Biosimilar structural comparability assessment by NMR: from small proteins to monoclonal antibodies

NASA Astrophysics Data System (ADS)

Japelj, Boštjan; Ilc, Gregor; Marušič, Jaka; Senčar, Jure; Kuzman, Drago; Plavec, Janez

2016-08-01

Biosimilar drug products must have a demonstrated similarity with respect to the reference product’s molecules in order to ensure both the effectiveness of the drug and the patients’ safety. In this paper the fusion framework of a highly sensitive NMR fingerprinting approach for conformational changes and mathematically-based biosimilarity metrics is introduced. The final goal is to translate the complex spectral information into biosimilarity scores, which are then used to estimate the degree of similarity between the biosimilar and the reference product. The proposed method was successfully applied to a small protein, i.e., filgrastim (neutropenia treatment), which is the first biosimilar approved in the United States, and a relatively large protein, i.e., monoclonal antibody rituximab (lymphoma treatment). This innovative approach introduces a new level of sensitivity to structural changes that are induced by, e.g., a small pH shift or other changes in the protein formulation.

Simultaneous optimization of biomolecular energy function on features from small molecules and macromolecules

PubMed Central

Park, Hahnbeom; Bradley, Philip; Greisen, Per; Liu, Yuan; Mulligan, Vikram Khipple; Kim, David E.; Baker, David; DiMaio, Frank

2017-01-01

Most biomolecular modeling energy functions for structure prediction, sequence design, and molecular docking, have been parameterized using existing macromolecular structural data; this contrasts molecular mechanics force fields which are largely optimized using small-molecule data. In this study, we describe an integrated method that enables optimization of a biomolecular modeling energy function simultaneously against small-molecule thermodynamic data and high-resolution macromolecular structural data. We use this approach to develop a next-generation Rosetta energy function that utilizes a new anisotropic implicit solvation model, and an improved electrostatics and Lennard-Jones model, illustrating how energy functions can be considerably improved in their ability to describe large-scale energy landscapes by incorporating both small-molecule and macromolecule data. The energy function improves performance in a wide range of protein structure prediction challenges, including monomeric structure prediction, protein-protein and protein-ligand docking, protein sequence design, and prediction of the free energy changes by mutation, while reasonably recapitulating small-molecule thermodynamic properties. PMID:27766851

Structural Changes Fundamental to Gating of the Cystic Fibrosis Transmembrane Conductance Regulator Anion Channel Pore.

PubMed

Linsdell, Paul

2017-01-01

Cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an epithelial cell anion channel. Potentiator drugs used in the treatment of cystic fibrosis act on the channel to increase overall channel function, by increasing the stability of its open state and/or decreasing the stability of its closed state. The structure of the channel in either the open state or the closed state is not currently known. However, changes in the conformation of the protein as it transitions between these two states have been studied using functional investigation and molecular modeling techniques. This review summarizes our current understanding of the architecture of the transmembrane channel pore that controls the movement of chloride and other small anions, both in the open state and in the closed state. Evidence for different kinds of changes in the conformation of the pore as it transitions between open and closed states is described, as well as the mechanisms by which these conformational changes might be controlled to regulate normal channel gating. The ways that key conformational changes might be targeted by small compounds to influence overall CFTR activity are also discussed. Understanding the changes in pore structure that might be manipulated by such small compounds is key to the development of novel therapeutic strategies for the treatment of cystic fibrosis.

Journal Clubs and Case Conferences: From Academic Tradition to Communities of Practice

ERIC Educational Resources Information Center

Price, David W.; Felix, Kate G.

2008-01-01

Introduction: As small group learning sessions, Journal Clubs (JCs) and Case Conferences (CCs), if structured interactively, have potential as educational formats that can change practice. However, the degree to which these formats, as currently typically structured, lead to practice change is unknown. Methods: We used concepts of communities of…

Modeling the effects of fire severity and spatial complexity on Small Mammals in Yosemite National Park, California

USGS Publications Warehouse

Roberts, Susan L.; Van Wagtendonk, Jan W.; Miles, A. Keith; Kelt, Douglas A.; Lutz, James A.

2008-01-01

We evaluated the impact of fire severity and related spatial and vegetative parameters on small mammal populations in 2 yr- to 15 yr-old burns in Yosemite National Park, California, USA. We also developed habitat models that would predict small mammal responses to fires of differing severity. We hypothesized that fire severity would influence the abundances of small mammals through changes in vegetation composition, structure, and spatial habitat complexity. Deer mouse (Peromyscus maniculatus) abundance responded negatively to fire severity, and brush mouse (P. boylii) abundance increased with increasing oak tree (Quercus spp.) cover. Chipmunk (Neotamias spp.) abundance was best predicted through a combination of a negative response to oak tree cover and a positive response to spatial habitat complexity. California ground squirrel (Spermophilus beecheyi) abundance increased with increasing spatial habitat complexity. Our results suggest that fire severity, with subsequent changes in vegetation structure and habitat spatial complexity, can influence small mammal abundance patterns.

Folding propensity of intrinsically disordered proteins by osmotic stress

DOE PAGES

Mansouri, Amanda L.; Grese, Laura N.; Rowe, Erica L.; ...

2016-10-11

Proteins imparted with intrinsic disorder conduct a range of essential cellular functions. To better understand the folding and hydration properties of intrinsically disordered proteins (IDPs), we used osmotic stress to induce conformational changes in nuclear co-activator binding domain (NCBD) and activator for thyroid hormone and retinoid receptor (ACTR). Osmotic stress was applied by the addition of small and polymeric osmolytes, where we discovered that water contributions to NCBD folding always exceeded those for ACTR. Both NCBD and ACTR were found to gain a-helical structure with increasing osmotic stress, consistent with their folding upon NCBD/ACTR complex formation. Using small-angle neutron scatteringmore » (SANS), we further characterized NCBD structural changes with the osmolyte ethylene glycol. Here a large reduction in overall size initially occurred before substantial secondary structural change. In conclusion, by focusing on folding propensity, and linked hydration changes, we uncover new insights that may be important for how IDP folding contributes to binding.« less

Molecular dynamics simulation analysis of the effect of T790M mutation on epidermal growth factor receptor protein architecture in non-small cell lung carcinoma.

PubMed

Peng, Xiao-Nu; Wang, Jing; Zhang, Wei

2017-08-01

Non-small cell lung cancer etiology and its treatment failure are due to epidermal growth factor receptor (EGFR) kinase domain mutations at amino acid position 790. The mutational change from threonine to methionine at position 790 (T790M) is responsible for tyrosine kinase inhibition failure. Using molecular dynamic simulation, the present study investigated the architectural changes occurring at the atomic scale. The 50-nsec runs using a GROMOS force field for wild-type and mutant EGFR's kinase domains were investigated for contrasting variations using Gromacs inbuilt tools. The adenosine triphosphate binding domain and the active site of EGFR were studied extensively in order to understand the structural changes. All the parameters investigated in the present study revealed considerable changes in the studied structures, and the knowledge gained from this may be used to develop novel kinase inhibitors that will be effective irrespective of the structural alterations in kinase domain.

Folding propensity of intrinsically disordered proteins by osmotic stress

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

Mansouri, Amanda L.; Grese, Laura N.; Rowe, Erica L.

Proteins imparted with intrinsic disorder conduct a range of essential cellular functions. To better understand the folding and hydration properties of intrinsically disordered proteins (IDPs), we used osmotic stress to induce conformational changes in nuclear co-activator binding domain (NCBD) and activator for thyroid hormone and retinoid receptor (ACTR). Osmotic stress was applied by the addition of small and polymeric osmolytes, where we discovered that water contributions to NCBD folding always exceeded those for ACTR. Both NCBD and ACTR were found to gain a-helical structure with increasing osmotic stress, consistent with their folding upon NCBD/ACTR complex formation. Using small-angle neutron scatteringmore » (SANS), we further characterized NCBD structural changes with the osmolyte ethylene glycol. Here a large reduction in overall size initially occurred before substantial secondary structural change. In conclusion, by focusing on folding propensity, and linked hydration changes, we uncover new insights that may be important for how IDP folding contributes to binding.« less

A comprehensive visual rating scale of brain magnetic resonance imaging: application in elderly subjects with Alzheimer's disease, mild cognitive impairment, and normal cognition.

PubMed

Jang, Jae-Won; Park, So Young; Park, Young Ho; Baek, Min Jae; Lim, Jae-Sung; Youn, Young Chul; Kim, SangYun

2015-01-01

Brain magnetic resonance imaging (MRI) shows cerebral structural changes. However, a unified comprehensive visual rating scale (CVRS) has seldom been studied. Thus, we combined brain atrophy and small vessel disease scales and used an MRI template as a CVRS. The aims of this study were to design a simple and reliable CVRS, validate it by investigating cerebral structural changes in clinical groups, and made comparison to the volumetric measurements. Elderly subjects (n = 260) with normal cognition (NC, n = 65), mild cognitive impairment (MCI, n = 101), or Alzheimer's disease (AD, n = 94) were evaluated with brain MRI according to the CVRS of brain atrophy and small vessel disease. Validation of the CVRS with structural changes, neuropsychological tests, and volumetric analyses was performed. The CVRS revealed a high intra-rater and inter-rater agreement and it reflected the structural changes of subjects with NC, MCI, and AD better than volumetric measures (CVRS-coronal: F = 13.5, p < 0.001; CVRS-axial: F = 19.9, p < 0.001). The area under the receiver operation curve (aROC) of the CVRS showed higher accuracy than volumetric analyses. (NC versus MCI aROC: CVRS-coronal, 0.777; CVRS-axial, 0.773; MCI versus AD aROC: CVRS-coronal, 0.680; CVRS-axial, 0.681). The CVRS can be used clinically to conveniently measure structural changes of brain. It reflected cerebral structural changes of clinical groups and correlated with the age better than volumetric measures.

Low-rank network decomposition reveals structural characteristics of small-world networks

NASA Astrophysics Data System (ADS)

Barranca, Victor J.; Zhou, Douglas; Cai, David

2015-12-01

Small-world networks occur naturally throughout biological, technological, and social systems. With their prevalence, it is particularly important to prudently identify small-world networks and further characterize their unique connection structure with respect to network function. In this work we develop a formalism for classifying networks and identifying small-world structure using a decomposition of network connectivity matrices into low-rank and sparse components, corresponding to connections within clusters of highly connected nodes and sparse interconnections between clusters, respectively. We show that the network decomposition is independent of node indexing and define associated bounded measures of connectivity structure, which provide insight into the clustering and regularity of network connections. While many existing network characterizations rely on constructing benchmark networks for comparison or fail to describe the structural properties of relatively densely connected networks, our classification relies only on the intrinsic network structure and is quite robust with respect to changes in connection density, producing stable results across network realizations. Using this framework, we analyze several real-world networks and reveal new structural properties, which are often indiscernible by previously established characterizations of network connectivity.

Structure and mechanism of a molecular rheostat, an RNA thermometer that modulates immune evasion by Neisseria meningitidis

PubMed Central

Barnwal, Ravi Pratap; Loh, Edmund; Godin, Katherine S.; Yip, Jordan; Lavender, Hayley; Tang, Christoph M.; Varani, Gabriele

2016-01-01

Neisseria meningitidis causes bacterial meningitis and septicemia. It evades the host complement system by upregulating expression of immune evasion factors in response to changes in temperature. RNA thermometers within mRNAs control expression of bacterial immune evasion factors, including CssA, in the 5′-untranslated region of the operon for capsule biosynthesis. We dissect the molecular mechanisms of thermoregulation and report the structure of the CssA thermometer. We show that the RNA thermometer acts as a rheostat, whose stability is optimized to respond in a small temperature range around 37°C as occur within the upper airways during infection. Small increases in temperature gradually open up the structure to allow progressively increased access to the ribosome binding site. Even small changes in stability induced by mutations of imperfect base pairs, as in naturally occurring polymorphisms, shift the thermometer response outside of the desired temperature range, suggesting that its activity could be modulated by pharmacological intervention. PMID:27369378

Monitoring stress changes in a concrete bridge with coda wave interferometry.

PubMed

Stähler, Simon Christian; Sens-Schönfelder, Christoph; Niederleithinger, Ernst

2011-04-01

Coda wave interferometry is a recent analysis method now widely used in seismology. It uses the increased sensitivity of multiply scattered elastic waves with long travel-times for monitoring weak changes in a medium. While its application for structural monitoring has been shown to work under laboratory conditions, the usability on a real structure with known material changes had yet to be proven. This article presents experiments on a concrete bridge during construction. The results show that small velocity perturbations induced by a changing stress state in the structure can be determined even under adverse conditions. Theoretical estimations based on the stress calculations by the structural engineers are in good agreement with the measured velocity variations.

Visualization of molecular structures using HoloLens-based augmented reality

PubMed Central

Hoffman, MA; Provance, JB

2017-01-01

Biological molecules and biologically active small molecules are complex three dimensional structures. Current flat screen monitors are limited in their ability to convey the full three dimensional characteristics of these molecules. Augmented reality devices, including the Microsoft HoloLens, offer an immersive platform to change how we interact with molecular visualizations. We describe a process to incorporate the three dimensional structures of small molecules and complex proteins into the Microsoft HoloLens using aspirin and the human leukocyte antigen (HLA) as examples. Small molecular structures can be introduced into the HoloStudio application, which provides native support for rotating, resizing and performing other interactions with these molecules. Larger molecules can be imported through the Unity gaming development platform and then Microsoft Visual Developer. The processes described here can be modified to import a wide variety of molecular structures into augmented reality systems and improve our comprehension of complex structural features. PMID:28815109

Use of Small Angle Neutron Scattering to Study Various Properties of Wool and Mohair Fibres

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

Franklyn, C. B.; Toeroek, Gy.

2011-12-13

To maintain a competitive edge in the wool and mohair industry, a detailed knowledge and understanding of the properties of wool fibres is essential. Standard techniques are used to determine fibre diameter, length and strength; however, properties such as hydroscopicity, lustre and changes in fibre structure following chemical or mechanical treatment are not so well understood. The unique capabilities of small angle neutron scattering to study changes in the supermolecular structure of wool fibres, particularly at the level of the microfibril-matrix complex, have been used to provide previously unknown features of the fibres. The results of these studies are presented.

Revolution in the Small Colleges.

ERIC Educational Resources Information Center

Heger, Herbert K.

1982-01-01

Small and medium-sized institutions are seen as likely to experience major organizational change during the next few years in three areas: contracting out, academic franchising, and reacting to declining instruction. Colleges need to explore interinstitutional cooperation, new educational media, structural innovation, productivity improvement, and…

13 CFR 113.3-3 - Structural accommodations for handicapped clients.

Code of Federal Regulations, 2013 CFR

2013-01-01

... handicapped clients. 113.3-3 Section 113.3-3 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION... ADMINISTRATOR General Provisions § 113.3-3 Structural accommodations for handicapped clients. (a) Existing... by handicapped clients. Where structural changes are necessary to make the recipient's goods or...

13 CFR 113.3-3 - Structural accommodations for handicapped clients.

Code of Federal Regulations, 2012 CFR

2012-01-01

... handicapped clients. 113.3-3 Section 113.3-3 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION... ADMINISTRATOR General Provisions § 113.3-3 Structural accommodations for handicapped clients. (a) Existing... by handicapped clients. Where structural changes are necessary to make the recipient's goods or...

13 CFR 113.3-3 - Structural accommodations for handicapped clients.

Code of Federal Regulations, 2014 CFR

2014-01-01

... handicapped clients. 113.3-3 Section 113.3-3 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION... ADMINISTRATOR General Provisions § 113.3-3 Structural accommodations for handicapped clients. (a) Existing... by handicapped clients. Where structural changes are necessary to make the recipient's goods or...

13 CFR 113.3-3 - Structural accommodations for handicapped clients.

Code of Federal Regulations, 2010 CFR

2010-01-01

... handicapped clients. 113.3-3 Section 113.3-3 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION... ADMINISTRATOR General Provisions § 113.3-3 Structural accommodations for handicapped clients. (a) Existing... by handicapped clients. Where structural changes are necessary to make the recipient's goods or...

Electroporation of the photosynthetic membrane: structural changes in protein and lipid-protein domains.

PubMed Central

Rosemberg, Y; Rotenberg, M; Korenstein, R

1994-01-01

A biological membrane undergoes a reversible permeability increase through structural changes in the lipid domain when exposed to high external electric fields. The present study shows the occurrence of electric field-induced changes in the conductance of the proton channel of the H(+)-ATPase as well as electric field-induced structural changes in the lipid-protein domain of photosystem (PS) II in the photosynthetic membrane. The study was carried out by analyzing the electric field-stimulated delayed luminescence (EPL), which originates from charge recombination in the protein complexes of PS I and II of photosynthetic vesicles. We established that a small fraction of the total electric field-induced conductance change was abolished by N,N'-dicyclohexylcarbodiimide (DCCD), an inhibitor of the H(+)-ATPase. This reversible electric field-induced conductance change has characteristics of a small channel and possesses a lifetime < or = 1 ms. To detect electric field-induced changes in the lipid-protein domains of PS II, we examined the effects of phospholipase A2 (PLA2) on EPL. Higher values of EPL were observed from vesicles that were exposed in the presence of PLA2 to an electroporating electric field than to a nonelectroporating electric field. The effect of the electroporating field was a long-lived one, lasting for a period > or = 2 min. This effect was attributed to long-lived electric field-induced structural changes in the lipid-protein domains of PS II. PMID:7811916

13 CFR 108.410 - Changes in Control of NMVC Company (through change in ownership or otherwise).

Code of Federal Regulations, 2010 CFR

2010-01-01

... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false Changes in Control of NMVC Company (through change in ownership or otherwise). 108.410 Section 108.410 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION NEW MARKETS VENTURE CAPITAL (âNMVCâ) PROGRAM Changes in Ownership, Structure, or...

Mathematical modeling of sustainability of porous Al2O3 growth during two-stage anodization process

NASA Astrophysics Data System (ADS)

Aryslanova, Elizaveta M.; Alfimov, Anton V.; Chivilikhin, Sergey A.

2015-06-01

Currently, due to the development of nanotechnology and metamaterials, it has become important to obtain regular nanoporous structures with different parameters, such as porous anodic alumina films that are used for synthesis of various nanocomposites. In this work we consider the motion of the interfaces between electrolyte and alumina layers, and between alumina and aluminum layers. We also took into account the dynamics of moving boundaries and the change of small perturbations of these boundaries. Each area under Laplace's equation is solved for the potential of the electric field. The growth of porous alumina is described with the theory of small perturbations. Small perturbations of the interface are considered, which lead to small changes in potential and current in the boundaries. As a result of the developed model we obtained the minimum distance between centers of aluminum oxide pores in the beginning of anodizing process and the wavelength of porous structure irregularities.

Eight guidelines for developing a strategy for the '90s.

PubMed

Kaufman, N

1994-03-20

Regardless of the outcome of federal reform initiatives, health care is undergoing structural change of unprecedented magnitude. Structural change occurs when there is a fundamental, sustainable change in the values and purchasing behavior of buyers. During such times, market leaders are extremely vulnerable to competitive threats due to internal bureaucratic barriers. Witness the U.S. computer and automobile industries. As Robert Lutz, president of Chrysler, points out, "Being large doesn't mean being safe. The large won't eat the small. The swift will eat the slow." During this dynamic period in health care, it is critical that strategy be on target. Periods of structural change are filled with numerous threats as well as opportunities. The following are eight guidelines for developing health care strategy during the structural changes of the '90s.

Elevated-Confined Phase-Change Random Access Memory Cells

NASA Astrophysics Data System (ADS)

Lee; Koon, Hock; Shi; Luping; Zhao; Rong; Yang; Hongxin; Lim; Guan, Kian; Li; Jianming; Chong; Chong, Tow

2010-04-01

A new elevated-confined phase-change random access memory (PCRAM) cell structure to reduce power consumption was proposed. In this proposed structure, the confined phase-change region is sitting on top of a small metal column enclosed by a dielectric at the sides. Hence, more heat can be effectively sustained underneath the phase-change region. As for the conventional structure, the confined phase-change region is sitting directly above a large planar bottom metal electrode, which can easily conduct most of the induced heat away. From simulations, a more uniform temperature profile around the active region and a higher peak temperature at the phase-change layer (PCL) in an elevated-confined structure were observed. Experimental results showed that the elevated-confined PCRAM cell requires a lower programming power and has a better scalability than a conventional confined PCRAM cell.

Thermodynamics of water structural reorganization due to geometric confinement

NASA Astrophysics Data System (ADS)

Stroberg, Wylie; Lichter, Seth

2015-03-01

Models of aqueous solvation have successfully quantified the behavior of water near convex bodies. However, many important processes occurring in aqueous solution involve interactions between solutes and surfaces with complicated non-convex geometries. Examples include the folding of proteins, hydrophobic association of solutes, ligand-receptor binding, and water confined within nanotubes and pores. For these geometries, models for solvation of convex bodies fail to account for the added interactions associated with structural confinement. Due to water's propensity to form networks of hydrogen bonds, small alterations to the confining geometry can induce large structural rearrangement within the water. We perform systematic Monte Carlo simulations of water confined to cylindrical cavities of varying aspect ratio to investigate how small geometric changes to the confining geometry may cause large changes to the structure and thermodynamic state of water. Using the Wang-Landau algorithm, we obtain free energies, enthalpies, entropies, and heat capacities across a broad range of temperatures, and show how these quantities are influenced by the structural rearrangement of water molecules due to geometric perturbations.

Effect of UV light on different structural and transport parameters of cellophane membranes

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

Benavente, J.; Vazquez, M.I.; De Abajo, J.

1996-01-01

A comparative study of UV light influence on structural and transport parameters of cellophane membranes was made. Changes in the chemical structure and electrical behavior of cellophane membranes were considered by determining the hydraulic permeability, salt diffusion coefficient, and resistance values, as well as some geometrical parameters, for an untreated membrane and two differently UV-treated cellophane membranes. Differences in the characteristic parameters for the three samples showed that radiation mainly affected the membrane structure, while only small changes in membrane electrical behavior were determined.

Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

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

Hura, Greg L.; Menon, Angeli L.; Hammel, Michal

2009-07-20

We present an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving. We subjected 50 representative proteins, mostly from Pyrococcus furiosus, to this pipeline and found that 30 were multimeric structures in solution. SAXS analysis allowed us to distinguish aggregated and unfolded proteins, define global structural parameters and oligomeric states for most samples, identify shapes and similar structures for 25 unknown structures, and determine envelopes formore » 41 proteins. We believe that high-throughput SAXS is an enabling technology that may change the way that structural genomics research is done.« less

Off The Scale - Expansion or Development? A Small Town within a Metropolitan Zone as an Alternative Place of Residence

NASA Astrophysics Data System (ADS)

Wójtowicz-Wróbel, Agnieszka

2017-10-01

The goal of this paper is to point out the types of spatial changes that the small towns located in Krakow’s range of influence are currently undergoing, as well as what are the consequences of the various types of changes in these towns. The author asks the question whether the current changes seen in small towns that are under the influence of Krakow can be described as sustainable development - at the basis of which is the increasing of the quality of the functional and spatial structure of a town while preserving its qualities and character - or, on the contrary, that it is more appropriate to describe the changes in the spatial structure of towns as an expansion, which is related only to an increase in their surface area or an increase in the density of their built environment? An attempt has also been made to determine the cause of these changes. An analysis of a set of towns in terms of their accessibility in relation to Krakow, as well as the demographic changes in towns in recent years, has been carried out. This research was useful in determining the dynamic of urban changes or their stagnation. Afterwards, groups of towns with varying degrees of transformation (towns that have been intensively transformed, towns with a balanced degree of spatial changes and towns which remain on the side-lines) were established. In addition, various forms of changes were defined - ranging from cities which register an increase in attractiveness and the changes that it brings while preserving their qualities in accordance with the principles of sustainable development, to settlements which are losing their small-town character as a result of intensive change, at the same time undergoing unification both in terms of space and form of use. From among the groups of towns, example which most fully illustrate the varying degrees and character of the changes of small towns in the area of Krakow has been selected. Based on the research that has been conducted, we can state that small towns in the vicinity of Krakow are undergoing intensive changes and are an attractive alternative in terms of serving as a place of residence, for instance in comparison to the suburban zone of Krakow. However, it is necessary to channel the changes in small towns in a manner that would take advantage of the opportunities for spatial, social and economic development on the one hand, while at the same time causing the intensive changes in those areas to not lead to the loss of their uniqueness, identity and small-town character, as well as the qualities of both a given town and its surroundings on the other. The research that had been performed and the conclusions that were drawn from it can serve as comparative material for other types of small towns and for metropolitan areas.

2.5D change detection from satellite imagery to monitor small-scale mining activities in the Democratic Republic of the Congo

NASA Astrophysics Data System (ADS)

Kranz, Olaf; Lang, Stefan; Schoepfer, Elisabeth

2017-09-01

Mining natural resources serve fundamental societal needs or commercial interests, but it may well turn into a driver of violence and regional instability. In this study, very high resolution (VHR) optical stereo satellite data are analysed to monitor processes and changes in one of the largest artisanal and small-scale mining sites in the Democratic Republic of the Congo, which is among the world's wealthiest countries in exploitable minerals To identify the subtle structural changes, the applied methodological framework employs object-based change detection (OBCD) based on optical VHR data and generated digital surface models (DSM). Results prove the DSM-based change detection approach enhances the assessment gained from sole 2D analyses by providing valuable information about changes in surface structure or volume. Land cover changes as analysed by OBCD reveal an increase in bare soil area by a rate of 47% between April 2010 and September 2010, followed by a significant decrease of 47.5% until March 2015. Beyond that, DSM differencing enabled the characterisation of small-scale features such as pits and excavations. The presented Earth observation (EO)-based monitoring of mineral exploitation aims at a better understanding of the relations between resource extraction and conflict, and thus providing relevant information for potential mitigation strategies and peace building.

A New Modeling for the Changes in the Distribution of Scatterers in Cirrhotic Liver

NASA Astrophysics Data System (ADS)

Hara, Takashi; Hachiya, Hiroyuki

2000-05-01

The human liver is composed of small hexagonal structures called liver lobules. Cirrhosis destroys these liver lobules and replaces them with permanent connective tissue referred to as regenerative nodules. In this paper, we propose a new modeling technique for changes in the scatterer distribution in liver tissue considering the structure of liver lobules to obtain images of the cirrhotic liver over continuous stages. Using these images, we analyze the relationship between changes in characteristics of biological tissue and changes in B-mode images during progressive liver cirrhosis.

Digestive enzyme expression and epithelial structure of small intestine in neonatal rats after 16 days spaceflight

NASA Astrophysics Data System (ADS)

Miyake, M.; Yamasaki, M.; Hazama, A.; Ijiri, K.; Shimizu, T.

It is important to assure whether digestive system can develop normally in neonates during spaceflight. Because the small intestine changes its function and structure drastically around weaning known as redifferentiation. Lactase expression declines and sucrase increases in small intestine for digestion of solid food before weaning. In this paper, we compared this enzyme transition and structural development of small intestine in neonatal rats after spaceflight. To find digestive genes differentially expressed in fight rats, DNA membrane macroarray was also used. Eight-day old rats were loaded to Space Shuttle Columbia, and housed in the animal facility for 16 days in space (STS-90, Neurolab mission). Two control groups (AGC; asynchronous ground control and VIV; vivarium) against flight group (FLT) were prepared. There was no difference in structure (crypt depth) and cell differentiation of epithelium between FLT and AGC by immunohistochemical analysis. We found that the amount of sucrase mRNA compared to lactase was decreased in FLT by RT-PCR. It reflected the enzyme transition was inhibited. Increase of 5 genes (APO A-I, APO A-IV, ACE, aFABP and aminopeptidase M) and decrease of carboxypeptidase-D were detected in FLT using macroarray. We think nutrition differences (less nourishment and late weaning) during spaceflight may cause inhibition of enzyme transition at least partly. The weightlessness might contribute to the inhibition through behavioral change.

Dislocation dynamics simulations of plasticity at small scales

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

Zhou, Caizhi

2010-01-01

As metallic structures and devices are being created on a dimension comparable to the length scales of the underlying dislocation microstructures, the mechanical properties of them change drastically. Since such small structures are increasingly common in modern technologies, there is an emergent need to understand the critical roles of elasticity, plasticity, and fracture in small structures. Dislocation dynamics (DD) simulations, in which the dislocations are the simulated entities, offer a way to extend length scales beyond those of atomistic simulations and the results from DD simulations can be directly compared with the micromechanical tests. The primary objective of this researchmore » is to use 3-D DD simulations to study the plastic deformation of nano- and micro-scale materials and understand the correlation between dislocation motion, interactions and the mechanical response. Specifically, to identify what critical events (i.e., dislocation multiplication, cross-slip, storage, nucleation, junction and dipole formation, pinning etc.) determine the deformation response and how these change from bulk behavior as the system decreases in size and correlate and improve our current knowledge of bulk plasticity with the knowledge gained from the direct observations of small-scale plasticity. Our simulation results on single crystal micropillars and polycrystalline thin films can march the experiment results well and capture the essential features in small-scale plasticity. Furthermore, several simple and accurate models have been developed following our simulation results and can reasonably predict the plastic behavior of small scale materials.« less

Probing the transition state for nucleic acid hybridization using phi-value analysis.

PubMed

Kim, Jandi; Shin, Jong-Shik

2010-04-27

Genetic regulation by noncoding RNA elements such as microRNA and small interfering RNA (siRNA) involves hybridization of a short single-stranded RNA with a complementary segment in a target mRNA. The physical basis of the hybridization process between the structured nucleic acids is not well understood primarily because of the lack of information about the transition-state structure. Here we use transition-state theory, inspired by phi-value analysis in protein folding studies, to provide quantitative analysis of the relationship between changes in the secondary structure stability and the activation free energy. Time course monitoring of the hybridization reaction was performed under pseudo-steady-state conditions using a single fluorophore. The phi-value analysis indicates that the native secondary structure remains intact in the transition state. The nativelike transition state was confirmed via examination of the salt dependence of the hybridization kinetics, indicating that the number of sodium ions associated with the transition state was not substantially affected by changes in the native secondary structure. These results propose that hybridization between structured nucleic acids undergoes a transition state leading to formation of a nucleation complex and then is followed by sequential displacement of preexisting base pairings involving successive small energy barriers. The proposed mechanism might provide new insight into physical processes during small RNA-mediated gene silencing, which is essential to selection of a target mRNA segment for siRNA design.

Big Trouble for Small Schools

ERIC Educational Resources Information Center

Bailey, Jon; Preston, Kim

2007-01-01

An analysis of the proposed changes to Nebraska's school finance formula and school structure shows that many of Nebraska's rural schools could suffer from imposition of a "small by choice" factor. Research has consistently shown that smaller schools have some advantages over their larger counterparts. The 2005 session of the Nebraska…

13 CFR 107.470 - SBA approval of merger, consolidation, or reorganization of Licensee.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false SBA approval of merger, consolidation, or reorganization of Licensee. 107.470 Section 107.470 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION SMALL BUSINESS INVESTMENT COMPANIES Changes in Ownership, Control, or Structure of...

13 CFR 107.450 - Notification to SBA of pledge of Licensee's shares.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false Notification to SBA of pledge of Licensee's shares. 107.450 Section 107.450 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION SMALL BUSINESS INVESTMENT COMPANIES Changes in Ownership, Control, or Structure of Licensee; Transfer of...

The structural, functional, and nutritional adaptation of college basketball players over a season.

PubMed

Bolonchuk, W W; Lukaski, H C; Siders, W A

1991-06-01

The purpose of this study was to determine the structural, functional and nutritional adaptation of college basketball players over a season. Structure was determined by somatotype and body composition, function was determined by peak work capacity and work efficiency, and nutrition was determined by plasma metals analysis. The tests were performed twice on each of the eight subjects, one preseason (PRS) and one postseason (PST). A small structural adaptation was indicated by a mean decrease (less than 1 kg) in fat free weight and an increase in ectomorphy (less than 0.03). Body weight and skinfolds did not change significantly. Functional adaptation was indicated by a one minute decrease in running time for the work capacity test (p less than 0.002), and an increase (p less than 0.02) in VO2 for the work efficiency test. Nutritional adaptation was indicated by a greater mobilization of plasma Zn after exercise during PST than PRS. Plasma Cu apparently was mobilized during exercise in PST but the change during the season (-10 to -6.6%) was not statistically significant because of the large interindividual variability in response. Structural and functional adaptation to basketball training over a collegiate season is small; however, the change in Zn mobility and the tendency for a concomitant change in Cu mobilization offers a unique finding to help explain the nutritional adaptation to training.

Small mammal abundance in Mediterranean post-fire habitats: a role for predators?

NASA Astrophysics Data System (ADS)

Torre, I.; Díaz, M.

2004-05-01

We studied patterns of small mammal abundance and species richness in post-fire habitats by sampling 33 plots (225 m 2 each) representing different stages of vegetation recovery after fire. Small mammal abundance was estimated by live trapping during early spring 1999 and vegetation structure was sampled by visual estimation at the same plots. Recently-burnt areas were characterised by shrubby and herbaceous vegetation with low structural variability, and unburnt areas were characterised by well developed forest cover with high structural complexity. Small mammal abundance and species richness decreased with time elapsed since the last fire (from 5 to at least 50 years), and these differences were associated to the decreasing cover of short shrubs as the post-fire succession of plant communities advanced. However, relationships between vegetation structure and small mammals differed among areas burned in different times, with weak or negative relationship in recently burnt areas and positive and stronger relationship in unburnt areas. Furthermore, the abundance of small mammals was larger than expected from vegetation structure in plots burned recently whereas the contrary pattern was found in unburned areas. We hypothesised that the pattern observed could be related to the responses of small mammal predators to changes in vegetation and landscape structure promoted by fire. Fire-related fragmentation could have promoted the isolation of forest predators (owls and carnivores) in unburned forest patches, a fact that could have produced a higher predation pressure for small mammals. Conversely, small mammal populations would have been enhanced in early post-fire stages by lower predator numbers combined with better predator protection in areas covered by resprouting woody vegetation.

Implications of invasion by Juniperus virginiana on small mammals in the southern Great Plains

USGS Publications Warehouse

Horncastle, V.J.; Hellgren, E.C.; Mayer, P.M.; Ganguli, A.C.; Engle, David M.; Leslie, David M.

2005-01-01

Changes in landscape cover in the Great Plains are resulting from the range expansion and invasion of eastern red cedar (Juniperus virginiana). By altering the landscape and local vegetation, red cedar is changing the structure and function of habitat for small mammals. We examined effects of invasion by eastern red cedar on small mammals in 3 plant communities (tallgrass prairie, old field, and cross-timbers forest) in the cross-timbers ecoregion in Oklahoma. We sampled small mammals seasonally from May 2001 to August 2002 by using Sherman live traps and mark-recapture techniques on 3.24-ha, 450-trap grids in each plant community. We sampled vegetation in two hundred twenty-five 12 x 12-m cells within each grid. The structure of the small-mammal community differed among the 3 habitat types, with higher species diversity and richness in the tallgrass-prairie and old-field sites. Overall, the small-mammal community shifted along a gradient of increasing eastern red cedar. In the old-field and tallgrass-prairie plots, occurrence of grassland mammals decreased with increasing red cedar, whereas only 1 woodland mammal species increased. In the cross-timbers forest site, percent woody cover (<1 m in height), rather than cover of red cedar, was the most important factor affecting woodland mammal species. Examination of our data suggests that an increase in overstory cover from 0% to 30% red cedar can change a species-rich prairie community to a depauperate community dominated by 1 species, Peromyscus leucopus. Losses in species diversity and changes in mammal distribution paralleled those seen in avian communities invaded by eastern red cedar. Our results highlight ecological effects of invasion by eastern red cedar on diversity and function at multiple trophic levels. ?? 2005 American Society of Mammalogists.

Differences in macroinvertebrate community structure in streams and rivers with different hydrologic regimes in the semi-arid Colorado Plateau

USGS Publications Warehouse

Miller, Matthew P.; Brasher, Anne M.D.

2011-01-01

Aquatic macroinvertebrates are sensitive to changes in their chemical and physical environment, and as such, serve as excellent indicators of overall ecosystem health. Moreover, temporal and spatial differences in macroinvertebrate community structure can be used to investigate broad issues in aquatic science, such as the hypothesis that changes in climate are likely to have disproportionately large effects on small, intermittent stream ecosystems. We quantified macroinvertebrate community structure and abiotic conditions at ten stream sites with different dominant hydrologic regimes in the Colorado Plateau, ranging from small, intermittent desert streams to large perennial mountain rivers. Considerable differences were observed in community structure between sites with differing hydrologic regimes. Quantitative results of non-metric multidimensional scaling (NMDS) ordination and Spearman rank correlations between physical habitat and macroinvertebrate resemblance matrices indicate that discharge, geomorphic channel unit type (% pools vs. % riffles), percent of substrate composed of sand, and velocity were the subset of measured habitat variables that best explained the differences in macroinvertebrate community structure among sites. Of the 134 taxa identified, nine taxa explained 95 % of the variability in community structure between sites. These results add to a growing base of knowledge regarding the functioning of lotic ecosystems in the Colorado Plateau, and provide timely information on anticipated changes in the structure and function of aquatic ecosystems in response to predicted future environmental conditions.

Interferometric measurement of displacements and displacement velocities for nondestructive quality control

NASA Astrophysics Data System (ADS)

Shpeĭzman, V. V.; Peschanskaya, N. N.

2007-07-01

It is shown that the interferometric measurement of small displacements and small-displacement velocities can be used to determine internal stresses or the stresses induced by an applied load in solids and to control structural changes in them. The interferometric method based on the measurement of the reaction of a solid to a small perturbation in its state of stress is applied to determine stresses from the deviation of the reaction to perturbations from that in the standard stress-free case. For structural control, this method is employed to study the specific features of the characteristics of microplastic deformation that appear after material treatment or operation and manifest themselves in the temperature and force dependences of the rate of a small inelastic strain.

Small-Angle Neutron Scattering Reveals pH-Dependent Conformational Changes in Trichoderma reesei Cellobiohydrolase I: Implications for Enzymatic Activity

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

Pingali, Sai Venkatesh; O'Neill, Hugh Michael; McGaughey, Joseph

2011-01-01

Cellobiohydrolase I (Cel7A) of the fungus Trichoderma reesei (now classified as an anamorph of Hypocrea jecorina) hydrolyzes crystalline cellulose to soluble sugars, making it of key interest for producing fermentable sugars from biomass for biofuel production. The activity of the enzyme is pH-dependent, with its highest activity occurring at pH 4 5. To probe the response of the solution structure of Cel7A to changes in pH, we measured small angle neutron scattering of it in a series of solutions having pH values of 7.0, 6.0, 5.3, and 4.2. As the pH decreases from 7.0 to 5.3, the enzyme structure remainsmore » well defined, possessing a spatial differentiation between the cellulose binding domain and the catalytic core that only changes subtly. At pH 4.2, the solution conformation of the enzyme changes to a structure that is intermediate between a properly folded enzyme and a denatured, unfolded state, yet the secondary structure of the enzyme is essentially unaltered. The results indicate that at the pH of optimal activity, the catalytic core of the enzyme adopts a structure in which the compact packing typical of a fully folded polypeptide chain is disrupted and suggest that the increased range of structures afforded by this disordered state plays an important role in the increased activity of Cel7A through conformational selection.« less

Operando Grazing Incidence Small-Angle X-ray Scattering/X-ray Diffraction of Model Ordered Mesoporous Lithium-Ion Battery Anodes

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

Bhaway, Sarang M.; Qiang, Zhe; Xia, Yanfeng

Emergent lithium-ion (Li +) batteries commonly rely on nanostructuring of the active electrode materials to decrease the Li + ion diffusion path length and to accommodate the strains associated with the insertion and de-insertion of Li +, but in many cases these nanostructures evolve during electrochemical charging–discharging. This change in the nanostructure can adversely impact performance, and challenges remain regarding how to control these changes from the perspective of morphological design. In order to address these questions, operando grazing-incidence small-angle X-ray scattering and X-ray diffraction (GISAXS/GIXD) were used to assess the structural evolution of a family of model ordered mesoporousmore » NiCo 2O 4 anode films during battery operation. The pore dimensions were systematically varied and appear to impact the stability of the ordered nanostructure during the cycling. For the anodes with small mesopores (≈9 nm), the ordered nanostructure collapses during the first two charge–discharge cycles, as determined from GISAXS. This collapse is accompanied by irreversible Li-ion insertion within the oxide framework, determined from GIXD and irreversible capacity loss. Anodes with larger ordered mesopores (17–28 nm) mostly maintained their nanostructure through the first two cycles with reversible Li-ion insertion. During the second cycle, there was a small additional deformation of the mesostructure. Furthermore, this preservation of the ordered structure lead to significant improvement in capacity retention during these first two cycles; but, a gradual loss in the ordered nanostructure from continuing deformation of the ordered structure during additional charge–discharge cycles leads to capacity decay in battery performance. We translate these multiscale operando measurements provide insight into how changes at the atomic scale (lithium insertion and de-insertion) to the nanostructure during battery operation. Moreover, small changes in the nanostructure can build up to significant morphological transformations that adversely impact battery performance through multiple charge–discharge cycles.« less

Operando Grazing Incidence Small-Angle X-ray Scattering/X-ray Diffraction of Model Ordered Mesoporous Lithium-Ion Battery Anodes

DOE PAGES

Bhaway, Sarang M.; Qiang, Zhe; Xia, Yanfeng; ...

2017-02-07

Emergent lithium-ion (Li +) batteries commonly rely on nanostructuring of the active electrode materials to decrease the Li + ion diffusion path length and to accommodate the strains associated with the insertion and de-insertion of Li +, but in many cases these nanostructures evolve during electrochemical charging–discharging. This change in the nanostructure can adversely impact performance, and challenges remain regarding how to control these changes from the perspective of morphological design. In order to address these questions, operando grazing-incidence small-angle X-ray scattering and X-ray diffraction (GISAXS/GIXD) were used to assess the structural evolution of a family of model ordered mesoporousmore » NiCo 2O 4 anode films during battery operation. The pore dimensions were systematically varied and appear to impact the stability of the ordered nanostructure during the cycling. For the anodes with small mesopores (≈9 nm), the ordered nanostructure collapses during the first two charge–discharge cycles, as determined from GISAXS. This collapse is accompanied by irreversible Li-ion insertion within the oxide framework, determined from GIXD and irreversible capacity loss. Anodes with larger ordered mesopores (17–28 nm) mostly maintained their nanostructure through the first two cycles with reversible Li-ion insertion. During the second cycle, there was a small additional deformation of the mesostructure. Furthermore, this preservation of the ordered structure lead to significant improvement in capacity retention during these first two cycles; but, a gradual loss in the ordered nanostructure from continuing deformation of the ordered structure during additional charge–discharge cycles leads to capacity decay in battery performance. We translate these multiscale operando measurements provide insight into how changes at the atomic scale (lithium insertion and de-insertion) to the nanostructure during battery operation. Moreover, small changes in the nanostructure can build up to significant morphological transformations that adversely impact battery performance through multiple charge–discharge cycles.« less

Operando Grazing Incidence Small-Angle X-ray Scattering/X-ray Diffraction of Model Ordered Mesoporous Lithium-Ion Battery Anodes.

PubMed

Bhaway, Sarang M; Qiang, Zhe; Xia, Yanfeng; Xia, Xuhui; Lee, Byeongdu; Yager, Kevin G; Zhang, Lihua; Kisslinger, Kim; Chen, Yu-Ming; Liu, Kewei; Zhu, Yu; Vogt, Bryan D

2017-02-28

Emergent lithium-ion (Li + ) batteries commonly rely on nanostructuring of the active electrode materials to decrease the Li + ion diffusion path length and to accommodate the strains associated with the insertion and de-insertion of Li + , but in many cases these nanostructures evolve during electrochemical charging-discharging. This change in the nanostructure can adversely impact performance, and challenges remain regarding how to control these changes from the perspective of morphological design. In order to address these questions, operando grazing-incidence small-angle X-ray scattering and X-ray diffraction (GISAXS/GIXD) were used to assess the structural evolution of a family of model ordered mesoporous NiCo 2 O 4 anode films during battery operation. The pore dimensions were systematically varied and appear to impact the stability of the ordered nanostructure during the cycling. For the anodes with small mesopores (≈9 nm), the ordered nanostructure collapses during the first two charge-discharge cycles, as determined from GISAXS. This collapse is accompanied by irreversible Li-ion insertion within the oxide framework, determined from GIXD and irreversible capacity loss. Conversely, anodes with larger ordered mesopores (17-28 nm) mostly maintained their nanostructure through the first two cycles with reversible Li-ion insertion. During the second cycle, there was a small additional deformation of the mesostructure. This preservation of the ordered structure lead to significant improvement in capacity retention during these first two cycles; however, a gradual loss in the ordered nanostructure from continuing deformation of the ordered structure during additional charge-discharge cycles leads to capacity decay in battery performance. These multiscale operando measurements provide insight into how changes at the atomic scale (lithium insertion and de-insertion) are translated to the nanostructure during battery operation. Moreover, small changes in the nanostructure can build up to significant morphological transformations that adversely impact battery performance through multiple charge-discharge cycles.

76 FR 70667 - Small Business Size Standards: Educational Services

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-15

..., SBA has received comments that its size standards have not kept up with changes in the economy, in particular the changes in the Federal contracting marketplace and industry structure. The last time SBA... in the Federal Register on July 18, 2008 (73 FR 41237). Because of changes in the Federal marketplace...

Structure and interactions of human respiratory mucin

NASA Astrophysics Data System (ADS)

Purdy, Kirstin; Sheehan, John; Rubinstein, Michael; Wong, Gerard

2006-03-01

Human respiratory mucin plays a crucial role in the pathology of Cystic Fibrosis lung infections. Mucin is a flexible, linear polyelectrolyte, characterized by its many charged oligo-carbohydrate side chains that give it its bottle-brush structure. The macroscopic properties of a mucin suspension are known to change drastically with changes in ion concentration and solution pH, but little is known about the effect of these variables on individual mucin structure. We present preliminary results on the structural response of individual human respiratory mucin molecules to variations in concentration of ions of different valences via small angle x-ray diffraction.

Bi-Metallic Composite Structures With Designed Internal Residual Stress Field

NASA Technical Reports Server (NTRS)

Brice, Craig A.

2014-01-01

Shape memory alloys (SMA) have a unique ability to recover small amounts of plastic strain through a temperature induced phase change. For these materials, mechanical displacement can be accomplished by heating the structure to induce a phase change, through which some of the plastic strain previously introduced to the structure can be reversed. This paper introduces a concept whereby an SMA phase is incorporated into a conventional alloy matrix in a co-continuous reticulated arrangement forming a bi-metallic composite structure. Through memory activation of the mechanically constrained SMA phase, a controlled residual stress field is developed in the interior of the structure. The presented experimental data show that the memory activation of the SMA composite component significantly changes the residual stress distribution in the overall structure. Designing the structural arrangement of the two phases to produce a controlled residual stress field could be used to create structures that have much improved durability and damage tolerance properties.

Computational Search for Strong Topological Insulators: An Exercise in Data Mining and Electronic Structure

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

Klintenberg, M.; Haraldsen, Jason T.; Balatsky, Alexander V.

In this paper, we report a data-mining investigation for the search of topological insulators by examining individual electronic structures for over 60,000 materials. Using a data-mining algorithm, we survey changes in band inversion with and without spin-orbit coupling by screening the calculated electronic band structure for a small gap and a change concavity at high-symmetry points. Overall, we were able to identify a number of topological candidates with varying structures and composition. Lastly, our overall goal is expand the realm of predictive theory into the determination of new and exotic complex materials through the data mining of electronic structure.

Computational Search for Strong Topological Insulators: An Exercise in Data Mining and Electronic Structure

DOE PAGES

Klintenberg, M.; Haraldsen, Jason T.; Balatsky, Alexander V.

2014-06-19

In this paper, we report a data-mining investigation for the search of topological insulators by examining individual electronic structures for over 60,000 materials. Using a data-mining algorithm, we survey changes in band inversion with and without spin-orbit coupling by screening the calculated electronic band structure for a small gap and a change concavity at high-symmetry points. Overall, we were able to identify a number of topological candidates with varying structures and composition. Lastly, our overall goal is expand the realm of predictive theory into the determination of new and exotic complex materials through the data mining of electronic structure.

Informing the improvement of forest products durability using small angle neutron scattering

Treesearch

Nayomi Plaza Rodriguez; Sai Venkatesh Pingali; Shuo Qian; William T. Heller; Joseph E. Jakes

2016-01-01

A better understanding of how wood nanostructure swells with moisture is needed to accelerate the development of forest products with enhanced moisture durability. Despite its suitability to study nanostructures, small angle neutron scattering (SANS) remains an underutilized tool in forest products research. Nanoscale moisture-induced structural changes in intact and...

The Creative Opportunists: Conversations with the CEOs of Small Businesses.

ERIC Educational Resources Information Center

Bruce, James S.

Interviews with the chief executive officers of 14 small businesses revealed the leadership challenges that they face. Some of the challenges are the following: (1) creating change; (2) building a robust organization, with a well-defined structure, an effective management team, plans for succession, established delivery systems, and people who…

13 CFR 107.440 - Standards governing prior SBA approval for a proposed transfer of Control.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 13 Business Credit and Assistance 1 2012-01-01 2012-01-01 false Standards governing prior SBA approval for a proposed transfer of Control. 107.440 Section 107.440 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION SMALL BUSINESS INVESTMENT COMPANIES Changes in Ownership, Control, or Structure of...

13 CFR 107.440 - Standards governing prior SBA approval for a proposed transfer of Control.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 13 Business Credit and Assistance 1 2013-01-01 2013-01-01 false Standards governing prior SBA approval for a proposed transfer of Control. 107.440 Section 107.440 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION SMALL BUSINESS INVESTMENT COMPANIES Changes in Ownership, Control, or Structure of...

13 CFR 107.440 - Standards governing prior SBA approval for a proposed transfer of Control.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 13 Business Credit and Assistance 1 2011-01-01 2011-01-01 false Standards governing prior SBA approval for a proposed transfer of Control. 107.440 Section 107.440 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION SMALL BUSINESS INVESTMENT COMPANIES Changes in Ownership, Control, or Structure of...

13 CFR 107.440 - Standards governing prior SBA approval for a proposed transfer of Control.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 13 Business Credit and Assistance 1 2014-01-01 2014-01-01 false Standards governing prior SBA approval for a proposed transfer of Control. 107.440 Section 107.440 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION SMALL BUSINESS INVESTMENT COMPANIES Changes in Ownership, Control, or Structure of...

Optics-Only Calibration of a Neural-Net Based Optical NDE Method for Structural Health Monitoring

NASA Technical Reports Server (NTRS)

Decker, Arthur J.

2004-01-01

A calibration process is presented that uses optical measurements alone to calibrate a neural-net based NDE method. The method itself detects small changes in the vibration mode shapes of structures. The optics-only calibration process confirms previous work that the sensitivity to vibration-amplitude changes can be as small as 10 nanometers. A more practical value in an NDE service laboratory is shown to be 50 nanometers. Both model-generated and experimental calibrations are demonstrated using two implementations of the calibration technique. The implementations are based on previously published demonstrations of the NDE method and an alternative calibration procedure that depends on comparing neural-net and point sensor measurements. The optics-only calibration method, unlike the alternative method, does not require modifications of the structure being tested or the creation of calibration objects. The calibration process can be used to test improvements in the NDE process and to develop a vibration-mode-independence of damagedetection sensitivity. The calibration effort was intended to support NASA s objective to promote safety in the operations of ground test facilities or aviation safety, in general, by allowing the detection of the gradual onset of structural changes and damage.

The introduction of strain and its effects on the structure and stability of T4 lysozyme.

PubMed

Liu, R; Baase, W A; Matthews, B W

2000-01-07

In order to try to better understand the role played by strain in the structure and stability of a protein a series of "small-to-large" mutations was made within the core of T4 lysozyme. Three different alanine residues, one involved in backbone contacts, one in side-chain contacts, and the third adjacent to a small cavity, were each replaced with subsets of the larger residues, Val, Leu, Ile, Met, Phe and Trp. As expected, the protein is progressively destabilized as the size of the introduced side-chain becomes larger. There does, however, seem to be a limit to the destabilization, suggesting that a protein of a given size may be capable of maintaining only a certain amount of strain. The changes in stability vary greatly from site to site. Substitution of larger residues for both Ala42 and Ala98 substantially destabilize the protein, even though the primary contacts in one case are predominantly with side-chain atoms and in the other with backbone. The results suggest that it is neither practical nor meaningful to try to separate the effects of introduced strain on side-chains from the effects on the backbone. Substitutions at Ala129 are much less destabilizing than at sites 42 or 98. This is most easily understood in terms of the pre-existing cavity, which provides partial space to accommodate the introduced side-chains. Crystal structures were obtained for a number of the mutants. These show that the changes in structure to accommodate the introduced side-chains usually consist of essentially rigid-body displacements of groups of linked atoms, achieved through relatively small changes in torsion angles. On rare occasions, a side-chain close to the site of substitution may change to a different rotamer. When such rotomer changes occur, they permit the structure to dissipate strain by a response that is plastic rather than elastic. In one case, a surface loop moves 1.2 A, not in direct response to a mutation, but in an interaction mediated via an intermolecular contact. It illustrates how the structure of a protein can be modified by crystal contacts. Copyright 2000 Academic Press.

State autonomy, policy paralysis: paradoxes of institutions and culture in the French health care system.

PubMed

Rochaix, Lise; Wilsford, David

2005-01-01

In this article, we assess the recent performance of the French state at containing costs in health care using political science concepts such as path dependency and incentives, which are central to an economic approach. The article focuses on institutional capacities and cultural immobilism and attempts to lay bare the tensions at play in seizing (or not) opportunities for structural change. In particular, we attempt to delineate what constitutes real change in this policy arena (big reforms versus the accumulation of many small policy movements) and to understand the variables at play in the coming together of conjunctures that provide for the big, as well as the underlying structures that allow the accumulation of the small. Except in cases of favorable conjuncture, the analysis bodes very ill for nonincremental reform and, indeed, for significant change over the long term.

Microfluidic strategy to investigate dynamics of small blood vessel function

NASA Astrophysics Data System (ADS)

Yasotharan, Sanjesh; Bolz, Steffen-Sebastian; Guenther, Axel

2010-11-01

Resistance arteries (RAs, 30-300 microns in diameter) that are located within the terminal part of the vascular tree regulate the laminar perfusion of tissue with blood, via the peripheral vascular resistance, and hence controls the systemic blood pressure. The structure of RAs is adapted to actively controlling flow resistance by dynamically changing their diameter, which is non-linearly dependent on the temporal variation of the transmural pressure, perfusion flow rate and spatiotemporal changes in the chemical environment. Increases in systemic blood pressure (hypertension) resulting from pathologic changes in the RA response represent the primary risk factor for cardiovascular diseases. We use a microfluidic strategy to investigate small blood vessels by quantifying structural variations within the arterial wall, RA outer contour and diameter over time. First, we document the artery response to vasomotor drugs that were homogeneously applied at step-wise increasing concentration. Second, we investigate the response in the presence of well-defined axial and circumferential heterogeneities. Artery per- and superfusion is discussed based on microscale PIV measurements of the fluid velocity on both sides of the arterial wall. Structural changes in the arterial wall are quantified using cross-correlation and proper orthogonal decomposition analyses of bright-field micrographs.

Time-Resolved Small-Angle X-ray Scattering Reveals Millisecond Transitions of a DNA Origami Switch.

PubMed

Bruetzel, Linda K; Walker, Philipp U; Gerling, Thomas; Dietz, Hendrik; Lipfert, Jan

2018-04-11

Self-assembled DNA structures enable creation of specific shapes at the nanometer-micrometer scale with molecular resolution. The construction of functional DNA assemblies will likely require dynamic structures that can undergo controllable conformational changes. DNA devices based on shape complementary stacking interactions have been demonstrated to undergo reversible conformational changes triggered by changes in ionic environment or temperature. An experimentally unexplored aspect is how quickly conformational transitions of large synthetic DNA origami structures can actually occur. Here, we use time-resolved small-angle X-ray scattering to monitor large-scale conformational transitions of a two-state DNA origami switch in free solution. We show that the DNA device switches from its open to its closed conformation upon addition of MgCl 2 in milliseconds, which is close to the theoretical diffusive speed limit. In contrast, measurements of the dimerization of DNA origami bricks reveal much slower and concentration-dependent assembly kinetics. DNA brick dimerization occurs on a time scale of minutes to hours suggesting that the kinetics depend on local concentration and molecular alignment.

Functional and structural analysis of a highly-expressed Yersinia pestis small RNA following infection of cultured macrophages

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

Li, Nan; Hennelly, Scott P.; Stubben, Chris J.

Non-coding small RNAs (sRNAs) are found in practically all bacterial genomes and play important roles in regulating gene expression to impact bacterial metabolism, growth, and virulence. We performed transcriptomics analysis to identify sRNAs that are differentially expressed in Yersinia pestis that invaded the human macrophage cell line THP-1, compared to pathogens that remained extracellular in the presence of host. Using ultra high-throughput sequencing, we identified 37 novel and 143 previously known sRNAs in Y. pestis. In particular, the sRNA Ysr170 was highly expressed in intracellular Yersinia and exhibited a log2 fold change ~3.6 higher levels compared to extracellular bacteria. Wemore » found that knock-down of Ysr170 expression attenuated infection efficiency in cell culture and growth rate in response to different stressors. In addition, we applied selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE) analysis to determine the secondary structure of Ysr170 and observed structural changes resulting from interactions with the aminoglycoside antibiotic gentamycin and the RNA chaperone Hfq. Interestingly, gentamicin stabilized helix 4 of Ysr170, which structurally resembles the native gentamicin 16S ribosomal binding site. Lastly, we modeled the tertiary structure of Ysr170 binding to gentamycin using RNA motif modeling. Integration of these experimental and structural methods can provide further insight into the design of small molecules that can inhibit function of sRNAs required for pathogen virulence.« less

Functional and structural analysis of a highly-expressed Yersinia pestis small RNA following infection of cultured macrophages

DOE PAGES

Li, Nan; Hennelly, Scott P.; Stubben, Chris J.; ...

2016-12-28

Non-coding small RNAs (sRNAs) are found in practically all bacterial genomes and play important roles in regulating gene expression to impact bacterial metabolism, growth, and virulence. We performed transcriptomics analysis to identify sRNAs that are differentially expressed in Yersinia pestis that invaded the human macrophage cell line THP-1, compared to pathogens that remained extracellular in the presence of host. Using ultra high-throughput sequencing, we identified 37 novel and 143 previously known sRNAs in Y. pestis. In particular, the sRNA Ysr170 was highly expressed in intracellular Yersinia and exhibited a log2 fold change ~3.6 higher levels compared to extracellular bacteria. Wemore » found that knock-down of Ysr170 expression attenuated infection efficiency in cell culture and growth rate in response to different stressors. In addition, we applied selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE) analysis to determine the secondary structure of Ysr170 and observed structural changes resulting from interactions with the aminoglycoside antibiotic gentamycin and the RNA chaperone Hfq. Interestingly, gentamicin stabilized helix 4 of Ysr170, which structurally resembles the native gentamicin 16S ribosomal binding site. Lastly, we modeled the tertiary structure of Ysr170 binding to gentamycin using RNA motif modeling. Integration of these experimental and structural methods can provide further insight into the design of small molecules that can inhibit function of sRNAs required for pathogen virulence.« less

Social structure, infectious diseases, disasters, secularism, and cultural change in America.

PubMed

Grossmann, Igor; Varnum, Michael E W

2015-03-01

Why do cultures change? The present work examined cultural change in eight cultural-level markers, or correlates, of individualism in the United States, all of which increased over the course of the 20th century: frequency of individualist themes in books, preference for uniqueness in baby naming, frequency of single-child relative to multichild families, frequency of single-generation relative to multigeneration households, percentage of adults and percentage of older adults living alone, small family size, and divorce rates (relative to marriage rates). We tested five key hypotheses regarding cultural change in individualism-collectivism. As predicted by previous theories, changes in socioeconomic structure, pathogen prevalence, and secularism accompanied changes in individualism averaged across all measures. The relationship with changes in individualism was less robust for urbanization. Contrary to previous theories, changes in individualism were positively (as opposed to negatively) related to the frequency of disasters. Time-lagged analyses suggested that only socioeconomic structure had a robust effect on individualism; changes in socioeconomic structure preceded changes in individualism. Implications for anthropology, psychology, and sociology are discussed. © The Author(s) 2015.

Thresholds for conservation and management: structured decision making as a conceptual framework

USGS Publications Warehouse

Nichols, James D.; Eaton, Mitchell J.; Martin, Julien; Edited by Guntenspergen, Glenn R.

2014-01-01

changes in system dynamics. They are frequently incorporated into ecological models used to project system responses to management actions. Utility thresholds are components of management objectives and are values of state or performance variables at which small changes yield substantial changes in the value of the management outcome. Decision thresholds are values of system state variables at which small changes prompt changes in management actions in order to reach specified management objectives. Decision thresholds are derived from the other components of the decision process.We advocate a structured decision making (SDM) approach within which the following components are identified: objectives (possibly including utility thresholds), potential actions, models (possibly including ecological thresholds), monitoring program, and a solution algorithm (which produces decision thresholds). Adaptive resource management (ARM) is described as a special case of SDM developed for recurrent decision problems that are characterized by uncertainty. We believe that SDM, in general, and ARM, in particular, provide good approaches to conservation and management. Use of SDM and ARM also clarifies the distinct roles of ecological thresholds, utility thresholds, and decision thresholds in informed decision processes.

Strategic Planning at a Small College--Executive Overview

ERIC Educational Resources Information Center

Agnew, Robert

2004-01-01

In 1994, Baldwin-Wallace College produced a Strategic Plan for Information Technology. This plan mandated changes in the influx of technology, the structure of IT, and technology committees. The published plan included the organizational structure of the College, a SWOT analysis (strengths, weaknesses, opportunities, and threats), ten proposed…

The Educational Implications of Regionalisation.

ERIC Educational Resources Information Center

Macdonald, R.

As of May 1975 the structure of Scottish local government will experience a change that will affect rural education, as districts will be reorganized for purposes of encouraging local control. In reference to this new structuring, the following questions must be considered: (1) Since it has been claimed that existing small school authorities lack…

Spectroscopic Identification of Lipid, Protein and DNA Changes in Breast Cancer tissues

NASA Astrophysics Data System (ADS)

Badr, Y. A.; Hassab Elnaby, S. I.

2007-02-01

The FTIR spectroscopy, at the range 4000 - 6000 cm-1 showed a clear distinction between normal and cancer tissues. Normal tissues spectra contain a doublet structure at 4258 and 4332 cm-1. This structure is usually on top of a small band that extends from 3950 cm-1 to 4400 cm-1. This structure us also observed from pure lipid tissues from control patients. The origin of this structure could be attributed to combinations of lipid lines. This structure is completely absent in cancer tissues, instead a broad intense band appears from 5100 cm-1 to 5200 cm-1. The intensity of this band varies from one patient to another. The shape of this broad band indicates that it is the due to random orientation changes in the proteins. This band has a peak at 5164 cm-1, it contains another small kink at 4882 cm-1. This may lead also to the conclusion that this window band is associated with a short half life time energy levels. On The other hand the photoacoustic spectrum of the same tissues , shows that in normal tissues there are three very distinct peaks (namely 1097,1159 and 1232 cm-1) they disappear in malignant tissues and replaced by many weak ripples. Two peaks (1578, 1690 cm-1) changes their position in malignant tissues(1626, 1678 cm-1). A change in DNA markers was also noticed in the range 600-1700 cm-1.

Scale characters analysis for gully structure in the watersheds of loess landforms based on digital elevation models

NASA Astrophysics Data System (ADS)

Zhu, Hongchun; Zhao, Yipeng; Liu, Haiying

2018-04-01

Scale is the basic attribute for expressing and describing spatial entity and phenomena. It offers theoretical significance in the study of gully structure information, variable characteristics of watershed morphology, and development evolution at different scales. This research selected five different areas in China's Loess Plateau as the experimental region and used DEM data at different scales as the experimental data. First, the change rule of the characteristic parameters of the data at different scales was analyzed. The watershed structure information did not change along with a change in the data scale. This condition was proven by selecting indices of gully bifurcation ratio and fractal dimension as characteristic parameters of watershed structure information. Then, the change rule of the characteristic parameters of gully structure with different analysis scales was analyzed by setting the scale sequence of analysis at the extraction gully. The gully structure of the watershed changed with variations in the analysis scale, and the change rule was obvious when the gully level changed. Finally, the change rule of the characteristic parameters of the gully structure at different areas was analyzed. The gully fractal dimension showed a significant numerical difference in different areas, whereas the variation of the gully branch ratio was small. The change rule indicated that the development degree of the gully obviously varied in different regions, but the morphological structure was basically similar.

Scale characters analysis for gully structure in the watersheds of loess landforms based on digital elevation models

NASA Astrophysics Data System (ADS)

Zhu, Hongchun; Zhao, Yipeng; Liu, Haiying

2018-06-01

Scale is the basic attribute for expressing and describing spatial entity and phenomena. It offers theoretical significance in the study of gully structure information, variable characteristics of watershed morphology, and development evolution at different scales. This research selected five different areas in China's Loess Plateau as the experimental region and used DEM data at different scales as the experimental data. First, the change rule of the characteristic parameters of the data at different scales was analyzed. The watershed structure information did not change along with a change in the data scale. This condition was proven by selecting indices of gully bifurcation ratio and fractal dimension as characteristic parameters of watershed structure information. Then, the change rule of the characteristic parameters of gully structure with different analysis scales was analyzed by setting the scale sequence of analysis at the extraction gully. The gully structure of the watershed changed with variations in the analysis scale, and the change rule was obvious when the gully level changed. Finally, the change rule of the characteristic parameters of the gully structure at different areas was analyzed. The gully fractal dimension showed a significant numerical difference in different areas, whereas the variation of the gully branch ratio was small. The change rule indicated that the development degree of the gully obviously varied in different regions, but the morphological structure was basically similar.

Transport and magnetic properties of Fe doped CaMnO3

NASA Astrophysics Data System (ADS)

Neetika; Das, A.; Dhiman, I.; Nigam, A. K.; Yadav, A. K.; Bhattacharyya, D.; Meena, S. S.

2012-12-01

The structural, transport, and magnetic properties of CaMn1-xFexO3-δ (0.0 ≤ x ≤ 0.3) have been studied by using resistivity, magnetization, and neutron powder diffraction techniques. The compounds are found to be isostructural and crystallize in GdFeO3-type orthorhombic structure (space group Pnma). With Fe doping, no structural change is observed. Mössbauer and paramagnetic susceptibility measurements show that Fe substitutes in 4+ valence state, and XANES measurements indicate the presence of mixed valence state of Mn. The compounds exhibit insulating behavior in the studied temperature range. The temperature dependence of resistivity is found to be described by small polaron model for x = 0 and variable range hopping model for x = 0.1. For higher x values, it follows a parallel combination resistance model. A small reduction in TN from 120 K to 100 K with increase in x is found. The magnetic structure changes from Gz-type collinear antiferromagnetic (AFM) structure for x = 0.0 to canted AFM structure GZFY-type for Fe doped compounds. The AFM component of the moment progressively decreases with x while FM component exhibits a maximum at x = 0.2.

Structural and phase transition changes of sodium dodecyl sulfate micellar solution in alcohols probed by small-angle neutron scattering (SANS)

NASA Astrophysics Data System (ADS)

Putra, Edy Giri Rachman; Patriati, Arum

2015-04-01

Small-angle neutron scattering (SANS) measurements on 0.3M sodium dodecyl sulfate (SDS) micellar solutions have been performed in the presence of n-alcohols, from ethanol to decanol at different alcohol concentrations, 2-10 wt%. The ellipsoid micellar structure which occurred in the 0.3M SDS in aqueous solution with the size range of 30-50 Å has different behavior at various hydrocarbon chain length and concentration of alcohols. At low concentration and short chain-length of alcohols, such as ethanol, propanol, and butanol, the size of micelles reduced and had a spherical-like structure. The opposite effect occurred as medium to long chain alcohols, such as hexanol, octanol and decanol was added into the 0.3M SDS micellar solutions. The micelles structure changed to be more elongated in major axis and then crossed the critical phase transition from micellar solution into liquid crystal phase as lamellar structure emerged by further addition of alcohols. The inter-lamellar distances were also depending on the hydrocarbon chain length and concentration of alcohols. In the meantime, the persistent micellar structures occurred in addition of medium chain of n-alcohol, pentanol at all concentrations.

On the Propagation of Small Perturbations in Two Simple Aeroelastic Systems

NASA Technical Reports Server (NTRS)

Iollo, Angelo; Salas, Manuel D.

1998-01-01

In this paper we investigate the wave propagation patterns for two simple flow-structure problems. We focus on the study of the propagation speeds of the waves in the fluid and in the structure, as the rigidity of the structure and the Mach number of the undisturbed flow are changing. Some implications concerning the sound emission by inhomogeneities eventually present in the structure are discussed.

A Small-Scale, Feasibility Study of Academic Language Time in Primary Grade Language Arts

ERIC Educational Resources Information Center

Roskos, Kathleen A.; Zuzolo, Nicole; Primm, Ashley

2017-01-01

A small-scale feasibility study was conducted to explore the implementation of academic language time (ALT) in primary grade classrooms with and without access to digital devices. Academic language time is a structural change that dedicates a portion of language arts instructional time to direct vocabulary instruction using evidence-based…

Emergence of small-world structure in networks of spiking neurons through STDP plasticity.

PubMed

Basalyga, Gleb; Gleiser, Pablo M; Wennekers, Thomas

2011-01-01

In this work, we use a complex network approach to investigate how a neural network structure changes under synaptic plasticity. In particular, we consider a network of conductance-based, single-compartment integrate-and-fire excitatory and inhibitory neurons. Initially the neurons are connected randomly with uniformly distributed synaptic weights. The weights of excitatory connections can be strengthened or weakened during spiking activity by the mechanism known as spike-timing-dependent plasticity (STDP). We extract a binary directed connection matrix by thresholding the weights of the excitatory connections at every simulation step and calculate its major topological characteristics such as the network clustering coefficient, characteristic path length and small-world index. We numerically demonstrate that, under certain conditions, a nontrivial small-world structure can emerge from a random initial network subject to STDP learning.

Influence of ordering change on the optical and thermal properties of inflation polyethylene films

NASA Astrophysics Data System (ADS)

Morikawa, Junko; Orie, Akihiro; Hikima, Yuta; Hashimoto, Toshimasa; Juodkazis, Saulius

2011-04-01

Changes of thermal diffusivity inside femtosecond laser-structured volumes as small as few percent were reliably determined (with standard deviation less than 1%) with miniaturized sensors. An increase of thermal diffusivity of a crystalline high-density polyethylene (HDPE) inflation films by 10-20% from the measured (1.16 ± 0.01) × 10 -7 m 2 s -1 value in regions not structured by femtosecond laser pulses is considerably larger than that of non-crystalline polymers, 0-3%. The origin of the change of thermal diffusivity are interplay between the laser induced disordering, voids' formation, compaction, and changes in molecular orientation. It is shown that laser structuring can be used to modify thermal and optical properties. The birefringence and infrared spectroscopy with thermal imaging of CH 2 vibrations are confirming inter-relation between structural, optical, and thermal properties of the laser-structured crystalline HDPE inflation films. Birefringence modulation as high as Δ n ˜ ± 1 × 10 -3 is achieved with grating structures.

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

Climate-mediated changes in zooplankton community structure for the eastern Bering Sea

NASA Astrophysics Data System (ADS)

Eisner, Lisa B.; Napp, Jeffrey M.; Mier, Kathryn L.; Pinchuk, Alexei I.; Andrews, Alexander G.

2014-11-01

Zooplankton are critical to energy transfer between higher and lower trophic levels in the eastern Bering Sea ecosystem. Previous studies from the southeastern Bering Sea shelf documented substantial differences in zooplankton taxa in the Middle and Inner Shelf Domains between warm and cold years. Our investigation expands this analysis into the northern Bering Sea and the south Outer Domain, looking at zooplankton community structure during a period of climate-mediated, large-scale change. Elevated air temperatures in the early 2000s resulted in regional warming and low sea-ice extent in the southern shelf whereas the late 2000s were characterized by cold winters, extensive spring sea ice, and a well-developed pool of cold water over the entire Middle Domain. The abundance of large zooplankton taxa such as Calanus spp. (C. marshallae and C. glacialis), and Parasagitta elegans, increased from warm to cold periods, while the abundance of gelatinous zooplankton (Cnidaria) and small taxa decreased. Biomass followed the same trends as abundance, except that the biomass of small taxa in the southeastern Bering Sea remained constant due to changes in abundance of small copepod taxa (increases in Acartia spp. and Pseudocalanus spp. and decreases in Oithona spp.). Statistically significant changes in zooplankton community structure and individual species were greatest in the Middle Domain, but were evident in all shelf domains, and in both the northern and southern portions of the eastern shelf. Changes in community structure did not occur abruptly during the transition from warm to cold, but seemed to begin gradually and build as the influence of the sea ice and cold water temperatures persisted. The change occurred one year earlier in the northern than the southern Middle Shelf. These and previous observations demonstrate that lower trophic levels within the eastern Bering Sea respond to climate-mediated changes on a variety of time scales, including those shorter than the commonly accepted quasi-decadal time periods. This lack of resilience or inertia at the lowest trophic levels affects production at higher trophic levels and must be considered in management strategy evaluations of living marine resources.

Performance-Based Funding: State Policy Influences on Small Rural Community Colleges

ERIC Educational Resources Information Center

Thornton, Zoë Mercedes; Friedel, Janice Nahra

2016-01-01

Performance-based funding (PBF) models intend to increase efficiency and productivity of the institution, thereby influencing organizational change. This change may be structural, programmatic, or procedural, and it may affect institutional practice and/or policy. The purpose of this qualitative case study was to understand the organizational…

Structural changes and fluctuations of proteins. I. A statistical thermodynamic model.

PubMed

Ikegami, A

1977-01-01

A general theory of the structural changes and fluctuations of proteins has been proposed based on statistical thermodynamic considerations at the chain level. The "structure" of protein was assumed to be characterized by the state of secondary bonds between unique pairs of specific sites on peptide chains. Every secondary bond changes between the bonded and unbonded states by thermal agitation and the "structure" is continuously fluctuating. The free energy of the "structural state" that is defined by the fraction of secondary bonds in the bonded state has been expressed by the bond energy, the cooperative interaction between bonds, the mixing entropy of bonds, and the entropy of polypeptide chains. The most probable "structural state" can be simply determined by graphical analysis and the effect of temperature or solvent composition on it is discussed. The temperature dependence of the free energy, the probability distribution of structural states and the specific heat have been calculted for two examples of structural change. The theory predicts two different types of structural changes from the ordered to disorderd state, a "structured transition" and a "gradual structural change" with rising temperature. In the "structural transition", the probability distribution has two maxima in the temperature range of transition. In the "gradual structural change", the probabilty distribution has only one maximum during the change. A considerable fraction of secondary bonds is in the unbounded state and is always fluctuating even in the ordered state at room temperature. Such structural flucutations in a single protein molecule have been discussed quantitatively. The theory is extended to include small molecules which bind to the protein molecule and affect the structural state. The changes of structural state caused by specific and non-specific binding and allosteric effects are explained in a unified manner.

Understanding molecular structure dependence of exciton diffusion in conjugated small molecules

NASA Astrophysics Data System (ADS)

Li, Zi; Zhang, Xu; Woellner, Cristiano F.; Lu, Gang

2014-04-01

First-principles simulations are carried out to understand molecular structure dependence of exciton diffusion in a series of small conjugated molecules arranged in a disordered, crystalline, and blend structure. Exciton diffusion length (LD), lifetime, and diffusivity in four diketopyrrolopyrrole derivatives are calculated and the results compare very well with experimental values. The correlation between exciton diffusion and molecular structure is examined in detail. In the disordered molecule structure, a longer backbone length leads to a shorter exciton lifetime and a higher exciton diffusivity, but it does not change LD substantially. Removal of the end alkyl chains or the extra branch on the side alkyl chains reduces LD. In the crystalline structure, exciton diffusion exhibits a strong anisotropy whose origin can be elucidated from the intermolecular transition density interaction point of view. In the blend structure, LD increases with the crystalline ratios, which are estimated and consistent with the experimental results.

Cognitive and brain structural changes in a lung cancer population.

PubMed

Simó, Marta; Root, James C; Vaquero, Lucía; Ripollés, Pablo; Jové, Josep; Ahles, Tim; Navarro, Arturo; Cardenal, Felipe; Bruna, Jordi; Rodríguez-Fornells, Antoni

2015-01-01

No study has examined structural brain changes specifically associated with chemotherapy in a lung cancer population. The aim of this cross-sectional study was to assess differences in brain structure between small-cell lung cancer patients (C+) following chemotherapy, non-small-cell lung cancer patients (C-) before chemotherapy and healthy controls (HC). Twenty-eight small-cell lung cancer patients underwent a neuropsychological assessment and a structural magnetic resonance imaging, including T1-weighted and diffusion tensor imaging to examine gray matter density and white matter (WM) integrity, respectively, 1 month following completion of platinum-based chemotherapy. This group was compared with 20 age and education-matched non-small-cell lung cancer patients before receiving chemotherapy and 20 HC. Both C+ and C- groups exhibited cognitive impairment compared with the HC group. The C+ group performed significantly worse than HC in verbal fluency and visuospatial subtests; C- performed significantly worse than both C+ and HC in verbal memory. Voxel-based morphometry analysis revealed lower gray matter density in the insula and parahippocampal gyrus bilaterally, and left anterior cingulate cortex in C+ compared with HC. Diffusion tensor imaging indices showed focal decreased WM integrity in left cingulum and bilateral inferior longitudinal fasciculus in the C+ group and more widespread decreased integrity in the C- group compared with the HC group. This study demonstrates that lung cancer patients exhibit cognitive impairment before and after chemotherapy. Before the treatment, C- showed verbal memory deficits as well as a widespread WM damage. Following treatment, the C+ group performed exhibited lower visuospatial and verbal fluency abilities, together with structural gray matter and WM differences in bilateral regions integrating the paralimbic system.

Improving the Small-Business Role in Turkish Defense Acquisitions: Recommendations from U.S. Best Practices

DTIC Science & Technology

2010-06-01

not take into account the effects of the Global Crisis as it impacts the small business assistance programs. Data related to Small and Medium Sized...unanticipated by many scholars and members of the policy community , but what was even more surprising than the resurgence itself was the primary...innovative because of their responsiveness to “changing market demands,” flexible structures, and “efficient internal communication ” (Mogee, 2003, p. 3

Lake warming favours small-sized planktonic diatom species

PubMed Central

Winder, Monika; Reuter, John E.; Schladow, S. Geoffrey

2008-01-01

Diatoms contribute to a substantial portion of primary production in the oceans and many lakes. Owing to their relatively heavy cell walls and high nutrient requirements, planktonic diatoms are expected to decrease with climate warming because of reduced nutrient redistribution and increasing sinking velocities. Using a historical dataset, this study shows that diatoms were able to maintain their biovolume with increasing stratification in Lake Tahoe over the last decades; however, the diatom community structure changed. Increased stratification and reduced nitrogen to phosphorus ratios selected for small-celled diatoms, particularly within the Cyclotella genus. An empirical model showed that a shift in phytoplankton species composition and cell size was consistent within different depth strata, indicating that altered nutrient concentrations were not responsible for the change. The increase in small-celled species was sufficient to decrease the average diatom size and thus sinking velocity, which strongly influences energy transfer through the food web and carbon cycling. Our results show that within the diverse group of diatoms, small-sized species with a high surface area to volume ratio were able to adapt to a decrease in mixing intensity, supporting the hypotheses that abiotic drivers affect the size structure of planktonic communities and that warmer climate favours small-sized diatom cells. PMID:18812287

Probing the emitter site of Renilla luciferase using small organic molecules; an attempt to understand the molecular architecture of the emitter site.

PubMed

Salehi, Farajollah; Emamzadeh, Rahman; Nazari, Mahboobeh; Rasa, Seyed Mohammad Mahdi

2016-12-01

Renilla luciferase is a sensitive enzyme and has wide applications in biotechnology such as drug screening. Previous studies have tried to show the catalytic residues, nevertheless, the accurate architecture and molecular behavior of its emitter site remains uncharacterized. In this study, the activity of Renilla luciferase, in the presence of two small organic molecules including dimethyl sulfoxide (DMSO) and isopropanol was considered and the structure was studied by circular dichroism (CD) and fluorescence spectroscopy. Moreover, the interaction of small organic molecules with the Renilla luciferase was studied using molecular dynamics simulations. Kinetics studies showed that at low concentration of DMSO (16.6-66mM) and isopropanol (19.3-76mM) the K m changed and a competitive inhibition pattern was observed. Moreover, spectroscopy studies reveled that the changes of activity of Renilla luciferase in the presence of low concentrations of small organic molecules was not associated with structural collapse or severe changes in the enzyme conformation. Molecular dynamics simulations indicated that DMSO and isopropanol, as probing molecules, were both able to bind to the emitter site and remained with the residues of the emitter site. Based on the probing data, the architecture of the emitter site in the "non-binding" model was proposed. Copyright © 2016 Elsevier B.V. All rights reserved.

Atomic Force Microscopy Studies on DNA Structural Changes Induced by Vincristine Sulfate and Aspirin

NASA Astrophysics Data System (ADS)

Zhu, Yi; Zeng, Hu; Xie, Jianming; Ba, Long; Gao, Xiang; Lu, Zuhong

2004-04-01

We report that atomic force microscopy (AFM) studies on structural variations of a linear plasmid DNA interact with various concentrations of vincristine sulfate and aspirin. The different binding images show that vincrinstine sulfate binding DNA chains caused some loops and cleavages of the DNA fragments, whereas aspirin interaction caused the width changes and conformational transition of the DNA fragments. Two different DNA structural alternations could be explained by the different mechanisms of the interactions with these two components. Our work indicates that the AFM is a powerful tool in studying the interaction between DNA and small molecules.

Large Lateral Photovoltaic Effect in Metal-(Oxide-) Semiconductor Structures

PubMed Central

Yu, Chongqi; Wang, Hui

2010-01-01

The lateral photovoltaic effect (LPE) can be used in position-sensitive detectors to detect very small displacements due to its output of lateral photovoltage changing linearly with light spot position. In this review, we will summarize some of our recent works regarding LPE in metal-semiconductor and metal-oxide-semiconductor structures, and give a theoretical model of LPE in these two structures. PMID:22163463

Small-angle neutron scattering study of a monoclonal antibody using free-energy constraints.

PubMed

Clark, Nicholas J; Zhang, Hailiang; Krueger, Susan; Lee, Hyo Jin; Ketchem, Randal R; Kerwin, Bruce; Kanapuram, Sekhar R; Treuheit, Michael J; McAuley, Arnold; Curtis, Joseph E

2013-11-14

Monoclonal antibodies (mAbs) contain hinge-like regions that enable structural flexibility of globular domains that have a direct effect on biological function. A subclass of mAbs, IgG2, have several interchain disulfide bonds in the hinge region that could potentially limit structural flexibility of the globular domains and affect the overall configuration space available to the mAb. We have characterized human IgG2 mAb in solution via small-angle neutron scattering (SANS) and interpreted the scattering data using atomistic models. Molecular Monte Carlo combined with molecular dynamics simulations of a model mAb indicate that a wide range of structural configurations are plausible, spanning radius of gyration values from ∼39 to ∼55 Å. Structural ensembles and representative single structure solutions were derived by comparison of theoretical SANS profiles of mAb models to experimental SANS data. Additionally, molecular mechanical and solvation free-energy calculations were carried out on the ensemble of best-fitting mAb structures. The results of this study indicate that low-resolution techniques like small-angle scattering combined with atomistic molecular simulations with free-energy analysis may be helpful to determine the types of intramolecular interactions that influence function and could lead to deleterious changes to mAb structure. This methodology will be useful to analyze small-angle scattering data of many macromolecular systems.

Small-scale spatial variability in phylogenetic community structure during early plant succession depends on soil properties.

PubMed

Ulrich, Werner; Piwczyński, Marcin; Zaplata, Markus Klemens; Winter, Susanne; Schaaf, Wolfgang; Fischer, Anton

2014-07-01

During early plant succession, the phylogenetic structure of a community changes in response to important environmental filters and emerging species interactions. We traced the development of temperate-zone plant communities during the first 7 years of primary succession on catchment soils to explore patterns of initial species assembly. We found pronounced small-scale differences in the phylogenetic composition of neighbouring plant assemblages and a large-scale trend towards phylogenetic evenness. This small-scale variability appears to be mediated by soil properties, particularly carbonate content. Therefore, abiotic environmental conditions might counteract or even supersede the effects of interspecific competition among closely related species, which are usually predicted to exhibit patterns of phylogenetic evenness. We conclude that theories on phylogenetic community composition need to incorporate effects of small-scale variability of environmental factors.

One-dimensional Confinement Effect on the Self-assembly of Symmetric H-shaped Copolymers in a Thin Film.

PubMed

Mu, Dan; Li, Jian-Quan; Feng, Sheng-Yu

2017-10-19

The self-assembly of a reformed symmetric H-shaped copolymer with four hydrophilic branches and one hydrophobic stem was systematically investigated. The existence of vacancies is vital to regulate the sizes of self-assembled cylinders to be able to form a hexagonal arrangement. With the introduction of horizontal-orientated confinement, a micellar structure is formed through a coalescence mechanism. The short acting distance and large influencing area of the confinement produces numerous small-sized micelles. Additionally, the cycled "contraction-expansion" change helps achieve hexagonal arrangement. In contrast, the introduction of lateral-oriented confinement with long acting distance and small influencing area cannot change the cylindrical structure. Under the fission mechanism, in which the larger cylinder splits into smaller ones, it is quite efficient to generate hierarchical-sized cylinders from larger-sized cylinders in the middle region and smaller-sized cylinders near both walls. The results indicate the possibility of regulating the characteristics of a nanomaterial by tuning the molecular structure of the copolymer and the parameters of the introduced confinement, which are closely related to the self-assembly structure.

Variable stiffness mechanisms with SMA actuators

NASA Astrophysics Data System (ADS)

Siler, Damin J.; Demoret, Kimberly B. J.

1996-05-01

Variable stiffness is a new branch of smart structures development with several applications related to aircraft. Previous research indicates that temporarily reducing the stiffness of an airplane wing can decrease control actuator sizing and improve aeroelastic roll performance. Some smart materials like shape memory alloys (SMA) can change their material stiffness properties, but they tend to gain stiffness in their `power on' state. An alternative is to integrate mechanisms into a structure and change stiffness by altering boundary conditions and structural load paths. An innovative concept for an axial strut mechanism was discovered as part of research into variable stiffness. It employs SMA springs (specifically Ni-Ti) in a way that reduces overall stiffness when the SMA springs gain stiffness. A simplified mathematical model for static analysis was developed, and a 70% reduction in stiffness was obtained for a particular selection of springs. The small force capacity of commercially available SMA springs limits the practicality of this concept for large load applications. However, smart material technology is still immature, and future advances may permit development of a heavy-duty, variable stiffness strut that is small and light enough for use in aircraft structures.

Time simulation of flutter with large stiffness changes

NASA Technical Reports Server (NTRS)

Karpel, M.; Wieseman, C. D.

1992-01-01

Time simulation of flutter, involving large local structural changes, is formulated with a state-space model that is based on a relatively small number of generalized coordinates. Free-free vibration modes are first calculated for a nominal finite-element model with relatively large fictitious masses located at the area of structural changes. A low-frequency subset of these modes is then transformed into a set of structural modal coordinates with which the entire simulation is performed. These generalized coordinates and the associated oscillatory aerodynamic force coefficient matrices are used to construct an efficient time-domain, state-space model for basic aeroelastic case. The time simulation can then be performed by simply changing the mass, stiffness and damping coupling terms when structural changes occur. It is shown that the size of the aeroelastic model required for time simulation with large structural changes at a few a priori known locations is similar to that required for direct analysis of a single structural case. The method is applied to the simulation of an aeroelastic wind-tunnel model. The diverging oscillations are followed by the activation of a tip-ballast decoupling mechanism that stabilizes the system but may cause significant transient overshoots.

Time simulation of flutter with large stiffness changes

NASA Technical Reports Server (NTRS)

Karpel, Mordechay; Wieseman, Carol D.

1992-01-01

Time simulation of flutter, involving large local structural changes, is formulated with a state-space model that is based on a relatively small number of generalized coordinates. Free-free vibration modes are first calculated for a nominal finite-element model with relatively large fictitious masses located at the area of structural changes. A low-frequency subset of these modes is then transformed into a set of structural modal coordinates with which the entire simulation is performed. These generalized coordinates and the associated oscillatory aerodynamic force coefficient matrices are used to construct an efficient time-domain, state-space model for a basic aeroelastic case. The time simulation can then be performed by simply changing the mass, stiffness, and damping coupling terms when structural changes occur. It is shown that the size of the aeroelastic model required for time simulation with large structural changes at a few apriori known locations is similar to that required for direct analysis of a single structural case. The method is applied to the simulation of an aeroelastic wind-tunnel model. The diverging oscillations are followed by the activation of a tip-ballast decoupling mechanism that stabilizes the system but may cause significant transient overshoots.

Patterns of Distribution and Spatial Indicators of Ecosystem Change Based on Key Species in the Southern Benguela.

PubMed

Watermeyer, Katherine E; Hutchings, Laurence; Jarre, Astrid; Shannon, Lynne J

2016-01-01

Several commercially and ecologically important species in the southern Benguela have undergone southward and eastward shifts in their distributions over previous decades, most notably the small pelagic fish sardine Sardinops sagax and anchovy Engraulis encrasicolus. Understanding these changes and their implications is essential in implementing an ecosystem approach to fisheries in the southern Benguela and attempting to appreciate the potential impacts of future environmental change. To investigate possible impacts of these shifts at an ecosystem level, distribution maps for before (1985-1991), during (1997-2000) and after (2003-2008) the shift in small pelagic fish were constructed for 14 key species from catch and survey data, and used to calculate spatial indicators including proportion east and west of Cape Agulhas, relative overlap in biomass and area, index of diversity, connectivity. Potential interactions on the south and west coasts were also compared. For several species (redeye; chub mackerel; kingklip; chokka squid; yellowtail), previously unidentified increases in the proportion of biomass east of Cape Agulhas were shown to have occurred over the same period as that of small pelagic fish, although none to the same degree. On average, overlap with small pelagic fish increased over time and overall system connectivity was lowest in the intermediate period, possibly indicating a system under transition. Connectivity declined over time on the west coast while increasing on the east coast. Distributions of other species have changed over time, with the region east of Cape Agulhas becoming increasingly important in terms of potential trophic interaction. Variations in distribution of biomass and structural complexity affect the trophic structure and hence functioning of the system, and implications should be considered when attempting to identify the possible ecosystem impacts of current and future system-level change.

Effect of high intensity ultrasound on the mesostructure of hydrated zirconia

NASA Astrophysics Data System (ADS)

Kopitsa, G. P.; Baranchikov, A. E.; Ivanova, O. S.; Yapryntsev, A. D.; Grigoriev, S. V.; Pranzas, P. Klaus; Ivanov, V. K.

2012-02-01

We report structural changes in amorphous hydrated zirconia caused by high intensity ultrasonic treatment studied by means of small-angle neutron scattering (SANS) and X-ray diffraction (XRD). It was established that sonication affects the mesostructure of ZrO2×xH2O gels (i.e. decreases their homogeneity, increases surface fractal dimension and the size of monomer particles). Ultrasound induced structural changes in hydrated zirconia governs its thermal behaviour, namely decreases the rate of tetragonal to monoclinic zirconia phase transition.

Conjugated-Backbone Effect of Organic Small Molecules for n-Type Thermoelectric Materials with ZT over 0.2.

PubMed

Huang, Dazhen; Yao, Huiying; Cui, Yutao; Zou, Ye; Zhang, Fengjiao; Wang, Chao; Shen, Hongguang; Jin, Wenlong; Zhu, Jia; Diao, Ying; Xu, Wei; Di, Chong-An; Zhu, Daoben

2017-09-20

Conjugated backbones play a fundamental role in determining the electronic properties of organic semiconductors. On the basis of two solution-processable dihydropyrrolo[3,4-c]pyrrole-1,4-diylidenebis(thieno[3,2-b]thiophene) derivatives with aromatic and quinoid structures, we have carried out a systematic study of the relationship between the conjugated-backbone structure and the thermoelectric properties. In particular, a combination of UV-vis-NIR spectra, photoemission spectroscopy, and doping optimization are utilized to probe the interplay between energy levels, chemical doping, and thermoelectric performance. We found that a moderate change in the conjugated backbone leads to varied doping mechanisms and contributes to dramatic changes in the thermoelectric performance. Notably, the chemically doped A-DCV-DPPTT, a small molecule with aromatic structure, exhibits an electrical conductivity of 5.3 S cm -1 and a high power factor (PF 373 K ) up to 236 μW m -1 K -2 , which is 50 times higher than that of Q-DCM-DPPTT with a quinoid structure. More importantly, the low thermal conductivity enables A-DCV-DPPTT to possess a figure of merit (ZT) of 0.23 ± 0.03, which is the highest value reported to date for thermoelectric materials based on organic small molecules. These results demonstrate that the modulation of the conjugated backbone represents a powerful strategy for tuning the electronic structure and mobility of organic semiconductors toward a maximum thermoelectric performance.

Element-selective investigation of domain structure in CoPd and FePd alloys using small-angle soft X-ray scattering

NASA Astrophysics Data System (ADS)

Weier, C.; Adam, R.; Frömter, R.; Bach, J.; Winkler, G.; Kobs, A.; Oepen, H. P.; Grychtol, P.; Kapteyn, H. C.; Murnane, M. M.; Schneider, C. M.

2014-03-01

Recent optical pump-probe experiments on magnetic multilayers and alloys identified perpendicular spin superdiffusion as one of possible mechanisms responsible for femtosecond magnetization dynamics. On the other hand, no strong evidence for the ultrafast lateral spin transport has been reported, so far. To address this question, we studied magnetic domain structure of CoPd and FePd thin films using small-angle scattering of soft X-rays. By tuning the synchrotron-generated X-rays to the absorption edges of Fe or Co we recorded Fourier images of the magnetic domain structure corresponding to a chosen element. Applying in - situ magnetic fields resulted in pronounced rearrangement of domain structure that was clearly observed in scattering images. Our analysis of both the stand-alone, as well as magnetically coupled CoPd/FePd layers provides insight into the formation of domains under small magnetic field perturbations and pave the way to better understanding of transient changes expected in magneto-dynamic measurements.

The effect of truncation on very small cardiac SPECT camerasystems

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

Rohmer, Damien; Eisner, Robert L.; Gullberg, Grant T.

2006-08-01

Background: The limited transaxial field-of-view (FOV) of avery small cardiac SPECT camera system causes view-dependent truncationof the projection of structures exterior to, but near the heart. Basictomographic principles suggest that the reconstruction of non-attenuatedtruncated data gives a distortion-free image in the interior of thetruncated region, but the DC term of the Fourier spectrum of thereconstructed image is incorrect, meaning that the intensity scale of thereconstruction is inaccurate. The purpose of this study was tocharacterize the reconstructed image artifacts from truncated data, andto quantify their effects on the measurement of tracer uptake in themyocardial. Particular attention was given to instances wheremore » the heartwall is close to hot structures (structures of high activity uptake).Methods: The MCAT phantom was used to simulate a 2D slice of the heartregion. Truncated and non-truncated projections were formed both with andwithout attenuation. The reconstructions were analyzed for artifacts inthe myocardium caused by truncation, and for the effect that attenuationhas relative to increasing those artifacts. Results: The inaccuracy dueto truncation is primarily caused by an incorrect DC component. Forvisualizing theleft ventricular wall, this error is not worse than theeffect of attenuation. The addition of a small hot bowel-like structurenear the left ventricle causes few changes in counts on the wall. Largerartifacts due to the truncation are located at the boundary of thetruncation and can be eliminated by sinogram interpolation. Finally,algebraic reconstruction methods are shown to give better reconstructionresults than an analytical filtered back-projection reconstructionalgorithm. Conclusion: Small inaccuracies in reconstructed images fromsmall FOV camera systems should have little effect on clinicalinterpretation. However, changes in the degree of inaccuracy in countsfrom slice toslice are due to changes in the truncated structures. Thesecan result in a visual 3-dimensional distortion. As with conventionallarge FOV systems attenuation effects have a much more significant effecton image accuracy.« less

Volcanology and morphology

NASA Technical Reports Server (NTRS)

Bryan, W. B.

1976-01-01

Apollo 15 photographs of the southern parts of Serenitatis and Imbrium were used for a study of the morphology and distribution of wrinkle ridges. Volcanic and structural features along the south margin of Serenitatis were also studied, including the Dawes basalt cinder cones. Volcanic and structural features in crater Aitken were investigated as well. Study of crater Goclenius showed a close relationship between morphology of the impact crater and grabens which tend to parallel directions of the lunar grid. Similar trends were observed in the walls of crater Tsiolkovsky and other linear structures. Small craters of possible volcanic origin were also studied. Possible cinder cones were found associated with the Dawes basalt and in the floor of craters Aitken and Goclenius. Small pit craters were observed in the floors of these craters. Attempts were made to obtain contour maps of specific small features and to compare Orbiter and Apollo photographs to determine short term changes associated with other processes.

Equilibrium geometries, electronic and magnetic properties of small AunNi- (n = 1-9) clusters

NASA Astrophysics Data System (ADS)

Tang, Cui-Ming; Chen, Xiao-Xu; Yang, Xiang-Dong

2014-05-01

Geometrical, electronic and magnetic properties of small AunNi- (n = 1-9) clusters have been investigated based on density functional theory (DFT) at PW91P86 level. An extensive structural search shows that the relative stable structures of AunNi- (n = 1-9) clusters adopt 2D structure for n = 1-5, 7 and 3D structure for n = 6, 8-9. And the substitution of a Ni atom for an Au atom in the Au-n+1 cluster obviously changes the structure of the host cluster. Moreover, an odd-even alternation phenomenon has been found for HOMO-LUMO energy gaps, indicating that the relative stable structures of the AunNi- clusters with odd-numbered gold atoms have a higher relative stability. Finally, the natural population analysis (NPA) and the vertical detachment energies (VDE) are studied, respectively. The theoretical values of VDE are reported for the first time to our best knowledge.

Structure and function of small heat shock/alpha-crystallin proteins: established concepts and emerging ideas.

PubMed

MacRae, T H

2000-06-01

Small heat shock/alpha-crystallin proteins are defined by conserved sequence of approximately 90 amino acid residues, termed the alpha-crystallin domain, which is bounded by variable amino- and carboxy-terminal extensions. These proteins form oligomers, most of uncertain quaternary structure, and oligomerization is prerequisite to their function as molecular chaperones. Sequence modelling and physical analyses show that the secondary structure of small heat shock/alpha-crystallin proteins is predominately beta-pleated sheet. Crystallography, site-directed spin-labelling and yeast two-hybrid selection demonstrate regions of secondary structure within the alpha-crystallin domain that interact during oligomer assembly, a process also dependent on the amino terminus. Oligomers are dynamic, exhibiting subunit exchange and organizational plasticity, perhaps leading to functional diversity. Exposure of hydrophobic residues by structural modification facilitates chaperoning where denaturing proteins in the molten globule state associate with oligomers. The flexible carboxy-terminal extension contributes to chaperone activity by enhancing the solubility of small heat shock/alpha-crystallin proteins. Site-directed mutagenesis has yielded proteins where the effect of the change on structure and function depends upon the residue modified, the organism under study and the analytical techniques used. Most revealing, substitution of a conserved arginine residue within the alpha-crystallin domain has a major impact on quaternary structure and chaperone action probably through realignment of beta-sheets. These mutations are linked to inherited diseases. Oligomer size is regulated by a stress-responsive cascade including MAPKAP kinase 2/3 and p38. Phosphorylation of small heat shock/alpha-crystallin proteins has important consequences within stressed cells, especially for microfilaments.

Measurement of local structural configurations associated with reversible photostructural changes in arsenic trisulfide films

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

Yang, C.Y.; Paesler, M.A.; Sayers, D.E.

1987-12-15

Extended x-ray-absorption fine-structure measurements have been made on three reversible and reproducible cycles of thermally annealed and light-soaked amorphous As/sub 2/S/sub 3/ films. Associated with the light-soaked material are (1) a very small increase in the population of wrong bonds in the first shell, (2) an enlarged As: S: As bond angle with an expansion of As: As distance in the second shell, (3) a larger spread in the distribution of As: S: As bond angles, and (4) an absence of any change in the third As: S shell. From these data, we present the first quantitative correlation between observedmore » local atomic structural changes and measured macroscopic properties that are associated with photodarkening. Our data demonstrate that the photoinduced structural changes mainly involve bonding alterations at S atoms as well as a change in the dihedral angle relationship between adjacent AsS/sub 3/ pyramids joined at S atoms.« less

Raman characterization of Avocado Sunblotch viroid and its response to external perturbations and self-cleavage

PubMed Central

2014-01-01

Background Viroids are the smallest pathogens of plants. To date the structural and conformational details of the cleavage of Avocado sunblotch viroid (ASBVd) and the catalytic role of Mg2+ ions in efficient self-cleavage are of crucial interest. Results We report the first Raman characterization of the structure and activity of ASBVd, for plus and minus viroid strands. Both strands exhibit a typical A-type RNA conformation with an ordered double-helical content and a C3′-endo/anti sugar pucker configuration, although small but specific differences are found in the sugar puckering and base-stacking regions. The ASBVd(-) is shown to self-cleave 3.5 times more actively than ASBVd(+). Deuteration and temperature increase perturb differently the double-helical content and the phosphodiester conformation, as revealed by corresponding characteristic Raman spectral changes. Our data suggest that the structure rigidity and stability are higher and the D2O accessibility to H-bonding network is lower for ASBVd(+) than for ASBVd(-). Remarkably, the Mg2+-activated self-cleavage of the viroid does not induce any significant alterations of the secondary viroid structure, as evidenced from the absence of intensity changes of Raman marker bands that, however exhibit small but noticeable frequency downshifts suggesting several minor changes in phosphodioxy, internal loops and hairpins of the cleaved viroids. Conclusions Our results demonstrate the sensitivity of Raman spectroscopy in monitoring structural and conformational changes of the viroid and constitute the basis for further studies of its interactions with therapeutic agents and cell membranes. PMID:24655924

Pair distribution function study and mechanical behavior of as-cast and structurally relaxed Zr-based bulk metallic glasses

NASA Astrophysics Data System (ADS)

Fan, Cang; Liaw, P. K.; Wilson, T. W.; Choo, H.; Gao, Y. F.; Liu, C. T.; Proffen, Th.; Richardson, J. W.

2006-12-01

Contrary to reported results on structural relaxation inducing brittleness in amorphous alloys, the authors found that structural relaxation actually caused an increase in the strength of Zr55Cu35Al10 bulk metallic glass (BMG) without changing the plasticity. Three dimensional models were rebuilt for the as-cast and structurally relaxed BMGs by reverse Monte Carlo (RMC) simulations based on the pair distribution function (PDF) measured by neutron scattering. Only a small portion of the atom pairs was found to change to more dense packing. The concept of free volume was defined based on the PDF and RMC studies, and the mechanism of mechanical behavior was discussed.

Effect of gamma radiation on low density polyethylene (LDPE) films: optical, dielectric and FTIR studies.

PubMed

Moez, A Abdel; Aly, S S; Elshaer, Y H

2012-07-01

The low density polyethylene (LDPE) films were irradiated with gamma radiation in the dose range varied from 20 to 400 kGy. The induced changes in the chemical structure and dielectric properties for the irradiated films were investigated. The structure modifications: crystallinity as well as possible molecular changes of the polymer were recognized using Fourier Transform Infrared Spectroscopy (FTIR). The optical results were determined from transmission, reflection and absorption spectra for these films. The dielectric properties of these films were calculated using optical methods. Result indicates small variation in crystallinity which could be increased or decreased depending on the relative importance of the structural and chemical changes. Copyright © 2012 Elsevier B.V. All rights reserved.

Characterization of zein assemblies by ultra-small-angle X-ray scattering

DOE PAGES

Uzun, Suzan; Ilavsky, Jan; Padua, Graciela Wild

2017-03-23

Zein, a protein of corn, has an amphiphilic molecule capable of self-assembly into distinctly different structures. In this work, ultra-small-angle X-ray scattering (USAXS) was applied to investigate the formation of self-assembled zein structures in binary solvent systems of ethanol and water. Our study included observing structural changes due to aging. Three hierarchical structures were identified in zein-solvent systems, molecular zein 2D films, believed to be formed by zein rods assembled first into one-dimensional fibers and then into two-dimensional films, and 3D spherical aggregates. Aging did not change the size or shape of primary units, but promoted their self-assembly into intermediatemore » 2D structures and shaped 3D structures into well19 defined spheres. We found that the rheological parameters, consistency index (K) and behavior index (n), storage and loss moduli (G’ and G”) were also measured. K and n, changed markedly with aging, from nearly Newtonian low consistency fresh samples to highly viscous pseudoplastic aged samples. G’ and G” increased with aging for all samples reflecting increased interactions among zein self-assembled structures. Furthermore, viscoelastic parameters indicated that zein dispersions formed gels upon aging. It was observed that USAX reported on molecular scale self-assembly processes, while rheological measurements reported on the macroscale interaction between self-assembled particles. Raman spectra suggested that α-helix to β-sheet transformations prompted zein self-assembly, which influenced the size and morphology of molecular assemblies and ultimately the rheological properties of zein dispersions.« less

Multi-scale structures and pasting characteristics of starch in whole-wheat flour treated by superfine grinding.

PubMed

Niu, Meng; Zhang, Binjia; Jia, Caihua; Zhao, Siming

2017-11-01

The multi-scale structures and pasting properties of starch in WWF were investigated after superfine grinding. Five particle size distributions of WWF and their corresponding starch were obtained. The grinding process reduced the particle size of WWF and starch. However, a slight increase of fragments from starch granules was observed with enhanced grinding strength because of the small decrease in starch particle size and the existence of other WWF components that undertook some of shearing force and friction during grinding. A prominent reduction in starch crystallinity was resulted due to the destruction of crystalline structure by grinding. Small-angle X-ray scattering analyses indicated the disordering in starch semi-crystalline lamellae with thinner lamellae thickness. Additionally, the 13 C Nuclear Magnetic Resonance spectra demonstrated the alterations in starch chain conformation by varying peak areas of starch carbons (C1 and C4). Along with these structural changes, Starch pasting characteristics showed substantial variations, indicating decreased viscosities and higher pasting stability. The results suggest that the grinding treatments influenced the structures and pasting properties of starch even at a non-separated state, the changes in starch structures were related to the variations in starch gelatinization characteristics. Copyright © 2017 Elsevier B.V. All rights reserved.

A tale of two seas: contrasting patterns of population structure in the small-spotted catshark across Europe

PubMed Central

Gubili, Chrysoula; Sims, David W.; Veríssimo, Ana; Domenici, Paolo; Ellis, Jim; Grigoriou, Panagiotis; Johnson, Andrew F.; McHugh, Matthew; Neat, Francis; Satta, Andrea; Scarcella, Giuseppe; Serra-Pereira, Bárbara; Soldo, Alen; Genner, Martin J.; Griffiths, Andrew M.

2014-01-01

Elasmobranchs represent important components of marine ecosystems, but they can be vulnerable to overexploitation. This has driven investigations into the population genetic structure of large-bodied pelagic sharks, but relatively little is known of population structure in smaller demersal taxa, which are perhaps more representative of the biodiversity of the group. This study explores spatial population genetic structure of the small-spotted catshark (Scyliorhinus canicula), across European seas. The results show significant genetic differences among most of the Mediterranean sample collections, but no significant structure among Atlantic shelf areas. The data suggest the Mediterranean populations are likely to have persisted in a stable and structured environment during Pleistocene sea-level changes. Conversely, the Northeast Atlantic populations would have experienced major changes in habitat availability during glacial cycles, driving patterns of population reduction and expansion. The data also provide evidence of male-biased dispersal and female philopatry over large spatial scales, implying complex sex-determined differences in the behaviour of elasmobranchs. On the basis of this evidence, we suggest that patterns of connectivity are determined by trends of past habitat stability that provides opportunity for local adaptation in species exhibiting philopatric behaviour, implying that resilience of populations to fisheries and other stressors may differ across the range of species. PMID:26064555

Structural and phase transition changes of sodium dodecyl sulfate micellar solution in alcohols probed by small-angle neutron scattering (SANS)

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

Putra, Edy Giri Rachman; Patriati, Arum; Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Gadjah Mada, Bulaksumur, Yogyakarta 55281, Indonesia giri@batan.go.id

2015-04-16

Small-angle neutron scattering (SANS) measurements on 0.3M sodium dodecyl sulfate (SDS) micellar solutions have been performed in the presence of n-alcohols, from ethanol to decanol at different alcohol concentrations, 2–10 wt%. The ellipsoid micellar structure which occurred in the 0.3M SDS in aqueous solution with the size range of 30–50 Å has different behavior at various hydrocarbon chain length and concentration of alcohols. At low concentration and short chain-length of alcohols, such as ethanol, propanol, and butanol, the size of micelles reduced and had a spherical-like structure. The opposite effect occurred as medium to long chain alcohols, such as hexanol,more » octanol and decanol was added into the 0.3M SDS micellar solutions. The micelles structure changed to be more elongated in major axis and then crossed the critical phase transition from micellar solution into liquid crystal phase as lamellar structure emerged by further addition of alcohols. The inter-lamellar distances were also depending on the hydrocarbon chain length and concentration of alcohols. In the meantime, the persistent micellar structures occurred in addition of medium chain of n-alcohol, pentanol at all concentrations.« less

Longitudinal decline in structural networks predicts dementia in cerebral small vessel disease

PubMed Central

Lawrence, Andrew J.; Zeestraten, Eva A.; Benjamin, Philip; Lambert, Christian P.; Morris, Robin G.; Barrick, Thomas R.

2018-01-01

Objective To determine whether longitudinal change in white matter structural network integrity predicts dementia and future cognitive decline in cerebral small vessel disease (SVD). To investigate whether network disruption has a causal role in cognitive decline and mediates the association between conventional MRI markers of SVD with both cognitive decline and dementia. Methods In the prospective longitudinal SCANS (St George's Cognition and Neuroimaging in Stroke) Study, 97 dementia-free individuals with symptomatic lacunar stroke were followed with annual MRI for 3 years and annual cognitive assessment for 5 years. Conversion to dementia was recorded. Structural networks were constructed from diffusion tractography using a longitudinal registration pipeline, and network global efficiency was calculated. Linear mixed-effects regression was used to assess change over time. Results Seventeen individuals (17.5%) converted to dementia, and significant decline in global cognition occurred (p = 0.0016). Structural network measures declined over the 3-year MRI follow-up, but the degree of change varied markedly between individuals. The degree of reductions in network global efficiency was associated with conversion to dementia (B = −2.35, odds ratio = 0.095, p = 0.00056). Change in network global efficiency mediated much of the association of conventional MRI markers of SVD with cognitive decline and progression to dementia. Conclusions Network disruption has a central role in the pathogenesis of cognitive decline and dementia in SVD. It may be a useful disease marker to identify that subgroup of patients with SVD who progress to dementia. PMID:29695593

Irradiation induced structural change in Mo 2Zr intermetallic phase

DOE PAGES

Gan, J.; Keiser, Jr., D. D.; Miller, B. D.; ...

2016-05-14

The Mo 2Zr phase has been identified as a major interaction product at the interface of U-10Mo and Zr. Transmission electron microscopy in-situ irradiation with Kr ions at 200 °C with doses up to 2.0E+16 ions/cm 2 was carried out to investigate the radiation stability of the Mo 2Zr. The Mo 2Zr undergoes a radiation-induced structural change, from a large cubic (cF24) to a small cubic (cI2), along with an estimated 11.2% volume contraction without changing its composition. The structural change begins at irradiation dose below 1.0E+14 ions/cm 2. Furthermore, the transformed Mo 2Zr phase demonstrates exceptional radiation tolerance withmore » the development of dislocations without bubble formation.« less

Changes in the northern Gulf of St. Lawrence ecosystem estimated by inverse modelling: Evidence of a fishery-induced regime shift?

NASA Astrophysics Data System (ADS)

Savenkoff, Claude; Castonguay, Martin; Chabot, Denis; Hammill, Mike O.; Bourdages, Hugo; Morissette, Lyne

2007-07-01

Mass-balance models have been constructed using inverse methodology for the northern Gulf of St. Lawrence for the mid-1980s, the mid-1990s, and the early 2000s to describe ecosystem structure, trophic group interactions, and the effects of fishing and predation on the ecosystem for each time period. Our analyses indicate that the ecosystem structure shifted dramatically from one previously dominated by demersal (cod, redfish) and small-bodied forage (e.g., capelin, mackerel, herring, shrimp) species to one now dominated by small-bodied forage species. Overfishing removed a functional group in the late 1980s, large piscivorous fish (primarily cod and redfish), which has not recovered 14 years after the cessation of heavy fishing. This has left only marine mammals as top predators during the mid-1990s, and marine mammals and small Greenland halibut during the early 2000s. Predation by marine mammals on fish increased from the mid-1980s to the early 2000s while predation by large fish on fish decreased. Capelin and shrimp, the main prey in each period, showed an increase in biomass over the three periods. A switch in the main predators of capelin from cod to marine mammals occurred, while Greenland halibut progressively replaced cod as shrimp predators. Overfishing influenced community structure directly through preferential removal of larger-bodied fishes and indirectly through predation release because larger-bodied fishes exerted top-down control upon other community species or competed with other species for the same prey. Our modelling estimates showed that a change in predation structure or flows at the top of the trophic system led to changes in predation at all lower trophic levels in the northern Gulf of St. Lawrence. These changes represent a case of fishery-induced regime shift.

Network marketing on a small-world network

NASA Astrophysics Data System (ADS)

Kim, Beom Jun; Jun, Tackseung; Kim, Jeong-Yoo; Choi, M. Y.

2006-02-01

We investigate a dynamic model of network marketing in a small-world network structure artificially constructed similarly to the Watts-Strogatz network model. Different from the traditional marketing, consumers can also play the role of the manufacturer's selling agents in network marketing, which is stimulated by the referral fee the manufacturer offers. As the wiring probability α is increased from zero to unity, the network changes from the one-dimensional regular directed network to the star network where all but one player are connected to one consumer. The price p of the product and the referral fee r are used as free parameters to maximize the profit of the manufacturer. It is observed that at α=0 the maximized profit is constant independent of the network size N while at α≠0, it increases linearly with N. This is in parallel to the small-world transition. It is also revealed that while the optimal value of p stays at an almost constant level in a broad range of α, that of r is sensitive to a change in the network structure. The consumer surplus is also studied and discussed.

Constructing Disability in Bhutan: Schools, Structures, Policies, and Global Discourses

ERIC Educational Resources Information Center

Schuelka, Matthew John

2014-01-01

Bhutan is a small country in the Himalaya that has experienced rapid societal changes in the past 60 years. Perhaps the most significant change in Bhutan has occurred in its educational system, which grew from a very limited presence in 1961 to now serving the entire youth population of Bhutan. With this massive increase in educational service…

Segmentation of the Knee for Analysis of Osteoarthritis

NASA Astrophysics Data System (ADS)

Zerfass, Peter; Museyko, Oleg; Bousson, Valérie; Laredo, Jean-Denis; Kalender, Willi A.; Engelke, Klaus

Osteoarthritis changes the load distribution within joints and also changes bone density and structure. Within typical timelines of clinical studies these changes can be very small. Therefore precise definition of evaluation regions which are highly robust and show little to no interand intra-operator variance are essential for high quality quantitative analysis. To achieve this goal we have developed a system for the definition of such regions with minimal user input.

Electrophoretic mobility shift in native gels indicates calcium-dependent structural changes of neuronal calcium sensor proteins.

PubMed

Viviano, Jeffrey; Krishnan, Anuradha; Wu, Hao; Venkataraman, Venkat

2016-02-01

In proteins of the neuronal calcium sensor (NCS) family, changes in structure as well as function are brought about by the binding of calcium. In this article, we demonstrate that these structural changes, solely due to calcium binding, can be assessed through electrophoresis in native gels. The results demonstrate that the NCS proteins undergo ligand-dependent conformational changes that are detectable in native gels as a gradual decrease in mobility with increasing calcium but not other tested divalent cations such as magnesium, strontium, and barium. Surprisingly, such a gradual change over the entire tested range is exhibited only by the NCS proteins but not by other tested calcium-binding proteins such as calmodulin and S100B, indicating that the change in mobility may be linked to a unique NCS family feature--the calcium-myristoyl switch. Even within the NCS family, the changes in mobility are characteristic of the protein, indicating that the technique is sensitive to the individual features of the protein. Thus, electrophoretic mobility on native gels provides a simple and elegant method to investigate calcium (small ligand)-induced structural changes at least in the superfamily of NCS proteins. Copyright © 2015 Elsevier Inc. All rights reserved.

Local and global structural drivers for the photoactivation of the orange carotenoid protein

DOE PAGES

Gupta, Sayan; Guttman, Miklos; Leverenz, Ryan L.; ...

2015-09-18

Here, photoprotective mechanisms are of fundamental importance for the survival of photosynthetic organisms. In cyanobacteria, the orange carotenoid protein (OCP), when activated by intense blue light, binds to the light-harvesting antenna and triggers the dissipation of excess captured light energy. Using a combination of small angle X-ray scattering (SAXS), X-ray hydroxyl radical footprinting, circular dichroism, and H/D exchange mass spectrometry, we identified both the local and global structural changes in the OCP upon photoactivation. SAXS and H/D exchange data showed that global tertiary structural changes, including complete domain dissociation, occur upon photoactivation, but with alteration of secondary structure confined tomore » only the N terminus of the OCP. Microsecond radiolytic labeling identified rearrangement of the H-bonding network associated with conserved residues and structural water molecules. Collectively, these data provide experimental evidence for an ensemble of local and global structural changes, upon activation of the OCP, that are essential for photoprotection.« less

Local and global structural drivers for the photoactivation of the orange carotenoid protein

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

Gupta, Sayan; Guttman, Miklos; Leverenz, Ryan L.

Here, photoprotective mechanisms are of fundamental importance for the survival of photosynthetic organisms. In cyanobacteria, the orange carotenoid protein (OCP), when activated by intense blue light, binds to the light-harvesting antenna and triggers the dissipation of excess captured light energy. Using a combination of small angle X-ray scattering (SAXS), X-ray hydroxyl radical footprinting, circular dichroism, and H/D exchange mass spectrometry, we identified both the local and global structural changes in the OCP upon photoactivation. SAXS and H/D exchange data showed that global tertiary structural changes, including complete domain dissociation, occur upon photoactivation, but with alteration of secondary structure confined tomore » only the N terminus of the OCP. Microsecond radiolytic labeling identified rearrangement of the H-bonding network associated with conserved residues and structural water molecules. Collectively, these data provide experimental evidence for an ensemble of local and global structural changes, upon activation of the OCP, that are essential for photoprotection.« less

Local structure of the SnTe topological crystalline insulator: Rhombohedral distortions emerging from the rocksalt phase

NASA Astrophysics Data System (ADS)

Mitrofanov, K. V.; Kolobov, A. V.; Fons, P.; Krbal, M.; Shintani, T.; Tominaga, J.; Uruga, T.

2014-10-01

AIVBVI crystals are believed to possess a rhombohedral (ferroelectric) structure at low temperature that changes to the rocksalt (paraelectric) structure above the Curie temperature. For GeTe it has been recently demonstrated that locally the structure retains the subsets of the shorter and longer bonds across the ferroelectric-to-paraelectric transition despite acquiring the cubic structure on average. Nothing is known about the existence of local distortions in SnTe, a prototypical topological crystalline insulator, where the crystal symmetry plays a crucial role. In this work we report the results of x-ray absorption measurements. We find that the structure is locally rhombohedrally distorted, and the distortions increase at T >100K, breaking the rocksalt average symmetry. Our density functional theory simulations performed at 0 K indicate that the role of spin-orbit coupling in the formation of the local structure of SnTe at low temperature is negligibly small. The small stochastic distortions do not affect the intrinsic band inversion of SnTe.

Study of the gel films of Acetobacter Xylinum cellulose and its modified samples by {sup 1}H NMR cryoporometry and small-angle X-ray scattering

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

Babushkina, T. A.; Klimova, T. P.; Shtykova, E. V.

2010-03-15

Gel films of Acetobacter Xylinum cellulose and its modified samples have been investigated by 1H nuclear magnetic resonance (NMR) cryoporometry and small-angle X-ray scattering. The joint use of these two methods made it possible to characterize the sizes of aqueous pores in gel films and estimate the sizes of structural inhomogeneities before and after the sorption of polyvinylpyrrolidone and Se{sub 0} nanoparticles (stabilized by polyvinylpyrrolidone) into the films. According to small-angle X-ray scattering data, the sizes of inhomogeneities in a gel film change only slightly upon the sorption of polyvinylpyrrolidone and nanoparticles. The impregnated material is sorbed into water-filled cavitiesmore » that are present in the gel film. {sup 1}H NMR cryoporometry allowed us to reveal the details of changes in the sizes of small aqueous pores during modifications.« less

Consultant-Client Relationship and Knowledge Transfer in Small- and Medium-Sized Enterprises Change Processes.

PubMed

Martinez, Luis F; Ferreira, Aristides I; Can, Amina B

2016-04-01

Based on Szulanski's knowledge transfer model, this study examined how the communicational, motivational, and sharing of understanding variables influenced knowledge transfer and change processes in small- and medium-sized enterprises, particularly under projects developed by funded programs. The sample comprised 144 entrepreneurs, mostly male (65.3%) and mostly ages 35 to 45 years (40.3%), who filled an online questionnaire measuring the variables of "sharing of understanding," "motivation," "communication encoding competencies," "source credibility," "knowledge transfer," and "organizational change." Data were collected between 2011 and 2012 and measured the relationship between clients and consultants working in a Portuguese small- and medium-sized enterprise-oriented action learning program. To test the hypotheses, structural equation modeling was conducted to identify the antecedents of sharing of understanding, motivational, and communicational variables, which were positively correlated with the knowledge transfer between consultants and clients. This transfer was also positively correlated with organizational change. Overall, the study provides important considerations for practitioners and academicians and establishes new avenues for future studies concerning the issues of consultant-client relationship and the efficacy of Government-funded programs designed to improve performance of small- and medium-sized enterprises. © The Author(s) 2016.

Nanophase change for data storage applications.

PubMed

Shi, L P; Chong, T C

2007-01-01

Phase change materials are widely used for date storage. The most widespread and important applications are rewritable optical disc and Phase Change Random Access Memory (PCRAM), which utilizes the light and electric induced phase change respectively. For decades, miniaturization has been the major driving force to increase the density. Now the working unit area of the current data storage media is in the order of nano-scale. On the nano-scale, extreme dimensional and nano-structural constraints and the large proportion of interfaces will cause the deviation of the phase change behavior from that of bulk. Hence an in-depth understanding of nanophase change and the related issues has become more and more important. Nanophase change can be defined as: phase change at the scale within nano range of 100 nm, which is size-dependent, interface-dominated and surrounding materials related. Nanophase change can be classified into two groups, thin film related and structure related. Film thickness and clapping materials are key factors for thin film type, while structure shape, size and surrounding materials are critical parameters for structure type. In this paper, the recent development of nanophase change is reviewed, including crystallization of small element at nano size, thickness dependence of crystallization, effect of clapping layer on the phase change of phase change thin film and so on. The applications of nanophase change technology on data storage is introduced, including optical recording such as super lattice like optical disc, initialization free disc, near field, super-RENS, dual layer, multi level, probe storage, and PCRAM including, superlattice-like structure, side edge structure, and line type structure. Future key research issues of nanophase change are also discussed.

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

Gargarella, P., E-mail: piter@ufscar.br; Departamento de Engenharia de Materiais, Universidade Federal de São Carlos, Rodovia Washington Luiz, Km 235, 13565-905 São Carlos, São Paulo; Pauly, S.

The structural evolution of Ti{sub 50}Cu{sub 43}Ni{sub 7} and Ti{sub 55}Cu{sub 35}Ni{sub 10} metallic glasses during heating was investigated by in-situ synchrotron X-ray diffraction. The width of the most intense diffraction maximum of the glassy phase decreases slightly during relaxation below the glass transition temperature. Significant structural changes only occur above the glass transition manifesting in a change in the respective peak positions. At even higher temperatures, nanocrystals of the shape memory B2-Ti(Cu,Ni) phase precipitate, and their small size hampers the occurrence of a martensitic transformation.

Metal surface coloration by oxide periodic structures formed with nanosecond laser pulses

NASA Astrophysics Data System (ADS)

Veiko, Vadim; Karlagina, Yulia; Moskvin, Mikhail; Mikhailovskii, Vladimir; Odintsova, Galina; Olshin, Pavel; Pankin, Dmitry; Romanov, Valery; Yatsuk, Roman

2017-09-01

In this work, we studied a method of laser-induced coloration of metals, where small-scale spatially periodic structures play a key role in the process of color formation. The formation of such structures on a surface of AISI 304 stainless steel was demonstrated for the 1.06 μm fiber laser with nanosecond duration of pulses and random (elliptical) polarization. The color of the surface depends on the period, height and orientation of periodic surface structures. Adjustment of the polarization of the laser radiation or change of laser incidence angle can be used to control the orientation of the structures. The formation of markings that change their color under the different viewing angles becomes possible. The potential application of the method is metal product protection against falsification.

Crystal Structures and Small-angle X-ray Scattering Analysis of UDP-galactopyranose Mutase from the Pathogenic Fungus Aspergillus fumigatus

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

Dhatwalia, Richa; Singh, Harkewal; Oppenheimer, Michelle

2015-10-15

UDP-galactopyranose mutase (UGM) is a flavoenzyme that catalyzes the conversion of UDP-galactopyranose to UDP-galactofuranose, which is a central reaction in galactofuranose biosynthesis. Galactofuranose has never been found in humans but is an essential building block of the cell wall and extracellular matrix of many bacteria, fungi, and protozoa. The importance of UGM for the viability of many pathogens and its absence in humans make UGM a potential drug target. Here we report the first crystal structures and small-angle x-ray scattering data for UGM from the fungus Aspergillus fumigatus, the causative agent of aspergillosis. The structures reveal that Aspergillus UGM hasmore » several extra secondary and tertiary structural elements that are not found in bacterial UGMs yet are important for substrate recognition and oligomerization. Small-angle x-ray scattering data show that Aspergillus UGM forms a tetramer in solution, which is unprecedented for UGMs. The binding of UDP or the substrate induces profound conformational changes in the enzyme. Two loops on opposite sides of the active site move toward each other by over 10 {angstrom} to cover the substrate and create a closed active site. The degree of substrate-induced conformational change exceeds that of bacterial UGMs and is a direct consequence of the unique quaternary structure of Aspergillus UGM. Galactopyranose binds at the re face of the FAD isoalloxazine with the anomeric carbon atom poised for nucleophilic attack by the FAD N5 atom. The structural data provide new insight into substrate recognition and the catalytic mechanism and thus will aid inhibitor design.« less

Self-assembled phase-change nanowire for nonvolatile electronic memory

NASA Astrophysics Data System (ADS)

Jung, Yeonwoong

One of the most important subjects in nanosciences is to identify and exploit the relationship between size and structural/physical properties of materials and to explore novel material properties at a small-length scale. Scale-down of materials is not only advantageous in realizing miniaturized devices but nanometer-sized materials often exhibit intriguing physical/chemical properties that greatly differ from their bulk counterparts. This dissertation studies self-assembled phase-change nanowires for future nonvolatile electronic memories, mainly focusing on their size-dependent memory switching properties. Owing to the one-dimensional, unique geometry coupled with the small and tunable sizes, bottom-designed nanowires offer great opportunities in terms for both fundamental science and practical engineering perspectives, which would be difficult to realize in conventional top-down based approaches. We synthesized chalcogenide phase-change nanowires of different compositions and sizes, and studied their electronic memory switching owing to the structural change between crystalline and amorphous phases. In particular, we investigated nanowire size-dependent memory switching parameters, including writing current, power consumption, and data retention times, as well as studying composition-dependent electronic properties. The observed size and composition-dependent switching and recrystallization kinetics are explained based on the heat transport model and heterogeneous nucleation theories, which help to design phase-change materials with better properties. Moreover, we configured unconventional heterostructured phase-change nanowire memories and studied their multiple memory states in single nanowire devices. Finally, by combining in-situ/ex-situ electron microscopy techniques and electrical measurements, we characterized the structural states involved in electrically-driven phase-change in order to understand the atomistic mechanism that governs the electronic memory switching through phase-change.

Bridging Enzymatic Structure Function via Mechanics: A Coarse-Grain Approach.

PubMed

Sacquin-Mora, S

2016-01-01

Flexibility is a central aspect of protein function, and ligand binding in enzymes involves a wide range of structural changes, ranging from large-scale domain movements to small loop or side-chain rearrangements. In order to understand how the mechanical properties of enzymes, and the mechanical variations that are induced by ligand binding, relate to enzymatic activity, we carried out coarse-grain Brownian dynamics simulations on a set of enzymes whose structures in the unbound and ligand-bound forms are available in the Protein Data Bank. Our results show that enzymes are remarkably heterogeneous objects from a mechanical point of view and that the local rigidity of individual residues is tightly connected to their part in the protein's overall structure and function. The systematic comparison of the rigidity of enzymes in their unbound and bound forms highlights the fact that small conformational changes can induce large mechanical effects, leading to either more or less flexibility depending on the enzyme's architecture and the location of its ligand-biding site. These mechanical variations target a limited number of specific residues that occupy key locations for enzymatic activity, and our approach thus offers a mean to detect perturbation-sensitive sites in enzymes, where the addition or removal of a few interactions will lead to important changes in the proteins internal dynamics. © 2016 Elsevier Inc. All rights reserved.

Salts employed in hydrophobic interaction chromatography can change protein structure - insights from protein-ligand interaction thermodynamics, circular dichroism spectroscopy and small angle X-ray scattering.

PubMed

Komaromy, Andras Z; Kulsing, Chadin; Boysen, Reinhard I; Hearn, Milton T W

2015-03-01

Key requirements of protein purification by hydrophobic interaction chromatography (HIC) are preservation of the tertiary/quaternary structure, maintenance of biological function, and separation of the correctly folded protein from its unfolded forms or aggregates. This study examines the relationship between the HIC retention behavior of hen egg white lysozyme (HEWL) in high concentrations of several kosmotropic salts and its conformation, assessed by circular dichroism (CD) spectroscopy. Further, the physicochemical properties of HEWL in the presence of high concentrations of ammonium sulfate, sodium chloride and magnesium chloride were investigated by small angle X-ray scattering (SAXS) at different temperatures. Radii of gyration were extrapolated from Guinier approximations and the indirect transform program GNOM with protein-protein interaction and contrast variation taken into account. A bead model simulation provided information on protein structural changes using ab initio reconstruction with GASBOR. These results correlated to the secondary structure content obtained from CD spectroscopy of HEWL. These changes in SAXS and CD data were consistent with heat capacity ΔCp -values obtained from van't Hoff plot analyses of the retention data. Collectively, these insights enable informed decisions to be made on the choice of chromatographic conditions, leading to improved separation selectivity and opportunities for innovative column-assisted protein refolding methods. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evolution of a flipped pathway creates metabolic innovation in tomato trichomes through BAHD enzyme promiscuity.

PubMed

Fan, Pengxiang; Miller, Abigail M; Liu, Xiaoxiao; Jones, A Daniel; Last, Robert L

2017-12-12

Plants produce hundreds of thousands of structurally diverse specialized metabolites via multistep biosynthetic networks, including compounds of ecological and therapeutic importance. These pathways are restricted to specific plant groups, and are excellent systems for understanding metabolic evolution. Tomato and other plants in the nightshade family synthesize protective acylated sugars in the tip cells of glandular trichomes on stems and leaves. We describe a metabolic innovation in wild tomato species that contributes to acylsucrose structural diversity. A small number of amino acid changes in two acylsucrose acyltransferases alter their acyl acceptor preferences, resulting in reversal of their order of reaction and increased product diversity. This study demonstrates how small numbers of amino acid changes in multiple pathway enzymes can lead to diversification of specialized metabolites in plants. It also highlights the power of a combined genetic, genomic and in vitro biochemical approach to identify the evolutionary mechanisms leading to metabolic novelty.

Warming and Resource Availability Shift Food Web Structure and Metabolism

PubMed Central

O'Connor, Mary I.; Piehler, Michael F.; Leech, Dina M.; Anton, Andrea; Bruno, John F.

2009-01-01

Climate change disrupts ecological systems in many ways. Many documented responses depend on species' life histories, contributing to the view that climate change effects are important but difficult to characterize generally. However, systematic variation in metabolic effects of temperature across trophic levels suggests that warming may lead to predictable shifts in food web structure and productivity. We experimentally tested the effects of warming on food web structure and productivity under two resource supply scenarios. Consistent with predictions based on universal metabolic responses to temperature, we found that warming strengthened consumer control of primary production when resources were augmented. Warming shifted food web structure and reduced total biomass despite increases in primary productivity in a marine food web. In contrast, at lower resource levels, food web production was constrained at all temperatures. These results demonstrate that small temperature changes could dramatically shift food web dynamics and provide a general, species-independent mechanism for ecological response to environmental temperature change. PMID:19707271

Structural changes of malt proteins during boiling.

PubMed

Jin, Bei; Li, Lin; Liu, Guo-Qin; Li, Bing; Zhu, Yu-Kui; Liao, Liao-Ning

2009-03-09

Changes in the physicochemical properties and structure of proteins derived from two malt varieties (Baudin and Guangmai) during wort boiling were investigated by differential scanning calorimetry, SDS-PAGE, two-dimensional electrophoresis, gel filtration chromatography and circular dichroism spectroscopy. The results showed that both protein content and amino acid composition changed only slightly during boiling, and that boiling might cause a gradual unfolding of protein structures, as indicated by the decrease in surface hydrophobicity and free sulfhydryl content and enthalpy value, as well as reduced alpha-helix contents and markedly increased random coil contents. It was also found that major component of both worts was a boiling-resistant protein with a molecular mass of 40 kDa, and that according to the two-dimensional electrophoresis and SE-HPLC analyses, a small amount of soluble aggregates might be formed via hydrophobic interactions. It was thus concluded that changes of protein structure caused by boiling that might influence beer quality are largely independent of malt variety.

Temporal efficiency evaluation and small-worldness characterization in temporal networks

PubMed Central

Dai, Zhongxiang; Chen, Yu; Li, Junhua; Fam, Johnson; Bezerianos, Anastasios; Sun, Yu

2016-01-01

Numerous real-world systems can be modeled as networks. To date, most network studies have been conducted assuming stationary network characteristics. Many systems, however, undergo topological changes over time. Temporal networks, which incorporate time into conventional network models, are therefore more accurate representations of such dynamic systems. Here, we introduce a novel generalized analytical framework for temporal networks, which enables 1) robust evaluation of the efficiency of temporal information exchange using two new network metrics and 2) quantitative inspection of the temporal small-worldness. Specifically, we define new robust temporal network efficiency measures by incorporating the time dependency of temporal distance. We propose a temporal regular network model, and based on this plus the redefined temporal efficiency metrics and widely used temporal random network models, we introduce a quantitative approach for identifying temporal small-world architectures (featuring high temporal network efficiency both globally and locally). In addition, within this framework, we can uncover network-specific dynamic structures. Applications to brain networks, international trade networks, and social networks reveal prominent temporal small-world properties with distinct dynamic network structures. We believe that the framework can provide further insight into dynamic changes in the network topology of various real-world systems and significantly promote research on temporal networks. PMID:27682314

Temporal efficiency evaluation and small-worldness characterization in temporal networks

NASA Astrophysics Data System (ADS)

Dai, Zhongxiang; Chen, Yu; Li, Junhua; Fam, Johnson; Bezerianos, Anastasios; Sun, Yu

2016-09-01

Numerous real-world systems can be modeled as networks. To date, most network studies have been conducted assuming stationary network characteristics. Many systems, however, undergo topological changes over time. Temporal networks, which incorporate time into conventional network models, are therefore more accurate representations of such dynamic systems. Here, we introduce a novel generalized analytical framework for temporal networks, which enables 1) robust evaluation of the efficiency of temporal information exchange using two new network metrics and 2) quantitative inspection of the temporal small-worldness. Specifically, we define new robust temporal network efficiency measures by incorporating the time dependency of temporal distance. We propose a temporal regular network model, and based on this plus the redefined temporal efficiency metrics and widely used temporal random network models, we introduce a quantitative approach for identifying temporal small-world architectures (featuring high temporal network efficiency both globally and locally). In addition, within this framework, we can uncover network-specific dynamic structures. Applications to brain networks, international trade networks, and social networks reveal prominent temporal small-world properties with distinct dynamic network structures. We believe that the framework can provide further insight into dynamic changes in the network topology of various real-world systems and significantly promote research on temporal networks.

Anomalous diffusion in neutral evolution of model proteins.

PubMed

Nelson, Erik D; Grishin, Nick V

2015-06-01

Protein evolution is frequently explored using minimalist polymer models, however, little attention has been given to the problem of structural drift, or diffusion. Here, we study neutral evolution of small protein motifs using an off-lattice heteropolymer model in which individual monomers interact as low-resolution amino acids. In contrast to most earlier models, both the length and folded structure of the polymers are permitted to change. To describe structural change, we compute the mean-square distance (MSD) between monomers in homologous folds separated by n neutral mutations. We find that structural change is episodic, and, averaged over lineages (for example, those extending from a single sequence), exhibits a power-law dependence on n. We show that this exponent depends on the alignment method used, and we analyze the distribution of waiting times between neutral mutations. The latter are more disperse than for models required to maintain a specific fold, but exhibit a similar power-law tail.

Anomalous diffusion in neutral evolution of model proteins

NASA Astrophysics Data System (ADS)

Nelson, Erik D.; Grishin, Nick V.

2015-06-01

Protein evolution is frequently explored using minimalist polymer models, however, little attention has been given to the problem of structural drift, or diffusion. Here, we study neutral evolution of small protein motifs using an off-lattice heteropolymer model in which individual monomers interact as low-resolution amino acids. In contrast to most earlier models, both the length and folded structure of the polymers are permitted to change. To describe structural change, we compute the mean-square distance (MSD) between monomers in homologous folds separated by n neutral mutations. We find that structural change is episodic, and, averaged over lineages (for example, those extending from a single sequence), exhibits a power-law dependence on n . We show that this exponent depends on the alignment method used, and we analyze the distribution of waiting times between neutral mutations. The latter are more disperse than for models required to maintain a specific fold, but exhibit a similar power-law tail.

Structural environments of carboxyl groups in natural organic molecules from terrestrial systems. Part 1: Infrared spectroscopy

NASA Astrophysics Data System (ADS)

Hay, Michael B.; Myneni, Satish C. B.

2007-07-01

Carboxyls play an important role in the chemistry of natural organic molecules (NOM) in the environment, and their behavior is dependent on local structural environment within the macromolecule. We studied the structural environments of carboxyl groups in dissolved NOM from the Pine Barrens (New Jersey, USA), and IHSS NOM isolates from soils and river waters using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy. It is well established that the energies of the asymmetric stretching vibrations of the carboxylate anion (COO -) are sensitive to the structural environment of the carboxyl group. These energies were compiled from previous infrared studies on small organic acids for a wide variety of carboxyl structural environments and compared with the carboxyl spectral features of the NOM samples. We found that the asymmetric stretching peaks for all NOM samples occur within a narrow range centered at 1578 cm -1, suggesting that all NOM samples examined primarily contain very similar carboxyl structures, independent of sample source and isolation techniques employed. The small aliphatic acids containing hydroxyl (e.g., D-lactate, gluconate), ether/ester (methoxyacetate, acetoxyacetate), and carboxylate (malonate) substitutions on the α-carbon, and the aromatic acids salicylate ( ortho-OH) and furancarboxylate ( O-heterocycle), exhibit strong overlap with the NOM range, indicating that similar structures may be common in NOM. The width of the asymmetric peak suggests that the structural heterogeneity among the predominant carboxyl configurations in NOM is small. Changes in peak area with pH at energies distant from the peak at 1578 cm -1, however, may be indicative of a small fraction of other aromatic carboxyls and aliphatic structures lacking α-substitution. This information is important in understanding NOM-metal and mineral-surface complexation, and in building appropriate structural and mechanistic models of humic materials.

Portable mini-chamber for temperature dependent studies using small angle and wide angle x-ray scattering

NASA Astrophysics Data System (ADS)

Dev, Arun Singh; Kumar, Dileep; Potdar, Satish; Pandit, Pallavi; Roth, Stephan V.; Gupta, Ajay

2018-04-01

The present work describes the design and performance of a vacuum compatible portable mini chamber for temperature dependent GISAXS and GIWAXS studies of thin films and multilayer structures. The water cooled body of the chamber allows sample annealing up to 900 K using ultra high vacuum compatible (UHV) pyrolytic boron nitride heater, thus making it possible to study the temperature dependent evolution of structure and morphology of two-dimensional nanostructured materials. Due to its light weight and small size, the chamber is portable and can be accommodated at synchrotron facilities worldwide. A systematic illustration of the versatility of the chamber has been demonstrated at beamline P03, PETRA-III, DESY, Hamburg, Germany. Temperature dependent grazing incidence small angle x-ray scattering (GISAXS) and grazing incidence wide angle x-ray scattering (GIWAXS) measurements were performed on oblique angle deposited Co/Ag multilayer structure, which jointly revealed that the surface diffusion in Co columns in Co/Ag multilayer enhances by increasing temperature from RT to ˜573 K. This results in a morphology change from columnar tilted structure to densely packed morphological isotropic multilayer.

ARC-1979-AC79-7102

NASA Image and Video Library

1979-07-03

Range : 6 Million km. ( 3.72 million miles ) This photograph of Jupiter, shot from Voyager 2, shows the equator to the southern polar latitudes, near the Great Red Spot. The white oval that appears here is different from the one seen in a similiar position when voyager 1 passed years before. The region of white clouds now extends from east of The Red Spot and around it's northern boundary, preventing small cloud vortices from circling the feature. The disturbed region west of The Red Spot has also changed since Voyager1. It shows more small scale structure and cloud vortices being formed out of the wave structures.

A Theoretical Study of Structural, Electronic and Vibrational Properties of Small Fluoride Clusters

NASA Astrophysics Data System (ADS)

Waters, Kevin; Pandey, Ratnesh; Nigam, Sandeep; He, Haiying; Pingle, Subhash; Pandey, Avinash; Pandey, Ravindra

2014-03-01

Alkaline earth metal fluorides are an interesting family of ionic crystals having a wide range of applications in solid state lasers, luminescence, scintillators, to name just a few. In this work, small stoichiometric clusters of (MF2)n (M = Mg, Ca Sr, Ba, n =1-6) were studied for structural, vibrational and electronic properties using first-principles methods based on density functional theory. A clear trend of structural and electronic structure evolution was found for all the alkaline earth metal fluorides when the cluster size n increases from 1 to 6. Our study reveals that these fluoride clusters mimic the bulk-like behavior at the very small size. Among the four series of metal fluorides, however, (MgF2)n clusters stands out to be different in its preference of equilibrium structures owing to the much smaller ionic radius of Mg and the higher degree of covalency in the Mg-F bonding. The calculated binding energy, highest stretching frequency, ionization potential, and HOMO-LUMO gap decrease from MgF2 to BaF2 for the same cluster size. These variations are explained in terms of the change in the ionic radius and the basicity of the metal ions.

The impact of structural adjustment and the changing nature of women's work in the People's Republic of China.

PubMed

Roy, S

2000-01-01

This paper examines the impact of structural adjustment and the changing nature of women's work in the People's Republic of China (PRC). It is noted that more than two-thirds of the developing countries have adopted structural adjustment policy packages as an answer to the economic crisis they are facing. Such an adjustment is a conscious change in the fundamental nature of economic relationships within a society. In relation to women, the structural changes have resulted to the collapse of many small and home-based industries, thus changing the role of women in economy. It is noted that although the policy shifts have created a wide range of job opportunities for women in other countries, in PRC gender inequalities exist in the economic area wherein women experience low employment and lack of work benefits. In addition, the fact that the rate of women's employment in China is higher than other developing and some developed countries worsens the situation as it indicates that more women suffer under the discriminatory employment system.

Changes in the pore network structure of Hanford sediment after reaction with caustic tank wastes.

PubMed

Crandell, L E; Peters, C A; Um, W; Jones, K W; Lindquist, W B

2012-04-01

At the former nuclear weapon production site in Hanford, WA, caustic radioactive tank waste leaks into subsurface sediments and causes dissolution of quartz and aluminosilicate minerals, and precipitation of sodalite and cancrinite. This work examines changes in pore structure due to these reactions in a previously-conducted column experiment. The column was sectioned and 2D images of the pore space were generated using backscattered electron microscopy and energy dispersive X-ray spectroscopy. A pre-precipitation scenario was created by digitally removing mineral matter identified as secondary precipitates. Porosity, determined by segmenting the images to distinguish pore space from mineral matter, was up to 0.11 less after reaction. Erosion-dilation analysis was used to compute pore and throat size distributions. Images with precipitation had more small and fewer large pores. Precipitation decreased throat sizes and the abundance of large throats. These findings agree with previous findings based on 3D X-ray CMT imaging, observing decreased porosity, clogging of small throats, and little change in large throats. However, 2D imaging found an increase in small pores, mainly in intragranular regions or below the resolution of the 3D images. Also, an increase in large pores observed via 3D imaging was not observed in the 2D analysis. Changes in flow conducting throats that are the key permeability-controlling features were observed in both methods. Copyright © 2012 Elsevier B.V. All rights reserved.

PREPARATION OF WHOLE SMALL FISH FOR HISTOLOGICAL EVALUATION

EPA Science Inventory

Toxicologic pathology, which is primarily concerned with chemically-induced structural changes in cells or tissues, depends on the proper histological processing of test specimens. In fishes, histopathological examination is widely recognized as a reliable method for disease diag...

Structure-activity relationships in the fusion of small unilamellar phosphatidylcholine vesicles induced by a model peptide.

PubMed

da Costa, M H; Chaimovich, H

1997-09-01

Limited proteolysis of fatty acid-free bovine serum albumin by pepsin yields several well characterized peptides, one of which (P9, M(r) 9,000), induces fusion of small unilamellar vesicles (SUV) of phosphatidylcholine at pH 3.6. Circular dichroism (CD) of P9 solutions confirmed that the peptide undergoes a reversible transition between pH 7 and pH 3.6. The spectral changes observed with CD suggest that in the low pH conformation there is a decrease in the alpha-helical contents and an exposure of hydrophobic residues. CD and differential ultraviolet spectroscopy demonstrated that P9 binds to micelles of hexadecylphosphorylcholine and the binding produces changes in the tertiary structure of the peptide. Reduction and carboxymethylation of the two disulfide bridges of P9 produced loss of the ability to induce fusion of SUV, although the reduced peptide binds to vesicles, induces loss of entrapped marker and produces vesicle disruption. In the active form P9 exposes hydrophobic groups, one amphiphilic alpha-helix and requires the integrity of the disulfide bridge-stabilized tertiary structure.

Phenyl-β-D-glucopyranoside and Phenyl-β-D-galactopyranoside dimers: Small Structural differences but Very Different Interactions

NASA Astrophysics Data System (ADS)

Usabiaga, Imanol; Camiruaga, Ander; Insausti, Aran; Çarçabal, Pierre; Cocinero, Emilio J.; León, Iker; Fernández, José A.

2018-02-01

We report a combination of laser spectroscopy in molecular jets and quantum mechanical calculations to characterize the aggregation preferences of phenyl-β-D-glucopyranoside (β-PhGlc) and phenyl-β-D-galactopyranoside (β-PhGal) homodimers. At least two structures of β-PhGlc dimer were found maintaining the same intramolecular interactions of the monomers, but with additional intermolecular interactions between the hydroxyl groups. Several isomers were also found for the dimer of β-PhGal forming extensive hydrogen bond networks between the interacting molecules, of very different shape. All the species found present several CH•••Pi and OH•••Pi interactions that add stability to the aggregates. The results show how even the smallest change in a substituent, from axial to equatorial position, plays a decisive role in the formation of the dimers. These conclusions reinforce the idea that the small structural changes between sugar units are amplified by formation of intra and intermolecular hydrogen bond networks, helping other molecules (proteins, receptors) to easily read the sugar code of glycans.

High sensitivity refractive index sensor based on a tapered small core single-mode fiber structure.

PubMed

Liu, Dejun; Mallik, Arun Kumar; Yuan, Jinhui; Yu, Chongxiu; Farrell, Gerald; Semenova, Yuliya; Wu, Qiang

2015-09-01

A high sensitivity refractive index (RI) sensor based on a tapered small core single-mode fiber (SCSMF) structure sandwiched between two traditional single-mode fibers (SMF28) is reported. The microheater brushing technique was employed to fabricate the tapered fiber structures with different waist diameters of 12.5, 15.0, and 18.8 μm. Experiments demonstrate that the fiber sensor with a waist diameter of 12.5 μm offers the best sensitivity of 19212.5  nm/RIU (RI unit) in the RI range of 1.4304 to 1.4320. All sensors fabricated in this Letter show good linearity in terms of the spectral wavelength shift versus changes in RI. Furthermore, the sensor with the best sensitivity to RI was also used to measure relative humidity (RH) without any coating materials applied to the fiber surface. Experimental results show that the spectral wavelength shift changes exponentially as the RH varies from 60% to 95%. A maximum sensitivity of 18.3 nm per relative humidity unit (RHU) was achieved in the RH range of 90.4% to 94.5% RH.

Neural network approach for characterizing structural transformations by X-ray absorption fine structure

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

Timoshenko, Janis; Frenkel, Anatoly I.; Cintins, Arturs

The knowledge of coordination environment around various atomic species in many functional materials provides a key for explaining their properties and working mechanisms. Many structural motifs and their transformations are difficult to detect and quantify in the process of work (operando conditions), due to their local nature, small changes, low dimensionality of the material, and/or extreme conditions. Here we use artificial neural network approach to extract the information on the local structure and its in-situ changes directly from the X-ray absorption fine structure spectra. We illustrate this capability by extracting the radial distribution function (RDF) of atoms in ferritic andmore » austenitic phases of bulk iron across the temperature-induced transition. Integration of RDFs allows us to quantify the changes in the iron coordination and material density, and to observe the transition from body-centered to face-centered cubic arrangement of iron atoms. Furthermore, this method is attractive for a broad range of materials and experimental conditions« less

Neural network approach for characterizing structural transformations by X-ray absorption fine structure

DOE PAGES

Timoshenko, Janis; Frenkel, Anatoly I.; Cintins, Arturs; ...

2018-05-25

The knowledge of coordination environment around various atomic species in many functional materials provides a key for explaining their properties and working mechanisms. Many structural motifs and their transformations are difficult to detect and quantify in the process of work (operando conditions), due to their local nature, small changes, low dimensionality of the material, and/or extreme conditions. Here we use artificial neural network approach to extract the information on the local structure and its in-situ changes directly from the X-ray absorption fine structure spectra. We illustrate this capability by extracting the radial distribution function (RDF) of atoms in ferritic andmore » austenitic phases of bulk iron across the temperature-induced transition. Integration of RDFs allows us to quantify the changes in the iron coordination and material density, and to observe the transition from body-centered to face-centered cubic arrangement of iron atoms. Furthermore, this method is attractive for a broad range of materials and experimental conditions« less

Neural Network Approach for Characterizing Structural Transformations by X-Ray Absorption Fine Structure Spectroscopy

NASA Astrophysics Data System (ADS)

Timoshenko, Janis; Anspoks, Andris; Cintins, Arturs; Kuzmin, Alexei; Purans, Juris; Frenkel, Anatoly I.

2018-06-01

The knowledge of the coordination environment around various atomic species in many functional materials provides a key for explaining their properties and working mechanisms. Many structural motifs and their transformations are difficult to detect and quantify in the process of work (operando conditions), due to their local nature, small changes, low dimensionality of the material, and/or extreme conditions. Here we use an artificial neural network approach to extract the information on the local structure and its in situ changes directly from the x-ray absorption fine structure spectra. We illustrate this capability by extracting the radial distribution function (RDF) of atoms in ferritic and austenitic phases of bulk iron across the temperature-induced transition. Integration of RDFs allows us to quantify the changes in the iron coordination and material density, and to observe the transition from a body-centered to a face-centered cubic arrangement of iron atoms. This method is attractive for a broad range of materials and experimental conditions.

A fluorescent probe-labeled Escherichia coli aspartate transcarbamoylase that monitors the allosteric conformational state.

PubMed

West, Jay M; Tsuruta, Hiro; Kantrowitz, Evan R

2004-01-09

A new system has been developed capable of monitoring conformational changes of the 240s loop of aspartate transcarbamoylase, which are tightly correlated with the quaternary structural transition, with high sensitivity in solution. Pyrene, a fluorescent probe, was conjugated to residue 241 in the 240s loop of aspartate transcarbamoylase to monitor changes in conformation by fluorescence spectroscopy. Pyrene maleimide was conjugated to a cysteine residue on the 240s loop of a previously constructed double catalytic chain mutant version of the enzyme, C47A/A241C. The pyrene-labeled enzyme undergoes the normal T to R structural transition, as demonstrated by small-angle x-ray scattering. Like the wild-type enzyme, the pyrene-labeled enzyme exhibits cooperativity toward aspartate, and is activated by ATP and inhibited by CTP at subsaturating concentrations of aspartate. The binding of the bisubstrate analogue N-(phosphonoacetyl)-l-aspartate (PALA), or the aspartate analogue succinate, in the presence of saturating carbamoyl phosphate, to the pyrenelabeled enzyme caused a sigmoidal change in the fluorescence emission. Saturation with ATP and CTP (in the presence of either subsaturating amounts of PALA or succinate and carbamoyl phosphate) caused a hyperbolic increase and decrease, respectively, in the fluorescence emission. The half-saturation values from the fluorescence saturation curves and kinetic saturation curves were, within error, identical. Fluorescence and small-angle x-ray scattering stopped-flow experiments, using aspartate and carbamoyl phosphate, confirm that the change in excimer fluorescence and the quaternary structure change correlate. These results in conjunction with previous studies suggest that the allosteric transition involves both global and local conformational changes and that the heterotropic effect of the nucleotides may be exerted through local conformational changes in the active site by directly influencing the conformation of the 240s loop.

Structural changes in C–S–H gel during dissolution: Small-angle neutron scattering and Si-NMR characterization

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

Trapote-Barreira, Ana, E-mail: anatrapotebarreira@gmail.com; Porcar, Lionel; Large Scale Structure Group, Institut Laue Langevin, Grenoble

2015-06-15

Flow-through experiments were conducted to study the calcium–silicate–hydrate (C–S–H) gel dissolution kinetics. During C–S–H gel dissolution the initial aqueous Ca/Si ratio decreases to reach the stoichiometric value of the Ca/Si ratio of a tobermorite-like phase (Ca/Si = 0.83). As the Ca/Si ratio decreases, the solid C–S–H dissolution rate increases from (4.5 × 10{sup −} {sup 14} to 6.7 × 10{sup −} {sup 12}) mol m{sup −} {sup 2} s{sup −} {sup 1}. The changes in the microstructure of the dissolving C–S–H gel were characterized by small-angle neutron scattering (SANS) and {sup 29}Si magic-angle-spinning nuclear magnetic resonance ({sup 29}Si-MAS NMR). Themore » SANS data were fitted using a fractal model. The SANS specific surface area tends to increase with time and the obtained fit parameters reflect the changes in the nanostructure of the dissolving solid C–S–H within the gel. The {sup 29}Si MAS NMR analyses show that with dissolution the solid C–S–H structure tends to a more ordered tobermorite structure, in agreement with the Ca/Si ratio evolution.« less

Measuring forest structure along productivity gradients in the Canadian boreal with small-footprint Lidar.

PubMed

Bolton, Douglas K; Coops, Nicholas C; Wulder, Michael A

2013-08-01

The structure and productivity of boreal forests are key components of the global carbon cycle and impact the resources and habitats available for species. With this research, we characterized the relationship between measurements of forest structure and satellite-derived estimates of gross primary production (GPP) over the Canadian boreal. We acquired stand level indicators of canopy cover, canopy height, and structural complexity from nearly 25,000 km of small-footprint discrete return Light Detection and Ranging (Lidar) data and compared these attributes to GPP estimates derived from the MODerate resolution Imaging Spectroradiometer (MODIS). While limited in our capacity to control for stand age, we removed recently disturbed and managed forests using information on fire history, roads, and anthropogenic change. We found that MODIS GPP was strongly linked to Lidar-derived canopy cover (r = 0.74, p < 0.01), however was only weakly related to Lidar-derived canopy height and structural complexity as these attributes are largely a function of stand age. A relationship was apparent between MODIS GPP and the maximum sampled heights derived from Lidar as growth rates and resource availability likely limit tree height in the prolonged absence of disturbance. The most structurally complex stands, as measured by the coefficient of variation of Lidar return heights, occurred where MODIS GPP was highest as productive boreal stands are expected to contain a wider range of tree heights and transition to uneven-aged structures faster than less productive stands. While MODIS GPP related near-linearly to Lidar-derived canopy cover, the weaker relationships to Lidar-derived canopy height and structural complexity highlight the importance of stand age in determining the structure of boreal forests. We conclude that an improved quantification of how both productivity and disturbance shape stand structure is needed to better understand the current state of boreal forests in Canada and how these forests are changing in response to changing climate and disturbance regimes.

Changes in children's time with parents: United States, 1981-1997.

PubMed

Sandberg, J F; Hofferth, S L

2001-08-01

In this paper we examine changes in the time American children spent with their parents between 1981 and 1997, and the contribution to these changes made by shifting patterns of female labor force participation, family structure, and parental education. We decompose changes into the parts attributable to changes in demographic characteristics and the parts probably due to changes in behavior. In general, children's time with parents did not decrease over the period; in two-parent families it increased substantially. Population-level changes in demographic characteristics exerted only small direct effects on the time children spent with parents.

Organization and dynamics of the actin cytoskeleton during dendritic spine morphological remodeling.

PubMed

Chazeau, Anaël; Giannone, Grégory

2016-08-01

In the central nervous system, most excitatory post-synapses are small subcellular structures called dendritic spines. Their structure and morphological remodeling are tightly coupled to changes in synaptic transmission. The F-actin cytoskeleton is the main driving force of dendritic spine remodeling and sustains synaptic plasticity. It is therefore essential to understand how changes in synaptic transmission can regulate the organization and dynamics of actin binding proteins (ABPs). In this review, we will provide a detailed description of the organization and dynamics of F-actin and ABPs in dendritic spines and will discuss the current models explaining how the actin cytoskeleton sustains both structural and functional synaptic plasticity.

[In situ Raman spectroscopic observation of micro-processes of methane hydrate formation and dissociation].

PubMed

Liu, Chang-Ling; Ye, Yu-Guang; Meng, Qing-Guo; Lü, Wan-Jun; Wang, Fei-Fei

2011-06-01

Micro laser Raman spectroscopic technique was used for in situ observation of the micro-processes of methane hydrate formed and decomposed in a high pressure transparent capillary. The changes in clathrate structure of methane hydrate were investigated during these processes. The results show that, during hydrate formation, the Raman peak (2 917 cm(-1)) of methane gas gradually splits into two peaks (2 905 and 2 915 cm(-1)) representing large and small cages, respectively, suggesting that the dissolved methane molecules go into two different chemical environments. In the meantime, the hydrogen bonds interaction is strengthened because water is changing from liquid to solid state gradually. As a result, the O-H stretching vibrations of water shift to lower wavenumber. During the decomposition process of methane hydrates, the Raman peaks of the methane molecules both in the large and small cages gradually clear up, and finally turn into a single peak of methane gas. The experimental results show that laser Raman spectroscopy can accurately demonstrate some relevant information of hydrate crystal structure changes during the formation and dissociation processes of methane hydrate.

Structured decision making as a conceptual framework to identify thresholds for conservation and management

USGS Publications Warehouse

Martin, J.; Runge, M.C.; Nichols, J.D.; Lubow, B.C.; Kendall, W.L.

2009-01-01

Thresholds and their relevance to conservation have become a major topic of discussion in the ecological literature. Unfortunately, in many cases the lack of a clear conceptual framework for thinking about thresholds may have led to confusion in attempts to apply the concept of thresholds to conservation decisions. Here, we advocate a framework for thinking about thresholds in terms of a structured decision making process. The purpose of this framework is to promote a logical and transparent process for making informed decisions for conservation. Specification of such a framework leads naturally to consideration of definitions and roles of different kinds of thresholds in the process. We distinguish among three categories of thresholds. Ecological thresholds are values of system state variables at which small changes bring about substantial changes in system dynamics. Utility thresholds are components of management objectives (determined by human values) and are values of state or performance variables at which small changes yield substantial changes in the value of the management outcome. Decision thresholds are values of system state variables at which small changes prompt changes in management actions in order to reach specified management objectives. The approach that we present focuses directly on the objectives of management, with an aim to providing decisions that are optimal with respect to those objectives. This approach clearly distinguishes the components of the decision process that are inherently subjective (management objectives, potential management actions) from those that are more objective (system models, estimates of system state). Optimization based on these components then leads to decision matrices specifying optimal actions to be taken at various values of system state variables. Values of state variables separating different actions in such matrices are viewed as decision thresholds. Utility thresholds are included in the objectives component, and ecological thresholds may be embedded in models projecting consequences of management actions. Decision thresholds are determined by the above-listed components of a structured decision process. These components may themselves vary over time, inducing variation in the decision thresholds inherited from them. These dynamic decision thresholds can then be determined using adaptive management. We provide numerical examples (that are based on patch occupancy models) of structured decision processes that include all three kinds of thresholds. ?? 2009 by the Ecological Society of America.

45 CFR 84.22 - Existing facilities.

Code of Federal Regulations, 2011 CFR

2011-10-01

..., welfare, or other social services at alternate accessible sites, alteration of existing facilities and... to make structural changes in existing facilities where other methods are effective in achieving... handicapped persons in the most integrated setting appropriate. (c) Small health, welfare, or other social...

45 CFR 84.22 - Existing facilities.

Code of Federal Regulations, 2010 CFR

2010-10-01

..., welfare, or other social services at alternate accessible sites, alteration of existing facilities and... to make structural changes in existing facilities where other methods are effective in achieving... handicapped persons in the most integrated setting appropriate. (c) Small health, welfare, or other social...

Structural changes of homodimers in the PDB.

PubMed

Koike, Ryotaro; Amemiya, Takayuki; Horii, Tatsuya; Ota, Motonori

2018-04-01

Protein complexes are involved in various biological phenomena. These complexes are intrinsically flexible, and structural changes are essential to their functions. To perform a large-scale automated analysis of the structural changes of complexes, we combined two original methods. An application, SCPC, compares two structures of protein complexes and decides the match of binding mode. Another application, Motion Tree, identifies rigid-body motions in various sizes and magnitude from the two structural complexes with the same binding mode. This approach was applied to all available homodimers in the Protein Data Bank (PDB). We defined two complex-specific motions: interface motion and subunit-spanning motion. In the former, each subunit of a complex constitutes a rigid body, and the relative movement between subunits occurs at the interface. In the latter, structural parts from distinct subunits constitute a rigid body, providing the relative movement spanning subunits. All structural changes were classified and examined. It was revealed that the complex-specific motions were common in the homodimers, detected in around 40% of families. The dimeric interfaces were likely to be small and flat for interface motion, while large and rugged for subunit-spanning motion. Interface motion was accompanied by a drastic change in contacts at the interface, while the change in the subunit-spanning motion was moderate. These results indicate that the interface properties of homodimers correlated with the type of complex-specific motion. The study demonstrates that the pipeline of SCPC and Motion Tree is useful for the massive analysis of structural change of protein complexes. Copyright © 2017 Elsevier Inc. All rights reserved.

Pre-exposure to drought increases the resistance of tropical forest soil bacterial communities to extended drought

PubMed Central

Bouskill, Nicholas J; Lim, Hsiao Chien; Borglin, Sharon; Salve, Rohit; Wood, Tana E; Silver, Whendee L; Brodie, Eoin L

2013-01-01

Global climate models project a decrease in the magnitude of precipitation in tropical regions. Changes in rainfall patterns have important implications for the moisture content and redox status of tropical soils, yet little is known about how these changes may affect microbial community structure. Specifically, does exposure to prior stress confer increased resistance to subsequent perturbation? Here we reduced the quantity of precipitation throughfall to tropical forest soils in the Luquillo Mountains, Puerto Rico. Treatments included newly established throughfall exclusion plots (de novo excluded), plots undergoing reduction for a second time (pre-excluded) and ambient control plots. Ten months of throughfall exclusion led to a small but statistically significant decline in soil water potential and bacterial populations clearly adapted to increased osmotic stress. Although the water potential decline was small and microbial biomass did not change, phylogenetic diversity in the de novo-excluded plots decreased by ∼40% compared with the control plots, yet pre-excluded plots showed no significant change. On the other hand, the relative abundances of bacterial taxa in both the de novo-excluded and pre-excluded plots changed significantly with throughfall exclusion compared with control plots. Changes in bacterial community structure could be explained by changes in soil pore water chemistry and suggested changes in soil redox. Soluble iron declined in treatment plots and was correlated with decreased soluble phosphorus concentrations, which may have significant implications for microbial productivity in these P-limited systems. PMID:23151641

Structural comparison of nickel electrodes and precursor phases

NASA Technical Reports Server (NTRS)

Cornilsen, Bahne C.; Shan, Xiaoyin; Loyselle, Patricia

1989-01-01

Researchers summarize previous Raman spectroscopic results and discuss important structural differences in the various phases of active mass and active mass precursors. Raman spectra provide unique signatures for these phases, and allow one to distinguish each phase, even when the compound is amorphous to x rays (i.e., does not scatter x rays because of a lack of order and/or small particle size). The structural changes incurred during formation, charge and discharge, cobalt addition, and aging are discussed. The oxidation states and dopant contents are explained in terms of the nonstoichiometric structures.

How do Small Groups Promote Behaviour Change? An Integrative Conceptual Review of Explanatory Mechanisms.

PubMed

Borek, Aleksandra J; Abraham, Charles

2018-03-01

Small groups are used to promote health, well-being, and personal change by altering members' perceptions, beliefs, expectations, and behaviour patterns. An extensive cross-disciplinary literature has articulated and tested theories explaining how such groups develop, function, and facilitate change. Yet these theoretical understandings are rarely applied in the development, description, and evaluation of health-promotion, group-based, behaviour-change interventions. Medline database, library catalogues, search engines, specific journals and reference lists were searched for relevant texts. Texts were reviewed for explanatory concepts or theories describing change processes in groups, which were integrated into the developing conceptual structure. This was designed to be a parsimonious conceptual framework that could be applied to design and delivery. Five categories of interacting processes and concepts were identified and defined: (1) group development processes, (2) dynamic group processes, (3) social change processes, (4) personal change processes, and (5) group design and operating parameters. Each of these categories encompasses a variety of theorised mechanisms explaining individual change in small groups. The final conceptual model, together with the design issues and practical recommendations derived from it, provides a practical basis for linking research and theory explaining group functioning to optimal design of group-based, behaviour-change interventions. © 2018 The Authors. Applied Psychology: Health and Well-Being published by John Wiley & Sons Ltd on behalf of International Association of Applied Psychology.

Joint Services Electronics Program: Electronics Research at the University of Texas at Austin

DTIC Science & Technology

1988-12-31

structures. This system is also used routinely as an in-situ measure of alloy composition. We have shown that significant changes in the principal...RHEED streak intensity and shape are produced by very small changes in adatom coverage and that the profile is noticeably different for Ga and As...characteristic impedance measurement instruments. The oscillation frequency in the waveguide circuit could be varied from 8 to 12 GHz by changing the dc bias

Random close packing of disks and spheres in confined geometries

NASA Astrophysics Data System (ADS)

Desmond, Kenneth W.; Weeks, Eric R.

2009-11-01

Studies of random close packing of spheres have advanced our knowledge about the structure of systems such as liquids, glasses, emulsions, granular media, and amorphous solids. In confined geometries, the structural properties of random-packed systems will change. To understand these changes, we study random close packing in finite-sized confined systems, in both two and three dimensions. Each packing consists of a 50-50 binary mixture with particle size ratio of 1.4. The presence of confining walls significantly lowers the overall maximum area fraction (or volume fraction in three dimensions). A simple model is presented, which quantifies the reduction in packing due to wall-induced structure. This wall-induced structure decays rapidly away from the wall, with characteristic length scales comparable to the small particle diameter.

Small-scale genetic structure in an endangered wetland specialist: possible effects of landscape change and population recovery

USGS Publications Warehouse

van Rees, Charles B.; Reed, J. Michael; Wilson, Robert E.; Underwood, Jared G.; Sonsthagen, Sarah A.

2018-01-01

The effects of anthropogenic landscape change on genetic population structure are well studied, but the temporal and spatial scales at which genetic structure can develop, especially in taxa with high dispersal capabilities like birds, are less well understood. We investigated population structure in the Hawaiian gallinule (Gallinula galeata sandvicensis), an endangered wetland specialist bird on the island of O`ahu (Hawai`i, USA). Hawaiian gallinules have experienced a gradual population recovery from near extinction in the 1950s, and have recolonized wetlands on O`ahu in the context of a rapidly urbanizing landscape. We genotyped 152 Hawaiian gallinules at 12 microsatellite loci and sequenced a 520 base-pair fragment of the ND2 region of mitochondrial DNA (mtDNA) from individuals captured at 13 wetland locations on O`ahu in 2014–2016. We observed moderate to high genetic structuring (overall microsatellite FST = 0.098, mtDNA FST = 0.248) among populations of Hawaiian gallinules occupying wetlands at very close geographic proximity (e.g., 1.5–55 km). Asymmetry in gene flow estimates suggests that Hawaiian gallinules may have persisted in 2–3 strongholds which served as source populations that recolonized more recently restored habitats currently supporting large numbers of birds. Our results highlight that genetic structure can develop in taxa that are expanding their range after severe population decline, and that biologically significant structuring can occur over small geographic distances, even in avian taxa.

Influence of small-scale turbulence on cup anemometer calibrations

NASA Astrophysics Data System (ADS)

Marraccini, M.; Bak-Kristensen, K.; Horn, A.; Fifield, E.; Hansen, S. O.

2017-11-01

The paper presents and discusses the calibration results of cup anemometers under different levels of small-scale turbulence. Small-scale turbulence is known to govern the curvature of shear layers around structures and is not related to the traditional under and over speeding of cup anemometers originating from large-scale turbulence components. The paper has shown that the small-scale turbulence has a significant effect on the calibration results obtained for cup anemometers. At 10m/s the rotational speed seems to change by approx. 0.5% due to different simulations of the small-scale turbulence. The work which this paper is based on, is part of the TrueWind research project, aiming to increase accuracy of mast top-mounted cup anemometer measurements.

Pyrvinium pamoate changes alternative splicing of the serotonin receptor 2C by influencing its RNA structure

PubMed Central

Shen, Manli; Bellaousov, Stanislav; Hiller, Michael; de La Grange, Pierre; Creamer, Trevor P.; Malina, Orit; Sperling, Ruth; Mathews, David H.; Stoilov, Peter; Stamm, Stefan

2013-01-01

The serotonin receptor 2C plays a central role in mood and appetite control. It undergoes pre-mRNA editing as well as alternative splicing. The RNA editing suggests that the pre-mRNA forms a stable secondary structure in vivo. To identify substances that promote alternative exons inclusion, we set up a high-throughput screen and identified pyrvinium pamoate as a drug-promoting exon inclusion without editing. Circular dichroism spectroscopy indicates that pyrvinium pamoate binds directly to the pre-mRNA and changes its structure. SHAPE (selective 2′-hydroxyl acylation analysed by primer extension) assays show that part of the regulated 5′-splice site forms intramolecular base pairs that are removed by this structural change, which likely allows splice site recognition and exon inclusion. Genome-wide analyses show that pyrvinium pamoate regulates >300 alternative exons that form secondary structures enriched in A–U base pairs. Our data demonstrate that alternative splicing of structured pre-mRNAs can be regulated by small molecules that directly bind to the RNA, which is reminiscent to an RNA riboswitch. PMID:23393189

Volume change measurements of rice by environmental scanning electron microscopy and stereoscopy.

PubMed

Tang, Xiaohu; De Rooij, Mario; De Jong, Liesbeth

2007-01-01

The measurement of volume change, which is induced by changing the relative humidity, is performed on rice by using environmental scanning electron microscope (ESEM) and stereoscopy techniques. The typical DeltaV% approximately RH curve of rice in both sorption and desorption can be categorized into three regions: low, intermediate, and high dependence on relative humidity from low- to high-relative humidity. The volume changes faster for rice samples with lower crystallinity, which is because the amorphous component is easier to absorb moisture than the crystalline component. The volume change behavior in various relative humidity environments is comparable with rice isotherm curve in sorption process though discrepancies exist in desorption, which are thought to be the presence of small pores and microstructure changes at high relative humidity. The volume in the desorption branch is less than that in the sorption branch at the same relative humidity, which can be attributed to the collapse of interior structures, existence of small pores, surface topography loss, and amylose leach.

Effect of elastic collisions and electronic excitation on lattice structure of NiTi bulk intermetallic compound irradiated with energetic ions

NASA Astrophysics Data System (ADS)

Ochi, M.; Kojima, H.; Hori, F.; Kaneno, Y.; Semboshi, S.; Saitoh, Y.; Okamoto, Y.; Ishikawa, N.; Iwase, A.

2018-07-01

NiTi bulk intermetallic compound with the B19‧ structure was irradiated with 1 MeV He, 5 MeV Al, 16 MeV Au and 200 MeV Xe ions, and the change in lattice structure near the surface by the ion bombardment was investigated by using the grazing incidence X-ray diffraction (GIXD) and the extended X-ray absorption fine structure (EXAFS). The lattice structure transformation by the irradiation strongly depends on ion species and/or energies. For the 1 MeV He irradiation, the lattice structure changed from B19‧ to the A2 structure, but did not show an amorphization even after the high fluence irradiation. For the 5 MeV Al irradiation, the samples are partially amorphized. For the 16 MeV Au irradiation, the lattice structure of the NiTi samples changed nearly completely from the B19‧ structure to the amorphous state via the A2 structure. The value of dpa (displacement per atom) which is needed for the amorphization is, however, much smaller than the case of the Al ion irradiation. For the 200 MeV Xe ion irradiation, the lattice structure completely changed to the A2 structure even by a small ion fluence. The dependence of the lattice structure transformation on elastic collisions (dpa), the spectrum of the primary knock-on (PKA) atoms and the density of energy deposited through electronic excitation was discussed.

Different in the dark: The effect of habitat characteristics on community composition and beta diversity in bromeliad microfauna.

PubMed

Busse, Annika; Antiqueira, Pablo A P; Neutzling, Alexandre S; Wolf, Anna M; Romero, Gustavo Q; Petermann, Jana S

2018-01-01

The mechanisms which structure communities have been the focus of a large body of research. Here, we address the question if habitat characteristics describing habitat quality may drive changes in community composition and beta diversity of bromeliad-inhabiting microfauna. In our system, changes in canopy cover along an environmental gradient may affect resource availability, disturbance in form of daily water temperature fluctuations and predation, and thus may lead to changes in community structure of bromeliad microfauna through differences in habitat quality along this gradient. Indeed, we observed distinct changes in microfauna community composition along the environmental gradient explained by changes in the extent of daily water temperature fluctuations. We found beta diversity to be higher under low habitat quality (low canopy cover) than under high habitat quality (high canopy cover), which could potentially be explained by a higher relative importance of stochastic processes under low habitat quality. We also partitioned beta diversity into turnover and nestedness components and we found a nested pattern of beta diversity along the environmental gradient, with communities from the lower-quality habitat being nested subsets of communities from the higher-quality habitat. However, this pattern resulted from an increase in microfauna alpha diversity with an increase in habitat quality. By providing insights into microfauna-environment relationships our results contribute to the mechanistic understanding of community dynamics in small freshwater bodies. Here, we highlight the importance of habitat characteristics representing habitat quality in structuring communities, and suggest that this information may help to improve conservation practices of small freshwater ecosystems.

Different in the dark: The effect of habitat characteristics on community composition and beta diversity in bromeliad microfauna

PubMed Central

Antiqueira, Pablo A. P.; Neutzling, Alexandre S.; Wolf, Anna M.; Romero, Gustavo Q.; Petermann, Jana S.

2018-01-01

The mechanisms which structure communities have been the focus of a large body of research. Here, we address the question if habitat characteristics describing habitat quality may drive changes in community composition and beta diversity of bromeliad-inhabiting microfauna. In our system, changes in canopy cover along an environmental gradient may affect resource availability, disturbance in form of daily water temperature fluctuations and predation, and thus may lead to changes in community structure of bromeliad microfauna through differences in habitat quality along this gradient. Indeed, we observed distinct changes in microfauna community composition along the environmental gradient explained by changes in the extent of daily water temperature fluctuations. We found beta diversity to be higher under low habitat quality (low canopy cover) than under high habitat quality (high canopy cover), which could potentially be explained by a higher relative importance of stochastic processes under low habitat quality. We also partitioned beta diversity into turnover and nestedness components and we found a nested pattern of beta diversity along the environmental gradient, with communities from the lower-quality habitat being nested subsets of communities from the higher-quality habitat. However, this pattern resulted from an increase in microfauna alpha diversity with an increase in habitat quality. By providing insights into microfauna-environment relationships our results contribute to the mechanistic understanding of community dynamics in small freshwater bodies. Here, we highlight the importance of habitat characteristics representing habitat quality in structuring communities, and suggest that this information may help to improve conservation practices of small freshwater ecosystems. PMID:29401522

Conformational Changes Allow Processing of Bulky Substrates by a Haloalkane Dehalogenase with a Small and Buried Active Site.

PubMed

Kokkonen, Piia; Bednar, David; Dockalova, Veronika; Prokop, Zbynek; Damborsky, Jiri

2018-06-01

Haloalkane dehalogenases catalyze the hydrolysis of halogen-carbon bonds in organic halogenated compounds and as such are of great utility as biocatalysts. The crystal structures of the haloalkane dehalogenase DhlA from the bacterium from Xanthobacter autotrophicus GJ10, specifically adapted for the conversion of the small 1,2-dichloroethane (DCE) molecule, display the smallest catalytic site (110 Å3) within this enzyme family. However, during a substrate-specificity screening, we noted that DhlA can catalyze the conversion of far bulkier substrates, such as the 4-(bromomethyl)-6,7-dimethoxy-coumarin (220 Å3). This large substrate cannot bind to DhlA without conformational alterations. These conformational changes have been previously inferred from kinetic analysis, but their structural basis has not been understood. Using molecular dynamic simulations, we demonstrate here the intrinsic flexibility of part of the cap domain that allows DhlA to accommodate bulky substrates. The simulations displayed two routes for transport of substrates to the active site, one of which requires the conformational change and which is likely the route for bulky substrates. These results provide insights into the structure-dynamics-function relationships in enzymes with deeply buried active sites. Moreover, understanding the structural basis for the molecular adaptation of DhlA to DCE introduced into the biosphere during the industrial revolution provides a valuable lesson in enzyme design by nature. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Seasonality in the dung beetle community in a Brazilian tropical dry forest: Do small changes make a difference?

PubMed

Medina, Anderson Matos; Lopes, Priscila Paixão

2014-01-01

Dung beetle (Coleoptera: Scarabaeoidea: Scarabaeinae) activity is influenced by rainfall seasonality. We hypothesized that rainfall might also play a major role in regulating the community structure of this group. In this study, we describe seasonal changes in the richness, composition, and structure of the Scarabaeinae community in a Brazilian tropical dry forest. A fragment of arboreal Caatinga was sampled using baited pitfall traps during the early dry season (EDS), late dry season (LDS), early wet season (EWS), and middle wet season (MWS). We compared the dung beetle community in each season in relationship to species richness, rank-dominance, curves, and composition. We collected 1352 Scarabaeinae individuals , belonging to 15 species. Dichotomius aff. laevicollis Felsche (Coleoptera: Scarabaeidae) was the dominant species, representing 73.89% of the individuals. There were no seasonal changes in the rank dominance curves; all had a single dominant species and a few species with low abundance, typical for arid areas. Estimated richness was highest in MWS, followed by EWS. Dry-season samples (EDS and LDS) had lower richness, with no significant difference between the dry seasons. Although species richness increased as the habitat became wetter, the difference between the wet and dry seasons was small, which differs completely from the findings of other studies in Neotropical dry forests, where almost all species cease activities in the dry season. Species composition changes were found in non-metric multidimensional scaling and sustained by analysis of similarity. All the seasons had pairwise differences in composition, with the exception of EDS and MWS, which indicates that the dung beetle community in this fragment requires more than three months of drought to trigger changes in species composition; this is probably due to small changes in the forest canopy. There was no difference in composition between EDS and MWS. As in other tropical dry forests, although to a lesser extent, the dung beetle community of this fragment responded to rainfall seasonality with changes in species composition and reduced species richness. Such responses, even to this lesser extent, may occur because of small changes in tree cover and minor microclimate changes. This is an open access paper. We use the Creative Commons Attribution 3.0 license that permits unrestricted use, provided that the paper is properly attributed.

Changes in coral-reef structure through the Miocene in the Mediterranean province: Adaptive versus environmental influence

NASA Astrophysics Data System (ADS)

Pomar, Luis; Hallock, Pamela

2007-10-01

Well-documented Mediterranean examples of Miocene carbonate platforms, with complete exposures from shallow-water to basinal facies, provide evidence for temporal changes in reef-building capacity of zooxanthellate corals. In pre-late Tortonian platforms, small coralgal patches and mounds occur from platform top to the toe of slope, but they did not build to sea level. In contrast, barrier reefs with unequivocal reef-crest structures that reached sea level are documented in late Tortonian-early Messinian platforms. We suggest that a change in both calcification rates and bathymetric zonation was the result of coevolution of corals and Symbiodinium zooxanthellae, coeval to global cooling and, at least at a regional scale, a geochemical change that supported widespread aragonite precipitation through the late Miocene.

Modeling protein conformational changes by iterative fitting of distance constraints using reoriented normal modes.

PubMed

Zheng, Wenjun; Brooks, Bernard R

2006-06-15

Recently we have developed a normal-modes-based algorithm that predicts the direction of protein conformational changes given the initial state crystal structure together with a small number of pairwise distance constraints for the end state. Here we significantly extend this method to accurately model both the direction and amplitude of protein conformational changes. The new protocol implements a multisteps search in the conformational space that is driven by iteratively minimizing the error of fitting the given distance constraints and simultaneously enforcing the restraint of low elastic energy. At each step, an incremental structural displacement is computed as a linear combination of the lowest 10 normal modes derived from an elastic network model, whose eigenvectors are reorientated to correct for the distortions caused by the structural displacements in the previous steps. We test this method on a list of 16 pairs of protein structures for which relatively large conformational changes are observed (root mean square deviation >3 angstroms), using up to 10 pairwise distance constraints selected by a fluctuation analysis of the initial state structures. This method has achieved a near-optimal performance in almost all cases, and in many cases the final structural models lie within root mean square deviation of 1 approximately 2 angstroms from the native end state structures.

Protein Structural Analysis via Mass Spectrometry-Based Proteomics

PubMed Central

Artigues, Antonio; Nadeau, Owen W.; Rimmer, Mary Ashley; Villar, Maria T.; Du, Xiuxia; Fenton, Aron W.; Carlson, Gerald M.

2017-01-01

Modern mass spectrometry (MS) technologies have provided a versatile platform that can be combined with a large number of techniques to analyze protein structure and dynamics. These techniques include the three detailed in this chapter: 1) hydrogen/deuterium exchange (HDX), 2) limited proteolysis, and 3) chemical crosslinking (CX). HDX relies on the change in mass of a protein upon its dilution into deuterated buffer, which results in varied deuterium content within its backbone amides. Structural information on surface exposed, flexible or disordered linker regions of proteins can be achieved through limited proteolysis, using a variety of proteases and only small extents of digestion. CX refers to the covalent coupling of distinct chemical species and has been used to analyze the structure, function and interactions of proteins by identifying crosslinking sites that are formed by small multi-functional reagents, termed crosslinkers. Each of these MS applications is capable of revealing structural information for proteins when used either with or without other typical high resolution techniques, including NMR and X-ray crystallography. PMID:27975228

75 FR 34202 - The Future of Aviation Advisory Committee (FAAC) Subcommittee on Competitiveness and Viability...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-16

..., which will be held in Washington, DC on June 30, 2010. This notice provides details on the date, time... changing competitive structure of the U.S. airline industry is likely to transform travel habits of small...

34 CFR 104.22 - Existing facilities.

Code of Federal Regulations, 2010 CFR

2010-07-01

..., delivery of health, welfare, or other social services at alternate accessible sites, alteration of existing... not required to make structural changes in existing facilities where other methods are effective in... handicapped persons in the most integrated setting appropriate. (c) Small health, welfare, or other social...

Photographer : JPL Range : 6 Million km. ( 3.72 million miles ) This photograph of Jupiter, shot

NASA Technical Reports Server (NTRS)

1979-01-01

Photographer : JPL Range : 6 Million km. ( 3.72 million miles ) This photograph of Jupiter, shot from Voyager 2, shows the equator to the southern polar latitudes, near the Great Red Spot. The white oval that appears here is different from the one seen in a similiar position when voyager 1 passed years before. The region of white clouds now extends from east of The Red Spot and around it's northern boundary, preventing small cloud vortices from circling the feature. The disturbed region west of The Red Spot has also changed since Voyager1. It shows more small scale structure and cloud vortices being formed out of the wave structures.

Application of kaizen methodology to foster departmental engagement in quality improvement.

PubMed

Knechtges, Paul; Decker, Michael Christopher

2014-12-01

The Toyota Production System, also known as Lean, is a structured approach to continuous quality improvement that has been developed over the past 50 years to transform the automotive manufacturing process. In recent years, these techniques have been successfully applied to quality and safety improvement in the medical field. One of these techniques is kaizen, which is the Japanese word for "good change." The central tenant of kaizen is the quick analysis of the small, manageable components of a problem and the rapid implementation of a solution with ongoing, real-time reassessment. Kaizen adds an additional "human element" that all stakeholders, not just management, must be involved in such change. Because of the small size of the changes involved in a kaizen event and the inherent focus on human factors and change management, a kaizen event can serve as good introduction to continuous quality improvement for a radiology department. Copyright © 2014. Published by Elsevier Inc.

Fusion of small unilamellar vesicles induced by a serum albumin fragment of molecular weight 9000.

PubMed

Garcia, L A; Araújo, P S; Chaimovich, H

1984-05-16

A peptide (P-9) comprising amino acids 307 to 385 of bovine serum albumin induced the fusion of small unilamellar vesicles of phosphatidylcholine at low pH. Upon acidification P-9 exhibited a ultraviolet differential spectrum characteristic of hydrophilic exposure of chromophores. This conformational change, and the structure of P-9 composed of three amphiphilic helixes , suggested a general working hypothesis for the description of protein-induced membrane fusion.

A venture capital view of challenges, opportunities, and innovation in biomedical research.

PubMed

Ratcliffe, L T

2011-02-01

Small biotech companies have been an important source of innovation, pipelines, and new products for the pharmaceutical industry, and are primarily financed by venture capital (VC). The significant changes happening within the VC industry have broad implications for these small companies. This includes a shift to financing later-stage programs with increasing interest in orphan or specialty indications. Nontraditional sources of capital and innovative risk-sharing structures can enable early-stage companies.

Profiling protein function with small molecule microarrays

PubMed Central

Winssinger, Nicolas; Ficarro, Scott; Schultz, Peter G.; Harris, Jennifer L.

2002-01-01

The regulation of protein function through posttranslational modification, local environment, and protein–protein interaction is critical to cellular function. The ability to analyze on a genome-wide scale protein functional activity rather than changes in protein abundance or structure would provide important new insights into complex biological processes. Herein, we report the application of a spatially addressable small molecule microarray to an activity-based profile of proteases in crude cell lysates. The potential of this small molecule-based profiling technology is demonstrated by the detection of caspase activation upon induction of apoptosis, characterization of the activated caspase, and inhibition of the caspase-executed apoptotic phenotype using the small molecule inhibitor identified in the microarray-based profile. PMID:12167675

Using stable isotopes to track the effects of deforestation on small-mammal ecology in the Pacific Northwest over the last 100 years

NASA Astrophysics Data System (ADS)

Packard, N. R.; Cotton, J. M.; Smiley, T. M.; Terry, R. C.

2017-12-01

Landscape, land-use, and climate change are important factors in determining ecosystem change over a range of spatio-temporal scales. For example, within small-mammal communities, the spread of agriculture, rapid urbanization, and deforestation have been shown to alter species composition and diet, thus potentially disrupting ecological interactions and reshaping ecosystems. Small mammals integrate the isotopic composition of their diet and drinking water into their hair and therefore serve as useful proxies for vegetation and water resources in their habitat. To better understand how forest loss and land-cover change influence small-mammal ecology in the Pacific Northwest (PNW), we analyzed the hydrogen (H) and oxygen (O) isotopic composition of hair from historical Peromyscus maniculatus (North American deer mouse) specimens housed in natural history museums across the country. While deforestation along the east coast occurred hundreds of years ago, the loss of forests on the west coast occurred more recently, beginning around 1930. We use early 20th century specimens of this widespread and abundant generalist species to better understand ecosystem changes that occurred over the past 100 years of local and regional deforestation. Changing forest composition and structure during deforestation can influence both broad-scale hydrological cycling and local ecosystems. Variation in O and H isotopic composition corresponds to changes in the hydrological cycle, such as changes in the source and amount of precipitation, and changes in the moisture conditions in local ecosystems. We will present this spatial and temporal variability in the form of isoscapes, or δ18O and δD isotope landscape models, of P. maniculatus hair in the western forests of the PNW through time. Investigating isotopic signatures in small mammals can help us better understand ecosystem response to anthropogenic land-use and climate change.

Ultra-Structure database design methodology for managing systems biology data and analyses

PubMed Central

Maier, Christopher W; Long, Jeffrey G; Hemminger, Bradley M; Giddings, Morgan C

2009-01-01

Background Modern, high-throughput biological experiments generate copious, heterogeneous, interconnected data sets. Research is dynamic, with frequently changing protocols, techniques, instruments, and file formats. Because of these factors, systems designed to manage and integrate modern biological data sets often end up as large, unwieldy databases that become difficult to maintain or evolve. The novel rule-based approach of the Ultra-Structure design methodology presents a potential solution to this problem. By representing both data and processes as formal rules within a database, an Ultra-Structure system constitutes a flexible framework that enables users to explicitly store domain knowledge in both a machine- and human-readable form. End users themselves can change the system's capabilities without programmer intervention, simply by altering database contents; no computer code or schemas need be modified. This provides flexibility in adapting to change, and allows integration of disparate, heterogenous data sets within a small core set of database tables, facilitating joint analysis and visualization without becoming unwieldy. Here, we examine the application of Ultra-Structure to our ongoing research program for the integration of large proteomic and genomic data sets (proteogenomic mapping). Results We transitioned our proteogenomic mapping information system from a traditional entity-relationship design to one based on Ultra-Structure. Our system integrates tandem mass spectrum data, genomic annotation sets, and spectrum/peptide mappings, all within a small, general framework implemented within a standard relational database system. General software procedures driven by user-modifiable rules can perform tasks such as logical deduction and location-based computations. The system is not tied specifically to proteogenomic research, but is rather designed to accommodate virtually any kind of biological research. Conclusion We find Ultra-Structure offers substantial benefits for biological information systems, the largest being the integration of diverse information sources into a common framework. This facilitates systems biology research by integrating data from disparate high-throughput techniques. It also enables us to readily incorporate new data types, sources, and domain knowledge with no change to the database structure or associated computer code. Ultra-Structure may be a significant step towards solving the hard problem of data management and integration in the systems biology era. PMID:19691849

Multiplex social ecological network analysis reveals how social changes affect community robustness more than resource depletion.

PubMed

Baggio, Jacopo A; BurnSilver, Shauna B; Arenas, Alex; Magdanz, James S; Kofinas, Gary P; De Domenico, Manlio

2016-11-29

Network analysis provides a powerful tool to analyze complex influences of social and ecological structures on community and household dynamics. Most network studies of social-ecological systems use simple, undirected, unweighted networks. We analyze multiplex, directed, and weighted networks of subsistence food flows collected in three small indigenous communities in Arctic Alaska potentially facing substantial economic and ecological changes. Our analysis of plausible future scenarios suggests that changes to social relations and key households have greater effects on community robustness than changes to specific wild food resources.

Small structural changes on a hydroquinone scaffold determine the complex I inhibition or uncoupling of tumoral oxidative phosphorylation

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

Urra, Félix A., E-mail: felix.urra@qf.uchile.cl; Córdova-Delgado, Miguel; Lapier, Michel

2016-01-15

Mitochondria participate in several distinctiveness of cancer cell, being a promising target for the design of anti-cancer compounds. Previously, we described that ortho-carbonyl hydroquinone scaffold 14 inhibits the complex I-dependent respiration with selective anti-proliferative effect on mouse mammary adenocarcinoma TA3/Ha cancer cells; however, the structural requirements of this hydroquinone scaffold to affect the oxidative phosphorylation (OXPHOS) of cancer cells have not been studied in detail. Here, we characterize the mitochondrial metabolism of TA3/Ha cancer cells, which exhibit a high oxidative metabolism, and evaluate the effect of small structural changes of the hydroquinone scaffold 14 on the respiration of this cellmore » line. Our results indicate that these structural changes modify the effect on OXPHOS, obtaining compounds with three alternative actions: inhibitors of complex I-dependent respiration, uncoupler of OXPHOS and compounds with both actions. To confirm this, the effect of a bicyclic hydroquinone (9) was evaluated in isolated mitochondria. Hydroquinone 9 increased mitochondrial respiration in state 4o without effects on the ADP-stimulated respiration (state 3{sub ADP}), decreasing the complexes I and II-dependent respiratory control ratio. The effect on mitochondrial respiration was reversed by 6-ketocholestanol addition, indicating that this hydroquinone is a protonophoric uncoupling agent. In intact TA3/Ha cells, hydroquinone 9 caused mitochondrial depolarization, decreasing intracellular ATP and NAD(P)H levels and GSH/GSSG ratio, and slightly increasing the ROS levels. Moreover, it exhibited selective NAD(P)H availability-dependent anti-proliferative effect on cancer cells. Therefore, our results indicate that the ortho-carbonyl hydroquinone scaffold offers the possibility to design compounds with specific actions on OXPHOS of cancer cells. - Highlights: • Small changes on a hydroquinone scaffold modify the action on OXPHOS of cancer cells. • Complex I Inhibitors, uncoupler of OXPHOS and agents with dual action are described. • Cpd. 9 is an uncoupler agent of OXPHOS with selective anti-proliferative effects. • Useful information to design agents with a selective mechanism on OXPHOS is provided.« less

Detection of Subtle Hydromechanical Medium Changes Caused By a Small-Magnitude Earthquake Swarm in NE Brazil

NASA Astrophysics Data System (ADS)

D'Hour, V.; Schimmel, M.; Do Nascimento, A. F.; Ferreira, J. M.; Lima Neto, H. C.

2016-04-01

Ambient noise correlation analyses are largely used in seismology to map heterogeneities and to monitor the temporal evolution of seismic velocity changes associated mostly with stress field variations and/or fluid movements. Here we analyse a small earthquake swarm related to a main mR 3.7 intraplate earthquake in North-East of Brazil to study the corresponding post-seismic effects on the medium. So far, post-seismic effects have been observed mainly for large magnitude events. In our study, we show that we were able to detect localized structural changes even for a small earthquake swarm in an intraplate setting. Different correlation strategies are presented and their performances are also shown. We compare the classical auto-correlation with and without pre-processing, including 1-bit normalization and spectral whitening, and the phase auto-correlation. The worst results were obtained for the pre-processed data due to the loss of waveform details. The best results were achieved with the phase cross-correlation which is amplitude unbiased and sensitive to small amplitude changes as long as there exist waveform coherence superior to other unrelated signals and noise. The analysis of 6 months of data using phase auto-correlation and cross-correlation resulted in the observation of a progressive medium change after the major recorded event. The progressive medium change is likely related to the swarm activity through opening new path ways for pore fluid diffusion. We further observed for the auto-correlations a lag time frequency-dependent change which likely indicates that the medium change is localized in depth. As expected, the main change is observed along the fault.

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

Mechanisms and chemistry of dye adsorption on manganese oxides-modified diatomite.

PubMed

Al-Ghouti, Mohammad A; Al-Degs, Yehya S; Khraisheh, Majeda A M; Ahmad, Mohammad N; Allen, Stephen J

2009-08-01

The investigations into structural changes which occur during adsorbent modification and the adsorption mechanisms are essential for an effective design of adsorption systems. Manganese oxides were impregnated onto diatomite to form the type known as delta-birnessite. Initial investigations established the effectiveness of manganese oxides-modified diatomite (MOMD) to remove basic and reactive dyes from aqueous solution. The adsorption capacity of MOMD for methylene blue (MB), hydrolysed reactive black (RB) and hydrolysed reactive yellow (RY) was 320, 419, and 204mg/g, respectively. Various analytical techniques were used to characterise the structure and the mechanisms of the dye adsorption process onto MOMD such as Fourier transform infrared (FTIR), X-ray diffraction (XRD) and atomic absorption spectrometry (A.A.). A small shift to higher values of the d-spacing of dye/MOMD was observed indicating that a small amount of the dye molecules were intercalated in the MOMD structure and other molecules were adsorbed on the external surface of MOMD. Two mechanisms of dye adsorption onto MOMD were proposed; intercalation of the dye in the octahedral layers and adsorption of the dye on the MOMD external surface. Moreover, the results demonstrated that the MOMD structure was changed upon insertion of MB and RY with an obvious decrease in the intensity of the second main peak of the MOMD X-ray pattern.

Small-Angle X-Ray Scattering Analysis of the Bifunctional Antibiotic Resistance Enzyme Aminoglycoside (6′) Acetyltransferase-Ie/Aminoglycoside (2″) Phosphotransferase-Ia Reveals a Rigid Solution Structure

PubMed Central

Caldwell, Shane J.

2012-01-01

Aminoglycoside (6′) acetyltransferase-Ie/aminoglycoside (2″) phosphotransferase-Ia [AAC(6′)-Ie/APH(2″)-Ia] is one of the most problematic aminoglycoside resistance factors in clinical pathogens, conferring resistance to almost every aminoglycoside antibiotic available to modern medicine. Despite 3 decades of research, our understanding of the structure of this bifunctional enzyme remains limited. We used small-angle X-ray scattering (SAXS) to model the structure of this bifunctional enzyme in solution and to study the impact of substrate binding on the enzyme. It was observed that the enzyme adopts a rigid conformation in solution, where the N-terminal AAC domain is fixed to the C-terminal APH domain and not loosely tethered. The addition of acetyl-coenzyme A, coenzyme A, GDP, guanosine 5′-[β,γ-imido]triphosphate (GMPPNP), and combinations thereof to the protein resulted in only modest changes to the radius of gyration (RG) of the enzyme, which were not consistent with any large changes in enzyme structure upon binding. These results imply some selective advantage to the bifunctional enzyme beyond coexpression as a single polypeptide, likely linked to an improvement in enzymatic properties. We propose that the rigid structure contributes to improved electrostatic steering of aminoglycoside substrates toward the two active sites, which may provide such an advantage. PMID:22290965

Dynamically variable negative stiffness structures.

PubMed

Churchill, Christopher B; Shahan, David W; Smith, Sloan P; Keefe, Andrew C; McKnight, Geoffrey P

2016-02-01

Variable stiffness structures that enable a wide range of efficient load-bearing and dexterous activity are ubiquitous in mammalian musculoskeletal systems but are rare in engineered systems because of their complexity, power, and cost. We present a new negative stiffness-based load-bearing structure with dynamically tunable stiffness. Negative stiffness, traditionally used to achieve novel response from passive structures, is a powerful tool to achieve dynamic stiffness changes when configured with an active component. Using relatively simple hardware and low-power, low-frequency actuation, we show an assembly capable of fast (<10 ms) and useful (>100×) dynamic stiffness control. This approach mitigates limitations of conventional tunable stiffness structures that exhibit either small (<30%) stiffness change, high friction, poor load/torque transmission at low stiffness, or high power active control at the frequencies of interest. We experimentally demonstrate actively tunable vibration isolation and stiffness tuning independent of supported loads, enhancing applications such as humanoid robotic limbs and lightweight adaptive vibration isolators.

A role for recombination junctions in the segregation of mitochondrial DNA in yeast.

PubMed

Lockshon, D; Zweifel, S G; Freeman-Cook, L L; Lorimer, H E; Brewer, B J; Fangman, W L

1995-06-16

In S. cerevisiae, mitochondrial DNA (mtDNA) molecules, in spite of their high copy number, segregate as if there were a small number of heritable units. The rapid segregation of mitochondrial genomes can be analyzed using mtDNA deletion variants. These small, amplified genomes segregate preferentially from mixed zygotes relative to wild-type mtDNA. This segregation advantage is abolished by mutations in a gene, MGT1, that encodes a recombination junction-resolving enzyme. We show here that resolvase deficiency causes a larger proportion of molecules to be linked together by recombination junctions, resulting in the aggregation of mtDNA into a small number of cytological structures. This change in mtDNA structure can account for the increased mitotic loss of mtDNA and the altered pattern of mtDNA segregation from zygotes. We propose that the level of unresolved recombination junctions influences the number of heritable units of mtDNA.

Long-term changes after brief dynamic psychotherapy: symptomatic versus dynamic assessments.

PubMed

Høglend, P; Sørlie, T; Sørbye, O; Heyerdahl, O; Amlo, S

1992-08-01

Dynamic change in psychotherapy, as measured by theory-related or mode-specific instruments, have been criticized for being too intercorrelated with symptomatic change measures. In this study, long-term changes after brief dynamic psychotherapy were studied in 45 moderately disturbed neurotic patients by a reliable outcome battery. The factor structure of all the change variables suggested that they tapped 2 distinct and stable sources of variance: dynamic and symptomatic change. The categories of overall dynamic change were different from categories of change on the Global Assessment Scale. A small systematic difference was found between the categories of overall dynamic change and the categories of target complaints change also, due to false solutions of dynamic conflicts.

Disrupted Structural and Functional Networks and Their Correlation with Alertness in Right Temporal Lobe Epilepsy: A Graph Theory Study.

PubMed

Jiang, Wenyu; Li, Jianping; Chen, Xuemei; Ye, Wei; Zheng, Jinou

2017-01-01

Previous studies have shown that temporal lobe epilepsy (TLE) involves abnormal structural or functional connectivity in specific brain areas. However, limited comprehensive studies have been conducted on TLE associated changes in the topological organization of structural and functional networks. Additionally, epilepsy is associated with impairment in alertness, a fundamental component of attention. In this study, structural networks were constructed using diffusion tensor imaging tractography, and functional networks were obtained from resting-state functional MRI temporal series correlations in 20 right temporal lobe epilepsy (rTLE) patients and 19 healthy controls. Global network properties were computed by graph theoretical analysis, and correlations were assessed between global network properties and alertness. The results from these analyses showed that rTLE patients exhibit abnormal small-world attributes in structural and functional networks. Structural networks shifted toward more regular attributes, but functional networks trended toward more random attributes. After controlling for the influence of the disease duration, negative correlations were found between alertness, small-worldness, and the cluster coefficient. However, alertness did not correlate with either the characteristic path length or global efficiency in rTLE patients. Our findings show that disruptions of the topological construction of brain structural and functional networks as well as small-world property bias are associated with deficits in alertness in rTLE patients. These data suggest that reorganization of brain networks develops as a mechanism to compensate for altered structural and functional brain function during disease progression.

Bone structure studies with holographic interferometric nondestructive testing and x-ray methods

NASA Astrophysics Data System (ADS)

Silvennoinen, Raimo; Nygren, Kaarlo; Rouvinen, Juha; Petrova, Valentina V.

1994-02-01

Changes in the biomechanics and in the molecular texture and structure of isolated radioulnar bones of subadult European moose (Alces alces L.) collected in various environmentally polluted areas of Finland were investigated by means of holographic interferometric non- destructive testing (HNDT), radiological, morphometrical, and x-ray diffraction methods. By means of small caudal-cranial bending forces, the surface movements of the lower end (distal epiphysis) of the radial bone were recorded with the HNDT method. To study bone molecular texture and structure changes under external compressing forces, the samples for x-ray diffraction analysis were taken from the upper end of the ulnar bone (olecranon tip). Results showed that the bones obtained from the Harjavalta area and those of North Karelian moose showing malnutrition and healing femoral fractures produced different HNDT pictures compared with the four normally developed North Karelian moose. In the x-ray diffraction, the Harjavalta samples showed changes in molecular texture and structure compared with the samples from the apparently normal North Karelian animals.

Whole-Cell-Based Assay To Evaluate Structure Permeation Relationships for Carbapenem Passage through the Pseudomonas aeruginosa Porin OprD.

PubMed

Iyer, Ramkumar; Sylvester, Mark A; Velez-Vega, Camilo; Tommasi, Ruben; Durand-Reville, Thomas F; Miller, Alita A

2017-04-14

The global emergence of antibiotic resistance, especially in Gram-negative bacteria, is an urgent threat to public health. Discovery of novel classes of antibiotics with activity against these pathogens has been impeded by a fundamental lack of understanding of the molecular drivers underlying small molecule uptake. Although it is well-known that outer membrane porins represent the main route of entry for small, hydrophilic molecules across the Gram-negative cell envelope, the structure-permeation relationship for porin passage has yet to be defined. To address this knowledge gap, we developed a sensitive and specific whole-cell approach in Escherichia coli called titrable outer membrane permeability assay system (TOMAS). We used TOMAS to characterize the structure porin-permeation relationships of a set of novel carbapenem analogues through the Pseudomonas aeruginosa porin OprD. Our results show that small structural modifications, especially the number and nature of charges and their position, have dramatic effects on the ability of these molecules to permeate cells through OprD. This is the first demonstration of a defined relationship between specific molecular changes in a substrate and permeation through an isolated porin. Understanding the molecular mechanisms that impact antibiotic transit through porins should provide valuable insights to antibacterial medicinal chemistry and may ultimately allow for the rational design of porin-mediated uptake of small molecules into Gram-negative bacteria.

ASSOCIATIONS OF EASTERN REDCEDAR AND COMMUNITY STRUCTURE OF SMALL MAMMALS

EPA Science Inventory

Increased abundance of eastern redcedar (Juniperus virginianas), a native but invasive species in the Great Plains, has been associated with several changes in ecosystem function. It can lead to a reduction in herbaceous biomass in the canopy zone, alter species composition, and...

Fine Structure in Quasar Flows Revealed by Lens-Aided Multi-Angle Spectroscopy (LAMAS)

NASA Astrophysics Data System (ADS)

Green, Paul J.

2006-09-01

Spectral differences between lensed quasar image components are common. Since lensing is intrinsically achromatic, these differences are typically explained as the effect of either microlensing, or as light path time delays sampling intrinsic quasar spectral variability. In some cases, neither explanation seems sufficient. Here we advance a novel third hypothesis: some spectral differences are due to small line-of- sight differences through quasar disk wind outflows, taking the widest separation lens SDSSJ1004+4112 as a key example. We show that small changes in sightline may traverse streams with significantly differing columns. The implications are many. Fine structure in these outflows may change the observed spectra on arcsec scales. Though difficult to detect observationally, high ionization, high velocity-width streams may sculpt the optical and X-ray spectra of most quasars. We discuss existing multi-epoch optical/UV spectroscopy and results from X-ray observations both by Chandra and XMM in this context, and sketch further possible tests. The author gratefully acknowledges support through NASA contract NAS8-03060 (CXC).

Computed microtomography and X-ray fluorescence analysis for comprehensive analysis of structural changes in bone.

PubMed

Buzmakov, Alexey; Chukalina, Marina; Nikolaev, Dmitry; Schaefer, Gerald; Gulimova, Victoria; Saveliev, Sergey; Tereschenko, Elena; Seregin, Alexey; Senin, Roman; Prun, Victor; Zolotov, Denis; Asadchikov, Victor

2013-01-01

This paper presents the results of a comprehensive analysis of structural changes in the caudal vertebrae of Turner's thick-toed geckos by computer microtomography and X-ray fluorescence analysis. We present algorithms used for the reconstruction of tomographic images which allow to work with high noise level projections that represent typical conditions dictated by the nature of the samples. Reptiles, due to their ruggedness, small size, belonging to the amniote and a number of other valuable features, are an attractive model object for long-orbital experiments on unmanned spacecraft. Issues of possible changes in their bone tissue under the influence of spaceflight are the subject of discussions between biologists from different laboratories around the world.

Structural analysis, electronic properties, and band gaps of a graphene nanoribbon: A new 2D materials

NASA Astrophysics Data System (ADS)

Dass, Devi

2018-03-01

Graphene nanoribbon (GNR), a new 2D carbon nanomaterial, has some unique features and special properties that offer a great potential for interconnect, nanoelectronic devices, optoelectronics, and nanophotonics. This paper reports the structural analysis, electronic properties, and band gaps of a GNR considering different chirality combinations obtained using the pz orbital tight binding model. In structural analysis, the analytical expressions for GNRs have been developed and verified using the simulation for the first time. It has been found that the total number of unit cells and carbon atoms within an overall unit cell and molecular structure of a GNR have been changed with the change in their chirality values which are similar to the values calculated using the developed analytical expressions thus validating both the simulation as well as analytical results. Further, the electronic band structures at different chirality values have been shown for the identification of metallic and semiconductor properties of a GNR. It has been concluded that all zigzag edge GNRs are metallic with very small band gaps range whereas all armchair GNRs show both the metallic and semiconductor nature with very small and high band gaps range. Again, the total number of subbands in each electronic band structure is equal to the total number of carbon atoms present in overall unit cell of the corresponding GNR. The semiconductors GNRs can be used as a channel material in field effect transistor suitable for advanced CMOS technology whereas the metallic GNRs could be used for interconnect.

Change in single cystathionine β-synthase domain-containing protein from a bent to flat conformation upon adenosine monophosphate binding.

PubMed

Jeong, Byung-Cheon; Park, Si Hoon; Yoo, Kyoung Shin; Shin, Jeong Sheop; Song, Hyun Kyu

2013-07-01

Cystathionine β-synthase (CBS) domains are small intracellular modules that can act as binding domains for adenosine derivatives, and they may regulate the activity of associated enzymes or other functional domains. Among these, the single CBS domain-containing proteins, CBSXs, from Arabidopsis thaliana, have recently been identified as redox regulators of the thioredoxin system. Here, the crystal structure of CBSX2 in complex with adenosine monophosphate (AMP) is reported at 2.2Å resolution. The structure of dimeric CBSX2 with bound-AMP is shown to be approximately flat, which is in stark contrast to the bent form of apo-CBSXs. This conformational change in quaternary structure is triggered by a local structural change of the unique α5 helix, and by moving each loop P into an open conformation to accommodate incoming ligands. Furthermore, subtle rearrangement of the dimer interface triggers movement of all subunits, and consequently, the bent structure of the CBSX2 dimer becomes a flat structure. This reshaping of the structure upon complex formation with adenosine-containing ligand provides evidence that ligand-induced conformational reorganization of antiparallel CBS domains is an important regulatory mechanism. Copyright © 2013 Elsevier Inc. All rights reserved.

Electronic structure change of NiS2- x Se x in the metal-insulator transition probed by X-ray absorption spectroscopy

NASA Astrophysics Data System (ADS)

Jeong, Jinwon; Park, Kyung Ja; Cho, En-Jin; Noh, Han-Jin; Kim, Sung Baek; Kim, Hyeong-Do

2018-01-01

The electronic structure change of NiS2- x Se x as a function of Se concentration x has been studied by Ni L-edge X-ray absorption spectroscopy (XAS). The XAS spectra show distinct features in Ni L 3 edge, indicating whether the system is insulating or metallic. These features can be semi-quantitatively explained within the framework of the configurational interaction cluster model (CICM). In the S-rich region, relatively large charge-transfer energy (Δ 5 eV) from ligand p to Ni 3 d states and a little small p- d hybridization strength ( V pdσ 1.1 eV) can reproduce the experimental spectra in the CICM calculation, and vice versa in the Se-rich region. Our analysis result is consistent with the Zaanen-Sawatzky-Allen scheme that the systems in S-rich side ( x ≤ 0.5) are a charge transfer insulator. However, it also requires that the Δ value must change abruptly in spite of the small change of x near x = 0.5. As a possible microscopic origin, we propose a percolation scenario where a long range connection of Ni[(S,Se)2]6 octahedra with Se-Se dimers plays a key role to gap closure.

Effects of Didymosphenia geminata massive growth on stream communities: Smaller organisms and simplified food web structure

PubMed Central

Gomà, Joan; Prat, Narcís

2018-01-01

This study aims to contribute to the understanding of the impact of Didymosphenia geminata massive growths upon river ecosystem communities’ composition and functioning. This is the first study to jointly consider the taxonomic composition and functional structure of diatom and macroinvertebrate assemblages in order to determine changes in community structure, and the food web alterations associated with this invasive alga. This study was carried out in the Lumbreras River (Ebro Basin, La Rioja, Northern Spain), which has been affected by a considerable massive growth of D. geminata since 2011. The study shows a profound alteration in both the river community composition and in the food web structure at the sites affected by the massive growth, which is primarily due to the alteration of the environmental conditions, thus demonstrating that D. geminata has an important role as an ecosystem engineer in the river. Thick filamentous mats impede the movement of large invertebrates—especially those that move and feed up on it—and favor small, opportunistic, herbivorous organisms, mainly chironomids, that are capable of moving between filaments and are aided by the absence of large trophic competitors and predators -prey release effect-. Only small predators, such as hydra, are capable of surviving in the new environment, as they are favored by the increase in chironomids, a source of food, and by the reduction in both their own predators and other midge predators -mesopredator release-. This change in the top-down control affects the diatom community, since chironomids may feed on large diatoms, increasing the proportion of small diatoms in the substrate. The survival of small and fast-growing pioneer diatoms is also favored by the mesh of filaments, which offers them a new habitat for colonization. Simultaneously, D. geminata causes a significant reduction in the number of diatoms with similar ecological requirements (those attached to the substrate). Overall, D. geminata creates a community dominated by small organisms that is clearly different from the existing communities in the same stream where there is an absence of massive growths. PMID:29494699

Using the heterogeneity distribution in Earth's mantle to study structure and flow

NASA Astrophysics Data System (ADS)

Rost, S.; Frost, D. A.; Bentham, H. L.

2016-12-01

The Earth's interior contains heterogeneities on many scale-lengths ranging from continent sized structures such as Large-Low Shear Velocity Provinces (LLSVPs) to grain-sized anomalies resolved using geochemistry. Sources of heterogeneity in Earth's mantle are for example the recycling of crustal material through the subduction process as well as partial melting and compositional variations. The subduction and recycling of oceanic crust throughout Earth's history leads to strong heterogeneities in the mantle that can be detected using seismology and geochemistry. Current models of mantle convection show that the subducted crustal material can be long-lived and is transported passively throughout the mantle by convective flows. Settling and entrainment is dependent on the density structure of the heterogeneity. Imaging heterogeneities throughout the mantle therefore allows imaging mantle flow especially in areas of inhibited flow due to e.g. viscosity changes or changes in composition or dynamics. The short-period seismic wavefield is dominated by scattered seismic energy partly originating from scattering at small-scale heterogeneities in Earth's mantle. Using specific raypath configurations we are able to sample different depths throughout Earth's mantle for the existence and properties of heterogeneities. These scattering probes show distinct variations in energy content with frequency indicating dominant heterogeneity length-scales in the mantle. We detect changes in heterogeneity structure both in lateral and radial directions. The radial heterogeneity structure requires changes in mantle structure at depths of 1000 km and 1800 to 2000 km that could indicate a change in viscosity structure in the mid mantle partly changing the flow of subducted crustal material into the deep mantle. Lateral changes in heterogeneity structure close to the core mantle boundary indicate lateral transport inhibited by the compositional anomalies of the LLSVPs.

The effects of burial diagenesis on multiscale porosity in the St. Peter Sandstone: An imaging, small-angle, and ultra-small-angle neutron scattering analysis

DOE PAGES

Anovitz, Lawrence M.; Freiburg, Jared T.; Wasbrough, Matthew; ...

2017-11-06

To examine the effects of burial diagenesis on heirarchical pore structures in sandstone and compare those with the effects of overgrowth formation, we obtained samples of St. Peter Sandstone from drill cores obtained in the Illinois and Michigan Basins. The multiscale pore structure of rocks in sedimentary reservoirs and the mineralogy associated with those pores are critical factors for estimating reservoir properties, including fluid mass in place, permeability, and capillary pressures, as well as geochemical interactions between the rock and the fluid. The combination of small- and ultra-small-angle neutron scattering with backscattered electron or X ray-computed tomographic imaging, or both,more » provided a means by which pore structures were quantified at scales ranging from aproximately 1 nm to 1 cm—seven orders of magnitude. Larger scale (>10 µm) porosity showed the expected logarithmic decrease in porosity with depth, although there was significant variation in each sample group. However, small- and ultra-small-angle neutron scattering data showed that the proportion of small-scale porosity increased with depth. Porosity distributions were not continuous, but consisted of a series of log normal-like distributions at several distinct scales within these rocks. Fractal dimensions at larger scales decreased (surfaces smoothed) with increasing depth, and those at smaller scales increased (surfaces roughened) and pores become more isolated (higher lacunarity). Furthermore, data suggest that changes in pore-size distributions are controlled by both physical (compaction) and chemical effects (precipitation, cementation, dissolution).« less

The effects of burial diagenesis on multiscale porosity in the St. Peter Sandstone: An imaging, small-angle, and ultra-small-angle neutron scattering analysis

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

Anovitz, Lawrence M.; Freiburg, Jared T.; Wasbrough, Matthew

To examine the effects of burial diagenesis on heirarchical pore structures in sandstone and compare those with the effects of overgrowth formation, we obtained samples of St. Peter Sandstone from drill cores obtained in the Illinois and Michigan Basins. The multiscale pore structure of rocks in sedimentary reservoirs and the mineralogy associated with those pores are critical factors for estimating reservoir properties, including fluid mass in place, permeability, and capillary pressures, as well as geochemical interactions between the rock and the fluid. The combination of small- and ultra-small-angle neutron scattering with backscattered electron or X ray-computed tomographic imaging, or both,more » provided a means by which pore structures were quantified at scales ranging from aproximately 1 nm to 1 cm—seven orders of magnitude. Larger scale (>10 µm) porosity showed the expected logarithmic decrease in porosity with depth, although there was significant variation in each sample group. However, small- and ultra-small-angle neutron scattering data showed that the proportion of small-scale porosity increased with depth. Porosity distributions were not continuous, but consisted of a series of log normal-like distributions at several distinct scales within these rocks. Fractal dimensions at larger scales decreased (surfaces smoothed) with increasing depth, and those at smaller scales increased (surfaces roughened) and pores become more isolated (higher lacunarity). Furthermore, data suggest that changes in pore-size distributions are controlled by both physical (compaction) and chemical effects (precipitation, cementation, dissolution).« less

Functional and phylogenetic structure of island bird communities.

PubMed

Si, Xingfeng; Cadotte, Marc W; Zeng, Di; Baselga, Andrés; Zhao, Yuhao; Li, Jiaqi; Wu, Yiru; Wang, Siyu; Ding, Ping

2017-05-01

Biodiversity change in anthropogenically transformed habitats is often nonrandom, yet the nature and importance of the different mechanisms shaping community structure are unclear. Here, we extend the classic Theory of Island Biogeography (TIB) to account for nonrandom processes by incorporating species traits and phylogenetic relationships into a study of faunal relaxation following habitat loss and fragmentation. Two possible mechanisms can create nonrandom community patterns on fragment islands. First, small and isolated islands might consist of similar or closely related species because they are environmentally homogeneous or select for certain shared traits, such as dispersal ability. Alternatively, communities on small islands might contain more dissimilar or distantly related species than on large islands because limited space and resource availability result in greater competitive exclusion among species with high niche overlap. Breeding birds were surveyed on 36 islands and two mainland sites annually from 2010 to 2014 in the Thousand Island Lake region, China. We assessed community structure of breeding birds on these subtropical land-bridge islands by integrating species' trait and evolutionary distances. We additionally analysed habitat heterogeneity and variance in size ratios to distinguish biotic and abiotic processes of community assembly. Results showed that functional-phylogenetic diversity increased with island area, and decreased with isolation. Bird communities on the mainland were more diverse and generally less clustered than island bird communities and not different than randomly assembled communities. Bird communities on islands tend to be functionally similar and phylogenetically clustered, especially on small and isolated islands. The nonrandom decline in species diversity and change in bird community structure with island area and isolation, along with the relatively homogeneous habitats on small islands, support the environmental filtering hypothesis. Our study demonstrates the importance of integrating multiple forms of diversity for understanding the effects of habitat loss and fragmentation, and further reveals that TIB could be extended to community measures by moving beyond assumptions of species equivalency in colonisation rates and extinction susceptibilities. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

A Method for Selecting Structure-switching Aptamers Applied to a Colorimetric Gold Nanoparticle Assay

PubMed Central

Martin, Jennifer A.; Smith, Joshua E.; Warren, Mercedes; Chávez, Jorge L.; Hagen, Joshua A.; Kelley-Loughnane, Nancy

2015-01-01

Small molecules provide rich targets for biosensing applications due to their physiological implications as biomarkers of various aspects of human health and performance. Nucleic acid aptamers have been increasingly applied as recognition elements on biosensor platforms, but selecting aptamers toward small molecule targets requires special design considerations. This work describes modification and critical steps of a method designed to select structure-switching aptamers to small molecule targets. Binding sequences from a DNA library hybridized to complementary DNA capture probes on magnetic beads are separated from nonbinders via a target-induced change in conformation. This method is advantageous because sequences binding the support matrix (beads) will not be further amplified, and it does not require immobilization of the target molecule. However, the melting temperature of the capture probe and library is kept at or slightly above RT, such that sequences that dehybridize based on thermodynamics will also be present in the supernatant solution. This effectively limits the partitioning efficiency (ability to separate target binding sequences from nonbinders), and therefore many selection rounds will be required to remove background sequences. The reported method differs from previous structure-switching aptamer selections due to implementation of negative selection steps, simplified enrichment monitoring, and extension of the length of the capture probe following selection enrichment to provide enhanced stringency. The selected structure-switching aptamers are advantageous in a gold nanoparticle assay platform that reports the presence of a target molecule by the conformational change of the aptamer. The gold nanoparticle assay was applied because it provides a simple, rapid colorimetric readout that is beneficial in a clinical or deployed environment. Design and optimization considerations are presented for the assay as proof-of-principle work in buffer to provide a foundation for further extension of the work toward small molecule biosensing in physiological fluids. PMID:25870978

Electrostatic effects in the collapse transition of phospholiquid monolayer

NASA Astrophysics Data System (ADS)

Nguyen, Toan T.; Gopal, Ajaykumar; Lee, Ka Yee C.; Witten, Thomas A.

2004-03-01

We study the collapse transition of fluidic phospholipid surfactant monolayers under lateral compression. DMPC, DPPC or POPG surfactants and their binary mixtures are used. Various collapsed structures (circular discs, cylinderical tubes and pearls-on-a-string) were observed during the transition. We show that electrostatics plays an important role in the formation of these structures. By changing the composition of charged surfactant (POGP) or the screening condition of the solution, one can change the dominant collapsed structure from discs to tubes to pearls in the order of increasing the strength of electrostatic interactions, in accordance with theoretical estimates. We also study a complimentary electrostatic effect due charge relaxation in the transitions between these structures. It is shown that free energy gained from relaxations of charge molecule is small and can be neglected when considering electrostatics of these systems.

Magneto-elastic coupling across the first-order transition in the distorted kagome lattice antiferromagnet Dy3Ru4Al12

PubMed Central

Henriques, M.S.; Gorbunov, D.I.; Kriegner, D.; Vališka, M.; Andreev, A.V.; Matěj, Z.

2018-01-01

Structural changes through the first-order paramagnetic-antiferromagnetic phase transition of Dy3Ru4Al12 at 7 K have been studied by means of X-ray diffraction and thermal expansion measurements. The compound crystallizes in a hexagonal crystal structure of Gd3Ru4Al12 type (P63/mmc space group), and no structural phase transition has been found in the temperature interval between 2.5 and 300 K. Nevertheless, due to the spin-lattice coupling the crystal volume undergoes a small orthorhombic distortion of the order of 2×10-5 as the compound enters the antiferromagnetic state. We propose that the first-order phase transition is not driven by the structural changes but rather by the exchange interactions present in the system. PMID:29445250

Physical Processes Contributing To Small-scale Vertical Movements During Changing Inplane Stresses In Rift Basins and At Passive Continental Margins

NASA Astrophysics Data System (ADS)

Paulsen, G. E.; Nielsen, S. B.; Hansen, D. L.

The vertical movements during a regional stress reversal in a rifted basin or on a passive continental margin are examined using a numerical 2D thermo-mechanical finite element model with a visco-elastic-plastic rheology. Three different physical mechanisms are recognized in small-scale vertical movements at small inplane force variations: elastic dilatation, elastic flexure, and permanent deformation. Their rela- tive importance depend on the applied force, the duration of the force, and the thermal structure of the lithosphere. Elastic material dilatation occurs whenever the stress state changes. A reversal from extension to compression therefore immediately leads to elastic dilatation, and re- sults in an overall subsidence of the entire profile. Simultaneously with dilatation the lithosphere reacts with flexure. The significance of the flexural component strongly depends on the thermal structure of the lithosphere. The polarity and amplitude of the flexure depends on the initial (before compression) loading of the lithosphere. Gener- ally, the flexural effects lead to subsidence of the overdeep in the landward part of the basin and a small amount of uplift at the basin flanks. The amplitudes of the flexural response are small and comparable with the amplitudes of the elastic dilatation. With continuing compression permanent deformation and lithospheric thickening becomes increasingly important. Ultimately, the thickened part of the lithosphere stands out as an inverted zone. The amount of permanent deformation is directly connected with the size and duration of the applied force, but even a relatively small force leads to inversion tectonics in the landward part of the basin. The conclusions are: 1) small stress induced vertical movements in rift basins and at passive continental margins are the result of a complex interaction of at least three different processes, 2) the total sediment loaded amplitudes resulting from these pro- cesses are small (2-300 m) for inplane forces up to 1.5·1012 N/m.

Mitochondrial-nuclear interactions and accelerated compensatory evolution: evidence from the primate cytochrome C oxidase complex.

PubMed

Osada, Naoki; Akashi, Hiroshi

2012-01-01

Accelerated rates of mitochondrial protein evolution have been proposed to reflect Darwinian coadaptation for efficient energy production for mammalian flight and brain activity. However, several features of mammalian mtDNA (absence of recombination, small effective population size, and high mutation rate) promote genome degradation through the accumulation of weakly deleterious mutations. Here, we present evidence for "compensatory" adaptive substitutions in nuclear DNA- (nDNA) encoded mitochondrial proteins to prevent fitness decline in primate mitochondrial protein complexes. We show that high mutation rate and small effective population size, key features of primate mitochondrial genomes, can accelerate compensatory adaptive evolution in nDNA-encoded genes. We combine phylogenetic information and the 3D structure of the cytochrome c oxidase (COX) complex to test for accelerated compensatory changes among interacting sites. Physical interactions among mtDNA- and nDNA-encoded components are critical in COX evolution; amino acids in close physical proximity in the 3D structure show a strong tendency for correlated evolution among lineages. Only nuclear-encoded components of COX show evidence for positive selection and adaptive nDNA-encoded changes tend to follow mtDNA-encoded amino acid changes at nearby sites in the 3D structure. This bias in the temporal order of substitutions supports compensatory weak selection as a major factor in accelerated primate COX evolution.

Difference structures from time-resolved small-angle and wide-angle x-ray scattering

NASA Astrophysics Data System (ADS)

Nepal, Prakash; Saldin, D. K.

2018-05-01

Time-resolved small-angle x-ray scattering/wide-angle x-ray scattering (SAXS/WAXS) is capable of recovering difference structures directly from difference SAXS/WAXS curves. It does so by means of the theory described here because the structural changes in pump-probe detection in a typical time-resolved experiment are generally small enough to be confined to a single residue or group in close proximity which is identified by a method akin to the difference Fourier method of time-resolved crystallography. If it is assumed, as is usual with time-resolved structures, that the moved atoms lie within the residue, the 100-fold reduction in the search space (assuming a typical protein has about 100 residues) allows the exaction of the structure by a simulated annealing algorithm with a huge reduction in computing time and leads to a greater resolution by varying the positions of atoms only within that residue. This reduction in the number of potential moved atoms allows us to identify the actual motions of the individual atoms. In the case of a crystal, time-resolved calculations are normally performed using the difference Fourier method, which is, of course, not directly applicable to SAXS/WAXS. The method developed in this paper may be thought of as a substitute for that method which allows SAXS/WAXS (and hence disordered molecules) to also be used for time-resolved structural work.

Imaging Live Drosophila Brain with Two-Photon Fluorescence Microscopy

NASA Astrophysics Data System (ADS)

Ahmed, Syeed Ehsan

Two-photon fluorescence microscopy is an imaging technique which delivers distinct benefits for in vivo cellular and molecular imaging. Cyclic adenosine monophosphate (cAMP), a second messenger molecule, is responsible for triggering many physiological changes in neural system. However, the mechanism by which this molecule regulates responses in neuron cells is not yet clearly understood. When cAMP binds to a target protein, it changes the structure of that protein. Therefore, studying this molecular structure change with fluorescence resonance energy transfer (FRET) imaging can shed light on the cAMP functioning mechanism. FRET is a non-radiative dipole-dipole coupling which is sensitive to small distance change in nanometer scale. In this study we have investigated the effect of dopamine in cAMP dynamics in vivo. In our study two-photon fluorescence microscope was used for imaging mushroom bodies inside live Drosophila melanogaster brain and we developed a method for studying the change in cyclic AMP level.

Smart Textiles for Strengthening of Structures

NASA Astrophysics Data System (ADS)

Górski, Marcin; Krzywoń, Rafał; Dawczyński, Szymon; Szojda, Leszek; Salvado, Rita; Lopes, Catarina; Araujo, Pedro; Velez, Fernando Jose; Castro-Gomes, Joao

2016-11-01

This paper presents results of mechanical tests on a prototype of an innovative structural strengthening in form of self-monitoring fabric. Smart textile employs carbon fibers conductivity for measuring strains while monitoring changes of electric resistance under increasing load. A general solution was tested in a series of calibrating tests on strengthening of small size concrete slabs. Promising results of simple specimen, has encouraged the research team to perform the next tests using mastered carbon fibre reinforced fabric. Main tests were performed on natural scale RC beam. Smart textile proved its efficiency in both: strengthening and monitoring of strains during load increase. New strengthening proposal was given 10% increase of loading capacity and the readings of strain changes were similar to those obtained in classical methods. In order to calibrate the prototype and to define range limits of solution usability, textile sensor was tested in areas of large deformations (timber beam) and aswell as very small strains (bridge bearing block). In both cases, the prototype demonstrated excellent performance in the range of importance for structural engineering. This paper also presents an example of use of the smart strengthening in situ, in a real life conditions.

Small Angle Neutron Scattering (SANS) Studies on the Structural Evolution of Pyromellitamide Self-assembled Gels

DOE PAGES

Scott, Jamieson; Tong, Katie; William, Hamilton; ...

2014-10-31

The kinetics of aggregation of two pyromellitamide gelators; tetrabutyl- (C4) and tetrahexylpyromellitamide (C6), in deuterated cyclohexane has been investigated by small angle neutron scattering (SANS) for up to six days. The purpose of this study was to improve our understanding of how self-assembled gels are formed. Short-term (< 3 hour) time scales revealed multiple phases with the data for the tetrabutylpyromellitamide C4 indicating one dimensional stacking and aggregation corresponding to a multi-fiber braided cluster arrangement that is about 35 Å in diameter. The corresponding tetrahexylpyromellitamide C6 data suggests that the C6 also forms one-dimensional stacks but that these aggregate tomore » a thicker multi-fiber braided cluster that have a diameter of 61.8 Å. Over a longer period of time, the radius, persistence length and contour length all continue to increase in 6 days after cooling. This data suggests that structural changes in self-assembled gels occur over a period exceeding several days and that fairly subtle changes in the structure (e.g. tail-length) can influence the packing of molecules in self-assembled gels on the single-to-few fiber bundle stage.« less

Small angle neutron scattering (SANS) studies on the structural evolution of pyromellitamide self-assembled gels.

PubMed

Jamieson, Scott A; Tong, Katie W K; Hamilton, William A; He, Lilin; James, Michael; Thordarson, Pall

2014-11-25

The kinetics of aggregation of two pyromellitamide gelators, tetrabutyl- (C4) and tetrahexyl-pyromellitamide (C6), in deuterated cyclohexane has been investigated by small angle neutron scattering (SANS) for up to 6 days. The purpose of this study was to improve our understanding of how self-assembled gels are formed. Short-term (< 3 h) time scales revealed multiple phases with the data for the tetrabutylpyromellitamide C4, indicating one-dimensional stacking and aggregation corresponding to a multifiber braided cluster arrangement that is about 35 Å in diameter. The corresponding tetrahexylpyromellitamide C6 data suggest that the C6 also forms one-dimensional stacks but that these aggregate to a thicker multifiber braided cluster that has a diameter of about 62 Å. Over a longer period of time, the radius, persistence length, and contour length all continue to increase in 6 days after cooling. These data suggest that structural changes in self-assembled gels occur over a period exceeding several days and that fairly subtle changes in the structure (e.g., tail-length) can influence the packing of molecules in self-assembled gels on the single-to-few fiber bundle stage.

Small Angle Neutron Scattering (SANS) Studies on the Structural Evolution of Pyromellitamide Self-assembled Gels

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

Scott, Jamieson; Tong, Katie; William, Hamilton

The kinetics of aggregation of two pyromellitamide gelators; tetrabutyl- (C4) and tetrahexylpyromellitamide (C6), in deuterated cyclohexane has been investigated by small angle neutron scattering (SANS) for up to six days. The purpose of this study was to improve our understanding of how self-assembled gels are formed. Short-term (< 3 hour) time scales revealed multiple phases with the data for the tetrabutylpyromellitamide C4 indicating one dimensional stacking and aggregation corresponding to a multi-fiber braided cluster arrangement that is about 35 Å in diameter. The corresponding tetrahexylpyromellitamide C6 data suggests that the C6 also forms one-dimensional stacks but that these aggregate tomore » a thicker multi-fiber braided cluster that have a diameter of 61.8 Å. Over a longer period of time, the radius, persistence length and contour length all continue to increase in 6 days after cooling. This data suggests that structural changes in self-assembled gels occur over a period exceeding several days and that fairly subtle changes in the structure (e.g. tail-length) can influence the packing of molecules in self-assembled gels on the single-to-few fiber bundle stage.« less

Is urbanisation scrambling the genetic structure of human populations? A case study

PubMed Central

Ashrafian-Bonab, Maziar; Handley, Lori Lawson; Balloux, François

2007-01-01

Recent population expansion and increased migration linked to urbanisation are assumed to be eroding the genetic structure of human populations. We investigated change in population structure over three generations by analysing both demographic and mitochondrial DNA (mtDNA) data from a random sample of 2351 men from twenty-two Iranian populations. Potential changes in genetic diversity (θ) and genetic distance (FST) over the last three generations were analysed by assigning mtDNA sequences to populations based on the individual's place of birth or that of their mother or grandmother. Despite the fact that several areas included cities of over one million inhabitants, we detected no change in genetic diversity, and only a small decrease in population structure, except in the capital city (Tehran), which was characterised by massive immigration, increased θ and a large decrease in FST over time. Our results suggest that recent erosion of human population structure might not be as important as previously thought, except in some large conurbations, and this clearly has important implications for future sampling strategies. PMID:17106453

Effects of prey size and foraging mode on the ontogenetic change in feeding niche ofColostethus stepheni (Anura: Dendrobatidae).

PubMed

Lima, Albertina P; Moreira, Gloria

1993-03-01

The feeding niche ofColostethus stepheni changes during ontogeny. Small individuals eat small arthropods, principally mites and collembolans, and larger frogs eat bigger prey of other types. The shift in prey types is not a passive effect of selection for bigger prey. There is a strong relationship between electivity for prey types and frog size, independent of electivity for prey size. Four indices of general activity during foraging (number of movements, velocity, total area utilized and time spent moving), which are associated with electivity for prey types in adult frogs and lizards, did not predict the ontogenetic change in the diet ofC. stepheni. Apparently, the behavioral changes that cause the ontogenetic change inC. stepheni are more subtle than shifts in general activity during foraging. Studies of niche partitioning in communities of anurans that do not take into consideration ontogenetic changes in diet and seasonal changes in the size structures of populations present a partial and possibly erroneous picture of the potential interactions among species.

Development of a very small telescope for a milli-arcsec space astrometry

NASA Astrophysics Data System (ADS)

Suganuma, M.; Kobayashi, Y.; Gouda, N.; Yano, T.; Yamada, Y.; Takato, N.; Yamauchi, M.

2008-07-01

We are preparing a reflecting telescope for Nano-JASMINE, a very small satellite for global space astrometry of milli-arcsecond accuracy. The telescope has a 5-cm diameter primary mirror and a beam-combiner in front of it. It occupies only about 12x12x17cm and is entirely made out of aluminum alloy. The telescope and its surrounding structures are carefully designed for thermal stability of the optics, especially to control changes in the relative angle of the beam-combiner.

Gravitational considerations with animal rhythms

NASA Technical Reports Server (NTRS)

Wunder, C. C.

1974-01-01

As established in the laboratory and largely confirmed by others, simulated high-g environments influence growth and development of animals as small as or smaller than baby turtles, sometimes accelerating and sometimes decelerating these processes. High-g environments result in many functional changes or adjustments in feeding, metabolism, circulation, fluid balances, and structures for support, and influence life expectancy. An assembly of equipment suitable for measuring oxygen consumption of small mammals as influenced by chronic centrifugation and/or by day-night rhythms is discussed.

Succession and regulation factors of small eukaryote community composition in a lacustrine ecosystem (Lake Pavin).

PubMed

Lepère, Cécile; Boucher, Delphine; Jardillier, Ludwig; Domaizon, Isabelle; Debroas, Didier

2006-04-01

The structure and dynamics of small eukaryotes (cells with a diameter less than 5 microm) were studied over two consecutive years in an oligomesotrophic lake (Lake Pavin in France). Water samples were collected at 5 and 30 m below the surface; when the lake was stratified, these depths corresponded to the epilimnion and hypolimnion. Changes in small-eukaryote structure were analyzed using terminal restriction fragment length polymorphism (T-RFLP) and cloning and sequencing of the 18S rRNA genes. Terminal restriction fragments from clones were used to reveal the dominant taxa in T-RFLP profiles of the environmental samples. Spumella-like cells (Chrysophyceae) did not dominate the small eukaryote community identified by molecular techniques in lacustrine ecosystems. Small eukaryotes appeared to be dominated by heterotrophic cells, particularly Cercozoa, which represented nearly half of the identified phylotypes, followed by the Fungi-LKM11 group (25%), choanoflagellates (10.3%) and Chrysophyceae (8.9%). Bicosoecida, Cryptophyta, and ciliates represented less than 9% of the community studied. No seasonal reproducibility in temporal evolution of the small-eukaryote community was observed from 1 year to the next. The T-RFLP patterns were related to bottom-up (resources) and top-down (grazing) variables using canonical correspondence analysis. The results showed a strong top-down regulation of small eukaryotes by zooplankton, more exactly, by cladocerans at 5 m and copepods at 30 m. Among bottom-up factors, temperature had a significant effect at both depths. The concentrations of nitrogenous nutrients and total phosphorus also had an effect on small-eukaryote dynamics at 5 m, whereas bacterial abundance and dissolved oxygen played a more important structuring role in the deeper zone.

Connecting synthetic chemistry decisions to cell and genome biology using small-molecule phenotypic profiling

PubMed Central

Wagner, Bridget K.; Clemons, Paul A.

2009-01-01

Discovering small-molecule modulators for thousands of gene products requires multiple stages of biological testing, specificity evaluation, and chemical optimization. Many cellular profiling methods, including cellular sensitivity, gene-expression, and cellular imaging, have emerged as methods to assess the functional consequences of biological perturbations. Cellular profiling methods applied to small-molecule science provide opportunities to use complex phenotypic information to prioritize and optimize small-molecule structures simultaneously against multiple biological endpoints. As throughput increases and cost decreases for such technologies, we see an emerging paradigm of using more information earlier in probe- and drug-discovery efforts. Moreover, increasing access to public datasets makes possible the construction of “virtual” profiles of small-molecule performance, even when multiplexed measurements were not performed or when multidimensional profiling was not the original intent. We review some key conceptual advances in small-molecule phenotypic profiling, emphasizing connections to other information, such as protein-binding measurements, genetic perturbations, and cell states. We argue that to maximally leverage these measurements in probe and drug discovery requires a fundamental connection to synthetic chemistry, allowing the consequences of synthetic decisions to be described in terms of changes in small-molecule profiles. Mining such data in the context of chemical structure and synthesis strategies can inform decisions about chemistry procurement and library development, leading to optimal small-molecule screening collections. PMID:19825513

Structural Changes in 2D BiSe Bilayers as n Increases in (BiSe)1+δ(NbSe2)n (n = 1-4) Heterostructures.

PubMed

Mitchson, Gavin; Hadland, Erik; Göhler, Fabian; Wanke, Martina; Esters, Marco; Ditto, Jeffrey; Bigwood, Erik; Ta, Kim; Hennig, Richard G; Seyller, Thomas; Johnson, David C

2016-09-28

(BiSe) 1+δ (NbSe 2 ) n heterostructures with n = 1-4 were synthesized using modulated elemental reactants. The BiSe bilayer structure changed from a rectangular basal plane with n = 1 to a square basal plane for n = 2-4. The BiSe in-plane structure was also influenced by small changes in the structure of the precursor, without significantly changing the out-of-plane diffraction pattern or value of the misfit parameter, δ. Density functional theory calculations on isolated BiSe bilayers showed that its lattice is very flexible, which may explain its readiness to adjust shape and size depending on the environment. Correlated with the changes in the BiSe basal plane structure, analysis of scanning transmission electron microscope images revealed that the occurrence of antiphase boundaries, found throughout the n = 1 compound, is dramatically reduced for the n = 2-4 compounds. X-ray photoelectron spectroscopy measurements showed that the Bi 5d 3/2 , 5d 5/2 doublet peaks narrowed toward higher binding energies as n increased from 1 to 2, also consistent with a reduction in the number of antiphase boundaries. Temperature-dependent electrical resistivity and Hall coefficient measurements of nominally stoichiometric samples in conjunction with structural refinements and XPS data suggest a constant amount of interlayer charge transfer independent of n. Constant interlayer charge transfer is surprising given the changes in the BiSe in-plane structure. The structural flexibility of the BiSe layer may be useful in designing multiple constituent heterostructures as an interlayer between structurally dissimilar constituents.

The interplay of plant and animal disease in a changing landscape: the role of sudden aspen decline in moderating Sin Nombre virus prevalence in natural deer mouse populations.

PubMed

Lehmer, Erin M; Korb, Julie; Bombaci, Sara; McLean, Nellie; Ghachu, Joni; Hart, Lacey; Kelly, Ashley; Jara-Molinar, Edlin; O'Brien, Colleen; Wright, Kimberly

2012-06-01

We examined how climate-mediated forest dieback regulates zoonotic disease prevalence using the relationship between sudden aspen decline (SAD) and Sin Nombre virus (SNV) as a model system. We compared understory plant community structure, small mammal community composition, and SNV prevalence on 12 study sites within aspen forests experiencing levels of SAD ranging from <10.0% crown fade to >95.0% crown fade. Our results show that sites with the highest levels of SAD had reduced canopy cover, stand density, and basal area, and these differences were reflected by reductions in understory vegetation cover. Conversely, sites with the highest levels of SAD had greater understory standing biomass, suggesting that vegetation on these sites was highly clustered. Changes in forest and understory vegetation structure likely resulted in shifts in small mammal community composition across the SAD gradient, as we found reduced species diversity and higher densities of deer mice, the primary host for SNV, on sites with the highest levels of SAD. Sites with the highest levels of SAD also had significantly greater SNV prevalence compared to sites with lower levels of SAD, which is likely a result of their abundance of deer mice. Collectively, results of our research provide strong evidence to show SAD has considerable impacts on vegetation community structure, small mammal density and biodiversity and the prevalence of SNV.

Changes in Brain Structural Networks and Cognitive Functions in Testicular Cancer Patients Receiving Cisplatin-Based Chemotherapy.

PubMed

Amidi, Ali; Hosseini, S M Hadi; Leemans, Alexander; Kesler, Shelli R; Agerbæk, Mads; Wu, Lisa M; Zachariae, Robert

2017-12-01

Cisplatin-based chemotherapy may have neurotoxic effects within the central nervous system. The aims of this study were 1) to longitudinally investigate the impact of cisplatin-based chemotherapy on whole-brain networks in testicular cancer patients undergoing treatment and 2) to explore whether possible changes are related to decline in cognitive functioning. Sixty-four newly orchiectomized TC patients underwent structural magnetic resonance imaging (T1-weighted and diffusion-weighted imaging) and cognitive testing at baseline prior to further treatment and again at a six-month follow-up. At follow-up, 22 participants had received cisplatin-based chemotherapy (CT) while 42 were in active surveillance (S). Brain structural networks were constructed for each participant, and network properties were investigated using graph theory and longitudinally compared across groups. Cognitive functioning was evaluated using standardized neuropsychological tests. All statistical tests were two-sided. Compared with the S group, the CT group demonstrated altered global and local brain network properties from baseline to follow-up as evidenced by decreases in important brain network properties such as small-worldness (P = .04), network clustering (P = .04), and local efficiency (P = .02). In the CT group, poorer overall cognitive performance was associated with decreased small-worldness (r = -0.46, P = .04) and local efficiency (r = -0.51, P = .02), and verbal fluency was associated with decreased local efficiency (r = -0.55, P = .008). Brain structural networks may be disrupted following treatment with cisplatin-based chemotherapy. Impaired brain networks may underlie poorer performance over time on both specific and nonspecific cognitive functions in patients undergoing chemotherapy. To the best of our knowledge, this is the first study to longitudinally investigate changes in structural brain networks in a cancer population, providing novel insights regarding the neurobiological mechanisms of cancer-related cognitive impairment.

A continuous record of intereruption velocity change at Mount St. Helens from coda wave interferometry

USGS Publications Warehouse

Hotovec-Ellis, Alicia J.; Gomberg, Joan S.; Vidale, John; Creager, Ken C.

2014-01-01

In September 2004, Mount St. Helens volcano erupted after nearly 18 years of quiescence. However, it is unclear from the limited geophysical observations when or if the magma chamber replenished following the 1980–1986 eruptions in the years before the 2004–2008 extrusive eruption. We use coda wave interferometry with repeating earthquakes to measure small changes in the velocity structure of Mount St. Helens volcano that might indicate magmatic intrusion. By combining observations of relative velocity changes from many closely located earthquake sources, we solve for a continuous function of velocity changes with time. We find that seasonal effects dominate the relative velocity changes. Seismicity rates and repeating earthquake occurrence also vary seasonally; therefore, velocity changes and seismicity are likely modulated by snow loading, fluid saturation, and/or changes in groundwater level. We estimate hydrologic effects impart stress changes on the order of tens of kilopascals within the upper 4 km, resulting in annual velocity variations of 0.5 to 1%. The largest nonseasonal change is a decrease in velocity at the time of the deep Mw = 6.8 Nisqually earthquake. We find no systematic velocity changes during the most likely times of intrusions, consistent with a lack of observable surface deformation. We conclude that if replenishing intrusions occurred, they did not alter seismic velocities where this technique is sensitive due to either their small size or the finite compressibility of the magma chamber. We interpret the observed velocity changes and shallow seasonal seismicity as a response to small stress changes in a shallow, pressurized system.

Small is beautiful: features of the smallest insects and limits to miniaturization.

PubMed

Polilov, Alexey A

2015-01-07

Miniaturization leads to considerable reorganization of structures in insects, affecting almost all organs and tissues. In the smallest insects, comparable in size to unicellular organisms, modifications arise not only at the level of organs, but also at the cellular level. Miniaturization is accompanied by allometric changes in many organ systems. The consequences of miniaturization displayed by different insect taxa include both common and unique changes. Because the smallest insects are among the smallest metazoans and have the most complex organization among organisms of the same size, their peculiar structural features and the factors that limit their miniaturization are of considerable theoretical interest to general biology.

Multiscale spatial and small-scale temporal variation in the composition of Riverine fish communities.

PubMed

Growns, Ivor; Astles, Karen; Gehrke, Peter

2006-03-01

We studied the multiscale (sites, river reaches and rivers) and short-term temporal (monthly) variability in a freshwater fish assemblage. We found that small-scale spatial variation and short-term temporal variability significantly influenced fish community structure in the Macquarie and Namoi Rivers. However, larger scale spatial differences between rivers were the largest source of variation in the data. The interaction between temporal change and spatial variation in fish community structure, whilst statistically significant, was smaller than the variation between rivers. This suggests that although the fish communities within each river changed between sampling occasions, the underlying differences between rivers were maintained. In contrast, the strongest interaction between temporal and spatial effects occurred at the smallest spatial scale, at the level of individual sites. This means whilst the composition of the fish assemblage at a given site may fluctuate, the magnitude of these changes is unlikely to affect larger scale differences between reaches within rivers or between rivers. These results suggest that sampling at any time within a single season will be sufficient to show spatial differences that occur over large spatial scales, such as comparisons between rivers or between biogeographical regions.

Novel Methods at Molecular Level for Neurotoxicity Testing in 21st Century-Utility of Structure-Activity Relationship

EPA Science Inventory

Current neurotoxicity and developmental neurotoxicity testing methods for hazard identification rely on in vivo neurobehavior, neurophysiological, and gross pathology of the nervous system. These measures may not be sensitive enough to detect small changes caused by realistic ex...

Schoolyard Microclimate

ERIC Educational Resources Information Center

Fontaine, Joseph J.; Stier, Samuel C.; Maggio, Melissa L.; Decker, Karie L.

2007-01-01

Students can gain an appreciation for the structure and function of local environments by studying the potential impacts of small changes in local microclimate on plant distribution. The concept of microclimate is easy for students to comprehend, simple to measure, exists in all schoolyards, and has important and tangible ecological implications.…

3-D imaging of temporal and spatial development of Puccinia striiformis haustoria in wheat.

PubMed

Sørensen, Chris K; Justesen, Annemarie F; Hovmøller, Mogens S

2012-01-01

Differentiation of haustoria on primary infection hyphae of the fungal pathogen Puccinia striiformis was studied in wheat seedlings with two-photon microscopy in combination with a classical staining technique. Our results showed a significant increase in the average haustorium size 22, 44, 68, 92 and 116 h after inoculation (hai). After 116 hai no significant change was observed until 336 hai. Haustorium morphology also changed significantly during the time of infection. Initially small spherical haustoria were seen, but as they grew the haustoria gradually became apically branched. At 22 hai all observed haustoria were spherical, but at 44 hai most haustoria had an irregular structure, and at 92 hai all observed haustoria appeared branched. Along with the changes of the haustorial body the haustorial neck changed from narrow and slender to having an expanded appearance with a rough and invaginated structure. The structural changes were similar in two susceptible wheat varieties, 514W and Cartago, although the mean haustorium size was larger in 514W than in Cartago at all intervals.

Structural changes of deposited casein micelles induced by membrane filtration.

PubMed

Gebhardt, R; Steinhauer, T; Meyer, P; Sterr, J; Perlich, J; Kulozik, U

2012-01-01

Casein micelles undergo shape changes when subjected to frontal filtration forces. Grazing incidence small angle X-ray scattering (GISAXS) and atomic force microscopy (AFM) allow a quantification of such structural changes on filtration cakes deposited on smooth silicon micro-sieves. A trans-membrane pressure of deltap = 400 mbar across the micro-sieve leads to an immediate film formation after deposition of casein solution. We observe significant changes in the GISAXS pattern depending on how many layers are stacked on top of each other. Compared to a deposit formed by one layer, GISAXS on a deposit formed by three layers of casein micelles leads to less scattering in the vertical and more scattering in the horizontal direction. Simulations show that the experimental results can be interpreted by a structural transformation from an originally spherical micelle shape to an ellipsoidal-deformed shape. The results are supported by AFM measurements showing a reduced lateral size of casein micelles deposited on top of a membrane pore. The observed shape changes could be due to filtration forces acting on densely packed deposits confining the micelles into ellipsoidal shapes.

Structural and Functional Analysis of BipA, a Regulator of Virulence in Enteropathogenic Escherichia coli

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

Fan, Haitian; Hahm, Joseph; Diggs, Stephen

The translational GTPase BipA regulates the expression of virulence and pathogenicity factors in several eubacteria. BipA-dependent expression of virulence factors occurs under starvation conditions, such as encountered during infection of a host. Under these conditions, BipA associates with the small ribosomal subunit. BipA also has a second function to promote the efficiency of late steps in biogenesis of large ribosomal subunits at low temperatures, presumably while bound to the ribosome. During starvation, the cellular concentration of stress alarmone guanosine-3', 5'-bis pyrophosphate (ppGpp) is increased. This increase allows ppGpp to bind to BipA and switch its binding specificity from ribosomes tomore » small ribosomal subunits. A conformational change of BipA upon ppGpp binding could explain the ppGpp regulation of the binding specificity of BipA. Here, we present the structures of the full-length BipA from Escherichia coli in apo, GDP-, and ppGpp-bound forms. The crystal structure and small-angle x-ray scattering data of the protein with bound nucleotides, together with a thermodynamic analysis of the binding of GDP and of ppGpp to BipA, indicate that the ppGpp-bound form of BipA adopts the structure of the GDP form. This suggests furthermore, that the switch in binding preference only occurs when both ppGpp and the small ribosomal subunit are present. Finally, this molecular mechanism would allow BipA to interact with both the ribosome and the small ribosomal subunit during stress response.« less

Structural and Functional Analysis of BipA, a Regulator of Virulence in Enteropathogenic Escherichia coli

DOE PAGES

Fan, Haitian; Hahm, Joseph; Diggs, Stephen; ...

2015-07-10

The translational GTPase BipA regulates the expression of virulence and pathogenicity factors in several eubacteria. BipA-dependent expression of virulence factors occurs under starvation conditions, such as encountered during infection of a host. Under these conditions, BipA associates with the small ribosomal subunit. BipA also has a second function to promote the efficiency of late steps in biogenesis of large ribosomal subunits at low temperatures, presumably while bound to the ribosome. During starvation, the cellular concentration of stress alarmone guanosine-3', 5'-bis pyrophosphate (ppGpp) is increased. This increase allows ppGpp to bind to BipA and switch its binding specificity from ribosomes tomore » small ribosomal subunits. A conformational change of BipA upon ppGpp binding could explain the ppGpp regulation of the binding specificity of BipA. Here, we present the structures of the full-length BipA from Escherichia coli in apo, GDP-, and ppGpp-bound forms. The crystal structure and small-angle x-ray scattering data of the protein with bound nucleotides, together with a thermodynamic analysis of the binding of GDP and of ppGpp to BipA, indicate that the ppGpp-bound form of BipA adopts the structure of the GDP form. This suggests furthermore, that the switch in binding preference only occurs when both ppGpp and the small ribosomal subunit are present. Finally, this molecular mechanism would allow BipA to interact with both the ribosome and the small ribosomal subunit during stress response.« less

Redox-dependent structure change and hyperfine nuclear magnetic resonance shifts in cytochrome c

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

Feng, Yiquing; Roder, H.; Englander, S.W.

1990-04-10

Proton nuclear magnetic resonance assignments for reduced and oxidized equine cytochrome c show that many individual protons exhibit different chemical shifts in the two protein forms, reflecting diamagnetic shift effects due to structure change, and in addition contact and pseudocontact shifts that occur only in the paramagnetic oxidized form. To evaluate the chemical shift differences for structure change, the authors removed the pseudocontact shift contribution by a calculation based on knowledge of the electron spin g tensor. The g-tensor calculation, when repeated using only 12 available C{sub {alpha}}H proton resonances for cytochrom c from tuna, proved to be remarkably stable.more » The derived g tensor was then used together with spatial coordinates for the oxidized form to calculate the pseudocontact shift contribution to proton resonances at 400 identifiable sites throughout the protein, so that the redox-dependent chemical shift discrepancy, could be evaluated. Large residual changes in chemical shift define the Fermi contact shifts, where are found as expected to be limited to the immediate covalent structure of the heme and its ligands and to be asymmetrically distributed over the heme. The chemical shift discrepancies observed appear in the main to reflect structure-dependent diamagnetic shifts rather than hyperfine effects due to displacements in the pseudocontact shift field. Although 51 protons in 29 different residues exhibit significant chemical shift changes, the general impressions one of small structural adjustments to redox-dependent strain rather than sizeable structural displacements or rearrangements.« less

Structure of the Jovian Magnetodisk Current Sheet: Initial Galileo Observations

NASA Technical Reports Server (NTRS)

Russell, C. T.; Huddleston, D. E.; Khurana, K. K.; Kivelson, M. G.

2001-01-01

The ten-degree tilt of the Jovian magnetic dipole causes the magnetic equator to move back and forth across Jupiter's rotational equator and tile Galileo orbit that lies therein. Beyond about 24 Jovian radii, the equatorial current sheet thins and tile magnetic structure changes from quasi-dipolar into magnetodisk-like with two regions of nearly radial but antiparallel magnetic field separated by a strong current layer. The magnetic field at the center of the current sheet is very weak in this region. Herein we examine tile current sheet at radial distances from 24 55 Jovian radii. We find that the magnetic structure very much resembles tile structure seen at planetary magnetopause and tail current sheet crossings. Tile magnetic field variation is mainly linear with little rotation of the field direction, At times there is almost no small-scale structure present and the normal component of the magnetic field is almost constant through the current sheet. At other times there are strong small-scale structures present in both the southward and northward directions. This small-scale structure appears to grow with radial distance and may provide the seeds for tile explosive reconnection observed at even greater radial distances oil tile nightside. Beyond about 40 Jovian radii, the thin current sheet also appears to be almost constantly in oscillatory motion with periods of about 10 min. The amplitude of these oscillations also appears to grow with radial distance. The source of these fluctuations may be dynamical events in tile more distant magnetodisk.

[Changes in the peritoneum of the small intestine and diaphragm in experimental portal hypertension].

PubMed

Khoroshaev, V A; Vorozheĭkin, V M; Baĭbekov, I M

1991-04-01

Diaphragm and small intestine peritoneum morphology was studied in experimental portal hypertension in rats with the help of luminescent, transmission and scanning electron microscopy techniques. Structural organizations of these peritoneum portions and performance function were different: fluid transudation realized through the small intestine peritoneum and resorption occurred via diaphragm peritoneum. Morphological signs allowed to judge about the increasing of fluid transudation in abdominal cavity and diaphragmatic resorption in early period of portal hypertension. Morphological alterations appeared in peritoneum resorption sites (pumping diaphragmatic hatchs) according to progress of portal hypertension that indicated decompensation process of peritoneal fluid absorption and led to ascites.

Effect of borax concentration on the structure of Poly(Vinyl Alcohol) gels

NASA Astrophysics Data System (ADS)

Lawrence, Mathias B.; Desa, J. A. E.; Aswal, V. K.

2012-06-01

Poly(Vinyl Alcohol) hydrogels cross-linked with varying concentrations of borax have been studied using Small-Angle Neutron Scattering and X-Ray Diffraction. The intensity of scattering increases with borax concentration from 1 mg/ml up to 2 mg/ml and falls thereafter for 4 mg/ml, increasing again for a concentration of 10 mg/ml. The mesoscopic structural changes that cause these trends in the SANS data are in keeping with the variations in the X-ray diffraction patterns pertaining to structures within the PVA chains.

Structure and evolutionary history of the solar system

NASA Technical Reports Server (NTRS)

Alfven, H.; Arrhenius, G.

1975-01-01

General principles and observational facts concerning the solar system are examined, taking into account the orbits of planets and satellites, the small bodies, the resonance structure, spin and tides, and postaccretional changes in the solar system. A description is given of the accretion of celestial bodies and the plasma phase is considered. Aspects of chemical differentiation and the matrix of the groups of bodies are also discussed, giving attention to chemical compositions in the solar system, meteorites and their precursor states, mass distribution and the critical velocity, and the structure of the groups.

Photonic Crystals: Tunable Design of Structural Colors Produced by Pseudo-1D Photonic Crystals of Graphene Oxide (Small 25/2016).

PubMed

Tong, Liping; Qi, Wei; Wang, Mengfan; Huang, Renliang; Su, Rongxin; He, Zhimin

2016-07-01

The production of structural colors based on graphene oxide (GO) pseudo-one-dimensional photonic crystals (p1D-PhCs) in the visible spectrum is reported on page 3433 by W. Qi and co-workers. The structural colors could be tuned by simply changing either the volume or concentration of the aqueous GO dispersion. Moreover, GO p1D-PhCs exhibit visible and rapid responsiveness to humidity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nanosecond retinal structure changes in K-590 during the room-temperature bacteriorhodopsin photocycle: picosecond time-resolved coherent anti-stokes Raman spectroscopy.

PubMed

Weidlich, O; Ujj, L; Jäger, F; Atkinson, G H

1997-05-01

Time-resolved vibrational spectra are used to elucidate the structural changes in the retinal chromophore within the K-590 intermediate that precedes the formation of the L-550 intermediate in the room-temperature (RT) bacteriorhodopsin (BR) photocycle. Measured by picosecond time-resolved coherent anti-Stokes Raman scattering (PTR/CARS), these vibrational data are recorded within the 750 cm-1 to 1720 cm-1 spectral region and with time delays of 50-260 ns after the RT/BR photocycle is optically initiated by pulsed (< 3 ps, 1.75 nJ) excitation. Although K-590 remains structurally unchanged throughout the 50-ps to 1-ns time interval, distinct structural changes do appear over the 1-ns to 260-ns period. Specifically, comparisons of the 50-ps PTR/CARS spectra with those recorded with time delays of 1 ns to 260 ns reveal 1) three types of changes in the hydrogen-out-of-plane (HOOP) region: the appearance of a strong, new feature at 984 cm-1; intensity decreases for the bands at 957 cm-1, 952 cm-1, and 939 cm-1; and small changes intensity and/or frequency of bands at 855 cm-1 and 805 cm-1; and 2) two types of changes in the C-C stretching region: the intensity increase in the band at 1196 cm-1 and small intensity changes and/or frequency shifts for bands at 1300 cm-1 and 1362 cm-1. No changes are observed in the C = C stretching region, and no bands assignable to the Schiff base stretching mode (C = NH+) mode are found in any of the PTR/CARS spectra assignable to K-590. These PTR/CARS data are used, together with vibrational mode assignments derived from previous work, to characterize the retinal structural changes in K-590 as it evolves from its 3.5-ps formation (ps/K-590) through the nanosecond time regime (ns/K-590) that precedes the formation of L-550. The PTR/CARS data suggest that changes in the torsional modes near the C14-C15 = N bonds are directly associated with the appearance of ns/K-590, and perhaps with the KL intermediate proposed in earlier studies. These vibrational data can be primarily interpreted in terms of the degree of twisting of the C14-C15 retinal bond. Such twisting may be accompanied by changes in the adjacent protein. Other smaller, but nonetheless clear, spectral changes indicate that alterations along the retinal polyene chain also occur. The changes in the retinal structure are preliminary to the deprotonation of the Schiff base nitrogen during the formation of M-412. The time constant for the ps/ns K-590 transformation is estimated from the amplitude change of four vibrational bands in the HOOP region to be 40-70 ns.

Structure of a nanobody-stabilized active state of the β(2) adrenoceptor.

PubMed

Rasmussen, Søren G F; Choi, Hee-Jung; Fung, Juan Jose; Pardon, Els; Casarosa, Paola; Chae, Pil Seok; Devree, Brian T; Rosenbaum, Daniel M; Thian, Foon Sun; Kobilka, Tong Sun; Schnapp, Andreas; Konetzki, Ingo; Sunahara, Roger K; Gellman, Samuel H; Pautsch, Alexander; Steyaert, Jan; Weis, William I; Kobilka, Brian K

2011-01-13

G protein coupled receptors (GPCRs) exhibit a spectrum of functional behaviours in response to natural and synthetic ligands. Recent crystal structures provide insights into inactive states of several GPCRs. Efforts to obtain an agonist-bound active-state GPCR structure have proven difficult due to the inherent instability of this state in the absence of a G protein. We generated a camelid antibody fragment (nanobody) to the human β(2) adrenergic receptor (β(2)AR) that exhibits G protein-like behaviour, and obtained an agonist-bound, active-state crystal structure of the receptor-nanobody complex. Comparison with the inactive β(2)AR structure reveals subtle changes in the binding pocket; however, these small changes are associated with an 11 Å outward movement of the cytoplasmic end of transmembrane segment 6, and rearrangements of transmembrane segments 5 and 7 that are remarkably similar to those observed in opsin, an active form of rhodopsin. This structure provides insights into the process of agonist binding and activation.

Conservation of protein structure over four billion years.

PubMed

Ingles-Prieto, Alvaro; Ibarra-Molero, Beatriz; Delgado-Delgado, Asuncion; Perez-Jimenez, Raul; Fernandez, Julio M; Gaucher, Eric A; Sanchez-Ruiz, Jose M; Gavira, Jose A

2013-09-03

Little is known about the evolution of protein structures and the degree of protein structure conservation over planetary time scales. Here, we report the X-ray crystal structures of seven laboratory resurrections of Precambrian thioredoxins dating up to approximately four billion years ago. Despite considerable sequence differences compared with extant enzymes, the ancestral proteins display the canonical thioredoxin fold, whereas only small structural changes have occurred over four billion years. This remarkable degree of structure conservation since a time near the last common ancestor of life supports a punctuated-equilibrium model of structure evolution in which the generation of new folds occurs over comparatively short periods and is followed by long periods of structural stasis. Copyright © 2013 Elsevier Ltd. All rights reserved.

Probing metamaterials with structured light

DOE PAGES

Xu, Yun; Sun, Jingbo; Walasik, Wiktor; ...

2016-11-03

Photonic metamaterials and metasurfaces are nanostructured optical materials engineered to enable properties that have not been found in nature. Optical characterization of these structures is a challenging task. We report a reliable technique that is particularly useful for characterization of phase properties introduced by small and spatially inhomogeneous samples of metamaterials and metasurfaces. The proposed structured light, or vortex based interferometric method is used to directly visualize phase changes introduced by subwavelength-thick nanostructures. In order to demonstrate the efficiency of the proposed technique, we designed and fabricated several metasurface samples consisting of metal nano-antennas introducing different phase shifts and experimentallymore » measured phase shifts of the transmitted light. The experimental results are in good agreement with numerical simulations and with the designed properties of the antenna arrays. Finally, due to the presence of the singularity in the vortex beam, one of the potential applications of the proposed approach based on structured light is step-by-step probing of small fractions of the micro-scale samples or images.« less

Structural basis of ligand interaction with atypical chemokine receptor 3

NASA Astrophysics Data System (ADS)

Gustavsson, Martin; Wang, Liwen; van Gils, Noortje; Stephens, Bryan S.; Zhang, Penglie; Schall, Thomas J.; Yang, Sichun; Abagyan, Ruben; Chance, Mark R.; Kufareva, Irina; Handel, Tracy M.

2017-01-01

Chemokines drive cell migration through their interactions with seven-transmembrane (7TM) chemokine receptors on cell surfaces. The atypical chemokine receptor 3 (ACKR3) binds chemokines CXCL11 and CXCL12 and signals exclusively through β-arrestin-mediated pathways, without activating canonical G-protein signalling. This receptor is upregulated in numerous cancers making it a potential drug target. Here we collected over 100 distinct structural probes from radiolytic footprinting, disulfide trapping, and mutagenesis to map the structures of ACKR3:CXCL12 and ACKR3:small-molecule complexes, including dynamic regions that proved unresolvable by X-ray crystallography in homologous receptors. The data are integrated with molecular modelling to produce complete and cohesive experimentally driven models that confirm and expand on the existing knowledge of the architecture of receptor:chemokine and receptor:small-molecule complexes. Additionally, we detected and characterized ligand-induced conformational changes in the transmembrane and intracellular regions of ACKR3 that elucidate fundamental structural elements of agonism in this atypical receptor.

Structural basis of ligand interaction with atypical chemokine receptor 3

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

Gustavsson, Martin; Wang, Liwen; van Gils, Noortje

2017-01-18

Chemokines drive cell migration through their interactions with seven-transmembrane (7TM) chemokine receptors on cell surfaces. The atypical chemokine receptor 3 (ACKR3) binds chemokines CXCL11 and CXCL12 and signals exclusively through β-arrestin-mediated pathways, without activating canonical G-protein signalling. This receptor is upregulated in numerous cancers making it a potential drug target. Here we collected over 100 distinct structural probes from radiolytic footprinting, disulfide trapping, and mutagenesis to map the structures of ACKR3:CXCL12 and ACKR3:small-molecule complexes, including dynamic regions that proved unresolvable by X-ray crystallography in homologous receptors. The data are integrated with molecular modelling to produce complete and cohesive experimentally drivenmore » models that confirm and expand on the existing knowledge of the architecture of receptor:chemokine and receptor:small-molecule complexes. Additionally, we detected and characterized ligand-induced conformational changes in the transmembrane and intracellular regions of ACKR3 that elucidate fundamental structural elements of agonism in this atypical receptor.« less

Imaging radiation pneumonitis in a rat model of a radiological terrorism incident

NASA Astrophysics Data System (ADS)

Molthen, Robert; Wu, QingPing; Krenz, Gary; Medhora, Meetha; Jacobs, Elizabeth; Moulder, John E.

2009-02-01

We have developed a rat model of single, sub-lethal thoracic irradiation. Our irradiation protocol is considered representative of exposures near the detonation site of a dirty bomb or small nuclear device. The model is being used to investigate techniques for identifying, triaging and treating possible victims. In addition to physiological markers of right ventricular hypertrophy, pulmonary vascular resistance, and arterial distensibility, we present two methods for quantifying microvascular density. We used methods including microfocal X-ray imaging to investigate changes in lung structure/function resulting from radiation exposure. Radiation pneumonitis is a complication in subjects receiving thoracic irradiation. A radiographic hallmark of acute radiation pneumonitis is a diffuse infiltrate corresponding to the radiation treatment field. We describe two methods for quantifying small artery dropout that occurs in the model at the same time-period. Rats were examined 3-days, 2-weeks, 1-month (m), 2-m, 5-m, and 12-m post-irradiation and compared with aged-matched controls. Right ventricular hypertrophy and increases in pulmonary vascular resistance were present during the pneumonitis phase. Vascular injury was dependent on dose and post-irradiation duration. Rats irradiated with 5 Gy had few detectable changes, whereas 10 Gy resulted in a significant decrease in both microvascular density and arterial distensibility around 2- m, the decrease in each lessening, but extending through 12-m. In conclusion, rats irradiated with a 10 Gy dose had changes in vascular structure concurrent with the onset of radiation pneumonitis that were detectable with our imaging techniques and these structural changes persist after resolution of the pneumonitis.

A crystallographic perspective on sharing data and knowledge

NASA Astrophysics Data System (ADS)

Bruno, Ian J.; Groom, Colin R.

2014-10-01

The crystallographic community is in many ways an exemplar of the benefits and practices of sharing data. Since the inception of the technique, virtually every published crystal structure has been made available to others. This has been achieved through the establishment of several specialist data centres, including the Cambridge Crystallographic Data Centre, which produces the Cambridge Structural Database. Containing curated structures of small organic molecules, some containing a metal, the database has been produced for almost 50 years. This has required the development of complex informatics tools and an environment allowing expert human curation. As importantly, a financial model has evolved which has, to date, ensured the sustainability of the resource. However, the opportunities afforded by technological changes and changing attitudes to sharing data make it an opportune moment to review current practices.

Characterizing fuels in treated areas.

Treesearch

Roger D. Ottmar; Clinton S. Wright

2002-01-01

Small-log utilization or thinning operations followed by a fuel treatment such as prescribed fire can be used to change the composition and structure of fuelbeds, thereby mitigating deleterious fire effects and reducing the potential for catastrophic wildfires in some forested landscapes. We are developing a national system, Fuel Characteristic Classification (FCC),...

Novel Methods at Molecular Level for Developmental Neurotoxicity Testing in 21st Century-Utility of Structure-Activity Relationship

EPA Science Inventory

Current neurotoxicity and developmental neurotoxicity testing methods for hazard identification rely on in vivo neurobehavior, neurophysiological, and gross pathology of the nervous system. These measures may not be sensitive enough to detect small changes caused by realistic ex...

School Principals--Entrepreneurial Professionals.

ERIC Educational Resources Information Center

Jenkins, Hugh

This paper examines the ways in which a small number of school principals in England and Wales are making changes in their management structures and processes to cope with an increasingly turbulent environment. Using evidence on a comparative basis from organizations outside education, this paper looks at the way in which a number of principals…

Vocational Education: Options and Directions. Working Paper 18.

ERIC Educational Resources Information Center

Stokes, Helen; Holdsworth, Roger

This paper presents practical options for school development in relation to vocational education ranging from small and specific steps to larger whole school change. Chapter 1 describes the context. Chapter 2 highlights three interlocked imperatives to attain this objective: a comprehensive and well-structured educational program that deals…

Wood for structural and architectural purposes

Treesearch

C.W. Boyd; P. Koch; H.B. MeKean; C.R. Morschauser; S.B. Preston; F.F. Wangaard

1976-01-01

In recent years major emphasis has been placed on nonrenewable resources in relation to potential national problems that may arise from possible changes in materials supply or utilization. Renewable resources, however, have received disproportionately small attention in spite of their current importance as industrial raw materials and their potential for the future. In...

An Integrative Concept for Technical, Personnel and Organizational Development for Professional Skill Enhancement.

ERIC Educational Resources Information Center

Kroll, Martin

1997-01-01

Training needed to implement technological and organizational change in small- and medium-sized enterprises is restrained by lack of systematic organization, negative effects of organizational and personnel structures, and different interpretations of managerial tasks. Article suggests that managers should strive to create the necessary…

Strong genetic structure corresponds to small-scale geographic breaks in the Australian alpine grasshopper Kosciuscola tristis.

PubMed

Slatyer, Rachel A; Nash, Michael A; Miller, Adam D; Endo, Yoshinori; Umbers, Kate D L; Hoffmann, Ary A

2014-10-02

Mountain landscapes are topographically complex, creating discontinuous 'islands' of alpine and sub-alpine habitat with a dynamic history. Changing climatic conditions drive their expansion and contraction, leaving signatures on the genetic structure of their flora and fauna. Australia's high country covers a small, highly fragmented area. Although the area is thought to have experienced periods of relative continuity during Pleistocene glacial periods, small-scale studies suggest deep lineage divergence across low-elevation gaps. Using both DNA sequence data and microsatellite markers, we tested the hypothesis that genetic partitioning reflects observable geographic structuring across Australia's mainland high country, in the widespread alpine grasshopper Kosciuscola tristis (Sjösted). We found broadly congruent patterns of regional structure between the DNA sequence and microsatellite datasets, corresponding to strong divergence among isolated mountain regions. Small and isolated mountains in the south of the range were particularly distinct, with well-supported divergence corresponding to climate cycles during the late Pliocene and Pleistocene. We found mixed support, however, for divergence among other mountain regions. Interestingly, within areas of largely contiguous alpine and sub-alpine habitat around Mt Kosciuszko, microsatellite data suggested significant population structure, accompanied by a strong signature of isolation-by-distance. Consistent patterns of strong lineage divergence among different molecular datasets indicate genetic breaks between populations inhabiting geographically distinct mountain regions. Three primary phylogeographic groups were evident in the highly fragmented Victorian high country, while within-region structure detected with microsatellites may reflect more recent population isolation. Despite the small area of Australia's alpine and sub-alpine habitats, their low topographic relief and lack of extensive glaciation, divergence among populations was on the same scale as that detected in much more extensive Northern hemisphere mountain systems. The processes driving divergence in the Australian mountains might therefore differ from their Northern hemisphere counterparts.

Propagation properties of cylindrical sinc Gaussian beam

NASA Astrophysics Data System (ADS)

Eyyuboğlu, Halil T.; Bayraktar, Mert

2016-09-01

We investigate the propagation properties of cylindrical sinc Gaussian beam in turbulent atmosphere. Since an analytic solution is hardly derivable, the study is carried out with the aid of random phase screens. Evolutions of the beam intensity profile, beam size and kurtosis parameter are analysed. It is found that on the source plane, cylindrical sinc Gaussian beam has a dark hollow appearance, where the side lobes also start to emerge with increase in width parameter and Gaussian source size. During propagation, beams with small width and Gaussian source size exhibit off-axis behaviour, losing the dark hollow shape, accumulating the intensity asymmetrically on one side, whereas those with large width and Gaussian source size retain dark hollow appearance even at long propagation distances. It is seen that the beams with large widths expand more in beam size than the ones with small widths. The structure constant values chosen do not seem to alter this situation. The kurtosis parameters of the beams having small widths are seen to be larger than the ones with the small widths. Again the choice of the structure constant does not change this trend.

Small-world human brain networks: Perspectives and challenges.

PubMed

Liao, Xuhong; Vasilakos, Athanasios V; He, Yong

2017-06-01

Modelling the human brain as a complex network has provided a powerful mathematical framework to characterize the structural and functional architectures of the brain. In the past decade, the combination of non-invasive neuroimaging techniques and graph theoretical approaches enable us to map human structural and functional connectivity patterns (i.e., connectome) at the macroscopic level. One of the most influential findings is that human brain networks exhibit prominent small-world organization. Such a network architecture in the human brain facilitates efficient information segregation and integration at low wiring and energy costs, which presumably results from natural selection under the pressure of a cost-efficiency balance. Moreover, the small-world organization undergoes continuous changes during normal development and ageing and exhibits dramatic alterations in neurological and psychiatric disorders. In this review, we survey recent advances regarding the small-world architecture in human brain networks and highlight the potential implications and applications in multidisciplinary fields, including cognitive neuroscience, medicine and engineering. Finally, we highlight several challenging issues and areas for future research in this rapidly growing field. Copyright © 2017 Elsevier Ltd. All rights reserved.

The structure of some cytoplasmic components of plant cells in relation to the biochemical properties of isolated particles.

PubMed

HODGE, A J; MARTIN, E M; MORTON, R K

1957-01-25

1. Electron micrographs of thin sections of material fixed with buffered osmium tetroxide have been used for comparison of the fine structure of isolated cytoplasmic particles from silver beet petioles and roots of germinating wheat with that of the cytoplasm of the intact cells. 2. Mitochondria of wheat roots have an external double membrane and poorly oriented internal double membranes. As compared with the structures seen in situ, the isolated mitochondria showed evidence of some disorganisation of the fine internal structure, probably due to osmotic effects. The possible influence of such changes on the enzymic properties of the isolated mitochondria is discussed. 3. The isolated plant microsomes are mainly spherical vesicular structures consisting of (a) an outer membrane enclosing (b) either an homogeneous slightly dense material (wheat root microsomes) or some granular dense material (silver beet microsomes) and (c) small dense particles, mostly associated with the vesicle membranes. 4. The cytoplasm of the wheat root cells does not contain any structures similar to the isolated microsomes but has a very dense reticular network, consisting of membranes with associated small dense particles, here called the endoplasmic reticulum. The observations indicate that the isolated microsomes arise mainly by rupture and transformation of the membranes of this structure. The effects of such extensive changes in the lipoprotein membranes on the enzymic activities of the endoplasmic reticulum, as studied in isolated microsomes, is discussed. 5. Meristematic wheat root cells contain structures which consist of smooth membranes with associated vacuoles and are similar to the Golgi zones of animal cells. The membranes of these zones probably contribute to the microsomal fraction under the conditions of preparation used for the enzymic and chemical studies previously reported.

THE STRUCTURE OF SOME CYTOPLASMIC COMPONENTS OF PLANT CELLS IN RELATION TO THE BIOCHEMICAL PROPERTIES OF ISOLATED PARTICLES

PubMed Central

Hodge, A. J.; Martin, E. M.; Morton, R. K.

1957-01-01

1. Electron micrographs of thin sections of material fixed with buffered osmium tetroxide have been used for comparison of the fine structure of isolated cytoplasmic particles from silver beet petioles and roots of germinating wheat with that of the cytoplasm of the intact cells. 2. Mitochondria of wheat roots have an external double membrane and poorly oriented internal double membranes. As compared with the structures seen in situ, the isolated mitochondria showed evidence of some disorganisation of the fine internal structure, probably due to osmotic effects. The possible influence of such changes on the enzymic properties of the isolated mitochondria is discussed. 3. The isolated plant microsomes are mainly spherical vesicular structures consisting of (a) an outer membrane enclosing (b) either an homogeneous slightly dense material (wheat root microsomes) or some granular dense material (silver beet microsomes) and (c) small dense particles, mostly associated with the vesicle membranes. 4. The cytoplasm of the wheat root cells does not contain any structures similar to the isolated microsomes but has a very dense reticular network, consisting of membranes with associated small dense particles, here called the endoplasmic reticulum. The observations indicate that the isolated microsomes arise mainly by rupture and transformation of the membranes of this structure. The effects of such extensive changes in the lipoprotein membranes on the enzymic activities of the endoplasmic reticulum, as studied in isolated microsomes, is discussed. 5. Meristematic wheat root cells contain structures which consist of smooth membranes with associated vacuoles and are similar to the Golgi zones of animal cells. The membranes of these zones probably contribute to the microsomal fraction under the conditions of preparation used for the enzymic and chemical studies previously reported. PMID:13416311

Structure and Properties of Sn2Se3, a mixed valent tin selenium compound

NASA Astrophysics Data System (ADS)

Xing, Guangzong; Li, Yuwei; Fan, Xiaofeng; Zhang, Lijun; Singh, David

Sn2Se3 is a possibly expected phase based on analogy with Sn2S3 but it has never been reported. It is of interest due to reported phase change memories using this composition using transitions between an amorphous phase and an unknown crystalline phase. We identify the crystal structure Sn2Se3 and report its properties at ambient pressure based on the ab initio evolutionary methodology for crystal structure prediction implemented in the Calypso code. We find a structure based on Sn-Se ribbons with clear Sn(II)and Sn(IV)sites similar to the structure of Sn2S3. Compared with the known phase SnSe (Pnma) +SnSe2 (P-3m1), the energy is only 2.3meV/atom higher. The electronic structure of this phase shows mixed valent tins Sn2+ and Sn4+ in this compound. A small band gap of 0.023 eV is obtained from the band structure consistent with the small resistance reported by Kyung-Min Chung et al. Work at the University of Missouri is supported by DOE through the S3TEC EFRC.

Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography

NASA Astrophysics Data System (ADS)

Stagno, J. R.; Liu, Y.; Bhandari, Y. R.; Conrad, C. E.; Panja, S.; Swain, M.; Fan, L.; Nelson, G.; Li, C.; Wendel, D. R.; White, T. A.; Coe, J. D.; Wiedorn, M. O.; Knoska, J.; Oberthuer, D.; Tuckey, R. A.; Yu, P.; Dyba, M.; Tarasov, S. G.; Weierstall, U.; Grant, T. D.; Schwieters, C. D.; Zhang, J.; Ferré-D'Amaré, A. R.; Fromme, P.; Draper, D. E.; Liang, M.; Hunter, M. S.; Boutet, S.; Tan, K.; Zuo, X.; Ji, X.; Barty, A.; Zatsepin, N. A.; Chapman, H. N.; Spence, J. C. H.; Woodson, S. A.; Wang, Y.-X.

2017-01-01

Riboswitches are structural RNA elements that are generally located in the 5‧ untranslated region of messenger RNA. During regulation of gene expression, ligand binding to the aptamer domain of a riboswitch triggers a signal to the downstream expression platform. A complete understanding of the structural basis of this mechanism requires the ability to study structural changes over time. Here we use femtosecond X-ray free electron laser (XFEL) pulses to obtain structural measurements from crystals so small that diffusion of a ligand can be timed to initiate a reaction before diffraction. We demonstrate this approach by determining four structures of the adenine riboswitch aptamer domain during the course of a reaction, involving two unbound apo structures, one ligand-bound intermediate, and the final ligand-bound conformation. These structures support a reaction mechanism model with at least four states and illustrate the structural basis of signal transmission. The three-way junction and the P1 switch helix of the two apo conformers are notably different from those in the ligand-bound conformation. Our time-resolved crystallographic measurements with a 10-second delay captured the structure of an intermediate with changes in the binding pocket that accommodate the ligand. With at least a 10-minute delay, the RNA molecules were fully converted to the ligand-bound state, in which the substantial conformational changes resulted in conversion of the space group. Such notable changes in crystallo highlight the important opportunities that micro- and nanocrystals may offer in these and similar time-resolved diffraction studies. Together, these results demonstrate the potential of ‘mix-and-inject’ time-resolved serial crystallography to study biochemically important interactions between biomacromolecules and ligands, including those that involve large conformational changes.

Recent research on inherent molecular structure, physiochemical properties, and bio-functions of food and feed-type Avena sativa oats and processing-induced changes revealed with molecular microspectroscopic techniques

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

Prates, Luciana Louzada; Yu, Peiqiang

Avena sativa oat is a cereal widely used as human food and livestock feed. However, the low metabolized energy and the rapid rumen degradations of protein and starch have limited the use of A. sativa oat grains. To overcome this disadvantage, new A. sativa oat varieties have been developed. Additionally, heat-related processing has been performed to decrease the degradation rate and improve the absorption of amino acids in the small intestine. The nutritive value is reflected by both chemical composition and inherent molecular structure conformation. However, the traditional wet chemical analysis is not able to detect the inherent molecular structuresmore » within an intact tissue. The advanced synchrotron-radiation and globar-based molecular microspectroscopy have been developed recently and applied to study internal molecular structures and the processing induced structure changes in A. sativa oats and reveal how molecular structure changes in relation to nutrient availability. This review aimed to obtain the recent information regarding physiochemical properties, molecular structures, metabolic characteristics of protein, and the heat-induced changes in new A. sativa oat varieties. The use of the advanced vibrational molecular spectroscopy was emphasized, synchrotron- and globar-based (micro)spectroscopy, to reveal the inherent structure of A. sativa oats at cellular and molecular levels and to reveal the heat processing effect on the degradation characteristics and the protein molecular structure in A. sativa oats. The relationship between nutrient availability and protein molecular inherent structure was also presented. Information described in this review gives better insight in the physiochemical properties, molecular structure, and the heat-induced changes in A. sativa oat detected with advanced molecular spectroscopic techniques in combinination with conventional nutrition study techniques.« less

Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography

PubMed Central

Stagno, J. R.; Liu, Y.; Bhandari, Y. R.; Conrad, C. E.; Panja, S.; Swain, M.; Fan, L.; Nelson, G.; Li, C.; Wendel, D. R.; White, T. A.; Coe, J. D.; Wiedorn, M. O.; Knoska, J.; Oberthuer, D.; Tuckey, R. A.; Yu, P.; Dyba, M.; Tarasov, S. G.; Weierstall, U.; Grant, T. D.; Schwieters, C. D.; Zhang, J.; Ferré-D’Amaré, A. R.; Fromme, P.; Draper, D. E.; Liang, M.; Hunter, M. S.; Boutet, S.; Tan, K.; Zuo, X.; Ji, X.; Barty, A.; Zatsepin, N. A.; Chapman, H. N.; Spence, J. C. H.; Woodson, S. A.; Wang, Y.-X.

2017-01-01

Riboswitches are structural RNA elements that are generally located in the 5′ untranslated region of messenger RNA. During regulation of gene expression, ligand binding to the aptamer domain of a riboswitch triggers a signal to the downstream expression platform1–3. A complete understanding of the structural basis of this mechanism requires the ability to study structural changes over time4. Here we use femtosecond X-ray free electron laser (XFEL) pulses5,6 to obtain structural measurements from crystals so small that diffusion of a ligand can be timed to initiate a reaction before diffraction. We demonstrate this approach by determining four structures of the adenine riboswitch aptamer domain during the course of a reaction, involving two unbound apo structures, one ligand-bound intermediate, and the final ligand-bound conformation. These structures support a reaction mechanism model with at least four states and illustrate the structural basis of signal transmission. The three-way junction and the P1 switch helix of the two apo conformers are notably different from those in the ligand-bound conformation. Our time-resolved crystallographic measurements with a 10-second delay captured the structure of an intermediate with changes in the binding pocket that accommodate the ligand. With at least a 10-minute delay, the RNA molecules were fully converted to the ligand-bound state, in which the substantial conformational changes resulted in conversion of the space group. Such notable changes in crystallo highlight the important opportunities that micro- and nanocrystals may offer in these and similar time-resolved diffraction studies. Together, these results demonstrate the potential of ‘mix-and-inject’ time-resolved serial crystallography to study biochemically important interactions between biomacromolecules and ligands, including those that involve large conformational changes. PMID:27841871

Timescales for exploratory tactical behaviour in football small-sided games.

PubMed

Ric, Angel; Hristovski, Robert; Gonçalves, Bruno; Torres, Lorena; Sampaio, Jaime; Torrents, Carlota

2016-09-01

The aim of this study was to identify the dynamics of tactical behaviour emerging on different timescales in football small-sided games and to quantify short- and long-term exploratory behaviour according to the number of opponents. Two teams of four professional male footballers played small-sided games against two different teams with a variable number of opponents (3, 5 and 7). Data were collected using a combination of systematic observation and a non-differential global positioning system (15 Hz). The temporal diversity and structural flexibility of the players were determined by calculating the dynamic overlap order parameter q, entropy and trapping strength. Analysis of the exploratory dynamics revealed two different timescales, forming a different metastable landscape of action for each constraint. Fast dynamics lasted on average a few seconds and consisted of changes in tactical patterns. The long timescale corresponded to the shared tasks of offence and defence lasting tens of seconds. The players' tactical diversity decreased with an increasing number of opponents, especially in defence. Manipulating numerical imbalance is likely to promote changes in the diversity, unpredictability and flexibility of tactical solutions. The fact that the temporally nested structure of constraints shaped the emergence of tactical behaviour provides a new rationale for practice task design. The manipulation of numerical imbalance on the timescale of a few tens of seconds, on which the exploratory behaviour of players saturates, may help coaches to optimise the exploratory efficiency of the small-sided games.

Consequences of extreme life history traits on population persistence: do short-lived gobies face demographic bottlenecks?

NASA Astrophysics Data System (ADS)

Lefèvre, Carine D.; Nash, Kirsty L.; González-Cabello, Alonso; Bellwood, David R.

2016-06-01

The majority of coral reef goby species are short-lived, with some highly abundant species living less than 100 d. To understand the role and consequences of this extreme life history in shaping coral reef fish populations, we quantitatively documented the structure of small reef fish populations over a 26-month period (>14 short-lived fish generations) at an inshore reef on the Great Barrier Reef, Australia. Most species with life spans >1 yr, such as pomacentrids, exhibited a peak in recruitment during the austral summer, driving seasonal changes in the small fish community composition. In contrast, there were no clear changes in goby community composition, despite the abundance of short-lived, high turnover species. Species of Eviota, the most abundant gobiid genus observed, showed remarkably similar demographic profiles year-round, with consistent densities of adults as well as recently recruited juveniles. Our results demonstrate ongoing recruitment of these small cryptic fishes, which appears to compensate for an exceptionally short life span on the reef. Our results suggest that gobiid populations are able to overcome demographic limitations, and by maintaining reproduction, larval survival and recruitment throughout the year, they may avoid population bottlenecks. These findings also underline the potential trophodynamic importance of these small species; because of this constant turnover, Eviota species and other short-lived fishes may be particularly valuable contributors to the flow of energy on coral reefs, underpinning the year-round trophic structure.

Change of hydrogen bonding structure in ionic liquid mixtures by anion type

NASA Astrophysics Data System (ADS)

Cha, Seoncheol; Kim, Doseok

2018-05-01

Ionic liquid mixtures have gained attention as a way of tuning material properties continuously with composition changes. For some mixture systems, physicochemical properties such as excess molar volume have been found to be significantly different from the value expected by linear interpolation, but the origin of this deviation is not well understood yet. The microstructure of the mixture, which can range from an ideal mixture of two initial consisting ionic liquids to a different structure from those of pure materials, has been suggested as the origin of the observed deviation. The structures of several different ionic liquid mixtures are studied by IR spectroscopy to confirm this suggestion, as a particular IR absorption band (νC(2)-D) for the moiety participating in the hydrogen bonding changes sensitively with the change of the anion in the ionic liquid. The absorbance of νC(2)-D changes proportionally with the composition, and a relatively small excess molar volume is observed for the mixtures containing an electronegative halide anion. By contrast, the absorbance changes nonlinearly, and the excess molar volumes are larger for the mixtures of which one of the anions has multiple interaction sites.

Ab initio studies of ultrafast x-ray scattering of the photodissociation of iodine

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

Debnarova, Andrea; Techert, Simone; Schmatz, Stefan

2010-09-28

We computationally examine various aspects of the reaction dynamics of the photodissociation and recombination of molecular iodine. We use our recently proposed formalism to calculate time-dependent x-ray scattering signal changes from first principles. Different aspects of the dynamics of this prototypical reaction are studied, such as coherent and noncoherent processes, features of structural relaxation that are periodic in time versus nonperiodic dissociative processes, as well as small electron density changes caused by electronic excitation, all with respect to x-ray scattering. We can demonstrate that wide-angle x-ray scattering offers a possibility to study the changes in electron densities in nonperiodic systems,more » which render it a suitable technique for the investigation of chemical reactions from a structural dynamics point of view.« less

Circular dichroism study of the carbohydrate-modified opioid peptides

NASA Astrophysics Data System (ADS)

Horvat, Štefica; Otvos, Laszlo; Urge, Laszlo; Horvat, Jaroslav; Čudić, Mare; Varga-Defterdarović, Lidija

1999-09-01

The conformational preferences of enkephalins and the related glycoconjugates in which free or protected carbohydrate moieties were linked to the opioid peptides through an ether, ester or amide bond were investigated by circular dichroism spectroscopy in water, trifluoroethanol and water-trifluoroethanol mixtures. The analysis of the spectra revealed that the conformation of the enkephalin molecule is very sensitive to slight changes in the peptide structure around the C-terminal region. It was found that the type II β-turn structures are populated in N-terminal tetrapeptide enkephalin fragment, while leucine-enkephalin amide feature a type I (III) β-turn structure in solution. Incorporation of the sugar moiety into opioid peptide compound did not significantly influence the overall conformation of the peptide backbone, although minor intensity changes may reflect shifts in the population of the different turn systems. These small structural alterations can be responsible for the receptor-subtype selectivity of the various carbohydrate-modified enkephalin analogs.

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

Nigro, Valentina, E-mail: nigro@fis.uniroma3.it; Bruni, Fabio; Ricci, Maria Antonietta

The temperature dependence of the local intra-particle structure of colloidal microgel particles, composed of interpenetrated polymer networks, has been investigated by small-angle neutron scattering at different pH and concentrations, in the range (299÷315) K, where a volume phase transition from a swollen to a shrunken state takes place. Data are well described by a theoretical model that takes into account the presence of both interpenetrated polymer networks and cross-linkers. Two different behaviors are found across the volume phase transition. At neutral pH and T ≈ 307 K, a sharp change of the local structure from a water rich open inhomogeneousmore » interpenetrated polymer network to a homogeneous porous solid-like structure after expelling water is observed. Differently, at acidic pH, the local structure changes almost continuously. These findings demonstrate that a fine control of the pH of the system allows to tune the sharpness of the volume-phase transition.« less

Atomic resolution structure of the E. coli YajR transporter YAM domain.

PubMed

Jiang, Daohua; Zhao, Yan; Fan, Junping; Liu, Xuehui; Wu, Yan; Feng, Wei; Zhang, Xuejun C

2014-07-25

YajR is an Escherichia coli transporter that belongs to the major facilitator superfamily. Unlike most MFS transporters, YajR contains a carboxyl terminal, cytosolic domain of 67 amino acid residues termed YAM domain. Although it is speculated that the function of this small soluble domain is to regulate the conformational change of the 12-helix transmembrane domain, its precise regulatory role remains unclear. Here, we report the crystal structure of the YAM domain at 1.07-Å resolution, along with its structure determined using nuclear magnetic resonance. Detailed analysis of the high resolution structure revealed a symmetrical dimer in which a belt of well-ordered poly-pentagonal water molecules is embedded. A mutagenesis experiment and a thermal stability assay were used to analyze the putative role of this dimerization in response to changes in halogen concentration. Copyright © 2014 Elsevier Inc. All rights reserved.

Impact of aggregation on scaling behavior of Internet backbone traffic

NASA Astrophysics Data System (ADS)

Zhang, Zhi-Li; Ribeiro, Vinay J.; Moon, Sue B.; Diot, Christophe

2002-07-01

We study the impact of aggregation on the scaling behavior of Internet backbone tra ffic, based on traces collected from OC3 and OC12 links in a tier-1 ISP. We make two striking observations regarding the sub-second small time scaling behaviors of Internet backbone traffic: 1) for a majority of these traces, the Hurst parameters at small time scales (1ms - 100ms) are fairly close to 0.5. Hence the traffic at these time scales are nearly uncorrelated; 2) the scaling behaviors at small time scales are link-dependent, and stay fairly invariant over changing utilization and time. To understand the scaling behavior of network traffic, we develop analytical models and employ them to demonstrate how traffic composition -- aggregation of traffic with different characteristics -- affects the small-time scalings of network traffic. The degree of aggregation and burst correlation structure are two major factors in traffic composition. Our trace-based data analysis confirms this. Furthermore, we discover that traffic composition on a backbone link stays fairly consistent over time and changing utilization, which we believe is the cause for the invariant small-time scalings we observe in the traces.

Small-angle X-ray scattering reveals the solution structure of the full-length DNA gyrase a subunit.

PubMed

Costenaro, Lionel; Grossmann, J Günter; Ebel, Christine; Maxwell, Anthony

2005-02-01

DNA gyrase is the topoisomerase uniquely able to actively introduce negative supercoils into DNA. Vital in all bacteria, but absent in humans, this enzyme is a successful target for antibacterial drugs. From biophysical experiments in solution, we report the low-resolution structure of the full-length A subunit (GyrA). Analytical ultracentrifugation shows that GyrA is dimeric, but nonglobular. Ab initio modeling from small-angle X-ray scattering allows us to retrieve the molecular envelope of GyrA and thereby the organization of its domains. The available crystallographic structure of the amino-terminal domain (GyrA59) forms a dimeric core, and two additional pear-shaped densities closely flank it in an unexpected position. Each accommodates very well a carboxyl-terminal domain (GyrA-CTD) built from a homologous crystallographic structure. The uniqueness of gyrase is due to the ability of the GyrA-CTDs to wrap DNA. Their position within the GyrA structure strongly suggests a large conformation change of the enzyme upon DNA binding.

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.

Conservation of forest birds: evidence of a shifting baseline in community structure.

PubMed

Rittenhouse, Chadwick D; Pidgeon, Anna M; Albright, Thomas P; Culbert, Patrick D; Clayton, Murray K; Flather, Curtis H; Huang, Chengquan; Masek, Jeffrey G; Stewart, Susan I; Radeloff, Volker C

2010-08-02

Quantifying changes in forest bird diversity is an essential task for developing effective conservation actions. When subtle changes in diversity accumulate over time, annual comparisons may offer an incomplete perspective of changes in diversity. In this case, progressive change, the comparison of changes in diversity from a baseline condition, may offer greater insight because changes in diversity are assessed over longer periods of times. Our objectives were to determine how forest bird diversity has changed over time and whether those changes were associated with forest disturbance. We used North American Breeding Bird Survey data, a time series of Landsat images classified with respect to land cover change, and mixed-effects models to associate changes in forest bird community structure with forest disturbance, latitude, and longitude in the conterminous United States for the years 1985 to 2006. We document a significant divergence from the baseline structure for all birds of similar migratory habit and nest location, and all forest birds as a group from 1985 to 2006. Unexpectedly, decreases in progressive similarity resulted from small changes in richness (<1 species per route for the 22-year study period) and modest losses in abundance (-28.7 - -10.2 individuals per route) that varied by migratory habit and nest location. Forest disturbance increased progressive similarity for Neotropical migrants, permanent residents, ground nesting, and cavity nesting species. We also documented highest progressive similarity in the eastern United States. Contemporary forest bird community structure is changing rapidly over a relatively short period of time (e.g., approximately 22 years). Forest disturbance and forest regeneration are primary factors associated with contemporary forest bird community structure, longitude and latitude are secondary factors, and forest loss is a tertiary factor. Importantly, these findings suggest some regions of the United States may already fall below the habitat amount threshold where fragmentation effects become important predictors of forest bird community structure.

Small bowel carcinomas in celiac or Crohn's disease: distinctive histophenotypic, molecular and histogenetic patterns.

PubMed

Vanoli, Alessandro; Di Sabatino, Antonio; Martino, Michele; Klersy, Catherine; Grillo, Federica; Mescoli, Claudia; Nesi, Gabriella; Volta, Umberto; Fornino, Daniele; Luinetti, Ombretta; Fociani, Paolo; Villanacci, Vincenzo; D'Armiento, Francesco P; Cannizzaro, Renato; Latella, Giovanni; Ciacci, Carolina; Biancone, Livia; Paulli, Marco; Sessa, Fausto; Rugge, Massimo; Fiocca, Roberto; Corazza, Gino R; Solcia, Enrico

2017-10-01

Non-familial small bowel carcinomas are relatively rare and have a poor prognosis. Two small bowel carcinoma subsets may arise in distinct immune-inflammatory diseases (celiac disease and Crohn's disease) and have been recently suggested to differ in prognosis, celiac disease-associated carcinoma cases showing a better outcome, possibly due to their higher DNA microsatellite instability and tumor-infiltrating T lymphocytes. In this study, we investigated the histological structure (glandular vs diffuse/poorly cohesive, mixed or solid), cell phenotype (intestinal vs gastric/pancreatobiliary duct type) and Wnt signaling activation (β-catenin and/or SOX-9 nuclear expression) in a series of 26 celiac disease-associated small bowel carcinoma, 25 Crohn's disease-associated small bowel carcinoma and 25 sporadic small bowel carcinoma cases, searching for new prognostic parameters. In addition, non-tumor mucosa of celiac and Crohn's disease patients was investigated for epithelial precursor changes (hyperplastic, metaplastic or dysplastic) to help clarify carcinoma histogenesis. When compared with non-glandular structure and non-intestinal phenotype, both glandular structure and intestinal phenotype were associated with a more favorable outcome at univariable or stage- and microsatellite instability/tumor-infiltrating lymphocyte-inclusive multivariable analysis. The prognostic power of histological structure was independent of the clinical groups while the non-intestinal phenotype, associated with poor outcome, was dominant among Crohn's disease-associated carcinoma. Both nuclear β-catenin and SOX-9 were preferably expressed among celiac disease-associated carcinomas; however, they were devoid, per se, of prognostic value. We obtained findings supporting an origin of celiac disease-associated carcinoma in SOX-9-positive immature hyperplastic crypts, partly through flat β-catenin-positive dysplasia, and of Crohn's disease-associated carcinoma in a metaplastic (gastric and/or pancreatobiliary-type) mucosa, often through dysplastic polypoid growths of metaplastic phenotype. In conclusion, despite their common origin in a chronically inflamed mucosa, celiac disease-associated and Crohn's disease-associated small bowel carcinomas differ substantially in histological structure, phenotype, microsatellite instability/tumor-infiltrating lymphocyte status, Wnt pathway activation, mucosal precursor lesions and prognosis.

Mcl-1–Bim complexes accommodate surprising point mutations via minor structural changes

PubMed Central

Fire, Emiko; Gullá, Stefano V; Grant, Robert A; Keating, Amy E

2010-01-01

Mcl-1 is an antiapoptotic Bcl-2-family protein that protects cells against death. Structures of Mcl-1, and of other anti-apoptotic Bcl-2 proteins, reveal a surface groove into which the α-helical BH3 regions of certain proapoptotic proteins can bind. Despite high overall structural conservation, differences in this groove afford binding specificity that is important for the mechanism of Bcl-2 family function. We report the crystal structure of human Mcl-1 bound to a BH3 peptide derived from human Bim and the structures for three complexes that accommodate large physicochemical changes at conserved Bim sites. The mutations had surprisingly modest effects on complex stability, and the structures show that Mcl-1 can undergo small changes to accommodate the mutant ligands. For example, a shift in a leucine side chain fills a hole left by an isoleucine-to-alanine mutation at the first hydrophobic buried position of Bim BH3. Larger changes are also observed, with shifting of helix α3 accommodating an isoleucine-to-tyrosine mutation at this same position. We surveyed the variation in available Mcl-1 and Bcl-xL structures and observed moderate flexibility that is likely critical for facilitating interactions of diverse BH3-only proteins with Mcl-1. With the antiapoptotic Bcl-2 family members attracting significant attention as therapeutic targets, these structures contribute to our growing understanding of how specificity is achieved and can help to guide the design of novel inhibitors that target Mcl-1. PMID:20066663

Technology for organization of the onboard system for processing and storage of ERS data for ultrasmall spacecraft

NASA Astrophysics Data System (ADS)

Strotov, Valery V.; Taganov, Alexander I.; Konkin, Yuriy V.; Kolesenkov, Aleksandr N.

2017-10-01

Task of processing and analysis of obtained Earth remote sensing data on ultra-small spacecraft board is actual taking into consideration significant expenditures of energy for data transfer and low productivity of computers. Thereby, there is an issue of effective and reliable storage of the general information flow obtained from onboard systems of information collection, including Earth remote sensing data, into a specialized data base. The paper has considered peculiarities of database management system operation with the multilevel memory structure. For storage of data in data base the format has been developed that describes a data base physical structure which contains required parameters for information loading. Such structure allows reducing a memory size occupied by data base because it is not necessary to store values of keys separately. The paper has shown architecture of the relational database management system oriented into embedment into the onboard ultra-small spacecraft software. Data base for storage of different information, including Earth remote sensing data, can be developed by means of such database management system for its following processing. Suggested database management system architecture has low requirements to power of the computer systems and memory resources on the ultra-small spacecraft board. Data integrity is ensured under input and change of the structured information.

Can integrative catchment management mitigate future water quality issues caused by climate change and socio-economic development?

NASA Astrophysics Data System (ADS)

Honti, Mark; Schuwirth, Nele; Rieckermann, Jörg; Stamm, Christian

2017-03-01

The design and evaluation of solutions for integrated surface water quality management requires an integrated modelling approach. Integrated models have to be comprehensive enough to cover the aspects relevant for management decisions, allowing for mapping of larger-scale processes such as climate change to the regional and local contexts. Besides this, models have to be sufficiently simple and fast to apply proper methods of uncertainty analysis, covering model structure deficits and error propagation through the chain of sub-models. Here, we present a new integrated catchment model satisfying both conditions. The conceptual iWaQa model was developed to support the integrated management of small streams. It can be used to predict traditional water quality parameters, such as nutrients and a wide set of organic micropollutants (plant and material protection products), by considering all major pollutant pathways in urban and agricultural environments. Due to its simplicity, the model allows for a full, propagative analysis of predictive uncertainty, including certain structural and input errors. The usefulness of the model is demonstrated by predicting future surface water quality in a small catchment with mixed land use in the Swiss Plateau. We consider climate change, population growth or decline, socio-economic development, and the implementation of management strategies to tackle urban and agricultural point and non-point sources of pollution. Our results indicate that input and model structure uncertainties are the most influential factors for certain water quality parameters. In these cases model uncertainty is already high for present conditions. Nevertheless, accounting for today's uncertainty makes management fairly robust to the foreseen range of potential changes in the next decades. The assessment of total predictive uncertainty allows for selecting management strategies that show small sensitivity to poorly known boundary conditions. The identification of important sources of uncertainty helps to guide future monitoring efforts and pinpoints key indicators, whose evolution should be closely followed to adapt management. The possible impact of climate change is clearly demonstrated by water quality substantially changing depending on single climate model chains. However, when all climate trajectories are combined, the human land use and management decisions have a larger influence on water quality against a time horizon of 2050 in the study.

Discussion on back-to-back two-stage centrifugal compressor compact design techniques

NASA Astrophysics Data System (ADS)

Huo, Lei; Liu, Huoxing

2013-12-01

Design a small flow back-to-back two-stage centrifugal compressor in the aviation turbocharger, the compressor is compact structure, small axial length, light weighted. Stationary parts have a great influence on their overall performance decline. Therefore, the stationary part of the back-to-back two-stage centrifugal compressor should pay full attention to the diffuser, bend, return vane and volute design. Volute also impact downstream return vane, making the flow in circumferential direction is not uniformed, and several blade angle of attack is drastically changed in downstream of the volute with the airflow can not be rotated to required angle. Loading of high-pressure rotor blades change due to non-uniformed of flow in circumferential direction, which makes individual blade load distribution changed, and affected blade passage load decreased to reduce the capability of work, the tip low speed range increases.

Vegetative community control of freshwater availability: Phoenix Islands case study

NASA Astrophysics Data System (ADS)

Engels, M.; Heinse, R.

2014-12-01

On small low islands with limited freshwater resources, terrestrial plant communities play a large role in moderating freshwater availability. Freshwater demands of vegetative communities are variable depending on the composition of the community. Hence, changes to community structure from production crop introductions, non-native species invasions, and climate change, may have significant implications for freshwater availability. Understanding how vegetative community changes impact freshwater availability will allow for better management and forecasting of limited freshwater supplies. To better understand these dynamics, we investigated three small tropical atolls in the Phoenix Island Protected Area, Kiribati. Despite their close proximity, these islands receive varying amounts of rainfall, are host to different plant communities and two of the islands have abandoned coconut plantations. Using electromagnetic induction, ground penetrating radar, soil samples, climate and satellite data, we present preliminary estimates of vegetative water demand for different tropical plant communities.

Control of finite critical behaviour in a small-scale social system

NASA Astrophysics Data System (ADS)

Daniels, Bryan C.; Krakauer, David C.; Flack, Jessica C.

2017-02-01

Many adaptive systems sit near a tipping or critical point. For systems near a critical point small changes to component behaviour can induce large-scale changes in aggregate structure and function. Criticality can be adaptive when the environment is changing, but entails reduced robustness through sensitivity. This tradeoff can be resolved when criticality can be tuned. We address the control of finite measures of criticality using data on fight sizes from an animal society model system (Macaca nemestrina, n=48). We find that a heterogeneous, socially organized system, like homogeneous, spatial systems (flocks and schools), sits near a critical point; the contributions individuals make to collective phenomena can be quantified; there is heterogeneity in these contributions; and distance from the critical point (DFC) can be controlled through biologically plausible mechanisms exploiting heterogeneity. We propose two alternative hypotheses for why a system decreases the distance from the critical point.

Changes in Structural Connectivity Following a Cognitive Intervention in Children With Traumatic Brain Injury.

PubMed

Yuan, Weihong; Treble-Barna, Amery; Sohlberg, McKay M; Harn, Beth; Wade, Shari L

2017-02-01

Structural connectivity analysis based on graph theory and diffusion tensor imaging tractography is a novel method that quantifies the topological characteristics in the brain network. This study aimed to examine structural connectivity changes following the Attention Intervention and Management (AIM) program designed to improve attention and executive function (EF) in children with traumatic brain injury (TBI). Seventeen children with complicated mild to severe TBI (13.66 ± 2.68 years; >12 months postinjury) completed magnetic resonance imaging (MRI) and neurobehavioral measures at time 1, 10 of whom completed AIM and assessment at time 2. Eleven matched healthy comparison (HC) children (13.37 ± 2.08 years) completed MRI and neurobehavioral assessment at both time points, but did not complete AIM. Network characteristics were analyzed to quantify the structural connectivity before and after the intervention. Mixed model analyses showed that small-worldness was significantly higher in the TBI group than the HC group at time 1, and both small-worldness and normalized clustering coefficient decreased significantly at time 2 in the TBI group whereas the HC group remained relatively unchanged. Reductions in mean local efficiency were significantly correlated with improvements in verbal inhibition and both parent- and child-reported EF. Increased normalized characteristic path length was significantly correlated with improved sustained attention. The results provide preliminary evidence suggesting that graph theoretical analysis may be a sensitive tool in pediatric TBI for detecting ( a) abnormalities of structural connectivity in brain network and ( b) structural neuroplasticity associated with neurobehavioral improvement following a short-term intervention for attention and EF.

The small angle x-ray scattering of globular proteins in solution during heat denaturation

NASA Astrophysics Data System (ADS)

Banuelos, Jose; Urquidi, Jacob

2008-10-01

The ability of proteins to change their conformation in response to changes in their environment has consequences in biological processes like metabolism, chemical regulation in cells, and is believed to play a role in the onset of several neurodegenerative diseases. Factors such as a change in temperature, pressure, and the introduction of ions into the aqueous environment of a protein can give rise to the folding/unfolding of a protein. As a protein unfolds, the ratio of nonpolar to polar groups exposed to water changes, affecting a protein's thermodynamic properties. Using small angle x-ray scattering (SAXS), we are currently studying the intermediate protein conformations that arise during the folding/unfolding process as a function of temperature for five globular proteins. Trends in the observed intermediate structures of these globular proteins, along with correlations with data on protein thermodynamics may help elucidate shared characteristics between all proteins in the folding/unfolding process. Experimental design considerations will be discussed and preliminary results for some of these systems will be presented.

Quantifying changes in the bone microarchitecture using Minkowski-functionals and scaling vectors: a comparative study

NASA Astrophysics Data System (ADS)

Raeth, Christoph W.; Mueller, Dirk; Link, Thomas M.; Boehm, Holger; Monetti, Roberto

2006-03-01

Osteoporosis is a metabolic bone disease leading to de-mineralization and increased risk of fracture. The two major factors that determine the biomechanical competence of bone are the degree of mineralization and the micro-architectural integrity. Today, modern imaging modalities exist that allow to depict structural details of trabecular bone tissue. Recently, non-linear techniques in 2D and 3D based on the scaling vector method (SVM) and the Minkowski functionals (MF) have been introduced, which show excellent performance in predicting bone strength and fracture risk. However, little is known about the performance of the various parameters with respect to monitoring structural changes due to progression of osteoporosis or as a result of medical treatment. We test and compare the two methodologies using realistic two-dimensional simulations of bone structures, which model the effect of osteoblasts and osteoclasts on the local change of relative bone density. Different realizations with slightly varying control parameters are considered. Our results show that even small changes in the trabecular structures, which are induced by variation of a control parameter of the system, become discernible by applying both the MF and the locally adapted scaling vector method. The results obtained with SVM are superior to those obtained with the Minkowski functionals. An additive combination of both measures drastically increases the sensitivity to slight changes in bone structures. These findings may be especially important for monitoring the treatment of patients, where the early recognition of (drug-induced) changes in the trabecular structure is crucial.

The relationship between manuscript title structure and success: editorial decisions and citation performance for an ecological journal

PubMed Central

Fox, Charles W; Burns, C Sean

2015-01-01

A poorly chosen article title may make a paper difficult to discover or discourage readership when discovered, reducing an article's impact. Yet, it is unclear how the structure of a manuscript's title influences readership and impact. We used manuscript tracking data for all manuscripts submitted to the journal Functional Ecology from 2004 to 2013 and citation data for papers published in this journal from 1987 to 2011 to examine how title features changed and whether a manuscript's title structure was predictive of success during the manuscript review process and/or impact (citation) after publication. Titles of manuscripts submitted to Functional Ecology became marginally longer (after controlling for other variables), broader in focus (less frequent inclusion of genus and species names), and included more humor and subtitles over the period of the study. Papers with subtitles were less likely to be rejected by editors both pre- and post-peer review, although both effects were small and the presence of subtitles in published papers was not predictive of citations. Papers with specific names of study organisms in their titles fared poorly during editorial (but not peer) review and, if published, were less well cited than papers whose titles did not include specific names. Papers with intermediate length titles were more successful during editorial review, although the effect was small and title word count was not predictive of citations. No features of titles were predictive of reviewer willingness to review papers or the length of time a paper was in peer review. We conclude that titles have changed in structure over time, but features of title structure have only small or no relationship with success during editorial review and post-publication impact. The title feature that was most predictive of manuscript success: papers whose titles emphasize broader conceptual or comparative issues fare better both pre- and post-publication than do papers with organism-specific titles. PMID:26045949

The relationship between manuscript title structure and success: editorial decisions and citation performance for an ecological journal.

PubMed

Fox, Charles W; Burns, C Sean

2015-05-01

A poorly chosen article title may make a paper difficult to discover or discourage readership when discovered, reducing an article's impact. Yet, it is unclear how the structure of a manuscript's title influences readership and impact. We used manuscript tracking data for all manuscripts submitted to the journal Functional Ecology from 2004 to 2013 and citation data for papers published in this journal from 1987 to 2011 to examine how title features changed and whether a manuscript's title structure was predictive of success during the manuscript review process and/or impact (citation) after publication. Titles of manuscripts submitted to Functional Ecology became marginally longer (after controlling for other variables), broader in focus (less frequent inclusion of genus and species names), and included more humor and subtitles over the period of the study. Papers with subtitles were less likely to be rejected by editors both pre- and post-peer review, although both effects were small and the presence of subtitles in published papers was not predictive of citations. Papers with specific names of study organisms in their titles fared poorly during editorial (but not peer) review and, if published, were less well cited than papers whose titles did not include specific names. Papers with intermediate length titles were more successful during editorial review, although the effect was small and title word count was not predictive of citations. No features of titles were predictive of reviewer willingness to review papers or the length of time a paper was in peer review. We conclude that titles have changed in structure over time, but features of title structure have only small or no relationship with success during editorial review and post-publication impact. The title feature that was most predictive of manuscript success: papers whose titles emphasize broader conceptual or comparative issues fare better both pre- and post-publication than do papers with organism-specific titles.

Climate Change Impact on the Southeastern Europe Security Environment and the Increasing Role of the Bulgarian Army as the World Warms

DTIC Science & Technology

2016-06-10

expected risks posed by climate change will reshape the Bulgarian Army structure and capabilities if the Army is to develop the proficiency to face...thousands of local timber based manufacturers and small scaled industries, and a few big and international oriented pulp, paper and board producers...prevention, social timber supply, etc.55 54 Union of Concerned Scientists, “Climate Hot Map,” accessed 20

Multivariate Analysis of Two-Dimensional 1H, 13C Methyl NMR Spectra of Monoclonal Antibody Therapeutics To Facilitate Assessment of Higher Order Structure.

PubMed

Arbogast, Luke W; Delaglio, Frank; Schiel, John E; Marino, John P

2017-11-07

Two-dimensional (2D) 1 H- 13 C methyl NMR provides a powerful tool to probe the higher order structure (HOS) of monoclonal antibodies (mAbs), since spectra can readily be acquired on intact mAbs at natural isotopic abundance, and small changes in chemical environment and structure give rise to observable changes in corresponding spectra, which can be interpreted at atomic resolution. This makes it possible to apply 2D NMR spectral fingerprinting approaches directly to drug products in order to systematically characterize structure and excipient effects. Systematic collections of NMR spectra are often analyzed in terms of the changes in specifically identified peak positions, as well as changes in peak height and line widths. A complementary approach is to apply principal component analysis (PCA) directly to the matrix of spectral data, correlating spectra according to similarities and differences in their overall shapes, rather than according to parameters of individually identified peaks. This is particularly well-suited for spectra of mAbs, where some of the individual peaks might not be well resolved. Here we demonstrate the performance of the PCA method for discriminating structural variation among systematic sets of 2D NMR fingerprint spectra using the NISTmAb and illustrate how spectral variability identified by PCA may be correlated to structure.

Assessment of flood-induced changes of phytoplankton along a river-floodplain system using the morpho-functional approach.

PubMed

Mihaljević, Melita; Spoljarić, Dubravka; Stević, Filip; Zuna Pfeiffer, Tanja

2013-10-01

In this research, we aimed to find out how the differences in hydrological connectivity between the main river channel and adjacent floodplain influence the changes in phytoplankton community structure along a river-floodplain system. The research was performed in the River Danube floodplain (Croatian river section) in the period 2008-2009 characterised by different flooding pattern on an annual time scale. By utilising the morpho-functional approach and multivariate analyses, the flood-derived structural changes of phytoplankton were analysed. The lake stability during the isolation phase triggered the specific pattern of morpho-functional groups (MFG) which were characterised by cyanobacterial species achieving very high biomass. Adversely, the high water turbulence in the lake during the frequent and extreme flooding led to evident similarity between lake and river assemblages. Besides different diatom species (groups of small and large centrics and pennates), which are the most abundant representatives in the river phytoplankton, many other groups such as cryptophytes and colonial phytomonads appeared to indicate altered conditions in the floodplain driven by flooding. Having different functional properties, small centric diatom taxa sorted to only one MFG cannot clearly reflect environmental changes that are shown by the species-level pattern. Disadvantages in using the MFG approach highlight that it is still necessary to combine it with taxonomical approach in monitoring of phytoplankton in the river-floodplain ecosystems.

When is an Inhibitory Synapse Effective?

NASA Astrophysics Data System (ADS)

Qian, Ning; Sejnowski, Terrence J.

1990-10-01

Interactions between excitatory and inhibitory synaptic inputs on dendrites determine the level of activity in neurons. Models based on the cable equation predict that silent shunting inhibition can strongly veto the effect of an excitatory input. The cable model assumes that ionic concentrations do not change during the electrical activity, which may not be a valid assumption, especially for small structures such as dendritic spines. We present here an analysis and computer simulations to show that for large Cl^- conductance changes, the more general Nernst-Planck electrodiffusion model predicts that shunting inhibition on spines should be much less effective than that predicted by the cable model. This is a consequence of the large changes in the intracellular ionic concentration of Cl^- that can occur in small structures, which would alter the reversal potential and reduce the driving force for Cl^-. Shunting inhibition should therefore not be effective on spines, but it could be significantly more effective on the dendritic shaft at the base of the spine. In contrast to shunting inhibition, hyperpolarizing synaptic inhibition mediated by K^+ currents can be very effective in reducing the excitatory synaptic potentials on the same spine if the excitatory conductance change is less than 10 nS. We predict that if the inhibitory synapses found on cortical spines are to be effective, then they should be mediated by K^+ through GABA_B receptors.

Beyond just sea-level rise: Considering macroclimatic drivers within coastal wetland vulnerability assessments to climate change

USGS Publications Warehouse

Osland, Michael J.; Enwright, Nicholas M.; Day, Richard H.; Gabler, Christopher A.; Stagg, Camille L.; Grace, James B.

2016-01-01

Due to their position at the land-sea interface, coastal wetlands are vulnerable to many aspects of climate change. However, climate change vulnerability assessments for coastal wetlands generally focus solely on sea-level rise without considering the effects of other facets of climate change. Across the globe and in all ecosystems, macroclimatic drivers (e.g., temperature and rainfall regimes) greatly influence ecosystem structure and function. Macroclimatic drivers have been the focus of climate-change related threat evaluations for terrestrial ecosystems, but largely ignored for coastal wetlands. In some coastal wetlands, changing macroclimatic conditions are expected to result in foundation plant species replacement, which would affect the supply of certain ecosystem goods and services and could affect ecosystem resilience. As examples, we highlight several ecological transition zones where small changes in macroclimatic conditions would result in comparatively large changes in coastal wetland ecosystem structure and function. Our intent in this communication is not to minimize the importance of sea-level rise. Rather, our overarching aim is to illustrate the need to also consider macroclimatic drivers within vulnerability assessments for coastal wetlands.

Early overfeed-induced obesity leads to brown adipose tissue hypoactivity in rats.

PubMed

de Almeida, Douglas L; Fabrício, Gabriel S; Trombini, Amanda B; Pavanello, Audrei; Tófolo, Laize P; da Silva Ribeiro, Tatiane A; de Freitas Mathias, Paulo C; Palma-Rigo, Kesia

2013-01-01

Brown adipose tissue activation has been considered a potential anti-obesity mechanism because it is able to expend energy through thermogenesis. In contrast, white adipose tissue stores energy, contributing to obesity. We investigated whether the early programming of obesity by overfeeding during lactation changes structure of interscapular brown adipose tissue in adulthood and its effects on thermogenesis. Birth of litters was considered day 0. On day 2, litter size was adjusted to normal (9 pups) and small (3 pups) litters. On day 21, the litters were weaned. A temperature transponder was implanted underneath interscapular brown adipose tissue pads of 81-day-old animals; local temperature was measured during light and dark periods between days 87 and 90. The animals were euthanized, and tissue and blood samples were collected for further analysis. The vagus and retroperitoneal sympathetic nerve activity was recorded. Small litter rats presented significant lower interscapular brown adipose tissue temperature during the light (NL 37.6°C vs. SL 37.2°C) and dark (NL 38°C vs. SL 37.6°C) periods compared to controls. Morphology of small litter brown adipose tissue showed fewer lipid droplets in the tissue center and more and larger in the periphery. The activity of vagus nerve was 19,9% greater in the small litter than in control (p<0.01), and no difference was observed in the sympathetic nerve activity. In adulthood, the small litter rats were 11,7% heavier than the controls and presented higher glycemia 13,1%, insulinemia 70% and corticosteronemia 92,6%. Early overfeeding programming of obesity changes the interscapular brown adipose tissue structure in adulthood, leading to local thermogenesis hypoactivity, which may contribute to obesity in adults. © 2013 S. Karger AG, Basel.

3D printing cybersecurity: detecting and preventing attacks that seek to weaken a printed object by changing fill level

NASA Astrophysics Data System (ADS)

Straub, Jeremy

2017-06-01

Prior work by Zeltmann, et al. has demonstrated the impact of small defects and other irregularities on the structural integrity of 3D printed objects. It posited that such defects could be introduced intentionally. The current work looks at the impact of changing the fill level on object structural integrity. It considers whether the existence of an appropriate level of fill can be determined through visible light imagery-based assessment of a 3D printed object. A technique for assessing the quality and sufficiency of quantity of 3D printed fill material is presented. It is assessed experimentally and results are presented and analyzed.

Structural changes and triacetin migration of starch acetate film contacting with distilled water as food simulant.

PubMed

Zhu, Jie; Li, Xiaoxi; Huang, Chen; Chen, Ling; Li, Lin

2014-04-15

This work studied the structural changes and the migration of triacetin plasticizer in starch acetate films in the presence of distilled water as food simulant. Fourier-transform infrared spectroscopy result showed that the macromolecular interaction was enhanced to form compact aggregation of amorphous chains. The characterization of aggregation structures via wide and small angle X-ray scattering techniques indicated that the orderly microregion was compressed and the crystallites inside were "squeezed" to form interference and further aggregation. The compact aggregation structures restricted the mobility of macromolecules, triacetin and water molecules. The overall kinetic and the diffusion model analysis manifested that Fick's second law was the predominant mechanism for the short-term migration of triacetin. The increasing relaxation within film matrix caused the subsequent migration to deviate from Fick's law. The safe and reasonable application of the starch-based materials with restrained plasticizer migration could be accomplished by controlling the molecular interaction and aggregation structures. Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.

Riboswitches: emerging themes in RNA structure and function.

PubMed

Montange, Rebecca K; Batey, Robert T

2008-01-01

Riboswitches are RNAs capable of binding cellular metabolites using a diverse array of secondary and tertiary structures to modulate gene expression. The recent determination of the three-dimensional structures of parts of six different riboswitches illuminates common features that allow riboswitches to be grouped into one of two types. Type I riboswitches, as exemplified by the purine riboswitch, are characterized by a single, localized binding pocket supported by a largely pre-established global fold. This arrangement limits ligand-induced conformational changes in the RNA to a small region. In contrast, Type II riboswitches, such as the thiamine pyrophosphate riboswitch, contain binding pockets split into at least two spatially distinct sites. As a result, binding induces both local changes to the binding pocket and global architecture. Similar organizational themes are found in other noncoding RNAs, making it possible to begin to build a hierarchical classification of RNA structure based on the spatial organization of their active sites and associated secondary structural elements.

Dynamically variable negative stiffness structures

PubMed Central

Churchill, Christopher B.; Shahan, David W.; Smith, Sloan P.; Keefe, Andrew C.; McKnight, Geoffrey P.

2016-01-01

Variable stiffness structures that enable a wide range of efficient load-bearing and dexterous activity are ubiquitous in mammalian musculoskeletal systems but are rare in engineered systems because of their complexity, power, and cost. We present a new negative stiffness–based load-bearing structure with dynamically tunable stiffness. Negative stiffness, traditionally used to achieve novel response from passive structures, is a powerful tool to achieve dynamic stiffness changes when configured with an active component. Using relatively simple hardware and low-power, low-frequency actuation, we show an assembly capable of fast (<10 ms) and useful (>100×) dynamic stiffness control. This approach mitigates limitations of conventional tunable stiffness structures that exhibit either small (<30%) stiffness change, high friction, poor load/torque transmission at low stiffness, or high power active control at the frequencies of interest. We experimentally demonstrate actively tunable vibration isolation and stiffness tuning independent of supported loads, enhancing applications such as humanoid robotic limbs and lightweight adaptive vibration isolators. PMID:26989771

Structural studies of Saccharomyces cerevesiae mitochondrial NADP-dependent isocitrate dehydrogenase in different enzymatic states reveal substantial conformational changes during the catalytic reaction.

PubMed

Peng, Yingjie; Zhong, Chen; Huang, Wei; Ding, Jianping

2008-09-01

Isocitrate dehydrogenases (IDHs) catalyze oxidative decarboxylation of isocitrate (ICT) into alpha-ketoglutarate (AKG). We report here the crystal structures of Saccharomyces cerevesiae mitochondrial NADP-IDH Idp1p in binary complexes with coenzyme NADP, or substrate ICT, or product AKG, and in a quaternary complex with NADPH, AKG, and Ca(2+), which represent different enzymatic states during the catalytic reaction. Analyses of these structures identify key residues involved in the binding of these ligands. Comparisons among these structures and with the previously reported structures of other NADP-IDHs reveal that eukaryotic NADP-IDHs undergo substantial conformational changes during the catalytic reaction. Binding or release of the ligands can cause significant conformational changes of the structural elements composing the active site, leading to rotation of the large domain relative to the small and clasp domains along two hinge regions (residues 118-124 and residues 284-287) while maintaining the integrity of its secondary structural elements, and thus, formation of at least three distinct overall conformations. Specifically, the enzyme adopts an open conformation when bound to NADP, a quasi-closed conformation when bound to ICT or AKG, and a fully closed conformation when bound to NADP, ICT, and Ca(2+) in the pseudo-Michaelis complex or with NADPH, AKG, and Ca(2+) in the product state. The conformational changes of eukaryotic NADP-IDHs are quite different from those of Escherichia coli NADP-IDH, for which significant conformational changes are observed only between two forms of the apo enzyme, suggesting that the catalytic mechanism of eukaryotic NADP-IDHs is more complex than that of EcIDH, and involves more fine-tuned conformational changes.

Structural studies of Saccharomyces cerevesiae mitochondrial NADP-dependent isocitrate dehydrogenase in different enzymatic states reveal substantial conformational changes during the catalytic reaction

PubMed Central

Peng, Yingjie; Zhong, Chen; Huang, Wei; Ding, Jianping

2008-01-01

Isocitrate dehydrogenases (IDHs) catalyze oxidative decarboxylation of isocitrate (ICT) into α-ketoglutarate (AKG). We report here the crystal structures of Saccharomyces cerevesiae mitochondrial NADP-IDH Idp1p in binary complexes with coenzyme NADP, or substrate ICT, or product AKG, and in a quaternary complex with NADPH, AKG, and Ca2+, which represent different enzymatic states during the catalytic reaction. Analyses of these structures identify key residues involved in the binding of these ligands. Comparisons among these structures and with the previously reported structures of other NADP-IDHs reveal that eukaryotic NADP-IDHs undergo substantial conformational changes during the catalytic reaction. Binding or release of the ligands can cause significant conformational changes of the structural elements composing the active site, leading to rotation of the large domain relative to the small and clasp domains along two hinge regions (residues 118–124 and residues 284–287) while maintaining the integrity of its secondary structural elements, and thus, formation of at least three distinct overall conformations. Specifically, the enzyme adopts an open conformation when bound to NADP, a quasi-closed conformation when bound to ICT or AKG, and a fully closed conformation when bound to NADP, ICT, and Ca2+ in the pseudo-Michaelis complex or with NADPH, AKG, and Ca2+ in the product state. The conformational changes of eukaryotic NADP-IDHs are quite different from those of Escherichia coli NADP-IDH, for which significant conformational changes are observed only between two forms of the apo enzyme, suggesting that the catalytic mechanism of eukaryotic NADP-IDHs is more complex than that of EcIDH, and involves more fine-tuned conformational changes. PMID:18552125

Enhancement and inhibition of light tunneling mediated by resonant mode conversion.

PubMed

Kartashov, Yaroslav V; Vysloukh, Victor A; Torner, Lluis

2014-02-15

We show that the rate at which light tunnels between neighboring multimode waveguides can be drastically increased or reduced by the presence of small longitudinal periodic modulations of the waveguide properties that stimulate resonant conversion between the eigenmodes of each waveguide. Such a conversion, available only in multimode guiding structures, leads to periodic power transfer into higher-order modes, whose tails may considerably overlap with neighboring waveguides. As a result, the effective coupling constant for neighboring waveguides may change by several orders of magnitude upon small variations in the longitudinal modulation parameters.

Rapid change with depth in megabenthic structure-forming communities of the Makapu'u deep-sea coral bed

NASA Astrophysics Data System (ADS)

Long, Dustin J.; Baco, Amy R.

2014-01-01

Seamounts are largely unexplored undersea mountains rising abruptly from the ocean floor, which can support an increased abundance and diversity of organisms. Deep-sea corals are important benthic structure-formers on current-swept hard substrates in these habitats. While depth is emerging as a factor structuring the fauna of seamounts on a large spatial scale, most work addressing deep-sea coral and seamount community structure has not considered the role of small-scale variation in species distributions. Video from six ROV dives over a depth range of ~320-530 m were analyzed to assess the diversity and density of benthic megafaunal invertebrates across the Makapu'u deep-sea coral bed, offshore of Oahu, Hawaii. At the same time, the physical environment along the dive track was surveyed to relate biotic patterns with abiotic variables including depth, aspect, rugosity, substrate, slope and relief to test the factors structuring community assemblages. Despite the narrow range examined, depth was found to be the strongest structuring gradient, and six unique macrobenthic communities were found, with a 93% faunal dissimilarity over the depth surveyed. Relief, rugosity and slope were also factors in the final model. Alcyonacean octocorals were the dominant macrofaunal invertebrates at all but the deepest depth zone. The commercially harvested precious coral C. secundum was the dominant species at depths 370-470 m, with a distribution that is on average deeper than similar areas. This may be artificial due to the past harvesting of this species on the shallower portion of its range. Primnoid octocorals were the most abundant octocoral family overall. This work yields new insight on the spatial ecology of seamounts, pointing out that community changes can occur over narrow depth ranges and that communities can be structured by small-scale physiography.

Small Animal Retinal Imaging

NASA Astrophysics Data System (ADS)

Choi, WooJhon; Drexler, Wolfgang; Fujimoto, James G.

Developing and validating new techniques and methods for small animal imaging is an important research area because there are many small animal models of retinal diseases such as diabetic retinopathy, age-related macular degeneration, and glaucoma [1-6]. Because the retina is a multilayered structure with distinct abnormalities occurring in different intraretinal layers at different stages of disease progression, there is a need for imaging techniques that enable visualization of these layers individually at different time points. Although postmortem histology and ultrastructural analysis can be performed for investigating microscopic changes in the retina in small animal models, this requires sacrificing animals, which makes repeated assessment of the same animal at different time points impossible and increases the number of animals required. Furthermore, some retinal processes such as neurovascular coupling cannot be fully characterized postmortem.

On the structural properties of small-world networks with range-limited shortcut links

NASA Astrophysics Data System (ADS)

Jia, Tao; Kulkarni, Rahul V.

2013-12-01

We explore a new variant of Small-World Networks (SWNs), in which an additional parameter (r) sets the length scale over which shortcuts are uniformly distributed. When r=0 we have an ordered network, whereas r=1 corresponds to the original Watts-Strogatz SWN model. These limited range SWNs have a similar degree distribution and scaling properties as the original SWN model. We observe the small-world phenomenon for r≪1, indicating that global shortcuts are not necessary for the small-world effect. For limited range SWNs, the average path length changes nonmonotonically with system size, whereas for the original SWN model it increases monotonically. We propose an expression for the average path length for limited range SWNs based on numerical simulations and analytical approximations.

Tunable Encapsulation Structure of Block Copolymer Coated Single-Walled Carbon Nanotubes in Aqueous Solution

DOE PAGES

Han, Youngkyu; Ahn, Suk-Kyun; Zhang, Zhe; ...

2015-05-15

The nano-sized and shape-tunable molecular building blocks can provide great opportunities for the fabrication of precisely controlled nanostructures. In this work, we have fabricated a molecular building block of single-walled carbon nanotubes (SWNTs) coated by PPO-PEO-PPO block copolymers whose encapsulation structure can be controlled via temperature or addition of small molecules. The structure and optical properties of SWNT-block copolymers have been investigated by small angle neutron scattering (SANS), ultraviolet-visible (UV-vis) spectroscopy, atomic force microscopy (AFM), and molecular dynamics (MD) simulation. The structure of the hydrated block copolymer layer surrounding SWNT can be controlled reversibly by varying temperature as well asmore » by irreversibly adding 5-methylsalicylic acid (5MS). Increasing hydrophobicity of the polymers with temperature and strong tendency of 5MS to interact with both block copolymers and orbitals of the SWNTs are likely to be responsible for the significant structural change of the block copolymer encapsulation layer, from loose corona shell to tightly encapsulating compact shell. These result shows an efficient and simple way to fabricate and manipulate carbon-based nano building blocks in aqueous systems with tunable structure.« less

Increased variability in ApcMin/+ intestinal tissue can be measured with microultrasound

NASA Astrophysics Data System (ADS)

Fatehullah, A.; Sharma, S.; Newton, I. P.; Langlands, A. J.; Lay, H.; Nelson, S. A.; McMahon, R. K.; McIlvenny, N.; Appleton, P. L.; Cochran, S.; Näthke, I. S.

2016-07-01

Altered tissue structure is a feature of many disease states and is usually measured by microscopic methods, limiting analysis to small areas. Means to rapidly and quantitatively measure the structure and organisation of large tissue areas would represent a major advance not just for research but also in the clinic. Here, changes in tissue organisation that result from heterozygosity in Apc, a precancerous situation, are comprehensively measured using microultrasound and three-dimensional high-resolution microscopy. Despite its normal appearance in conventionally examined cross-sections, both approaches revealed a significant increase in the variability of tissue organisation in Apc heterozygous tissue. These changes preceded the formation of aberrant crypt foci or adenoma. Measuring these premalignant changes using microultrasound provides a potential means to detect microscopically abnormal regions in large tissue samples, independent of visual examination or biopsies. Not only does this provide a powerful tool for studying tissue structure in experimental settings, the ability to detect and monitor tissue changes by microultrasound could be developed into a powerful adjunct to screening endoscopy in the clinic.

Grating-based X-ray Dark-field Computed Tomography of Living Mice.

PubMed

Velroyen, A; Yaroshenko, A; Hahn, D; Fehringer, A; Tapfer, A; Müller, M; Noël, P B; Pauwels, B; Sasov, A; Yildirim, A Ö; Eickelberg, O; Hellbach, K; Auweter, S D; Meinel, F G; Reiser, M F; Bech, M; Pfeiffer, F

2015-10-01

Changes in x-ray attenuating tissue caused by lung disorders like emphysema or fibrosis are subtle and thus only resolved by high-resolution computed tomography (CT). The structural reorganization, however, is of strong influence for lung function. Dark-field CT (DFCT), based on small-angle scattering of x-rays, reveals such structural changes even at resolutions coarser than the pulmonary network and thus provides access to their anatomical distribution. In this proof-of-concept study we present x-ray in vivo DFCTs of lungs of a healthy, an emphysematous and a fibrotic mouse. The tomographies show excellent depiction of the distribution of structural - and thus indirectly functional - changes in lung parenchyma, on single-modality slices in dark field as well as on multimodal fusion images. Therefore, we anticipate numerous applications of DFCT in diagnostic lung imaging. We introduce a scatter-based Hounsfield Unit (sHU) scale to facilitate comparability of scans. In this newly defined sHU scale, the pathophysiological changes by emphysema and fibrosis cause a shift towards lower numbers, compared to healthy lung tissue.

Grating-based X-ray Dark-field Computed Tomography of Living Mice

PubMed Central

Velroyen, A.; Yaroshenko, A.; Hahn, D.; Fehringer, A.; Tapfer, A.; Müller, M.; Noël, P.B.; Pauwels, B.; Sasov, A.; Yildirim, A.Ö.; Eickelberg, O.; Hellbach, K.; Auweter, S.D.; Meinel, F.G.; Reiser, M.F.; Bech, M.; Pfeiffer, F.

2015-01-01

Changes in x-ray attenuating tissue caused by lung disorders like emphysema or fibrosis are subtle and thus only resolved by high-resolution computed tomography (CT). The structural reorganization, however, is of strong influence for lung function. Dark-field CT (DFCT), based on small-angle scattering of x-rays, reveals such structural changes even at resolutions coarser than the pulmonary network and thus provides access to their anatomical distribution. In this proof-of-concept study we present x-ray in vivo DFCTs of lungs of a healthy, an emphysematous and a fibrotic mouse. The tomographies show excellent depiction of the distribution of structural – and thus indirectly functional – changes in lung parenchyma, on single-modality slices in dark field as well as on multimodal fusion images. Therefore, we anticipate numerous applications of DFCT in diagnostic lung imaging. We introduce a scatter-based Hounsfield Unit (sHU) scale to facilitate comparability of scans. In this newly defined sHU scale, the pathophysiological changes by emphysema and fibrosis cause a shift towards lower numbers, compared to healthy lung tissue. PMID:26629545

Effects of Age, Task Performance, and Structural Brain Development on Face Processing

PubMed Central

Cohen Kadosh, Kathrin; Johnson, Mark H; Dick, Frederic; Cohen Kadosh, Roi; Blakemore, Sarah-Jayne

2013-01-01

In this combined structural and functional MRI developmental study, we tested 48 participants aged 7–37 years on 3 simple face-processing tasks (identity, expression, and gaze task), which were designed to yield very similar performance levels across the entire age range. The same participants then carried out 3 more difficult out-of-scanner tasks, which provided in-depth measures of changes in performance. For our analysis we adopted a novel, systematic approach that allowed us to differentiate age- from performance-related changes in the BOLD response in the 3 tasks, and compared these effects to concomitant changes in brain structure. The processing of all face aspects activated the core face-network across the age range, as well as additional and partially separable regions. Small task-specific activations in posterior regions were found to increase with age and were distinct from more widespread activations that varied as a function of individual task performance (but not of age). Our results demonstrate that activity during face-processing changes with age, and these effects are still observed when controlling for changes associated with differences in task performance. Moreover, we found that changes in white and gray matter volume were associated with changes in activation with age and performance in the out-of-scanner tasks. PMID:22661406

Parvovirus Capsid Structures Required for Infection: Mutations Controlling Receptor Recognition and Protease Cleavages

PubMed Central

Callaway, Heather M.; Feng, Kurtis H.; Lee, Donald W.; Pinard, Melissa; McKenna, Robert; Agbandje-McKenna, Mavis; Hafenstein, Susan

2016-01-01

ABSTRACT Parvovirus capsids are small but complex molecular machines responsible for undertaking many of the steps of cell infection, genome packing, and cell-to-cell as well as host-to-host transfer. The details of parvovirus infection of cells are still not fully understood, but the processes must involve small changes in the capsid structure that allow the endocytosed virus to escape from the endosome, pass through the cell cytoplasm, and deliver the single-stranded DNA (ssDNA) genome to the nucleus, where viral replication occurs. Here, we examine capsid substitutions that eliminate canine parvovirus (CPV) infectivity and identify how those mutations changed the capsid structure or altered interactions with the infectious pathway. Amino acid substitutions on the exterior surface of the capsid (Gly299Lys/Ala300Lys) altered the binding of the capsid to transferrin receptor type 1 (TfR), particularly during virus dissociation from the receptor, but still allowed efficient entry into both feline and canine cells without successful infection. These substitutions likely control specific capsid structural changes resulting from TfR binding required for infection. A second set of changes on the interior surface of the capsid reduced viral infectivity by >100-fold and included two cysteine residues and neighboring residues. One of these substitutions, Cys270Ser, modulates a VP2 cleavage event found in ∼10% of the capsid proteins that also was shown to alter capsid stability. A neighboring substitution, Pro272Lys, significantly reduced capsid assembly, while a Cys273Ser change appeared to alter capsid transport from the nucleus. These mutants reveal additional structural details that explain cell infection processes of parvovirus capsids. IMPORTANCE Parvoviruses are commonly found in both vertebrate and invertebrate animals and cause widespread disease. They are also being developed as oncolytic therapeutics and as gene therapy vectors. Most functions involved in infection or transduction are mediated by the viral capsid, but the structure-function correlates of the capsids and their constituent proteins are still incompletely understood, especially in relation to identifying capsid processes responsible for infection and release from the cell. Here, we characterize the functional effects of capsid protein mutations that result in the loss of virus infectivity, giving a better understanding of the portions of the capsid that mediate essential steps in successful infection pathways and how they contribute to viral infectivity. PMID:27847360

Parvovirus Capsid Structures Required for Infection: Mutations Controlling Receptor Recognition and Protease Cleavages.

PubMed

Callaway, Heather M; Feng, Kurtis H; Lee, Donald W; Allison, Andrew B; Pinard, Melissa; McKenna, Robert; Agbandje-McKenna, Mavis; Hafenstein, Susan; Parrish, Colin R

2017-01-15

Parvovirus capsids are small but complex molecular machines responsible for undertaking many of the steps of cell infection, genome packing, and cell-to-cell as well as host-to-host transfer. The details of parvovirus infection of cells are still not fully understood, but the processes must involve small changes in the capsid structure that allow the endocytosed virus to escape from the endosome, pass through the cell cytoplasm, and deliver the single-stranded DNA (ssDNA) genome to the nucleus, where viral replication occurs. Here, we examine capsid substitutions that eliminate canine parvovirus (CPV) infectivity and identify how those mutations changed the capsid structure or altered interactions with the infectious pathway. Amino acid substitutions on the exterior surface of the capsid (Gly299Lys/Ala300Lys) altered the binding of the capsid to transferrin receptor type 1 (TfR), particularly during virus dissociation from the receptor, but still allowed efficient entry into both feline and canine cells without successful infection. These substitutions likely control specific capsid structural changes resulting from TfR binding required for infection. A second set of changes on the interior surface of the capsid reduced viral infectivity by >100-fold and included two cysteine residues and neighboring residues. One of these substitutions, Cys270Ser, modulates a VP2 cleavage event found in ∼10% of the capsid proteins that also was shown to alter capsid stability. A neighboring substitution, Pro272Lys, significantly reduced capsid assembly, while a Cys273Ser change appeared to alter capsid transport from the nucleus. These mutants reveal additional structural details that explain cell infection processes of parvovirus capsids. Parvoviruses are commonly found in both vertebrate and invertebrate animals and cause widespread disease. They are also being developed as oncolytic therapeutics and as gene therapy vectors. Most functions involved in infection or transduction are mediated by the viral capsid, but the structure-function correlates of the capsids and their constituent proteins are still incompletely understood, especially in relation to identifying capsid processes responsible for infection and release from the cell. Here, we characterize the functional effects of capsid protein mutations that result in the loss of virus infectivity, giving a better understanding of the portions of the capsid that mediate essential steps in successful infection pathways and how they contribute to viral infectivity. Copyright © 2017 American Society for Microbiology.

Small angle neutron scattering study on the structural variation of lysozyme in bioprotectants

NASA Astrophysics Data System (ADS)

Koda, Shota; Takayama, Haruki; Shibata, Tomohiko; Mori, Tatsuya; Kojima, Seiji; Park, In-Sung; Shin, Tae-Gyu

2015-05-01

The thermal denaturation and subsequent structural variation of lysozyme in various bioprotectant candidate solutions such as trehalose and choline acetate have been investigated by using small angle neutron scattering and differential scanning calorimetry. The gyration radius shows little change with the addition of additives in a native state at room temperature. On heating the lysozyme solution, a remarkable increase in the gyration radius is observed at temperatures above the denaturation temperature without any bioprotectants. Such an increase is suppressed by the additives owing to the intermolecular interactions between the lysozyme molecules and the bioprotectants of trehalose and choline acetate. The fractal dimension of lysozyme varies slightly with the addition of the bioprotectant solutions, and shows a remarkable drop in the vicinity of the denaturation temperature for all the solutions.

Improvement of chemical composition, structure and mechanical properties of heat-resistant chromium-nickel alloy

NASA Astrophysics Data System (ADS)

Varlamova, S.; Trushnikova, A.; Rumyantsev, B.; Butrim, V.; Simonov, V.

2018-04-01

A thermodynamic analysis of a multicomponent system of the Cr-Ni alloy (Cr-32Ni-1,5W-0,25V-0,5Ti) with small additions of refractory metals was carried out. The microstructure and phase composition of the base alloy (I) and alloy with additional alloying (II) were studied. The effect of additives on the mechanical properties of the Cr-Ni alloy at 20, 900 and 1080 °C was shown. The microstructure of alloys I and II was studied in the fracture zone of samples after tensile tests at different temperatures. We studied the effect of small additives on the microstructure of alloys and changes in the morphology of the structural components (phases) as a function of temperature and degree of deformation.

Structural characterization of casein micelles: shape changes during film formation.

PubMed

Gebhardt, R; Vendrely, C; Kulozik, U

2011-11-09

The objective of this study was to determine the effect of size-fractionation by centrifugation on the film structure of casein micelles. Fractionated casein micelles in solution were asymmetrically distributed with a small distribution width as measured by dynamic light scattering. Films prepared from the size-fractionated samples showed a smooth surface in optical microscopy images and a homogeneous microstructure in atomic force micrographs. The nano- and microstructure of casein films was probed by micro-beam grazing incidence small angle x-ray scattering (μGISAXS). Compared to the solution measurements, the sizes determined in the film were larger and broadly distributed. The measured GISAXS patterns clearly deviate from those simulated for a sphere and suggest a deformation of the casein micelles in the film. © 2011 IOP Publishing Ltd

Targeting Mycobacterium tuberculosis nucleoid-associated protein HU with structure-based inhibitors

NASA Astrophysics Data System (ADS)

Bhowmick, Tuhin; Ghosh, Soumitra; Dixit, Karuna; Ganesan, Varsha; Ramagopal, Udupi A.; Dey, Debayan; Sarma, Siddhartha P.; Ramakumar, Suryanarayanarao; Nagaraja, Valakunja

2014-06-01

The nucleoid-associated protein HU plays an important role in maintenance of chromosomal architecture and in global regulation of DNA transactions in bacteria. Although HU is essential for growth in Mycobacterium tuberculosis (Mtb), there have been no reported attempts to perturb HU function with small molecules. Here we report the crystal structure of the N-terminal domain of HU from Mtb. We identify a core region within the HU-DNA interface that can be targeted using stilbene derivatives. These small molecules specifically inhibit HU-DNA binding, disrupt nucleoid architecture and reduce Mtb growth. The stilbene inhibitors induce gene expression changes in Mtb that resemble those induced by HU deficiency. Our results indicate that HU is a potential target for the development of therapies against tuberculosis.

Protein structure refinement using a quantum mechanics-based chemical shielding predictor.

PubMed

Bratholm, Lars A; Jensen, Jan H

2017-03-01

The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of a protein backbone and CB chemical shifts (ProCS15, PeerJ , 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1-0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiments that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differ in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural change may be due to force field deficiencies. The overall accuracy of the empirical methods are slightly improved by annealing the CHARMM structure with ProCS15, which may suggest that the minor structural changes introduced by ProCS15-based annealing improves the accuracy of the protein structures. Having established that QM-based chemical shift prediction can deliver the same accuracy as empirical shift predictors we hope this can help increase the accuracy of related approaches such as QM/MM or linear scaling approaches or interpreting protein structural dynamics from QM-derived chemical shift.

The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery.

PubMed

Papaleo, Elena; Saladino, Giorgio; Lambrughi, Matteo; Lindorff-Larsen, Kresten; Gervasio, Francesco Luigi; Nussinov, Ruth

2016-06-08

Proteins are dynamic entities that undergo a plethora of conformational changes that may take place on a wide range of time scales. These changes can be as small as the rotation of one or a few side-chain dihedral angles or involve concerted motions in larger portions of the three-dimensional structure; both kinds of motions can be important for biological function and allostery. It is becoming increasingly evident that "connector regions" are important components of the dynamic personality of protein structures. These regions may be either disordered loops, i.e., poorly structured regions connecting secondary structural elements, or linkers that connect entire protein domains. Experimental and computational studies have, however, revealed that these regions are not mere connectors, and their role in allostery and conformational changes has been emerging in the last few decades. Here we provide a detailed overview of the structural properties and classification of loops and linkers, as well as a discussion of the main computational methods employed to investigate their function and dynamical properties. We also describe their importance for protein dynamics and allostery using as examples key proteins in cellular biology and human diseases such as kinases, ubiquitinating enzymes, and transcription factors.

Photonic crystal-based optical biosensor: a brief investigation

NASA Astrophysics Data System (ADS)

Divya, J.; Selvendran, S.; Sivanantha Raja, A.

2018-06-01

In this paper, a two-dimensional photonic crystal biosensor for medical applications based on two waveguides and a nanocavity was explored with different shoulder-coupled nanocavity structures. The most important biosensor parameters, like the sensitivity and quality factor, can be significantly improved. By injecting an analyte into a sensing hole, the refractive index of the hole was changed. This refractive index biosensor senses the changes and shifts its operating wavelength accordingly. The transmission characteristics of light in the biosensor under different refractive indices that correspond to the change in the analyte concentration are analyzed by the finite-difference time-domain method. The band gap for each structure is designed and observed by the plane wave expansion method. These proposed structures are designed to obtain an analyte refractive index variation of about 1–1.5 in an optical wavelength range of 1.250–1.640 µm. Accordingly, an improved sensitivity of 136.6 nm RIU‑1 and a quality factor as high as 3915 is achieved. An important feature of this structure is its very small dimensions. Such a combination of attributes makes the designed structure a promising element for label-free biosensing applications.

Reconceptualizing gender and reconstructing social life: Ugandan women and the path to national development.

PubMed

Wakoko, F; Lobao, L

1996-01-01

This article focuses on how women's responses to crisis and social change in Uganda signal attempts to achieve a more gender-equal social life while facilitating national development. After an introduction, the article reviews research on women's response to change and points out the limitations of this research. In the next section, the article provides a historical overview of Uganda's gender system and the political and economic changes that occurred during the 1970s and early 1980s. The third main section argues that while the social structural changes created widespread hardship, they also provided openings for women to advance their interests. Thus, the National Resistance Movement of the mid-1980s responded to the mobilization of women by creating new avenues for women to participate in political life and have control over financial resources. Traditional ideologies, divisions of labor, and the social construction of gender have also been altered by such factors as the involvement of women in the guerrilla movement and the key developmental role played by nongovernmental organizations and women's groups. The article continues by considering the effect of these changes on contemporary gender relations. Data from a sampling of women and men from two regions of the country and of small business owners provide the basis for a discussion of the different strategies (such as small scale entrepreneurship and networking) employed by women to meet their daily and longterm needs. It is concluded that women's attempts to change their lives have influenced macrolevel social structure. However, it remains to be seen whether these postinsurgency gains can be sustained.

Robustness of plant-insect herbivore interaction networks to climate change in a fragmented temperate forest landscape.

PubMed

Bähner, K W; Zweig, K A; Leal, I R; Wirth, R

2017-10-01

Forest fragmentation and climate change are among the most severe and pervasive forms of human impact. Yet, their combined effects on plant-insect herbivore interaction networks, essential components of forest ecosystems with respect to biodiversity and functioning, are still poorly investigated, particularly in temperate forests. We addressed this issue by analysing plant-insect herbivore networks (PIHNs) from understories of three managed beech forest habitats: small forest fragments (2.2-145 ha), forest edges and forest interior areas within three continuous control forests (1050-5600 ha) in an old hyper-fragmented forest landscape in SW Germany. We assessed the impact of forest fragmentation, particularly edge effects, on PIHNs and the resulting differences in robustness against climate change by habitat-wise comparison of network topology and biologically realistic extinction cascades of networks following scores of vulnerability to climate change for the food plant species involved. Both the topological network metrics (complexity, nestedness, trophic niche redundancy) and robustness to climate change strongly increased in forest edges and fragments as opposed to the managed forest interior. The nature of the changes indicates that human impacts modify network structure mainly via host plant availability to insect herbivores. Improved robustness of PIHNs in forest edges/small fragments to climate-driven extinction cascades was attributable to an overall higher thermotolerance across plant communities, along with positive effects of network structure. The impoverishment of PIHNs in managed forest interiors and the suggested loss of insect diversity from climate-induced co-extinction highlight the need for further research efforts focusing on adequate silvicultural and conservation approaches.

13 CFR 108.470 - SBA approval of merger, consolidation, or reorganization of NMVC Company.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false SBA approval of merger, consolidation, or reorganization of NMVC Company. 108.470 Section 108.470 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION NEW MARKETS VENTURE CAPITAL (âNMVCâ) PROGRAM Changes in Ownership, Structure, or...

Production Process for Strong, Light Ceramic Tiles

NASA Technical Reports Server (NTRS)

Holmquist, G. R.; Cordia, E. R.; Tomer, R. S.

1985-01-01

Proportions of ingredients and sintering time/temperature schedule changed. Production process for lightweight, high-strength ceramic insulating tiles for Space Shuttle more than just scaled-up version of laboratory process for making small tiles. Boron in aluminum borosilicate fibers allows fusion at points where fibers contact each other during sintering, thereby greatly strengthening tiles structure.

Biomimetic Nanosensor Arrays for Selective Small Molecule Detection

DTIC Science & Technology

2012-02-21

Nanowires. Science 303, 213-217 (2004). 22. Pesenti, M. E. et al. Structural Basis of the Honey Bee PBP Pheromone and pH-Induced Conformational Change. J...receptors on the antennal olfactory sensilla. The exceptional ability of insects to detect chemical signatures has led to the use of trained bees in a

13 CFR 108.440 - Standards governing prior SBA approval for a proposed transfer of Control.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false Standards governing prior SBA approval for a proposed transfer of Control. 108.440 Section 108.440 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION NEW MARKETS VENTURE CAPITAL (âNMVCâ) PROGRAM Changes in Ownership, Structure, or...

13 CFR 108.440 - Standards governing prior SBA approval for a proposed transfer of Control.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 13 Business Credit and Assistance 1 2013-01-01 2013-01-01 false Standards governing prior SBA approval for a proposed transfer of Control. 108.440 Section 108.440 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION NEW MARKETS VENTURE CAPITAL (âNMVCâ) PROGRAM Changes in Ownership, Structure, or...

13 CFR 108.440 - Standards governing prior SBA approval for a proposed transfer of Control.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 13 Business Credit and Assistance 1 2012-01-01 2012-01-01 false Standards governing prior SBA approval for a proposed transfer of Control. 108.440 Section 108.440 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION NEW MARKETS VENTURE CAPITAL (âNMVCâ) PROGRAM Changes in Ownership, Structure, or...

13 CFR 108.440 - Standards governing prior SBA approval for a proposed transfer of Control.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 13 Business Credit and Assistance 1 2011-01-01 2011-01-01 false Standards governing prior SBA approval for a proposed transfer of Control. 108.440 Section 108.440 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION NEW MARKETS VENTURE CAPITAL (âNMVCâ) PROGRAM Changes in Ownership, Structure, or...

Interface colloidal robotic manipulator

DOEpatents

Aronson, Igor; Snezhko, Oleksiy

2015-08-04

A magnetic colloidal system confined at the interface between two immiscible liquids and energized by an alternating magnetic field dynamically self-assembles into localized asters and arrays of asters. The colloidal system exhibits locomotion and shape change. By controlling a small external magnetic field applied parallel to the interface, structures can capture, transport, and position target particles.

In vivo digestion of bovine milk fat globules: effect of processing and interfacial structural changes. II. Upper digestive tract digestion.

PubMed

Gallier, Sophie; Zhu, Xiang Q; Rutherfurd, Shane M; Ye, Aiqian; Moughan, Paul J; Singh, Harjinder

2013-12-01

The aim of this research was to study the effect of milk processing on the in vivo upper digestive tract digestion of milk fat globules. Fasted rats were serially gavaged over a 5h period with cream from raw, pasteurised, or pasteurised and homogenised milk. Only a few intact dietary proteins and peptides were present in the small intestinal digesta. Significantly (P<0.05) more longer chain (C≥10) fatty acids were present in the digesta of rats gavaged with raw (448 mg g(-1) digesta dry matter (DDM)) and homogenised creams (528 mg g(-1) DDM), as compared to pasteurised and homogenised cream (249 mg g(-1) DDM). Microscopy techniques were used to investigate the structural changes during digestion. Liquid-crystalline lamellar phases surrounding the fat globules, fatty acid soap crystals and lipid-mucin interactions were evident in all small intestinal digesta. Overall, the pasteurised and homogenised cream appeared to be digested to a greater extent. Copyright © 2013 Elsevier Ltd. All rights reserved.

Imaging phase slip dynamics in micron-size superconducting rings

NASA Astrophysics Data System (ADS)

Polshyn, Hryhoriy; Naibert, Tyler R.; Budakian, Raffi

2018-05-01

We present a scanning probe technique for measuring the dynamics of individual fluxoid transitions in multiply connected superconducting structures. In these measurements, a small magnetic particle attached to the tip of a silicon cantilever is scanned over a micron-size superconducting ring fabricated from a thin aluminum film. We find that near the superconducting transition temperature of the aluminum, the dissipation and frequency of the cantilever changes significantly at particular locations where the tip-induced magnetic flux penetrating the ring causes the two lowest-energy fluxoid states to become nearly degenerate. In this regime, we show that changes in the cantilever frequency and dissipation are well-described by a stochastic resonance (SR) process, wherein small oscillations of the cantilever in the presence of thermally activated phase slips (TAPS) in the ring give rise to a dynamical force that modifies the mechanical properties of the cantilever. Using the SR model, we calculate the average fluctuation rate of the TAPS as a function of temperature over a 32-dB range in frequency, and we compare it to the Langer-Ambegaokar-McCumber-Halperin theory for TAPS in one-dimensional superconducting structures.

Reversible electric-field manipulation of the adsorption morphology and magnetic anisotropy of small Fe and Co clusters on graphene

NASA Astrophysics Data System (ADS)

Tanveer, M.; Dorantes-Dávila, J.; Pastor, G. M.

2017-12-01

First-principles electronic calculations show how the adsorption morphology, orbital magnetism, and magnetic anisotropy energy (MAE) of small CoN and FeN clusters (N ≤3 ) on graphene (G) can be reversibly controlled under the action of an external electric field (EF). A variety of cluster-specific and EF-induced effects are revealed, including (i) perpendicular or canted adsorption configurations of the dimers and trimers, (ii) significant morphology-dependent permanent dipole moments and electric susceptibilities, (iii) EF-induced reversible transitions among the different metastable adsorption morphologies of Fe3 and Co3 on graphene, (iv) qualitative changes in the MAE landscape driven by structural changes, (v) colossal values of the magnetic anisotropy Δ E ≃45 meV per atom in Co2/G , (vi) EF-induced spin-reorientation transitions in Co3/G , and (vii) reversibly tunable coercive field and blocking temperatures, which in some cases allow a barrierless magnetization reversal of the cluster. These remarkable electric and magnetic fingerprints open new possibilities of characterizing and exploiting the size- and structural-dependent properties of magnetic nanostructures at surfaces.

Morphological transformations in the magnetite biomineralizing protein Mms6 in iron solutions: A small-angle x-ray scattering study

DOE PAGES

Zhang, Honghu; Liu, Xunpei; Feng, Shuren; ...

2015-02-10

In this study, magnetotactic bacteria that produce magnetic nanocrystals of uniform size and well-defined morphologies have inspired the use of biomineralization protein Mms6 to promote formation of uniform magnetic nanocrystals in vitro. Small angle X-ray scattering (SAXS) studies in physiological solutions reveal that Mms6 forms compact globular three-dimensional (3D) micelles (approximately 10 nm in diameter) that are, to a large extent, independent of concentration. In the presence of iron ions in the solutions, the general micellar morphology is preserved, however, with associations among micelles that are induced by iron ions. Compared with Mms6, the m2Mms6 mutant (with the sequence ofmore » hydroxyl/carboxyl containing residues in the C-terminal domain shuffled) exhibits subtle morphological changes in the presence of iron ions in solutions. The analysis of the SAXS data is consistent with a hierarchical core–corona micellar structure similar to that found in amphiphilic polymers. The addition of ferric and ferrous iron ions to the protein solution induces morphological changes in the micellar structure by transforming the 3D micelles into objects of reduced dimensionality of 2, with fractal-like characteristics (including Gaussian-chain-like) or, alternatively, platelet-like structures.« less

Innovative design of parabolic reflector light guiding structure

NASA Astrophysics Data System (ADS)

Whang, Allen J.; Tso, Chun-Hsien; Chen, Yi-Yung

2008-02-01

Due to the idea of everlasting green architecture, it is of increasing importance to guild natural light into indoors. The advantages are multifold - to have better color rendering index, excellent energy savings from environments viewpoints and make humans more healthy, etc. Our search is to design an innovative structure, to convert outdoor sun light impinges on larger surfaces, into near linear light beam sources, later convert this light beam into near point sources which enters the indoor spaces then can be used as lighting sources indoors. We are not involved with the opto-electrical transformation, to the guild light into to the building, to perform the illumination, as well as the imaging function. Because non-imaging optics, well known for apply to the solar concentrators, that can use non-imaging structures to fulfill our needs, which can also be used as energy collectors in solar energy devices. Here, we have designed a pair of large and small parabolic reflector, which can be used to collect daylight and change area from large to small. Then we make a light-guide system that is been designed by us use of this parabolic reflector to guide the collection light, can pick up the performance for large surface source change to near linear source and a larger collection area.

Structural basis for drug-induced allosteric changes to human β-cardiac myosin motor activity

PubMed Central

Winkelmann, Donald A.; Forgacs, Eva; Miller, Matthew T.; Stock, Ann M.

2015-01-01

Omecamtiv Mecarbil (OM) is a small molecule allosteric effector of cardiac myosin that is in clinical trials for treatment of systolic heart failure. A detailed kinetic analysis of cardiac myosin has shown that the drug accelerates phosphate release by shifting the equilibrium of the hydrolysis step towards products, leading to a faster transition from weak to strong actin-bound states. The structure of the human β-cardiac motor domain (cMD) with OM bound reveals a single OM-binding site nestled in a narrow cleft separating two domains of the human cMD where it interacts with the key residues that couple lever arm movement to the nucleotide state. In addition, OM induces allosteric changes in three strands of the β-sheet that provides the communication link between the actin-binding interface and the nucleotide pocket. The OM-binding interactions and allosteric changes form the structural basis for the kinetic and mechanical tuning of cardiac myosin. PMID:26246073

Modeling structure and resilience of the dark network.

PubMed

De Domenico, Manlio; Arenas, Alex

2017-02-01

While the statistical and resilience properties of the Internet are no longer changing significantly across time, the Darknet, a network devoted to keep anonymous its traffic, still experiences rapid changes to improve the security of its users. Here we study the structure of the Darknet and find that its topology is rather peculiar, being characterized by a nonhomogeneous distribution of connections, typical of scale-free networks; very short path lengths and high clustering, typical of small-world networks; and lack of a core of highly connected nodes. We propose a model to reproduce such features, demonstrating that the mechanisms used to improve cybersecurity are responsible for the observed topology. Unexpectedly, we reveal that its peculiar structure makes the Darknet much more resilient than the Internet (used as a benchmark for comparison at a descriptive level) to random failures, targeted attacks, and cascade failures, as a result of adaptive changes in response to the attempts of dismantling the network across time.

Modeling structure and resilience of the dark network

NASA Astrophysics Data System (ADS)

De Domenico, Manlio; Arenas, Alex

2017-02-01

While the statistical and resilience properties of the Internet are no longer changing significantly across time, the Darknet, a network devoted to keep anonymous its traffic, still experiences rapid changes to improve the security of its users. Here we study the structure of the Darknet and find that its topology is rather peculiar, being characterized by a nonhomogeneous distribution of connections, typical of scale-free networks; very short path lengths and high clustering, typical of small-world networks; and lack of a core of highly connected nodes. We propose a model to reproduce such features, demonstrating that the mechanisms used to improve cybersecurity are responsible for the observed topology. Unexpectedly, we reveal that its peculiar structure makes the Darknet much more resilient than the Internet (used as a benchmark for comparison at a descriptive level) to random failures, targeted attacks, and cascade failures, as a result of adaptive changes in response to the attempts of dismantling the network across time.

Excitation energy shift and size difference of low-energy levels in p -shell Λ hypernuclei

NASA Astrophysics Data System (ADS)

Kanada-En'yo, Yoshiko

2018-02-01

Structures of low-lying 0 s -orbit Λ states in p -shell Λ hypernuclei (ZAΛ) are investigated by applying microscopic cluster models for nuclear structure and a single-channel folding potential model for a Λ particle. For A >10 systems, the size reduction of core nuclei is small, and the core polarization effect is regarded as a higher-order perturbation in the Λ binding. The present calculation qualitatively describes the systematic trend of experimental data for excitation energy change from Z-1A to ZAΛ, in A >10 systems. The energy change shows a clear correlation with the nuclear size difference between the ground and excited states. In Li7Λ and Be9Λ, the significant shrinkage of cluster structures occurs consistently with the prediction of other calculations.

Collective Structural Changes in Vermiculite Clay Suspensions Induced by Cesium Ions

NASA Astrophysics Data System (ADS)

Motokawa, Ryuhei; Endo, Hitoshi; Yokoyama, Shingo; Nishitsuji, Shotaro; Kobayashi, Tohru; Suzuki, Shinichi; Yaita, Tsuyoshi

2014-10-01

Following the Fukushima Daiichi nuclear disaster in 2011, Cs radioisotopes have been dispersed over a wide area. Most of the Cs has remained on the surface of the soil because Cs+ is strongly adsorbed in the interlayer spaces of soil clays, particularly vermiculite. We have investigated the microscopic structure of an aqueous suspension of vermiculite clay over a wide length scale (1-1000 Å) by small-angle X-ray scattering. We determined the effect of the adsorption behavior of Cs+ on the structural changes in the clay. It was found that the abruption of the clay sheets was induced by the localization of Cs+ at the interlayer. This work provides important information for predicting the environmental fate of radioactive Cs in polluted areas, and for developing methods to extract Cs from the soil and reduce radioactivity.

Structural integrity and containment aspects of small gas turbine engines

NASA Astrophysics Data System (ADS)

Gupta, S. S.; Gomuc, R.

1994-03-01

Structural integrity of rotating components in gas turbine engines is very crucial since their failure implies high impact energy, which, if uncontained, could mean damage to aircraft structures, controls, and so forth, and, in the worst scenario, even loss of lives. This final consequence has led to very stringent airworthiness regulations for engine/aircraft certifications. This paper discusses the historical statistics of noncontainment events in turbofans, turboprops, and turboshafts and shows how the damage severity varies between different applications and how changes to regulations are continuing in order to improve the reliability of aircraft/rotorcraft. The paper also presents design challenges resulting from the analysis complexity of containment/noncontainment event and the way Pratt & Whitney Canada design/analysis/test system caters to all the requirements. The weight and cost impact of possible changes to current regulations are also presented.

Molecular-Scale Features that Govern the Effects of O-Glycosylation on a Carbohydrate-Binding Module

DOE PAGES

Guan, Xiaoyang; Chaffey, Patrick K.; Zeng, Chen; ...

2015-09-21

The protein glycosylation is a ubiquitous post-translational modification in all kingdoms of life. Despite its importance in molecular and cellular biology, the molecular-level ramifications of O-glycosylation on biomolecular structure and function remain elusive. Here, we took a small model glycoprotein and changed the glycan structure and size, amino acid residues near the glycosylation site, and glycosidic linkage while monitoring any corresponding changes to physical stability and cellulose binding affinity. The results of this study reveal the collective importance of all the studied features in controlling the most pronounced effects of O-glycosylation in this system. This study suggests the possibility ofmore » designing proteins with multiple improved properties by simultaneously varying the structures of O-glycans and amino acids local to the glycosylation site.« less

The effect of low temperature thermal annealing on the magnetic properties of Heusler Ni-Mn-Sn melt-spun ribbons

NASA Astrophysics Data System (ADS)

Llamazares, J. L. Sánchez; Quintana-Nedelcos, A.; Ríos-Jara, D.; Sánchez-Valdes, C. F.; García-Fernández, T.; García, C.

2016-03-01

We report the effect of low temperature vacuum annealing (823 K; 550 °C) on the elemental chemical composition, structural phase transition temperatures, phase structure, and magnetic properties of Ni50.6Mn36.3Sn13.1 as-solidified ribbons. Their elemental chemical composition, highly oriented columnar-like microstructure and single-phase character (L21-type crystal structure for austenite) remain unchanged after this low temperature annealing. Annealed ribbons show a reduction of interatomic distances which lead to a small change in the characteristic phase transition temperatures ( 3-6 K) but to a significant rise of 73 and 63% in the saturation magnetization of the martensite and austenite phases, respectively, that can be strictly ascribed to the strengthening of ferromagnetic interactions due to the change in interatomic distances.

Effect of laser irradiation on the functional activity of enzymes with different structural complexity

NASA Astrophysics Data System (ADS)

Ostrovtsova, Svetlana A.; Volodenkov, Alexander P.; Maskevich, Alexander A.; Artsukevich, Irina M.; Anufrik, Slavomir S.; Makarchikov, Alexander F.; Chernikevich, Ivan P.; Stepuro, Vitali I.

1998-05-01

Three enzymes differing in their structural composition were irradiated by UV lasers to study the effect of temperature, protein concentration and addition of small molecules on their sensitivity to radiation exposure. The laser-induced effects were due to the structural complexity of the protein molecules and depended on the dose applied, the wavelength and the density of irradiation. The multi-enzyme 2- oxoglutarate dehydrogenase complex was subjected to pronounced irradiation-induced changes whereas the response of the two other enzymes was less significant. Reduction of the protein levels in irradiated samples was important under the XeCl laser coercion and the effects depended on the doses applied. The laser irradiation effects are suggested to be realized by means of conformational changes in the protein molecules and intermolecular association- dissociation processes.

The crust structure of the Morasko meteorite - a preliminary hypothesis

NASA Astrophysics Data System (ADS)

Stankowski, Wojciech T. J.

2017-03-01

A small piece of the Morasko meteorite, weighing 970 g, yields traces of its journey through the Earth's atmosphere and of its impact into a mineral substrate, such as reflected in the meteorite's crust. This is seen in the crust structure in the form of sintered as well as fusion and semi-fusion layers for which ablative niches are optimum sites. Subsequent weathering processes have resulted in significant mineralogical changes in the crusts. The meteorite crusts originated during polygenetic processes.

Fatigue Technology Assessment and Strategies for Fatigue Avoidance in Marine Structures

DTIC Science & Technology

1992-06-01

time history. xii MODELING ERROR (Xme) : Typically defined as the ratio of actual behavior of the structure to the one predicted by the model. It is...and temperature changes may be important to fatigue in a local component, these loadings are not a major concern in the global behavior of typical...Reference 3.1) to assess fracture behavior in a low toughness HAZ indicated that a small low- toughness area in the HAZ can be masked by the higher

Structure and mechanical properties of parts obtained by selective laser melting of metal powder based on intermetallic compounds Ni3Al

NASA Astrophysics Data System (ADS)

Smelov, V. G.; Sotov, A. V.; Agapovichev, A. V.; Nosova, E. A.

2018-03-01

The structure and mechanical properties of samples are obtained from metal powder based on intermetallic compound by selective laser melting. The chemical analysis of the raw material and static tensile test of specimens were made. Change in the samples’ structure and mechanical properties after homogenization during four and twenty-four hours were investigated. A small-sized combustion chamber of a gas turbine engine was performed by the selective laser melting method. The print combustion chamber was subjected to the gas-dynamic test in a certain temperature and time range.

Structural and magnetic properties of non-stoichiometric Fe1-xO thin films

NASA Astrophysics Data System (ADS)

Muhammed Shameem P., V.; Mekala, Laxman; Kumar, M. Senthil

2018-04-01

The Fe1-xO thin films of various iron deficiencies (x) have been grown at ambient temperature by reactive dc magnetron sputtering technique and their structural and magnetic properties are studied. The structural study shows that the films are polycrystalline. As the iron content (1-x) varies from 0.924 to 0.855 a clear consistent change in the preferential orientation of the grains from [111] to the [200] direction is observed. The magnetization measurements show the possible existence of small superparamagnetic defect clusters at 300 K and large spinel-type defect clusters below the Neel temperature.

Small structural changes on a hydroquinone scaffold determine the complex I inhibition or uncoupling of tumoral oxidative phosphorylation.

PubMed

Urra, Félix A; Córdova-Delgado, Miguel; Lapier, Michel; Orellana-Manzano, Andrea; Acevedo-Arévalo, Luis; Pessoa-Mahana, Hernán; González-Vivanco, Jaime M; Martínez-Cifuentes, Maximiliano; Ramírez-Rodríguez, Oney; Millas-Vargas, Juan Pablo; Weiss-López, Boris; Pavani, Mario; Ferreira, Jorge; Araya-Maturana, Ramiro

2016-01-15

Mitochondria participate in several distinctiveness of cancer cell, being a promising target for the design of anti-cancer compounds. Previously, we described that ortho-carbonyl hydroquinone scaffold 14 inhibits the complex I-dependent respiration with selective anti-proliferative effect on mouse mammary adenocarcinoma TA3/Ha cancer cells; however, the structural requirements of this hydroquinone scaffold to affect the oxidative phosphorylation (OXPHOS) of cancer cells have not been studied in detail. Here, we characterize the mitochondrial metabolism of TA3/Ha cancer cells, which exhibit a high oxidative metabolism, and evaluate the effect of small structural changes of the hydroquinone scaffold 14 on the respiration of this cell line. Our results indicate that these structural changes modify the effect on OXPHOS, obtaining compounds with three alternative actions: inhibitors of complex I-dependent respiration, uncoupler of OXPHOS and compounds with both actions. To confirm this, the effect of a bicyclic hydroquinone (9) was evaluated in isolated mitochondria. Hydroquinone 9 increased mitochondrial respiration in state 4o without effects on the ADP-stimulated respiration (state 3ADP), decreasing the complexes I and II-dependent respiratory control ratio. The effect on mitochondrial respiration was reversed by 6-ketocholestanol addition, indicating that this hydroquinone is a protonophoric uncoupling agent. In intact TA3/Ha cells, hydroquinone 9 caused mitochondrial depolarization, decreasing intracellular ATP and NAD(P)H levels and GSH/GSSG ratio, and slightly increasing the ROS levels. Moreover, it exhibited selective NAD(P)H availability-dependent anti-proliferative effect on cancer cells. Therefore, our results indicate that the ortho-carbonyl hydroquinone scaffold offers the possibility to design compounds with specific actions on OXPHOS of cancer cells.

Crystal Structure of an Activated Variant of Small Heat Shock Protein Hsp16.5

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

Mchaourab, Hassane S.; Lin, Yi-Lun; Spiller, Benjamin W.

How does the sequence of a single small heat shock protein (sHSP) assemble into oligomers of different sizes? To gain insight into the underlying structural mechanism, we determined the crystal structure of an engineered variant of Methanocaldococcus jannaschii Hsp16.5 wherein a 14 amino acid peptide from human heat shock protein 27 (Hsp27) was inserted at the junction of the N-terminal region and the {alpha}-crystallin domain. In response to this insertion, the oligomer shell expands from 24 to 48 subunits while maintaining octahedral symmetry. Oligomer rearrangement does not alter the fold of the conserved {alpha}-crystallin domain nor does it disturb themore » interface holding the dimeric building block together. Rather, the flexible C-terminal tail of Hsp16.5 changes its orientation relative to the {alpha}-crystallin domain which enables alternative packing of dimers. This change in orientation preserves a peptide-in-groove interaction of the C-terminal tail with an adjacent {beta}-sandwich, thereby holding the assembly together. The interior of the expanded oligomer, where substrates presumably bind, retains its predominantly nonpolar character relative to the outside surface. New large windows in the outer shell provide increased access to these substrate-binding regions, thus accounting for the higher affinity of this variant to substrates. Oligomer polydispersity regulates sHSPs chaperone activity in vitro and has been implicated in their physiological roles. The structural mechanism of Hsp16.5 oligomer flexibility revealed here, which is likely to be highly conserved across the sHSP superfamily, explains the relationship between oligomer expansion observed in disease-linked mutants and changes in chaperone activity.« less

Crystal structure of an activated variant of small heat shock protein Hsp16.5.

PubMed

McHaourab, Hassane S; Lin, Yi-Lun; Spiller, Benjamin W

2012-06-26

How does the sequence of a single small heat shock protein (sHSP) assemble into oligomers of different sizes? To gain insight into the underlying structural mechanism, we determined the crystal structure of an engineered variant of Methanocaldococcus jannaschii Hsp16.5 wherein a 14 amino acid peptide from human heat shock protein 27 (Hsp27) was inserted at the junction of the N-terminal region and the α-crystallin domain. In response to this insertion, the oligomer shell expands from 24 to 48 subunits while maintaining octahedral symmetry. Oligomer rearrangement does not alter the fold of the conserved α-crystallin domain nor does it disturb the interface holding the dimeric building block together. Rather, the flexible C-terminal tail of Hsp16.5 changes its orientation relative to the α-crystallin domain which enables alternative packing of dimers. This change in orientation preserves a peptide-in-groove interaction of the C-terminal tail with an adjacent β-sandwich, thereby holding the assembly together. The interior of the expanded oligomer, where substrates presumably bind, retains its predominantly nonpolar character relative to the outside surface. New large windows in the outer shell provide increased access to these substrate-binding regions, thus accounting for the higher affinity of this variant to substrates. Oligomer polydispersity regulates sHSPs chaperone activity in vitro and has been implicated in their physiological roles. The structural mechanism of Hsp16.5 oligomer flexibility revealed here, which is likely to be highly conserved across the sHSP superfamily, explains the relationship between oligomer expansion observed in disease-linked mutants and changes in chaperone activity.

Measuring hemodynamics in the developing heart tube with four-dimensional gated Doppler optical coherence tomography

NASA Astrophysics Data System (ADS)

Jenkins, Michael W.; Peterson, Lindsy; Gu, Shi; Gargesha, Madhusudhana; Wilson, David L.; Watanabe, Michiko; Rollins, Andrew M.

2010-11-01

Hemodynamics is thought to play a major role in heart development, yet tools to quantitatively assess hemodynamics in the embryo are sorely lacking. The especially challenging analysis of hemodynamics in the early embryo requires new technology. Small changes in blood flow could indicate when anomalies are initiated even before structural changes can be detected. Furthermore, small changes in the early embryo that affect blood flow could lead to profound abnormalities at later stages. We present a demonstration of 4-D Doppler optical coherence tomography (OCT) imaging of structure and flow, and present several new hemodynamic measurements on embryonic avian hearts at early stages prior to the formation of the four chambers. Using 4-D data, pulsed Doppler measurements could accurately be attained in the inflow and outflow of the heart tube. Also, by employing an en-face slice from the 4-D Doppler image set, measurements of stroke volume and cardiac output are obtained without the need to determine absolute velocity. Finally, an image plane orthogonal to the blood flow is used to determine shear stress by calculating the velocity gradient normal to the endocardium. Hemodynamic measurements will be crucial to identifying genetic and environmental factors that lead to congenital heart defects.

Tuning Interfacial Properties and Processes by Controlling the Rheology and Structure of Poly( N-isopropylacrylamide) Particles at Air/Water Interfaces.

PubMed

Maestro, Armando; Jones, Daniel; Sánchez de Rojas Candela, Carmen; Guzman, Eduardo; Duits, Michel H G; Cicuta, Pietro

2018-06-05

By combining controlled experiments on single interfaces with measurements on solitary bubbles and liquid foams, we show that poly( N-isopropylacrylamide) (PNIPAM) microgels assembled at air/water interfaces exhibit a solid to liquid transition changing the temperature, and that this is associated with the change in the interfacial microstructure of the PNIPAM particles around their volume phase transition temperature. We show that the solid behaves as a soft 2D colloidal glass, and that the existence of this solid/liquid transition offers an ideal platform to tune the permeability of air bubbles covered by PNIPAM and to control macroscopic foam properties such as drainage, stability, and foamability. PNIPAM particles on fluid interfaces allow new tunable materials, for example foam structures with variable mechanical properties upon small temperature changes.

The dead do not lie: using skeletal remains for rapid assessment of historical small-mammal community baselines

PubMed Central

Terry, Rebecca C.

2010-01-01

Conservation and restoration efforts are often hindered by a lack of historical baselines that pre-date intense anthropogenic environmental change. In this paper I document that natural accumulations of skeletal remains represent a potential source of high-quality data on the historical composition and structure of small-mammal communities. I do so by assessing the fidelity of modern, decadal and centennial-scale time-averaged samples of skeletal remains (concentrated by raptor predation) to the living small-mammal communities from which they are derived. To test the power of skeletal remains to reveal baseline shifts, I employ the design of a natural experiment, comparing two taphonomically similar Great Basin cave localities in areas where anthropogenic land-use practices have diverged within the last century. I find relative stasis at the undisturbed site, but document rapid restructuring of the small-mammal community at the site subjected to recent disturbance. I independently validate this result using historical trapping records to show that dead remains accurately capture both the magnitude and direction of this baseline shift. Surveys of skeletal remains therefore provide a simple, powerful and rapid alternative approach for gaining insight into the historical structure and dynamics of modern small-mammal communities. PMID:20031992

Structural characterization of metal binding to a cold-adapted frataxin.

PubMed

Noguera, Martín E; Roman, Ernesto A; Rigal, Juan B; Cousido-Siah, Alexandra; Mitschler, André; Podjarny, Alberto; Santos, Javier

2015-06-01

Frataxin is an evolutionary conserved protein that participates in iron metabolism. Deficiency of this small protein in humans causes a severe neurodegenerative disease known as Friedreich's ataxia. A number of studies indicate that frataxin binds iron and regulates Fe-S cluster biosynthesis. Previous structural studies showed that metal binding occurs mainly in a region of high density of negative charge. However, a comprehensive characterization of the binding sites is required to gain further insights into the mechanistic details of frataxin function. In this work, we have solved the X-ray crystal structures of a cold-adapted frataxin from a psychrophilic bacterium in the presence of cobalt or europium ions. We have identified a number of metal-binding sites, mainly solvent exposed, several of which had not been observed in previous studies on mesophilic homologues. No major structural changes were detected upon metal binding, although the structures exhibit significant changes in crystallographic B-factors. The analysis of these B-factors, in combination with crystal packing and RMSD among structures, suggests the existence of localized changes in the internal motions. Based on these results, we propose that bacterial frataxins possess binding sites of moderate affinity for a quick capture and transfer of iron to other proteins and for the regulation of Fe-S cluster biosynthesis, modulating interactions with partner proteins.

Multi-scale characterization of pore evolution in a combustion metamorphic complex, Hatrurim basin, Israel: Combining (ultra) small-angle neutron scattering and image analysis

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

Wang, Hsiu-Wen; Anovitz, Lawrence; Burg, Avihu

Backscattered scanning electron micrograph and ultra small- and small-angle neutron scattering data have been combined to provide statistically meaningful data on the pore/grain structure and pore evolution of combustion metamorphic complexes from the Hatrurim basin, Israel. Three processes, anti-sintering roughening, alteration of protolith (dehydration, decarbonation, and oxidation) and crystallization of high-temperature minerals, occurred simultaneously, leading to significant changes in observed pore/grain structures. Pore structures in the protoliths, and in lowand high-grade metamorphic rocks show surface (Ds) and mass (Dm) pore fractal geometries with gradual increases in both Ds and Dm values as a function of metamorphic grade. This suggests thatmore » increases in pore volume and formation of less branching pore networks are accompanied by a roughening of pore/grain interfaces. Additionally, pore evolution during combustion metamorphism is also characterized by reduced contributions from small-scale pores to the cumulative porosity in the high-grade rocks. At high temperatures, small-scale pores may be preferentially closed by the formation of high-temperature minerals, producing a rougher morphology with increasing temperature. Alternatively, large-scale pores may develop at the expense of small-scale pores. These observations (pore fractal geometry and cumulative porosity) indicate that the evolution of pore/grain structures is correlated with the growth of high-temperature phases and is a consequence of the energy balance between pore/grain surface energy and energy arising from heterogeneous phase contacts. The apparent pore volume density further suggests that the localized time/temperature development of the high-grade Hatrurim rocks is not simply an extension of that of the low-grade rocks. The former likely represents the "hot spots (burning foci)" in the overall metamorphic terrain while the latter may represent contact aureoles.« less

Mach-Zehnder Interferometer Refractive Index Sensor Based on a Plasmonic Channel Waveguide

PubMed Central

Lee, Da Eun; Lee, Young Jin; Shin, Eunso; Kwon, Soon-Hong

2017-01-01

A Mach-Zehnder interferometer based on a plasmonic channel waveguide is proposed for refractive index sensing. The structure, with a small physical footprint of 20 × 120 μm2, achieved a high figure of merit of 294. The cut-off frequency behaviour in the plasmonic channel waveguide resulted in a flat dispersion curve, which induces a 1.8 times larger change of the propagation constant for the given refractive index change compared with previously reported results. PMID:29120381

Effect of wrinkles on the surface area of graphene: toward the design of nanoelectronics.

PubMed

Qin, Zhao; Taylor, Michael; Hwang, Mary; Bertoldi, Katia; Buehler, Markus J

2014-11-12

Graphene has attracted intense attention to the use in extreme applications. However, its small thickness facilitates wrinkle formation, and it is not clear how such structural change affects its area-specific capacitance. Herein, we combine molecular dynamics and continuum mechanics-based simulations to study the changes in surface area induced by wrinkles. We find that the high specific surface area of graphene can only be affected up to 2% regardless of loading conditions, geometry, and defects.

Parasites Affect Food Web Structure Primarily through Increased Diversity and Complexity

PubMed Central

Dunne, Jennifer A.; Lafferty, Kevin D.; Dobson, Andrew P.; Hechinger, Ryan F.; Kuris, Armand M.; Martinez, Neo D.; McLaughlin, John P.; Mouritsen, Kim N.; Poulin, Robert; Reise, Karsten; Stouffer, Daniel B.; Thieltges, David W.; Williams, Richard J.; Zander, Claus Dieter

2013-01-01

Comparative research on food web structure has revealed generalities in trophic organization, produced simple models, and allowed assessment of robustness to species loss. These studies have mostly focused on free-living species. Recent research has suggested that inclusion of parasites alters structure. We assess whether such changes in network structure result from unique roles and traits of parasites or from changes to diversity and complexity. We analyzed seven highly resolved food webs that include metazoan parasite data. Our analyses show that adding parasites usually increases link density and connectance (simple measures of complexity), particularly when including concomitant links (links from predators to parasites of their prey). However, we clarify prior claims that parasites “dominate” food web links. Although parasites can be involved in a majority of links, in most cases classic predation links outnumber classic parasitism links. Regarding network structure, observed changes in degree distributions, 14 commonly studied metrics, and link probabilities are consistent with scale-dependent changes in structure associated with changes in diversity and complexity. Parasite and free-living species thus have similar effects on these aspects of structure. However, two changes point to unique roles of parasites. First, adding parasites and concomitant links strongly alters the frequency of most motifs of interactions among three taxa, reflecting parasites' roles as resources for predators of their hosts, driven by trophic intimacy with their hosts. Second, compared to free-living consumers, many parasites' feeding niches appear broader and less contiguous, which may reflect complex life cycles and small body sizes. This study provides new insights about generic versus unique impacts of parasites on food web structure, extends the generality of food web theory, gives a more rigorous framework for assessing the impact of any species on trophic organization, identifies limitations of current food web models, and provides direction for future structural and dynamical models. PMID:23776404

Parasites affect food web structure primarily through increased diversity and complexity

USGS Publications Warehouse

Dunne, Jennifer A.; Lafferty, Kevin D.; Dobson, Andrew P.; Hechinger, Ryan F.; Kuris, Armand M.; Martinez, Neo D.; McLaughlin, John P.; Mouritsen, Kim N.; Poulin, Robert; Reise, Karsten; Stouffer, Daniel B.; Thieltges, David W.; Williams, Richard J.; Zander, Claus Dieter

2013-01-01

Comparative research on food web structure has revealed generalities in trophic organization, produced simple models, and allowed assessment of robustness to species loss. These studies have mostly focused on free-living species. Recent research has suggested that inclusion of parasites alters structure. We assess whether such changes in network structure result from unique roles and traits of parasites or from changes to diversity and complexity. We analyzed seven highly resolved food webs that include metazoan parasite data. Our analyses show that adding parasites usually increases link density and connectance (simple measures of complexity), particularly when including concomitant links (links from predators to parasites of their prey). However, we clarify prior claims that parasites ‘‘dominate’’ food web links. Although parasites can be involved in a majority of links, in most cases classic predation links outnumber classic parasitism links. Regarding network structure, observed changes in degree distributions, 14 commonly studied metrics, and link probabilities are consistent with scale-dependent changes in structure associated with changes in diversity and complexity. Parasite and free-living species thus have similar effects on these aspects of structure. However, two changes point to unique roles of parasites. First, adding parasites and concomitant links strongly alters the frequency of most motifs of interactions among three taxa, reflecting parasites’ roles as resources for predators of their hosts, driven by trophic intimacy with their hosts. Second, compared to free-living consumers, many parasites’ feeding niches appear broader and less contiguous, which may reflect complex life cycles and small body sizes. This study provides new insights about generic versus unique impacts of parasites on food web structure, extends the generality of food web theory, gives a more rigorous framework for assessing the impact of any species on trophic organization, identifies limitations of current food web models, and provides direction for future structural and dynamical models.

Parasites affect food web structure primarily through increased diversity and complexity.

PubMed

Dunne, Jennifer A; Lafferty, Kevin D; Dobson, Andrew P; Hechinger, Ryan F; Kuris, Armand M; Martinez, Neo D; McLaughlin, John P; Mouritsen, Kim N; Poulin, Robert; Reise, Karsten; Stouffer, Daniel B; Thieltges, David W; Williams, Richard J; Zander, Claus Dieter

2013-01-01

Comparative research on food web structure has revealed generalities in trophic organization, produced simple models, and allowed assessment of robustness to species loss. These studies have mostly focused on free-living species. Recent research has suggested that inclusion of parasites alters structure. We assess whether such changes in network structure result from unique roles and traits of parasites or from changes to diversity and complexity. We analyzed seven highly resolved food webs that include metazoan parasite data. Our analyses show that adding parasites usually increases link density and connectance (simple measures of complexity), particularly when including concomitant links (links from predators to parasites of their prey). However, we clarify prior claims that parasites "dominate" food web links. Although parasites can be involved in a majority of links, in most cases classic predation links outnumber classic parasitism links. Regarding network structure, observed changes in degree distributions, 14 commonly studied metrics, and link probabilities are consistent with scale-dependent changes in structure associated with changes in diversity and complexity. Parasite and free-living species thus have similar effects on these aspects of structure. However, two changes point to unique roles of parasites. First, adding parasites and concomitant links strongly alters the frequency of most motifs of interactions among three taxa, reflecting parasites' roles as resources for predators of their hosts, driven by trophic intimacy with their hosts. Second, compared to free-living consumers, many parasites' feeding niches appear broader and less contiguous, which may reflect complex life cycles and small body sizes. This study provides new insights about generic versus unique impacts of parasites on food web structure, extends the generality of food web theory, gives a more rigorous framework for assessing the impact of any species on trophic organization, identifies limitations of current food web models, and provides direction for future structural and dynamical models.

Dynamic Edge Effects in Small Mammal Communities across a Conservation-Agricultural Interface in Swaziland

PubMed Central

Hurst, Zachary M.; McCleery, Robert A.; Collier, Bret A.; Fletcher, Robert J.; Silvy, Nova J.; Taylor, Peter J.; Monadjem, Ara

2013-01-01

Across the planet, high-intensity farming has transformed native vegetation into monocultures, decreasing biodiversity on a landscape scale. Yet landscape-scale changes to biodiversity and community structure often emerge from processes operating at local scales. One common process that can explain changes in biodiversity and community structure is the creation of abrupt habitat edges, which, in turn, generate edge effects. Such effects, while incredibly common, can be highly variable across space and time; however, we currently lack a general analytical framework that can adequately capture such spatio-temporal variability. We extend previous approaches for estimating edge effects to a non-linear mixed modeling framework that captures such spatio-temporal heterogeneity and apply it to understand how agricultural land-uses alter wildlife communities. We trapped small mammals along a conservation-agriculture land-use interface extending 375 m into sugarcane plantations and conservation land-uses at three sites during dry and wet seasons in Swaziland, Africa. Sugarcane plantations had significant reductions in species richness and heterogeneity, and showed an increase in community similarity, suggesting a more homogenized small mammal community. Furthermore, our modeling framework identified strong variation in edge effects on communities across sites and seasons. Using small mammals as an indicator, intensive agricultural practices appear to create high-density communities of generalist species while isolating interior species in less than 225 m. These results illustrate how agricultural land-use can reduce diversity across the landscape and that effects can be masked or magnified, depending on local conditions. Taken together, our results emphasize the need to create or retain natural habitat features in agricultural mosaics. PMID:24040269

Quantum Theory of Atoms in Molecules Charge-Charge Transfer-Dipolar Polarization Classification of Infrared Intensities.

PubMed

Duarte, Leonardo J; Richter, Wagner E; Silva, Arnaldo F; Bruns, Roy E

2017-10-26

Fundamental infrared vibrational transition intensities of gas-phase molecules are sensitive probes of changes in electronic structure accompanying small molecular distortions. Models containing charge, charge transfer, and dipolar polarization effects are necessary for a successful classification of the C-H, C-F, and C-Cl stretching and bending intensities. C-H stretching and in-plane bending vibrations involving sp 3 carbon atoms have small equilibrium charge contributions and are accurately modeled by the charge transfer-counterpolarization contribution and its interaction with equilibrium charge movement. Large C-F and C═O stretching intensities have dominant equilibrium charge movement contributions compared to their charge transfer-dipolar polarization ones and are accurately estimated by equilibrium charge and the interaction contribution. The C-F and C-Cl bending modes have charge and charge transfer-dipolar polarization contribution sums that are of similar size but opposite sign to their interaction values resulting in small intensities. Experimental in-plane C-H bends have small average intensities of 12.6 ± 10.4 km mol -1 owing to negligible charge contributions and charge transfer-counterpolarization cancellations, whereas their average out-of-plane experimental intensities are much larger, 65.7 ± 20.0 km mol -1 , as charge transfer is zero and only dipolar polarization takes place. The C-F bending intensities have large charge contributions but very small intensities. Their average experimental out-of-plane intensity of 9.9 ± 12.6 km mol -1 arises from the cancellation of large charge contributions by dipolar polarization contributions. The experimental average in-plane C-F bending intensity, 5.8 ± 7.3 km mol -1 , is also small owing to charge and charge transfer-counterpolarization sums being canceled by their interaction contributions. Models containing only atomic charges and their fluxes are incapable of describing electronic structure changes for simple molecular distortions that are of interest in classifying infrared intensities. One can expect dipolar polarization effects to also be important for larger distortions of chemical interest.

Protein–Mineral Interactions: Molecular Dynamics Simulations Capture Importance of Variations in Mineral Surface Composition and Structure

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

Andersen, Amity; Reardon, Patrick N.; Chacon, Stephany S.

Molecular dynamics simulations, conventional and metadynamics, were performed to determine the interaction of model protein Gb1 over kaolinite (001), Na+-montmorillonite (001), Ca2+-montmorillonite (001), goethite (100), and Na+-birnessite (001) mineral surfaces. Gb1, a small (56 residue) protein with a well-characterized solution-state nuclear magnetic resonance (NMR) structure and having α-helix, four-fold β-sheet, and hydrophobic core features, is used as a model protein to study protein soil mineral interactions and gain insights on structural changes and potential degradation of protein. From our simulations, we observe little change to the hydrated Gb1 structure over the kaolinite, montmorillonite, and goethite surfaces relative to its solvatedmore » structure without these mineral surfaces present. Over the Na+-birnessite basal surface, however, the Gb1 structure is highly disturbed as a result of interaction with this birnessite surface. Unraveling of the Gb1 β-sheet at specific turns and a partial unraveling of the α-helix is observed over birnessite, which suggests specific vulnerable residue sites for oxidation or hydrolysis possibly leading to fragmentation.« less

Development and application of induced-strain actuators for building structures

NASA Astrophysics Data System (ADS)

Morita, Koichi; Fujita, Takafumi; Ise, Shiro; Kawaguchi, Ken-ichi; Kamada, Takayoshi; Fujitani, Hideo

2001-07-01

Induced strain actuator (ISA) can change their own shapes according to external electric/magnetic fields, and vice versa. Recently these materials have been widely used for the small/precision. The objectives in this study are to develop smart members for building and to realize the smart, comfortable and safe structures. The research items are 1) Semi-active isolation of structures using piezoelectric actuator, 2) Using ISA as sensor materials and 3) Improvement of Acoustic Environment. Semi-active base isolation system with controllable friction damper using piezoelectric actuators is proposed. Simulation study was carried out, and by semi-active isolation, it could be realized to reduce response displacement of the structure to 50% of values of the passive isolation. ISA materials can act as sensors because they cause change of electric or magnetic fields under deformation. PVDF sensors are suitable for membrane structures. We evaluate performance of PVDF sensors for membrane structures by experiment. Polymer based ISA films or distributed ISA devices can control vibration mode of plane members. Applications to music halls or dwelling partition walls are expected. Results of experimental studies of noise control are discussed.

An In-Situ XAS Study of the Structural Changes in a CuO-CeO2/Al2O3 Catalyst during Total Oxidation of Propane

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

Silversmith, Geert; Poelman, Hilde; Poelman, Dirk

2007-02-02

A CuOx-CeOx/Al2O3 catalyst was studied with in-situ transmission Cu K XAS for the total oxidation of propane as model reaction for the catalytic elimination of volatile organic compounds. The local Cu structure was determined for the catalyst as such, after pre-oxidation and after reduction with propane. The catalyst as such has a local CuO structure. No structural effect was observed upon heating in He up to 600 deg. C or after pre-oxidation at 150 deg. C. A full reduction of the Cu2+ towards metallic Cu0 occurred, when propane was fed to the catalyst. The change in local Cu structure duringmore » propane reduction was followed with a time resolution of 1 min. The {chi}(k) scans appeared as linear combinations of start and end spectra, CuO and Cu structure, respectively. However, careful examination of the XANES edge spectra indicates the presence of a small amount of additional Cu1+ species.« less

In vitro isolation of small-molecule-binding aptamers with intrinsic dye-displacement functionality

PubMed Central

Yu, Haixiang; Yang, Weijuan; Alkhamis, Obtin; Canoura, Juan; Yang, Kyung-Ae; Xiao, Yi

2018-01-01

Abstract Aptamer-based sensors offer a powerful tool for molecular detection, but the practical implementation of these biosensors is hindered by costly and laborious sequence engineering and chemical modification procedures. We report a simple strategy for directly isolating signal-reporting aptamers in vitro through systematic evolution of ligands by exponential enrichment (SELEX) that transduce binding events into a detectable change of absorbance via target-induced displacement of a small-molecule dye. We first demonstrate that diethylthiatricarbocyanine (Cy7) can stack into DNA three-way junctions (TWJs) in a sequence-independent fashion, greatly altering the dye's absorbance spectrum. We then design a TWJ-containing structured library and isolate an aptamer against 3,4-methylenedioxypyrovalerone (MDPV), a synthetic cathinone that is an emerging drug of abuse. This aptamer intrinsically binds Cy7 within its TWJ domain, but MDPV efficiently displaces the dye, resulting in a change in absorbance within seconds. This assay is label-free, and detects nanomolar concentrations of MDPV. It also recognizes other synthetic cathinones, offering the potential to detect newly-emerging designer drugs, but does not detect structurally-similar non-cathinone compounds or common cutting agents. Moreover, we demonstrate that the Cy7-displacement colorimetric assay is more sensitive than a conventional strand-displacement fluorescence assay. We believe our strategy offers an effective generalized approach for the development of sensitive dye-displacement colorimetric assays for other small-molecule targets. PMID:29361056

Supramolecular Architectures and Mimics of Complex Natural Folds Derived from Rationally Designed alpha-Helical Protein Structures

NASA Astrophysics Data System (ADS)

Tavenor, Nathan Albert

Protein-based supramolecular polymers (SMPs) are a class of biomaterials which draw inspiration from and expand upon the many examples of complex protein quaternary structures observed in nature: collagen, microtubules, viral capsids, etc. Designing synthetic supramolecular protein scaffolds both increases our understanding of natural superstructures and allows for the creation of novel materials. Similar to small-molecule SMPs, protein-based SMPs form due to self-assembly driven by intermolecular interactions between monomers, and monomer structure determines the properties of the overall material. Using protein-based monomers takes advantage of the self-assembly and highly specific molecular recognition properties encodable in polypeptide sequences to rationally design SMP architectures. The central hypothesis underlying our work is that alpha-helical coiled coils, a well-studied protein quaternary folding motif, are well-suited to SMP design through the addition of synthetic linkers at solvent-exposed sites. Through small changes in the structures of the cross-links and/or peptide sequence, we have been able to control both the nanoscale organization and the macroscopic properties of the SMPs. Changes to the linker and hydrophobic core of the peptide can be used to control polymer rigidity, stability, and dimensionality. The gaps in knowledge that this thesis sought to fill on this project were 1) the relationship between the molecular structure of the cross-linked polypeptides and the macroscopic properties of the SMPs and 2) a means of creating materials exhibiting multi-dimensional net or framework topologies. Separate from the above efforts on supramolecular architectures was work on improving backbone modification strategies for an alpha-helix in the context of a complex protein tertiary fold. Earlier work in our lab had successfully incorporated unnatural building blocks into every major secondary structure (beta-sheet, alpha-helix, loops and beta-turns) of a small protein with a tertiary fold. Although the tertiary fold of the native sequence was mimicked by the resulting artificial protein, the thermodynamic stability was greatly compromised. Most of this energetic penalty derived from the modifications present in the alpha-helix. The contribution within this thesis was direct comparison of several alpha-helical design strategies and establishment of the thermodynamic consequences of each.

Effects of seed predators of different body size on seed mortality in Bornean logged forest.

PubMed

Hautier, Yann; Saner, Philippe; Philipson, Christopher; Bagchi, Robert; Ong, Robert C; Hector, Andy

2010-07-19

The Janzen-Connell hypothesis proposes that seed and seedling enemies play a major role in maintaining high levels of tree diversity in tropical forests. However, human disturbance may alter guilds of seed predators including their body size distribution. These changes have the potential to affect seedling survival in logged forest and may alter forest composition and diversity. We manipulated seed density in plots beneath con- and heterospecific adult trees within a logged forest and excluded vertebrate predators of different body sizes using cages. We show that small and large-bodied predators differed in their effect on con- and heterospecific seedling mortality. In combination small and large-bodied predators dramatically decreased both con- and heterospecific seedling survival. In contrast, when larger-bodied predators were excluded small-bodied predators reduced conspecific seed survival leaving seeds coming from the distant tree of a different species. Our results suggest that seed survival is affected differently by vertebrate predators according to their body size. Therefore, changes in the body size structure of the seed predator community in logged forests may change patterns of seed mortality and potentially affect recruitment and community composition.

Effects of Seed Predators of Different Body Size on Seed Mortality in Bornean Logged Forest

PubMed Central

Hautier, Yann; Saner, Philippe; Philipson, Christopher; Bagchi, Robert; Ong, Robert C.; Hector, Andy

2010-01-01

Background The Janzen-Connell hypothesis proposes that seed and seedling enemies play a major role in maintaining high levels of tree diversity in tropical forests. However, human disturbance may alter guilds of seed predators including their body size distribution. These changes have the potential to affect seedling survival in logged forest and may alter forest composition and diversity. Methodology/Principal Findings We manipulated seed density in plots beneath con- and heterospecific adult trees within a logged forest and excluded vertebrate predators of different body sizes using cages. We show that small and large-bodied predators differed in their effect on con- and heterospecific seedling mortality. In combination small and large-bodied predators dramatically decreased both con- and heterospecific seedling survival. In contrast, when larger-bodied predators were excluded small-bodied predators reduced conspecific seed survival leaving seeds coming from the distant tree of a different species. Conclusions/Significance Our results suggest that seed survival is affected differently by vertebrate predators according to their body size. Therefore, changes in the body size structure of the seed predator community in logged forests may change patterns of seed mortality and potentially affect recruitment and community composition. PMID:20657841

Multiple image x-radiography for functional lung imaging

NASA Astrophysics Data System (ADS)

Aulakh, G. K.; Mann, A.; Belev, G.; Wiebe, S.; Kuebler, W. M.; Singh, B.; Chapman, D.

2018-01-01

Detection and visualization of lung tissue structures is impaired by predominance of air. However, by using synchrotron x-rays, refraction of x-rays at the interface of tissue and air can be utilized to generate contrast which may in turn enable quantification of lung optical properties. We utilized multiple image radiography, a variant of diffraction enhanced imaging, at the Canadian light source to quantify changes in unique x-ray optical properties of lungs, namely attenuation, refraction and ultra small-angle scatter (USAXS or width) contrast ratios as a function of lung orientation in free-breathing or respiratory-gated mice before and after intra-nasal bacterial endotoxin (lipopolysaccharide) instillation. The lung ultra small-angle scatter and attenuation contrast ratios were significantly higher 9 h post lipopolysaccharide instillation compared to saline treatment whereas the refraction contrast decreased in magnitude. In ventilated mice, end-expiratory pressures result in an increase in ultra small-angle scatter contrast ratio when compared to end-inspiratory pressures. There were no detectable changes in lung attenuation or refraction contrast ratio with change in lung pressure alone. In effect, multiple image radiography can be applied towards following optical properties of lung air-tissue barrier over time during pathologies such as acute lung injury.

Effects of Clostridium perfringens iota toxin in the small intestine of mice.

PubMed

Redondo, Leandro M; Redondo, Enzo A; Dailoff, Gabriela C; Leiva, Carlos L; Díaz-Carrasco, Juan M; Bruzzone, Octavio A; Cangelosi, Adriana; Geoghegan, Patricia; Fernandez-Miyakawa, Mariano E

2017-12-01

Iota toxin is a binary toxin solely produced by Clostridium perfringens type E strains, and is structurally related to CDT from C. difficile and CST from C. spiroforme. As type E causes hemorrhagic enteritis in cattle, it is usually assumed that associated diseases are mediated by iota toxin, although evidence in this regard has not been provided. In the present report, iota toxin intestinal effects were evaluated in vivo using a mouse model. Histological damage was observed in ileal loops treated with purified iota toxin after 4 h of incubation. Luminal iota toxin induced fluid accumulation in the small intestine in a dose dependent manner, as determined by the enteropooling and the intestinal loop assays. None of these changes were observed in the large intestine. These results suggest that C. perfringens iota toxin alters intestinal permeability, predominantly by inducing necrosis and degenerative changes in the mucosal epithelium of the small intestine, as well as changes in intestinal motility. The obtained results suggest a central role for iota toxin in the pathogenesis of C. perfringens type E hemorrhagic enteritis, and contribute to remark the importance of clostridial binary toxins in digestive diseases. Published by Elsevier Ltd.

Refoldable Foldamers: Global Conformational Switching by Deletion or Insertion of a Single Hydrogen Bond

PubMed Central

Le Bailly, Bryden A. F.; Byrne, Liam

2016-01-01

Abstract Small changes in the structure of a foldamer may lead to gross changes in conformational preference. We show that the simple insertion or deletion of a single hydrogen bond by changes in pH or by photochemical deprotection is sufficient to refold a helical oligomer, interconverting M and P screw‐sense preference. As a consequence of the switch, information may be transmitted to a remote catalytic site, selectively directing the formation of either of two enantiomeric products by a reaction involving 1,22‐remote intermolecular asymmetric induction. PMID:26762559

Doping-dependent correlation effects in (Sr1-xLax) 3Ir2O7

NASA Astrophysics Data System (ADS)

Affeldt, Gregory; Hogan, Tom; Denlinger, Jonathan D.; Vishwanath, Ashvin; Wilson, Stephen D.; Lanzara, Alessandra

2018-03-01

We have measured the signatures of electronic energy scales and their doping evolution in the band structure of (Sr1-xLax) 3Ir2O7 using angle-resolved photoemission spectroscopy. While band splittings and positions corresponding to the bilayer splitting and spin-orbit coupling undergo only small changes, the Mott gap and effective mass of both the lower Hubbard band and conduction band exhibit strong variations with doping. These changes correspond to similar observations in the cuprate superconductors, and are likely connected to the changing effective Coulomb interaction upon addition of itinerant carriers.

The convergence of maturational change and structural covariance in human cortical networks.

PubMed

Alexander-Bloch, Aaron; Raznahan, Armin; Bullmore, Ed; Giedd, Jay

2013-02-13

Large-scale covariance of cortical thickness or volume in distributed brain regions has been consistently reported by human neuroimaging studies. The mechanism of this population covariance of regional cortical anatomy has been hypothetically related to synchronized maturational changes in anatomically connected neuronal populations. Brain regions that grow together, i.e., increase or decrease in volume at the same rate over the course of years in the same individual, are thus expected to demonstrate strong structural covariance or anatomical connectivity across individuals. To test this prediction, we used a structural MRI dataset on healthy young people (N = 108; aged 9-22 years at enrollment), comprising 3-6 longitudinal scans on each participant over 6-12 years of follow-up. At each of 360 regional nodes, and for each participant, we estimated the following: (1) the cortical thickness in the median scan and (2) the linear rate of change in cortical thickness over years of serial scanning. We constructed structural and maturational association matrices and networks from these measurements. Both structural and maturational networks shared similar global and nodal topological properties, as well as mesoscopic features including a modular community structure, a relatively small number of highly connected hub regions, and a bias toward short distance connections. Using resting-state functional magnetic resonance imaging data on a subset of the sample (N = 32), we also demonstrated that functional connectivity and network organization was somewhat predictable by structural/maturational networks but demonstrated a stronger bias toward short distance connections and greater topological segregation. Brain structural covariance networks are likely to reflect synchronized developmental change in distributed cortical regions.

Age-related changes in the plasticity and toughness of human cortical bone at multiple length-scales

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

Zimmermann, Elizabeth A.; Schaible, Eric; Bale, Hrishikesh

2011-08-10

The structure of human cortical bone evolves over multiple length-scales from its basic constituents of collagen and hydroxyapatite at the nanoscale to osteonal structures at nearmillimeter dimensions, which all provide the basis for its mechanical properties. To resist fracture, bone’s toughness is derived intrinsically through plasticity (e.g., fibrillar sliding) at structural-scales typically below a micron and extrinsically (i.e., during crack growth) through mechanisms (e.g., crack deflection/bridging) generated at larger structural-scales. Biological factors such as aging lead to a markedly increased fracture risk, which is often associated with an age-related loss in bone mass (bone quantity). However, we find that age-relatedmore » structural changes can significantly degrade the fracture resistance (bone quality) over multiple lengthscales. Using in situ small-/wide-angle x-ray scattering/diffraction to characterize sub-micron structural changes and synchrotron x-ray computed tomography and in situ fracture-toughness measurements in the scanning electron microscope to characterize effects at micron-scales, we show how these age-related structural changes at differing size-scales degrade both the intrinsic and extrinsic toughness of bone. Specifically, we attribute the loss in toughness to increased non-enzymatic collagen cross-linking which suppresses plasticity at nanoscale dimensions and to an increased osteonal density which limits the potency of crack-bridging mechanisms at micron-scales. The link between these processes is that the increased stiffness of the cross-linked collagen requires energy to be absorbed by “plastic” deformation at higher structural levels, which occurs by the process of microcracking.« less

Mcl-1-Bim complexes accommodate surprising point mutations via minor structural changes

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

Fire, Emiko; Gullá, Stefano V.; Grant, Robert A.

2010-06-25

Mcl-1 is an antiapoptotic Bcl-2-family protein that protects cells against death. Structures of Mcl-1, and of other anti-apoptotic Bcl-2 proteins, reveal a surface groove into which the {alpha}-helical BH3 regions of certain proapoptotic proteins can bind. Despite high overall structural conservation, differences in this groove afford binding specificity that is important for the mechanism of Bcl-2 family function. We report the crystal structure of human Mcl-1 bound to a BH3 peptide derived from human Bim and the structures for three complexes that accommodate large physicochemical changes at conserved Bim sites. The mutations had surprisingly modest effects on complex stability, andmore » the structures show that Mcl-1 can undergo small changes to accommodate the mutant ligands. For example, a shift in a leucine side chain fills a hole left by an isoleucine-to-alanine mutation at the first hydrophobic buried position of Bim BH3. Larger changes are also observed, with shifting of helix {alpha}3 accommodating an isoleucine-to-tyrosine mutation at this same position. We surveyed the variation in available Mcl-1 and Bcl-x{sub L} structures and observed moderate flexibility that is likely critical for facilitating interactions of diverse BH3-only proteins with Mcl-1. With the antiapoptotic Bcl-2 family members attracting significant attention as therapeutic targets, these structures contribute to our growing understanding of how specificity is achieved and can help to guide the design of novel inhibitors that target Mcl-1.« less

Anomalous Hall conductivity and electronic structures of Si-substituted Mn2CoAl epitaxial films

NASA Astrophysics Data System (ADS)

Arima, K.; Kuroda, F.; Yamada, S.; Fukushima, T.; Oguchi, T.; Hamaya, K.

2018-02-01

We study anomalous Hall conductivity (σAHC) and electronic band structures of Si-substituted Mn2CoAl (Mn2CoAl1 -xSix ). First-principles calculations reveal that the electronic band structure is like a spin-gapless system even after substituting a quaternary element of Si for Al up to x =0.2 in Mn2CoAl1 -xSix . This means that the Si substitution enables the Fermi-level shift without largely changing the electronic structures in Mn2CoAl . By using molecular beam epitaxy techniques, Mn2CoAl1 -xSix epitaxial films can be grown, leading to the systematic control of x (0 ⩽x ⩽0.3 ). In addition to the electrical conductivity, the values of σAHC for the Mn2CoAl1 -xSix films are similar to those in Mn2CoAl films shown in previous reports. We note that a very small σAHC of ˜1.1 S/cm is obtained for x = 0.225, and the sign of σAHC is changed from positive to negative at around x = 0.25. We discuss the origin of the sign reversal of σAHC as a consequence of the Fermi-level shift in Mn2CoAl . Considering the presence of the structural disorder in the Mn2CoAl1 -xSix films, we can conclude that the small value and sign reversal of σAHC are not related to the characteristics of spin-gapless semiconductors.

Computational study of solution behavior of magainin 2 monomers.

PubMed

Petkov, P; Marinova, R; Kochev, V; Ilieva, N; Lilkova, E; Litov, L

2018-03-27

Antimicrobial peptides (AMPs) play crucial role as mediators of the primary host defense against microbial invasion. They are considered a promising alternative to antibiotics for multidrug resistant bacterial strains. For complete understanding of the antimicrobial defense mechanism, a detailed knowledge of the dynamics of peptide-membrane interactions, including atomistic studies on AMPs geometry and both peptide and membrane structural changes during the whole process is a prerequisite. We aim at clarifying the conformation dynamics of small linear AMPs in solution as a first step of in silico protocol for establishing a correspondence between certain amino-acid sequence motifs, secondary-structure elements, conformational dynamics in solution and the intensity and mode of interaction with the bacterial membrane. To this end, we use molecular dynamics simulations augmented by well-tempered metadynamics to study the free-energy landscape of two AMPs with close primary structure and different antibacterial activity - the native magainin 2 (MG2) and an analog (MG2m, with substitutions F5Y and F16W) in aqueous solution. We observe that upon solvation, the initial α-helical structures change differently. The native form remains structured, with three shorter α-helical motifs, connected by random coils, while the synthetic analog tends predominantly to a disordered conformation. Our results indicate the importance of the side-chains at positions 5 and 16 for maintaining the solvated peptide conformation. They also provide a modeling background for recent experimental observations, relating the higher α-helical content in solution (peptide pre-folding) in the case of small linear AMPs to a lower antibacterial activity.

Free-Energy Landscape of Protein-Ligand Interactions Coupled with Protein Structural Changes.

PubMed

Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

2017-02-02

Protein-ligand interactions are frequently coupled with protein structural changes. Focusing on the coupling, we present the free-energy surface (FES) of the ligand-binding process for glutamine-binding protein (GlnBP) and its ligand, glutamine, in which glutamine binding accompanies large-scale domain closure. All-atom simulations were performed in explicit solvents by multiscale enhanced sampling (MSES), which adopts a multicopy and multiscale scheme to achieve enhanced sampling of systems with a large number of degrees of freedom. The structural ensemble derived from the MSES simulation yielded the FES of the coupling, described in terms of both the ligand's and protein's degrees of freedom at atomic resolution, and revealed the tight coupling between the two degrees of freedom. The derived FES led to the determination of definite structural states, which suggested the dominant pathways of glutamine binding to GlnBP: first, glutamine migrates via diffusion to form a dominant encounter complex with Arg75 on the large domain of GlnBP, through strong polar interactions. Subsequently, the closing motion of GlnBP occurs to form ligand interactions with the small domain, finally completing the native-specific complex structure. The formation of hydrogen bonds between glutamine and the small domain is considered to be a rate-limiting step, inducing desolvation of the protein-ligand interface to form the specific native complex. The key interactions to attain high specificity for glutamine, the "door keeper" existing between the two domains (Asp10-Lys115) and the "hydrophobic sandwich" formed between the ligand glutamine and Phe13/Phe50, have been successfully mapped on the pathway derived from the FES.

An examination on the influence of small and medium enterprise (SME) stakeholder on green supply chain management practices

NASA Astrophysics Data System (ADS)

Shahlan, M. Z.; Sidek, A. A.; Suffian, S. A.; Hazza, M. H. F. A.; Daud, M. R. C.

2018-01-01

In this paper, climate change and global warming are the biggest current issues in the industrial sectors. The green supply chain managements (GSCM) is one of the crucial input to these issues. Effective GSCM can potentially secure the organization’s competitive advantage and improve the environmental performance of the network activities. In this study, the aim is to investigate and examine how a small and medium enterprises (SMEs) stakeholder pressure and top management influence green supply chain management practices. The study is further advance green supply chain management research in Malaysia focusing on SMEs manufacturing sector using structural equation modelling. Structural equation modelling is a multivariate statistical analysis technique used to examine structural relationship. It is the combination of factor analysis and multi regression analysis and used to analyse structural relationship between measure variable and latent factor. This research found that top management support and stakeholder pressure is the major influence for SMEs to adopt green supply chain management. The research also found that top management is fully mediate with the relationship between stakeholder pressure and monitoring supplier environmental performance.

Pressure and Temperature Effects on the Activity and Structure of the Catalytic Domain of Human MT1-MMP

PubMed Central

Decaneto, Elena; Suladze, Saba; Rosin, Christopher; Havenith, Martina; Lubitz, Wolfgang; Winter, Roland

2015-01-01

Membrane type 1-matrix metalloproteinase (MT1-MMP or MMP-14) is a zinc-transmembrane metalloprotease involved in the degradation of extracellular matrix and tumor invasion. While changes in solvation of MT1-MMP have been recently studied, little is known about the structural and energetic changes associated with MT1-MMP while interacting with substrates. Steady-state kinetic and thermodynamic data (including activation energies and activation volumes) were measured over a wide range of temperatures and pressures by means of a stopped-flow fluorescence technique. Complementary temperature- and pressure-dependent Fourier-transform infrared measurements provided corresponding structural information of the protein. MT1-MMP is stable and active over a wide range of temperatures (10–55°C). A small conformational change was detected at 37°C, which is responsible for the change in activity observed at the same temperature. Pressure decreases the enzymatic activity until complete inactivation occurs at 2 kbar. The inactivation is associated with changes in the rate-limiting step of the reaction caused by additional hydration of the active site upon compression and/or minor conformational changes in the active site region. Based on these data, an energy and volume diagram could be established for the various steps of the enzymatic reaction. PMID:26636948

Species Identity Supersedes the Dilution Effect Concerning Hantavirus Prevalence at Sites across Texas and México.

PubMed

Milholland, Matthew T; Castro-Arellano, Iván; Arellano, Elizabeth; Nava-García, Elizabeth; Rangel-Altamirano, Guadalupe; Gonzalez-Cozatl, Francisco X; Suzán, Gerardo; Schountz, Tony; González-Padrón, Shiara; Vigueras, Ana; Rubio, André V; Maikis, Troy J; Westrich, Bradford J; Martinez, Jose A; Esteve-Gassent, Maria D; Torres, Madison; Rodriguez-Ruiz, Erick R; Hahn, Dittmar; Lacher, Thomas E

2017-12-15

Recent models suggest a relationship exists between community diversity and pathogen prevalence, the proportion of individuals in a population that are infected by a pathogen, with most inferences tied to assemblage structure. Two contrasting outcomes of this relationship have been proposed: the "dilution effect" and the "amplification effect." Small mammal assemblage structure in disturbed habitats often differs from assemblages in sylvan environments, and hantavirus prevalence is often negatively correlated with habitats containing high species diversity via dilution effect dynamics. As species richness increases, prevalence of infection often is decreased. However, anthropogenic changes to sylvan landscapes have been shown to decrease species richness and/or increase phylogenetic similarities within assemblages. Between January 2011 and January 2016, we captured and tested 2406 individual small mammals for hantavirus antibodies at 20 sites across Texas and México and compared differences in hantavirus seroprevalence, species composition, and assemblage structure between sylvan and disturbed habitats. We found 313 small mammals positive for antibodies against hantaviruses, evincing an overall prevalence of 9.7% across all sites. In total, 40 species of small mammals were identified comprising 2 taxonomic orders (Rodentia and Eulipotyphla). By sampling both habitat types concurrently, we were able to make real-world inferences into the efficacy of dilution effect theory in terms of hantavirus ecology. Our hypothesis predicting greater species richness higher in sylvan habitats compared to disturbed areas was not supported, suggesting the characteristics of assemblage structure do not adhere to current conceptions of species richness negatively influencing prevalence via a dilution effect.

Protein structural dynamics in solution unveiled via 100-ps time-resolved x-ray scattering

PubMed Central

Anfinrud, Philip

2010-01-01

We have developed a time-resolved x-ray scattering diffractometer capable of probing structural dynamics of proteins in solution with 100-ps time resolution. This diffractometer, developed on the ID14B BioCARS (Consortium for Advanced Radiation Sources) beamline at the Advanced Photon Source, records x-ray scattering snapshots over a broad range of q spanning 0.02–2.5 Å-1, thereby providing simultaneous coverage of the small-angle x-ray scattering (SAXS) and wide-angle x-ray scattering (WAXS) regions. To demonstrate its capabilities, we have tracked structural changes in myoglobin as it undergoes a photolysis-induced transition from its carbon monoxy form (MbCO) to its deoxy form (Mb). Though the differences between the MbCO and Mb crystal structures are small (rmsd < 0.2 Å), time-resolved x-ray scattering differences recorded over 8 decades of time from 100 ps to 10 ms are rich in structure, illustrating the sensitivity of this technique. A strong, negative-going feature in the SAXS region appears promptly and corresponds to a sudden > 22 Å3 volume expansion of the protein. The ensuing conformational relaxation causes the protein to contract to a volume ∼2 Å3 larger than MbCO within ∼10 ns. On the timescale for CO escape from the primary docking site, another change in the SAXS/WAXS fingerprint appears, demonstrating sensitivity to the location of the dissociated CO. Global analysis of the SAXS/WAXS patterns recovered time-independent scattering fingerprints for four intermediate states of Mb. These SAXS/WAXS fingerprints provide stringent constraints for putative models of conformational states and structural transitions between them. PMID:20406909

Protein structural dynamics in solution unveiled via 100-ps time-resolved x-ray scattering.

PubMed

Cho, Hyun Sun; Dashdorj, Naranbaatar; Schotte, Friedrich; Graber, Timothy; Henning, Robert; Anfinrud, Philip

2010-04-20

We have developed a time-resolved x-ray scattering diffractometer capable of probing structural dynamics of proteins in solution with 100-ps time resolution. This diffractometer, developed on the ID14B BioCARS (Consortium for Advanced Radiation Sources) beamline at the Advanced Photon Source, records x-ray scattering snapshots over a broad range of q spanning 0.02-2.5 A(-1), thereby providing simultaneous coverage of the small-angle x-ray scattering (SAXS) and wide-angle x-ray scattering (WAXS) regions. To demonstrate its capabilities, we have tracked structural changes in myoglobin as it undergoes a photolysis-induced transition from its carbon monoxy form (MbCO) to its deoxy form (Mb). Though the differences between the MbCO and Mb crystal structures are small (rmsd < 0.2 A), time-resolved x-ray scattering differences recorded over 8 decades of time from 100 ps to 10 ms are rich in structure, illustrating the sensitivity of this technique. A strong, negative-going feature in the SAXS region appears promptly and corresponds to a sudden > 22 A(3) volume expansion of the protein. The ensuing conformational relaxation causes the protein to contract to a volume approximately 2 A(3) larger than MbCO within approximately 10 ns. On the timescale for CO escape from the primary docking site, another change in the SAXS/WAXS fingerprint appears, demonstrating sensitivity to the location of the dissociated CO. Global analysis of the SAXS/WAXS patterns recovered time-independent scattering fingerprints for four intermediate states of Mb. These SAXS/WAXS fingerprints provide stringent constraints for putative models of conformational states and structural transitions between them.

Evaluation of the molecular lipid organization in millimeter-sized stratum corneum by synchrotron X-ray diffraction.

PubMed

Suzuki, T; Uchino, T; Hatta, I; Miyazaki, Y; Kato, S; Sasaki, K; Kagawa, Y

2018-04-29

The aim of this study was to investigate whether the lamellar and lateral structure of intercellular lipid of stratum corneum (SC) can be evaluated from millimeter-sized SC (MSC) by X-ray diffraction. A 12 mm × 12 mm SC sheet from hairless mouse was divided into 16 pieces measuring 3 mm × 3 mm square. From another sheet, 4 pieces of ultramillimeter-sized SC (USC:1.5 mm × 1.5 mm square) were prepared. Small and wide-angle X-ray diffraction (SAXD and WAXD) measurements were performed on each piece. For MSC and USC, changes in the lamellar and lateral structure after the application of d-limonene were measured. The intensity of SAXD peaks due to the lamellar phase of long periodicity phase (LPP) and WAXD peaks due to the lateral hydrocarbon chain-packing structures varied in MSC and USC pieces, although over the 12 mm × 12 mm SC sheet. These results indicated that the intercellular lipid components and their proportion appeared nearly uniform. Application of d-limonene on MSC and USC piece with strong peaks in SAXD and the WAXD resulted in the disappearance of peaks due to the lamellar phase of LPP and decrease in peak intensity for the lateral hydrocarbon chain-packing structures. These changes are consistent with normal-sized sample results. We found that the selection of a sample piece with strong diffraction peaks due to the lamellar and lateral structure enabled evaluation of the SC structure in small-sized samples by X-ray diffraction. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Coevolutionary dynamics of opinion propagation and social balance: The key role of small-worldness

NASA Astrophysics Data System (ADS)

Chen, Yan; Chen, Lixue; Sun, Xian; Zhang, Kai; Zhang, Jie; Li, Ping

2014-03-01

The propagation of various opinions in social networks, which influences human inter-relationships and even social structure, and hence is a most important part of social life. We have incorporated social balance into opinion propagation in social networks are influenced by social balance. The edges in networks can represent both friendly or hostile relations, and change with the opinions of individual nodes. We introduce a model to characterize the coevolutionary dynamics of these two dynamical processes on Watts-Strogatz (WS) small-world network. We employ two distinct evolution rules (i) opinion renewal; and (ii) relation adjustment. By changing the rewiring probability, and thus the small-worldness of the WS network, we found that the time for the system to reach balanced states depends critically on both the average path length and clustering coefficient of the network, which is different than other networked process like epidemic spreading. In particular, the system equilibrates most quickly when the underlying network demonstrates strong small-worldness, i.e., small average path lengths and large clustering coefficient. We also find that opinion clusters emerge in the process of the network approaching the global equilibrium, and a measure of global contrariety is proposed to quantify the balanced state of a social network.

RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs.

PubMed

Bhattacharyya, Dhananjay; Halder, Sukanya; Basu, Sankar; Mukherjee, Debasish; Kumar, Prasun; Bansal, Manju

2017-02-01

Comprehensive analyses of structural features of non-canonical base pairs within a nucleic acid double helix are limited by the availability of a small number of three dimensional structures. Therefore, a procedure for model building of double helices containing any given nucleotide sequence and base pairing information, either canonical or non-canonical, is seriously needed. Here we describe a program RNAHelix, which is an updated version of our widely used software, NUCGEN. The program can regenerate duplexes using the dinucleotide step and base pair orientation parameters for a given double helical DNA or RNA sequence with defined Watson-Crick or non-Watson-Crick base pairs. The original structure and the corresponding regenerated structure of double helices were found to be very close, as indicated by the small RMSD values between positions of the corresponding atoms. Structures of several usual and unusual double helices have been regenerated and compared with their original structures in terms of base pair RMSD, torsion angles and electrostatic potentials and very high agreements have been noted. RNAHelix can also be used to generate a structure with a sequence completely different from an experimentally determined one or to introduce single to multiple mutation, but with the same set of parameters and hence can also be an important tool in homology modeling and study of mutation induced structural changes.

Homeostatic structural plasticity can account for topology changes following deafferentation and focal stroke.

PubMed

Butz, Markus; Steenbuck, Ines D; van Ooyen, Arjen

2014-01-01

After brain lesions caused by tumors or stroke, or after lasting loss of input (deafferentation), inter- and intra-regional brain networks respond with complex changes in topology. Not only areas directly affected by the lesion but also regions remote from the lesion may alter their connectivity-a phenomenon known as diaschisis. Changes in network topology after brain lesions can lead to cognitive decline and increasing functional disability. However, the principles governing changes in network topology are poorly understood. Here, we investigated whether homeostatic structural plasticity can account for changes in network topology after deafferentation and brain lesions. Homeostatic structural plasticity postulates that neurons aim to maintain a desired level of electrical activity by deleting synapses when neuronal activity is too high and by providing new synaptic contacts when activity is too low. Using our Model of Structural Plasticity, we explored how local changes in connectivity induced by a focal loss of input affected global network topology. In accordance with experimental and clinical data, we found that after partial deafferentation, the network as a whole became more random, although it maintained its small-world topology, while deafferentated neurons increased their betweenness centrality as they rewired and returned to the homeostatic range of activity. Furthermore, deafferentated neurons increased their global but decreased their local efficiency and got longer tailed degree distributions, indicating the emergence of hub neurons. Together, our results suggest that homeostatic structural plasticity may be an important driving force for lesion-induced network reorganization and that the increase in betweenness centrality of deafferentated areas may hold as a biomarker for brain repair.

Complex pattern of variation in neurocranial ontogeny revealed by CT-scanning.

PubMed

Anzelmo, Marisol; Ventrice, Fernando; Kelmansky, Diana; Sardi, Marina

2018-05-01

The neurocranium of hominid species has been largely studied with reference to the midsagittal plane, with variations being attributed to brain evolution. By contrast, there is limited information on variation in non-midsagittal regions, which are the points of insertion of muscles and bony structures related to mastication. This work aims to analyze ontogenetic changes and sexual dimorphism (SD) in midsagittal and non-midsagittal neurocranial structures from a contemporary human sample comprising 138 computed tomography (CT) cranial images of individuals ranging from infants to adults. Morphology of the vault and the base was assessed by registering landmarks and semilandmarks, which were analyzed by geometric morphometrics, and the endocranial volume (EV). The results of regressions and Kruskal-Wallis test indicate that the major size and shape changes in both midsagittal and non-midsagittal regions occur during infancy and juvenility; shape changes are also associated with an increase in EV. The size of the midsagittal vault, the shape of the non-midsagittal vault and the size of the base show an extension of ontogenetic trajectories. Sexes show similar changes in shape but different changes in size. We conclude that brain growth appears to be an important factor influencing the morphology of the neurocranium, at least during infancy and childhood. Subsequent changes may be attributed to osteogenic activity and the differential growth of the brain lobes. Masticatory-related bony structures and muscles may not be strong enough factors to induce independent modifications in non-midsagittal structures. The small influence of the cranial muscles would explain why the human neurocranium is a quite integrated structure.

Understanding the structure and functioning of polar pelagic ecosystems to predict the impacts of change

PubMed Central

Drinkwater, K. F.; Grant, S. M.; Heymans, J. J.; Hofmann, E. E.; Hunt, G. L.; Johnston, N. M.

2016-01-01

The determinants of the structure, functioning and resilience of pelagic ecosystems across most of the polar regions are not well known. Improved understanding is essential for assessing the value of biodiversity and predicting the effects of change (including in biodiversity) on these ecosystems and the services they maintain. Here we focus on the trophic interactions that underpin ecosystem structure, developing comparative analyses of how polar pelagic food webs vary in relation to the environment. We highlight that there is not a singular, generic Arctic or Antarctic pelagic food web, and, although there are characteristic pathways of energy flow dominated by a small number of species, alternative routes are important for maintaining energy transfer and resilience. These more complex routes cannot, however, provide the same rate of energy flow to highest trophic-level species. Food-web structure may be similar in different regions, but the individual species that dominate mid-trophic levels vary across polar regions. The characteristics (traits) of these species are also different and these differences influence a range of food-web processes. Low functional redundancy at key trophic levels makes these ecosystems particularly sensitive to change. To develop models for projecting responses of polar ecosystems to future environmental change, we propose a conceptual framework that links the life histories of pelagic species and the structure of polar food webs. PMID:27928038

Understanding the structure and functioning of polar pelagic ecosystems to predict the impacts of change.

PubMed

Murphy, E J; Cavanagh, R D; Drinkwater, K F; Grant, S M; Heymans, J J; Hofmann, E E; Hunt, G L; Johnston, N M

2016-12-14

The determinants of the structure, functioning and resilience of pelagic ecosystems across most of the polar regions are not well known. Improved understanding is essential for assessing the value of biodiversity and predicting the effects of change (including in biodiversity) on these ecosystems and the services they maintain. Here we focus on the trophic interactions that underpin ecosystem structure, developing comparative analyses of how polar pelagic food webs vary in relation to the environment. We highlight that there is not a singular, generic Arctic or Antarctic pelagic food web, and, although there are characteristic pathways of energy flow dominated by a small number of species, alternative routes are important for maintaining energy transfer and resilience. These more complex routes cannot, however, provide the same rate of energy flow to highest trophic-level species. Food-web structure may be similar in different regions, but the individual species that dominate mid-trophic levels vary across polar regions. The characteristics (traits) of these species are also different and these differences influence a range of food-web processes. Low functional redundancy at key trophic levels makes these ecosystems particularly sensitive to change. To develop models for projecting responses of polar ecosystems to future environmental change, we propose a conceptual framework that links the life histories of pelagic species and the structure of polar food webs. © 2016 The Authors.

Oligomeric structure and chaperone-like activity of Drosophila melanogaster mitochondrial small heat shock protein Hsp22 and arginine mutants in the alpha-crystallin domain.

PubMed

Dabbaghizadeh, Afrooz; Finet, Stéphanie; Morrow, Genevieve; Moutaoufik, Mohamed Taha; Tanguay, Robert M

2017-07-01

The structure and chaperone function of DmHsp22WT, a small Hsp of Drosophila melanogaster localized within mitochondria were examined. Mutations of conserved arginine mutants within the alpha-crystallin domain (ACD) domain (R105G, R109G, and R110G) were introduced, and their effects on oligomerization and chaperone function were assessed. Arginine to glycine mutations do not induce significant changes in tryptophan fluorescence, and the mutated proteins form oligomers that are of equal or smaller size than the wild-type protein. They all form oligomer with one single peak as determined by size exclusion chromatography. While all mutants demonstrate the same efficiency as the DmHsp22WT in a DTT-induced insulin aggregation assay, all are more efficient chaperones to prevent aggregation of malate dehydrogenase. Arginine mutants of DmHsp22 are efficient chaperones to retard aggregation of CS and Luc. In summary, this study shows that mutations of arginine to glycine in DmHsp22 ACD induce a number of structural changes, some of which differ from those described in mammalian sHsps. Interestingly, only the R110G-DmHsp22 mutant, and not the expected R109G equivalent to human R140-HspB1, R116-HspB4, and R120-HspB5, showed different structural properties compared with the DmHsp22WT.

Flavonoid interactions with human transthyretin: combined structural and thermodynamic analysis.

PubMed

Trivella, Daniela B B; dos Reis, Caio V; Lima, Luís Maurício T R; Foguel, Débora; Polikarpov, Igor

2012-10-01

Transthyretin (TTR) is a carrier protein involved in human amyloidosis. The development of small molecules that may act as TTR amyloid inhibitors is a promising strategy to treat these pathologies. Here we selected and characterized the interaction of flavonoids with the wild type and the V30M amyloidogenic mutant TTR. TTR acid aggregation was evaluated in vitro in the presence of the different flavonoids. The best TTR aggregation inhibitors were studied by Isothermal Titration Calorimetry (ITC) in order to reveal their thermodynamic signature of binding to TTRwt. Crystal structures of TTRwt in complex with the top binders were also obtained, enabling us to in depth inspect TTR interactions with these flavonoids. The results indicate that changing the number and position of hydroxyl groups attached to the flavonoid core strongly influence flavonoid recognition by TTR, either by changing ligand affinity or its mechanism of interaction with the two sites of TTR. We also compared the results obtained for TTRwt with the V30M mutant structure in the apo form, allowing us to pinpoint structural features that may facilitate or hamper ligand binding to the V30M mutant. Our data show that the TTRwt binding site is labile and, in particular, the central region of the cavity is sensible for the small differences in the ligands tested and can be influenced by the Met30 amyloidogenic mutation, therefore playing important roles in flavonoid binding affinity, mechanism and mutant protein ligand binding specificities. Copyright © 2012 Elsevier Inc. All rights reserved.

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

Li, Shuning; Roy, Amitava; Lichtenberg, Henning

The micro-segmented flow technique was applied for continuous synthesis of ZnO micro- and nanoparticles with short residence times of 9.4 s and 21.4 s, respectively. The obtained particles were characterized by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Small angle X-ray scattering (SAXS) and photoluminescence spectroscopy were used to determine the size and optical properties of ZnO nanoparticles. In addition, extended X-ray absorption fine structure (EXAFS) spectroscopy was employed to investigate local structural properties. The EXAFS measurements reveal a larger degree of structural disorder in the nanoparticles than the microparticles. These structural changes should be taken into considerationmore » while evaluating the size-dependent visible emission of ZnO nanoparticles.« less

Fast, label-free super-resolution live-cell imaging using rotating coherent scattering (ROCS) microscopy

NASA Astrophysics Data System (ADS)

Jünger, Felix; Olshausen, Philipp V.; Rohrbach, Alexander

2016-07-01

Living cells are highly dynamic systems with cellular structures being often below the optical resolution limit. Super-resolution microscopes, usually based on fluorescence cell labelling, are usually too slow to resolve small, dynamic structures. We present a label-free microscopy technique, which can generate thousands of super-resolved, high contrast images at a frame rate of 100 Hertz and without any post-processing. The technique is based on oblique sample illumination with coherent light, an approach believed to be not applicable in life sciences because of too many interference artefacts. However, by circulating an incident laser beam by 360° during one image acquisition, relevant image information is amplified. By combining total internal reflection illumination with dark-field detection, structures as small as 150 nm become separable through local destructive interferences. The technique images local changes in refractive index through scattered laser light and is applied to living mouse macrophages and helical bacteria revealing unexpected dynamic processes.

Synthesis and atomic scale characterization of Er2O3 nanoparticles: enhancement of magnetic properties and changes in the local structure

NASA Astrophysics Data System (ADS)

Corrêa, Eduardo L.; Bosch-Santos, Brianna; Freitas, Rafael S.; Potiens, Maria da Penha A.; Saiki, Mitiko; Carbonari, Artur W.

2018-05-01

In the investigation reported in this paper a modified thermal decomposition method was developed to produce very small Er2O3 nanoparticles (NPs). Particles structure, shape and size were characterized by x-ray diffraction and transmission electron microscopy which showed that the synthesis by thermal decomposition under O2 atmosphere produced very small and monodisperse NPs, allowing the investigation of finite-size and surface effects. Results of magnetization measurements showed that the smallest particles present the highest values of susceptibility that decrease as particle size increases. Specific heat measurements indicate that the sample with the smallest NPs (diameter ∼5 nm) has a Néel temperature of 0.54 K. The local structure of particles was investigated by measurements of hyperfine interactions with perturbed angular correlation spectroscopy using 111Cd as probe nuclei replacing the cationic sites. Results showed that the relative population of sites 8b increases in both the core and surface layer of particles.

Bidirectional synaptic structural plasticity after chronic cocaine administration occurs through Rap1 small GTPase signaling

PubMed Central

Cahill, Michael E.; Bagot, Rosemary C.; Gancarz, Amy M.; Walker, Deena M.; Sun, HaoSheng; Wang, Zi-Jun; Heller, Elizabeth A.; Feng, Jian; Kennedy, Pamela J.; Koo, Ja Wook; Cates, Hannah M.; Neve, Rachael L.; Shen, Li; Dietz, David M.

2016-01-01

Summary Dendritic spines are the sites of most excitatory synapses in the CNS, and opposing alterations in the synaptic structure of medium spiny neurons (MSNs) of the nucleus accumbens, a primary brain reward region, are seen at early vs. late time points after cocaine administration. Here we investigate the time-dependent molecular and biochemical processes that regulate this bidirectional synaptic structural plasticity of NAc MSNs and associated changes in cocaine reward in response to chronic cocaine exposure. Our findings reveal key roles for the bidirectional synaptic expression of the Rap1b small GTPase and an associated local-synaptic protein translation network in this process. The transcriptional mechanisms and pathway-specific inputs to NAc that regulate Rap1b expression are also characterized. Collectively, these findings provide a precise mechanism by which nuclear to synaptic interactions induce “metaplasticity” in NAc MSNs, and we reveal the specific effects of this plasticity on reward behavior in a brain circuit-specific manner. PMID:26844834

Fast, label-free super-resolution live-cell imaging using rotating coherent scattering (ROCS) microscopy

PubMed Central

Jünger, Felix; Olshausen, Philipp v.; Rohrbach, Alexander

2016-01-01

Living cells are highly dynamic systems with cellular structures being often below the optical resolution limit. Super-resolution microscopes, usually based on fluorescence cell labelling, are usually too slow to resolve small, dynamic structures. We present a label-free microscopy technique, which can generate thousands of super-resolved, high contrast images at a frame rate of 100 Hertz and without any post-processing. The technique is based on oblique sample illumination with coherent light, an approach believed to be not applicable in life sciences because of too many interference artefacts. However, by circulating an incident laser beam by 360° during one image acquisition, relevant image information is amplified. By combining total internal reflection illumination with dark-field detection, structures as small as 150 nm become separable through local destructive interferences. The technique images local changes in refractive index through scattered laser light and is applied to living mouse macrophages and helical bacteria revealing unexpected dynamic processes. PMID:27465033

The small heat shock protein Hsp27 affects assembly dynamics and structure of keratin intermediate filament networks.

PubMed

Kayser, Jona; Haslbeck, Martin; Dempfle, Lisa; Krause, Maike; Grashoff, Carsten; Buchner, Johannes; Herrmann, Harald; Bausch, Andreas R

2013-10-15

The mechanical properties of living cells are essential for many processes. They are defined by the cytoskeleton, a composite network of protein fibers. Thus, the precise control of its architecture is of paramount importance. Our knowledge about the molecular and physical mechanisms defining the network structure remains scarce, especially for the intermediate filament cytoskeleton. Here, we investigate the effect of small heat shock proteins on the keratin 8/18 intermediate filament cytoskeleton using a well-controlled model system of reconstituted keratin networks. We demonstrate that Hsp27 severely alters the structure of such networks by changing their assembly dynamics. Furthermore, the C-terminal tail domain of keratin 8 is shown to be essential for this effect. Combining results from fluorescence and electron microscopy with data from analytical ultracentrifugation reveals the crucial role of kinetic trapping in keratin network formation. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Synthesis and atomic scale characterization of Er2O3 nanoparticles: enhancement of magnetic properties and changes in the local structure.

PubMed

Corrêa, Eduardo L; Bosch-Santos, Brianna; Freitas, Rafael S; da Penha A Potiens, Maria; Saiki, Mitiko; Carbonari, Artur W

2018-05-18

In the investigation reported in this paper a modified thermal decomposition method was developed to produce very small Er 2 O 3 nanoparticles (NPs). Particles structure, shape and size were characterized by x-ray diffraction and transmission electron microscopy which showed that the synthesis by thermal decomposition under O 2 atmosphere produced very small and monodisperse NPs, allowing the investigation of finite-size and surface effects. Results of magnetization measurements showed that the smallest particles present the highest values of susceptibility that decrease as particle size increases. Specific heat measurements indicate that the sample with the smallest NPs (diameter ∼5 nm) has a Néel temperature of 0.54 K. The local structure of particles was investigated by measurements of hyperfine interactions with perturbed angular correlation spectroscopy using 111 Cd as probe nuclei replacing the cationic sites. Results showed that the relative population of sites 8b increases in both the core and surface layer of particles.

On the adsorption properties of magnetic fluids: Impact of bulk structure

NASA Astrophysics Data System (ADS)

Kubovcikova, Martina; Gapon, Igor V.; Zavisova, Vlasta; Koneracka, Martina; Petrenko, Viktor I.; Soltwedel, Olaf; Almasy, László; Avdeev, Mikhail V.; Kopcansky, Peter

2017-04-01

Adsorption of nanoparticles from magnetic fluids (MFs) on solid surface (crystalline silicon) was studied by neutron reflectometry (NR) and related to the bulk structural organization of MFs concluded from small-angle neutron scattering (SANS). The initial aqueous MF with nanomagnetite (co-precipitation reaction) stabilized by sodium oleate and MF modified by a biocompatible polymer, poly(ethylene glycol) (PEG), were considered. Regarding the bulk structure it was confirmed in the SANS experiment that comparatively small and compact (size 30 nm) aggregates of nanoparticle in the initial sample transfer to large and developed (size>130 nm, fractal dimension 2.7) associates in the PEG modified MF. This reorganization in the aggregates correlates with the changes in the neutron reflectivity that showed that a single adsorption layer of individual nanoparticles on the oxidized silicon surface for the initial MF disappears after the PEG modification. It is concluded that all particles in the modified fluid are in the aggregates that are not adsorbed by silicon.

Structural basis for profilin-mediated actin nucleotide exchange

PubMed Central

Porta, Jason C.; Borgstahl, Gloria E.O.

2015-01-01

Actin is a ubiquitous eukaryotic protein that is responsible for cellular scaffolding, motility and division. The ability of actin to form a helical filament is the driving force behind these cellular activities. Formation of a filament is dependent the successful exchange of actin’s ADP for ATP. Mammalian profilin is a small actin binding protein that catalyzes the exchange of nucleotide and facilitates the addition of an actin monomer to a growing filament. Here, crystal structures of profilin:actin have been determined showing an actively exchanging ATP. The structural analysis shows how the binding of profilin to the barbed end of actin causes a rotation of the small domain relative to the large domain. This conformational change is propagated to the ATP site and causes a shift in the nucleotide loops which in turn causes a repositioning of Ca2+ to its canonical position as the cleft closes around ATP. Reversing the solvent exposure of Trp-356 is also involved in cleft closure. In addition, secondary calcium binding sites were identified. PMID:22366544

Evaluation of Seismic Performance and Effectiveness of Multiple Slim-Type Damper System for Seismic Response Control of Building Structures

PubMed Central

Kim, David; Sung, Eun Hee; Park, Kwan-Soon; Park, Jaegyun

2014-01-01

This paper presents the evaluation of seismic performance and cost-effectiveness of a multiple slim-type damper system developed for the vibration control of earthquake excited buildings. The multiple slim-type damper (MSD) that consists of several small slim-type dampers and linkage units can control damping capacity easily by changing the number of small dampers. To evaluate the performance of the MSD, dynamic loading tests are performed with three slim-type dampers manufactured at a real scale. Numerical simulations are also carried out by nonlinear time history analysis with a ten-story earthquake excited building structure. The seismic performance and cost-effectiveness of the MSD system are investigated according to the various installation configurations of the MSD system. From the results of numerical simulation and cost-effectiveness evaluation, it is shown that combinations of the MSD systems can effectively improve the seismic performance of earthquake excited building structures. PMID:25301387

Creating an Institutional Identity out of "Differences": A Case Study of Multicultural Organizational Change.

ERIC Educational Resources Information Center

Bensimon, Estela Mara

This case study examines the efforts of one small private liberal arts college to exchange a monocultural organizational structure for one that is grounded in the racial, ethnic, and cultural diversity of the student body. The paper is based on interviews with faculty, administrators, students, and trustees and provides a detailed description of…

"What Did I Change and Why Did I Do It?": Young Writers' Revision Practices

ERIC Educational Resources Information Center

Dix, Stephanie

2006-01-01

The article presents findings from a research project that investigated young, fluent writers' revision practices. The project adopted a qualitative approach, using semi-structured interviews based on the students' written scripts. This article focuses on a small sample of children and profiles the extent of their ability to reflect on their…

Small and Perfectly Formed? Is Democracy an Alternative Approach to School Leadership?

ERIC Educational Resources Information Center

Hope, Max A.

2012-01-01

In recent decades, education policy has changed considerably so that now, numerous types of schools are available in the "marketplace". The most recent additions to this landscape are Academies and Free Schools, with freedoms to make more choices about curriculum, structures and leadership. In this climate, this paper takes one school as…

77 FR 11001 - Small Business Size Standards: Health Care and Social Assistance

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-24

... the changes in the Federal contracting marketplace and industry structure. The last time SBA conducted... size standards at one time, SBA is reviewing size standards on a Sector by Sector basis. A NAICS Sector... nonmanufacturer rule. See 13 CFR 121.406(b). These long-standing anchor size standards have stood the test of time...

Reenergizing Small Communities: A Vital Role for Rural Schools

ERIC Educational Resources Information Center

Wright, Kathleen Anne

2007-01-01

New ways of participating in rural communities and in community development have evolved as the structure of rural communities has changed. In some communities, the impetus to redefine and reenergize is strong while, in others, ways to move forward have yet to be identified (Pomeroy 1997). Rural schools serve a vital role in recreating communities…

Small-diameter success stories III.

Treesearch

Jean Livingston

2008-01-01

More than 73 million acres of our national forests and millions more in public and private forestlands are in need of some form of restoration. Our forests are declining in health because of major changes over the years in forest structure and composition. However, restoration of these overstocked stands is extremely expensive. If new, economical, and value-added uses...

Gage for evaluating rheumatoid hands

NASA Technical Reports Server (NTRS)

Houge, J. C.; Plautz, K. A.

1981-01-01

Two-axis goniometer accurately measures movements of fingers about knuckle joints, diagnosing hands structurally changed by rheumatoid arthritis. Instrument measures lateral movement which is small in normal knuckles but increased in diseased joints. Goniometer is two connected protractors that simultaneously measure angles in perpindicular planes. Dials are offset to clear bony protuberances; extension and offset adjustments span any hand size.

Connecting Common Genetic Polymorphisms to Protein Function: A Modular Project Sequence for Lecture or Lab

ERIC Educational Resources Information Center

Berndsen, Christopher E.; Young, Byron H.; McCormick, Quinlin J.; Enke, Raymond A.

2016-01-01

Single nucleotide polymorphisms (SNPs) in DNA can result in phenotypes where the biochemical basis may not be clear due to the lack of protein structures. With the growing number of modeling and simulation software available on the internet, students can now participate in determining how small changes in genetic information impact cellular…

Technology, Learning, and Change: Community Development Revisited

ERIC Educational Resources Information Center

Moore, Anne H.

2004-01-01

Bordering on North Carolina, the Dan River region of Southside Virginia is a largely rural area south of the state capitol, Richmond, and 135 miles east of Virginia Tech's main residential campus in Blacksburg. The structural problems evident today in this expanse of wooded areas, fields, small cities, and towns were born, in large measure, of the…

Shared community patterns following experimental fire in a semiarid grassland

Treesearch

Paulette L. Ford

2007-01-01

This paper presents a synthesis of experimental research testing effects of seasonal fire on community structure of plants, arthropods, and small mammals in shortgrass steppe. These groups of plants and animals share the same environment, and therefore, the species in the groups were predicted to respond in a similar way to changes in their environment resulting from...

Economic Conditions and the Divorce Rate: A Time-Series Analysis of the Postwar United States.

ERIC Educational Resources Information Center

South, Scott J.

1985-01-01

Challenges the belief that the divorce rate rises during prosperity and falls during economic recessions. Time-series regression analysis of postwar United States reveals small but positive effects of unemployment on divorce rate. Stronger influences on divorce rates are changes in age structure and labor-force participation rate of women.…

13 CFR 108.460 - Restrictions on Common Control or ownership of two (or more) NMVC Companies.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false Restrictions on Common Control or ownership of two (or more) NMVC Companies. 108.460 Section 108.460 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION NEW MARKETS VENTURE CAPITAL (âNMVCâ) PROGRAM Changes in Ownership, Structure, or...

Global analysis of tomato gene expression during potato spindle tuber viroid infection reveals a complex array of changes affecting hormone signaling

USDA-ARS?s Scientific Manuscript database

Viroids are the smallest known agents of infectious disease – small, single-stranded, highly structured, circular RNAs that lack detectable messenger RNA activity yet are able to replicate autonomously in susceptible plant species. Potato spindle tuber viroid (PSTVd) infection in tomato is accompan...

Understanding ponderosa pine forest-grassland vegetation dynamics at Fort Valley Experimental Forest using phytolith analysis

Treesearch

Becky K. Kerns; Margaret M. Moore; Stephen C. Hart

2008-01-01

In the last century, ponderosa pine forests in the Southwest have changed from more open park-like stands of older trees to denser stands of younger, small-diameter trees. Considerable information exists regarding ponderosa pine forest fire history and recent shifts in stand structure and composition, yet quantitative studies investigating understory reference...

Observation of an angular change in the structure of an RNA complex using Fluorescence Resonance Energy Transfer

NASA Astrophysics Data System (ADS)

Rahmanseresht, Sheema; Milas, Peker; Parrot, Louis; Goldner, Lori S.

Single-molecular-pair FRET is often used to study distance fluctuations of single molecules. It is harder to capture angular changes using FRET, because rotational motion of the dyes tends to wash out the angular sensitivity. Using a dye labeling scheme that minimizes the rotational motion of the dyes with respect to the RNA, we use spFRET to measure an angular change in structure of an RNA kissing complex upon protein binding. The model system studied here, R1inv-R2inv, is derived from the RNAI-RNAII complex in E.coli. RNA II is a primer for replication of the ColE1 plasmid; its function is modulated by interaction with RNA I, Rop protein is known to stabilize the bent R1inv-R2inv kissing complex against dissociation. The effect, if any, of Rop protein on the conformation of the kissing complex is not known. The eight minimized-energy NMR structures reported for R1inv-R2inv show a small difference in end-to-end distances and much larger differences in twist and bend angles. We compare a first-principles model with spFRET data to determine if the observed change in FRET is consistent with an angular change in structure, as suggested by the model. Grant Number: NSF DBI-1152386.

Transcriptome-Wide Analysis of UTRs in Non-Small Cell Lung Cancer Reveals Cancer-Related Genes with SNV-Induced Changes on RNA Secondary Structure and miRNA Target Sites

PubMed Central

Novotny, Peter; Tang, Xiaojia; Kalari, Krishna R.; Gorodkin, Jan

2014-01-01

Traditional mutation assessment methods generally focus on predicting disruptive changes in protein-coding regions rather than non-coding regulatory regions like untranslated regions (UTRs) of mRNAs. The UTRs, however, are known to have many sequence and structural motifs that can regulate translational and transcriptional efficiency and stability of mRNAs through interaction with RNA-binding proteins and other non-coding RNAs like microRNAs (miRNAs). In a recent study, transcriptomes of tumor cells harboring mutant and wild-type KRAS (V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog) genes in patients with non-small cell lung cancer (NSCLC) have been sequenced to identify single nucleotide variations (SNVs). About 40% of the total SNVs (73,717) identified were mapped to UTRs, but omitted in the previous analysis. To meet this obvious demand for analysis of the UTRs, we designed a comprehensive pipeline to predict the effect of SNVs on two major regulatory elements, secondary structure and miRNA target sites. Out of 29,290 SNVs in 6462 genes, we predict 472 SNVs (in 408 genes) affecting local RNA secondary structure, 490 SNVs (in 447 genes) affecting miRNA target sites and 48 that do both. Together these disruptive SNVs were present in 803 different genes, out of which 188 (23.4%) were previously known to be cancer-associated. Notably, this ratio is significantly higher (one-sided Fisher's exact test p-value = 0.032) than the ratio (20.8%) of known cancer-associated genes (n = 1347) in our initial data set (n = 6462). Network analysis shows that the genes harboring disruptive SNVs were involved in molecular mechanisms of cancer, and the signaling pathways of LPS-stimulated MAPK, IL-6, iNOS, EIF2 and mTOR. In conclusion, we have found hundreds of SNVs which are highly disruptive with respect to changes in the secondary structure and miRNA target sites within UTRs. These changes hold the potential to alter the expression of known cancer genes or genes linked to cancer-associated pathways. PMID:24416147

Transcriptome-wide analysis of UTRs in non-small cell lung cancer reveals cancer-related genes with SNV-induced changes on RNA secondary structure and miRNA target sites.

PubMed

Sabarinathan, Radhakrishnan; Wenzel, Anne; Novotny, Peter; Tang, Xiaojia; Kalari, Krishna R; Gorodkin, Jan

2014-01-01

Traditional mutation assessment methods generally focus on predicting disruptive changes in protein-coding regions rather than non-coding regulatory regions like untranslated regions (UTRs) of mRNAs. The UTRs, however, are known to have many sequence and structural motifs that can regulate translational and transcriptional efficiency and stability of mRNAs through interaction with RNA-binding proteins and other non-coding RNAs like microRNAs (miRNAs). In a recent study, transcriptomes of tumor cells harboring mutant and wild-type KRAS (V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog) genes in patients with non-small cell lung cancer (NSCLC) have been sequenced to identify single nucleotide variations (SNVs). About 40% of the total SNVs (73,717) identified were mapped to UTRs, but omitted in the previous analysis. To meet this obvious demand for analysis of the UTRs, we designed a comprehensive pipeline to predict the effect of SNVs on two major regulatory elements, secondary structure and miRNA target sites. Out of 29,290 SNVs in 6462 genes, we predict 472 SNVs (in 408 genes) affecting local RNA secondary structure, 490 SNVs (in 447 genes) affecting miRNA target sites and 48 that do both. Together these disruptive SNVs were present in 803 different genes, out of which 188 (23.4%) were previously known to be cancer-associated. Notably, this ratio is significantly higher (one-sided Fisher's exact test p-value = 0.032) than the ratio (20.8%) of known cancer-associated genes (n = 1347) in our initial data set (n = 6462). Network analysis shows that the genes harboring disruptive SNVs were involved in molecular mechanisms of cancer, and the signaling pathways of LPS-stimulated MAPK, IL-6, iNOS, EIF2 and mTOR. In conclusion, we have found hundreds of SNVs which are highly disruptive with respect to changes in the secondary structure and miRNA target sites within UTRs. These changes hold the potential to alter the expression of known cancer genes or genes linked to cancer-associated pathways.

Degrees of Isolation: The Impact of Climate Change on the Dispersal and Population Genetic Structure of Two Antarctic Fish Species

NASA Astrophysics Data System (ADS)

Young, E. F.; Belchier, M.; Meredith, M. P.; Tysklind, N.; Carvalho, G. R.

2016-02-01

Understanding the key drivers of larval dispersal and population connectivity in the marine environment is essential for estimating the potential impacts of climate change on the genetic structure and resilience of populations. Small, isolated and fragmented communities will differ fundamentally in their response and resilience to environmental stress, compared with species that are broadly distributed, abundant, and with a frequent exchange of members. Using a `seascape genetics' approach, combining oceanographic modelling and genetic analyses, we have elucidated the fundamental roles of oceanographic transport and planktonic duration on the connectivity and population genetic structure of two Antarctic fish species with contrasting early life histories, Champsocephalus gunnari and Notothenia rossii. Here, we extend these analyses to consider the impact of rising sea temperatures due to climate change on planktonic dispersal and population connectivity. Using a theoretical approach, the effect of increased water temperatures on mortality rates and species-specific egg and larval phase durations has been incorporated into the models, and the relative impact of these climate-related influences on connectivity and population genetic structure has been investigated. Here we present the key findings of our research and consider the roles of early life history and oceanography in the response of fragmented fish populations to climate change.

Signaling and sensory adaptation in Escherichia coli chemoreceptors: 2015 update

PubMed Central

Parkinson, John S.; Hazelbauer, Gerald L.; Falke, Joseph J.

2015-01-01

Motile Escherichia coli cells track gradients of attractant and repellent chemicals in their environment with transmembrane chemoreceptor proteins. These receptors operate in cooperative arrays to produce large changes in the activity of a signaling kinase CheA in response to small changes in chemoeffector concentration. Recent research has provided much deeper understanding of the structure and function of core receptor signaling complexes and the architecture of higher-order receptor arrays, which in turn has led to new insights into the molecular signaling mechanisms of chemoreceptor networks. Current evidence supports a new view of receptor signaling in which stimulus information travels within receptor molecules through shifts in the dynamic properties of adjoining structural elements rather than through a few discrete conformational states. PMID:25834953

Crystal structure and phase transitions of sodium potassium niobate perovskites

NASA Astrophysics Data System (ADS)

Tellier, J.; Malic, B.; Dkhil, B.; Jenko, D.; Cilensek, J.; Kosec, M.

2009-02-01

This paper presents the crystal structure and the phase transitions of K xNa 1- xNbO 3 (0.4 ≤ x ≤ 0.6). X-ray diffraction measurements were used to follow the change of the unit-cell parameters and the symmetry in the temperature range 100-800 K. At room temperature all the compositions exhibited a monoclinic metric of the unit cell with a small monoclinic distortion (90.32° ≤ β ≤ 90.34°). No major change of symmetry was evidenced in the investigated compositional range, which should be characteristic of the morphotropic phase-boundary region. With increasing temperature, the samples underwent first-order monoclinic-tetragonal and tetragonal-cubic transitions. Only the potassium-rich phases were rhombohedral at 100 K.

Origin and development of plains-type folds in the mid-continent (United States) during the late Paleozoic

USGS Publications Warehouse

Merriam, D.F.

2005-01-01

Plains-type folds are local, subtle anticlines formed in the thin sedimentary package overlying a shallow, crystalline basement on the craton. They are small in areal extent (usually less than 1-3 km 2 [0.4-1.2 mi2]), and their amplitude increases with depth (usually tens of meters), which is mainly the result of differential compaction of sediments (usually clastic units) over tilted, rigid, basement fault blocks. The development of these structural features by continuous but intermittent movement of the basement fault blocks in the late Paleozoic in the United States mid-continent is substantiated by a record of stratigraphic and sedimentological evidence. The recurrent structural movement, which reflects adjustment to external stresses, is expressed by the change in thickness of stratigraphic units over the crest of the fold compared to the flanks. By plotting the change in thickness for different stratigraphic units of anticlines on different fault blocks, it is possible to determine the timing of movement of the blocks that reflect structural adjustment. These readjustments are confirmed by sedimentological evidence, such as convolute, soft-sediment deformation features and small intraformational faults. The stratigraphic interval change in thickness for numerous structures in the Cherokee, Forest City, and Salina basins and on the Nemaha anticline of the mid-continent United States was determined and compared for location and timing of the adjustments. Most of the adjustment occurred during and after time of deposition of the Permian-Pennsylvanian clastic units, which, in turn, reflect tectonic disturbance in adjacent areas, and the largest amount of movement on the plains-type structures occurred on those nearest and semiparallel to major positive features, such as the Nemaha anticline. Depending on the time of origin and development of plains-type folds, they may control the entrapment and occurrence of oil and gas. Copyright ??2005. The American Association of Petroleum Geologists. All rights reserved.

Impact of hygrothermal aging on structure/function relationship of perfluorosulfonic-acid membrane

DOE PAGES

Shi, Shouwen; Dursch, Thomas J.; Blake, Colin; ...

2015-10-20

Perfluorosulfonic-acid (PFSA) membranes are widely used as the solid electrolyte in electrochemical devices where their main functionalities are ion (proton) conduction and gas separation in a thermomechanically stable matrix. Due to prolonged operational requirements in these devices, PFSA membranes’ properties change with time due to hygrothermal aging. This paper studies the evolution of PFSA structure/property relationship changes during hygrothermal aging, including chemical changes leading to changes in ion-exchange capacity (IEC), nanostructure, water-uptake behavior, conductivity, and mechanical properties. Our findings demonstrate that with hygrothermal aging, the storage modulus increases, while IEC and water content decrease, consistent with the changes in nanostructure,more » that is, water- and crystalline-domain spacings inferred from small- and wide-angle X-ray scattering (SAXS/WAXS) experiments. In addition, the impact of aging is found to depend on the membrane's thermal prehistory and post-treatments, although universal correlations exist between nanostructural changes and water uptake. Lastly, the findings have impact on understanding lifetime, durability, and use of these and related polymers in various technologies.« less

Pressure-actuated cellular structures.

PubMed

Pagitz, M; Lamacchia, E; Hol, J M A M

2012-03-01

Shape changing structures will play an important role in future engineering designs since rigid structures are usually only optimal for a small range of service conditions. Hence, a concept for reliable and energy-efficient morphing structures that possess a large strength to self-weight ratio would be widely applicable. We propose a novel concept for morphing structures that is inspired by the nastic movement of plants. The idea is to connect prismatic cells with tailored pentagonal and/or hexagonal cross sections such that the resulting cellular structure morphs into given target shapes for certain cell pressures. An efficient algorithm for computing equilibrium shapes as well as cross-sectional geometries is presented. The potential of this novel concept is demonstrated by several examples that range from a flagellum like propulsion device to a morphing aircraft wing.

Influence of ceramide on the internal structure and hydration of the phospholipid bilayer studied by neutron and X-ray scattering

NASA Astrophysics Data System (ADS)

Kiselev, M. A.; Zemlyanaya, E. V.; Ryabova, N. Y.; Hauss, T.; Almasy, L.; Funari, S. S.; Zbytovska, J.; Lombardo, D.

2014-07-01

Small angle neutron scattering (SANS), neutron diffraction and X-ray powder diffraction were used to investigate influence of N-stearoyl phytosphingosine (CER[NP]) and α-hydroxy- N-stearoyl phytosphingosine (CER[AP]) on the internal structure and hydration of DMPC membrane in fully and partly hydrated states at T = 30 °C. Application of Fourier analysis for diffraction data and model calculations for the SANS data evidence that addition of both CER[NP] and CER[AP] in small concentrations promotes significant changes in the organization of DMPC bilayers, such as the increase of the hydrophobic core region. SANS data evidence a decrease in the average radius and polydispersity of the vesicles that can be ascribed to hydrogen bonds interactions that favor tight lipid packing with a compact, more rigid character.

Beyond simple small-angle X-ray scattering: developments in online complementary techniques and sample environments.

PubMed

Bras, Wim; Koizumi, Satoshi; Terrill, Nicholas J

2014-11-01

Small- and wide-angle X-ray scattering (SAXS, WAXS) are standard tools in materials research. The simultaneous measurement of SAXS and WAXS data in time-resolved studies has gained popularity due to the complementary information obtained. Furthermore, the combination of these data with non X-ray based techniques, via either simultaneous or independent measurements, has advanced understanding of the driving forces that lead to the structures and morphologies of materials, which in turn give rise to their properties. The simultaneous measurement of different data regimes and types, using either X-rays or neutrons, and the desire to control parameters that initiate and control structural changes have led to greater demands on sample environments. Examples of developments in technique combinations and sample environment design are discussed, together with a brief speculation about promising future developments.

Beyond simple small-angle X-ray scattering: developments in online complementary techniques and sample environments

PubMed Central

Bras, Wim; Koizumi, Satoshi; Terrill, Nicholas J

2014-01-01

Small- and wide-angle X-ray scattering (SAXS, WAXS) are standard tools in materials research. The simultaneous measurement of SAXS and WAXS data in time-resolved studies has gained popularity due to the complementary information obtained. Furthermore, the combination of these data with non X-ray based techniques, via either simultaneous or independent measurements, has advanced understanding of the driving forces that lead to the structures and morphologies of materials, which in turn give rise to their properties. The simultaneous measurement of different data regimes and types, using either X-rays or neutrons, and the desire to control parameters that initiate and control structural changes have led to greater demands on sample environments. Examples of developments in technique combinations and sample environment design are discussed, together with a brief speculation about promising future developments. PMID:25485128

Serial population extinctions in a small mammal indicate Late Pleistocene ecosystem instability

PubMed Central

Brace, Selina; Palkopoulou, Eleftheria; Dalén, Love; Lister, Adrian M.; Miller, Rebecca; Otte, Marcel; Germonpré, Mietje; Blockley, Simon P. E.; Stewart, John R.; Barnes, Ian

2012-01-01

The Late Pleistocene global extinction of many terrestrial mammal species has been a subject of intensive scientific study for over a century, yet the relative contributions of environmental changes and the global expansion of humans remain unresolved. A defining component of these extinctions is a bias toward large species, with the majority of small-mammal taxa apparently surviving into the present. Here, we investigate the population-level history of a key tundra-specialist small mammal, the collared lemming (Dicrostonyx torquatus), to explore whether events during the Late Pleistocene had a discernible effect beyond the large mammal fauna. Using ancient DNA techniques to sample across three sites in North-West Europe, we observe a dramatic reduction in genetic diversity in this species over the last 50,000 y. We further identify a series of extinction-recolonization events, indicating a previously unrecognized instability in Late Pleistocene small-mammal populations, which we link with climatic fluctuations. Our results reveal climate-associated, repeated regional extinctions in a keystone prey species across the Late Pleistocene, a pattern likely to have had an impact on the wider steppe-tundra community, and one that is concordant with environmental change as a major force in structuring Late Pleistocene biodiversity. PMID:23185018

Three-dimensional elastic-plastic finite-element analysis of fatigue crack propagation

NASA Technical Reports Server (NTRS)

Goglia, G. L.; Chermahini, R. G.

1985-01-01

Fatigue cracks are a major problem in designing structures subjected to cyclic loading. Cracks frequently occur in structures such as aircraft and spacecraft. The inspection intervals of many aircraft structures are based on crack-propagation lives. Therefore, improved prediction of propagation lives under flight-load conditions (variable-amplitude loading) are needed to provide more realistic design criteria for these structures. The main thrust was to develop a three-dimensional, nonlinear, elastic-plastic, finite element program capable of extending a crack and changing boundary conditions for the model under consideration. The finite-element model is composed of 8-noded (linear-strain) isoparametric elements. In the analysis, the material is assumed to be elastic-perfectly plastic. The cycle stress-strain curve for the material is shown Zienkiewicz's initial-stress method, von Mises's yield criterion, and Drucker's normality condition under small-strain assumptions are used to account for plasticity. The three-dimensional analysis is capable of extending the crack and changing boundary conditions under cyclic loading.

Structure of the β-form of human MK2 in complex with the non-selective kinase inhibitor TEI-L03090

PubMed Central

Fujino, Aiko; Fukushima, Kei; Kubota, Takaharu; Matsumoto, Yoshiyuki; Takimoto-Kamimura, Midori

2013-01-01

Mitogen-activated protein kinase-activated protein kinase 2 (MK2 or MAPKAP-K2), a serine/threonine kinase from the p38 mitogen-activated protein kinase signalling pathway, plays an important role in the production of TNF-α and other cytokines. In a previous report, it was shown that MK2 in complex with the selective inhibitor TEI-I01800 adopts an α-helical glycine-rich loop that is induced by the stable nonplanar conformer of TEI-I01800. To understand the mechanism of the structural change, the structure of MK2 bound to TEI-L03090, which lacks the key substituent found in TEI-I01800, was determined. MK2–TEI-L03090 has a β-sheet glycine-rich loop in common with other kinases, as predicted. This result suggests that a small compound can induce a drastic conformational change in the target protein structure and can be used to design potent and selective inhibitors. PMID:24316826

Automated polarization control for the precise alignment of laser-induced self-organized nanostructures

NASA Astrophysics Data System (ADS)

Hermens, Ulrike; Pothen, Mario; Winands, Kai; Arntz, Kristian; Klocke, Fritz

2018-02-01

Laser-induced periodic surface structures (LIPSS) found in particular applications in the fields of surface functionalization have been investigated since many years. The direction of these ripple structures with a periodicity in the nanoscale can be manipulated by changing the laser polarization. For industrial use, it is useful to manipulate the direction of these structures automatically and to obtain smooth changes of their orientation without any visible inhomogeneity. However, currently no system solution exists that is able to control the polarization direction completely automated in one software solution so far. In this paper, a system solution is presented that includes a liquid crystal polarizer to control the polarization direction. It is synchronized with a scanner, a dynamic beam expander and a five axis-system. It provides fast switching times and small step sizes. First results of fabricated structures are also presented. In a systematic study, the conjunction of LIPSS with different orientation in two parallel line scans has been investigated.

Structure and Inhibition of Microbiome β-Glucuronidases Essential to the Alleviation of Cancer Drug Toxicity

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

Wallace, Bret D.; Roberts, Adam B.; Pollet, Rebecca M.

The selective inhibition of bacterial β-glucuronidases was recently shown to alleviate drug-induced gastrointestinal toxicity in mice, including the damage caused by the widely used anticancer drug irinotecan. Here, we report crystal structures of representative β-glucuronidases from the Firmicutes Streptococcus agalactiae and Clostridium perfringens and the Proteobacterium Escherichia coli, and the characterization of a β-glucuronidase from the Bacteroidetes Bacteroides fragilis. While largely similar in structure, these enzymes exhibit marked differences in catalytic properties and propensities for inhibition, indicating that the microbiome maintains functional diversity in orthologous enzymes. Small changes in the structure of designed inhibitors can induce significant conformational changes inmore » the β-glucuronidase active site. Finally, we establish that β-glucuronidase inhibition does not alter the serum pharmacokinetics of irinotecan or its metabolites in mice. Together, the data presented advance our in vitro and in vivo understanding of the microbial β-glucuronidases, a promising new set of targets for controlling drug-induced gastrointestinal toxicity.« less

Mammalian HspB1 (Hsp27) is a molecular sensor linked to the physiology and environment of the cell.

PubMed

Arrigo, André-Patrick

2017-07-01

Constitutively expressed small heat shock protein HspB1 regulates many fundamental cellular processes and plays major roles in many human pathological diseases. In that regard, this chaperone has a huge number of apparently unrelated functions that appear linked to its ability to recognize many client polypeptides that are subsequently modified in their activity and/or half-life. A major parameter to understand how HspB1 is dedicated to interact with particular clients in defined cellular conditions relates to its complex oligomerization and phosphorylation properties. Indeed, HspB1 structural organization displays dynamic and complex rearrangements in response to changes in the cellular environment or when the cell physiology is modified. These structural modifications probably reflect the formation of structural platforms aimed at recognizing specific client polypeptides. Here, I have reviewed data from the literature and re-analyzed my own studies to describe and discuss these fascinating changes in HspB1 structural organization.

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

Xiong, J.-P.; Stehle, T.; Zhang, R.

The structural basis for the divalent cation-dependent binding of heterodimeric alpha beta integrins to their ligands, which contain the prototypical Arg-Gly-Asp sequence, is unknown. Interaction with ligands triggers tertiary and quaternary structural rearrangements in integrins that are needed for cell signaling. Here we report the crystal structure of the extracellular segment of integrin alpha Vbeta 3 in complex with a cyclic peptide presenting the Arg-Gly-Asp sequence. The ligand binds at the major interface between the alpha V and beta 3 subunits and makes extensive contacts with both. Both tertiary and quaternary changes are observed in the presence of ligand. Themore » tertiary rearrangements take place in beta A, the ligand-binding domain of beta 3; in the complex, beta A acquires two cations, one of which contacts the ligand Asp directly and the other stabilizes the ligand-binding surface. Ligand binding induces small changes in the orientation of alpha V relative to beta 3.« less

Probing Conformational Change of Bovine Serum Albumin–Dextran Conjugates under Controlled Dry Heating

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

Xia, Shuqin; Li, Yunqi; Zhao, Qin

2015-04-29

The time-dependent conformational change of bovine serum album (BSA) during Maillard reaction with dextran under controlled dry heating has been studied by small-angle X-ray scattering, fluorescence spectroscopy, dynamic light scattering, and circular dichroism analysis. Through the research on the radii of gyration (R g), intrinsic fluorescence, and secondary structure, conjugates with dextran coating were found to inhibit BSA aggregation and preserve the secondary structure of native BSA against long-time heat treatment during Maillard reaction. The results suggested that the hydrophilic dextran was conjugated to the compact protein surface and enclosed it and more dextran chains were attached to BSA withmore » the increase of the heating time. The study presented here will be beneficial to the understanding of the conformational evolution of BSA molecules during the dry-heating Maillard reaction and to the control of the protein–polysaccharide conjugate structure.« less

Density, Velocity and Ionization Structure in Accretion-Disc Winds

NASA Technical Reports Server (NTRS)

Sonneborn, George (Technical Monitor); Long, Knox

2004-01-01

This was a project to exploit the unique capabilities of FUSE to monitor variations in the wind- formed spectral lines of the luminous, low-inclination, cataclysmic variables(CV) -- RW Sex. (The original proposal contained two additional objects but these were not approved.) These observations were intended to allow us to determine the relative roles of density and ionization state changes in the outflow and to search for spectroscopic signatures of stochastic small-scale structure and shocked gas. By monitoring the temporal behavior of blue-ward extended absorption lines with a wide range of ionization potentials and excitation energies, we proposed to track the changing physical conditions in the outflow. We planned to use a new Monte Carlo code to calculate the ionization structure of and radiative transfer through the CV wind. The analysis therefore was intended to establish the wind geometry, kinematics and ionization state, both in a time-averaged sense and as a function of time.

Analysis of angle effect on particle flocculation in branch flow

NASA Astrophysics Data System (ADS)

Prasad, Karthik; Fink, Kathryn; Liepmann, Dorian

2014-11-01

Hollow point microneedle drug delivery systems are known to be highly susceptible to blockage, owing to their very small structures. This problem has been especially noted when delivering suspended particle solutions, such as vaccines. Attempts to reduce particle flocculation in such devices through surface treatments of the particles have been largely unsuccessful. Furthermore, the particle clog only forms at the mouths of the microneedle structures, leaving the downstream walls clear. This implies that the sudden change in length scales alter the hydrodynamic interactions, creating the conditions for particle flocculation. However, while it is known that particle flocculation occurs, the physics behind the event are obscure. We utilize micro-PIV to observe how the occurrence and formation of particle flocculation changes in relation to the angle encountered by particle laden flow into microfluidic branch structures. The results offer the ability to optimize particle flocculation in MEMS devices, increasing device efficacy and longevity.

On-wire lithography: synthesis, encoding and biological applications

PubMed Central

Banholzer, Matthew J; Qin, Lidong; Millstone, Jill E; Osberg, Kyle D; Mirkin, Chad A

2014-01-01

The next step in the maturing field of nanotechnology is to develop ways to introduce unusual architectural changes to simple building blocks. For nanowires, on-wire lithography (OWL) has emerged as a powerful way of synthesizing a segmented structure and subsequently introducing architectural changes through post-chemical treatment. In the OWL protocol presented here, multisegmented nanowires are grown and a support layer is deposited on one side of each nanostructure. After selective chemical etching of sacrificial segments, structures with gaps as small as 2 nm and disks as thin as 20 nm can be created. These nanostructures are highly tailorable and can be used in electrical transport, Raman enhancement and energy conversion. Such nanostructures can be functionalized with many types of adsorbates, enabling the use of OWL-generated structures as bioactive probes for diagnostic assays and molecular transport junctions. The process takes 13–36 h depending on the type of adsorbate used to functionalize the nanostructures. PMID:19444241

Relativistic shock waves in an electron-positron plasma

NASA Astrophysics Data System (ADS)

Tsintsadze, Levan N.

1995-12-01

The equations describing the detailed structure of radiation electromagnetic hydrodynamics for a relativistically hot electron-positron plasma are derived. Various discontinuities are studied by these equations. It is shown that the dependence of the electron (positron) mass on the temperature changes the structure of discontinuities, including shock waves, both qualitatively and quantitatively. Steady radiative shocks are considered, which can arise in steady flows, and which also can be used to describe the propagation of shocks when the shock thickness is very small as compared to the characteristic length over which the ambient medium changes significantly. First, the magnetohydrodynamic shock wave is treated as a discontinuity and jump relations, which relate the equilibrium states of the upstream and downstream plasma far from the front, are derived. Then the structure of the front itself is considered and tangential, contact (or entropy) and rotational discontinuities are investigated.

Insight into the microscopic structure of an AdS black hole from a thermodynamical phase transition.

PubMed

Wei, Shao-Wen; Liu, Yu-Xiao

2015-09-11

Comparing with an ordinary thermodynamic system, we investigate the possible microscopic structure of a charged anti-de Sitter black hole completely from the thermodynamic viewpoint. The number density of the black hole molecules is introduced to measure the microscopic degrees of freedom of the black hole. We found that the number density suffers a sudden change accompanied by a latent heat when the black hole system crosses the small-large black hole coexistence curve, while when the system passes the critical point, it encounters a second-order phase transition with a vanishing latent heat due to the continuous change of the number density. Moreover, the thermodynamic scalar curvature suggests that there is a weak attractive interaction between two black hole molecules. These phenomena might cast new insight into the underlying microscopic structure of a charged anti-de Sitter black hole.

Dynamic Changes in Cervical Glycosaminoglycan Composition during Normal Pregnancy and Preterm Birth

PubMed Central

Akgul, Yucel; Holt, Roxane; Mummert, Mark; Word, Ann

2012-01-01

Glycosaminoglycans (GAG) have diverse functions that regulate macromolecular assembly in the extracellular matrix. During pregnancy, the rigid cervix transforms to a pliable structure to allow birth. Quantitative assessment of cervical GAG is a prerequisite to identify GAG functions in term and preterm birth. In the current study, total GAG levels increased at term, yet the abundance, chain length, and sulfation levels of sulfated GAG remained constant. The increase in total GAG resulted exclusively from an increase in hyaluronan (HA). HA can form large structures that promote increased viscosity, hydration, and matrix disorganization as well as small structures that have roles in inflammation. HA levels increased from 19% of total GAG in early pregnancy to 71% at term. Activity of the HA-metabolizing enzyme, hyaluronidase, increased in labor, resulting in metabolism of large to small HA. Similar to mice, HA transitions from high to low molecular weight in term human cervix. Mouse preterm models were also characterized by an increase in HA resulting from differential expression of the HA synthase (Has) genes, with increased Has1 in preterm in contrast to Has2 induction at term. The Has2 gene but not Has1 is regulated in part by estrogen. These studies identify a shift in sulfated GAG dominance in the early pregnant cervix to HA dominance in term and preterm ripening. Increased HA synthesis along with hyaluronidase-induced changes in HA size in mice and women suggest diverse contributions of HA to macromolecular changes in the extracellular matrix, resulting in loss of tensile strength during parturition. PMID:22529214

Chronic uremia induces permeability changes, increased nitric oxide synthase expression, and structural modifications in the peritoneum.

PubMed

Combet, S; Ferrier, M L; Van Landschoot, M; Stoenoiu, M; Moulin, P; Miyata, T; Lameire, N; Devuyst, O

2001-10-01

Advanced glycation end products (AGE), growth factors, and nitric oxide contribute to alterations of the peritoneum during peritoneal dialysis (PD). These mediators are also involved in chronic uremia, a condition associated with increased permeability of serosal membranes. It is unknown whether chronic uremia per se modifies the peritoneum before PD initiation. A rat model of subtotal nephrectomy was used to measure peritoneal permeability after 3, 6, and 9 wk, in parallel with peritoneal nitric oxide synthase (NOS) isoform expression and activity and structural changes. Uremic rats were characterized by a higher peritoneal permeability for small solutes and an increased NOS activity due to the up-regulation of endothelial and neuronal NOS. The permeability changes and increased NOS activities correlated with the degree of renal failure. Focal areas of vascular proliferation and fibrosis were detected in uremic rats, in relation with a transient up-regulation of vascular endothelial growth factor and basic fibroblast growth factor, as well as vascular deposits of the AGE carboxymethyllysine and pentosidine. Correction of anemia with erythropoietin did not prevent the permeability or structural changes in uremic rats. Thus, in this rat model, uremia induces permeability and structural changes in the peritoneum, in parallel with AGE deposits and up-regulation of specific NOS isoforms and growth factors. These data suggest an independent contribution of uremia in the peritoneal changes during PD and offer a paradigm to better understand the modifications of serosal membranes in uremia.

The roles of RIIbeta linker and N-terminal cyclic nucleotide-binding domain in determining the unique structures of Type IIbeta Protein Kinase A. A small angle X-ray and neutron scattering study

DOE PAGES

Blumenthal, Donald K.; Copps, Jeffrey; Smith-Nguyen, Eric V.; ...

2014-08-11

Protein kinase A (PKA) is ubiquitously expressed and is responsible for regulating many important cellular functions in response to changes in intracellular cAMP concentrations. Moreover, the PKA holoenzyme is a tetramer (R 2:C 2), with a regulatory subunit homodimer (R 2) that binds and inhibits two catalytic (C) subunits; binding of cAMP to the regulatory subunit homodimer causes activation of the catalytic subunits. Four different R subunit isoforms exist in mammalian cells, and these confer different structural features, subcellular localization, and biochemical properties upon the PKA holoenzymes they form. The holoenzyme containing RIIβ is structurally unique in that the typemore » IIβ holoenzyme is much more compact than the free RIIβ homodimer. We have used small angle x-ray scattering and small angle neutron scattering to study the solution structure and subunit organization of a holoenzyme containing an RIIβ C-terminal deletion mutant (RIIβ(1–280)), which is missing the C-terminal cAMP-binding domain to better understand the structural organization of the type IIβ holoenzyme and the RIIβ domains that contribute to stabilizing the holoenzyme conformation. These results demonstrate that compaction of the type IIβ holoenzyme does not require the C-terminal cAMP-binding domain but rather involves large structural rearrangements within the linker and N-terminal cyclic nucleotide-binding domain of the RIIβ homodimer. The structural rearrangements are significantly greater than seen previously with RIIα and are likely to be important in mediating short range and long range interdomain and intersubunit interactions that uniquely regulate the activity of the type IIβ isoform of PKA.« less

Damage severity assessment in wind turbine blade laboratory model through fuzzy finite element model updating

NASA Astrophysics Data System (ADS)

Turnbull, Heather; Omenzetter, Piotr

2017-04-01

The recent shift towards development of clean, sustainable energy sources has provided a new challenge in terms of structural safety and reliability: with aging, manufacturing defects, harsh environmental and operational conditions, and extreme events such as lightning strikes wind turbines can become damaged resulting in production losses and environmental degradation. To monitor the current structural state of the turbine, structural health monitoring (SHM) techniques would be beneficial. Physics based SHM in the form of calibration of a finite element model (FEMs) by inverse techniques is adopted in this research. Fuzzy finite element model updating (FFEMU) techniques for damage severity assessment of a small-scale wind turbine blade are discussed and implemented. The main advantage is the ability of FFEMU to account in a simple way for uncertainty within the problem of model updating. Uncertainty quantification techniques, such as fuzzy sets, enable a convenient mathematical representation of the various uncertainties. Experimental frequencies obtained from modal analysis on a small-scale wind turbine blade were described by fuzzy numbers to model measurement uncertainty. During this investigation, damage severity estimation was investigated through addition of small masses of varying magnitude to the trailing edge of the structure. This structural modification, intended to be in lieu of damage, enabled non-destructive experimental simulation of structural change. A numerical model was constructed with multiple variable additional masses simulated upon the blades trailing edge and used as updating parameters. Objective functions for updating were constructed and minimized using both particle swarm optimization algorithm and firefly algorithm. FFEMU was able to obtain a prediction of baseline material properties of the blade whilst also successfully predicting, with sufficient accuracy, a larger magnitude of structural alteration and its location.

The roles of the RIIβ linker and N-terminal cyclic nucleotide-binding domain in determining the unique structures of the type IIβ protein kinase A: a small angle x-ray and neutron scattering study.

PubMed

Blumenthal, Donald K; Copps, Jeffrey; Smith-Nguyen, Eric V; Zhang, Ping; Heller, William T; Taylor, Susan S

2014-10-10

Protein kinase A (PKA) is ubiquitously expressed and is responsible for regulating many important cellular functions in response to changes in intracellular cAMP concentrations. The PKA holoenzyme is a tetramer (R2:C2), with a regulatory subunit homodimer (R2) that binds and inhibits two catalytic (C) subunits; binding of cAMP to the regulatory subunit homodimer causes activation of the catalytic subunits. Four different R subunit isoforms exist in mammalian cells, and these confer different structural features, subcellular localization, and biochemical properties upon the PKA holoenzymes they form. The holoenzyme containing RIIβ is structurally unique in that the type IIβ holoenzyme is much more compact than the free RIIβ homodimer. We have used small angle x-ray scattering and small angle neutron scattering to study the solution structure and subunit organization of a holoenzyme containing an RIIβ C-terminal deletion mutant (RIIβ(1-280)), which is missing the C-terminal cAMP-binding domain to better understand the structural organization of the type IIβ holoenzyme and the RIIβ domains that contribute to stabilizing the holoenzyme conformation. Our results demonstrate that compaction of the type IIβ holoenzyme does not require the C-terminal cAMP-binding domain but rather involves large structural rearrangements within the linker and N-terminal cyclic nucleotide-binding domain of the RIIβ homodimer. The structural rearrangements are significantly greater than seen previously with RIIα and are likely to be important in mediating short range and long range interdomain and intersubunit interactions that uniquely regulate the activity of the type IIβ isoform of PKA. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Hollow carbon nanospheres using an asymmetric triblock copolymer structure directing agent.

PubMed

Li, Yunqi; Tan, Haibo; Salunkhe, Rahul R; Tang, Jing; Shrestha, Lok Kumar; Bastakoti, Bishnu Prasad; Rong, Hongpan; Takei, Toshiaki; Henzie, Joel; Yamauchi, Yusuke; Ariga, Katsuhiko

2016-12-20

We introduce a simple method to prepare hollow carbon nanospheres (HCNs) by using triblock copolymer poly(styrene-b-2-vinylpyridine-b-ethylene oxide) (PS-b-P2VP-b-PEO) micelles as a new class of soft-templates. Simply by changing the solvent we can prepare ultra-small sized micelles of the triblock copolymer PS-b-P2VP-b-PEO soft template to obtain HCNs with ultra-small diameters (43 nm) and hollow cores (19 nm). Furthermore, we use these HCNs to make electric double-layer capacitors (EDLCs) that exhibit superior performance.

Batch-batch stable microbial community in the traditional fermentation process of huyumei broad bean pastes.

PubMed

Zhu, Linjiang; Fan, Zihao; Kuai, Hui; Li, Qi

2017-09-01

During natural fermentation processes, a characteristic microbial community structure (MCS) is naturally formed, and it is interesting to know about its batch-batch stability. This issue was explored in a traditional semi-solid-state fermentation process of huyumei, a Chinese broad bean paste product. The results showed that this MCS mainly contained four aerobic Bacillus species (8 log CFU per g), including B. subtilis, B. amyloliquefaciens, B. methylotrophicus, and B. tequilensis, and the facultative anaerobe B. cereus with a low concentration (4 log CFU per g), besides a very small amount of the yeast Zygosaccharomyces rouxii (2 log CFU per g). The dynamic change of the MCS in the brine fermentation process showed that the abundance of dominant species varied within a small range, and in the beginning of process the growth of lactic acid bacteria was inhibited and Staphylococcus spp. lost its viability. Also, the MCS and its dynamic change were proved to be highly reproducible among seven batches of fermentation. Therefore, the MCS naturally and stably forms between different batches of the traditional semi-solid-state fermentation of huyumei. Revealing microbial community structure and its batch-batch stability is helpful for understanding the mechanisms of community formation and flavour production in a traditional fermentation. This issue in a traditional semi-solid-state fermentation of huyumei broad bean paste was firstly explored. This fermentation process was revealed to be dominated by a high concentration of four aerobic species of Bacillus, a low concentration of B. cereus and a small amount of Zygosaccharomyces rouxii. Lactic acid bacteria and Staphylococcus spp. lost its viability at the beginning of fermentation. Such the community structure was proved to be highly reproducible among seven batches. © 2017 The Society for Applied Microbiology.

Probing Na+ Induced Changes in the HIV-1 TAR Conformational Dynamics using NMR Residual Dipolar Couplings: New Insights into the Role of Counterions and Electrostatic Interactions in Adaptive Recognition†

PubMed Central

Casiano-Negroni, Anette; Sun, Xiaoyan; Al-Hashimi, Hashim M.

2012-01-01

Many regulatory RNAs undergo large changes in structure upon recognition of proteins and ligands but the mechanism by which this occur remains poorly understood. Using NMR residual dipolar coupling (RDCs), we characterized Na+ induced changes in the structure and dynamics of the bulge-containing HIV-1 transactivation response element (TAR) RNA that mirror changes induced by small molecules bearing a different number of cationic groups. Increasing the Na+ concentration from 25 mM to 320 mM led to a continuous reduction in the average inter-helical bend angle (from 46° to 22°), inter-helical twist angle (from 66° to −18°) and inter-helix flexibility (as measured by an increase in the internal generalized degree of order from 0.56 to 0.74). Similar conformational changes were observed with Mg2+, indicating that non-specific electrostatic interactions drive the conformational transition, although results also suggest that Na+ and Mg2+ may associate with TAR in distinct modes. The transition can be rationalized based on a population-weighted average of two ensembles comprising an electrostatically relaxed bent and flexible TAR conformation that is weakly associated with counterions, and a globally rigid coaxial conformation which has stronger electrostatic potential and association with counterions. The TAR inter-helical orientations that are stabilized by small molecules fall around the metal-induced conformational pathway, indicating that counterions may help predispose the TAR conformation for target recognition. Our results underscore the intricate sensitivity of RNA conformational dynamics to environmental conditions and demonstrate the ability to detect subtle conformational changes using NMR RDCs. PMID:17488097

Beyond just sea-level rise: considering macroclimatic drivers within coastal wetland vulnerability assessments to climate change.

PubMed

Osland, Michael J; Enwright, Nicholas M; Day, Richard H; Gabler, Christopher A; Stagg, Camille L; Grace, James B

2016-01-01

Due to their position at the land-sea interface, coastal wetlands are vulnerable to many aspects of climate change. However, climate change vulnerability assessments for coastal wetlands generally focus solely on sea-level rise without considering the effects of other facets of climate change. Across the globe and in all ecosystems, macroclimatic drivers (e.g., temperature and rainfall regimes) greatly influence ecosystem structure and function. Macroclimatic drivers have been the focus of climate change-related threat evaluations for terrestrial ecosystems, but largely ignored for coastal wetlands. In some coastal wetlands, changing macroclimatic conditions are expected to result in foundation plant species replacement, which would affect the supply of certain ecosystem goods and services and could affect ecosystem resilience. As examples, we highlight several ecological transition zones where small changes in macroclimatic conditions would result in comparatively large changes in coastal wetland ecosystem structure and function. Our intent in this communication is not to minimize the importance of sea-level rise. Rather, our overarching aim is to illustrate the need to also consider macroclimatic drivers within vulnerability assessments for coastal wetlands. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

Imaging of the stroke-related changes in the vascular system of the mouse brain with the use of extended focus optical coherence microscopy

NASA Astrophysics Data System (ADS)

Tamborski, Szymon; Lyu, Hong Chou; Bukowska, Danuta; Dolezyczek, Hubert; Wilczynski, Grzegorz; Szlag, Daniel; Lasser, Theo; Wojtkowski, Maciej; Szkulmowski, Maciej

2016-03-01

We used Optical Coherence Microscopy (OCM) to monitor structural and functional changes due to ischemic stroke in small animals brains in vivo. To obtain lateral resolution of 2.2 μm over the range of 600 μm we used extended focus configuration of OCM instrument involving Bessel beam. It provided access to detailed 3D information about the changes in brain vascular system up to the level of capillaries across I and II/III layers of neocortex. We used photothrombotic stroke model involving photoactive application of rose bengal to assure minimal invasiveness of the procedure and precise localization of the clot distribution center. We present the comparative analysis involving structural and angiographic maps of the stroke-affected brain enabling in-depth insight to the process of development of the disorder.

Diffusion of molecules and macromolecules in thylakoid membranes.

PubMed

Kirchhoff, Helmut

2014-04-01

The survival and fitness of photosynthetic organisms is critically dependent on the flexible response of the photosynthetic machinery, harbored in thylakoid membranes, to environmental changes. A central element of this flexibility is the lateral diffusion of membrane components along the membrane plane. As demonstrated, almost all functions of photosynthetic energy conversion are dependent on lateral diffusion. The mobility of both small molecules (plastoquinone, xanthophylls) as well as large protein supercomplexes is very sensitive to changes in structural boundary conditions. Knowledge about the design principles that govern the mobility of photosynthetic membrane components is essential to understand the dynamic response of the photosynthetic machinery. This review summarizes our knowledge about the factors that control diffusion in thylakoid membranes and bridges structural membrane alterations to changes in mobility and function. This article is part of a Special Issue entitled: Dynamic and ultrastructure of bioenergetic membranes and their components. Copyright © 2013 Elsevier B.V. All rights reserved.

Molecular basis of ancestral vertebrate electroreception

PubMed Central

Bellono, Nicholas W.; Leitch, Duncan B.; Julius, David

2017-01-01

Elasmobranch fishes, including sharks, rays, and skates, use specialized electrosensory organs called Ampullae of Lorenzini to detect extremely small changes in environmental electric fields. Electrosensory cells within these ampullae are able to discriminate and respond to minute changes in environmental voltage gradients through an as-yet unknown mechanism. Here we show that the voltage-gated calcium channel CaV1.3 and big conductance calcium-activated potassium (BK) channel are preferentially expressed by electrosensory cells in little skate (Leucoraja erinacea) and functionally couple to mediate electrosensory cell membrane voltage oscillations, which are important in the detection of specific, weak electrical signals. Both channels exhibit unique properties compared with their mammalian orthologues to support electrosensory functions: structural adaptations in CaV1.3 mediate a low voltage threshold for activation, while alterations in BK support specifically tuned voltage oscillations. These findings reveal a molecular basis of electroreception and demonstrate how discrete evolutionary changes in ion channel structure facilitate sensory adaptation. PMID:28264196

The roles of biological interactions and pollutant contamination in shaping microbial benthic community structure.

PubMed

Louati, Hela; Said, Olfa Ben; Soltani, Amel; Got, Patrice; Mahmoudi, Ezzeddine; Cravo-Laureau, Cristiana; Duran, Robert; Aissa, Patricia; Pringault, Olivier

2013-11-01

Biological interactions between metazoans and the microbial community play a major role in structuring food webs in aquatic sediments. Pollutants can also strongly affect the structure of meiofauna and microbial communities. This study aims investigating, in a non-contaminated sediment, the impact of meiofauna on bacteria facing contamination by a mixture of three PAHs (fluoranthene, phenanthrene and pyrene). Sediment microcosms were incubated in the presence or absence of meiofauna during 30 days. Bioremediation treatments, nutrient amendment and addition of a hydrocarbon-degrading bacterium, were also tested to enhance PAH biodegradation. Results clearly show the important role of meiofauna as structuring factor for bacterial communities with significant changes observed in the molecular fingerprints. However, these structural changes were not concomitant with changes in biomass or function. PAH contamination had a severe impact on total meiofaunal abundance with a strong decrease of nematodes and the complete disappearance of polychaetes and copepods. In contrast, correspondence analysis, based on T-RFLP fingerprints, showed that contamination by PAH resulted in small shifts in microbial composition, with or without meiofauna, suggesting a relative tolerance of bacteria to the PAH cocktail. The PAH bioremediation treatments were highly efficient with more than 95% biodegradation. No significant difference was observed in presence or absence of meiofauna. Nutrient addition strongly enhanced bacterial and meiofaunal abundances as compared to control and contaminated microcosms, as well as inducing important changes in the bacterial community structure. Nutrients thus were the main structural factor in shaping bacterial community composition, while the role of meiofauna was less evident.

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

Tao, Jinhui; Buchko, Garry W.; Shaw, Wendy J.

The interactions between proteins and surfaces are critical to a number of important processes including biomineralization, the biocompatibility of biomaterials, and the function of biosensors. Although many proteins exist as monomers or small oligomers, amelogenin is a unique protein that self-assembles into supramolecular structures called “nanospheres,” aggregates of 100’s of monomers that are 20-60 nm in diameter. The nanosphere quaternary structure is observed in solution, however, the quaternary structure of amelogenin adsorbed onto hydroxyapatite (HAP) surfaces is not known even though it may be important to amelogenin’s function in forming highly elongated and intricately assembled HAP crystallites during enamel formation.more » We report studies of the interactions of the enamel protein, amelogenin (rpM179), with a well-defined (100) face prepared by synthesis of large crystals of HAP. High resolution, in-situ atomic force microscopy (AFM) was used to directly observe protein adsorption onto HAP at the molecular level within an aqueous solution environment. Our study shows that the amelogenin nanospheres disassemble onto the HAP surface, breaking down into oligomeric (25-mer) subunits of the larger nanosphere. In some cases, the disassembly event is directly observed by in situ imaging for the first time. Quantification of the adsorbate amounts by size analysis led to the determination of a protein binding energy (17.1 kbT) to a specific face of HAP (100). The kinetics of disassembly are greatly slowed in aged solutions, indicating there are time-dependent increases in oligomer-oligomer binding interactions within the nanosphere. A small change in the sequence of amelogenin by the attachment of a histidine tag to the N-terminus of rpM179 to form rp(H)M180 results in the adsorption of a complete second layer on top of the underlying first layer. Our research elucidates how supramolecular protein structures interact and break down at surfaces and how small changes in the primary sequence of amelogenin can affect the disassembly process.« less

Serial femtosecond X-ray diffraction of enveloped virus microcrystals

DOE PAGES

Lawrence, Robert M.; Conrad, Chelsie E.; Zatsepin, Nadia A.; ...

2015-08-20

Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has produced high-resolution, room temperature, time-resolved protein structures. We report preliminary SFX of Sindbis virus, an enveloped icosahedral RNA virus with ~700 Å diameter. Microcrystals delivered in viscous agarose medium diffracted to ~40 Å resolution. Small-angle diffuse X-ray scattering overlaid Bragg peaks and analysis suggests this results from molecular transforms of individual particles. Viral proteins undergo structural changes during entry and infection, which could, in principle, be studied with SFX. This is a pertinent step toward determining room temperature structures from virus microcrystals that may enable time-resolved studies of enveloped viruses.

Analysis of neighborhood behavior in lead optimization and array design.

PubMed

Papadatos, George; Cooper, Anthony W J; Kadirkamanathan, Visakan; Macdonald, Simon J F; McLay, Iain M; Pickett, Stephen D; Pritchard, John M; Willett, Peter; Gillet, Valerie J

2009-02-01

Neighborhood behavior describes the extent to which small structural changes defined by a molecular descriptor are likely to lead to small property changes. This study evaluates two methods for the quantification of neighborhood behavior: the optimal diagonal method of Patterson et al. and the optimality criterion method of Horvath and Jeandenans. The methods are evaluated using twelve different types of fingerprint (both 2D and 3D) with screening data derived from several lead optimization projects at GlaxoSmithKline. The principal focus of the work is the design of chemical arrays during lead optimization, and the study hence considers not only biological activity but also important drug properties such as metabolic stability, permeability, and lipophilicity. Evidence is provided to suggest that the optimality criterion method may provide a better quantitative description of neighborhood behavior than the optimal diagonal method.

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

Xu, Gui -Liang; Sheng, Tian; Chong, Lina

Sodium-ion batteries (SIBs) have been considered as one of the promising power source candidates for the stationary storage industries owing to the much lower cost of sodium than lithium. It is well-known that the electrode materials largely determine the energy density of the battery systems. However, recent discoveries on the electrode materials showed that most of them present distinct lithium and sodium storage performance, which is not yet well understood. In this work, we performed a comparative understanding on the structural changes of porous cobalt oxide during its electrochemical lithiation and sodiation process by in operando synchrotron small angel X-raymore » scattering, X-ray diffraction, and X-ray absorption spectroscopy. It was found that compared to the lithiation process, the porous cobalt oxide undergoes less pore structure changes, oxidation state, and local structure changes as well as crystal structure evolution during its sodiation process, which is attributed to the intrinsic low sodiation activity of cobalt oxide as evidenced by ab initio molecular dynamics simulations. Moreover, it was indicated that the sodiation activity of metal sulfides is higher than that of metal oxides, indicating a better candidate for SIBs. Furthermore, such understanding is crucial for future design and improvement of high-performance electrode materials for SIBs.« less

Desert mammal populations are limited by introduced predators rather than future climate change

PubMed Central

Wardle, Glenda M.; Dickman, Chris R.

2017-01-01

Climate change is predicted to place up to one in six species at risk of extinction in coming decades, but extinction probability is likely to be influenced further by biotic interactions such as predation. We use structural equation modelling to integrate results from remote camera trapping and long-term (17–22 years) regional-scale (8000 km2) datasets on vegetation and small vertebrates (greater than 38 880 captures) to explore how biotic processes and two key abiotic drivers influence the structure of a diverse assemblage of desert biota in central Australia. We use our models to predict how changes in rainfall and wildfire are likely to influence the cover and productivity of the dominant vegetation and the impacts of predators on their primary rodent prey over a 100-year timeframe. Our results show that, while vegetation cover may decline due to climate change, the strongest negative effect on prey populations in this desert system is top-down suppression from introduced predators. PMID:29291051

Structure of FcRY, an avian immunoglobulin receptor related to mammalian mannose receptors, and its complex with IgY

PubMed Central

He, Yongning; Bjorkman, Pamela J.

2011-01-01

Fc receptors transport maternal antibodies across epithelial cell barriers to passively immunize newborns. FcRY, the functional counterpart of mammalian FcRn (a major histocompatibility complex homolog), transfers IgY across the avian yolk sac, and represents a new class of Fc receptor related to the mammalian mannose receptor family. FcRY and FcRn bind immunoglobulins at pH ≤6.5, but not pH ≥7, allowing receptor–ligand association inside intracellular vesicles and release at the pH of blood. We obtained structures of monomeric and dimeric FcRY and an FcRY–IgY complex and explored FcRY's pH-dependent binding mechanism using electron cryomicroscopy (cryoEM) and small-angle X-ray scattering. The cryoEM structure of FcRY at pH 6 revealed a compact double-ring “head,” in which the N-terminal cysteine-rich and fibronectin II domains were folded back to contact C-type lectin-like domains 1–6, and a “tail” comprising C-type lectin-like domains 7–8. Conformational changes at pH 8 created a more elongated structure that cannot bind IgY. CryoEM reconstruction of FcRY dimers at pH 6 and small-angle X-ray scattering analysis at both pH values confirmed both structures. The cryoEM structure of the FcRY–IgY revealed symmetric binding of two FcRY heads to the dimeric FcY, each head contacting the CH4 domain of one FcY chain. FcRY shares structural properties with mannose receptor family members, including a head and tail domain organization, multimerization that may regulate ligand binding, and pH-dependent conformational changes. Our results facilitate understanding of immune recognition by the structurally related mannose receptor family and comparison of diverse methods of Ig transport across evolution. PMID:21746914

Evolution of cooperation with shared costs and benefits

PubMed Central

Brown, Joel S; Vincent, Thomas L

2008-01-01

The quest to determine how cooperation evolves can be based on evolutionary game theory, in spite of the fact that evolutionarily stable strategies (ESS) for most non-zero-sum games are not cooperative. We analyse the evolution of cooperation for a family of evolutionary games involving shared costs and benefits with a continuum of strategies from non-cooperation to total cooperation. This cost–benefit game allows the cooperator to share in the benefit of a cooperative act, and the recipient to be burdened with a share of the cooperator's cost. The cost–benefit game encompasses the Prisoner's Dilemma, Snowdrift game and Partial Altruism. The models produce ESS solutions of total cooperation, partial cooperation, non-cooperation and coexistence between cooperation and non-cooperation. Cooperation emerges from an interplay between the nonlinearities in the cost and benefit functions. If benefits increase at a decelerating rate and costs increase at an accelerating rate with the degree of cooperation, then the ESS has an intermediate level of cooperation. The game also exhibits non-ESS points such as unstable minima, convergent-stable minima and unstable maxima. The emergence of cooperative behaviour in this game represents enlightened self-interest, whereas non-cooperative solutions illustrate the Tragedy of the Commons. Games having either a stable maximum or a stable minimum have the property that small changes in the incentive structure (model parameter values) or culture (starting frequencies of strategies) result in correspondingly small changes in the degree of cooperation. Conversely, with unstable maxima or unstable minima, small changes in the incentive structure or culture can result in a switch from non-cooperation to total cooperation (and vice versa). These solutions identify when human or animal societies have the potential for cooperation and whether cooperation is robust or fragile. PMID:18495622

Small-scale structure and the Lyman-α forest baryon acoustic oscillation feature

NASA Astrophysics Data System (ADS)

Hirata, Christopher M.

2018-02-01

The baryon-acoustic oscillation (BAO) feature in the Lyman-α forest is a key probe of the cosmic expansion rate at redshifts z ˜ 2.5, well before dark energy is believed to have become significant. A key advantage of the BAO as a standard ruler is that it is a sharp feature and hence is more robust against broad-band systematic effects than other cosmological probes. However, if the Lyman-α forest transmission is sensitive to the initial streaming velocity of the baryons relative to the dark matter, then the BAO peak position can be shifted. Here we investigate this sensitivity using a suite of hydrodynamic simulations of small regions of the intergalactic medium with a range of box sizes and physics assumptions; each simulation starts from initial conditions at the kinematic decoupling era (z ˜ 1059), undergoes a discrete change from neutral gas to ionized gas thermal evolution at reionization (z ˜ 8), and is finally processed into a Lyman-α forest transmitted flux cube. Streaming velocities suppress small-scale structure, leading to less violent relaxation after reionization. The changes in the gas distribution and temperature-density relation at low redshift are more subtle, due to the convergent temperature evolution in the ionized phase. The change in the BAO scale is estimated to be of the order of 0.12 per cent at z = 2.5; some of the major uncertainties and avenues for future improvement are discussed. The predicted streaming velocity shift would be a subdominant but not negligible effect (of order 0.26σ) for the upcoming DESI Lyman-α forest survey, and exceeds the cosmic variance floor.

Microstructure Characterization Of Lead-Free Solders Depending On Alloy Composition

NASA Astrophysics Data System (ADS)

Panchenko, Iuliana; Mueller, Maik; Wolter, Klaus-Juergen

2010-11-01

Fatigue and crack nucleation in solder joints is basically associated with changes in the microstructure. Therefore the microstructure evolution of SnAgCu solder joints during solidification and subsequent application is an important subject for reliability investigations and physics of failure analysis. The scope of this study is a systematic overview of the as-cast microstructures in small sized lead-free SnAgCu solder spheres after solidification. A total of 32 alloy compositions have been investigated with varying Ag content from 0 to 5 wt.% and varying Cu content from 0 to 1.2 wt.%. The solder spheres had a diameter of approx. 270 μm and were all manufactured under the similar conditions. Subsequent cross-sectioning was carried out in order to analyze the microstructure by optical and electron microscopy as well as Electron Backscatter Diffraction and Energy Dispersive X-ray Spectroscopy. The results allow a comprehensive overview of the dependence of the as-cast microstructure on the solder composition. It is shown that strong changes in microstructure can be caused by small changes in solder composition. In addition, a solidification phenomenon known as cyclic twinning has been found in the samples. Three different microstructures related to that phenomenon will be presented and detailed characterizations of these structures are given in this study. These microstructures differ in their appearance by solidification morphology, phase distribution as well as grain structure and can be described as follows: 1. large dentritic areas of different grain orientations which are characterized by approx. 60° twin boundaries; 2. areas of small β-Sn cells with approx. 60° twin relation and larger intermetallic precipitates; 3. large grains consisting of a β-Sn matrix with very fine intermetallic precipitates and high angle grain boundaries between adjacent grains.

Toward understanding the structural heterogeneity and ion pair stability in dicationic ionic liquids.

PubMed

Li, Song; Bañuelos, José Leobardo; Zhang, Pengfei; Feng, Guang; Dai, Sheng; Rother, Gernot; Cummings, Peter T

2014-12-07

The structural and dynamical properties of dicationic ionic liquids (DILs) [Cn(mim)2](Tf2N)2, that is, 3-methylimidazolium dications separated by an alkyl chain and with bis(trifluoromethylsulfonyl)amide as the anion, were investigated by molecular dynamics (MD) simulation in combination with small/wide-angle X-ray scattering (SWAXS) measurements. Enhanced spatial heterogeneity is observed as the DIL chain length is increased, characterized by the changes in the scattering and the increased heterogeneity order parameter (HOP). Temperature variation imposes only slight influences on the local structures of DILs compared to monocationic ionic liquids (MILs). The peaks at 0.9 Å(-1) and 1.4 Å(-1) of the structure function shift towards low Q as the temperature increases, in a similar manner to MILs, and changes in peak positions in response to temperature changes are reflected in HOP variations. However, the prepeak shift with increasing temperature is ∼3 times smaller in DILs compared to MILs, and both MD and SWAXS indicate a DIL-specific prepeak shifting. Furthermore, the high ion pair/ion cage stability in DILs is indicative of high thermal stability and relative insensitivity of structural heterogeneity to temperature variation, which might be caused by the stronger Coulombic interactions in DILs.

Bulk electronic structure of non-centrosymmetric Eu T Ge3 (T =Co , Ni, Rh, Ir) studied by hard x-ray photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Utsumi, Yuki; Kasinathan, Deepa; Swatek, Przemysław; Bednarchuk, Oleksandr; Kaczorowski, Dariusz; Ablett, James M.; Rueff, Jean-Pascal

2018-03-01

Non-centrosymmetric Eu T Ge3 (T = Co, Ni, Rh, and Ir) possesses magnetic Eu2 + ions, and antiferromagnetic ordering appears at low temperatures. Transition-metal substitution leads to changes in the unit-cell volume and in the magnetic ordering. However, the magnetic ordering temperature does not scale with the volume change, and the Eu valence is expected to remain divalent. Here we study the bulk electronic structure of non-centrosymmetric Eu T Ge3 (T = Co, Ni, Rh, and Ir) by hard x-ray photoelectron spectroscopy. The Eu 3 d core-level spectrum confirms the robust Eu2 + valence state against the transition-metal substitution with a small contribution from Eu3 +. The estimated Eu mean valence is around 2.1 in these compounds, as confirmed by multiplet calculations. In contrast, the Ge 2 p spectrum shifts to higher binding energy upon changing the transition metal from 3 d to 4 d to 5 d elements, hinting at a change in the Ge-T bonding strength. The valence bands of the different compounds are found to be well reproduced by ab initio band structure calculations.

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

Borodin, Oleg; Price, David L.; Aoun, Bachir

The influence of water on the structure of a prototype ionic liquid (IL) 1-octyl-3-methyimidazolium tetrafluoroborate (C8mimBF4) is examined in the IL-rich regime using high-energy x-ray diffraction (HEXRD) and molecular dynamics (MD) simulations. A many-body polarizable force field APPLE&P was developed for C8mimBF4 water mixture. It predicts structure factors of pure IL and IL-water mixture in excellent agreement with the HEXRD experiments. The MD results provide detailed insights into the structural changes from the partial structure factors, 2-D projections of the simulation box and 3-D distribution functions. Water partitioning with IL and its competition with BF4- for complexing the imidazolium ringsmore » was examined. The added water molecules occupy a diffuse coordination shell around the imidazolium ring but are not present around the alkyl tail. The strong coordination of the fluorine atoms of the BF4- anions to the imidazolium ring is not significantly changed by the addition of water. These results are consistent with the very small differences in the average structure between the pure IL and the mixture.« less

Conformational Changes in Small Ligands Upon Tetanus Toxin Binding

DTIC Science & Technology

2008-06-01

lectin-like N-terminal jelly -roll domain and a C-terminal P-trefoil domain;2’ see Figure 2. The ganglioside binding site has been found to occur along...C-terminal P-trefoil and N-terminal jelly -roll sub- domains.’ 0 The site has been identified as the most highly conserved pocket in the structures of...the TeNT and botulinum toxins.23 p-trefoil jelly -roll Figure 2: Crystal Structure of TetC Determined to 1.6 A Resolution. a-Helices are red, P-sheets

Numerical analysis of stiffened shells of revolution. Volume 4: Engineer's program manual for STARS-2S shell theory automated for rotational structures - 2 (statics) digital computer program

NASA Technical Reports Server (NTRS)

Svalbonas, V.; Ogilvie, P.

1973-01-01

The engineering programming information for the digital computer program for analyzing shell structures is presented. The program is designed to permit small changes such as altering the geometry or a table size to fit the specific requirements. Each major subroutine is discussed and the following subjects are included: (1) subroutine description, (2) pertinent engineering symbols and the FORTRAN coded counterparts, (3) subroutine flow chart, and (4) subroutine FORTRAN listing.

An overview of the Douglas Aircraft Company Aeroelastic Design Optimization Program (ADOP)

NASA Technical Reports Server (NTRS)

Dodd, Alan J.

1989-01-01

From a program manager's viewpoint, the history, scope and architecture of a major structural design program at Douglas Aircraft Company called Aeroelastic Design Optimization Program (ADOP) are described. ADOP was originally intended for the rapid, accurate, cost-effective evaluation of relatively small structural models at the advanced design level, resulting in improved proposal competitiveness and avoiding many costly changes later in the design cycle. Before release of the initial version in November 1987, however, the program was expanded to handle very large production-type analyses.

SPS attitude control and stationkeeping: Requirements and tradeoffs

NASA Technical Reports Server (NTRS)

Oglevie, R. E.

1980-01-01

The dominant control requirements of solar power satellites change appreciably relative to small contemporary spacecraft. Trade studies and analyses illustrated preferred control approaches. It was found that the geosynchronous equatorial orbit is preferred over the alternative orbits considered, that the solar pressure orbit perturbation dominates stationkeeping propulsion requirements and that a combined AC and SK system using ion electric propulsion can satisfy the attitude control requirements. It was also found that control system/structural dynamic interaction stability can be obtained through frequency separation with reasonable structural dynamic requirements and simplify spacecraft design.

Radiation-damage-assisted ferroelectric domain structuring in magnesium-doped lithium niobate

NASA Astrophysics Data System (ADS)

Jentjens, L.; Peithmann, K.; Maier, K.; Steigerwald, H.; Jungk, T.

2009-06-01

Irradiation of 5% magnesium-doped lithium niobate crystals (LiNbO3:Mg) with high-energy, low-mass 3He ions, which are transmitted through the crystal, changes the domain reversal properties of the material. This enables easier domain engineering compared to non-irradiated material and assists the formation of small-sized periodically poled domains in LiNbO3:Mg. Periodic domain structures exhibiting a width of ≈520 nm are obtained in radiation-damaged sections of the crystals. The ferroelectric poling behavior between irradiated and non-treated material is compared.

Protein structure refinement using a quantum mechanics-based chemical shielding predictor† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc04344e Click here for additional data file.

PubMed Central

2017-01-01

The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of a protein backbone and CB chemical shifts (ProCS15, PeerJ, 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1–0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiments that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differ in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural change may be due to force field deficiencies. The overall accuracy of the empirical methods are slightly improved by annealing the CHARMM structure with ProCS15, which may suggest that the minor structural changes introduced by ProCS15-based annealing improves the accuracy of the protein structures. Having established that QM-based chemical shift prediction can deliver the same accuracy as empirical shift predictors we hope this can help increase the accuracy of related approaches such as QM/MM or linear scaling approaches or interpreting protein structural dynamics from QM-derived chemical shift. PMID:28451325

Multifunctional Nanoparticles Self-Assembled from Small Organic Building Blocks for Biomedicine.

PubMed

Xing, Pengyao; Zhao, Yanli

2016-09-01

Supramolecular self-assembly shows significant potential to construct responsive materials. By tailoring the structural parameters of organic building blocks, nanosystems can be fabricated, whose performance in catalysis, energy storage and conversion, and biomedicine has been explored. Since small organic building blocks are structurally simple, easily modified, and reproducible, they are frequently employed in supramolecular self-assembly and materials science. The dynamic and adaptive nature of self-assembled nanoarchitectures affords an enhanced sensitivity to the changes in environmental conditions, favoring their applications in controllable drug release and bioimaging. Here, recent significant research advancements of small-organic-molecule self-assembled nanoarchitectures toward biomedical applications are highlighted. Functionalized assemblies, mainly including vesicles, nanoparticles, and micelles are categorized according to their topological morphologies and functions. These nanoarchitectures with different topologies possess distinguishing advantages in biological applications, well incarnating the structure-property relationship. By presenting some important discoveries, three domains of these nanoarchitectures in biomedical research are covered, including biosensors, bioimaging, and controlled release/therapy. The strategies regarding how to design and characterize organic assemblies to exhibit biomedical applications are also discussed. Up-to-date research developments in the field are provided and research challenges to be overcome in future studies are revealed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface.

PubMed

Johnson, David K; Karanicolas, John

2013-01-01

Despite intense interest and considerable effort via high-throughput screening, there are few examples of small molecules that directly inhibit protein-protein interactions. This suggests that many protein interaction surfaces may not be intrinsically "druggable" by small molecules, and elevates in importance the few successful examples as model systems for improving our fundamental understanding of druggability. Here we describe an approach for exploring protein fluctuations enriched in conformations containing surface pockets suitable for small molecule binding. Starting from a set of seven unbound protein structures, we find that the presence of low-energy pocket-containing conformations is indeed a signature of druggable protein interaction sites and that analogous surface pockets are not formed elsewhere on the protein. We further find that ensembles of conformations generated with this biased approach structurally resemble known inhibitor-bound structures more closely than equivalent ensembles of unbiased conformations. Collectively these results suggest that "druggability" is a property encoded on a protein surface through its propensity to form pockets, and inspire a model in which the crude features of the predisposed pocket(s) restrict the range of complementary ligands; additional smaller conformational changes then respond to details of a particular ligand. We anticipate that the insights described here will prove useful in selecting protein targets for therapeutic intervention.

Investigation of point and extended defects in electron irradiated silicon—Dependence on the particle energy

NASA Astrophysics Data System (ADS)

Radu, R.; Pintilie, I.; Nistor, L. C.; Fretwurst, E.; Lindstroem, G.; Makarenko, L. F.

2015-04-01

This work is focusing on generation, time evolution, and impact on the electrical performance of silicon diodes impaired by radiation induced active defects. n-type silicon diodes had been irradiated with electrons ranging from 1.5 MeV to 27 MeV. It is shown that the formation of small clusters starts already after irradiation with high fluence of 1.5 MeV electrons. An increase of the introduction rates of both point defects and small clusters with increasing energy is seen, showing saturation for electron energies above ˜15 MeV. The changes in the leakage current at low irradiation fluence-values proved to be determined by the change in the configuration of the tri-vacancy (V3). Similar to V3, other cluster related defects are showing bistability indicating that they might be associated with larger vacancy clusters. The change of the space charge density with irradiation and with annealing time after irradiation is fully described by accounting for the radiation induced trapping centers. High resolution electron microscopy investigations correlated with the annealing experiments revealed changes in the spatial structure of the defects. Furthermore, it is shown that while the generation of point defects is well described by the classical Non Ionizing Energy Loss (NIEL), the formation of small defect clusters is better described by the "effective NIEL" using results from molecular dynamics simulations.

Myosin head orientation: a structural determinant for the Frank-Starling relationship

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

Farman, Gerrie P.; Gore, David; Allen, Edward

The cellular mechanism underlying the Frank-Starling law of the heart is myofilament length-dependent activation. The mechanism(s) whereby sarcomeres detect changes in length and translate this into increased sensitivity to activating calcium has been elusive. Small-angle X-ray diffraction studies have revealed that the intact myofilament lattice undergoes numerous structural changes upon an increase in sarcomere length (SL): lattice spacing and the I{sub 1,1}/I{sub 1,0} intensity ratio decreases, whereas the M3 meridional reflection intensity (I{sub M3}) increases, concomitant with increases in diastolic and systolic force. Using a short ({approx}10 ms) X-ray exposure just before electrical stimulation, we were able to obtain detailedmore » structural information regarding the effects of external osmotic compression (with mannitol) and obtain SL on thin intact electrically stimulated isolated rat right ventricular trabeculae. We show that over the same incremental increases in SL, the relative changes in systolic force track more closely to the relative changes in myosin head orientation (as reported by IM3) than to the relative changes in lattice spacing. We conclude that myosin head orientation before activation determines myocardial sarcomere activation levels and that this may be the dominant mechanism for length-dependent activation.« less

Coping with change: Household structure and composition in rural South Africa, 1992 – 20031

PubMed Central

MADHAVAN, SANGEETHA; SCHATZ, ENID J.

2010-01-01

Aim To describe household change over a 10-year period of tremendous social, political, economic and health transformation in South Africa using data from the Agincourt health and demographic surveillance system in the rural northeast of South Africa. Methods Examination of household structure and composition at three points: 1992, 1997, and 2003. These three years loosely represent conditions immediately before the elections (1992), short term post-elections (1997), and longer term (2003), and span a period of notable increase in HIV prevalence. Results Average household size decreased and the proportion headed by females increased. The within-household dependency ratios for children and elders both decreased, as did the proportion of households containing foster children. The proportion with at least one maternal orphan doubled, but was still relatively small at 5.5%. Conclusions This analysis is a starting point for future investigations aimed at explaining how HIV/AIDS and other sociocultural changes post-apartheid have impacted on household organization. The analysis shows both consistency and change in measures of household structure and composition between 1992 and 2003. The changes do not include an increase in various types of “fragile families”, such as child-headed or skipped-generation households that might be expected due to HIV/AIDS. PMID:17676508

Volume-of-Change Cone-Beam CT for Image-Guided Surgery

PubMed Central

Lee, Junghoon; Stayman, J. Webster; Otake, Yoshito; Schafer, Sebastian; Zbijewski, Wojciech; Khanna, A. Jay; Prince, Jerry L.; Siewerdsen, Jeffrey H.

2012-01-01

C-arm cone-beam CT (CBCT) can provide intraoperative 3D imaging capability for surgical guidance, but workflow and radiation dose are the significant barriers to broad utilization. One main reason is that each 3D image acquisition requires a complete scan with a full radiation dose to present a completely new 3D image every time. In this paper, we propose to utilize patient-specific CT or CBCT as prior knowledge to accurately reconstruct the aspects of the region that have changed by the surgical procedure from only a sparse set of x-rays. The proposed methods consist of a 3D-2D registration between the prior volume and a sparse set of intraoperative x-rays, creating digitally reconstructed radiographs (DRR) from the registered prior volume, computing difference images by subtracting DRRs from the intraoperative x-rays, a penalized likelihood reconstruction of the volume of change (VOC) from the difference images, and finally a fusion of VOC reconstruction with the prior volume to visualize the entire surgical field. When the surgical changes are local and relatively small, the VOC reconstruction involves only a small volume size and a small number of projections, allowing less computation and lower radiation dose than is needed to reconstruct the entire surgical field. We applied this approach to sacroplasty phantom data obtained from a CBCT test bench and vertebroplasty data with a fresh cadaver acquired from a C-arm CBCT system with a flat-panel detector (FPD). The VOCs were reconstructed from varying number of images (10–66 images) and compared to the CBCT ground truth using four different metrics (mean squared error, correlation coefficient, structural similarity index, and perceptual difference model). The results show promising reconstruction quality with structural similarity to the ground truth close to 1 even when only 15–20 images were used, allowing dose reduction by the factor of 10–20. PMID:22801026

Volume-of-change cone-beam CT for image-guided surgery

NASA Astrophysics Data System (ADS)

Lee, Junghoon; Webster Stayman, J.; Otake, Yoshito; Schafer, Sebastian; Zbijewski, Wojciech; Khanna, A. Jay; Prince, Jerry L.; Siewerdsen, Jeffrey H.

2012-08-01

C-arm cone-beam CT (CBCT) can provide intraoperative 3D imaging capability for surgical guidance, but workflow and radiation dose are the significant barriers to broad utilization. One main reason is that each 3D image acquisition requires a complete scan with a full radiation dose to present a completely new 3D image every time. In this paper, we propose to utilize patient-specific CT or CBCT as prior knowledge to accurately reconstruct the aspects of the region that have changed by the surgical procedure from only a sparse set of x-rays. The proposed methods consist of a 3D-2D registration between the prior volume and a sparse set of intraoperative x-rays, creating digitally reconstructed radiographs (DRRs) from the registered prior volume, computing difference images by subtracting DRRs from the intraoperative x-rays, a penalized likelihood reconstruction of the volume of change (VOC) from the difference images, and finally a fusion of VOC reconstruction with the prior volume to visualize the entire surgical field. When the surgical changes are local and relatively small, the VOC reconstruction involves only a small volume size and a small number of projections, allowing less computation and lower radiation dose than is needed to reconstruct the entire surgical field. We applied this approach to sacroplasty phantom data obtained from a CBCT test bench and vertebroplasty data with a fresh cadaver acquired from a C-arm CBCT system with a flat-panel detector. The VOCs were reconstructed from a varying number of images (10-66 images) and compared to the CBCT ground truth using four different metrics (mean squared error, correlation coefficient, structural similarity index and perceptual difference model). The results show promising reconstruction quality with structural similarity to the ground truth close to 1 even when only 15-20 images were used, allowing dose reduction by the factor of 10-20.

Synchrotron x-ray modification of nanoparticle superlattice formation

NASA Astrophysics Data System (ADS)

Lu, Chenguang; Akey, Austin J.; Herman, Irving P.

2012-09-01

The synchrotron x-ray radiation used to perform small angle x-ray scattering (SAXS) during the formation of three-dimensional nanoparticle superlattices by drop casting nanoparticle solutions affects the structure and the local crystalline order of the resulting films. The domain size decreases due to the real-time SAXS analysis during drying and more macroscopic changes are visible to the eye.