics Data System (ADS)

Caldeira, S. M. G.; Petit Lobão, T. C.; Andrade, R. F. S.; Neme, A.; Miranda, J. G. V.

2006-02-01

Complex network theory is used to investigate the structure of meaningful concepts in written texts of individual authors. Networks have been constructed after a two phase filtering, where words with less meaning contents are eliminated and all remaining words are set to their canonical form, without any number, gender or time flexion. Each sentence in the text is added to the network as a clique. A large number of written texts have been scrutinised, and it is found that texts have small-world as well as scale-free structures. The growth process of these networks has also been investigated, and a universal evolution of network quantifiers have been found among the set of texts written by distinct authors. Further analyses, based on shuffling procedures taken either on the texts or on the constructed networks, provide hints on the role played by the word frequency and sentence length distributions to the network structure.

Hydrostar Thermal and Structural Deformation Analyses of Antenna Array Concept

NASA Technical Reports Server (NTRS)

Amundsen, Ruth M.; Hope, Drew J.

1998-01-01

The proposed Hydrostar mission used a large orbiting antenna array to demonstrate synthetic aperture technology in space while obtaining global soil moisture data. In order to produce accurate data, the array was required to remain as close as possible to its perfectly aligned placement while undergoing the mechanical and thermal stresses induced by orbital changes. Thermal and structural analyses for a design concept of this antenna array were performed. The thermal analysis included orbital radiation calculations, as well as parametric studies of orbit altitude, material properties and coating types. The thermal results included predicted thermal distributions over the array for several cases. The structural analysis provided thermally-driven deflections based on these cases, as well as based on a 1-g inertial load. In order to minimize the deflections of the array in orbit, the use of XN70, a carbon-reinforced polycyanate composite, was recommended.

“FRIED EGG”: AN OCEANIC IMPACT CRATER IN THE MID-ATLANTIC?

NASA Astrophysics Data System (ADS)

Dias, F. C.; Lourenco, N.; Lobo, A.; Santos de Campos, A.; Pinto de Abreu, M.

2009-12-01

Analysis of a multibeam echosounder hydrographic survey performed in the Southern Azores Platform under the scope of the Portuguese Continental Shelf Project has revealed a large scale bathymetric structure nicknamed “Fried Egg” due to its well defined morphology. Laying at about 2km depth, this structure consists of a roughly circular 6km wide depression 110m below the surrounding ocean bottom, with a circular dome shaped central uplift 3km in diameter and with a base to top height of 300m. The associated backscatter signal presents a distinctive ring-like signature corresponding to the lower flank section of the dome, suggesting the outcrop of hard rock material. The remaining backscatter signal seems to correspond to widespread sediments. No lava flows are apparent either within the structure or on its surroundings. All these properties are compatible with the record of terrestrial impact craters, thus making of “Fried Egg” a potential oceanic impact crater.

An Enzyme-Catalyzed Multistep DNA Refolding Mechanism in Hairpin Telomere Formation

PubMed Central

Shi, Ke; Huang, Wai Mun; Aihara, Hideki

2013-01-01

Hairpin telomeres of bacterial linear chromosomes are generated by a DNA cutting–rejoining enzyme protelomerase. Protelomerase resolves a concatenated dimer of chromosomes as the last step of chromosome replication, converting a palindromic DNA sequence at the junctions between chromosomes into covalently closed hairpins. The mechanism by which protelomerase transforms a duplex DNA substrate into the hairpin telomeres remains largely unknown. We report here a series of crystal structures of the protelomerase TelA bound to DNA that represent distinct stages along the reaction pathway. The structures suggest that TelA converts a linear duplex substrate into hairpin turns via a transient strand-refolding intermediate that involves DNA-base flipping and wobble base-pairs. The extremely compact di-nucleotide hairpin structure of the product is fully stabilized by TelA prior to strand ligation, which drives the reaction to completion. The enzyme-catalyzed, multistep strand refolding is a novel mechanism in DNA rearrangement reactions. PMID:23382649

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hushur, Anwar; Manghnani, Murli H.; Werheit, Helmut

Single-crystal B4.3C boron carbide is investigated concerning the pressure-dependence of optical properties and of Raman-active phonons up to ~70 GPa. The high concentration of structural defects determining the electronic properties of boron carbide at ambient conditions initially decrease and finally vanish with pressure increasing. We obtain this immediately from transparency photos, allowing to estimate the pressure-dependent variation of the absorption edge rapidly increasing around 55 GPa. Glass-like transparency at pressures exceeding 60 GPa indicate that the width of the band exceeds ~3.1 eV thus making boron carbide a wide-gap semiconductor. Furthermore, the spectra of Raman–active phonons indicate a pressure-dependent phasemore » transition in single-crystal natB4.3C boron carbide near 35 GPa., particularly related to structural changes in connection with the C-B-C chains, while the basic icosahedral structure remains largely unaffected.« less

Plant cell wall characterization using scanning probe microscopy techniques

PubMed Central

Yarbrough, John M; Himmel, Michael E; Ding, Shi-You

2009-01-01

Lignocellulosic biomass is today considered a promising renewable resource for bioenergy production. A combined chemical and biological process is currently under consideration for the conversion of polysaccharides from plant cell wall materials, mainly cellulose and hemicelluloses, to simple sugars that can be fermented to biofuels. Native plant cellulose forms nanometer-scale microfibrils that are embedded in a polymeric network of hemicelluloses, pectins, and lignins; this explains, in part, the recalcitrance of biomass to deconstruction. The chemical and structural characteristics of these plant cell wall constituents remain largely unknown today. Scanning probe microscopy techniques, particularly atomic force microscopy and its application in characterizing plant cell wall structure, are reviewed here. We also further discuss future developments based on scanning probe microscopy techniques that combine linear and nonlinear optical techniques to characterize plant cell wall nanometer-scale structures, specifically apertureless near-field scanning optical microscopy and coherent anti-Stokes Raman scattering microscopy. PMID:19703302

Structural stability of nonlinear population dynamics.

PubMed

Cenci, Simone; Saavedra, Serguei

2018-01-01

In population dynamics, the concept of structural stability has been used to quantify the tolerance of a system to environmental perturbations. Yet, measuring the structural stability of nonlinear dynamical systems remains a challenging task. Focusing on the classic Lotka-Volterra dynamics, because of the linearity of the functional response, it has been possible to measure the conditions compatible with a structurally stable system. However, the functional response of biological communities is not always well approximated by deterministic linear functions. Thus, it is unclear the extent to which this linear approach can be generalized to other population dynamics models. Here, we show that the same approach used to investigate the classic Lotka-Volterra dynamics, which is called the structural approach, can be applied to a much larger class of nonlinear models. This class covers a large number of nonlinear functional responses that have been intensively investigated both theoretically and experimentally. We also investigate the applicability of the structural approach to stochastic dynamical systems and we provide a measure of structural stability for finite populations. Overall, we show that the structural approach can provide reliable and tractable information about the qualitative behavior of many nonlinear dynamical systems.

Structural stability of nonlinear population dynamics

NASA Astrophysics Data System (ADS)

Cenci, Simone; Saavedra, Serguei

2018-01-01

In population dynamics, the concept of structural stability has been used to quantify the tolerance of a system to environmental perturbations. Yet, measuring the structural stability of nonlinear dynamical systems remains a challenging task. Focusing on the classic Lotka-Volterra dynamics, because of the linearity of the functional response, it has been possible to measure the conditions compatible with a structurally stable system. However, the functional response of biological communities is not always well approximated by deterministic linear functions. Thus, it is unclear the extent to which this linear approach can be generalized to other population dynamics models. Here, we show that the same approach used to investigate the classic Lotka-Volterra dynamics, which is called the structural approach, can be applied to a much larger class of nonlinear models. This class covers a large number of nonlinear functional responses that have been intensively investigated both theoretically and experimentally. We also investigate the applicability of the structural approach to stochastic dynamical systems and we provide a measure of structural stability for finite populations. Overall, we show that the structural approach can provide reliable and tractable information about the qualitative behavior of many nonlinear dynamical systems.

Pathways of information transmission among wild songbirds follow experimentally imposed changes in social foraging structure.

PubMed

Firth, Josh A; Sheldon, Ben C; Farine, Damien R

2016-06-01

Animals regularly use information from others to shape their decisions. Yet, determining how changes in social structure affect information flow and social learning strategies has remained challenging. We manipulated the social structure of a large community of wild songbirds by controlling which individuals could feed together at automated feeding stations (selective feeders). We then provided novel ephemeral food patches freely accessible to all birds and recorded the spread of this new information. We demonstrate that the discovery of new food patches followed the experimentally imposed social structure and that birds disproportionately learnt from those whom they could forage with at the selective feeders. The selective feeders reduced the number of conspecific information sources available and birds subsequently increased their use of information provided by heterospecifics. Our study demonstrates that changes to social systems carry over into pathways of information transfer and that individuals learn from tutors that provide relevant information in other contexts. © 2016 The Authors.

Clustered marginalization of minorities during social transitions induced by co-evolution of behaviour and network structure

NASA Astrophysics Data System (ADS)

Schleussner, Carl-Friedrich; Donges, Jonathan F.; Engemann, Denis A.; Levermann, Anders

2016-08-01

Large-scale transitions in societies are associated with both individual behavioural change and restructuring of the social network. These two factors have often been considered independently, yet recent advances in social network research challenge this view. Here we show that common features of societal marginalization and clustering emerge naturally during transitions in a co-evolutionary adaptive network model. This is achieved by explicitly considering the interplay between individual interaction and a dynamic network structure in behavioural selection. We exemplify this mechanism by simulating how smoking behaviour and the network structure get reconfigured by changing social norms. Our results are consistent with empirical findings: The prevalence of smoking was reduced, remaining smokers were preferentially connected among each other and formed increasingly marginalized clusters. We propose that self-amplifying feedbacks between individual behaviour and dynamic restructuring of the network are main drivers of the transition. This generative mechanism for co-evolution of individual behaviour and social network structure may apply to a wide range of examples beyond smoking.

Structure and activation of pro-activin A

PubMed Central

Wang, Xuelu; Fischer, Gerhard; Hyvönen, Marko

2016-01-01

Activins are growth factors with multiple roles in the development and homeostasis. Like all TGF-β family of growth factors, activins are synthesized as large precursors from which mature dimeric growth factors are released proteolytically. Here we have studied the activation of activin A and determined crystal structures of the unprocessed precursor and of the cleaved pro-mature complex. Replacing the natural furin cleavage site with a HRV 3C protease site, we show how the protein gains its bioactivity after proteolysis and is as active as the isolated mature domain. The complex remains associated in conditions used for biochemical analysis with a dissociation constant of 5 nM, but the pro-domain can be actively displaced from the complex by follistatin. Our high-resolution structures of pro-activin A share features seen in the pro-TGF-β1 and pro-BMP-9 structures, but reveal a new oligomeric arrangement, with a domain-swapped, cross-armed conformation for the protomers in the dimeric protein. PMID:27373274

Clustered marginalization of minorities during social transitions induced by co-evolution of behaviour and network structure.

PubMed

Schleussner, Carl-Friedrich; Donges, Jonathan F; Engemann, Denis A; Levermann, Anders

2016-08-11

Large-scale transitions in societies are associated with both individual behavioural change and restructuring of the social network. These two factors have often been considered independently, yet recent advances in social network research challenge this view. Here we show that common features of societal marginalization and clustering emerge naturally during transitions in a co-evolutionary adaptive network model. This is achieved by explicitly considering the interplay between individual interaction and a dynamic network structure in behavioural selection. We exemplify this mechanism by simulating how smoking behaviour and the network structure get reconfigured by changing social norms. Our results are consistent with empirical findings: The prevalence of smoking was reduced, remaining smokers were preferentially connected among each other and formed increasingly marginalized clusters. We propose that self-amplifying feedbacks between individual behaviour and dynamic restructuring of the network are main drivers of the transition. This generative mechanism for co-evolution of individual behaviour and social network structure may apply to a wide range of examples beyond smoking.

Limited plasticity in the phenotypic variance-covariance matrix for male advertisement calls in the black field cricket, Teleogryllus commodus

PubMed Central

Pitchers, W. R.; Brooks, R.; Jennions, M. D.; Tregenza, T.; Dworkin, I.; Hunt, J.

2013-01-01

Phenotypic integration and plasticity are central to our understanding of how complex phenotypic traits evolve. Evolutionary change in complex quantitative traits can be predicted using the multivariate breeders’ equation, but such predictions are only accurate if the matrices involved are stable over evolutionary time. Recent work, however, suggests that these matrices are temporally plastic, spatially variable and themselves evolvable. The data available on phenotypic variance-covariance matrix (P) stability is sparse, and largely focused on morphological traits. Here we compared P for the structure of the complex sexual advertisement call of six divergent allopatric populations of the Australian black field cricket, Teleogryllus commodus. We measured a subset of calls from wild-caught crickets from each of the populations and then a second subset after rearing crickets under common-garden conditions for three generations. In a second experiment, crickets from each population were reared in the laboratory on high- and low-nutrient diets and their calls recorded. In both experiments, we estimated P for call traits and used multiple methods to compare them statistically (Flury hierarchy, geometric subspace comparisons and random skewers). Despite considerable variation in means and variances of individual call traits, the structure of P was largely conserved among populations, across generations and between our rearing diets. Our finding that P remains largely stable, among populations and between environmental conditions, suggests that selection has preserved the structure of call traits in order that they can function as an integrated unit. PMID:23530814

Inner-outer interactions in the convective atmospheric boundary layer

NASA Astrophysics Data System (ADS)

Salesky, S.

2017-12-01

Recently, observational and numerical studies have revealed the existence of so-called large scale motions (LSMs) that populate the logarithmic layer of wall-bounded turbulent shear flows and modulate the amplitude and frequency of turbulence dynamics near the ground. Properties of LSMs are well understood in neutrally stratified flows over smooth and rough walls. However, the implications of previous studies for the convective atmospheric boundary layer (CBL) are not entirely clear, since the morphology of both small-scale and large-scale turbulent structures is known to be strongly affected by buoyancy [e.g. Salesky et al., Bound.-Layer Meteorol. 163:41-68 (2017)]. In the present study, inner-outer interactions in the CBL are investigated using a suite of large eddy simulations spanning neutral to highly convective conditions. Simulation results reveal that, as the atmosphere becomes increasingly unstable, the inclination angle of structures near the ground increases from 12-15° to nearly 90°. Furthermore, the scale separation between the inner and outer peaks in the premultiplied velocity spectra decreases until only a single peak remains (comparable in magnitude to the boundary layer depth). The extent to which the amplitude modulation of surface layer turbulence by outer layer structures changes with increasing instability will be considered, following the decoupling procedure proposed by Mathis et al. [J. Fluid Mech., vol 628, 311-337 (2009)]. Frequency modulation of surface layer turbulence also will be examined, following the wavelet analysis approach of Baars et al. [Exp. Fluids, 56:188, (2015)].

Ecohydrology of the coastal wetlands of Yucatan Peninsula are related with the submarine groundwater discharges?

NASA Astrophysics Data System (ADS)

Herrera Silveira, J. A.; Morales-Ojeda, S. M.; Medina Gomez, I.; Kantun Manzano, C.; Caamal Sosa, J.; Marino-Tapia, I.; Adame, F.; Teutli Hernandez, C.

2013-05-01

Submarine groundwater discharge (SGD) contributes significantly in the structure and function of coastal ecosystems favoring nutrients and salinity gradients, and with these spatial variability of wetland types and rates of primary production. However, the connectivity between SGD and coastal wetlands remains largely unexplored, especially in the tropics and karstic regions. On the other hand, coastal wetlands could represents exceptionally large carbon (C) stocks, whose protection and restoration can constitute an effective mitigation strategy for climate change. The Yucatán Peninsula is a low-relief carbonate platform and karst geology that permits fast rainfall infiltration, minimal surface flow, and high SGD., which is characterized by a continuum of freshwater wetland, mangroves, seagrasses meadows and coral reefs. Our studies around the Yucatan coastal wetlands related with the ecohydrology, suggest strong connectivity between SGD and mangrove and seagrasses structure and function. Some of the results indicate that SGD are the main source of nitrate and silicate favoring salinity gradient along the coastal lagoons and bays like estuaries. Mangrove forests show the best structural developments where a spring of groundwater is located, these types of mangroves are called locally "petenes" and show large C stocks. Respect to seagrasses, high shoots density has been observed at sites characterized by low salinity and peak nutrients concentration. Further research on groundwater flows among human activities on inland activities, coastal wetlands and marine ecosystems are required in order to develop management strategies for mitigation and adaptation to global climate change

Rolling hills on the core-mantle boundary

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Daoyuan; Helmberger, Don V.; Jackson, Jennifer M.

2014-07-17

Recent results suggest that an iron-rich oxide may have fractionally crystallized from a primordial magma ocean and settled on the core–mantle boundary (CMB). Based on experimental results, the presence of only a few percent of Fe-rich oxide could slow seismic waves down by several percent. This heavy layer can become highly undulating as predicted from dynamic modeling but can remain as a distinct structure with uniform velocity reductions. Here, we use the large USArray seismic network to search for such structures. Strong constraints on D" are provided by the core-phase SKS where it bifurcates, containing a short segment of P-wavemore » diffractions (P d) when crossing the CMB, called SKS d. Synthetics from models with moderate velocity drops (less than 10%) involving a layer with variable thickness, perhaps a composite of sharp small structures, with strong variation in thickness can explain both the observed SKS d waveforms and large scatter in differential times between SKKS and SKS. A smooth 3D image is obtained from inverting SKS d waveforms displaying rolling-hills with elongated dome-like structures sitting on the CMB. The most prominent one has an 80-km height, ~8° length, and ~4° width, thus adding still more structural complexity to the lower mantle. We suggest that these results can be explained by a dynamically-stabilized material containing small amounts (~5%) iron-rich (Mg,Fe)O providing a self-consistent physical interpretation.« less

DYNAMICS OF A PROMINENCE-HORN STRUCTURE DURING ITS EVAPORATION IN THE SOLAR CORONA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Bing; Chen, Yao; Fu, Jie

The physical connections among and formation mechanisms of various components of the prominence-horn cavity system remain elusive. Here we present observations of such a system, focusing on a section of the prominence that rises and separates gradually from the main body. This forms a configuration sufficiently simple to yield clues regarding the above issues. It is characterized by embedding horns, oscillations, and a gradual disappearance of the separated material. The prominence-horn structure exhibits a large-amplitude longitudinal oscillation with a period of ∼150 minutes and an amplitude of ∼30 Mm along the trajectory defined by the concave horn structure. The hornsmore » also experience a simultaneous transverse oscillation with a much smaller amplitude (∼3 Mm) and a shorter period (∼10–15 minutes), likely representative of a global mode of the large-scale magnetic structure. The gradual disappearance of the structure indicates that the horn, an observational manifestation of the field-aligned transition region separating the cool and dense prominence from the hot and tenuous corona, is formed due to the heating and diluting process of the central prominence mass; most previous studies suggested that it is the opposite process, i.e., the cooling and condensation of coronal plasmas, that formed the horn. This study also demonstrates how the prominence transports magnetic flux to the upper corona, a process essential for the gradual build-up of pre-eruption magnetic energy.« less

Abnormalities in the structural covariance of emotion regulation networks in major depressive disorder.

PubMed

Wu, Huawang; Sun, Hui; Wang, Chao; Yu, Lin; Li, Yilan; Peng, Hongjun; Lu, Xiaobing; Hu, Qingmao; Ning, Yuping; Jiang, Tianzi; Xu, Jinping; Wang, Jiaojian

2017-01-01

Major depressive disorder (MDD) is a common psychiatric disorder that is characterized by cognitive deficits and affective symptoms. To date, an increasing number of neuroimaging studies have focused on emotion regulation and have consistently shown that emotion dysregulation is one of the central features and underlying mechanisms of MDD. Although gray matter morphological abnormalities in regions within emotion regulation networks have been identified in MDD, the interactions and relationships between these gray matter structures remain largely unknown. Thus, in this study, we adopted a structural covariance method based on gray matter volume to investigate the brain morphological abnormalities within the emotion regulation networks in a large cohort of 65 MDD patients and 65 age- and gender-matched healthy controls. A permutation test with p < 0.05 was used to identify the significant changes in covariance connectivity strengths between MDD patients and healthy controls. The structural covariance analysis revealed an increased correlation strength of gray matter volume between the left angular gyrus and the left amygdala and between the right angular gyrus and the right amygdala, as well as a decreased correlation strength of the gray matter volume between the right angular gyrus and the posterior cingulate cortex in MDD. Our findings support the notion that emotion dysregulation is an underlying mechanism of MDD by revealing disrupted structural covariance patterns in the emotion regulation network. Copyright © 2016 Elsevier Ltd. All rights reserved.

Dynamic response analysis of a 24-story damped steel structure

NASA Astrophysics Data System (ADS)

Feng, Demin; Miyama, Takafumi

2017-10-01

In Japanese and Chinese building codes, a two-stage design philosophy, damage limitation (small earthquake, Level 1) and life safety (extreme large earthquake, Level 2), is adopted. It is very interesting to compare the design method of a damped structure based on the two building codes. In the Chinese code, in order to be consistent with the conventional seismic design method, the damped structure is also designed at the small earthquake level. The effect of damper systems is considered by the additional damping ratio concept. The design force will be obtained from the damped design spectrum considering the reduction due to the additional damping ratio. The additional damping ratio by the damper system is usually calculated by a time history analysis method at the small earthquake level. The velocity dependent type dampers such as viscous dampers can function well even in the small earthquake level. But, if steel damper is used, which usually remains elastic in the small earthquake, there will be no additional damping ratio achieved. On the other hand, a time history analysis is used in Japan both for small earthquake and extreme large earthquake level. The characteristics of damper system and ductility of the structure can be modelled well. An existing 24-story steel frame is modified to demonstrate the design process of the damped structure based on the two building codes. Viscous wall type damper and low yield steel panel dampers are studied as the damper system.

Spatial Distribution of a Large Herbivore Community at Waterholes: An Assessment of Its Stability over Years in Hwange National Park, Zimbabwe.

PubMed

Chamaillé-Jammes, Simon; Charbonnel, Anaïs; Dray, Stéphane; Madzikanda, Hillary; Fritz, Hervé

2016-01-01

The spatial structuring of populations or communities is an important driver of their functioning and their influence on ecosystems. Identifying the (in)stability of the spatial structure of populations is a first step towards understanding the underlying causes of these structures. Here we studied the relative importance of spatial vs. interannual variability in explaining the patterns of abundance of a large herbivore community (8 species) at waterholes in Hwange National Park (Zimbabwe). We analyzed census data collected over 13 years using multivariate methods. Our results showed that variability in the census data was mostly explained by the spatial structure of the community, as some waterholes had consistently greater herbivore abundance than others. Some temporal variability probably linked to Park-scale migration dependent on annual rainfall was noticeable, however. Once this was accounted for, little temporal variability remained to be explained, suggesting that other factors affecting herbivore abundance over time had a negligible effect at the scale of the study. The extent of spatial and temporal variability in census data was also measured for each species. This study could help in projecting the consequences of surface water management, and more generally presents a methodological framework to simultaneously address the relative importance of spatial vs. temporal effects in driving the distribution of organisms across landscapes.

Using local chromatin structure to improve CRISPR/Cas9 efficiency in zebrafish.

PubMed

Chen, Yunru; Zeng, Shiyang; Hu, Ruikun; Wang, Xiangxiu; Huang, Weilai; Liu, Jiangfang; Wang, Luying; Liu, Guifen; Cao, Ying; Zhang, Yong

2017-01-01

Although the CRISPR/Cas9 has been successfully applied in zebrafish, considerable variations in efficiency have been observed for different gRNAs. The workload and cost of zebrafish mutant screening is largely dependent on the mutation rate of injected embryos; therefore, selecting more effective gRNAs is especially important for zebrafish mutant construction. Besides the sequence features, local chromatin structures may have effects on CRISPR/Cas9 efficiency, which remain largely unexplored. In the only related study in zebrafish, nucleosome organization was not found to have an effect on CRISPR/Cas9 efficiency, which is inconsistent with recent studies in vitro and in mammalian cell lines. To understand the effects of local chromatin structure on CRISPR/Cas9 efficiency in zebrafish, we first determined that CRISPR/Cas9 introduced genome editing mainly before the dome stage. Based on this observation, we reanalyzed our published nucleosome organization profiles and generated chromatin accessibility profiles in the 256-cell and dome stages using ATAC-seq technology. Our study demonstrated that chromatin accessibility showed positive correlation with CRISPR/Cas9 efficiency, but we did not observe a clear correlation between nucleosome organization and CRISPR/Cas9 efficiency. We constructed an online database for zebrafish gRNA selection based on local chromatin structure features that could prove beneficial to zebrafish homozygous mutant construction via CRISPR/Cas9.

Spatial Distribution of a Large Herbivore Community at Waterholes: An Assessment of Its Stability over Years in Hwange National Park, Zimbabwe

PubMed Central

Chamaillé-Jammes, Simon; Charbonnel, Anaïs; Dray, Stéphane; Madzikanda, Hillary; Fritz, Hervé

2016-01-01

The spatial structuring of populations or communities is an important driver of their functioning and their influence on ecosystems. Identifying the (in)stability of the spatial structure of populations is a first step towards understanding the underlying causes of these structures. Here we studied the relative importance of spatial vs. interannual variability in explaining the patterns of abundance of a large herbivore community (8 species) at waterholes in Hwange National Park (Zimbabwe). We analyzed census data collected over 13 years using multivariate methods. Our results showed that variability in the census data was mostly explained by the spatial structure of the community, as some waterholes had consistently greater herbivore abundance than others. Some temporal variability probably linked to Park-scale migration dependent on annual rainfall was noticeable, however. Once this was accounted for, little temporal variability remained to be explained, suggesting that other factors affecting herbivore abundance over time had a negligible effect at the scale of the study. The extent of spatial and temporal variability in census data was also measured for each species. This study could help in projecting the consequences of surface water management, and more generally presents a methodological framework to simultaneously address the relative importance of spatial vs. temporal effects in driving the distribution of organisms across landscapes. PMID:27074044

Structure of rhenium-containing sodium borosilicate glass

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goel, Ashutosh; McCloy, John S.; Windisch, Charles F.

2013-03-01

A series of sodium borosilicate glasses were synthesized with increasing fractions of KReO4 or Re2O7, to 10000 ppm (1 mass%) target Re in glass, to assess the effects of large concentrations of rhenium on glass structure and to estimate the solubility of technetium, a radioactive component in typical low active waste nuclear waste glasses. Magic angle spinning nuclear magnetic resonance (MAS-NMR), Fourier transform infrared (FTIR) spectroscopy, and Raman spectroscopy were performed to characterize the glasses as a function of Re source additions. In general, silicon was found coordinated in a mixture of Q2 and Q3 structural units, while Al wasmore » 4-coordinated and B was largely 3-coordinate and partially 4-coordinated. The rhenium source did not appear to have significant effects on the glass structure. Thus, at the up to the concentrations that remain in dissolved in glass, ~3000 ppm Re by mass maximum. , the Re appeared to be neither a glass-former nor a strong glass modifier., Rhenium likely exists in isolated ReO4- anions in the interstices of the glass network, as evidenced by the polarized Raman spectrum of the Re glass in the absence of sulfate. Analogous to SO42-¬ in similar glasses, ReO4- is likely a network modifier and forms alkali salt phases on the surface and in the bulk glass above solubility.« less

Nonlinear pulse propagation in one-dimensional metal-dielectric multilayer stacks: ultrawide bandwidth optical limiting.

PubMed

Scalora, Michael; Mattiucci, Nadia; D'Aguanno, Giuseppe; Larciprete, MariaCristina; Bloemer, Mark J

2006-01-01

We numerically study the nonlinear optical properties of metal-dielectric photonic band gap structures in the pulsed regime. We exploit the high chi3 of copper metal to induce nonlinear effects such as broadband optical limiting, self-phase modulation, and unusual spectral narrowing of high intensity pulses. We show that in a single pass through a typical, chirped multilayer stack nonlinear transmittance and peak powers can be reduced by nearly two orders of magnitude compared to low light intensity levels across the entire visible range. Chirping dielectric layer thickness dramatically improves the linear transmittance through the stack and achieves large fields inside the copper to access the large nonlinearity. At the same time, the linear properties of the stack block most of the remaining electromagnetic spectrum.

Ecosystem Services Connect Environmental Change to Human Health Outcomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bayles, Brett R.; Brauman, Kate A.; Adkins, Joshua N.

Global environmental change, driven in large part by human activities, profoundly impacts the structure and functioning of Earth’s ecosystems (Millennium Ecosystem Assessment 2005). We are beginning to push beyond planetary boundaries (Steffan et al. 2015), and the consequences for human health remain largely unknown (Myers et al. 2013). Growing evidence suggests that ecological transformations can dramatically affect human health in ways that are both obvious and obscure (Myers and Patz 2009; Myers et al. 2013). The framework of ecosystem services, designed to evaluate the benefits that people derive from ecosystem products and processes, provides a compelling framework for integrating themore » many factors that influence the human health response to global change, as well as for integrating health impacts into broader analyses of the impacts of this change« less

Turbulent Dynamics of Epithelial Cell Cultures

NASA Astrophysics Data System (ADS)

Blanch-Mercader, C.; Yashunsky, V.; Garcia, S.; Duclos, G.; Giomi, L.; Silberzan, P.

2018-05-01

We investigate the large length and long time scales collective flows and structural rearrangements within in vitro human bronchial epithelial cell (HBEC) cultures. Activity-driven collective flows result in ensembles of vortices randomly positioned in space. By analyzing a large population of vortices, we show that their area follows an exponential law with a constant mean value and their rotational frequency is size independent, both being characteristic features of the chaotic dynamics of active nematic suspensions. Indeed, we find that HBECs self-organize in nematic domains of several cell lengths. Nematic defects are found at the interface between domains with a total number that remains constant due to the dynamical balance of nucleation and annihilation events. The mean velocity fields in the vicinity of defects are well described by a hydrodynamic theory of extensile active nematics.

IMG-ABC: An Atlas of Biosynthetic Gene Clusters to Fuel the Discovery of Novel Secondary Metabolites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, I-Min; Chu, Ken; Ratner, Anna

2014-10-28

In the discovery of secondary metabolites (SMs), large-scale analysis of sequence data is a promising exploration path that remains largely underutilized due to the lack of relevant computational resources. We present IMG-ABC (https://img.jgi.doe.gov/abc/) -- An Atlas of Biosynthetic gene Clusters within the Integrated Microbial Genomes (IMG) system1. IMG-ABC is a rich repository of both validated and predicted biosynthetic clusters (BCs) in cultured isolates, single-cells and metagenomes linked with the SM chemicals they produce and enhanced with focused analysis tools within IMG. The underlying scalable framework enables traversal of phylogenetic dark matter and chemical structure space -- serving as a doorwaymore » to a new era in the discovery of novel molecules.« less

Structural and Functional Loss in Restored Wetland Ecosystems

PubMed Central

Moreno-Mateos, David; Power, Mary E.; Comín, Francisco A.; Yockteng, Roxana

2012-01-01

Wetlands are among the most productive and economically valuable ecosystems in the world. However, because of human activities, over half of the wetland ecosystems existing in North America, Europe, Australia, and China in the early 20th century have been lost. Ecological restoration to recover critical ecosystem services has been widely attempted, but the degree of actual recovery of ecosystem functioning and structure from these efforts remains uncertain. Our results from a meta-analysis of 621 wetland sites from throughout the world show that even a century after restoration efforts, biological structure (driven mostly by plant assemblages), and biogeochemical functioning (driven primarily by the storage of carbon in wetland soils), remained on average 26% and 23% lower, respectively, than in reference sites. Either recovery has been very slow, or postdisturbance systems have moved towards alternative states that differ from reference conditions. We also found significant effects of environmental settings on the rate and degree of recovery. Large wetland areas (>100 ha) and wetlands restored in warm (temperate and tropical) climates recovered more rapidly than smaller wetlands and wetlands restored in cold climates. Also, wetlands experiencing more (riverine and tidal) hydrologic exchange recovered more rapidly than depressional wetlands. Restoration performance is limited: current restoration practice fails to recover original levels of wetland ecosystem functions, even after many decades. If restoration as currently practiced is used to justify further degradation, global loss of wetland ecosystem function and structure will spread. PMID:22291572

Structure-Activity Analysis of Biased Agonism at the Human Adenosine A3 Receptor

PubMed Central

Baltos, Jo-Anne; Paoletta, Silvia; Nguyen, Anh T. N.; Gregory, Karen J.; Tosh, Dilip K.; Christopoulos, Arthur; Jacobson, Kenneth A.

2016-01-01

Biased agonism at G protein–coupled receptors (GPCRs) has significant implications for current drug discovery, but molecular determinants that govern ligand bias remain largely unknown. The adenosine A3 GPCR (A3AR) is a potential therapeutic target for various conditions, including cancer, inflammation, and ischemia, but for which biased agonism remains largely unexplored. We now report the generation of bias “fingerprints” for prototypical ribose containing A3AR agonists and rigidified (N)-methanocarba 5′-N-methyluronamide nucleoside derivatives with regard to their ability to mediate different signaling pathways. Relative to the reference prototypical agonist IB-MECA, (N)-methanocarba 5′-N-methyluronamide nucleoside derivatives with significant N6 or C2 modifications, including elongated aryl-ethynyl groups, exhibited biased agonism. Significant positive correlation was observed between the C2 substituent length (in Å) and bias toward cell survival. Molecular modeling suggests that extended C2 substituents on (N)-methanocarba 5′-N-methyluronamide nucleosides promote a progressive outward shift of the A3AR transmembrane domain 2, which may contribute to the subset of A3AR conformations stabilized on biased agonist binding. PMID:27136943

Elevated correlations in neuronal ensembles of mouse auditory cortex following parturition.

PubMed

Rothschild, Gideon; Cohen, Lior; Mizrahi, Adi; Nelken, Israel

2013-07-31

The auditory cortex is malleable by experience. Previous studies of auditory plasticity have described experience-dependent changes in response profiles of single neurons or changes in global tonotopic organization. However, experience-dependent changes in the dynamics of local neural populations have remained unexplored. In this study, we examined the influence of a dramatic yet natural experience in the life of female mice, giving birth and becoming a mother on single neurons and neuronal ensembles in the primary auditory cortex (A1). Using in vivo two-photon calcium imaging and electrophysiological recordings from layer 2/3 in A1 of mothers and age-matched virgin mice, we monitored changes in the responses to a set of artificial and natural sounds. Population dynamics underwent large changes as measured by pairwise and higher-order correlations, with noise correlations increasing as much as twofold in lactating mothers. Concomitantly, changes in response properties of single neurons were modest and selective. Remarkably, despite the large changes in correlations, information about stimulus identity remained essentially the same in the two groups. Our results demonstrate changes in the correlation structure of neuronal activity as a result of a natural life event.

Nickel: The time-reversal symmetry conserving partner of iron on a chalcogenide topological insulator

NASA Astrophysics Data System (ADS)

Vondráček, M.; Cornils, L.; Minár, J.; Warmuth, J.; Michiardi, M.; Piamonteze, C.; Barreto, L.; Miwa, J. A.; Bianchi, M.; Hofmann, Ph.; Zhou, L.; Kamlapure, A.; Khajetoorians, A. A.; Wiesendanger, R.; Mi, J.-L.; Iversen, B.-B.; Mankovsky, S.; Borek, St.; Ebert, H.; Schüler, M.; Wehling, T.; Wiebe, J.; Honolka, J.

2016-10-01

We report on the quenching of single Ni adatom moments on Te-terminated Bi2Te2Se and Bi2Te3 topological insulator surfaces. The effect is noted as a missing x-ray magnetic circular dichroism for resonant L3 ,2 transitions into partially filled Ni 3 d states of theory-derived occupancy nd=9.2 . On the basis of a comparative study of Ni and Fe using scanning tunneling microscopy and ab initio calculations, we are able to relate the element specific moment formation to a local Stoner criterion. Our theory shows that while Fe adatoms form large spin moments of ms=2.54 μB with out-of-plane anisotropy due to a sufficiently large density of states at the Fermi energy, Ni remains well below an effective Stoner threshold for local moment formation. With the Fermi level remaining in the bulk band gap after adatom deposition, nonmagnetic Ni and preferentially out-of-plane oriented magnetic Fe with similar structural properties on Bi2Te2Se surfaces constitute a perfect platform to study the off-on effects of time-reversal symmetry breaking on topological surface states.

Reasons for measles cases not being vaccinated with MMR: investigation into parents' and carers' views following a large measles outbreak.

PubMed

McHale, P; Keenan, A; Ghebrehewet, S

2016-03-01

Uptake rates for the combined measles, mumps and rubella (MMR) vaccine have been below the required 95% in the UK since a retracted and discredited article linking the MMR vaccine with autism and inflammatory bowel disease was released in 1998. This study undertook semi-structured telephone interviews among parents or carers of 47 unvaccinated measles cases who were aged between 13 months and 9 years, during a large measles outbreak in Merseyside. Results showed that concerns over the specific links with autism remain an important cause of refusal to vaccinate, with over half of respondents stating this as a reason. A quarter stated child illness during scheduled vaccination time, while other reasons included general safety concerns and access issues. Over half of respondents felt that more information or a discussion with a health professional would help the decision-making process, while a third stated improved access. There was clear support for vaccination among respondents when asked about current opinions regarding MMR vaccine. The findings support the hypothesis that safety concerns remain a major barrier to MMR vaccination, and also support previous evidence that experience of measles is an important determinant in the decision to vaccinate.

Arterial extracellular matrix: a mechanobiological study of the contributions and interactions of elastin and collagen.

PubMed

Chow, Ming-Jay; Turcotte, Raphaël; Lin, Charles P; Zhang, Yanhang

2014-06-17

The complex network structure of elastin and collagen extracellular matrix (ECM) forms the primary load bearing components in the arterial wall. The structural and mechanobiological interactions between elastin and collagen are important for properly functioning arteries. Here, we examined the elastin and collagen organization, realignment, and recruitment by coupling mechanical loading and multiphoton imaging. Two-photon excitation fluorescence and second harmonic generation methods were performed with a multiphoton video-rate microscope to capture real time changes to the elastin and collagen structure during biaxial deformation. Enzymatic removal of elastin was performed to assess the structural changes of the remaining collagen structure. Quantitative analysis of the structural changes to elastin and collagen was made using a combination of two-dimensional fast Fourier transform and fractal analysis, which allows for a more complete understanding of structural changes. Our study provides new quantitative evidence, to our knowledge on the sequential engagement of different arterial ECM components in response to mechanical loading. The adventitial collagen exists as large wavy bundles of fibers that exhibit fiber engagement after 20% strain. The medial collagen is engaged throughout the stretching process, and prominent elastic fiber engagement is observed up to 20% strain after which the engagement plateaus. The fiber orientation distribution functions show remarkably different changes in the ECM structure in response to mechanical loading. The medial collagen shows an evident preferred circumferential distribution, however the fiber families of adventitial collagen are obscured by their waviness at no or low mechanical strains. Collagen fibers in both layers exhibit significant realignment in response to unequal biaxial loading. The elastic fibers are much more uniformly distributed and remained relatively unchanged due to loading. Removal of elastin produces similar structural changes in collagen as mechanical loading. Our study suggests that the elastic fibers are under tension and impart an intrinsic compressive stress on the collagen. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Evaluating and learning from RNA pseudotorsional space: quantitative validation of a reduced representation for RNA structure.

PubMed

Wadley, Leven M; Keating, Kevin S; Duarte, Carlos M; Pyle, Anna Marie

2007-09-28

Quantitatively describing RNA structure and conformational elements remains a formidable problem. Seven standard torsion angles and the sugar pucker are necessary to characterize the conformation of an RNA nucleotide completely. Progress has been made toward understanding the discrete nature of RNA structure, but classifying simple and ubiquitous structural elements such as helices and motifs remains a difficult task. One approach for describing RNA structure in a simple, mathematically consistent, and computationally accessible manner involves the invocation of two pseudotorsions, eta (C4'(n-1), P(n), C4'(n), P(n+1)) and theta (P(n), C4'(n), P(n+1), C4'(n+1)), which can be used to describe RNA conformation in much the same way that varphi and psi are used to describe backbone configuration of proteins. Here, we conduct an exploration and statistical evaluation of pseudotorsional space and of the Ramachandran-like eta-theta plot. We show that, through the rigorous quantitative analysis of the eta-theta plot, the pseudotorsional descriptors eta and theta, together with sugar pucker, are sufficient to describe RNA backbone conformation fully in most cases. These descriptors are also shown to contain considerable information about nucleotide base conformation, revealing a previously uncharacterized interplay between backbone and base orientation. A window function analysis is used to discern statistically relevant regions of density in the eta-theta scatter plot and then nucleotides in colocalized clusters in the eta-theta plane are shown to have similar 3-D structures through RMSD analysis of the RNA structural constituents. We find that major clusters in the eta-theta plot are few, underscoring the discrete nature of RNA backbone conformation. Like the Ramachandran plot, the eta-theta plot is a valuable system for conceptualizing biomolecular conformation, it is a useful tool for analyzing RNA tertiary structures, and it is a vital component of new approaches for solving the 3-D structures of large RNA molecules and RNA assemblies.

Insights into eukaryotic DNA priming from the structure and functional interactions of the 4Fe-4S cluster domain of human DNA primase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vaithiyalingam, Sivaraja; Warren, Eric M.; Eichman, Brandt F.

2010-10-19

DNA replication requires priming of DNA templates by enzymes known as primases. Although DNA primase structures are available from archaea and bacteria, the mechanism of DNA priming in higher eukaryotes remains poorly understood in large part due to the absence of the structure of the unique, highly conserved C-terminal regulatory domain of the large subunit (p58C). Here, we present the structure of this domain determined to 1.7-{angstrom} resolution by X-ray crystallography. The p58C structure reveals a novel arrangement of an evolutionarily conserved 4Fe-4S cluster buried deeply within the protein core and is not similar to any known protein structure. Analysismore » of the binding of DNA to p58C by fluorescence anisotropy measurements revealed a strong preference for ss/dsDNA junction substrates. This approach was combined with site-directed mutagenesis to confirm that the binding of DNA occurs to a distinctively basic surface on p58C. A specific interaction of p58C with the C-terminal domain of the intermediate subunit of replication protein A (RPA32C) was identified and characterized by isothermal titration calorimetry and NMR. Restraints from NMR experiments were used to drive computational docking of the two domains and generate a model of the p58C-RPA32C complex. Together, our results explain functional defects in human DNA primase mutants and provide insights into primosome loading on RPA-coated ssDNA and regulation of primase activity.« less

Disappearance of Anisotropic Intermittency in Large-amplitude MHD Turbulence and Its Comparison with Small-amplitude MHD Turbulence

NASA Astrophysics Data System (ADS)

Yang, Liping; Zhang, Lei; He, Jiansen; Tu, Chuanyi; Li, Shengtai; Wang, Xin; Wang, Linghua

2018-03-01

Multi-order structure functions in the solar wind are reported to display a monofractal scaling when sampled parallel to the local magnetic field and a multifractal scaling when measured perpendicularly. Whether and to what extent will the scaling anisotropy be weakened by the enhancement of turbulence amplitude relative to the background magnetic strength? In this study, based on two runs of the magnetohydrodynamic (MHD) turbulence simulation with different relative levels of turbulence amplitude, we investigate and compare the scaling of multi-order magnetic structure functions and magnetic probability distribution functions (PDFs) as well as their dependence on the direction of the local field. The numerical results show that for the case of large-amplitude MHD turbulence, the multi-order structure functions display a multifractal scaling at all angles to the local magnetic field, with PDFs deviating significantly from the Gaussian distribution and a flatness larger than 3 at all angles. In contrast, for the case of small-amplitude MHD turbulence, the multi-order structure functions and PDFs have different features in the quasi-parallel and quasi-perpendicular directions: a monofractal scaling and Gaussian-like distribution in the former, and a conversion of a monofractal scaling and Gaussian-like distribution into a multifractal scaling and non-Gaussian tail distribution in the latter. These results hint that when intermittencies are abundant and intense, the multifractal scaling in the structure functions can appear even if it is in the quasi-parallel direction; otherwise, the monofractal scaling in the structure functions remains even if it is in the quasi-perpendicular direction.

Alignments of Dark Matter Halos with Large-scale Tidal Fields: Mass and Redshift Dependence

NASA Astrophysics Data System (ADS)

Chen, Sijie; Wang, Huiyuan; Mo, H. J.; Shi, Jingjing

2016-07-01

Large-scale tidal fields estimated directly from the distribution of dark matter halos are used to investigate how halo shapes and spin vectors are aligned with the cosmic web. The major, intermediate, and minor axes of halos are aligned with the corresponding tidal axes, and halo spin axes tend to be parallel with the intermediate axes and perpendicular to the major axes of the tidal field. The strengths of these alignments generally increase with halo mass and redshift, but the dependence is only on the peak height, ν \\equiv {δ }{{c}}/σ ({M}{{h}},z). The scaling relations of the alignment strengths with the value of ν indicate that the alignment strengths remain roughly constant when the structures within which the halos reside are still in a quasi-linear regime, but decreases as nonlinear evolution becomes more important. We also calculate the alignments in projection so that our results can be compared directly with observations. Finally, we investigate the alignments of tidal tensors on large scales, and use the results to understand alignments of halo pairs separated at various distances. Our results suggest that the coherent structure of the tidal field is the underlying reason for the alignments of halos and galaxies seen in numerical simulations and in observations.

HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks

PubMed Central

Azad, Ariful; Ouzounis, Christos A; Kyrpides, Nikos C; Buluç, Aydin

2018-01-01

Abstract Biological networks capture structural or functional properties of relevant entities such as molecules, proteins or genes. Characteristic examples are gene expression networks or protein–protein interaction networks, which hold information about functional affinities or structural similarities. Such networks have been expanding in size due to increasing scale and abundance of biological data. While various clustering algorithms have been proposed to find highly connected regions, Markov Clustering (MCL) has been one of the most successful approaches to cluster sequence similarity or expression networks. Despite its popularity, MCL’s scalability to cluster large datasets still remains a bottleneck due to high running times and memory demands. Here, we present High-performance MCL (HipMCL), a parallel implementation of the original MCL algorithm that can run on distributed-memory computers. We show that HipMCL can efficiently utilize 2000 compute nodes and cluster a network of ∼70 million nodes with ∼68 billion edges in ∼2.4 h. By exploiting distributed-memory environments, HipMCL clusters large-scale networks several orders of magnitude faster than MCL and enables clustering of even bigger networks. HipMCL is based on MPI and OpenMP and is freely available under a modified BSD license. PMID:29315405

Structural connectivity of the developing human amygdala.

PubMed

Saygin, Zeynep M; Osher, David E; Koldewyn, Kami; Martin, Rebecca E; Finn, Amy; Saxe, Rebecca; Gabrieli, John D E; Sheridan, Margaret

2015-01-01

A large corpus of research suggests that there are changes in the manner and degree to which the amygdala supports cognitive and emotional function across development. One possible basis for these developmental differences could be the maturation of amygdalar connections with the rest of the brain. Recent functional connectivity studies support this conclusion, but the structural connectivity of the developing amygdala and its different nuclei remains largely unstudied. We examined age related changes in the DWI connectivity fingerprints of the amygdala to the rest of the brain in 166 individuals of ages 5-30. We also developed a model to predict age based on individual-subject amygdala connectivity, and identified the connections that were most predictive of age. Finally, we segmented the amygdala into its four main nucleus groups, and examined the developmental changes in connectivity for each nucleus. We observed that with age, amygdalar connectivity becomes increasingly sparse and localized. Age related changes were largely localized to the subregions of the amygdala that are implicated in social inference and contextual memory (the basal and lateral nuclei). The central nucleus' connectivity also showed differences with age but these differences affected fewer target regions than the basal and lateral nuclei. The medial nucleus did not exhibit any age related changes. These findings demonstrate increasing specificity in the connectivity patterns of amygdalar nuclei across age.

Partially acoustic dark matter, interacting dark radiation, and large scale structure

NASA Astrophysics Data System (ADS)

Chacko, Zackaria; Cui, Yanou; Hong, Sungwoo; Okui, Takemichi; Tsai, Yuhsinz

2016-12-01

The standard paradigm of collisionless cold dark matter is in tension with measurements on large scales. In particular, the best fit values of the Hubble rate H 0 and the matter density perturbation σ 8 inferred from the cosmic microwave background seem inconsistent with the results from direct measurements. We show that both problems can be solved in a framework in which dark matter consists of two distinct components, a dominant component and a subdominant component. The primary component is cold and collisionless. The secondary component is also cold, but interacts strongly with dark radiation, which itself forms a tightly coupled fluid. The growth of density perturbations in the subdominant component is inhibited by dark acoustic oscillations due to its coupling to the dark radiation, solving the σ 8 problem, while the presence of tightly coupled dark radiation ameliorates the H 0 problem. The subdominant component of dark matter and dark radiation continue to remain in thermal equilibrium until late times, inhibiting the formation of a dark disk. We present an example of a simple model that naturally realizes this scenario in which both constituents of dark matter are thermal WIMPs. Our scenario can be tested by future stage-IV experiments designed to probe the CMB and large scale structure.

HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks

DOE PAGES

Azad, Ariful; Pavlopoulos, Georgios A.; Ouzounis, Christos A.; ...

2018-01-05

Biological networks capture structural or functional properties of relevant entities such as molecules, proteins or genes. Characteristic examples are gene expression networks or protein–protein interaction networks, which hold information about functional affinities or structural similarities. Such networks have been expanding in size due to increasing scale and abundance of biological data. While various clustering algorithms have been proposed to find highly connected regions, Markov Clustering (MCL) has been one of the most successful approaches to cluster sequence similarity or expression networks. Despite its popularity, MCL’s scalability to cluster large datasets still remains a bottleneck due to high running times andmore » memory demands. In this paper, we present High-performance MCL (HipMCL), a parallel implementation of the original MCL algorithm that can run on distributed-memory computers. We show that HipMCL can efficiently utilize 2000 compute nodes and cluster a network of ~70 million nodes with ~68 billion edges in ~2.4 h. By exploiting distributed-memory environments, HipMCL clusters large-scale networks several orders of magnitude faster than MCL and enables clustering of even bigger networks. Finally, HipMCL is based on MPI and OpenMP and is freely available under a modified BSD license.« less

HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Azad, Ariful; Pavlopoulos, Georgios A.; Ouzounis, Christos A.

Biological networks capture structural or functional properties of relevant entities such as molecules, proteins or genes. Characteristic examples are gene expression networks or protein–protein interaction networks, which hold information about functional affinities or structural similarities. Such networks have been expanding in size due to increasing scale and abundance of biological data. While various clustering algorithms have been proposed to find highly connected regions, Markov Clustering (MCL) has been one of the most successful approaches to cluster sequence similarity or expression networks. Despite its popularity, MCL’s scalability to cluster large datasets still remains a bottleneck due to high running times andmore » memory demands. In this paper, we present High-performance MCL (HipMCL), a parallel implementation of the original MCL algorithm that can run on distributed-memory computers. We show that HipMCL can efficiently utilize 2000 compute nodes and cluster a network of ~70 million nodes with ~68 billion edges in ~2.4 h. By exploiting distributed-memory environments, HipMCL clusters large-scale networks several orders of magnitude faster than MCL and enables clustering of even bigger networks. Finally, HipMCL is based on MPI and OpenMP and is freely available under a modified BSD license.« less

Partially acoustic dark matter, interacting dark radiation, and large scale structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chacko, Zackaria; Cui, Yanou; Hong, Sungwoo

The standard paradigm of collisionless cold dark matter is in tension with measurements on large scales. In particular, the best fit values of the Hubble rate H 0 and the matter density perturbation σ 8 inferred from the cosmic microwave background seem inconsistent with the results from direct measurements. We show that both problems can be solved in a framework in which dark matter consists of two distinct components, a dominant component and a subdominant component. The primary component is cold and collisionless. The secondary component is also cold, but interacts strongly with dark radiation, which itself forms a tightlymore » coupled fluid. The growth of density perturbations in the subdominant component is inhibited by dark acoustic oscillations due to its coupling to the dark radiation, solving the σ 8 problem, while the presence of tightly coupled dark radiation ameliorates the H 0 problem. The subdominant component of dark matter and dark radiation continue to remain in thermal equilibrium until late times, inhibiting the formation of a dark disk. We present an example of a simple model that naturally realizes this scenario in which both constituents of dark matter are thermal WIMPs. Our scenario can be tested by future stage-IV experiments designed to probe the CMB and large scale structure.« less

Partially acoustic dark matter, interacting dark radiation, and large scale structure

DOE PAGES

Chacko, Zackaria; Cui, Yanou; Hong, Sungwoo; ...

2016-12-21

The standard paradigm of collisionless cold dark matter is in tension with measurements on large scales. In particular, the best fit values of the Hubble rate H 0 and the matter density perturbation σ 8 inferred from the cosmic microwave background seem inconsistent with the results from direct measurements. We show that both problems can be solved in a framework in which dark matter consists of two distinct components, a dominant component and a subdominant component. The primary component is cold and collisionless. The secondary component is also cold, but interacts strongly with dark radiation, which itself forms a tightlymore » coupled fluid. The growth of density perturbations in the subdominant component is inhibited by dark acoustic oscillations due to its coupling to the dark radiation, solving the σ 8 problem, while the presence of tightly coupled dark radiation ameliorates the H 0 problem. The subdominant component of dark matter and dark radiation continue to remain in thermal equilibrium until late times, inhibiting the formation of a dark disk. We present an example of a simple model that naturally realizes this scenario in which both constituents of dark matter are thermal WIMPs. Our scenario can be tested by future stage-IV experiments designed to probe the CMB and large scale structure.« less

Exact coherent structures and chaotic dynamics in a model of cardiac tissue

DOE Office of Scientific and Technical Information (OSTI.GOV)

Byrne, Greg; Marcotte, Christopher D.; Grigoriev, Roman O., E-mail: roman.grigoriev@physics.gatech.edu

Unstable nonchaotic solutions embedded in the chaotic attractor can provide significant new insight into chaotic dynamics of both low- and high-dimensional systems. In particular, in turbulent fluid flows, such unstable solutions are referred to as exact coherent structures (ECS) and play an important role in both initiating and sustaining turbulence. The nature of ECS and their role in organizing spatiotemporally chaotic dynamics, however, is reasonably well understood only for systems on relatively small spatial domains lacking continuous Euclidean symmetries. Construction of ECS on large domains and in the presence of continuous translational and/or rotational symmetries remains a challenge. This ismore » especially true for models of excitable media which display spiral turbulence and for which the standard approach to computing ECS completely breaks down. This paper uses the Karma model of cardiac tissue to illustrate a potential approach that could allow computing a new class of ECS on large domains of arbitrary shape by decomposing them into a patchwork of solutions on smaller domains, or tiles, which retain Euclidean symmetries locally.« less

Improved accuracy for finite element structural analysis via a new integrated force method

NASA Technical Reports Server (NTRS)

Patnaik, Surya N.; Hopkins, Dale A.; Aiello, Robert A.; Berke, Laszlo

1992-01-01

A comparative study was carried out to determine the accuracy of finite element analyses based on the stiffness method, a mixed method, and the new integrated force and dual integrated force methods. The numerical results were obtained with the following software: MSC/NASTRAN and ASKA for the stiffness method; an MHOST implementation method for the mixed method; and GIFT for the integrated force methods. The results indicate that on an overall basis, the stiffness and mixed methods present some limitations. The stiffness method generally requires a large number of elements in the model to achieve acceptable accuracy. The MHOST method tends to achieve a higher degree of accuracy for course models than does the stiffness method implemented by MSC/NASTRAN and ASKA. The two integrated force methods, which bestow simultaneous emphasis on stress equilibrium and strain compatibility, yield accurate solutions with fewer elements in a model. The full potential of these new integrated force methods remains largely unexploited, and they hold the promise of spawning new finite element structural analysis tools.

Radio structure effects on the optical and radio representations of the ICRF

NASA Astrophysics Data System (ADS)

Andrei, A. H.; da Silva Neto, D. N.; Assafin, M.; Vieira Martins, R.

Silva Neto et al. (2002) show that comparing the ICRF Ext.1 sources standard radio position (Ma et al. 1998) against their optical counterpart position (Zacharias et al. 1999, Monet et al., 1998), a systematic pattern appears, which depends on the radio structure index (Fey and Charlot, 2000). The optical to radio offsets produce a distribution suggestive of a coincidence of the optical and radio centroids worse for the radio extended than for the radio compact sources. On average, the coincidence between the optical and radio centroids is found 7.9±1.1 mas smaller for the compact than for the extended sources. Such an effect is reasonably large, and certainly much too large to be due to errors on the VLBI radio position. On the other hand, it is too small to be accounted to the errors on the optical position, which moreover should be independent from the radio stucture. Thus, other than a true pattern of centroids non-coincidence, the remaining explanation is of a hazard result. This paper summarizes the several statistical tests used to discard the hazard explanation.

Overview on Biological Activities and Molecular Characteristics of Sulfated Polysaccharides from Marine Green Algae in Recent Years

PubMed Central

Wang, Lingchong; Wang, Xiangyu; Wu, Hao; Liu, Rui

2014-01-01

Among the three main divisions of marine macroalgae (Chlorophyta, Phaeophyta and Rhodophyta), marine green algae are valuable sources of structurally diverse bioactive compounds and remain largely unexploited in nutraceutical and pharmaceutical areas. Recently, a great deal of interest has been developed to isolate novel sulfated polysaccharides (SPs) from marine green algae because of their numerous health beneficial effects. Green seaweeds are known to synthesize large quantities of SPs and are well established sources of these particularly interesting molecules such as ulvans from Ulva and Enteromorpha, sulfated rhamnans from Monostroma, sulfated arabinogalactans from Codium, sulfated galacotans from Caulerpa, and some special sulfated mannans from different species. These SPs exhibit many beneficial biological activities such as anticoagulant, antiviral, antioxidative, antitumor, immunomodulating, antihyperlipidemic and antihepatotoxic activities. Therefore, marine algae derived SPs have great potential for further development as healthy food and medical products. The present review focuses on SPs derived from marine green algae and presents an overview of the recent progress of determinations of their structural types and biological activities, especially their potential health benefits. PMID:25257786

Solid-state supercapacitors with rationally designed heterogeneous electrodes fabricated by large area spray processing for wearable energy storage applications.

PubMed

Huang, Chun; Zhang, Jin; Young, Neil P; Snaith, Henry J; Grant, Patrick S

2016-05-10

Supercapacitors are in demand for short-term electrical charge and discharge applications. Unlike conventional supercapacitors, solid-state versions have no liquid electrolyte and do not require robust, rigid packaging for containment. Consequently they can be thinner, lighter and more flexible. However, solid-state supercapacitors suffer from lower power density and where new materials have been developed to improve performance, there remains a gap between promising laboratory results that usually require nano-structured materials and fine-scale processing approaches, and current manufacturing technology that operates at large scale. We demonstrate a new, scalable capability to produce discrete, multi-layered electrodes with a different material and/or morphology in each layer, and where each layer plays a different, critical role in enhancing the dynamics of charge/discharge. This layered structure allows efficient utilisation of each material and enables conservative use of hard-to-obtain materials. The layered electrode shows amongst the highest combinations of energy and power densities for solid-state supercapacitors. Our functional design and spray manufacturing approach to heterogeneous electrodes provide a new way forward for improved energy storage devices.

Large heterogeneities in comet 67P as revealed by active pits from sinkhole collapse.

PubMed

Vincent, Jean-Baptiste; Bodewits, Dennis; Besse, Sébastien; Sierks, Holger; Barbieri, Cesare; Lamy, Philippe; Rodrigo, Rafael; Koschny, Detlef; Rickman, Hans; Keller, Horst Uwe; Agarwal, Jessica; A'Hearn, Michael F; Auger, Anne-Thérèse; Barucci, M Antonella; Bertaux, Jean-Loup; Bertini, Ivano; Capanna, Claire; Cremonese, Gabriele; Da Deppo, Vania; Davidsson, Björn; Debei, Stefano; De Cecco, Mariolino; El-Maarry, Mohamed Ramy; Ferri, Francesca; Fornasier, Sonia; Fulle, Marco; Gaskell, Robert; Giacomini, Lorenza; Groussin, Olivier; Guilbert-Lepoutre, Aurélie; Gutierrez-Marques, P; Gutiérrez, Pedro J; Güttler, Carsten; Hoekzema, Nick; Höfner, Sebastian; Hviid, Stubbe F; Ip, Wing-Huen; Jorda, Laurent; Knollenberg, Jörg; Kovacs, Gabor; Kramm, Rainer; Kührt, Ekkehard; Küppers, Michael; La Forgia, Fiorangela; Lara, Luisa M; Lazzarin, Monica; Lee, Vicky; Leyrat, Cédric; Lin, Zhong-Yi; Lopez Moreno, Josè J; Lowry, Stephen; Magrin, Sara; Maquet, Lucie; Marchi, Simone; Marzari, Francesco; Massironi, Matteo; Michalik, Harald; Moissl, Richard; Mottola, Stefano; Naletto, Giampiero; Oklay, Nilda; Pajola, Maurizio; Preusker, Frank; Scholten, Frank; Thomas, Nicolas; Toth, Imre; Tubiana, Cecilia

2015-07-02

Pits have been observed on many cometary nuclei mapped by spacecraft. It has been argued that cometary pits are a signature of endogenic activity, rather than impact craters such as those on planetary and asteroid surfaces. Impact experiments and models cannot reproduce the shapes of most of the observed cometary pits, and the predicted collision rates imply that few of the pits are related to impacts. Alternative mechanisms like explosive activity have been suggested, but the driving process remains unknown. Here we report that pits on comet 67P/Churyumov-Gerasimenko are active, and probably created by a sinkhole process, possibly accompanied by outbursts. We argue that after formation, pits expand slowly in diameter, owing to sublimation-driven retreat of the walls. Therefore, pits characterize how eroded the surface is: a fresh cometary surface will have a ragged structure with many pits, while an evolved surface will look smoother. The size and spatial distribution of pits imply that large heterogeneities exist in the physical, structural or compositional properties of the first few hundred metres below the current nucleus surface.

Unusual phonon behavior and ultra-low thermal conductance of monolayer InSe.

PubMed

Zhou, Hangbo; Cai, Yongqing; Zhang, Gang; Zhang, Yong-Wei

2017-12-21

Monolayer indium selenide (InSe) possesses numerous fascinating properties, such as high electron mobility, quantum Hall effect and anomalous optical response. However, its phonon properties, thermal transport properties and the origin of its structural stability remain unexplored. Using first-principles calculations, we show that the atoms in InSe are highly polarized and such polarization causes strong long-range dipole-dipole interaction (DDI). For acoustic modes, DDI is essential for maintaining its structural stability. For optical modes, DDI causes a significant frequency shift of its out-of-phase vibrations. Surprisingly, we observed that there were two isolated frequency regimes, which were completely separated from other frequency regimes with large frequency gaps. Within each frequency regime, only a single phonon mode exists. We further reveal that InSe possesses the lowest thermal conductance among the known two-dimensional materials due to the low cut-off frequency, low phonon group velocities and the presence of large frequency gaps. These unique behaviors of monolayer InSe can enable the fabrication of novel devices, such as thermoelectric module, single-mode phonon channel and phononic laser.

Design of focused and restrained subsets from extremely large virtual libraries.

PubMed

Jamois, Eric A; Lin, Chien T; Waldman, Marvin

2003-11-01

With the current and ever-growing offering of reagents along with the vast palette of organic reactions, virtual libraries accessible to combinatorial chemists can reach sizes of billions of compounds or more. Extracting practical size subsets for experimentation has remained an essential step in the design of combinatorial libraries. A typical approach to computational library design involves enumeration of structures and properties for the entire virtual library, which may be unpractical for such large libraries. This study describes a new approach termed as on the fly optimization (OTFO) where descriptors are computed as needed within the subset optimization cycle and without intermediate enumeration of structures. Results reported herein highlight the advantages of coupling an ultra-fast descriptor calculation engine to subset optimization capabilities. We also show that enumeration of properties for the entire virtual library may not only be unpractical but also wasteful. Successful design of focused and restrained subsets can be achieved while sampling only a small fraction of the virtual library. We also investigate the stability of the method and compare results obtained from simulated annealing (SA) and genetic algorithms (GA).

The telencephalon of the Göttingen minipig, cytoarchitecture and cortical surface anatomy.

PubMed

Bjarkam, Carsten R; Glud, Andreas N; Orlowski, Dariusz; Sørensen, Jens Christian H; Palomero-Gallagher, Nicola

2017-07-01

During the last 20 years pigs have become increasingly popular in large animal translational neuroscience research as an economical and ethical feasible substitute to non-human primates. The anatomy of the pig telencephalon is, however, not well known. We present, accordingly, a detailed description of the surface anatomy and cytoarchitecture of the Göttingen minipig telencephalon based on macrophotos and consecutive high-power microphotographs of 15 μm thick paraffin embedded Nissl-stained coronal sections. In 1-year-old specimens the formalin perfused brain measures approximately 55 × 47 × 36 mm (length, width, height) and weighs around 69 g. The telencephalic part of the Göttingen minipig cerebrum covers a large surface area, which can be divided into a neocortical gyrencephalic part located dorsal to the rhinal fissure, and a ventral subrhinal part dominated by olfactory, amygdaloid, septal, and hippocampal structures. This part of the telencephalon is named the subrhinal lobe, and based on cytoarchitectural and sulcal anatomy, can be discerned from the remaining dorsally located neocortical perirhinal/insular, pericallosal, frontal, parietal, temporal, and occipital lobes. The inner subcortical structure of the minipig telencephalon is dominated by a prominent ventricular system and large basal ganglia, wherein the putamen and the caudate nucleus posterior and dorsally are separated into two entities by the internal capsule, whereas both structures ventrally fuse into a large accumbens nucleus. The presented anatomical data is accompanied by surface renderings and high-power macrophotographs illustrating the telencephalic sulcal pattern, and the localization of the identified lobes and cytoarchitectonic areas. Additionally, 24 representative Nissl-stained telencephalic coronal sections are presented as supplementary material in atlas form on http://www.cense.dk/minipig_atlas/index.html and referred to as S1-S24 throughout the manuscript.

Use of stabilizing mutations to engineer a charged group within a ligand-binding hydrophobic cavity in T4 lysozyme.

PubMed

Liu, Lijun; Baase, Walter A; Michael, Miya M; Matthews, Brian W

2009-09-22

Both large-to-small and nonpolar-to-polar mutations in the hydrophobic core of T4 lysozyme cause significant loss in stability. By including supplementary stabilizing mutations we constructed a variant that combines the cavity-creating substitution Leu99 --> Ala with the buried charge mutant Met102 --> Glu. Crystal structure determination confirmed that this variant has a large cavity with the side chain of Glu102 located within the cavity wall. The cavity includes a large disk-shaped region plus a bulge. The disk-like region is essentially nonpolar, similar to L99A, while the Glu102 substituent is located in the vicinity of the bulge. Three ordered water molecules bind within this part of the cavity and appear to stabilize the conformation of Glu102. Glu102 has an estimated pKa of about 5.5-6.5, suggesting that it is at least partially charged in the crystal structure. The polar ligands pyridine, phenol and aniline bind within the cavity, and crystal structures of the complexes show one or two water molecules to be retained. Nonpolar ligands of appropriate shape can also bind in the cavity and in some cases exclude all three water molecules. This disrupts the hydrogen-bond network and causes the Glu102 side chain to move away from the ligand by up to 0.8 A where it remains buried in a completely nonpolar environment. Isothermal titration calorimetry revealed that the binding of these compounds stabilizes the protein by 4-6 kcal/mol. For both polar and nonpolar ligands the binding is enthalpically driven. Large negative changes in entropy adversely balance the binding of the polar ligands, whereas entropy has little effect on the nonpolar ligand binding.

Work-related factors influencing home care nurse intent to remain employed.

PubMed

Tourangeau, Ann E; Patterson, Erin; Saari, Margaret; Thomson, Heather; Cranley, Lisa

Health care is shifting out of hospitals into community settings. In Ontario, Canada, home care organizations continue to experience challenges recruiting and retaining nurses. However, factors influencing home care nurse retention that can be modified remain largely unexplored. Several groups of factors have been identified as influencing home care nurse intent to remain employed including job characteristics, work structures, relationships and communication, work environment, responses to work, and conditions of employment. The aim of this study was to test and refine a model that identifies which factors are related to home care nurse intentions to remain employed for the next 5 years with their current home care employer organization. A cross-sectional survey design was implemented to test and refine a hypothesized model of home care nurse intent to remain employed. Logistic regression was used to determine which factors influence home care nurse intent to remain employed. Home care nurse intent to remain employed for the next 5 years was associated with increasing age, higher nurse-evaluated quality of care, having greater variety of patients, experiencing greater meaningfulness of work, having greater income stability, having greater continuity of client care, experiencing more positive relationships with supervisors, experiencing higher work-life balance, and being more satisfied with salary and benefits. Home care organizations can promote home care nurse intent to remain employed by (a) ensuring nurses have adequate training and resources to provide quality client care, (b) improving employment conditions to increase income stability and satisfaction with pay and benefits, (c) ensuring manageable workloads to facilitate improved work-life balance, and (d) ensuring leaders are accessible and competent.

Facile fabrication of nanofluidic diode membranes using anodic aluminium oxide

NASA Astrophysics Data System (ADS)

Wu, Songmei; Wildhaber, Fabien; Vazquez-Mena, Oscar; Bertsch, Arnaud; Brugger, Juergen; Renaud, Philippe

2012-08-01

Active control of ion transport plays important roles in chemical and biological analytical processes. Nanofluidic systems hold the promise for such control through electrostatic interaction between ions and channel surfaces. Most existing experiments rely on planar geometry where the nanochannels are generally very long and shallow with large aspect ratios. Based on this configuration the concepts of nanofluidic gating and rectification have been successfully demonstrated. However, device minimization and throughput scaling remain significant challenges. We report here an innovative and facile realization of hetero-structured Al2O3/SiO2 (Si) nanopore array membranes by using pattern transfer of self-organized nanopore structures of anodic aluminum oxide (AAO). Thanks to the opposite surface charge states of Al2O3 (positive) and SiO2 (negative), the membrane exhibits clear rectification of ion current in electrolyte solutions with very low aspect ratios compared to previous approaches. Our hetero-structured nanopore arrays provide a valuable platform for high throughput applications such as molecular separation, chemical processors and energy conversion.Active control of ion transport plays important roles in chemical and biological analytical processes. Nanofluidic systems hold the promise for such control through electrostatic interaction between ions and channel surfaces. Most existing experiments rely on planar geometry where the nanochannels are generally very long and shallow with large aspect ratios. Based on this configuration the concepts of nanofluidic gating and rectification have been successfully demonstrated. However, device minimization and throughput scaling remain significant challenges. We report here an innovative and facile realization of hetero-structured Al2O3/SiO2 (Si) nanopore array membranes by using pattern transfer of self-organized nanopore structures of anodic aluminum oxide (AAO). Thanks to the opposite surface charge states of Al2O3 (positive) and SiO2 (negative), the membrane exhibits clear rectification of ion current in electrolyte solutions with very low aspect ratios compared to previous approaches. Our hetero-structured nanopore arrays provide a valuable platform for high throughput applications such as molecular separation, chemical processors and energy conversion. Electronic supplementary information (ESI) available: Pattern transfer of local AAO mask into Si layers of different thickness; characterization of the Ag/AgCl electrodes and the cell constant; control experiments of mono-charged nanopore membranes; and simulation of ionic transport in nanofluidic diodes. See DOI: 10.1039/c2nr31243c

Structural basis for immunization with postfusion respiratory syncytial virus fusion F glycoprotein (RSV F) to elicit high neutralizing antibody titers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swanson, Kurt A.; Settembre, Ethan C.; Shaw, Christine A.

2012-02-07

Respiratory syncytial virus (RSV), the main cause of infant bronchiolitis, remains a major unmet vaccine need despite more than 40 years of vaccine research. Vaccine candidates based on a chief RSV neutralization antigen, the fusion (F) glycoprotein, have foundered due to problems with stability, purity, reproducibility, and potency. Crystal structures of related parainfluenza F glycoproteins have revealed a large conformational change between the prefusion and postfusion states, suggesting that postfusion F antigens might not efficiently elicit neutralizing antibodies. We have generated a homogeneous, stable, and reproducible postfusion RSV F immunogen that elicits high titers of neutralizing antibodies in immunized animals.more » The 3.2-{angstrom} X-ray crystal structure of this substantially complete RSV F reveals important differences from homology-based structural models. Specifically, the RSV F crystal structure demonstrates the exposure of key neutralizing antibody binding sites on the surface of the postfusion RSV F trimer. This unanticipated structural feature explains the engineered RSV F antigen's efficiency as an immunogen. This work illustrates how structural-based antigen design can guide the rational optimization of candidate vaccine antigens.« less

Model representations of kerogen structures: An insight from density functional theory calculations and spectroscopic measurements

DOE PAGES

Weck, Philippe F.; Kim, Eunja; Wang, Yifeng; ...

2017-08-01

Molecular structures of kerogen control hydrocarbon production in unconventional reservoirs. Significant progress has been made in developing model representations of various kerogen structures. These models have been widely used for the prediction of gas adsorption and migration in shale matrix. However, using density functional perturbation theory (DFPT) calculations and vibrational spectroscopic measurements, we here show that a large gap may still remain between the existing model representations and actual kerogen structures, therefore calling for new model development. Using DFPT, we calculated Fourier transform infrared (FTIR) spectra for six most widely used kerogen structure models. The computed spectra were then systematicallymore » compared to the FTIR absorption spectra collected for kerogen samples isolated from Mancos, Woodford and Marcellus formations representing a wide range of kerogen origin and maturation conditions. Limited agreement between the model predictions and the measurements highlights that the existing kerogen models may still miss some key features in structural representation. A combination of DFPT calculations with spectroscopic measurements may provide a useful diagnostic tool for assessing the adequacy of a proposed structural model as well as for future model development. This approach may eventually help develop comprehensive infrared (IR)-fingerprints for tracing kerogen evolution.« less

Model representations of kerogen structures: An insight from density functional theory calculations and spectroscopic measurements.

PubMed

Weck, Philippe F; Kim, Eunja; Wang, Yifeng; Kruichak, Jessica N; Mills, Melissa M; Matteo, Edward N; Pellenq, Roland J-M

2017-08-01

Molecular structures of kerogen control hydrocarbon production in unconventional reservoirs. Significant progress has been made in developing model representations of various kerogen structures. These models have been widely used for the prediction of gas adsorption and migration in shale matrix. However, using density functional perturbation theory (DFPT) calculations and vibrational spectroscopic measurements, we here show that a large gap may still remain between the existing model representations and actual kerogen structures, therefore calling for new model development. Using DFPT, we calculated Fourier transform infrared (FTIR) spectra for six most widely used kerogen structure models. The computed spectra were then systematically compared to the FTIR absorption spectra collected for kerogen samples isolated from Mancos, Woodford and Marcellus formations representing a wide range of kerogen origin and maturation conditions. Limited agreement between the model predictions and the measurements highlights that the existing kerogen models may still miss some key features in structural representation. A combination of DFPT calculations with spectroscopic measurements may provide a useful diagnostic tool for assessing the adequacy of a proposed structural model as well as for future model development. This approach may eventually help develop comprehensive infrared (IR)-fingerprints for tracing kerogen evolution.

Family Structure and Adolescent Substance Use: An International Perspective.

PubMed

Hoffmann, John P

2017-11-10

Numerous studies indicate that family structure is a key correlate of adolescent substance use. Yet there are some important limitations to this research. Studies have been conducted mainly in the United States, with relatively few studies that have compared family structure and youth substance use across nations. There is also a lack of recognition of the complexity of family types prevalent in contemporary global society. Moreover, there remains a need to consider personal, interpersonal, and macro-level characteristics that may help account for the association between family structure and youth substance use. This study uses data from 37 countries to examine several models that purport to explain the association between family structure and substance use. The data are from the 2005-2006 WHO-sponsored Health Behaviour in School-Aged Children (HBSC) (n = 193,202). Multilevel models, including linear, probit, and structural equation models (SEMs), were used to test several hypotheses. The results suggest that time spent with friends largely accounted for the association between specific types of family structures and frequency of alcohol use and getting drunk, but that cannabis use was negatively associated with living with both biological parents irrespective of other factors.

Model representations of kerogen structures: An insight from density functional theory calculations and spectroscopic measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weck, Philippe F.; Kim, Eunja; Wang, Yifeng

Molecular structures of kerogen control hydrocarbon production in unconventional reservoirs. Significant progress has been made in developing model representations of various kerogen structures. These models have been widely used for the prediction of gas adsorption and migration in shale matrix. However, using density functional perturbation theory (DFPT) calculations and vibrational spectroscopic measurements, we here show that a large gap may still remain between the existing model representations and actual kerogen structures, therefore calling for new model development. Using DFPT, we calculated Fourier transform infrared (FTIR) spectra for six most widely used kerogen structure models. The computed spectra were then systematicallymore » compared to the FTIR absorption spectra collected for kerogen samples isolated from Mancos, Woodford and Marcellus formations representing a wide range of kerogen origin and maturation conditions. Limited agreement between the model predictions and the measurements highlights that the existing kerogen models may still miss some key features in structural representation. A combination of DFPT calculations with spectroscopic measurements may provide a useful diagnostic tool for assessing the adequacy of a proposed structural model as well as for future model development. This approach may eventually help develop comprehensive infrared (IR)-fingerprints for tracing kerogen evolution.« less

Structure of Gremlin-2 in Complex with GDF5 Gives Insight into DAN-Family-Mediated BMP Antagonism.

PubMed

Nolan, Kristof; Kattamuri, Chandramohan; Rankin, Scott A; Read, Randy J; Zorn, Aaron M; Thompson, Thomas B

2016-08-23

The DAN family, including Gremlin-1 and Gremlin-2 (Grem1 and Grem2), represents a large family of secreted BMP (bone morphogenetic protein) antagonists. However, how DAN proteins specifically inhibit BMP signaling has remained elusive. Here, we report the structure of Grem2 bound to GDF5 at 2.9-Å resolution. The structure reveals two Grem2 dimers binding perpendicularly to each GDF5 monomer, resembling an H-like structure. Comparison to the unbound Grem2 structure reveals a dynamic N terminus that undergoes significant transition upon complex formation, leading to simultaneous interaction with the type I and type II receptor motifs on GDF5. Binding studies show that DAN-family members can interact with BMP-type I receptor complexes, whereas Noggin outcompetes the type I receptor for ligand binding. Interestingly, Grem2-GDF5 forms a stable aggregate-like structure in vitro that is not clearly observed for other antagonists, including Noggin and Follistatin. These findings exemplify the structural and functional diversity across the various BMP antagonist families. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Seed dispersal of the Australian cycad Macrozamia miquelii (Zamiaceae): are cycads megafauna-dispersed "grove forming" plants?

PubMed

Hall, John A; Walter, Gimme H

2013-06-01

Plants that invest in large, heavy seeds and colorful, fleshy fruits or analogous structures seem adapted for dispersal by large vertebrates. Some such plants, like Australian cycads in the genus Macrozamia, do not disperse well, which could be explained by seed-dispersal relationships with megafauna that are rare or extinct in contemporary ecosystems. Such plants provide an opportunity to investigate the ecological consequences of low seed-dispersal distances. • We investigated seed dispersal of Macrozamia miquelii in Central Queensland by tracking the fate of marked seeds, identifying the dispersal fauna and quantifying population demography and spatial structure. • We found that 70-100% of marked seeds remained within 1 m of maternal females (cycads are dioecious). Of the 812 seeds recovered (from 840 originally marked) only 24 dispersed >1 m from maternal females, the greatest observed dispersal being 5 m. We found an average of 2.2 seedlings and 0.7 juveniles within 1.5 m of mature females, which suggests that most seeds that remain in the vicinity of maternal females perish. Within-stand densities ranged between 1000 and 5000 plants/ha. The brushtail possum Trichosurus vulpecula was the only animal observed to move the seeds. • Macrozamia are adapted for dispersal by megafauna that are rare or absent in contemporary ecosystems. We argue that Macrozamia are "grove forming" plants that derive ecological benefit from existing as high-density, spatially discrete populations, the function of megafaunal dispersal adaptations being the infrequent dispersal of seeds en masse to establish new such groves in the landscape.

Genome accessibility is widely preserved and locally modulated during mitosis

PubMed Central

Hsiung, Chris C.-S.; Morrissey, Christapher S.; Udugama, Maheshi; Frank, Christopher L.; Keller, Cheryl A.; Baek, Songjoon; Giardine, Belinda; Crawford, Gregory E.; Sung, Myong-Hee; Hardison, Ross C.

2015-01-01

Mitosis entails global alterations to chromosome structure and nuclear architecture, concomitant with transient silencing of transcription. How cells transmit transcriptional states through mitosis remains incompletely understood. While many nuclear factors dissociate from mitotic chromosomes, the observation that certain nuclear factors and chromatin features remain associated with individual loci during mitosis originated the hypothesis that such mitotically retained molecular signatures could provide transcriptional memory through mitosis. To understand the role of chromatin structure in mitotic memory, we performed the first genome-wide comparison of DNase I sensitivity of chromatin in mitosis and interphase, using a murine erythroblast model. Despite chromosome condensation during mitosis visible by microscopy, the landscape of chromatin accessibility at the macromolecular level is largely unaltered. However, mitotic chromatin accessibility is locally dynamic, with individual loci maintaining none, some, or all of their interphase accessibility. Mitotic reduction in accessibility occurs primarily within narrow, highly DNase hypersensitive sites that frequently coincide with transcription factor binding sites, whereas broader domains of moderate accessibility tend to be more stable. In mitosis, proximal promoters generally maintain their accessibility more strongly, whereas distal regulatory elements tend to lose accessibility. Large domains of DNA hypomethylation mark a subset of promoters that retain accessibility during mitosis and across many cell types in interphase. Erythroid transcription factor GATA1 exerts site-specific changes in interphase accessibility that are most pronounced at distal regulatory elements, but has little influence on mitotic accessibility. We conclude that features of open chromatin are remarkably stable through mitosis, but are modulated at the level of individual genes and regulatory elements. PMID:25373146

Modification of electronic structure, magnetic structure, and topological phase of bismuthene by point defects

NASA Astrophysics Data System (ADS)

Kadioglu, Yelda; Kilic, Sevket Berkay; Demirci, Salih; Aktürk, O. Üzengi; Aktürk, Ethem; Ciraci, Salim

2017-12-01

This paper reveals how the electronic structure, magnetic structure, and topological phase of two-dimensional (2D), single-layer structures of bismuth are modified by point defects. We first showed that a free-standing, single-layer, hexagonal structure of bismuth, named h-bismuthene, exhibits nontrivial band topology. We then investigated interactions between single foreign adatoms and bismuthene structures, which comprise stability, bonding, electronic structure, and magnetic structures. Localized states in diverse locations of the band gap and resonant states in band continua of bismuthene are induced upon the adsorption of different adatoms, which modify electronic and magnetic properties. Specific adatoms result in reconstruction around the adsorption site. Single vacancies and divacancies can form readily in bismuthene structures and remain stable at high temperatures. Through rebondings, Stone-Whales-type defects are constructed by divacancies, which transform into a large hole at high temperature. Like adsorbed adatoms, vacancies induce also localized gap states, which can be eliminated through rebondings in divacancies. We also showed that not only the optical and magnetic properties, but also the topological features of pristine h-bismuthene can be modified by point defects. The modification of the topological features depends on the energies of localized states and also on the strength of coupling between point defects.

Revealing and analyzing networks of environmental systems

NASA Astrophysics Data System (ADS)

Eveillard, D.; Bittner, L.; Chaffron, S.; Guidi, L.; Raes, J.; Karsenti, E.; Bowler, C.; Gorsky, G.

2015-12-01

Understanding the interactions between microbial communities and their environment well enough to be able to predict diversity on the basis of physicochemical parameters is a fundamental pursuit of microbial ecology that still eludes us. However, modeling microbial communities is a complicated task, because (i) communities are complex, (ii) most are described qualitatively, and (iii) quantitative understanding of the way communities interacts with their surroundings remains incomplete. Within this seminar, we will illustrate two complementary approaches that aim to overcome these points in different manners. First, we will present a network analysis that focus on the biological carbon pump in the global ocean. The biological carbon pump is the process by which photosynthesis transforms CO2 to organic carbon sinking to the deep-ocean as particles where it is sequestered. While the intensity of the pump correlate to plankton community composition, the underlying ecosystem structure and interactions driving this process remain largely uncharacterized Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve understanding of these drivers. We show that specific plankton communities correlate with carbon export and highlight unexpected and overlooked taxa such as Radiolaria, alveolate parasites and bacterial pathogens, as well as Synechococcus and their phages, as key players in the biological pump. Additionally, we show that the abundances of just a few bacterial and viral genes predict most of the global ocean carbon export's variability. Together these findings help elucidate ecosystem drivers of the biological carbon pump and present a case study for scaling from genes-to-ecosystems. Second, we will show preliminary results on a probabilistic modeling that predicts microbial community structure across observed physicochemical data, from a putative network and partial quantitative knowledge. This modeling shows that, despite distinct quantitative environmental perturbations, the constraints on community structure could remain stable.

Activator Protein-1: redox switch controlling structure and DNA-binding.

PubMed

Yin, Zhou; Machius, Mischa; Nestler, Eric J; Rudenko, Gabby

2017-11-02

The transcription factor, activator protein-1 (AP-1), binds to cognate DNA under redox control; yet, the underlying mechanism has remained enigmatic. A series of crystal structures of the AP-1 FosB/JunD bZIP domains reveal ordered DNA-binding regions in both FosB and JunD even in absence DNA. However, while JunD is competent to bind DNA, the FosB bZIP domain must undergo a large conformational rearrangement that is controlled by a 'redox switch' centered on an inter-molecular disulfide bond. Solution studies confirm that FosB/JunD cannot undergo structural transition and bind DNA when the redox-switch is in the 'OFF' state, and show that the mid-point redox potential of the redox switch affords it sensitivity to cellular redox homeostasis. The molecular and structural studies presented here thus reveal the mechanism underlying redox-regulation of AP-1 Fos/Jun transcription factors and provide structural insight for therapeutic interventions targeting AP-1 proteins. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Defying stereotypes: the elusive search for a universal model of LysR-type regulation.

PubMed

Momany, Cory; Neidle, Ellen L

2012-02-01

LysR-type transcriptional regulators (LTTRs) compose the largest family of homologous regulators in bacteria. Considering their prevalence, it is not surprising that LTTRs control diverse metabolic functions. Arguably, the most unexpected aspect of LTTRs is the paucity of available structural information. Solubility issues are notoriously problematic, and structural studies have only recently begun to flourish. In this issue of Molecular Microbiology, Taylor et al. (2012) present the structure of AphB, a LysR-type regulator of virulence in Vibrio cholerae. This contribution adds significantly to the group of known full-length atomic LTTR structures, which remains small. Importantly, this report also describes an active-form variant. Small conformational changes in the effector-binding domain translate to global reorganization of the DNA-binding domain. Emerging from these results is a model of theme-and-variation among LTTRs rather than a unified regulatory scheme. Despite common structural folds, LTTRs exhibit differences in oligomerization, promoter recognition and communication with RNA polymerase. Such variation mirrors the diversity in sequence and function associated with members of this very large family. © 2012 Blackwell Publishing Ltd.

Masking effects of speech and music: does the masker's hierarchical structure matter?

PubMed

Shi, Lu-Feng; Law, Yvonne

2010-04-01

Speech and music are time-varying signals organized by parallel hierarchical rules. Through a series of four experiments, this study compared the masking effects of single-talker speech and instrumental music on speech perception while manipulating the complexity of hierarchical and temporal structures of the maskers. Listeners' word recognition was found to be similar between hierarchically intact and disrupted speech or classical music maskers (Experiment 1). When sentences served as the signal, significantly greater masking effects were observed with disrupted than intact speech or classical music maskers (Experiment 2), although not with jazz or serial music maskers, which differed from the classical music masker in their hierarchical structures (Experiment 3). Removing the classical music masker's temporal dynamics or partially restoring it affected listeners' sentence recognition; yet, differences in performance between intact and disrupted maskers remained robust (Experiment 4). Hence, the effect of structural expectancy was largely present across maskers when comparing them before and after their hierarchical structure was purposefully disrupted. This effect seemed to lend support to the auditory stream segregation theory.

Harmonic template neurons in primate auditory cortex underlying complex sound processing

PubMed Central

Feng, Lei

2017-01-01

Harmonicity is a fundamental element of music, speech, and animal vocalizations. How the auditory system extracts harmonic structures embedded in complex sounds and uses them to form a coherent unitary entity is not fully understood. Despite the prevalence of sounds rich in harmonic structures in our everyday hearing environment, it has remained largely unknown what neural mechanisms are used by the primate auditory cortex to extract these biologically important acoustic structures. In this study, we discovered a unique class of harmonic template neurons in the core region of auditory cortex of a highly vocal New World primate, the common marmoset (Callithrix jacchus), across the entire hearing frequency range. Marmosets have a rich vocal repertoire and a similar hearing range to that of humans. Responses of these neurons show nonlinear facilitation to harmonic complex sounds over inharmonic sounds, selectivity for particular harmonic structures beyond two-tone combinations, and sensitivity to harmonic number and spectral regularity. Our findings suggest that the harmonic template neurons in auditory cortex may play an important role in processing sounds with harmonic structures, such as animal vocalizations, human speech, and music. PMID:28096341

Social Experiments in the Mesoscale: Humans Playing a Spatial Prisoner's Dilemma

PubMed Central

Grujić, Jelena; Fosco, Constanza; Araujo, Lourdes; Cuesta, José A.; Sánchez, Angel

2010-01-01

Background The evolutionary origin of cooperation among unrelated individuals remains a key unsolved issue across several disciplines. Prominent among the several mechanisms proposed to explain how cooperation can emerge is the existence of a population structure that determines the interactions among individuals. Many models have explored analytically and by simulation the effects of such a structure, particularly in the framework of the Prisoner's Dilemma, but the results of these models largely depend on details such as the type of spatial structure or the evolutionary dynamics. Therefore, experimental work suitably designed to address this question is needed to probe these issues. Methods and Findings We have designed an experiment to test the emergence of cooperation when humans play Prisoner's Dilemma on a network whose size is comparable to that of simulations. We find that the cooperation level declines to an asymptotic state with low but nonzero cooperation. Regarding players' behavior, we observe that the population is heterogeneous, consisting of a high percentage of defectors, a smaller one of cooperators, and a large group that shares features of the conditional cooperators of public goods games. We propose an agent-based model based on the coexistence of these different strategies that is in good agreement with all the experimental observations. Conclusions In our large experimental setup, cooperation was not promoted by the existence of a lattice beyond a residual level (around 20%) typical of public goods experiments. Our findings also indicate that both heterogeneity and a “moody” conditional cooperation strategy, in which the probability of cooperating also depends on the player's previous action, are required to understand the outcome of the experiment. These results could impact the way game theory on graphs is used to model human interactions in structured groups. PMID:21103058

Atypical sulcal anatomy in young children with autism spectrum disorder

PubMed Central

Auzias, G.; Viellard, M.; Takerkart, S.; Villeneuve, N.; Poinso, F.; Fonséca, D. Da; Girard, N.; Deruelle, C.

2014-01-01

Autism spectrum disorder is associated with an altered early brain development. However, the specific cortical structure abnormalities underlying this disorder remain largely unknown. Nonetheless, atypical cortical folding provides lingering evidence of early disruptions in neurodevelopmental processes and identifying changes in the geometry of cortical sulci is of primary interest for characterizing these structural abnormalities in autism and their evolution over the first stages of brain development. Here, we applied state-of-the-art sulcus-based morphometry methods to a large highly-selective cohort of 73 young male children of age spanning from 18 to 108 months. Moreover, such large cohort was selected through extensive behavioral assessments and stringent inclusion criteria for the group of 59 children with autism. After manual labeling of 59 different sulci in each hemisphere, we computed multiple shape descriptors for each single sulcus element, hereby separating the folding measurement into distinct factors such as the length and depth of the sulcus. We demonstrated that the central, intraparietal and frontal medial sulci showed a significant and consistent pattern of abnormalities across our different geometrical indices. We also found that autistic and control children exhibited strikingly different relationships between age and structural changes in brain morphology. Lastly, the different measures of sulcus shapes were correlated with the CARS and ADOS scores that are specific to the autistic pathology and indices of symptom severity. Inherently, these structural abnormalities are confined to regions that are functionally relevant with respect to cognitive disorders in ASD. In contrast to those previously reported in adults, it is very unlikely that these abnormalities originate from general compensatory mechanisms unrelated to the primary pathology. Rather, they most probably reflect an early disruption on developmental trajectory that could be part of the primary pathology. PMID:24936410

Fast 3D shape screening of large chemical databases through alignment-recycling

PubMed Central

Fontaine, Fabien; Bolton, Evan; Borodina, Yulia; Bryant, Stephen H

2007-01-01

Background Large chemical databases require fast, efficient, and simple ways of looking for similar structures. Although such tasks are now fairly well resolved for graph-based similarity queries, they remain an issue for 3D approaches, particularly for those based on 3D shape overlays. Inspired by a recent technique developed to compare molecular shapes, we designed a hybrid methodology, alignment-recycling, that enables efficient retrieval and alignment of structures with similar 3D shapes. Results Using a dataset of more than one million PubChem compounds of limited size (< 28 heavy atoms) and flexibility (< 6 rotatable bonds), we obtained a set of a few thousand diverse structures covering entirely the 3D shape space of the conformers of the dataset. Transformation matrices gathered from the overlays between these diverse structures and the 3D conformer dataset allowed us to drastically (100-fold) reduce the CPU time required for shape overlay. The alignment-recycling heuristic produces results consistent with de novo alignment calculation, with better than 80% hit list overlap on average. Conclusion Overlay-based 3D methods are computationally demanding when searching large databases. Alignment-recycling reduces the CPU time to perform shape similarity searches by breaking the alignment problem into three steps: selection of diverse shapes to describe the database shape-space; overlay of the database conformers to the diverse shapes; and non-optimized overlay of query and database conformers using common reference shapes. The precomputation, required by the first two steps, is a significant cost of the method; however, once performed, querying is two orders of magnitude faster. Extensions and variations of this methodology, for example, to handle more flexible and larger small-molecules are discussed. PMID:17880744

Structural and functional studies of a family of Dictyostelium discoideum developmentally regulated, prestalk genes coding for small proteins.

PubMed

Vicente, Juan J; Galardi-Castilla, María; Escalante, Ricardo; Sastre, Leandro

2008-01-03

The social amoeba Dictyostelium discoideum executes a multicellular development program upon starvation. This morphogenetic process requires the differential regulation of a large number of genes and is coordinated by extracellular signals. The MADS-box transcription factor SrfA is required for several stages of development, including slug migration and spore terminal differentiation. Subtractive hybridization allowed the isolation of a gene, sigN (SrfA-induced gene N), that was dependent on the transcription factor SrfA for expression at the slug stage of development. Homology searches detected the existence of a large family of sigN-related genes in the Dictyostelium discoideum genome. The 13 most similar genes are grouped in two regions of chromosome 2 and have been named Group1 and Group2 sigN genes. The putative encoded proteins are 87-89 amino acids long. All these genes have a similar structure, composed of a first exon containing a 13 nucleotides long open reading frame and a second exon comprising the remaining of the putative coding region. The expression of these genes is induced at10 hours of development. Analyses of their promoter regions indicate that these genes are expressed in the prestalk region of developing structures. The addition of antibodies raised against SigN Group 2 proteins induced disintegration of multi-cellular structures at the mound stage of development. A large family of genes coding for small proteins has been identified in D. discoideum. Two groups of very similar genes from this family have been shown to be specifically expressed in prestalk cells during development. Functional studies using antibodies raised against Group 2 SigN proteins indicate that these genes could play a role during multicellular development.

Spatial extent of analysis influences observed patterns of population genetic structure in a widespread darter species (Percidae)

USGS Publications Warehouse

Argentina, Jane E.; Angermeier, Paul L.; Hallerman, Eric M.; Welsh, Stuart A.

2018-01-01

Connectivity among stream fish populations allows for exchange of genetic material and helps maintain genetic diversity, adaptive potential and population stability over time. Changes in species demographics and population connectivity have the potential to permanently alter the genetic patterns of stream fish, although these changes through space and time are variable and understudied in small‐bodied freshwater fish.As a spatially widespread, common species of benthic freshwater fish, the variegate darter (Etheostoma variatum) is a model species for documenting how patterns of genetic structure and diversity respond to increasing isolation due to large dams and how scale of study may shape our understanding of these patterns. We sampled variegate darters from 34 sites across their range in the North American Ohio River basin and examined how patterns of genetic structure and diversity within and between populations responded to historical population changes and dams within and between populations.Spatial scale and configuration of genetic structure varied across the eight identified populations, from tributaries within a watershed, to a single watershed, to multiple watersheds that encompass Ohio River mainstem habitats. This multiwatershed pattern of population structuring suggests genetic dispersal across large distances was and may continue to be common, although some populations remain isolated despite no apparent structural dispersal barriers. Populations with low effective population sizes and evidence of past population bottlenecks showed low allelic richness, but diversity patterns were not related to watershed size, a surrogate for habitat availability. Pairwise genetic differentiation (FST) increased with fluvial distance and was related to both historic and contemporary processes. Genetic diversity changes were influenced by underlying population size and stability, and while instream barriers were not strong determinants of genetic structuring or loss of genetic diversity, they reduce population connectivity and may impact long‐term population persistence.The broad spatial scale of this study demonstrated the large spatial extent of some variegate darter populations and indicated that dispersal is more extensive than expected given the movement patterns typically observed for small‐bodied, benthic fish. Dam impacts depended on underlying population size and stability, with larger populations more resilient to genetic drift and allelic richness loss than smaller populations.Other darters that inhabit large river habitats may show similar patterns in landscape‐scale studies, and large river barriers may impact populations of small‐bodied fish more than previously expected. Estimation of dispersal rates and behaviours is critical to conservation of imperilled riverine species such as darters.

Mapping human genetic diversity in Asia.

PubMed

Abdulla, Mahmood Ameen; Ahmed, Ikhlak; Assawamakin, Anunchai; Bhak, Jong; Brahmachari, Samir K; Calacal, Gayvelline C; Chaurasia, Amit; Chen, Chien-Hsiun; Chen, Jieming; Chen, Yuan-Tsong; Chu, Jiayou; Cutiongco-de la Paz, Eva Maria C; De Ungria, Maria Corazon A; Delfin, Frederick C; Edo, Juli; Fuchareon, Suthat; Ghang, Ho; Gojobori, Takashi; Han, Junsong; Ho, Sheng-Feng; Hoh, Boon Peng; Huang, Wei; Inoko, Hidetoshi; Jha, Pankaj; Jinam, Timothy A; Jin, Li; Jung, Jongsun; Kangwanpong, Daoroong; Kampuansai, Jatupol; Kennedy, Giulia C; Khurana, Preeti; Kim, Hyung-Lae; Kim, Kwangjoong; Kim, Sangsoo; Kim, Woo-Yeon; Kimm, Kuchan; Kimura, Ryosuke; Koike, Tomohiro; Kulawonganunchai, Supasak; Kumar, Vikrant; Lai, Poh San; Lee, Jong-Young; Lee, Sunghoon; Liu, Edison T; Majumder, Partha P; Mandapati, Kiran Kumar; Marzuki, Sangkot; Mitchell, Wayne; Mukerji, Mitali; Naritomi, Kenji; Ngamphiw, Chumpol; Niikawa, Norio; Nishida, Nao; Oh, Bermseok; Oh, Sangho; Ohashi, Jun; Oka, Akira; Ong, Rick; Padilla, Carmencita D; Palittapongarnpim, Prasit; Perdigon, Henry B; Phipps, Maude Elvira; Png, Eileen; Sakaki, Yoshiyuki; Salvador, Jazelyn M; Sandraling, Yuliana; Scaria, Vinod; Seielstad, Mark; Sidek, Mohd Ros; Sinha, Amit; Srikummool, Metawee; Sudoyo, Herawati; Sugano, Sumio; Suryadi, Helena; Suzuki, Yoshiyuki; Tabbada, Kristina A; Tan, Adrian; Tokunaga, Katsushi; Tongsima, Sissades; Villamor, Lilian P; Wang, Eric; Wang, Ying; Wang, Haifeng; Wu, Jer-Yuarn; Xiao, Huasheng; Xu, Shuhua; Yang, Jin Ok; Shugart, Yin Yao; Yoo, Hyang-Sook; Yuan, Wentao; Zhao, Guoping; Zilfalil, Bin Alwi

2009-12-11

Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations.

''Football'' test coil: a simulated service test of internally-cooled, cabled superconductor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marston, P.G.; Iwasa, Y.; Thome, R.J.

Internally-cooled, cabled superconductor, (ICCS), appears from small-scale tests to be a viable alternative to pool-boiling cooled superconductors for large superconducting magnets. Potential advantages may include savings in helium inventory, smaller structure and ease of fabrication. Questions remain, however, about the structural performance of these systems. The ''football'' test coil has been designed to simulate the actual ''field-current-stress-thermal'' operating conditions of a 25 ka ICCS in a commercial scale MHD magnet. The test procedure will permit demonstration of the 20 year cyclic life of such a magnet in less than 20 days. This paper describes the design, construction and test ofmore » that coil which is wound of copper-stabilized niobium-titanium cable in steel conduit. 2 refs.« less

Evolving Systems: Adaptive Key Component Control and Inheritance of Passivity and Dissipativity

NASA Technical Reports Server (NTRS)

Frost, S. A.; Balas, M. J.

2010-01-01

We propose a new framework called Evolving Systems to describe the self-assembly, or autonomous assembly, of actively controlled dynamical subsystems into an Evolved System with a higher purpose. Autonomous assembly of large, complex flexible structures in space is a target application for Evolving Systems. A critical requirement for autonomous assembling structures is that they remain stable during and after assembly. The fundamental topic of inheritance of stability, dissipativity, and passivity in Evolving Systems is the primary focus of this research. In this paper, we develop an adaptive key component controller to restore stability in Nonlinear Evolving Systems that would otherwise fail to inherit the stability traits of their components. We provide sufficient conditions for the use of this novel control method and demonstrate its use on an illustrative example.

Observational Analysis of Coronal Fans

NASA Technical Reports Server (NTRS)

Talpeanu, D.-C.; Rachmeler, L; Mierla, Marilena

2017-01-01

Coronal fans (see Figure 1) are bright observational structures that extend to large distances above the solar surface and can easily be seen in EUV (174 angstrom) above the limb. They have a very long lifetime and can live up to several Carrington rotations (CR), remaining relatively stationary for many months. Note that they are not off-limb manifestation of similarly-named active region fans. The solar conditions required to create coronal fans are not well understood. The goal of this research was to find as many associations as possible of coronal fans with other solar features and to gain a better understanding of these structures. Therefore, we analyzed many fans and created an overview of their properties. We present the results of this statistical analysis and also a case study on the longest living fan.

Simulated observations of young gravitationally unstable protoplanetary discs

NASA Astrophysics Data System (ADS)

Douglas, T. A.; Caselli, P.; Ilee, J. D.; Boley, A. C.; Hartquist, T. W.; Durisen, R. H.; Rawlings, J. M. C.

2013-08-01

The formation and earliest stages of protoplanetary discs remain poorly constrained by observations. Atacama Large Millimetre/sub-millimetre Array (ALMA) will soon revolutionise this field. Therefore, it is important to provide predictions which will be valuable for the interpretation of future high sensitivity and high angular resolution observations. Here, we present simulated ALMA observations based on radiative transfer modelling of a relatively massive (0.39 M⊙) self-gravitating disc embedded in a 10 M⊙ dense core, with structure similar to the pre-stellar core L1544. We focus on simple species and conclude that C17O 3→2, HCO+ 3→2, OCS 26→25 and H2CO 404→303 lines can be used to probe the disc structure and kinematics at all scales.

Fast detection of the fuzzy communities based on leader-driven algorithm

NASA Astrophysics Data System (ADS)

Fang, Changjian; Mu, Dejun; Deng, Zhenghong; Hu, Jun; Yi, Chen-He

2018-03-01

In this paper, we present the leader-driven algorithm (LDA) for learning community structure in networks. The algorithm allows one to find overlapping clusters in a network, an important aspect of real networks, especially social networks. The algorithm requires no input parameters and learns the number of clusters naturally from the network. It accomplishes this using leadership centrality in a clever manner. It identifies local minima of leadership centrality as followers which belong only to one cluster, and the remaining nodes are leaders which connect clusters. In this way, the number of clusters can be learned using only the network structure. The LDA is also an extremely fast algorithm, having runtime linear in the network size. Thus, this algorithm can be used to efficiently cluster extremely large networks.

Dynamic analysis of rotor flex-structure based on nonlinear anisotropic shell models

NASA Astrophysics Data System (ADS)

Bauchau, Olivier A.; Chiang, Wuying

1991-05-01

In this paper an anisotropic shallow shell model is developed that accommodates transverse shearing deformations and arbitrarily large displacements and rotations, but strains are assumed to remain small. Two kinematic models are developed, the first using two DOF to locate the direction of the normal to the shell's midplane, the second using three. The latter model allows for an automatic compatibility of the shell model with beam models. The shell model is validated by comparing its predictions with several benchmark problems. In actual helicopter rotor blade problems, the shell model of the flex structure is shown to give very different results shown compared to beam models. The lead-lag and torsion modes in particular are strongly affected, whereas flapping modes seem to be less affected.

Solution conformation of a cohesin module and its scaffoldin linker from a prototypical cellulosome.

PubMed

Galera-Prat, Albert; Pantoja-Uceda, David; Laurents, Douglas V; Carrión-Vázquez, Mariano

2018-04-15

Bacterial cellulases are drawing increased attention as a means to obtain plentiful chemical feedstocks and fuels from renewable lignocellulosic biomass sources. Certain bacteria deploy a large extracellular multi-protein complex, called the cellulosome, to degrade cellulose. Scaffoldin, a key non-catalytic cellulosome component, is a large protein containing a cellulose-specific carbohydrate-binding module and several cohesin modules which bind and organize the hydrolytic enzymes. Despite the importance of the structure and protein/protein interactions of the cohesin module in the cellulosome, its structure in solution has remained unknown to date. Here, we report the backbone 1 H, 13 C and 15 N NMR assignments of the Cohesin module 5 from the highly stable and active cellulosome from Clostridium thermocellum. These data reveal that this module adopts a tightly packed, well folded and rigid structure in solution. Furthermore, since in scaffoldin, the cohesin modules are connected by linkers we have also characterized the conformation of a representative linker segment using NMR spectroscopy. Analysis of its chemical shift values revealed that this linker is rather stiff and tends to adopt extended conformations. This suggests that the scaffoldin linkers act to minimize interactions between cohesin modules. These results pave the way towards solution studies on cohesin/dockerin's fascinating dual-binding mode. Copyright © 2018 Elsevier Inc. All rights reserved.

Spanwise vorticity and wall normal velocity structure in the inertial region of turbulent boundary layers

NASA Astrophysics Data System (ADS)

Cuevas Bautista, Juan Carlos; Morrill-Winter, Caleb; White, Christopher; Chini, Gregory; Klewicki, Joseph

2017-11-01

The Reynolds shear stress gradient is a leading order mechanism on the inertial domain of turbulent wall-flows. This quantity can be described relative to the sum of two velocity-vorticity correlations, vωz and wωy . Recent studies suggest that the first of these correlates with the step-like structure of the instantaneous streamwise velocity profile on the inertial layer. This structure is comprised of large zones of uniform momentum segregated by slender regions of concentrated vorticity. In this talk we study the contributions of the v and ωz motions to the vorticity transport (vωz) mechanism through the use of experimental data at large friction Reynolds numbers, δ+. The primary contributions to v and ωz were estimated by identifying the peak wavelengths of their streamwise spectra. The magnitudes of these peaks are of the same order, and are shown to exhibit a weak δ+ dependence. The peak wavelengths of v, however, exhibit a strong wall-distance (y) dependence, while the peak wavelengths of ωz show only a weak y dependence, and remain almost O (√{δ+}) in size throughout the inertial domain. This research was partially supported by the National Science Foundation and partially supported by the Australian Research Council.

Crystal structure studies with the Paris-Edinburgh cell: Neutron scattering aspects

NASA Astrophysics Data System (ADS)

Loveday, J. S.; Wilson, R. M.; Nelmes, R. J.; Besson, J. M.; Klotz, S.; Hamel, G.; Hull, S.

1994-07-01

The count rates achieved in neutron powder diffraction experiments create difficulties for high-pressure experiments because large sample volumes (˜100 mm3) must be used. Until recently it has been difficult to build suitable pressure cells with such large volumes and hence the maximum pressure for neutron diffraction has remained at the relatively low value of 3 GPa. We have now developed a pressure cell (the Paris-Edinburgh cell) which is capable of exceeding 10 GPa with a sample volume of ˜100 mm3 for use at the U.K. spallation source ISIS. Considerable effort has been devoted to the opimization of the cell, shielding, and detector geometry to enable the best possible data to be recorded. Finite-element calculations to correct for the systematic errors introduced by the attenuation of the pressure-cell materials have been developed and tested. As a result of this work we are now able to obtain accurate structural data to ˜12 GPa and recent studies of phase IV of ND3, the behaviour of the O-D bondlength in D2O ice VIII, and the structural pressure dependence of B4C illustrate the importance of the extension of neutron-diffraction studies to such pressures.

On the cyclic nature of perception in vision versus audition

PubMed Central

VanRullen, Rufin; Zoefel, Benedikt; Ilhan, Barkin

2014-01-01

Does our perceptual awareness consist of a continuous stream, or a discrete sequence of perceptual cycles, possibly associated with the rhythmic structure of brain activity? This has been a long-standing question in neuroscience. We review recent psychophysical and electrophysiological studies indicating that part of our visual awareness proceeds in approximately 7–13 Hz cycles rather than continuously. On the other hand, experimental attempts at applying similar tools to demonstrate the discreteness of auditory awareness have been largely unsuccessful. We argue and demonstrate experimentally that visual and auditory perception are not equally affected by temporal subsampling of their respective input streams: video sequences remain intelligible at sampling rates of two to three frames per second, whereas audio inputs lose their fine temporal structure, and thus all significance, below 20–30 samples per second. This does not mean, however, that our auditory perception must proceed continuously. Instead, we propose that audition could still involve perceptual cycles, but the periodic sampling should happen only after the stage of auditory feature extraction. In addition, although visual perceptual cycles can follow one another at a spontaneous pace largely independent of the visual input, auditory cycles may need to sample the input stream more flexibly, by adapting to the temporal structure of the auditory inputs. PMID:24639585

Effects of magnetic fields on photoionized pillars and globules

NASA Astrophysics Data System (ADS)

Mackey, Jonathan; Lim, Andrew J.

2011-04-01

The effects of initially uniform magnetic fields on the formation and evolution of dense pillars and cometary globules at the boundaries of H II regions are investigated using 3D radiation-magnetohydrodynamics simulations. It is shown, in agreement with previous work, that a strong initial magnetic field is required to significantly alter the non-magnetized dynamics because the energy input from photoionization is so large that it remains the dominant driver of the dynamics in most situations. Additionally, it is found that for weak and medium field strengths an initially perpendicular field is swept into alignment with the pillar during its dynamical evolution, matching magnetic field observations of the 'Pillars of Creation' in M16 and also some cometary globules. A strong perpendicular magnetic field remains in its initial configuration and also confines the photoevaporation flow into a bar-shaped dense ionized ribbon which partially shields the ionization front and would be readily observable in recombination lines. A simple analytic model is presented to explain the properties of this bright linear structure. These results show that magnetic field strengths in star-forming regions can in principle be significantly constrained by the morphology of structures which form at the borders of H II regions.

Food-web dynamics in a large river discontinuum

USGS Publications Warehouse

Cross, Wyatt F.; Baxter, Colden V.; Rosi-Marshall, Emma J.; Hall, Robert O.; Kennedy, Theodore A.; Donner, Kevin C.; Kelly, Holly A. Wellard; Seegert, Sarah E.Z.; Behn, Kathrine E.; Yard, Michael D.

2013-01-01

Nearly all ecosystems have been altered by human activities, and most communities are now composed of interacting species that have not co-evolved. These changes may modify species interactions, energy and material flows, and food-web stability. Although structural changes to ecosystems have been widely reported, few studies have linked such changes to dynamic food-web attributes and patterns of energy flow. Moreover, there have been few tests of food-web stability theory in highly disturbed and intensely managed freshwater ecosystems. Such synthetic approaches are needed for predicting the future trajectory of ecosystems, including how they may respond to natural or anthropogenic perturbations. We constructed flow food webs at six locations along a 386-km segment of the Colorado River in Grand Canyon (Arizona, USA) for three years. We characterized food-web structure and production, trophic basis of production, energy efficiencies, and interaction-strength distributions across a spatial gradient of perturbation (i.e., distance from Glen Canyon Dam), as well as before and after an experimental flood. We found strong longitudinal patterns in food-web characteristics that strongly correlated with the spatial position of large tributaries. Above tributaries, food webs were dominated by nonnative New Zealand mudsnails (62% of production) and nonnative rainbow trout (100% of fish production). The simple structure of these food webs led to few dominant energy pathways (diatoms to few invertebrate taxa to rainbow trout), large energy inefficiencies (i.e., Below large tributaries, invertebrate production declined ∼18-fold, while fish production remained similar to upstream sites and comprised predominately native taxa (80–100% of production). Sites below large tributaries had increasingly reticulate and detritus-based food webs with a higher prevalence of omnivory, as well as interaction strength distributions more typical of theoretically stable food webs (i.e., nearly twofold higher proportion of weak interactions). Consistent with theory, downstream food webs were less responsive to the experimental flood than sites closest to the dam. We show how human-induced shifts to food-web structure can affect energy flow and interaction strengths, and we show that these changes have consequences for food-web function and response to perturbations.

Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses.

PubMed

Sarti, Edoardo; Gladich, Ivan; Zamuner, Stefano; Correia, Bruno E; Laio, Alessandro

2016-09-01

The prediction of protein-protein interactions and their structural configuration remains a largely unsolved problem. Most of the algorithms aimed at finding the native conformation of a protein complex starting from the structure of its monomers are based on searching the structure corresponding to the global minimum of a suitable scoring function. However, protein complexes are often highly flexible, with mobile side chains and transient contacts due to thermal fluctuations. Flexibility can be neglected if one aims at finding quickly the approximate structure of the native complex, but may play a role in structure refinement, and in discriminating solutions characterized by similar scores. We here benchmark the capability of some state-of-the-art scoring functions (BACH-SixthSense, PIE/PISA and Rosetta) in discriminating finite-temperature ensembles of structures corresponding to the native state and to non-native configurations. We produce the ensembles by running thousands of molecular dynamics simulations in explicit solvent starting from poses generated by rigid docking and optimized in vacuum. We find that while Rosetta outperformed the other two scoring functions in scoring the structures in vacuum, BACH-SixthSense and PIE/PISA perform better in distinguishing near-native ensembles of structures generated by molecular dynamics in explicit solvent. Proteins 2016; 84:1312-1320. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER.

PubMed

Smart, Oliver S; Womack, Thomas O; Flensburg, Claus; Keller, Peter; Paciorek, Włodek; Sharff, Andrew; Vonrhein, Clemens; Bricogne, Gérard

2012-04-01

Maximum-likelihood X-ray macromolecular structure refinement in BUSTER has been extended with restraints facilitating the exploitation of structural similarity. The similarity can be between two or more chains within the structure being refined, thus favouring NCS, or to a distinct 'target' structure that remains fixed during refinement. The local structural similarity restraints (LSSR) approach considers all distances less than 5.5 Å between pairs of atoms in the chain to be restrained. For each, the difference from the distance between the corresponding atoms in the related chain is found. LSSR applies a restraint penalty on each difference. A functional form that reaches a plateau for large differences is used to avoid the restraints distorting parts of the structure that are not similar. Because LSSR are local, there is no need to separate out domains. Some restraint pruning is still necessary, but this has been automated. LSSR have been available to academic users of BUSTER since 2009 with the easy-to-use -autoncs and -target target.pdb options. The use of LSSR is illustrated in the re-refinement of PDB entries 5rnt, where -target enables the correct ligand-binding structure to be found, and 1osg, where -autoncs contributes to the location of an additional copy of the cyclic peptide ligand.

Polarization of the prompt gamma-ray emission from the gamma-ray burst of 6 December 2002.

PubMed

Coburn, Wayne; Boggs, Steven E

2003-05-22

Observations of the afterglows of gamma-ray bursts (GRBs) have revealed that they lie at cosmological distances, and so correspond to the release of an enormous amount of energy. The nature of the central engine that powers these events and the prompt gamma-ray emission mechanism itself remain enigmatic because, once a relativistic fireball is created, the physics of the afterglow is insensitive to the nature of the progenitor. Here we report the discovery of linear polarization in the prompt gamma-ray emission from GRB021206, which indicates that it is synchrotron emission from relativistic electrons in a strong magnetic field. The polarization is at the theoretical maximum, which requires a uniform, large-scale magnetic field over the gamma-ray emission region. A large-scale magnetic field constrains possible progenitors to those either having or producing organized fields. We suggest that the large magnetic energy densities in the progenitor environment (comparable to the kinetic energy densities of the fireball), combined with the large-scale structure of the field, indicate that magnetic fields drive the GRB explosion.

Source-gated transistors for order-of-magnitude performance improvements in thin-film digital circuits

NASA Astrophysics Data System (ADS)

Sporea, R. A.; Trainor, M. J.; Young, N. D.; Shannon, J. M.; Silva, S. R. P.

2014-03-01

Ultra-large-scale integrated (ULSI) circuits have benefited from successive refinements in device architecture for enormous improvements in speed, power efficiency and areal density. In large-area electronics (LAE), however, the basic building-block, the thin-film field-effect transistor (TFT) has largely remained static. Now, a device concept with fundamentally different operation, the source-gated transistor (SGT) opens the possibility of unprecedented functionality in future low-cost LAE. With its simple structure and operational characteristics of low saturation voltage, stability under electrical stress and large intrinsic gain, the SGT is ideally suited for LAE analog applications. Here, we show using measurements on polysilicon devices that these characteristics lead to substantial improvements in gain, noise margin, power-delay product and overall circuit robustness in digital SGT-based designs. These findings have far-reaching consequences, as LAE will form the technological basis for a variety of future developments in the biomedical, civil engineering, remote sensing, artificial skin areas, as well as wearable and ubiquitous computing, or lightweight applications for space exploration.

Source-gated transistors for order-of-magnitude performance improvements in thin-film digital circuits

PubMed Central

Sporea, R. A.; Trainor, M. J.; Young, N. D.; Shannon, J. M.; Silva, S. R. P.

2014-01-01

Ultra-large-scale integrated (ULSI) circuits have benefited from successive refinements in device architecture for enormous improvements in speed, power efficiency and areal density. In large-area electronics (LAE), however, the basic building-block, the thin-film field-effect transistor (TFT) has largely remained static. Now, a device concept with fundamentally different operation, the source-gated transistor (SGT) opens the possibility of unprecedented functionality in future low-cost LAE. With its simple structure and operational characteristics of low saturation voltage, stability under electrical stress and large intrinsic gain, the SGT is ideally suited for LAE analog applications. Here, we show using measurements on polysilicon devices that these characteristics lead to substantial improvements in gain, noise margin, power-delay product and overall circuit robustness in digital SGT-based designs. These findings have far-reaching consequences, as LAE will form the technological basis for a variety of future developments in the biomedical, civil engineering, remote sensing, artificial skin areas, as well as wearable and ubiquitous computing, or lightweight applications for space exploration. PMID:24599023

Removing brakes on adult brain plasticity: from molecular to behavioral interventions

PubMed Central

Bavelier, D.; Levi, D.M.; Li, R.W.; Dan, Y.; Hensch, T.K.

2010-01-01

Adult brain plasticity, although possible, remains more restricted in scope than during development. Here, we address conditions under which circuit rewiring may be facilitated in the mature brain. At a cellular and molecular level, adult plasticity is actively limited. Some of these “brakes” are structural, such as peri-neuronal nets or myelin, which inhibit neurite outgrowth. Others are functional, acting directly upon excitatory-inhibitory balance within local circuits. Plasticity in adulthood can be induced either by lifting these brakes through invasive interventions or by exploiting endogenous permissive factors, such as neuromodulators. Using the amblyopic visual system as a model, we discuss genetic, pharmacological, and environmental removal of brakes to enable recovery of vision in adult rodents. Although these mechanisms remain largely uncharted in the human, we consider how they may provide a biological foundation for the remarkable increase in plasticity after action video game play by amblyopic subjects. PMID:21068299

Conformational transition of membrane-associated terminally-acylated HIV-1 Nef

PubMed Central

Akgun, Bulent; Satija, Sushil; Nanda, Hirsh; Pirrone, Gregory F.; Shi, Xiaomeng; Engen, John R.; Kent, Michael S.

2013-01-01

Many proteins are post-translationally modified by acylation targetting them to lipid membranes. While methods such as X-ray crystallography and NMR are available to determine the structure of folded proteins in solution, the precise position of folded domains relative to a membrane remains largely unknown. We used neutron and X-ray reflection methods to measure the displacement of the core domain of HIV Nef from lipid membranes upon insertion of the N-terminal myristate group. Nef is one of several HIV-1 accessory proteins and an essential factor in AIDS progression. Upon insertion of the myristate and residues from the N-terminal arm, Nef transitions from a closed to open conformation that positions the core domain 70 Å from the lipid headgroups. This work rules out speculation that the Nef core remains closely associated with the membrane to optimize interactions with the cytoplasmic domain of MHC-1. PMID:24035710

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Shiwang; Xie, Shi-Jie; Carrillo, Jan-Michael Y.

Polymer nanocomposites (PNCs) are important materials that are widely used in many current technologies and potentially have broader applications in the future due to their excellent property of tunability, light weight and low cost. But, expanding the limits in property enhancement remains a fundamental scientific challenge. We demonstrate that well-dispersed, small (diameter ~1.8 nm) nanoparticles with attractive interactions lead to unexpectedly large and qualitatively new changes in PNC structural dynamics in comparison to conventional composites based on particles of diameter ~10-50 nm. At the same time, the zero-shear viscosity at high temperatures remains comparable to that of the neat polymer,more » thereby retaining good processibility and resolving a major challenge in PNC applications. These results suggest that the nanoparticle mobility and relatively short lifetimes of nanoparticlepolymer associations open qualitatively new horizons in tunability of macroscopic properties in nanocomposites with high potential for the development of new functional materials.« less

Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction.

PubMed

Brylinski, Michal

2013-11-25

A common strategy for virtual screening considers a systematic docking of a large library of organic compounds into the target sites in protein receptors with promising leads selected based on favorable intermolecular interactions. Despite a continuous progress in the modeling of protein-ligand interactions for pharmaceutical design, important challenges still remain, thus the development of novel techniques is required. In this communication, we describe eSimDock, a new approach to ligand docking and binding affinity prediction. eSimDock employs nonlinear machine learning-based scoring functions to improve the accuracy of ligand ranking and similarity-based binding pose prediction, and to increase the tolerance to structural imperfections in the target structures. In large-scale benchmarking using the Astex/CCDC data set, we show that 53.9% (67.9%) of the predicted ligand poses have RMSD of <2 Å (<3 Å). Moreover, using binding sites predicted by recently developed eFindSite, eSimDock models ligand binding poses with an RMSD of 4 Å for 50.0-39.7% of the complexes at the protein homology level limited to 80-40%. Simulations against non-native receptor structures, whose mean backbone rearrangements vary from 0.5 to 5.0 Å Cα-RMSD, show that the ratio of docking accuracy and the estimated upper bound is at a constant level of ∼0.65. Pearson correlation coefficient between experimental and predicted by eSimDock Ki values for a large data set of the crystal structures of protein-ligand complexes from BindingDB is 0.58, which decreases only to 0.46 when target structures distorted to 3.0 Å Cα-RMSD are used. Finally, two case studies demonstrate that eSimDock can be customized to specific applications as well. These encouraging results show that the performance of eSimDock is largely unaffected by the deformations of ligand binding regions, thus it represents a practical strategy for across-proteome virtual screening using protein models. eSimDock is freely available to the academic community as a Web server at http://www.brylinski.org/esimdock .

A model for the evolution of the Earth's mantle structure since the Early Paleozoic

NASA Astrophysics Data System (ADS)

Zhang, Nan; Zhong, Shijie; Leng, Wei; Li, Zheng-Xiang

2010-06-01

Seismic tomography studies indicate that the Earth's mantle structure is characterized by African and Pacific seismically slow velocity anomalies (i.e., superplumes) and circum-Pacific seismically fast anomalies (i.e., a globally spherical harmonic degree 2 structure). However, the cause for and time evolution of the African and Pacific superplumes and the degree 2 mantle structure remain poorly understood with two competing proposals. First, the African and Pacific superplumes have remained largely unchanged for at least the last 300 Myr and possibly much longer. Second, the African superplume is formed sometime after the formation of Pangea (i.e., at 330 Ma) and the mantle in the African hemisphere is predominated by cold downwelling structures before and during the assembly of Pangea, while the Pacific superplume has been stable for the Pangea supercontinent cycle (i.e., globally a degree 1 structure before the Pangea formation). Here, we construct a proxy model of plate motions for the African hemisphere for the last 450 Myr since the Early Paleozoic using the paleogeographic reconstruction of continents constrained by paleomagnetic and geological observations. Coupled with assumed oceanic plate motions for the Pacific hemisphere, this proxy model for the plate motion history is used as time-dependent surface boundary condition in three-dimensional spherical models of thermochemical mantle convection to study the evolution of mantle structure, particularly the African mantle structure, since the Early Paleozoic. Our model calculations reproduce well the present-day mantle structure including the African and Pacific superplumes and generally support the second proposal with a dynamic cause for the superplume structure. Our results suggest that while the mantle in the African hemisphere before the assembly of Pangea is predominated by the cold downwelling structure resulting from plate convergence between Gondwana and Laurussia, it is unlikely that the bulk of the African superplume structure can be formed before ˜230 Ma (i.e., ˜100 Myr after the assembly of Pangea). Particularly, the last 120 Myr plate motion plays an important role in generating the African superplume. Our models have implications for understanding the global-scale magmatism, tectonics, mantle dynamics, and thermal evolution history for the Earth since the Early Paleozoic.

Comprehensive analysis of Curie-point depths and lithospheric effective elastic thickness at Arctic Region

NASA Astrophysics Data System (ADS)

Lu, Y.; Li, C. F.

2017-12-01

Arctic Ocean remains at the forefront of geological exploration. Here we investigate its deep geological structures and geodynamics on the basis of gravity, magnetic and bathymetric data. We estimate Curie-point depth and lithospheric effective elastic thickness to understand deep geothermal structures and Arctic lithospheric evolution. A fractal exponent of 3.0 for the 3D magnetization model is used in the Curie-point depth inversion. The result shows that Curie-point depths are between 5 and 50 km. Curie depths are mostly small near the active mid-ocean ridges, corresponding well to high heat flow and active shallow volcanism. Large curie depths are distributed mainly at continental marginal seas around the Arctic Ocean. We present a map of effective elastic thickness (Te) of the lithosphere using a multitaper coherence technique, and Te are between 5 and 110 km. Te primarily depends on geothermal gradient and composition, as well as structures in the lithosphere. We find that Te and Curie-point depths are often correlated. Large Te are distributed mainly at continental region and small Te are distributed at oceanic region. The Alpha-Mendeleyev Ridge (AMR) and The Svalbard Archipelago (SA) are symmetrical with the mid-ocean ridge. AMR and SA were formed before an early stage of Eurasian basin spreading, and they are considered as conjugate large igneous provinces, which show small Te and Curie-point depths. Novaya Zemlya region has large Curie-point depths and small Te. We consider that fault and fracture near the Novaya Zemlya orogenic belt cause small Te. A series of transform faults connect Arctic mid-ocean ridge with North Atlantic mid-ocean ridge. We can see large Te near transform faults, but small Curie-point depths. We consider that although temperature near transform faults is high, but mechanically the lithosphere near transform faults are strengthened.

Vertebral Adaptations to Large Body Size in Theropod Dinosaurs.

PubMed

Wilson, John P; Woodruff, D Cary; Gardner, Jacob D; Flora, Holley M; Horner, John R; Organ, Chris L

2016-01-01

Rugose projections on the anterior and posterior aspects of vertebral neural spines appear throughout Amniota and result from the mineralization of the supraspinous and interspinous ligaments via metaplasia, the process of permanent tissue-type transformation. In mammals, this metaplasia is generally pathological or stress induced, but is a normal part of development in some clades of birds. Such structures, though phylogenetically sporadic, appear throughout the fossil record of non-avian theropod dinosaurs, yet their physiological and adaptive significance has remained unexamined. Here we show novel histologic and phylogenetic evidence that neural spine projections were a physiological response to biomechanical stress in large-bodied theropod species. Metaplastic projections also appear to vary between immature and mature individuals of the same species, with immature animals either lacking them or exhibiting smaller projections, supporting the hypothesis that these structures develop through ontogeny as a result of increasing bending stress subjected to the spinal column. Metaplastic mineralization of spinal ligaments would likely affect the flexibility of the spinal column, increasing passive support for body weight. A stiff spinal column would also provide biomechanical support for the primary hip flexors and, therefore, may have played a role in locomotor efficiency and mobility in large-bodied species. This new association of interspinal ligament metaplasia in Theropoda with large body size contributes additional insight to our understanding of the diverse biomechanical coping mechanisms developed throughout Dinosauria, and stresses the significance of phylogenetic methods when testing for biological trends, evolutionary or not.

Bacteriophage Tail-Tube Assembly Studied by Proton-Detected 4D Solid-State NMR

DOE PAGES

Zinke, Maximilian; Fricke, Pascal; Samson, Camille; ...

2017-07-07

Obtaining unambiguous resonance assignments remains a major bottleneck in solid-state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three-dimensional (3D) spectra are used. Here, we present a proton-detected 4D solid-state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non-uniform sampling (as low as 2 %). As a proof of principle, we acquired 4D (H)COCANH,more » (H)CACONH, and (H)CBCANH spectra of the 20 kDa bacteriophage tail-tube protein gp17.1 in a total time of two and a half weeks. These spectra were sufficient to obtain complete resonance assignments in a straightforward manner without use of previous solution NMR data.« less

Bacteriophage Tail-Tube Assembly Studied by Proton-Detected 4D Solid-State NMR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zinke, Maximilian; Fricke, Pascal; Samson, Camille

Obtaining unambiguous resonance assignments remains a major bottleneck in solid-state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three-dimensional (3D) spectra are used. Here, we present a proton-detected 4D solid-state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non-uniform sampling (as low as 2 %). As a proof of principle, we acquired 4D (H)COCANH,more » (H)CACONH, and (H)CBCANH spectra of the 20 kDa bacteriophage tail-tube protein gp17.1 in a total time of two and a half weeks. These spectra were sufficient to obtain complete resonance assignments in a straightforward manner without use of previous solution NMR data.« less

The VIMOS Public Extragalactic Redshift Survey (VIPERS): Science Highlights and Final Data Release

NASA Astrophysics Data System (ADS)

Guzzo, L.; Vipers Team

2017-06-01

The VIMOS Public Extragalactic Redshift Survey (VIPERS) released its final set of nearly 90 000 galaxy redshifts in November 2016, together with a series of science papers that range from the detailed evolution of galaxies over the past 8 Gyr to the growth rate and the power spectrum of cosmological structures measured at about half the Hubble time. These are the results of a map of the distribution of galaxies and their properties which is unprecedented in its combination of large volume and detailed sampling at 0.5 < z < 1.2. In this article, the survey design and data properties are briefly summarised and an overview of the key scientific results published so far is provided. The VIPERS data, obtained within the framework of an ESO Large Programme over the equivalent of just under 55 nights at the Very Large Telescope, will remain the largest legacy of the VIMOS spectrograph and its still unsurpassed ability to reach target densities close to 10000 spectra per square degree.

High-resolution 2-D Bragg diffraction reveal heterogeneous domain transformation behavior in a bulk relaxor ferroelectric

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pramanick, Abhijit, E-mail: apramani@cityu.edu.hk; Stoica, Alexandru D.; An, Ke

2016-08-29

In-situ measurement of fine-structure of neutron Bragg diffraction peaks from a relaxor single-crystal using a time-of-flight instrument reveals highly heterogeneous mesoscale domain transformation behavior under applied electric fields. It is observed that only ∼25% of domains undergo reorientation or phase transition contributing to large average strains, while at least 40% remain invariant and exhibit microstrains. Such insights could be central for designing new relaxor materials with better performance and longevity. The current experimental technique can also be applied to resolve complex mesoscale phenomena in other functional materials.

Terahertz birefringence of potassium niobate crystals

NASA Astrophysics Data System (ADS)

Antsygin, V. D.; Mamrashev, A. A.; Nikolaev, N. A.

2018-03-01

We present terahertz optical properties (refractive indices and absorption coefficients) of potassium niobate crystals measured by time-domain spectroscopy in the range of 0.2-2.0 THz. We observe average refractive indices nx = 5.25, ny = 4.8, nz = 5.9 for corresponding optical axes X, Y, Z with the large birefringence of Δn = nz - ny = 1.1. We report rising absorption coefficient at higher frequencies (α ∼ 50 cm-1 at 1 THz for all three axes) while the dichroism is not pronounced. Somewhat higher absorption compared to the previous results could be attributed to some polydomain structure remaining in the crystal.

Plasma motions in planetary magnetospheres

NASA Technical Reports Server (NTRS)

Hill, T. W.; Dessler, A. J.

1991-01-01

Interplanetary space is pervaded by a supersonic 'solar wind' plasma; five planets, in addition to the earth, have magnetic fields of sufficient strength to form the cometlike cavities called 'magnetospheres'. Comparative studies of these structures have indicated the specific environmental factor that can result in dramatic differences in the behavior of any pair of magnetospheres. Although planetary magnetospheres are large enough to serve as laboratories for in situ study of cosmic plasma and magnetic field behavior effects on particle acceleration and EM emission, much work remains to be done toward relating magnetospheric physics results to the study of remote astrophysical plasmas.

High-resolution 2-D Bragg diffraction reveal heterogeneous domain transformation behavior in a bulk relaxor ferroelectric

DOE PAGES

Pramanick, Abhijit; Stoica, Alexandru D.; An, Ke

2016-09-02

In-situ measurement of fine-structure of neutron Bragg diffraction peaks from a relaxor single-crystal using a time-of-flight instrument reveals highly heterogeneous mesoscale domain transformation behavior under applied electric fields. We observed that only 25% of domains undergo reorienta- tion or phase transition contributing to large average strains, while at least 40% remain invariant and exhibit microstrains. Such insights could be central for designing new relaxor materials with better performance and longevity. The current experimental technique can also be applied to resolve com- plex mesoscale phenomena in other functional materials.

Persistence of soil organic matter as an ecosystem property.

PubMed

Schmidt, Michael W I; Torn, Margaret S; Abiven, Samuel; Dittmar, Thorsten; Guggenberger, Georg; Janssens, Ivan A; Kleber, Markus; Kögel-Knabner, Ingrid; Lehmann, Johannes; Manning, David A C; Nannipieri, Paolo; Rasse, Daniel P; Weiner, Steve; Trumbore, Susan E

2011-10-05

Globally, soil organic matter (SOM) contains more than three times as much carbon as either the atmosphere or terrestrial vegetation. Yet it remains largely unknown why some SOM persists for millennia whereas other SOM decomposes readily--and this limits our ability to predict how soils will respond to climate change. Recent analytical and experimental advances have demonstrated that molecular structure alone does not control SOM stability: in fact, environmental and biological controls predominate. Here we propose ways to include this understanding in a new generation of experiments and soil carbon models, thereby improving predictions of the SOM response to global warming.

Aluminum Foils of the Stardust Interstellar Collector: The Challenge of Recognizing Micrometer-sized Impact Craters made by Interstellar Grains

NASA Technical Reports Server (NTRS)

Kearsley, A. T.; Westphal, A. J.; Burchell, M. J.; Zolensky, Michael E.

2008-01-01

Preliminary Examination (PE) of the Stardust cometary collector revealed material embedded in aerogel and on aluminium (Al) foil. Large numbers of sub-micrometer impact craters gave size, structural and compositional information. With experience of finding and analyzing the picogram to nanogram mass remains of cometary particles, are we now ready for PE of the Interstellar (IS) collector? Possible interstellar particle (ISP) tracks in the aerogel are being identified by the stardust@home team. We are now assessing challenges facing PE of Al foils from the interstellar collector.

Magnetic tunnel junction thermocouple for thermoelectric power harvesting

NASA Astrophysics Data System (ADS)

Böhnert, T.; Paz, E.; Ferreira, R.; Freitas, P. P.

2018-05-01

The thermoelectric power generated in magnetic tunnel junctions (MTJs) is determined as a function of the tunnel barrier thickness for a matched electric circuit. This study suggests that lower resistance area product and higher tunnel magnetoresistance will maximize the thermoelectric power output of the MTJ structures. Further, the thermoelectric behavior of a series of two MTJs, a MTJ thermocouple, is investigated as a function of its magnetic configurations. In an alternating magnetic configurations the thermovoltages cancel each other, while the magnetic contribution remains. A large array of MTJ thermocouples could amplify the magnetic thermovoltage signal significantly.

Persistence of soil organic matter as an ecosystem property

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schmidt, M.W.; Torn, M. S.; Abiven, S.

2011-08-15

Globally, soil organic matter (SOM) contains more than three times as much carbon as either the atmosphere or terrestrial vegetation. Yet it remains largely unknown why some SOM persists for millennia whereas other SOM decomposes readily—and this limits our ability to predict how soils will respond to climate change. Recent analytical and experimental advances have demonstrated that molecular structure alone does not control SOM stability: in fact, environmental and biological controls predominate. Here we propose ways to include this understanding in a new generation of experiments and soil carbon models, thereby improving predictions of the SOM response to global warming.

Acid-sensing ion channels in pain and disease

PubMed Central

Wemmie, John A.; Taugher, Rebecca J.; Kreple, Collin J.

2015-01-01

Why do neurons sense extracellular acid? In large part, this question has driven increasing investigation on acid-sensing ion channels (ASICs) in the CNS and the peripheral nervous system for the past two decades. Significant progress has been made in understanding the structure and function of ASICs at the molecular level. Studies aimed at clarifying their physiological importance have suggested roles for ASICs in pain, neurological and psychiatric disease. This Review highlights recent findings linking these channels to physiology and disease. In addition, it discusses some of the implications for therapy and points out questions that remain unanswered. PMID:23783197

Acid-sensing ion channels in pain and disease.

PubMed

Wemmie, John A; Taugher, Rebecca J; Kreple, Collin J

2013-07-01

Why do neurons sense extracellular acid? In large part, this question has driven increasing investigation on acid-sensing ion channels (ASICs) in the CNS and the peripheral nervous system for the past two decades. Significant progress has been made in understanding the structure and function of ASICs at the molecular level. Studies aimed at clarifying their physiological importance have suggested roles for ASICs in pain, neurological and psychiatric disease. This Review highlights recent findings linking these channels to physiology and disease. In addition, it discusses some of the implications for therapy and points out questions that remain unanswered.

Associations between antimicrobial stewardship program elements and Clostridium difficile infection performance.

PubMed

Barlow, Giulia; Patterson, Julie; Stultz, Jeremy; Pakyz, Amy L

2017-12-01

Hospitals are categorized as better, no different, or worse at a national level based on their Clostridium difficile infection performance. Institutional antimicrobial stewardship programs seek to decrease the occurrence of C difficile by implementing strategies to address antibiotic usage; however, optimal structure and strategies for accomplishing this remain largely unknown. We found that a higher proportion of hospitals with either a worse or no different rank used a postprescription audit and feedback strategy than hospitals with a better rank. Copyright © 2017 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

The hubble constant.

PubMed

Huchra, J P

1992-04-17

The Hubble constant is the constant of proportionality between recession velocity and distance in the expanding universe. It is a fundamental property of cosmology that sets both the scale and the expansion age of the universe. It is determined by measurement of galaxy The Hubble constant is the constant of proportionality between recession velocity and development of new techniques for the measurements of galaxy distances, both calibration uncertainties and debates over systematic errors remain. Current determinations still range over nearly a factor of 2; the higher values favored by most local measurements are not consistent with many theories of the origin of large-scale structure and stellar evolution.

Effects of shallow natural gas well structures and associated roads on grassland songbird reproductive success in Alberta, Canada

PubMed Central

Koper, Nicola

2017-01-01

Grassland songbird populations across North America have experienced dramatic population declines due to habitat loss and degradation. In Canada, energy development continues to fragment and disturb prairie habitat, but effects of oil and gas development on reproductive success of songbirds in North American mixed-grass prairies remains largely unknown. From 2010–2012, in southeastern Alberta, Canada, we monitored 257 nests of two ground-nesting grassland songbird species, Savannah sparrow (Passerculus sandwichensis) and chestnut-collared longspur (Calcarius ornatus). Nest locations varied with proximity to and density of conventional shallow gas well structures and associated roads in forty-two 258-ha mixed-grass prairie sites. We estimated the probabilities of nest success and clutch size relative to gas well structures and roads. There was little effect of distance to or density of gas well structure on nest success; however, Savannah sparrow experienced lower nest success near roads. Clutch sizes were lower near gas well structures and cattle water sources. Minimizing habitat disturbance surrounding gas well structures, and reducing abundance of roads and trails, would help minimize impacts on reproductive success for some grassland songbirds. PMID:28355241

Assembly of Layered Monetite-Chitosan Nanocomposite and Its Transition to Organized Hydroxyapatite.

PubMed

Ruan, Qichao; Liberman, David; Zhang, Yuzheng; Ren, Dongni; Zhang, Yunpeng; Nutt, Steven; Moradian-Oldak, Janet

2016-06-13

Bioinspired synthesis of hierarchically structured calcium phosphate (CaP) material is a highly promising strategy for developing improved bone substitute materials. However, synthesis of CaP materials with outstanding mechanical properties still remains an ongoing challenge. Inspired by the formation of lamellar structure in nacre, we designed an organic matrix composed of chitosan and cis-butenediolic acid (maleic acid, MAc) that could assemble into a layered complex and further guide the mineralization of monetite crystals, resulting in the formation of organized and parallel arrays of monetite platelets with a brick-and-mortar structure. Using the layered monetite-chitosan composite as a precursor, we were able to synthesize hydroxyapatite (HAp) with multiscale hierarchically ordered structure via a topotactic phase transformation process. On the nanoscale, needlelike HAp crystallites assembled into organized bundles that aligned to form highly oriented plates on the microscale. On the large-scale level, these plates with different crystal orientations were stacked together to form a layered structure. The organized structures and composite feature yielded CaP materials with improved mechanical properties close to those of bone. Our study introduces a biomimetic approach that may be practical for the design of advanced, mechanically robust materials for biomedical applications.

Determinants of community structure of zooplankton in heavily polluted river ecosystems

NASA Astrophysics Data System (ADS)

Xiong, Wei; Li, Jie; Chen, Yiyong; Shan, Baoqing; Wang, Weimin; Zhan, Aibin

2016-02-01

River ecosystems are among the most affected habitats globally by human activities, such as the release of chemical pollutants. However, it remains largely unknown how and to what extent many communities such as zooplankton are affected by these environmental stressors in river ecosystems. Here, we aim to determine major factors responsible for shaping community structure of zooplankton in heavily polluted river ecosystems. Specially, we use rotifers in the Haihe River Basin (HRB) in North China as a case study to test the hypothesis that species sorting (i.e. species are “filtered” by environmental factors and occur at environmental suitable sites) plays a key role in determining community structure at the basin level. Based on an analysis of 94 sites across the plain region of HRB, we found evidence that both local and regional factors could affect rotifer community structure. Interestingly, further analyses indicated that local factors played a more important role in determining community structure. Thus, our results support the species sorting hypothesis in highly polluted rivers, suggesting that local environmental constraints, such as environmental pollution caused by human activities, can be stronger than dispersal limitation caused by regional factors to shape local community structure of zooplankton at the basin level.

Atomic scale chemical tomography of human bone

NASA Astrophysics Data System (ADS)

Langelier, Brian; Wang, Xiaoyue; Grandfield, Kathryn

2017-01-01

Human bone is a complex hierarchical material. Understanding bone structure and its corresponding composition at the nanometer scale is critical for elucidating mechanisms of biomineralization under healthy and pathological states. However, the three-dimensional structure and chemical nature of bone remains largely unexplored at the nanometer scale due to the challenges associated with characterizing both the structural and chemical integrity of bone simultaneously. Here, we use correlative transmission electron microscopy and atom probe tomography for the first time, to our knowledge, to reveal structures in human bone at the atomic level. This approach provides an overlaying chemical map of the organic and inorganic constituents of bone on its structure. This first use of atom probe tomography on human bone reveals local gradients, trace element detection of Mg, and the co-localization of Na with the inorganic-organic interface of bone mineral and collagen fibrils, suggesting the important role of Na-rich organics in the structural connection between mineral and collagen. Our findings provide the first insights into the hierarchical organization and chemical heterogeneity in human bone in three-dimensions at its smallest length scale - the atomic level. We demonstrate that atom probe tomography shows potential for new insights in biomineralization research on bone.

Effects of shallow natural gas well structures and associated roads on grassland songbird reproductive success in Alberta, Canada.

PubMed

Yoo, Jenny; Koper, Nicola

2017-01-01

Grassland songbird populations across North America have experienced dramatic population declines due to habitat loss and degradation. In Canada, energy development continues to fragment and disturb prairie habitat, but effects of oil and gas development on reproductive success of songbirds in North American mixed-grass prairies remains largely unknown. From 2010-2012, in southeastern Alberta, Canada, we monitored 257 nests of two ground-nesting grassland songbird species, Savannah sparrow (Passerculus sandwichensis) and chestnut-collared longspur (Calcarius ornatus). Nest locations varied with proximity to and density of conventional shallow gas well structures and associated roads in forty-two 258-ha mixed-grass prairie sites. We estimated the probabilities of nest success and clutch size relative to gas well structures and roads. There was little effect of distance to or density of gas well structure on nest success; however, Savannah sparrow experienced lower nest success near roads. Clutch sizes were lower near gas well structures and cattle water sources. Minimizing habitat disturbance surrounding gas well structures, and reducing abundance of roads and trails, would help minimize impacts on reproductive success for some grassland songbirds.

Investigating error structure of shuttle radar topography mission elevation data product

NASA Astrophysics Data System (ADS)

Becek, Kazimierz

2008-08-01

An attempt was made to experimentally assess the instrumental component of error of the C-band SRTM (SRTM). This was achieved by comparing elevation data of 302 runways from airports all over the world with the shuttle radar topography mission data product (SRTM). It was found that the rms of the instrumental error is about +/-1.55 m. Modeling of the remaining SRTM error sources, including terrain relief and pixel size, shows that downsampling from 30 m to 90 m (1 to 3 arc-sec pixels) worsened SRTM vertical accuracy threefold. It is suspected that the proximity of large metallic objects is a source of large SRTM errors. The achieved error estimates allow a pixel-based accuracy assessment of the SRTM elevation data product to be constructed. Vegetation-induced errors were not considered in this work.

An intense, quasi-steady thunderstorm over mountainous terrain. I - Evolution of the storm-initiating mesoscale circulation

NASA Technical Reports Server (NTRS)

Cotton, W. R.; George, R. L.; Knupp, K. R.

1982-01-01

The evolution of mesoscale systems that eventually lead to the formation of large quasi-steady storm systems is investigated. The morphological and turbulent structure of the quasi-steady storm is described. Data obtained during the South Park Area Cumulus Experiment from surface meteorological stations, rawinsondes and tethered balloons, conventional and Doppler radars, powered aircraft, and satellites, indicate that on July 19, 1977, a north-south oriented line of intense convective cells formed and remained within South Park. Elevated surface heating created a region of low-level convergence, importing Pacific moisture from west of the Rockies. The mesoscale thunderstorm line formed over this convergence zone, and a single large convective cell was observed to grow on the southern end of the mesoscale line, exhibiting supercell characteristics and substantial modifications of the environmental flow.

Fibrin mechanical properties and their structural origins.

PubMed

Litvinov, Rustem I; Weisel, John W

2017-07-01

Fibrin is a protein polymer that is essential for hemostasis and thrombosis, wound healing, and several other biological functions and pathological conditions that involve extracellular matrix. In addition to molecular and cellular interactions, fibrin mechanics has been recently shown to underlie clot behavior in the highly dynamic intra- and extravascular environments. Fibrin has both elastic and viscous properties. Perhaps the most remarkable rheological feature of the fibrin network is an extremely high elasticity and stability despite very low protein content. Another important mechanical property that is common to many filamentous protein polymers but not other polymers is stiffening occurring in response to shear, tension, or compression. New data has begun to provide a structural basis for the unique mechanical behavior of fibrin that originates from its complex multi-scale hierarchical structure. The mechanical behavior of the whole fibrin gel is governed largely by the properties of single fibers and their ensembles, including changes in fiber orientation, stretching, bending, and buckling. The properties of individual fibrin fibers are determined by the number and packing arrangements of double-stranded half-staggered protofibrils, which still remain poorly understood. It has also been proposed that forced unfolding of sub-molecular structures, including elongation of flexible and relatively unstructured portions of fibrin molecules, can contribute to fibrin deformations. In spite of a great increase in our knowledge of the structural mechanics of fibrin, much about the mechanisms of fibrin's biological functions remains unknown. Fibrin deformability is not only an essential part of the biomechanics of hemostasis and thrombosis, but also a rapidly developing field of bioengineering that uses fibrin as a versatile biomaterial with exceptional and tunable biochemical and mechanical properties. Copyright © 2016 Elsevier B.V. All rights reserved.

Anisotropic lattice softening near the structural phase transition in the thermosalient crystal 1,2,4,5-tetrabromobenzene.

PubMed

Zakharov, Boris A; Michalchuk, Adam A L; Morrison, Carole A; Boldyreva, Elena V

2018-03-28

The thermosalient effect (crystal jumping on heating) attracts much attention as both an intriguing academic phenomenon and in relation to its potential for the development of molecular actuators but its mechanism remains unclear. 1,2,4,5-Tetrabromobenzene (TBB) is one of the most extensively studied thermosalient compounds that has been shown previously to undergo a phase transition on heating, accompanied by crystal jumping and cracking. The difference in the crystal structures and intermolecular interaction energies of the low- and high-temperature phases is, however, too small to account for the large stress that arises over the course of the transformation. The energy is released spontaneously, and crystals jump across distances that exceed the crystal size by orders of magnitude. In the present work, the anisotropy of lattice strain is followed across the phase transition by single-crystal X-ray diffraction, focusing on the structural evolution from 273 to 343 K. A pronounced lattice softening is observed close to the transition point, with the structure becoming more rigid immediately after the phase transition. The diffraction studies are further supported by theoretical analysis of pairwise intermolecular energies and zone-centre lattice vibrations. Only three modes are found to monotonically soften up to the phase transition, with complex behaviour exhibited by the remaining lattice modes. The thermosalient effect is delayed with respect to the structural transformation itself. This can originate from the martensitic mechanism of the transformation, and the accumulation of stress associated with vibrational switching across the phase transition. The finding of this study sheds more light on the nature of the thermosalient effect in 1,2,4,5-tetrabromobenzene and can be applicable also to other thermosalient compounds.

Engineering Encodable Lanthanide-Binding Tags (LBTs) into Loop Regions of Proteins

PubMed Central

Barthelmes, Katja; Reynolds, Anne M.; Peisach, Ezra; Jonker, Hendrik R. A.; DeNunzio, Nicholas J.; Allen, Karen N.; Imperiali, Barbara; Schwalbe, Harald

2011-01-01

Lanthanide-binding-tags (LBTs) are valuable tools for investigation of protein structure, function, and dynamics by NMR spectroscopy, X-ray crystallography and luminescence studies. We have inserted LBTs into three different loop positions (denoted L, R, and S) of the model protein interleukin-1β and varied the length of the spacer between the LBT and the protein (denoted 1-3). Luminescence studies demonstrate that all nine constructs bind Tb3+ tightly in the low nanomolar range. No significant change in the fusion protein occurs from insertion of the LBT, as shown by two X-ray crystallographic structures of the IL1β-S1 and IL1β-L3 constructs and for the remaining constructs by comparing 1H-15N-HSQC NMR spectra with wild-type IL1β. Additionally, binding of LBT-loop IL1β proteins to their native binding partner in vitro remains unaltered. X-ray crystallographic phasing was successful using only the signal from the bound lanthanide. Large residual dipolar couplings (RDCs) could be determined by NMR spectroscopy for all LBT-loop-constructs and revealed that the LBT-2 series were rigidly incorporated into the interleukin-1β structure. The paramagnetic NMR spectra of loop-LBT mutant IL1β-R2 were assigned and the Δχ tensor components were calculated based on RDCs and pseudocontact shifts (PCSs). A structural model of the IL1β-R2 construct was calculated using the paramagnetic restraints. The current data provide support that encodable LBTs serve as versatile biophysical tags when inserted into loop regions of proteins of known structure or predicted via homology modelling. PMID:21182275

Top predators, mesopredators and their prey: interference ecosystems along bioclimatic productivity gradients.

PubMed

Elmhagen, B; Ludwig, G; Rushton, S P; Helle, P; Lindén, H

2010-07-01

1. The Mesopredator Release Hypothesis (MRH) suggests that top predator suppression of mesopredators is a key ecosystem function with cascading impacts on herbivore prey, but it remains to be shown that this top-down cascade impacts the large-scale structure of ecosystems. 2. The Exploitation Ecosystems Hypothesis (EEH) predicts that regional ecosystem structures are determined by top-down exploitation and bottom-up productivity. In contrast to MRH, EEH assumes that interference among predators has a negligible impact on the structure of ecosystems with three trophic levels. 3. We use the recolonization of a top predator in a three-level boreal ecosystem as a natural experiment to test if large-scale biomass distributions and population trends support MRH. Inspired by EEH, we also test if top-down interference and bottom-up productivity impact regional ecosystem structures. 4. We use data from the Finnish Wildlife Triangle Scheme which has monitored top predator (lynx, Lynx lynx), mesopredator (red fox, Vulpes vulpes) and prey (mountain hare, Lepus timidus) abundance for 17 years in a 200 000 km(2) study area which covers a distinct productivity gradient. 5. Fox biomass was lower than expected from productivity where lynx biomass was high, whilst hare biomass was lower than expected from productivity where fox biomass was high. Hence, where interference controlled fox abundance, lynx had an indirect positive impact on hare abundance as predicted by MRH. The rates of change indicated that lynx expansion gradually suppressed fox biomass. 6. Lynx status caused shifts between ecosystem structures. In the 'interference ecosystem', lynx and hare biomass increased with productivity whilst fox biomass did not. In the 'mesopredator release ecosystem', fox biomass increased with productivity but hare biomass did not. Thus, biomass controlled top-down did not respond to changes in productivity. This fulfils a critical prediction of EEH. 7. We conclude that the cascade involving top predators, mesopredators and their prey can determine large-scale biomass distribution patterns and regional ecosystem structures. Hence, interference within trophic levels has to be taken into account to understand how terrestrial ecosystem structures are shaped.

Lessons learned: Infrastructure development and financial management for large, publically funded, international trials

PubMed Central

Larson, Gregg S; Carey, Cate; Grarup, Jesper; Hudson, Fleur; Sachi, Karen; Vjecha, Michael J; Gordin, Fred

2015-01-01

Background/Aims Randomized clinical trials are widely recognized as essential to address world-wide clinical and public health research questions. However, for many conditions, their size and duration can overwhelm available public and private resources. To remain competitive in international research settings, advocates and practitioners of clinical trials must implement practices that reduce their cost. We identify approaches and practices for large, publicly-funded, international trials that reduce cost without compromising data integrity, and recommend an approach to cost reporting that permits comparison of clinical trials. Methods We describe the organizational and financial characteristics of INSIGHT, an infectious disease research network that conducts multiple, large, long-term, international trials, and examine challenges associated with simple and streamlined governance and an infrastructure and financial management model that is based on performance, transparency, and accountability. Results It is possible to reduce costs of participant follow-up and not compromise clinical trial quality or integrity. The INSIGHT network has successfully completed four large HIV trials using cost-efficient practices that have not adversely affected investigator enthusiasm, accrual rates, loss-to-follow-up, adherence to the protocol, and completion of data collection. This experience is relevant to the conduct of large, publically funded trials in other disease areas, particularly trials dependent on international collaborations. Conclusion New approaches, or creative adaption of traditional clinical trial infrastructure and financial management tools, can render large, international clinical trials more cost-efficient by emphasizing structural simplicity; minimal up-front costs; payments for performance; and uniform algorithms and fees-for-service, irrespective of location. However, challenges remain. They include institutional resistance to financial change, growing trial complexity, and the difficulty of sustaining network infrastructure absent stable research work. There is also a need for more central monitoring, improved and harmonized regulations, and a widely-applied metric for measuring and comparing cost efficiency in clinical trials. ClinicalTrials.gov is recommended as a location where standardized trial cost information could be made publicly accessible. PMID:26908541

Structure and stability of the ankyrin domain of the Drosophila Notch receptor.

PubMed

Zweifel, Mark E; Leahy, Daniel J; Hughson, Frederick M; Barrick, Doug

2003-11-01

The Notch receptor contains a conserved ankyrin repeat domain that is required for Notch-mediated signal transduction. The ankyrin domain of Drosophila Notch contains six ankyrin sequence repeats previously identified as closely matching the ankyrin repeat consensus sequence, and a putative seventh C-terminal sequence repeat that exhibits lower similarity to the consensus sequence. To better understand the role of the Notch ankyrin domain in Notch-mediated signaling and to examine how structure is distributed among the seven ankyrin sequence repeats, we have determined the crystal structure of this domain to 2.0 angstroms resolution. The seventh, C-terminal, ankyrin sequence repeat adopts a regular ankyrin fold, but the first, N-terminal ankyrin repeat, which contains a 15-residue insertion, appears to be largely disordered. The structure reveals a substantial interface between ankyrin polypeptides, showing a high degree of shape and charge complementarity, which may be related to homotypic interactions suggested from indirect studies. However, the Notch ankyrin domain remains largely monomeric in solution, demonstrating that this interface alone is not sufficient to promote tight association. Using the structure, we have classified reported mutations within the Notch ankyrin domain that are known to disrupt signaling into those that affect buried residues and those restricted to surface residues. We show that the buried substitutions greatly decrease protein stability, whereas the surface substitutions have only a marginal affect on stability. The surface substitutions are thus likely to interfere with Notch signaling by disrupting specific Notch-effector interactions and map the sites of these interactions.

Inferring coarse-grain histone-DNA interaction potentials from high-resolution structures of the nucleosome

NASA Astrophysics Data System (ADS)

Meyer, Sam; Everaers, Ralf

2015-02-01

The histone-DNA interaction in the nucleosome is a fundamental mechanism of genomic compaction and regulation, which remains largely unknown despite increasing structural knowledge of the complex. In this paper, we propose a framework for the extraction of a nanoscale histone-DNA force-field from a collection of high-resolution structures, which may be adapted to a larger class of protein-DNA complexes. We applied the procedure to a large crystallographic database extended by snapshots from molecular dynamics simulations. The comparison of the structural models first shows that, at histone-DNA contact sites, the DNA base-pairs are shifted outwards locally, consistent with locally repulsive forces exerted by the histones. The second step shows that the various force profiles of the structures under analysis derive locally from a unique, sequence-independent, quadratic repulsive force-field, while the sequence preferences are entirely due to internal DNA mechanics. We have thus obtained the first knowledge-derived nanoscale interaction potential for histone-DNA in the nucleosome. The conformations obtained by relaxation of nucleosomal DNA with high-affinity sequences in this potential accurately reproduce the experimental values of binding preferences. Finally we address the more generic binding mechanisms relevant to the 80% genomic sequences incorporated in nucleosomes, by computing the conformation of nucleosomal DNA with sequence-averaged properties. This conformation differs from those found in crystals, and the analysis suggests that repulsive histone forces are related to local stretch tension in nucleosomal DNA, mostly between adjacent contact points. This tension could play a role in the stability of the complex.

Assembly of RNA nanostructures on supported lipid bilayers

PubMed Central

Dabkowska, Aleksandra P.; Michanek, Agnes; Jaeger, Luc; Rabe, Michael; Chworos, Arkadiusz; Höök, Fredrik; Nylander, Tommy; Sparr, Emma

2014-01-01

The assembly of nucleic acid nanostructures with controlled size and shape has large impact in the fields of nanotechnology, nanomedicine and synthetic biology. The directed arrangement of nanostructures at interfaces is important for many applications. In spite of this, the use of laterally mobile lipid bilayers to control RNA three-dimensional nanostructure formation on surfaces remains largely unexplored. Here, we direct the self-assembly of RNA building blocks into three-dimensional structures of RNA on fluid lipid bilayers composed of cationic 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) or mixtures of zwitterionic 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) and cationic sphingosine. We demonstrate the stepwise supramolecular assembly of discrete building blocks through specific and selective RNA-RNA interactions, based on results from quartz crystal microbalance with dissipation (QCM-D), ellipsometry, fluorescence recovery after photobleaching (FRAP) and total internal reflection fluorescence microscopy (TIRF) experiments. The assembly can be controlled to give a densely packed single layer of RNA polyhedrons at the fluid lipid bilayer surface. We show that assembly of the 3D structure can be modulated by sequence specific interactions, surface charge and changes in the salt composition and concentration. In addition, the tertiary structure of the RNA polyhedron can be controllably switched from an extended structure to one that is dense and compact. The versatile approach to building up three-dimensional structures of RNA does not require modification of the surface or the RNA molecules, and can be used as a bottom-up means of nanofabrication of functionalized bio-mimicking surfaces. PMID:25417592

Large eddy simulation study of spanwise spacing effects on secondary flows in turbulent channel flow

NASA Astrophysics Data System (ADS)

Aliakbarimiyanmahaleh, Mohammad; Anderson, William

2015-11-01

The structure of turbulent flow over a complex topography composed of streamwise-aligned rows of cones with varying spanwise spacing, s is studied with large-eddy simulation (LES). Similar to the experimental study of Vanderwel and Ganapathisubramani, 2015: J. Fluid Mech., we investigate the relationship between secondary flow and s, for 0 . 25 <= s / δ <= 5 . For cases with s / δ > 2 , domain-scale rollers freely exist. These had previously been called ``turbulent secondary flows'' (Willingham et al., 2014: Phys. Fluids; Barros and Christensen, 2014: J. Fluid Mech.; Anderson et al., 2015: J. Fluid Mech.), but closer inspection of the statistics indicates these are a turbulent tertiary flow: they only remain ``anchored'' to the conical roughness elements for s / δ > 2 . For s / δ < 2 , turbulent tertiary flows are prevented from occupying the domain by virtue of proximity to adjacent, counter-rotating tertiary flows. Turbulent secondary flows are associated with the conical roughness elements. These turbulent secondary flows emanate from individual conical topographic elements and set the roughness sublayer depth. The turbulent secondary flows remain intact for large and small spacing. For s / δ < 1 , a mean tertiary flow is not present. This work was supported by the Air Force Office of Sci. Research, Young Inv. Program (PM: Dr. R. Ponnoppan and Ms. E. Montomery) under Grant # FA9550-14-1-0394. Computational resources were provided by the Texas Adv. Comp. Center at the Univ. of Texas.

MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive.

PubMed

Bernstein, Matthew N; Doan, AnHai; Dewey, Colin N

2017-09-15

The NCBI's Sequence Read Archive (SRA) promises great biological insight if one could analyze the data in the aggregate; however, the data remain largely underutilized, in part, due to the poor structure of the metadata associated with each sample. The rules governing submissions to the SRA do not dictate a standardized set of terms that should be used to describe the biological samples from which the sequencing data are derived. As a result, the metadata include many synonyms, spelling variants and references to outside sources of information. Furthermore, manual annotation of the data remains intractable due to the large number of samples in the archive. For these reasons, it has been difficult to perform large-scale analyses that study the relationships between biomolecular processes and phenotype across diverse diseases, tissues and cell types present in the SRA. We present MetaSRA, a database of normalized SRA human sample-specific metadata following a schema inspired by the metadata organization of the ENCODE project. This schema involves mapping samples to terms in biomedical ontologies, labeling each sample with a sample-type category, and extracting real-valued properties. We automated these tasks via a novel computational pipeline. The MetaSRA is available at metasra.biostat.wisc.edu via both a searchable web interface and bulk downloads. Software implementing our computational pipeline is available at http://github.com/deweylab/metasra-pipeline. cdewey@biostat.wisc.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Influence of the remaining coronal structure on the resistance of teeth with intraradicular retainer.

PubMed

Pereira, Jefferson Ricardo; Neto, Tatiany de Mendonça; Porto, Vinícius de Carvalho; Pegoraro, Luiz Fernando; do Valle, Accácio Lins

2005-01-01

The aim of this study was to compare the resistance of endodontically treated teeth with intraradicular retainer different amounts of remaining coronal structure. Fifty freshly extracted maxillary canines were endodontically treated and randomly assigned to five groups (n=10), as follows: group 1 (control) = teeth with custom cast post and core; group 2 = teeth without remaining coronal structure; group 3, 4 and 5 = teeth with 1 mm, 2 mm and 3 mm of remaining coronal structure, respectively. All specimens in groups 2 to 5 were restored with prefabricated post and resin core. The teeth were embedded in acrylic resin and the fracture strength was measured on a universal testing machine at 45 degrees to the long axis of the tooth until failure. Data were analyzed statistically by one-way analysis of variance and Tukey's test. There was no significant differences (p>0.05) between the control group and group 2, and between groups 3, 4 and 5 (p>0.05). Control group and group 2 had significantly higher resistance strength than groups 3, 4 and 5 (p<0.00001). The findings of this study showed that teeth without remaining coronal structure had significantly higher fracture strength than those with remaining coronal structure (1 mm, 2 mm and 3 mm). When the dental crown was not completely removed, the amount of remaining coronal dentin did not significantly affect the fracture strength of endodontically treated teeth with intraradicular retainer.

Temperate Snake Community in South America: Is Diet Determined by Phylogeny or Ecology?

PubMed Central

Etchepare, Eduardo G.

2015-01-01

Communities are complex and dynamic systems that change with time. The first attempts to explain how they were structured involve contemporary phenomena like ecological interactions between species (e.g., competition and predation) and led to the competition-predation hypothesis. Recently, the deep history hypothesis has emerged, which suggests that profound differences in the evolutionary history of organisms resulted in a number of ecological features that remain largely on species that are part of existing communities. Nevertheless, both phylogenetic structure and ecological interactions can act together to determine the structure of a community. Because diet is one of the main niche axes, in this study we evaluated, for the first time, the impact of ecological and phylogenetic factors on the diet of Neotropical snakes from the subtropical-temperate region of South America. Additionally, we studied their relationship with morphological and environmental aspects to understand the natural history and ecology of this community. A canonical phylogenetical ordination analysis showed that phylogeny explained most of the variation in diet, whereas ecological characters explained very little of this variation. Furthermore, some snakes that shared the habitat showed some degree of diet convergence, in accordance with the competition-predation hypothesis, although phylogeny remained the major determinant in structuring this community. The clade with the greatest variability was the subfamily Dipsadinae, whose members had a very different type of diet, based on soft-bodied invertebrates. Our results are consistent with the deep history hypothesis, and we suggest that the community under study has a deep phylogenetic effect that explains most of the variation in the diet. PMID:25945501

NanoSIMS Sheds Light on the Origin and Significance of Early Archean Organic Microstructures from the Pilbara of Australia

NASA Technical Reports Server (NTRS)

Oehler, Dorothy Z.; Robert, Francois; Meibom, Anders; Mostefaoui, Smail; Selo, Madeleine; Walter, Malcolm, R.; Sugitani, Kenichiro; Allwood, Abigail; Gibson, Everett K.

2008-01-01

NanoSIMS was used to characterize sub-micron scale morphology and elemental composition (C, N, S, Si, O) of organic microstructures in Early Archean (3 - 3.4 Ga) charts from the Pilbara of Western Australia. Three categories of structures were analyzed: small spheroids in clusters; spindle-shaped remains; and large spheroids. All are relatively poorly preserved and occur within the chert matrix of the samples. Carbonaceous material in a secondary hydrothermal vein also was analyzed, as an example of non-indigenous organic matter. Comparisons were made of NanoSIMS characteristics of the Archean samples and those from well-preserved, biogenic microfossils in the 0.8 Ga Bitter Springs Formation. The comparisons show that the Pilbara microstructures are generally distinct from material in the hydrothermal vein but similar in morphology and elemental composition to the Bitter Springs microfossils. In addition, the Pilbara structures exhibit a spatial relationship to silicon and oxygen that seemingly reflects silica nucleation on organic surfaces; this argues that the organic frameworks of the Archean structures were present in the sediment during crystallization of the silica matrix. The structures are thus interpreted as being indigenous to the enclosing sediment. While these results are suggestive of Early Archean biogenicity and are consistent with a growing body of data suggesting that life on Earth was well established by 3 to 3.4 Ga, work is continuing to determine the N/C and 13C ratios of individual forms, and this should provide additional insight into the derivation and significance of these ancient organic remains.

Condensins exert force on chromatin-nuclear envelope tethers to mediate nucleoplasmic reticulum formation in Drosophila melanogaster.

PubMed

Bozler, Julianna; Nguyen, Huy Q; Rogers, Gregory C; Bosco, Giovanni

2014-12-30

Although the nuclear envelope is known primarily for its role as a boundary between the nucleus and cytoplasm in eukaryotes, it plays a vital and dynamic role in many cellular processes. Studies of nuclear structure have revealed tissue-specific changes in nuclear envelope architecture, suggesting that its three-dimensional structure contributes to its functionality. Despite the importance of the nuclear envelope, the factors that regulate and maintain nuclear envelope shape remain largely unexplored. The nuclear envelope makes extensive and dynamic interactions with the underlying chromatin. Given this inexorable link between chromatin and the nuclear envelope, it is possible that local and global chromatin organization reciprocally impact nuclear envelope form and function. In this study, we use Drosophila salivary glands to show that the three-dimensional structure of the nuclear envelope can be altered with condensin II-mediated chromatin condensation. Both naturally occurring and engineered chromatin-envelope interactions are sufficient to allow chromatin compaction forces to drive distortions of the nuclear envelope. Weakening of the nuclear lamina further enhanced envelope remodeling, suggesting that envelope structure is capable of counterbalancing chromatin compaction forces. Our experiments reveal that the nucleoplasmic reticulum is born of the nuclear envelope and remains dynamic in that they can be reabsorbed into the nuclear envelope. We propose a model where inner nuclear envelope-chromatin tethers allow interphase chromosome movements to change nuclear envelope morphology. Therefore, interphase chromatin compaction may be a normal mechanism that reorganizes nuclear architecture, while under pathological conditions, such as laminopathies, compaction forces may contribute to defects in nuclear morphology. Copyright © 2015 Bozler et al.

Condensins Exert Force on Chromatin-Nuclear Envelope Tethers to Mediate Nucleoplasmic Reticulum Formation in Drosophila melanogaster

PubMed Central

Bozler, Julianna; Nguyen, Huy Q.; Rogers, Gregory C.; Bosco, Giovanni

2014-01-01

Although the nuclear envelope is known primarily for its role as a boundary between the nucleus and cytoplasm in eukaryotes, it plays a vital and dynamic role in many cellular processes. Studies of nuclear structure have revealed tissue-specific changes in nuclear envelope architecture, suggesting that its three-dimensional structure contributes to its functionality. Despite the importance of the nuclear envelope, the factors that regulate and maintain nuclear envelope shape remain largely unexplored. The nuclear envelope makes extensive and dynamic interactions with the underlying chromatin. Given this inexorable link between chromatin and the nuclear envelope, it is possible that local and global chromatin organization reciprocally impact nuclear envelope form and function. In this study, we use Drosophila salivary glands to show that the three-dimensional structure of the nuclear envelope can be altered with condensin II-mediated chromatin condensation. Both naturally occurring and engineered chromatin-envelope interactions are sufficient to allow chromatin compaction forces to drive distortions of the nuclear envelope. Weakening of the nuclear lamina further enhanced envelope remodeling, suggesting that envelope structure is capable of counterbalancing chromatin compaction forces. Our experiments reveal that the nucleoplasmic reticulum is born of the nuclear envelope and remains dynamic in that they can be reabsorbed into the nuclear envelope. We propose a model where inner nuclear envelope-chromatin tethers allow interphase chromosome movements to change nuclear envelope morphology. Therefore, interphase chromatin compaction may be a normal mechanism that reorganizes nuclear architecture, while under pathological conditions, such as laminopathies, compaction forces may contribute to defects in nuclear morphology. PMID:25552604

FOUR DUAL AGN CANDIDATES OBSERVED WITH THE VLBA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gabányi, K. É.; Frey, S.; An, T.

According to hierarchical structure formation models, merging galaxies are expected to be seen in different stages of coalescence. However, there are currently no straightforward observational methods to either select or to confirm a large number of dual active galactic nucleus (AGN) candidates. Most attempts involve obtaining a better understanding of double-peaked narrow emission line sources, in order to distinguish the objects for which the emission lines originate from narrow-line kinematics or jet-driven outflows, from those which might harbor dual AGNs. We observed four such candidate sources with the Very Long Baseline Array (VLBA), at 1.5 GHz with a ∼10 masmore » angular resolution, for which the spectral profiles of AGN optical emission suggested the existence of dual AGNs. In SDSS J210449.13–000919.1 and SDSS J23044.82–093345.3 the radio structures are aligned with the optical emission features, thus the double-peaked emission lines might be the results of jet-driven outflows. In the third detected source SDSS J115523.74+150756.9, the radio structure is less extended and is oriented nearly perpendicular to the position angle derived from optical spectroscopy. The fourth source remained undetected with the VLBA, but it was imaged with the Very Large Array at arcsec resolution a few months before our observations, suggesting the existence of an extended radio structure. We did not detect two radio-emitting cores in any of the four sources, a convincing signature of duality.« less

New insights into typical Archaean structures in greenstone terranes of western Ontario

NASA Technical Reports Server (NTRS)

Schwerdtner, W. M.

1986-01-01

Ongoing detailed field work in selected granitoid complexes of the western Wabigoon and Wawa Subprovinces, southern Canadian Shield, has led to several new conclusions: (1) Prominent gneiss domes are composed of prestrained tonalite-granodiorite and represent dense hoods of magmatic granitoid diapirs; (2) the deformation history of the prestrained gneiss remains to be unraveled; (3) the gneiss lacked a thick cover of mafic metavolcanics or other dense rocks at the time of magmatic diaprisim; (4) the synclinoral structure of large greenstone belts is older than the late gneiss domes and may have been initiated by volcano-tectonic processes; (5) small greenstone masses within the gneiss are complexly deformed, together with the gneiss; and, (6) no compelling evidence has been found of ductile early thrusting in the gneiss terranes. Zones of greenstone enclaves occur in hornblende-rich contaminated tonalite and are apt to be deformed magmatic septa. Elsewhere, the tonalite gneiss is biotite-rich and hornblende-poor. These conclusions rest on several new pieces of structural evidence; (1) oval plutons of syenite-diorite have magmatic strain fabrics and sharp contacts that are parallel to an axial-plane foliation in the surrounding refolded gneiss; (2) gneiss domes are lithologically composite and contain large sheath-like structures which are deformed early plutons, distorted earlier gneiss domes, or early ductile nappes produced by folding of planar plutonic septa, and (3) the predomal attitudes of gneissosity varied from point to point.

Tree Death Leading To Ecosystem Renewal? Forecasting Carbon Storage As Eastern Forests Age

NASA Astrophysics Data System (ADS)

Curtis, P.; Gough, C. M.; Bohrer, G.; Nadelhoffer, K. J.; Ivanov, V. Y.

2013-12-01

The future trajectory of North American carbon (C) stocks remains uncertain as a subset of maturing trees die in mixed deciduous forests of the U.S. Midwest and East transitioning from early to middle and late succession. We are studying disturbance-structure-function relationships of aging forests in northern Michigan using long-term ecological and meteorological C cycling studies, a large-scale disturbance experiment, a 200-year forest chronosequence, and flux comparisons across three tower sites. We find that ecosystem responses to mortality are characterized by several processes that affect structure-function relationships and alter the way ecosystem functioning interacts with meteorological forcing. We subjected 39 ha of forest to moderate experimental disturbance, similar to that of age-related or climatically induced tree mortality. We found that the mortality of a third of all canopy trees minimally altered the balance between forest C uptake and release, as growth-limiting light and nitrogen resources were rapidly reallocated from dead and dying trees to undisturbed trees. Although disturbance-induced mortality increased soil N mineralization rates, nitrification, and denitrification, N exports from soils remained low. Upper canopy gap formation and a rise in structural complexity allowed increased photosynthetic contribution of sub-canopy vegetation to compensate for the death of canopy dominant trees. However, we found large differences between the transpirational response of maples and oaks to VPD and soil moisture, which led to relative declines in maple transpiration post-disturbance. These hydrologic differences may affect a species' ability to compete for resources following such a disturbance. Changes to canopy structure had a relatively small effect on roughness length and the turbulence forcing of fluxes from the canopy. We currently are studying how tree mortality driven changes in canopy structure affects within-canopy resource distribution and subsequent changes in leaf morphological, physiological and biochemical traits, how disturbance severity relates to the magnitude of C storage resilience, the impacts of clouds and aerosols on surface diffuse light and how they interact with canopy structure to modify C uptake, and how these processes change overall C assimilation given different forest age and disturbance histories. Along a conceptual continuum from structural to functional attributes, our results show that leaf area distribution and its heterogeneity, canopy light, water and nutrient use efficiency, canopy roughness length and turbulent mixing of canopy air, and the coupling between soil moisture and canopy density, all change with successional and disturbance processes and affect ecosystem C fluxes. Patchy mortality and related increases in structural complexity could, against expectations, enhance the C storage of some forests. Our finding that increases in canopy structural complexity improve resource-use efficiency provides a mechanism for maintaining high rates of C storage in aging forests.

The internal structure of the Brunt Ice Shelf, Antarctica from ice-penetrating radar

NASA Astrophysics Data System (ADS)

King, Edward; De Rydt, Jan; Gudmundsson, Hilmar

2016-04-01

The Brunt Ice Shelf is a small feature on the Coats Land Coast of the Weddell Sea, Antarctica. It is unusual among Antarctic ice shelves because the ice crossing the grounding line from the ice sheet retains no structural integrity, so the ice shelf comprises icebergs of continental ice cemented together by sea ice, with the whole blanketed by in-situ snowfall. The size and distribution of the icebergs is governed by the thickness profile along the grounding line. Where bedrock troughs discharge thick ice to the ice shelf, the icebergs are large and remain close together with little intervening sea ice. Where bedrock ridges mean the ice crossing the grounding line is thin, the icebergs are small and widely-scattered with large areas of sea ice between them. To better understand the internal structure of the Brunt Ice Shelf and how this might affect the flow dynamics we conducted ice-penetrating radar surveys during December 2015 and January 2016. Three different ground-based radar systems were used, operating at centre frequencies of 400, 50 and 10 MHz respectively. The 400 MHz system gave detailed firn structure and accumulation profiles as well as time-lapse profiles of the active propagation of a crevasse. The 50 MHz system provided intermediate-level detail of iceberg distribution and thickness as well as information on the degree of salt water infiltration into the accumulating snow pack. The 10 MHz system used a high-power transmitter in an attempt to measure ice thickness beneath salt-impregnated ice. In this poster we will present example data from each of the three radar systems which will demonstrate the variability of the internal structure of the ice shelf. We will also present preliminary correlations between the internal structure and the surface topography from satellite data.

The SGC beyond structural genomics: redefining the role of 3D structures by coupling genomic stratification with fragment-based discovery.

PubMed

Bradley, Anthony R; Echalier, Aude; Fairhead, Michael; Strain-Damerell, Claire; Brennan, Paul; Bullock, Alex N; Burgess-Brown, Nicola A; Carpenter, Elisabeth P; Gileadi, Opher; Marsden, Brian D; Lee, Wen Hwa; Yue, Wyatt; Bountra, Chas; von Delft, Frank

2017-11-08

The ongoing explosion in genomics data has long since outpaced the capacity of conventional biochemical methodology to verify the large number of hypotheses that emerge from the analysis of such data. In contrast, it is still a gold-standard for early phenotypic validation towards small-molecule drug discovery to use probe molecules (or tool compounds), notwithstanding the difficulty and cost of generating them. Rational structure-based approaches to ligand discovery have long promised the efficiencies needed to close this divergence; in practice, however, this promise remains largely unfulfilled, for a host of well-rehearsed reasons and despite the huge technical advances spearheaded by the structural genomics initiatives of the noughties. Therefore the current, fourth funding phase of the Structural Genomics Consortium (SGC), building on its extensive experience in structural biology of novel targets and design of protein inhibitors, seeks to redefine what it means to do structural biology for drug discovery. We developed the concept of a Target Enabling Package (TEP) that provides, through reagents, assays and data, the missing link between genetic disease linkage and the development of usefully potent compounds. There are multiple prongs to the ambition: rigorously assessing targets' genetic disease linkages through crowdsourcing to a network of collaborating experts; establishing a systematic approach to generate the protocols and data that comprise each target's TEP; developing new, X-ray-based fragment technologies for generating high quality chemical matter quickly and cheaply; and exploiting a stringently open access model to build multidisciplinary partnerships throughout academia and industry. By learning how to scale these approaches, the SGC aims to make structures finally serve genomics, as originally intended, and demonstrate how 3D structures systematically allow new modes of druggability to be discovered for whole classes of targets. © 2017 The Author(s).

Discovery of small-scale-structure in the large molecule/dust distribution in the diffuse ISM

NASA Astrophysics Data System (ADS)

Cordiner, Martin A.; Fossey, Stephen J.; Sarre, Peter J.

There is mounting evidence that far from being homogeneously distributed, interstellar matter can have a clumpy or filamentary structure on the scale of 10s to a few 1000s of AU and which is commonly described as small scale structure (SSS). Initially confined to VLBI HI observations and HI observations of high-velocity pulsars, evidence for SSS has also come indirectly from molecular radio studies of e.g. HCO+ and infrared absorption by H3+. Much of the recent data on SSS has been obtained through optical/UV detection of atomic and diatomic molecular lines. Is there small scale structure in the large molecule/dust distribution? While this question could in principle be explored by measuring differences in the interstellar extinction towards the components of binary stars, in practice this would be difficult. Rather we chose to investigate this by recording very high signal-to-noise spectra of diffuse interstellar absorption bands. Although the carriers remain unidentified, the diffuse bands are generally considered to be tracers of the large molecule/dust distribution and scale well with reddening. Using the Anglo-Australian Telescope we have made UCLES observations of pairs of stars with separations ranging between 500 and 30000 AU. The signal-to-noise achieved was up to 2000, thus allowing variations in central depth of less than a few tenths of a percent to be discernible. Striking differences in diffuse band strengths for closely spaced lines of sight are found showing clearly that there exists small-scale-structure in the large molecule/dust distribution. For example, in the Ophiuchus star-formation region the central depths for the λ6614 diffuse band towards the ρ Oph stars A, B, C and D/E all differ and range between 0.966 and 0.930. Further interesting behaviour is found when comparing the relative strengths of diffuse bands between closely parallel lines of sight. Taking again the ρ Oph group, for λ5797 the strengths follow the order DE > B > C > A whereas the λ5850 band, which has been associated with λ5797 as a member of the same 'family', follows a very different intensity pattern with C > B > A > DE. This opens a new avenue of diffuse band research in its own right and provides a rigorous test for models and theories of diffuse band carrier structure and behaviour.

Complementary uses of small angle X-ray scattering and X-ray crystallography.

PubMed

Pillon, Monica C; Guarné, Alba

2017-11-01

Most proteins function within networks and, therefore, protein interactions are central to protein function. Although stable macromolecular machines have been extensively studied, dynamic protein interactions remain poorly understood. Small-angle X-ray scattering probes the size, shape and dynamics of proteins in solution at low resolution and can be used to study samples in a large range of molecular weights. Therefore, it has emerged as a powerful technique to study the structure and dynamics of biomolecular systems and bridge fragmented information obtained using high-resolution techniques. Here we review how small-angle X-ray scattering can be combined with other structural biology techniques to study protein dynamics. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

Plant cell wall engineering: applications in biofuel production and improved human health.

PubMed

Burton, Rachel A; Fincher, Geoffrey B

2014-04-01

Plant cell walls consist largely of cellulose, non-cellulosic polysaccharides and lignin. Concerted attempts are underway to convert wall polysaccharides from crop plant residues into renewable transport fuels and other valuable products, and to exploit the dietary benefits of cereal grain wall polysaccharides in human health. Attempts to improve plant performance for these applications have involved the manipulation of the levels and structures of wall components. Some successes in altering non-cellulosic polysaccharides has been achieved, but it would appear that drastic changes in cellulose are more difficult to engineer. Nevertheless, future prospects for both genetically modified (GM) and non-GM technologies to modify plant cell wall composition and structure remain bright, and will undoubtedly find applications beyond the current focus on human health and biofuel production. Copyright © 2013. Published by Elsevier Ltd.

Study of acoustic emission during mechanical tests of large flight weight tank structure

NASA Technical Reports Server (NTRS)

Mccauley, B. O.; Nakamura, Y.; Veach, C. L.

1973-01-01

A PPO-insulated, flight-weight, subscale, aluminum tank was monitored for acoustic emissions during a proof test and during 100 cycles of environmental test simulating space flights. The use of a combination of frequency filtering and appropriate spatial filtering to reduce background noise was found to be sufficient to detect acoustic emission signals of relatively small intensity expected from subcritical crack growth in the structure. Several emission source locations were identified, including the one where a flaw was detected by post-test x-ray inspections. For most source locations, however, post-test inspections did not detect flaws; this was partially attributed to the higher sensitivity of the acoustic emission technique than any other currently available NDT method for detecting flaws. For these non-verifiable emission sources, a problem still remains in correctly interpreting observed emission signals.

Inverse statistical physics of protein sequences: a key issues review.

PubMed

Cocco, Simona; Feinauer, Christoph; Figliuzzi, Matteo; Monasson, Rémi; Weigt, Martin

2018-03-01

In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques, sequence data accumulate at unprecedented pace. This provides large sets of so-called homologous, i.e. evolutionarily related protein sequences, to which methods of inverse statistical physics can be applied. Using sequence data as the basis for the inference of Boltzmann distributions from samples of microscopic configurations or observables, it is possible to extract information about evolutionary constraints and thus protein function and structure. Here we give an overview over some biologically important questions, and how statistical-mechanics inspired modeling approaches can help to answer them. Finally, we discuss some open questions, which we expect to be addressed over the next years.

Inverse statistical physics of protein sequences: a key issues review

NASA Astrophysics Data System (ADS)

Cocco, Simona; Feinauer, Christoph; Figliuzzi, Matteo; Monasson, Rémi; Weigt, Martin

2018-03-01

In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques, sequence data accumulate at unprecedented pace. This provides large sets of so-called homologous, i.e. evolutionarily related protein sequences, to which methods of inverse statistical physics can be applied. Using sequence data as the basis for the inference of Boltzmann distributions from samples of microscopic configurations or observables, it is possible to extract information about evolutionary constraints and thus protein function and structure. Here we give an overview over some biologically important questions, and how statistical-mechanics inspired modeling approaches can help to answer them. Finally, we discuss some open questions, which we expect to be addressed over the next years.

Controllability of structural brain networks

NASA Astrophysics Data System (ADS)

Gu, Shi; Pasqualetti, Fabio; Cieslak, Matthew; Telesford, Qawi K.; Yu, Alfred B.; Kahn, Ari E.; Medaglia, John D.; Vettel, Jean M.; Miller, Michael B.; Grafton, Scott T.; Bassett, Danielle S.

2015-10-01

Cognitive function is driven by dynamic interactions between large-scale neural circuits or networks, enabling behaviour. However, fundamental principles constraining these dynamic network processes have remained elusive. Here we use tools from control and network theories to offer a mechanistic explanation for how the brain moves between cognitive states drawn from the network organization of white matter microstructure. Our results suggest that densely connected areas, particularly in the default mode system, facilitate the movement of the brain to many easily reachable states. Weakly connected areas, particularly in cognitive control systems, facilitate the movement of the brain to difficult-to-reach states. Areas located on the boundary between network communities, particularly in attentional control systems, facilitate the integration or segregation of diverse cognitive systems. Our results suggest that structural network differences between cognitive circuits dictate their distinct roles in controlling trajectories of brain network function.

Multiparametric AFM reveals turgor-responsive net-like peptidoglycan architecture in live streptococci

NASA Astrophysics Data System (ADS)

Saar Dover, Ron; Bitler, Arkady; Shimoni, Eyal; Trieu-Cuot, Patrick; Shai, Yechiel

2015-05-01

Cell-wall peptidoglycan (PG) of Gram-positive bacteria is a strong and elastic multi-layer designed to resist turgor pressure and determine the cell shape and growth. Despite its crucial role, its architecture remains largely unknown. Here using high-resolution multiparametric atomic force microscopy (AFM), we studied how the structure and elasticity of PG change when subjected to increasing turgor pressure in live Group B Streptococcus. We show a new net-like arrangement of PG, which stretches and stiffens following osmotic challenge. The same structure also exists in isogenic mutants lacking surface appendages. Cell aging does not alter the elasticity of the cell wall, yet destroys the net architecture and exposes single segmented strands with the same circumferential orientation as predicted for intact glycans. Together, we show a new functional PG architecture in live Gram-positive bacteria.

Three-dimensional mapping of microcircuit correlation structure

PubMed Central

Cotton, R. James; Froudarakis, Emmanouil; Storer, Patrick; Saggau, Peter; Tolias, Andreas S.

2013-01-01

Great progress has been made toward understanding the properties of single neurons, yet the principles underlying interactions between neurons remain poorly understood. Given that connectivity in the neocortex is locally dense through both horizontal and vertical connections, it is of particular importance to characterize the activity structure of local populations of neurons arranged in three dimensions. However, techniques for simultaneously measuring microcircuit activity are lacking. We developed an in vivo 3D high-speed, random-access two-photon microscope that is capable of simultaneous 3D motion tracking. This allows imaging from hundreds of neurons at several hundred Hz, while monitoring tissue movement. Given that motion will induce common artifacts across the population, accurate motion tracking is absolutely necessary for studying population activity with random-access based imaging methods. We demonstrate the potential of this imaging technique by measuring the correlation structure of large populations of nearby neurons in the mouse visual cortex, and find that the microcircuit correlation structure is stimulus-dependent. Three-dimensional random access multiphoton imaging with concurrent motion tracking provides a novel, powerful method to characterize the microcircuit activity in vivo. PMID:24133414

Turbocharged molecular discovery of OLED emitters: from high-throughput quantum simulation to highly efficient TADF devices

NASA Astrophysics Data System (ADS)

Gómez-Bombarelli, Rafael; Aguilera-Iparraguirre, Jorge; Hirzel, Timothy D.; Ha, Dong-Gwang; Einzinger, Markus; Wu, Tony; Baldo, Marc A.; Aspuru-Guzik, Alán.

2016-09-01

Discovering new OLED emitters requires many experiments to synthesize candidates and test performance in devices. Large scale computer simulation can greatly speed this search process but the problem remains challenging enough that brute force application of massive computing power is not enough to successfully identify novel structures. We report a successful High Throughput Virtual Screening study that leveraged a range of methods to optimize the search process. The generation of candidate structures was constrained to contain combinatorial explosion. Simulations were tuned to the specific problem and calibrated with experimental results. Experimentalists and theorists actively collaborated such that experimental feedback was regularly utilized to update and shape the computational search. Supervised machine learning methods prioritized candidate structures prior to quantum chemistry simulation to prevent wasting compute on likely poor performers. With this combination of techniques, each multiplying the strength of the search, this effort managed to navigate an area of molecular space and identify hundreds of promising OLED candidate structures. An experimentally validated selection of this set shows emitters with external quantum efficiencies as high as 22%.

Application of PolyHIPE Membrane with Tricaprylmethylammonium Chloride for Cr(VI) Ion Separation: Parameters and Mechanism of Transport Relating to the Pore Structure

PubMed Central

Chen, Jyh-Herng; Le, Thi Tuyet Mai; Hsu, Kai-Chung

2018-01-01

The structural characteristics of membrane support directly affect the performance of carrier facilitated transport membrane. A highly porous PolyHIPE impregnated with Aliquat 336 is proposed for Cr(VI) separation. PolyHIPE consisting of poly(styrene-co-2-ethylhexyl acrylate) copolymer crosslinked with divinylbenzene has the pore structure characteristic of large pore spaces interconnected with small window throats. The unique pore structure provides the membrane with high flux and stability. The experimental results indicate that the effective diffusion coefficient D* of Cr(VI) through Aliquat 336/PolyHIPE membrane is as high as 1.75 × 10−11 m2 s−1. Transport study shows that the diffusion of Cr(VI) through Aliquat 336/PolyHIPE membrane can be attributed to the jumping transport mechanism. The hydraulic stability experiment shows that the membrane is quite stable, with recovery rates remaining at 95%, even after 10 consecutive cycles of operation. The separation study demonstrates the potential application of this new type of membrane for Cr(VI) recovery. PMID:29498709

Complex furrows in a 2D epithelial sheet code the 3D structure of a beetle horn.

PubMed

Matsuda, Keisuke; Gotoh, Hiroki; Tajika, Yuki; Sushida, Takamichi; Aonuma, Hitoshi; Niimi, Teruyuki; Akiyama, Masakazu; Inoue, Yasuhiro; Kondo, Shigeru

2017-10-24

The external organs of holometabolous insects are generated through two consecutive processes: the development of imaginal primordia and their subsequent transformation into the adult structures. During the latter process, many different phenomena at the cellular level (e.g. cell shape changes, cell migration, folding and unfolding of epithelial sheets) contribute to the drastic changes observed in size and shape. Because of this complexity, the logic behind the formation of the 3D structure of adult external organs remains largely unknown. In this report, we investigated the metamorphosis of the horn in the Japanese rhinoceros beetle Trypoxylus dichotomus. The horn primordia is essentially a 2D epithelial cell sheet with dense furrows. We experimentally unfolded these furrows using three different methods and found that the furrow pattern solely determines the 3D horn structure, indicating that horn formation in beetles occurs by two distinct processes: formation of the furrows and subsequently unfolding them. We postulate that this developmental simplicity offers an inherent advantage to understanding the principles that guide 3D morphogenesis in insects.

Crystal Structure of the Cul2-Rbx1-EloBC-VHL Ubiquitin Ligase Complex.

PubMed

Cardote, Teresa A F; Gadd, Morgan S; Ciulli, Alessio

2017-06-06

Cullin RING E3 ubiquitin ligases (CRLs) function in the ubiquitin proteasome system to catalyze the transfer of ubiquitin from E2 conjugating enzymes to specific substrate proteins. CRLs are large dynamic complexes and attractive drug targets for the development of small-molecule inhibitors and chemical inducers of protein degradation. The atomic details of whole CRL assembly and interactions that dictate subunit specificity remain elusive. Here we present the crystal structure of a pentameric CRL2 VHL complex, composed of Cul2, Rbx1, Elongin B, Elongin C, and pVHL. The structure traps a closed state of full-length Cul2 and a new pose of Rbx1 in a trajectory from closed to open conformation. We characterize hotspots and binding thermodynamics at the interface between Cul2 and pVHL-EloBC and identify mutations that contribute toward a selectivity switch for Cul2 versus Cul5 recognition. Our findings provide structural and biophysical insights into the whole Cul2 complex that could aid future drug targeting. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Application of PolyHIPE Membrane with Tricaprylmethylammonium Chloride for Cr(VI) Ion Separation: Parameters and Mechanism of Transport Relating to the Pore Structure.

PubMed

Chen, Jyh-Herng; Le, Thi Tuyet Mai; Hsu, Kai-Chung

2018-03-02

The structural characteristics of membrane support directly affect the performance of carrier facilitated transport membrane. A highly porous PolyHIPE impregnated with Aliquat 336 is proposed for Cr(VI) separation. PolyHIPE consisting of poly(styrene- co -2-ethylhexyl acrylate) copolymer crosslinked with divinylbenzene has the pore structure characteristic of large pore spaces interconnected with small window throats. The unique pore structure provides the membrane with high flux and stability. The experimental results indicate that the effective diffusion coefficient D* of Cr(VI) through Aliquat 336/PolyHIPE membrane is as high as 1.75 × 10 -11 m² s -1 . Transport study shows that the diffusion of Cr(VI) through Aliquat 336/PolyHIPE membrane can be attributed to the jumping transport mechanism. The hydraulic stability experiment shows that the membrane is quite stable, with recovery rates remaining at 95%, even after 10 consecutive cycles of operation. The separation study demonstrates the potential application of this new type of membrane for Cr(VI) recovery.

Chromatin insulator bodies are nuclear structures that form in response to osmotic stress and cell death

PubMed Central

Schoborg, Todd; Rickels, Ryan; Barrios, Josh

2013-01-01

Chromatin insulators assist in the formation of higher-order chromatin structures by mediating long-range contacts between distant genomic sites. It has been suggested that insulators accomplish this task by forming dense nuclear foci termed insulator bodies that result from the coalescence of multiple protein-bound insulators. However, these structures remain poorly understood, particularly the mechanisms triggering body formation and their role in nuclear function. In this paper, we show that insulator proteins undergo a dramatic and dynamic spatial reorganization into insulator bodies during osmostress and cell death in a high osmolarity glycerol–p38 mitogen-activated protein kinase–independent manner, leading to a large reduction in DNA-bound insulator proteins that rapidly repopulate chromatin as the bodies disassemble upon return to isotonicity. These bodies occupy distinct nuclear territories and contain a defined structural arrangement of insulator proteins. Our findings suggest insulator bodies are novel nuclear stress foci that can be used as a proxy to monitor the chromatin-bound state of insulator proteins and provide new insights into the effects of osmostress on nuclear and genome organization. PMID:23878275

Clustered marginalization of minorities during social transitions induced by co-evolution of behaviour and network structure

PubMed Central

Schleussner, Carl-Friedrich; Donges, Jonathan F.; Engemann, Denis A.; Levermann, Anders

2016-01-01

Large-scale transitions in societies are associated with both individual behavioural change and restructuring of the social network. These two factors have often been considered independently, yet recent advances in social network research challenge this view. Here we show that common features of societal marginalization and clustering emerge naturally during transitions in a co-evolutionary adaptive network model. This is achieved by explicitly considering the interplay between individual interaction and a dynamic network structure in behavioural selection. We exemplify this mechanism by simulating how smoking behaviour and the network structure get reconfigured by changing social norms. Our results are consistent with empirical findings: The prevalence of smoking was reduced, remaining smokers were preferentially connected among each other and formed increasingly marginalized clusters. We propose that self-amplifying feedbacks between individual behaviour and dynamic restructuring of the network are main drivers of the transition. This generative mechanism for co-evolution of individual behaviour and social network structure may apply to a wide range of examples beyond smoking. PMID:27510641

Backbone hydration determines the folding signature of amino acid residues.

PubMed

Bignucolo, Olivier; Leung, Hoi Tik Alvin; Grzesiek, Stephan; Bernèche, Simon

2015-04-08

The relation between the sequence of a protein and its three-dimensional structure remains largely unknown. A lasting dream is to elucidate the side-chain-dependent driving forces that govern the folding process. Different structural data suggest that aromatic amino acids play a particular role in the stabilization of protein structures. To better understand the underlying mechanism, we studied peptides of the sequence EGAAXAASS (X = Gly, Ile, Tyr, Trp) through comparison of molecular dynamics (MD) trajectories and NMR residual dipolar coupling (RDC) measurements. The RDC data for aromatic substitutions provide evidence for a kink in the peptide backbone. Analysis of the MD simulations shows that the formation of internal hydrogen bonds underlying a helical turn is key to reproduce the experimental RDC values. The simulations further reveal that the driving force leading to such helical-turn conformations arises from the lack of hydration of the peptide chain on either side of the bulky aromatic side chain, which can potentially act as a nucleation point initiating the folding process.

The application of quantum mechanics in structure-based drug design.

PubMed

Mucs, Daniel; Bryce, Richard A

2013-03-01

Computational chemistry has become an established and valuable component in structure-based drug design. However the chemical complexity of many ligands and active sites challenges the accuracy of the empirical potentials commonly used to describe these systems. Consequently, there is a growing interest in utilizing electronic structure methods for addressing problems in protein-ligand recognition. In this review, the authors discuss recent progress in the development and application of quantum chemical approaches to modeling protein-ligand interactions. The authors specifically consider the development of quantum mechanics (QM) approaches for studying large molecular systems pertinent to biology, focusing on protein-ligand docking, protein-ligand binding affinities and ligand strain on binding. Although computation of binding energies remains a challenging and evolving area, current QM methods can underpin improved docking approaches and offer detailed insights into ligand strain and into the nature and relative strengths of complex active site interactions. The authors envisage that QM will become an increasingly routine and valued tool of the computational medicinal chemist.

System-wide organization of actin cytoskeleton determines organelle transport in hypocotyl plant cells

PubMed Central

Nowak, Jacqueline; Ivakov, Alexander; Somssich, Marc; Persson, Staffan; Nikoloski, Zoran

2017-01-01

The actin cytoskeleton is an essential intracellular filamentous structure that underpins cellular transport and cytoplasmic streaming in plant cells. However, the system-level properties of actin-based cellular trafficking remain tenuous, largely due to the inability to quantify key features of the actin cytoskeleton. Here, we developed an automated image-based, network-driven framework to accurately segment and quantify actin cytoskeletal structures and Golgi transport. We show that the actin cytoskeleton in both growing and elongated hypocotyl cells has structural properties facilitating efficient transport. Our findings suggest that the erratic movement of Golgi is a stable cellular phenomenon that might optimize distribution efficiency of cell material. Moreover, we demonstrate that Golgi transport in hypocotyl cells can be accurately predicted from the actin network topology alone. Thus, our framework provides quantitative evidence for system-wide coordination of cellular transport in plant cells and can be readily applied to investigate cytoskeletal organization and transport in other organisms. PMID:28655850

Drug resistance conferred by mutations outside the active site through alterations in the dynamic and structural ensemble of HIV-1 protease.

PubMed

Ragland, Debra A; Nalivaika, Ellen A; Nalam, Madhavi N L; Prachanronarong, Kristina L; Cao, Hong; Bandaranayake, Rajintha M; Cai, Yufeng; Kurt-Yilmaz, Nese; Schiffer, Celia A

2014-08-27

HIV-1 protease inhibitors are part of the highly active antiretroviral therapy effectively used in the treatment of HIV infection and AIDS. Darunavir (DRV) is the most potent of these inhibitors, soliciting drug resistance only when a complex combination of mutations occur both inside and outside the protease active site. With few exceptions, the role of mutations outside the active site in conferring resistance remains largely elusive. Through a series of DRV-protease complex crystal structures, inhibition assays, and molecular dynamics simulations, we find that single and double site mutations outside the active site often associated with DRV resistance alter the structure and dynamic ensemble of HIV-1 protease active site. These alterations correlate with the observed inhibitor binding affinities for the mutants, and suggest a network hypothesis on how the effect of distal mutations are propagated to pivotal residues at the active site and may contribute to conferring drug resistance.