Aeroelastic characteristics of composite bearingless rotor blades

NASA Technical Reports Server (NTRS)

Bielawa, R. L.

1976-01-01

Owing to the inherent unique structural features of composite bearingless rotors, various assumptions upon which conventional rotor aeroelastic analyses are formulated, are violated. Three such features identified are highly nonlinear and time-varying structural twist, structural redundancy in bending and torsion, and for certain configurations a strongly coupled low frequency bending-torsion mode. An examination of these aeroelastic considerations and appropriate formulations required for accurate analyses of such rotor systems is presented. Also presented are test results from a dynamically scaled model rotor and complementary analytic results obtained with the appropriately reformulated aeroelastic analysis.

UbSRD: The Ubiquitin Structural Relational Database.

PubMed

Harrison, Joseph S; Jacobs, Tim M; Houlihan, Kevin; Van Doorslaer, Koenraad; Kuhlman, Brian

2016-02-22

The structurally defined ubiquitin-like homology fold (UBL) can engage in several unique protein-protein interactions and many of these complexes have been characterized with high-resolution techniques. Using Rosetta's structural classification tools, we have created the Ubiquitin Structural Relational Database (UbSRD), an SQL database of features for all 509 UBL-containing structures in the PDB, allowing users to browse these structures by protein-protein interaction and providing a platform for quantitative analysis of structural features. We used UbSRD to define the recognition features of ubiquitin (UBQ) and SUMO observed in the PDB and the orientation of the UBQ tail while interacting with certain types of proteins. While some of the interaction surfaces on UBQ and SUMO overlap, each molecule has distinct features that aid in molecular discrimination. Additionally, we find that the UBQ tail is malleable and can adopt a variety of conformations upon binding. UbSRD is accessible as an online resource at rosettadesign.med.unc.edu/ubsrd. Copyright © 2015 Elsevier Ltd. All rights reserved.

Structure and engineering of celluloses.

PubMed

Pérez, Serge; Samain, Daniel

2010-01-01

This chapter collates the developments and conclusions of many of the extensive studies that have been conducted on cellulose, with particular emphasis on the structural and morphological features while not ignoring the most recent results derived from the elucidation of unique biosynthetic pathways. The presentation of structural and morphological data gathered together in this chapter follows the historical development of our knowledge of the different structural levels of cellulose and its various organizational levels. These levels concern features such as chain conformation, chain polarity, chain association, crystal polarity, and microfibril structure and organization. This chapter provides some historical landmarks related to the evolution of concepts in the field of biopolymer science, which parallel the developments of novel methods for characterization of complex macromolecular structures. The elucidation of the different structural levels of organization opens the way to relating structure to function and properties. The chemical and biochemical methods that have been developed to dissolve and further modify cellulose chains are briefly covered. Particular emphasis is given to the facets of topochemistry and topoenzymology where the morphological features play a key role in determining unique physicochemical properties. A final chapter addresses what might be considered tomorrow's goal in amplifying the economic importance of cellulose in the context of sustainable development. Selected examples illustrate the types of result that can be obtained when cellulose fibers are no longer viewed as inert substrates, and when the polyhydroxyl nature of their surfaces, as well as their entire structural complexity, are taken into account. Copyright © 2010 Elsevier Inc. All rights reserved.

Reusable glucose sensing using carbon nanotube-based self-assembly

NASA Astrophysics Data System (ADS)

Bhattacharyya, Tamoghna; Samaddar, Sarbani; Dasgupta, Anjan Kr.

2013-09-01

Lipid functionalized single walled carbon nanotube-based self assembly forms a super-micellar structure. This assemblage has been exploited to trap glucose oxidase in a molecular cargo for glucose sensing. The advantage of such a molecular trap is that all components of this unique structure (both the trapping shell and the entrapped enzyme) are reusable and rechargeable. The unique feature of this sensing method lies in the solid state functionalization of single walled carbon nanotubes that facilitates liquid state immobilization of the enzyme. The method can be used for soft-immobilization (a new paradigm in enzyme immobilization) of enzymes with better thermostability that is imparted by the strong hydrophobic environment provided through encapsulation by the nanotubes.Lipid functionalized single walled carbon nanotube-based self assembly forms a super-micellar structure. This assemblage has been exploited to trap glucose oxidase in a molecular cargo for glucose sensing. The advantage of such a molecular trap is that all components of this unique structure (both the trapping shell and the entrapped enzyme) are reusable and rechargeable. The unique feature of this sensing method lies in the solid state functionalization of single walled carbon nanotubes that facilitates liquid state immobilization of the enzyme. The method can be used for soft-immobilization (a new paradigm in enzyme immobilization) of enzymes with better thermostability that is imparted by the strong hydrophobic environment provided through encapsulation by the nanotubes. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr02609d

Ecological Structure of Recent and Last Glacial Mammalian Faunas in Northern Eurasia: The Case of Altai-Sayan Refugium

PubMed Central

Pavelková Řičánková, Věra; Robovský, Jan; Riegert, Jan

2014-01-01

Pleistocene mammalian communities display unique features which differ from present-day faunas. The paleocommunities were characterized by the extraordinarily large body size of herbivores and predators and by their unique structure consisting of species now inhabiting geographically and ecologically distinct natural zones. These features were probably the result of the unique environmental conditions of ice age ecosystems. To analyze the ecological structure of Last Glacial and Recent mammal communities we classified the species into biome and trophic-size categories, using Principal Component analysis. We found a marked similarity in ecological structure between Recent eastern Altai-Sayan mammalian assemblages and comparable Pleistocene faunas. The composition of Last Glacial and Recent eastern Altai-Sayan assemblages were characterized by the occurrence of large herbivore and predator species associated with steppe, desert and alpine biomes. These three modern biomes harbor most of the surviving Pleistocene mammals. None of the analyzed Palearctic Last Glacial faunas showed affinity to the temperate forest, taiga, or tundra biome. The Eastern part of the Altai-Sayan region could be considered a refugium of the Last Glacial-like mammalian assemblages. Glacial fauna seems to persist up to present in those areas where the forest belt does not separate alpine vegetation from the steppes and deserts. PMID:24454791

Features and characterization needs of rubber composite structures

NASA Technical Reports Server (NTRS)

Tabaddor, Farhad

1989-01-01

Some of the major unique features of rubber composite structures are outlined. The features covered are those related to the material properties, but the analytical features are also briefly discussed. It is essential to recognize these features at the planning stage of any long-range analytical, experimental, or application program. The development of a general and comprehensive program which fully accounts for all the important characteristics of tires, under all the relevant modes of operation, may present a prohibitively expensive and impractical task at the near future. There is therefore a need to develop application methodologies which can utilize the less general models, beyond their theoretical limitations and yet with reasonable reliability, by proper mix of analytical, experimental, and testing activities.

Biomimetic surface structuring using cylindrical vector femtosecond laser beams

NASA Astrophysics Data System (ADS)

Skoulas, Evangelos; Manousaki, Alexandra; Fotakis, Costas; Stratakis, Emmanuel

2017-03-01

We report on a new, single-step and scalable method to fabricate highly ordered, multi-directional and complex surface structures that mimic the unique morphological features of certain species found in nature. Biomimetic surface structuring was realized by exploiting the unique and versatile angular profile and the electric field symmetry of cylindrical vector (CV) femtosecond (fs) laser beams. It is shown that, highly controllable, periodic structures exhibiting sizes at nano-, micro- and dual- micro/nano scales can be directly written on Ni upon line and large area scanning with radial and azimuthal polarization beams. Depending on the irradiation conditions, new complex multi-directional nanostructures, inspired by the Shark’s skin morphology, as well as superhydrophobic dual-scale structures mimicking the Lotus’ leaf water repellent properties can be attained. It is concluded that the versatility and features variations of structures formed is by far superior to those obtained via laser processing with linearly polarized beams. More important, by exploiting the capabilities offered by fs CV fields, the present technique can be further extended to fabricate even more complex and unconventional structures. We believe that our approach provides a new concept in laser materials processing, which can be further exploited for expanding the breadth and novelty of applications.

Structural and phylogenetic analysis of Rhodobacter capsulatus NifF: uncovering general features of nitrogen-fixation (nif)-flavodoxins.

PubMed

Pérez-Dorado, Inmaculada; Bortolotti, Ana; Cortez, Néstor; Hermoso, Juan A

2013-01-09

Analysis of the crystal structure of NifF from Rhodobacter capsulatus and its homologues reported so far reflects the existence of unique structural features in nif flavodoxins: a leucine at the re face of the isoalloxazine, an eight-residue insertion at the C-terminus of the 50's loop and a remarkable difference in the electrostatic potential surface with respect to non-nif flavodoxins. A phylogenetic study on 64 sequences from 52 bacterial species revealed four clusters, including different functional prototypes, correlating the previously defined as "short-chain" with the firmicutes flavodoxins and the "long-chain" with gram-negative species. The comparison of Rhodobacter NifF structure with other bacterial flavodoxin prototypes discloses the concurrence of specific features of these functional electron donors to nitrogenase.

A Content-Addressable Memory structure using quantum cells in nanotechnology with energy dissipation analysis

NASA Astrophysics Data System (ADS)

Sadoghifar, Ali; Heikalabad, Saeed Rasouli

2018-05-01

Quantum-dot cellular automata is one of the recent new technologies at the nanoscale that can be a suitable replacement for CMOS technology. The circuits constructed in QCA technology have desirable features such as low power consumption, high speed and small size. These features can be more distinct in memory structures. In this paper, we design a new structure for content addressable memory cell in QCA. For this purpose, first, a unique gate is introduced for mask operation in QCA and then this gate is used to improve the performance of CAM. These structures are evaluated with QCADesigner simulator.

Dioxygen Binding, Activation, and Reduction to H2O by Cu Enzymes.

PubMed

Solomon, Edward I

2016-07-05

Oxygen intermediates in copper enzymes exhibit unique spectroscopic features that reflect novel geometric and electronic structures that are key to reactivity. This perspective will describe: (1) the bonding origin of the unique spectroscopic features of the coupled binuclear copper enzymes and how this overcomes the spin forbiddenness of O2 binding and activates monooxygenase activity, (2) how the difference in exchange coupling in the non-coupled binuclear Cu enzymes controls the reaction mechanism, and (3) how the trinuclear Cu cluster present in the multicopper oxidases leads to a major structure/function difference in enabling the irreversible reductive cleavage of the O-O bond with little overpotential and generating a fully oxidized intermediate, different from the resting enzyme studied by crystallography, that is key in enabling fast PCET in the reductive half of the catalytic cycle.

Virus activated artificial ECM induces the osteoblastic differentiation of mesenchymal stem cells without osteogenic supplements

PubMed Central

Wang, Jianglin; Wang, Lin; Li, Xin; Mao, Chuanbin

2013-01-01

Biochemical and topographical features of an artificial extracellular matrix (aECM) can direct stem cell fate. However, it is difficult to vary only the biochemical cues without changing nanotopography to study their unique role. We took advantage of two unique features of M13 phage, a non-toxic nanofiber-like virus, to generate a virus-activated aECM with constant ordered ridge/groove nanotopography but displaying different fibronectin-derived peptides (RGD, its synergy site PHSRN, and a combination of RGD and PHSRN). One feature is the self-assembly of phage into a ridge/groove structure, another is the ease of genetically surface-displaying a peptide. We found that the unique ridge/groove nanotopography and the display of RGD and PHSRN could induce the osteoblastic differentiation of mesenchymal stem cells (MSCs) without any osteogenic supplements. The aECM formed through self-assembly and genetic engineering of phage can be used to understand the role of peptide cues in directing stem cell behavior while keeping nanotopography constant. PMID:23393624

Conceptual Structure within and between Modalities

PubMed Central

Dilkina, Katia; Lambon Ralph, Matthew A.

2012-01-01

Current views of semantic memory share the assumption that conceptual representations are based on multimodal experience, which activates distinct modality-specific brain regions. This proposition is widely accepted, yet little is known about how each modality contributes to conceptual knowledge and how the structure of this contribution varies across these multiple information sources. We used verbal feature lists, features from drawings, and verbal co-occurrence statistics from latent semantic analysis to examine the informational structure in four domains of knowledge: perceptual, functional, encyclopedic, and verbal. The goals of the analysis were three-fold: (1) to assess the structure within individual modalities; (2) to compare structures between modalities; and (3) to assess the degree to which concepts organize categorically or randomly. Our results indicated significant and unique structure in all four modalities: perceptually, concepts organize based on prominent features such as shape, size, color, and parts; functionally, they group based on use and interaction; encyclopedically, they arrange based on commonality in location or behavior; and verbally, they group associatively or relationally. Visual/perceptual knowledge gives rise to the strongest hierarchical organization and is closest to classic taxonomic structure. Information is organized somewhat similarly in the perceptual and encyclopedic domains, which differs significantly from the structure in the functional and verbal domains. Notably, the verbal modality has the most unique organization, which is not at all categorical but also not random. The idiosyncrasy and complexity of conceptual structure across modalities raise the question of how all of these modality-specific experiences are fused together into coherent, multifaceted yet unified concepts. Accordingly, both methodological and theoretical implications of the present findings are discussed. PMID:23293593

Radiation biology of HZE particles

NASA Technical Reports Server (NTRS)

Nelson, Gregory A.

1990-01-01

The biological effects of heavy charged particle (HZE) radiation are of particular interest to travellers and planners for long duration space flights where exposure levels represent a potential health hazard. The unique feature of HZE radiation is the structured pattern of its energy deposition in targets which may be related to charge, velocity, or rate of energy loss. There are many consequences of this feature to biological endpoints when compared to effects of ionizing photons. Dose vs response and dose rate kinetics are modified, DNA and cellular repair systems are altered in their abilities to cope with damage and, the qualitative features of damage are unique for different ions. These features must be incorporated into any risk assessment system for radiation health management. HZE induced mutation, cell inactivation and altered organogenesis will be discussed emphasizing studies with the nematode Caenorhabditis elegans and cultured cells. Observations from radiobiology experiments in space will also be reviewed along with plans for future space-based studies.

The Nature of Metastable AA’ Graphite: Low Dimensional Nano- and Single-Crystalline Forms

PubMed Central

Lee, Jae-Kap; Kim, Jin-Gyu; Hembram, K. P. S. S.; Kim, Yong-Il; Min, Bong-Ki; Park, Yeseul; Lee, Jeon-Kook; Moon, Dong Ju; Lee, Wooyoung; Lee, Sang-Gil; John, Phillip

2016-01-01

Over the history of carbon, it is generally acknowledged that Bernal AB stacking of the sp2 carbon layers is the unique crystalline form of graphite. The universal graphite structure is synthesized at 2,600~3,000 °C and exhibits a micro-polycrystalline feature. In this paper, we provide evidence for a metastable form of graphite with an AA’ structure. The non-Bernal AA’ allotrope of graphite is synthesized by the thermal- and plasma-treatment of graphene nanopowders at ~1,500 °C. The formation of AA’ bilayer graphene nuclei facilitates the preferred texture growth and results in single-crystal AA’ graphite in the form of nanoribbons (1D) or microplates (2D) of a few nm in thickness. Kinetically controlled AA’ graphite exhibits unique nano- and single-crystalline feature and shows quasi-linear behavior near the K-point of the electronic band structure resulting in anomalous optical and acoustic phonon behavior. PMID:28000780

Root, Successive-Cyclic and Feature-Splitting Internal Merge: Implications for Feature-Inheritance and Transfer

ERIC Educational Resources Information Center

Obata, Miki

2010-01-01

The goal of the dissertation is to determine aspects of the structure of the human language faculty, a cognitive system, specifically focusing on human syntactic systems, (unique in the animal kingdom) which enable us to creatively produce an unlimited number of grammatical sentences (like the one you just read, probably never before written or…

LSST camera grid structure made out of ceramic composite material, HB-Cesic

NASA Astrophysics Data System (ADS)

Kroedel, Matthias R.; Langton, J. Bryan

2016-08-01

In this paper we are presenting the ceramic design and the fabrication of the camera structure which is using the unique manufacturing features of the HB-Cesic technology and associated with a dedicated metrology device in order to ensure the challenging flatness requirement of 4 micron over the full array.

An interactive mutation database for human coagulation factor IX provides novel insights into the phenotypes and genetics of hemophilia B.

PubMed

Rallapalli, P M; Kemball-Cook, G; Tuddenham, E G; Gomez, K; Perkins, S J

2013-07-01

Factor IX (FIX) is important in the coagulation cascade, being activated to FIXa on cleavage. Defects in the human F9 gene frequently lead to hemophilia B. To assess 1113 unique F9 mutations corresponding to 3721 patient entries in a new and up-to-date interactive web database alongside the FIXa protein structure. The mutations database was built using MySQL and structural analyses were based on a homology model for the human FIXa structure based on closely-related crystal structures. Mutations have been found in 336 (73%) out of 461 residues in FIX. There were 812 unique point mutations, 182 deletions, 54 polymorphisms, 39 insertions and 26 others that together comprise a total of 1113 unique variants. The 64 unique mild severity mutations in the mature protein with known circulating protein phenotypes include 15 (23%) quantitative type I mutations and 41 (64%) predominantly qualitative type II mutations. Inhibitors were described in 59 reports (1.6%) corresponding to 25 unique mutations. The interactive database provides insights into mechanisms of hemophilia B. Type II mutations are deduced to disrupt predominantly those structural regions involved with functional interactions. The interactive features of the database will assist in making judgments about patient management. © 2013 International Society on Thrombosis and Haemostasis.

An examination of the relationship between childhood emotional abuse and borderline personality disorder features: the role of difficulties with emotion regulation.

PubMed

Kuo, Janice R; Khoury, Jennifer E; Metcalfe, Rebecca; Fitzpatrick, Skye; Goodwill, Alasdair

2015-01-01

Childhood abuse has been consistently linked with borderline personality disorder (BPD) and recent studies suggest that some forms of childhood abuse might be uniquely related to both BPD and BPD features. In addition, difficulties with emotion regulation have been found to be associated with childhood abuse, BPD, as well as BPD features. The present study examined (1) whether frequency of childhood emotional abuse is uniquely associated with BPD feature severity when controlling for other forms of childhood abuse and (2) whether difficulties with emotion regulation accounts for the relationship between childhood emotional abuse and BPD feature severity. A sample of undergraduates (n=243) completed the Childhood Trauma Questionnaire - Short Form, Difficulties in Emotion Regulation Scale, and Borderline Symptom List-23. Multiple regression analyses and Structural Equation Modeling were conducted. Results indicated that frequency of childhood emotional abuse (and not sexual or physical abuse) was uniquely associated with BPD feature severity. In addition, while there was no direct path between childhood emotional abuse, childhood physical abuse, or childhood sexual abuse and BPD features, there was an indirect relationship between childhood emotional abuse and BPD features through difficulties with emotion regulation. These findings suggest that, of the different forms of childhood abuse, emotional abuse specifically, may have a developmental role in BPD pathology. Prevention and treatment of BPD pathology might benefit from the provision of emotion regulation strategies. Copyright © 2014 Elsevier Ltd. All rights reserved.

Functional mesoporous silica nanoparticles for bio-imaging applications.

PubMed

Cha, Bong Geun; Kim, Jaeyun

2018-03-22

Biomedical investigations using mesoporous silica nanoparticles (MSNs) have received significant attention because of their unique properties including controllable mesoporous structure, high specific surface area, large pore volume, and tunable particle size. These unique features make MSNs suitable for simultaneous diagnosis and therapy with unique advantages to encapsulate and load a variety of therapeutic agents, deliver these agents to the desired location, and release the drugs in a controlled manner. Among various clinical areas, nanomaterials-based bio-imaging techniques have advanced rapidly with the development of diverse functional nanoparticles. Due to the unique features of MSNs, an imaging agent supported by MSNs can be a promising system for developing targeted bio-imaging contrast agents with high structural stability and enhanced functionality that enable imaging of various modalities. Here, we review the recent achievements on the development of functional MSNs for bio-imaging applications, including optical imaging, magnetic resonance imaging (MRI), positron emission tomography (PET), computed tomography (CT), ultrasound imaging, and multimodal imaging for early diagnosis. With further improvement in noninvasive bio-imaging techniques, the MSN-supported imaging agent systems are expected to contribute to clinical applications in the future. This article is categorized under: Diagnostic Tools > In vivo Nanodiagnostics and Imaging Nanotechnology Approaches to Biology > Nanoscale Systems in Biology. © 2018 Wiley Periodicals, Inc.

Understanding the molecular mechanism of substrate channeling and domain communication in protozoal bifunctional TS-DHFR.

PubMed

Anderson, Karen S

2017-03-01

Most species, such as humans, have monofunctional forms of thymidylate synthase (TS) and dihydrofolate reductase (DHFR) that are key folate metabolism enzymes making critical folate components required for DNA synthesis. In contrast, several parasitic protozoa, including Leishmania major (Lm), Plasmodium falciparum (Pf), Toxoplasma gondii (Tg) and Cryptosporidium hominis (Ch), contain a unique bifunctional thymidylate synthase-dihydrofolate reductase (TS-DHFR) having the two sequential catalytic activities contained on a single polypeptide chain. It has been suggested that the bifunctional nature of the two catalytic activities may enable substrate channeling. The 3D structures for each of these enzymes reveals distinct features for each species. While three of the four species (Pf, Tg and Ch) contain a junctional region linking the two domains, this is lacking in Lm. The Lm and Pf contain N-terminal amino acid extensions. A multidisciplinary approach using structural studies and transient kinetic analyses combined with mutational analysis has investigated the roles of these unique structural features for each enzyme. Additionally, the possibility of substrate channeling behavior was explored. These studies have identified unique, functional regions in both the TS and DHFR domains that govern efficient catalysis for each species. Surprisingly, even though there are structural similarities among the species, each is regulated in a distinct manner. This structural and mechanistic information was also used to exploit species-specific inhibitor design. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Bioinspired Single-Walled Carbon Nanotubes as a Spider Silk Structure for Ultrahigh Mechanical Property.

PubMed

Luo, Chengzhi; Li, Fangying; Li, Delong; Fu, Qiang; Pan, Chunxu

2016-11-16

Due to its unique hierarchical structure, natural spider silk features exceptional mechanical properties such as high tensile strength and great extensibility, making it one of the toughest materials. Herein, we design bioinspired spider silk single-walled carbon nanotubes (BISS-SWCNTs) that combine the hierarchical structure of spider silk and the high strength and conductivity of SWCNTs. To imitate the hierarchical structure, Fe nanoparticles are embedded on the surface of directly synthesized SWCNTs skeleton followed by coating an amorphous carbon layer. The carbon layer forms the spider silk-featured skin-core structure with SWCNTs, thus making the tube junction tougher. The embedded Fe nanoparticles act as glue spots for preventing interfacial slippages between the BISS-SWCNTs and the reinforced matrix. With only 2.1 wt % BISS-SWCNTs added, the tensile strength and Young's modulus of the BISS-SWCNTs/PMMA composites can be improved by 300%. More importantly, the BISS-SWCNTs also retain the high conductivity and transmittance of the pristine SWCNTs film. This unique bioinspired material will be of great importance in applications of multifunctional composite materials and has important implications for the future of biomimetic materials.

Conserved and variable domains of RNase MRP RNA.

PubMed

Dávila López, Marcela; Rosenblad, Magnus Alm; Samuelsson, Tore

2009-01-01

Ribonuclease MRP is a eukaryotic ribonucleoprotein complex consisting of one RNA molecule and 7-10 protein subunits. One important function of MRP is to catalyze an endonucleolytic cleavage during processing of rRNA precursors. RNase MRP is evolutionary related to RNase P which is critical for tRNA processing. A large number of MRP RNA sequences that now are available have been used to identify conserved primary and secondary structure features of the molecule. MRP RNA has structural features in common with P RNA such as a conserved catalytic core, but it also has unique features and is characterized by a domain highly variable between species. Information regarding primary and secondary structure features is of interest not only in basic studies of the function of MRP RNA, but also because mutations in the RNA give rise to human genetic diseases such as cartilage-hair hypoplasia.

Dynamic biophotonics: female squid exhibit sexually dimorphic tunable leucophores and iridocytes.

PubMed

DeMartini, Daniel G; Ghoshal, Amitabh; Pandolfi, Erica; Weaver, Aaron T; Baum, Mary; Morse, Daniel E

2013-10-01

Loliginid squid use tunable multilayer reflectors to modulate the optical properties of their skin for camouflage and communication. Contained inside specialized cells called iridocytes, these photonic structures have been a model for investigations into bio-inspired adaptive optics. Here, we describe two distinct sexually dimorphic tunable biophotonic features in the commercially important species Doryteuthis opalescens: bright stripes of rainbow iridescence on the mantle just beneath each fin attachment and a bright white stripe centered on the dorsal surface of the mantle between the fins. Both of these cellular features are unique to the female; positioned in the same location as the conspicuously bright white testis in the male, they are completely switchable, transitioning between transparency and high reflectivity. The sexual dimorphism, location and tunability of these features suggest that they may function in mating or reproduction. These features provide advantageous new models for investigation of adaptive biophotonics. The intensely reflective cells of the iridescent stripes provide a greater signal-to-noise ratio than the adaptive iridocytes studied thus far, while the cells constituting the white stripe are adaptive leucophores--unique biological tunable broadband scatterers containing Mie-scattering organelles activated by acetylcholine, and a unique complement of reflectin proteins.

Seafloor massive sulfide deposits support unique megafaunal assemblages: Implications for seabed mining and conservation.

PubMed

Boschen, Rachel E; Rowden, Ashley A; Clark, Malcolm R; Pallentin, Arne; Gardner, Jonathan P A

2016-04-01

Mining of seafloor massive sulfides (SMS) is imminent, but the ecology of assemblages at SMS deposits is poorly known. Proposed conservation strategies include protected areas to preserve biodiversity at risk from mining impacts. Determining site suitability requires biological characterisation of the mine site and protected area(s). Video survey of a proposed mine site and protected area off New Zealand revealed unique megafaunal assemblages at the mine site. Significant relationships were identified between assemblage structure and environmental conditions, including hydrothermal features. Unique assemblages occurred at both active and inactive chimneys and are particularly at risk from mining-related impacts. The occurrence of unique assemblages at the mine site suggests that the proposed protected area is insufficient alone and should instead form part of a network. These results provide support for including hydrothermally active and inactive features within networks of protected areas and emphasise the need for quantitative survey data of proposed sites. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Conjunction of Conducting Polymer Nanostructures with Macroporous Structured Graphene Thin Films for High-Performance Flexible Supercapacitors.

PubMed

Memon, Mushtaque A; Bai, Wei; Sun, Jinhua; Imran, Muhammad; Phulpoto, Shah Nawaz; Yan, Shouke; Huang, Yong; Geng, Jianxin

2016-05-11

Fabrication of hybridized structures is an effective strategy to promote the performances of graphene-based composites for energy storage/conversion applications. In this work, macroporous structured graphene thin films (MGTFs) are fabricated on various substrates including flexible graphene papers (GPs) through an ice-crystal-induced phase separation process. The MGTFs prepared on GPs (MGTF@GPs) are recognized with remarkable features such as interconnected macroporous configuration, sufficient exfoliation of the conductive RGO sheets, and good mechanical flexibility. As such, the flexible MGTF@GPs are demonstrated as a versatile conductive platform for depositing conducting polymers (CPs), e.g., polyaniline (PAn), polypyrrole, and polythiophene, through in situ electropolymerization. The contents of the CPs in the composite films are readily controlled by varying the electropolymerization time. Notably, electrodeposition of PAn leads to the formation of nanostructures of PAn nanofibers on the walls of the macroporous structured RGO framework (PAn@MGTF@GPs): thereafter, the PAn@MGTF@GPs display a unique structural feature that combine the nanostructures of PAn nanofibers and the macroporous structures of RGO sheets. Being used as binder-free electrodes for flexible supercapacitors, the PAn@MGTF@GPs exhibit excellent electrochemical performance, in particular a high areal specific capacity (538 mF cm(-2)), high cycling stability, and remarkable capacitive stability to deformation, due to the unique electrode structures.

Biomimetic surface structuring using cylindrical vector femtosecond laser beams

PubMed Central

Skoulas, Evangelos; Manousaki, Alexandra; Fotakis, Costas; Stratakis, Emmanuel

2017-01-01

We report on a new, single-step and scalable method to fabricate highly ordered, multi-directional and complex surface structures that mimic the unique morphological features of certain species found in nature. Biomimetic surface structuring was realized by exploiting the unique and versatile angular profile and the electric field symmetry of cylindrical vector (CV) femtosecond (fs) laser beams. It is shown that, highly controllable, periodic structures exhibiting sizes at nano-, micro- and dual- micro/nano scales can be directly written on Ni upon line and large area scanning with radial and azimuthal polarization beams. Depending on the irradiation conditions, new complex multi-directional nanostructures, inspired by the Shark’s skin morphology, as well as superhydrophobic dual-scale structures mimicking the Lotus’ leaf water repellent properties can be attained. It is concluded that the versatility and features variations of structures formed is by far superior to those obtained via laser processing with linearly polarized beams. More important, by exploiting the capabilities offered by fs CV fields, the present technique can be further extended to fabricate even more complex and unconventional structures. We believe that our approach provides a new concept in laser materials processing, which can be further exploited for expanding the breadth and novelty of applications. PMID:28327611

Isotropic and Anisotropic Growth of Metal-Organic Framework (MOF) on MOF: Logical Inference on MOF Structure Based on Growth Behavior and Morphological Feature.

PubMed

Choi, Sora; Kim, Taeho; Ji, Hoyeon; Lee, Hee Jung; Oh, Moonhyun

2016-11-02

The growth of one metal-organic framework (MOF) on another MOF for constructing a heterocompositional hybrid MOF is an interesting research topic because of the curiosity regarding the occurrence of this phenomenon and the value of hybrid MOFs as multifunctional materials or routes for fine-tuning MOF properties. In particular, the anisotropic growth of MOF on MOF is fascinating for the development of MOFs possessing atypical shapes and heterostructures or abnormal properties. Herein, we clarify the understanding of growth behavior of a secondary MOF on an initial MOF template, such as isotropic or anisotropic ways associated with their cell parameters. The isotropic growth of MIL-68-Br on the MIL-68 template results in the formation of core-shell-type MIL-68@MIL-68-Br. However, the unique anisotropic growth of a secondary MOF (MOF-NDC) on the MIL-68 template results in semitubular particles, and structural features of this unknown secondary MOF are successfully speculated for the first time on the basis of its unique growth behavior and morphological characteristics. Finally, the validation of this structural speculation is verified by the powder X-ray diffraction and the selected area electron diffraction studies. The results suggests that the growth behavior and morphological features of MOFs should be considered to be important factors for understanding the MOFs' structures.

Precursor state of oxygen molecules on the Si(001) surface during the initial room-temperature adsorption

NASA Astrophysics Data System (ADS)

Hwang, Eunkyung; Chang, Yun Hee; Kim, Yong-Sung; Koo, Ja-Yong; Kim, Hanchul

2012-10-01

The initial adsorption of oxygen molecules on Si(001) is investigated at room temperature. The scanning tunneling microscopy images reveal a unique bright O2-induced feature. The very initial sticking coefficient of O2 below 0.04 Langmuir is measured to be ˜0.16. Upon thermal annealing at 250-600 °C, the bright O2-induced feature is destroyed, and the Si(001) surface is covered with dark depressions that seem to be oxidized structures with -Si-O-Si- bonds. This suggests that the observed bright O2-induced feature is an intermediate precursor state that may be either a silanone species or a molecular adsorption structure.

Encapsulation of an interpenetrated diamondoid inorganic building block in a metal-organic framework.

PubMed

Zhang, Huabin; Lin, Ping; Chen, Erxia; Tan, Yanxi; Wen, Tian; Aldalbahi, Ali; Alshehri, Saad M; Yamauchi, Yusuke; Du, Shaowu; Zhang, Jian

2015-03-23

The first example of an inorganic-organic composite framework with an interpenetrated diamondoid inorganic building block, featuring unique {InNa}n helices and {In12 Na16 } nano-rings, has been constructed and structurally characterized. This framework also represents a unique example of encapsulation of an interpenetrated diamondoid inorganic building block in a metal-organic framework. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Feature Acquisition with Imbalanced Training Data

NASA Technical Reports Server (NTRS)

Thompson, David R.; Wagstaff, Kiri L.; Majid, Walid A.; Jones, Dayton L.

2011-01-01

This work considers cost-sensitive feature acquisition that attempts to classify a candidate datapoint from incomplete information. In this task, an agent acquires features of the datapoint using one or more costly diagnostic tests, and eventually ascribes a classification label. A cost function describes both the penalties for feature acquisition, as well as misclassification errors. A common solution is a Cost Sensitive Decision Tree (CSDT), a branching sequence of tests with features acquired at interior decision points and class assignment at the leaves. CSDT's can incorporate a wide range of diagnostic tests and can reflect arbitrary cost structures. They are particularly useful for online applications due to their low computational overhead. In this innovation, CSDT's are applied to cost-sensitive feature acquisition where the goal is to recognize very rare or unique phenomena in real time. Example applications from this domain include four areas. In stream processing, one seeks unique events in a real time data stream that is too large to store. In fault protection, a system must adapt quickly to react to anticipated errors by triggering repair activities or follow- up diagnostics. With real-time sensor networks, one seeks to classify unique, new events as they occur. With observational sciences, a new generation of instrumentation seeks unique events through online analysis of large observational datasets. This work presents a solution based on transfer learning principles that permits principled CSDT learning while exploiting any prior knowledge of the designer to correct both between-class and withinclass imbalance. Training examples are adaptively reweighted based on a decomposition of the data attributes. The result is a new, nonparametric representation that matches the anticipated attribute distribution for the target events.

Assessment of the Seattle Smart Traveler evaluation

DOT National Transportation Integrated Search

1999-09-01

The system was designed using a World Wide Web or Internet interface. Two of the unique features of the design were accommodating the desired travel times and identifying origins and destinations. A search structure was developed using a series of pu...

Extensive Evolution of Cereal Ribosome-Inactivating Proteins Translates into Unique Structural Features, Activation Mechanisms, and Physiological Roles

PubMed Central

De Zaeytijd, Jeroen; Van Damme, Els J. M.

2017-01-01

Ribosome-inactivating proteins (RIPs) are a class of cytotoxic enzymes that can depurinate rRNAs thereby inhibiting protein translation. Although these proteins have also been detected in bacteria, fungi, and even some insects, they are especially prevalent in the plant kingdom. This review focuses on the RIPs from cereals. Studies on the taxonomical distribution and evolution of plant RIPs suggest that cereal RIPs have evolved at an enhanced rate giving rise to a large and heterogeneous RIP gene family. Furthermore, several cereal RIP genes are characterized by a unique domain architecture and the lack of a signal peptide. This advanced evolution of cereal RIPs translates into distinct structures, activation mechanisms, and physiological roles. Several cereal RIPs are characterized by activation mechanisms that include the proteolytic removal of internal peptides from the N-glycosidase domain, a feature not documented for non-cereal RIPs. Besides their role in defense against pathogenic fungi or herbivorous insects, cereal RIPs are also involved in endogenous functions such as adaptation to abiotic stress, storage, induction of senescence, and reprogramming of the translational machinery. The unique properties of cereal RIPs are discussed in this review paper. PMID:28353660

Ketide Synthase (KS) Domain Prediction and Analysis of Iterative Type II PKS Gene in Marine Sponge-Associated Actinobacteria Producing Biosurfactants and Antimicrobial Agents

PubMed Central

Selvin, Joseph; Sathiyanarayanan, Ganesan; Lipton, Anuj N.; Al-Dhabi, Naif Abdullah; Valan Arasu, Mariadhas; Kiran, George S.

2016-01-01

The important biological macromolecules, such as lipopeptide and glycolipid biosurfactant producing marine actinobacteria were analyzed and their potential linkage between type II polyketide synthase (PKS) genes was explored. A unique feature of type II PKS genes is their high amino acid (AA) sequence homology and conserved gene organization. These enzymes mediate the biosynthesis of polyketide natural products with enormous structural complexity and chemical nature by combinatorial use of various domains. Therefore, deciphering the order of AA sequence encoded by PKS domains tailored the chemical structure of polyketide analogs still remains a great challenge. The present work deals with an in vitro and in silico analysis of PKS type II genes from five actinobacterial species to correlate KS domain architecture and structural features. Our present analysis reveals the unique protein domain organization of iterative type II PKS and KS domain of marine actinobacteria. The findings of this study would have implications in metabolic pathway reconstruction and design of semi-synthetic genomes to achieve rational design of novel natural products. PMID:26903957

Survey of natural products reported by Asian research groups in 2016.

PubMed

Liu, Yan-Fei; Yu, Shi-Shan

2017-11-01

The new natural products reported in peer-reviewed articles in 2016 in journals with good reputations were reviewed and analyzed. The advances that Asian research groups made in the field of natural products chemistry in 2016 were summarized. Compounds with unique structural features and/or promising bioactivities originating from Asian natural sources were discussed based on structural classification.

Crystal structure of the C-terminal SH3 domain of the adaptor protein GADS in complex with SLP-76 motif peptide reveals a unique SH3-SH3 interaction.

PubMed

Dimasi, Nazzareno

2007-01-01

The Grb2-like adaptor protein GADS is essential for tyrosine kinase-dependent signaling in T lymphocytes. Following T cell receptor ligation, GADS interacts through its C-terminal SH3 domain with the adaptors SLP-76 and LAT, to form a multiprotein signaling complex that is crucial for T cell activation. To understand the structural basis for the selective recognition of GADS by SLP-76, herein is reported the crystal structure at 1.54 Angstrom of the C-terminal SH3 domain of GADS bound to the SLP-76 motif 233-PSIDRSTKP-241, which represents the minimal binding site. In addition to the unique structural features adopted by the bound SLP-76 peptide, the complex structure reveals a unique SH3-SH3 interaction. This homophilic interaction, which is observed in presence of the SLP-76 peptide and is present in solution, extends our understanding of the molecular mechanisms that could be employed by modular proteins to increase their signaling transduction specificity.

On the structure and phase transitions of power-law Poissonian ensembles

NASA Astrophysics Data System (ADS)

Eliazar, Iddo; Oshanin, Gleb

2012-10-01

Power-law Poissonian ensembles are Poisson processes that are defined on the positive half-line, and that are governed by power-law intensities. Power-law Poissonian ensembles are stochastic objects of fundamental significance; they uniquely display an array of fractal features and they uniquely generate a span of important applications. In this paper we apply three different methods—oligarchic analysis, Lorenzian analysis and heterogeneity analysis—to explore power-law Poissonian ensembles. The amalgamation of these analyses, combined with the topology of power-law Poissonian ensembles, establishes a detailed and multi-faceted picture of the statistical structure and the statistical phase transitions of these elemental ensembles.

Project Ranger Adopter's Guide, 1979.

ERIC Educational Resources Information Center

Douglas, Randi; McCann, Karen, Comp.

Project Ranger is a program providing a combination of classroom study, outdoor survival, and environmental education to students having difficulty adapting to structured learning. The program has three unique features: it tries to reach younger children than most programs for "reluctant learners"; it provides affective counseling…

Radiobiological studies with the nematode Caenorhabditis elegans. Genetic and developmental effects of high LET radiation

NASA Technical Reports Server (NTRS)

Nelson, G. A.; Schubert, W. W.; Marshall, T. M.

1992-01-01

The biological effects of heavy charged particle (HZE) radiation are of particular interest to travellers and planners for long-duration space flights where exposure levels represent a potential health hazard. The unique feature of HZE radiation is the structured pattern of its energy deposition in targets. There are many consequences of this feature to biological endpoints when compared with effects of ionizing photons. Dose vs response and dose-rate kinetics may be modified, DNA and cellular repair systems may be altered in their abilities to cope with damage, and the qualitative features of damage may be unique for different ions. The nematode Caenorhabditis elegans is being used to address these and related questions associated with exposure to radiation. HZE-induced mutation, chromosome aberration, cell inactivation and altered organogenesis are discussed along with plans for radiobiological experiments in space.

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

Schürpf, Thomas; Chen, Qiang; Liu, Jin-huan

Developmental endothelial cell locus-1 (Del-1) glycoprotein is secreted by endothelial cells and a subset of macrophages. Del-1 plays a regulatory role in vascular remodeling and functions in innate immunity through interaction with integrin {alpha}{sub V}{beta}{sub 3}. Del-1 contains 3 epidermal growth factor (EGF)-like repeats and 2 discoidin-like domains. An Arg-Gly-Asp (RGD) motif in the second EGF domain (EGF2) mediates adhesion by endothelial cells and phagocytes. We report the crystal structure of its 3 EGF domains. The RGD motif of EGF2 forms a type II' {beta} turn at the tip of a long protruding loop, dubbed the RGD finger. Whereas EGF2more » and EGF3 constitute a rigid rod via an interdomain calcium ion binding site, the long linker between EGF1 and EGF2 lends considerable flexibility to EGF1. Two unique O-linked glycans and 1 N-linked glycan locate to the opposite side of EGF2 from the RGD motif. These structural features favor integrin binding of the RGD finger. Mutagenesis data confirm the importance of having the RGD motif at the tip of the RGD finger. A database search for EGF domain sequences shows that this RGD finger is likely an evolutionary insertion and unique to the EGF domain of Del-1 and its homologue milk fat globule-EGF 8. The RGD finger of Del-1 is a unique structural feature critical for integrin binding.« less

Synthesis, crystal structure and optical properties of two new layered cadmium iodates: Cd(IO{sub 3})X (X=Cl, OH)

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

Yang, Bing-Ping, E-mail: ybp@fjirsm.ac.cn; Mao, Jiang-Gao

Systematic explorations of new compounds in the cadmium iodate system by hydrothermal reactions led to two layered iodates, namely, Cd(IO{sub 3})X (X=Cl, OH). Cd(IO{sub 3})Cl crystallizes in the orthorhombic space group Cmca (No. 64) whereas Cd(IO{sub 3})(OH) crystallizes in the orthorhombic space group Pnma (No. 62). Cd(IO{sub 3})Cl displays a unique double layered structure composed of {sup 1}{sub ∞}[Cd−O{sub 3}Cl]{sub n} chains. Cadmium octahedrons form a 1D chain along the a-axis through edge sharing, and such chains are further interconnected via IO{sub 3} groups to form a special double layer on (020) plane. Cd(IO{sub 3})(OH) also exhibits a layered structuremore » that is composed of cadmium cations, IO{sub 3} groups and hydroxyl ions. Within a layer, chains of CdO{sub 6} edge-shared octahedra are observed along the b-axis. And these chains are connected by IO{sub 3} groups into a layer parallel to the bc plane. Spectroscopic characterizations, elemental analysis, and thermogravimetric analysis for the reported two compounds are also presented. - Graphical abstract: Two new layered cadmium iodates Cd(IO{sub 3})X (X=Cl, OH) are reported. Cd(IO{sub 3})Cl features a unique double layered structure whereas Cd(IO{sub 3})(OH) displays an ordinary layered structure. - Highlights: • Two new layered cadmium iodates Cd(IO{sub 3})X (X=Cl, OH) are reported. • Cd(IO{sub 3})Cl features a unique double layered structure. • Cd(IO{sub 3})(OH) displays an ordinary layered structure. • The spectroscopic and thermal properties have been studied in detail.« less

Structural Insights into the Transport Mechanism of the Human Sodium-dependent Lysophosphatidylcholine Transporter MFSD2A*♦

PubMed Central

Quek, Debra Q. Y.; Nguyen, Long N.; Fan, Hao; Silver, David L.

2016-01-01

Major facilitator superfamily domain containing 2A (MFSD2A) was recently characterized as a sodium-dependent lysophosphatidylcholine transporter expressed at the blood-brain barrier endothelium. It is the primary route for importation of docosohexaenoic acid and other long-chain fatty acids into fetal and adult brain and is essential for mouse and human brain growth and function. Remarkably, MFSD2A is the first identified major facilitator superfamily member that uniquely transports lipids, implying that MFSD2A harbors unique structural features and transport mechanism. Here, we present three three-dimensional structural models of human MFSD2A derived by homology modeling using MelB- and LacY-based crystal structures and refined by biochemical analysis. All models revealed 12 transmembrane helices and connecting loops and represented the partially outward-open, outward-partially occluded, and inward-open states of the transport cycle. In addition to a conserved sodium-binding site, three unique structural features were identified as follows: a phosphate headgroup binding site, a hydrophobic cleft to accommodate a hydrophobic hydrocarbon tail, and three sets of ionic locks that stabilize the outward-open conformation. Ligand docking studies and biochemical assays identified Lys-436 as a key residue for transport. It is seen forming a salt bridge with the negative charge on the phosphate headgroup. Importantly, MFSD2A transported structurally related acylcarnitines but not a lysolipid without a negative charge, demonstrating the necessity of a negatively charged headgroup interaction with Lys-436 for transport. These findings support a novel transport mechanism by which lysophosphatidylcholines are “flipped” within the transporter cavity by pivoting about Lys-436 leading to net transport from the outer to the inner leaflet of the plasma membrane. PMID:26945070

Substrate-bound Crystal Structures Reveal Features Unique to Mycobacterium tuberculosis N-Acetyl-glucosamine 1-Phosphate Uridyltransferase and a Catalytic Mechanism for Acetyl Transfer

PubMed Central

Jagtap, Pravin Kumar Ankush; Soni, Vijay; Vithani, Neha; Jhingan, Gagan Deep; Bais, Vaibhav Singh; Nandicoori, Vinay Kumar; Prakash, Balaji

2012-01-01

N-Acetyl-glucosamine-1-phosphate uridyltransferase (GlmU), a bifunctional enzyme involved in bacterial cell wall synthesis is exclusive to prokaryotes. GlmU, now recognized as a promising target to develop new antibacterial drugs, catalyzes two key reactions: acetyl transfer and uridyl transfer at two independent domains. Hitherto, we identified GlmU from Mycobacterium tuberculosis (GlmUMtb) to be unique in possessing a 30-residue extension at the C terminus. Here, we present the crystal structures of GlmUMtb in complex with substrates/products bound at the acetyltransferase active site. Analysis of these and mutational data, allow us to infer a catalytic mechanism operative in GlmUMtb. In this SN2 reaction, His-374 and Asn-397 act as catalytic residues by enhancing the nucleophilicity of the attacking amino group of glucosamine 1-phosphate. Ser-416 and Trp-460 provide important interactions for substrate binding. A short helix at the C-terminal extension uniquely found in mycobacterial GlmU provides the highly conserved Trp-460 for substrate binding. Importantly, the structures reveal an uncommon mode of acetyl-CoA binding in GlmUMtb; we term this the U conformation, which is distinct from the L conformation seen in the available non-mycobacterial GlmU structures. Residues, likely determining U/L conformation, were identified, and their importance was evaluated. In addition, we identified that the primary site for PknB-mediated phosphorylation is Thr-418, near the acetyltransferase active site. Down-regulation of acetyltransferase activity upon Thr-418 phosphorylation is rationalized by the structures presented here. Overall, this work provides an insight into substrate recognition, catalytic mechanism for acetyl transfer, and features unique to GlmUMtb, which may be exploited for the development of inhibitors specific to GlmU. PMID:22969087

Single trial decoding of belief decision making from EEG and fMRI data using independent components features

PubMed Central

Douglas, Pamela K.; Lau, Edward; Anderson, Ariana; Head, Austin; Kerr, Wesley; Wollner, Margalit; Moyer, Daniel; Li, Wei; Durnhofer, Mike; Bramen, Jennifer; Cohen, Mark S.

2013-01-01

The complex task of assessing the veracity of a statement is thought to activate uniquely distributed brain regions based on whether a subject believes or disbelieves a given assertion. In the current work, we present parallel machine learning methods for predicting a subject's decision response to a given propositional statement based on independent component (IC) features derived from EEG and fMRI data. Our results demonstrate that IC features outperformed features derived from event related spectral perturbations derived from any single spectral band, yet were similar to accuracy across all spectral bands combined. We compared our diagnostic IC spatial maps with our conventional general linear model (GLM) results, and found that informative ICs had significant spatial overlap with our GLM results, yet also revealed unique regions like amygdala that were not statistically significant in GLM analyses. Overall, these results suggest that ICs may yield a parsimonious feature set that can be used along with a decision tree structure for interpretation of features used in classifying complex cognitive processes such as belief and disbelief across both fMRI and EEG neuroimaging modalities. PMID:23914164

Isolation and synthesis of antibacterial prenylated acylphloroglu-cinols from Psorothamnus fremontii

USDA-ARS?s Scientific Manuscript database

Antibacterial assay-guided fractionation of the methanol extract of the native American plant Psorothamnus fremontii followed by structure elucidation afforded three prenylated acylphloroglucinol derivatives, psorothatins A-C (1-3). They feature a unique a,ß-epoxyketone functionality and an a,ß-hydr...

Use of Chemotypes for Profiling and Exploring the ToxCast Chemical-Assay Landscape (ACS Spring meeting)

EPA Science Inventory

EPA's ToxCast chemical library, currently exceeding 4000 unique chemicals, has successfully captured a broad diversity of chemical use-types, functionality, and structures and features potentially relevant to toxicity and environmental exposure landscapes. Chemical diversity in ...

Cerebral vascular amyloid seeds drive amyloid β-protein fibril assembly with a distinct anti-parallel structure

PubMed Central

Xu, Feng; Fu, Ziao; Dass, Sharmila; Kotarba, AnnMarie E.; Davis, Judianne; Smith, Steven O.; Van Nostrand, William E.

2016-01-01

Cerebrovascular accumulation of amyloid β-protein (Aβ), a condition known as cerebral amyloid angiopathy (CAA), is a common pathological feature of patients with Alzheimer's disease. Familial Aβ mutations, such as Dutch-E22Q and Iowa-D23N, can cause severe cerebrovascular accumulation of amyloid that serves as a potent driver of vascular cognitive impairment and dementia. The distinctive features of vascular amyloid that underlie its unique pathological properties remain unknown. Here, we use transgenic mouse models producing CAA mutants (Tg-SwDI) or overproducing human wild-type Aβ (Tg2576) to demonstrate that CAA-mutant vascular amyloid influences wild-type Aβ deposition in brain. We also show isolated microvascular amyloid seeds from Tg-SwDI mice drive assembly of human wild-type Aβ into distinct anti-parallel β-sheet fibrils. These findings indicate that cerebrovascular amyloid can serve as an effective scaffold to promote rapid assembly and strong deposition of Aβ into a unique structure that likely contributes to its distinctive pathology. PMID:27869115

PDB@: an offline toolkit for exploration and analysis of PDB files.

PubMed

Mani, Udayakumar; Ravisankar, Sadhana; Ramakrishnan, Sai Mukund

2013-12-01

Protein Data Bank (PDB) is a freely accessible archive of the 3-D structural data of biological molecules. Structure based studies offers a unique vantage point in inferring the properties of a protein molecule from structural data. This is too big a task to be done manually. Moreover, there is no single tool, software or server that comprehensively analyses all structure-based properties. The objective of the present work is to develop an offline computational toolkit, PDB@ containing in-built algorithms that help categorizing the structural properties of a protein molecule. The user has the facility to view and edit the PDB file to his need. Some features of the present work are unique in itself and others are an improvement over existing tools. Also, the representation of protein properties in both graphical and textual formats helps in predicting all the necessary details of a protein molecule on a single platform.

Structural characterization of the novel aminoglycoside phosphotransferase AphVIII from Streptomyces rimosus with enzymatic activity modulated by phosphorylation

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

Boyko, Konstantin M., E-mail: kmb@inbi.ras.ru; National Research Center “Kurchatov Institute”, Kurchatov Complex of NBICS-technologies, Akad. Kurchatova sqr., 1, Moscow, 123182; Gorbacheva, Marina A.

2016-09-02

Aminoglycoside phosphotransferases represent a broad class of enzymes that promote bacterial resistance to aminoglycoside antibiotics via the phosphorylation of hydroxyl groups in the latter. Here we report the spatial structure of the 3′-aminoglycoside phosphotransferase of novel VIII class (AphVIII) solved by X-ray diffraction method with a resolution of 2.15 Å. Deep analysis of APHVIII structure and its comparison with known structures of aminoglycoside phosphotransferases of various types reveals that AphVIII has a typical two-domain fold and, however, possesses some unique characteristics that distinguish the enzyme from its known homologues. The most important difference is the presence of the activation loop withmore » unique Ser146 residue. We demonstrate that in the apo-state of the enzyme the activation loop does not interact with other parts of the enzyme and seems to adopt catalytically competent state only after substrate binding. - Highlights: • 3D structure of the novel aminoglycoside phosphotransferase AphVIII was obtained. • AphVIII activation loop is clearly identified in the electron density. • AphVIII has some unique structural features in its substrate C-ring binding pocket.« less

Understanding Psychopathy through an Evaluation of Interpersonal Behavior: Testing the Factor Structure of the Interpersonal Measure of Psychopathy in a Large Sample of Jail Detainees

ERIC Educational Resources Information Center

Vitacco, Michael J.; Kosson, David S.

2010-01-01

Interpersonal characteristics are core features of the psychopathy construct which have a unique pattern of correlations with a variety of external correlates. To improve the assessment of interpersonal traits, the current study evaluated the internal structure of the Interpersonal Measure of Psychopathy (IM-P) through exploratory and confirmatory…

All-benzene carbon nanocages: size-selective synthesis, photophysical properties, and crystal structure.

PubMed

Matsui, Katsuma; Segawa, Yasutomo; Itami, Kenichiro

2014-11-19

The design and synthesis of a series of carbon nanocages consisting solely of benzene rings are described. Carbon nanocages are appealing molecules not only because they represent junction unit structures of branched carbon nanotubes, but also because of their potential utilities as unique optoelectronic π-conjugated materials and guest-encapsulating hosts. Three sizes of strained, conjugated [n.n.n]carbon nanocages (1, n = 4; 2, n = 5; 3, n = 6) were synthesized with perfect size-selectivity. Cyclohexane-containing units and 1,3,5-trisubstituted benzene-containing units were assembled to yield the minimally strained bicyclic precursors, which were successfully converted into the corresponding carbon nanocages via acid-mediated aromatization. X-ray crystallography of 1 confirmed the cage-shaped structure with an approximately spherical void inside the cage molecule. The present studies revealed the unique properties of carbon nanocages, including strain energies, size-dependent absorption and fluorescence, as well as unique size-dependency for the electronic features of 1-3.

The macromolecular aromatic domain in suberized tissue: a changing paradigm

NASA Technical Reports Server (NTRS)

Bernards, M. A.; Lewis, N. G.

1998-01-01

As a structural feature of specialized cell walls, suberization remains an enigma, despite its obvious importance both during normal growth and development and as a stress response in plants. While it is clear that suberized tissues contain both polyaromatic and polyaliphatic domains, and that each of these has its own unique characteristics, whether there is a contiguous macromolecule that can be called suberin is an open question. From a structural perspective, the aromatic domain is unique and distinct from lignin, and is apparently comprised primarily of (poly)hydroxycinnamates, such as amides (e.g., feruloyltyramine). The aliphatic domain is also unique, being quite distinct from cutin in terms of both its chemical composition and cellular location. In the present paper, histochemical, structural and biochemical data, particularly, regarding the polyaromatic domain of suberized tissues, are critically reviewed. A revised description of the polyaromatic domain of suberized tissues, based on the consensus that is emerging from the current data, is presented and especially includes a spatially distinct (poly)hydroxycinnamoyl-containing macromolecule.

A Systematic Review of Behavioral Interventions to Reduce Condomless Sex and Increase HIV Testing for Latino MSM.

PubMed

Pérez, Ashley; Santamaria, E Karina; Operario, Don

2017-12-15

Latino men who have sex with men (MSM) in the United States are disproportionately affected by HIV, and there have been calls to improve availability of culturally sensitive HIV prevention programs for this population. This article provides a systematic review of intervention programs to reduce condomless sex and/or increase HIV testing among Latino MSM. We searched four electronic databases using a systematic review protocol, screened 1777 unique records, and identified ten interventions analyzing data from 2871 Latino MSM. Four studies reported reductions in condomless anal intercourse, and one reported reductions in number of sexual partners. All studies incorporated surface structure cultural features such as bilingual study recruitment, but the incorporation of deep structure cultural features, such as machismo and sexual silence, was lacking. There is a need for rigorously designed interventions that incorporate deep structure cultural features in order to reduce HIV among Latino MSM.

Mass wasting features in Juventae Chasma, Mars

NASA Astrophysics Data System (ADS)

Sarkar, Ranjan; Singh, Pragya; Porwal, Alok; Ganesh, Indujaa

2016-07-01

Introduction : We report mass-wasting features preserved as debris aprons from Juventae Chasma. Diverse lines of evidence and associated geomorphological features indicate that fluidized ice or water within the wall rocks of the chasma could be responsible for mobilizing the debris. Description : The distinctive features of the landslides in Juvenate Chasma are: (1) lack of a well-defined crown or a clear-cut section at their point of origin and instead the presence of amphitheatre-headed tributary canyons; (2) absence of slump blocks; (3) overlapping of debris aprons; (4) a variety of surface textures from fresh and grooved to degraded and chaotic; (5) rounded lobes of debris aprons; (6) large variation of sizes from small lumps (~0.52 m2) to large tongue shaped ones (~ 80 m2); (7) smaller average size of landslides as compared to other chasmas; and (8) occasional preservation of fresh surficial features indicating recent emplacement. Discussion : Amphitheatre-headed tributary canyons, which are formed due to ground water sapping, indicate that the same was responsible for wall-section collapse, although a structural control cannot be completely ruled out. The emplacement of the mass wasting features preferentially at the mouths of amphitheatre-headed tributary canyons along with the rounded flow fronts of the debris suggest fluids may have played a vital role in their emplacement. The mass-wasting features in Juventae Chasma are unique compared to other landslides in Valles Marineris despite commonalities such as the radial furrows, fan-shaped outlines, overlapping aprons and overtopped obstacles. The unique set of features and close association with amphitheatre-headed tributary canyons imply that the trigger of the landslides was not structural or tectonic but possibly weakness imparted by the presence of water or ice in the pore-spaces of the wall. Craters with fluidized ejecta blankets and scalloped depressions in the surrounding plateau also support this possibility. Depending on the amounts of fluids involved at the time of emplacement, these mass movements may also qualify as debris flows. The role of fluids in the Valles Marineris landslides is still debated; however, in the Juventae Chasma landslides we see unique features which set these apart from other landslides in Valles Marineris. Further study is required to fully investigate the mechanism of emplacement of these debris.

An Evaluation of PC-Based Optical Character Recognition Systems.

ERIC Educational Resources Information Center

Schreier, E. M.; Uslan, M. M.

1991-01-01

The review examines six personal computer-based optical character recognition (OCR) systems designed for use by blind and visually impaired people. Considered are OCR components and terms, documentation, scanning and reading, command structure, conversion, unique features, accuracy of recognition, scanning time, speed, and cost. (DB)

Group Therapy Techniques for Sexually Abused Preteen Girls.

ERIC Educational Resources Information Center

Berman, Pearl

1990-01-01

Describes an open-ended, structured, highly intensive therapy group for sexually abused preteen girls that was the primary mode of treatment for 11 girls from low-income, rural White families with numerous problems. Unique features of the group included simultaneous group and individualized goals. (Author/BB)

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

DOE PAGES

Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.; ...

2017-07-13

The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the a CTD may play a role in Mtb transcription regulation. Here, our results reveal the structure of an Actinobacteria-unique insert ofmore » the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σ A, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.« less

Structural Basis For Antigenic Peptide Precursor Processing by the Endoplasmic Reticulum Aminopeptidase ERAP1

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

T Nguyen; S Chang; I Evnouchidou

2011-12-31

ERAP1 trims antigen precursors to fit into MHC class I proteins. To fulfill this function, ERAP1 has unique substrate preferences, trimming long peptides but sparing shorter ones. To identify the structural basis for ERAP1's unusual properties, we determined the X-ray crystal structure of human ERAP1 bound to bestatin. The structure reveals an open conformation with a large interior compartment. An extended groove originating from the enzyme's catalytic center can accommodate long peptides and has features that explain ERAP1's broad specificity for antigenic peptide precursors. Structural and biochemical analyses suggest a mechanism for ERAP1's length-dependent trimming activity, whereby binding of longmore » rather than short substrates induces a conformational change with reorientation of a key catalytic residue toward the active site. ERAP1's unique structural elements suggest how a generic aminopeptidase structure has been adapted for the specialized function of trimming antigenic precursors.« less

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

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

Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.

The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the αCTD may play a role in Mtb transcription regulation. Our results reveal the structure of an Actinobacteria-unique insert of the RNAPmore » β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σA, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.« less

Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures

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

Hubin, Elizabeth A.; Lilic, Mirjana; Darst, Seth A.

The mycobacteria RNA polymerase (RNAP) is a target for antimicrobials against tuberculosis, motivating structure/function studies. Here we report a 3.2 Å-resolution crystal structure of a Mycobacterium smegmatis (Msm) open promoter complex (RPo), along with structural analysis of the Msm RPo and a previously reported 2.76 Å-resolution crystal structure of an Msm transcription initiation complex with a promoter DNA fragment. We observe the interaction of the Msm RNAP α-subunit C-terminal domain (αCTD) with DNA, and we provide evidence that the a CTD may play a role in Mtb transcription regulation. Here, our results reveal the structure of an Actinobacteria-unique insert ofmore » the RNAP β' subunit. Finally, our analysis reveals the disposition of the N-terminal segment of Msm σ A, which may comprise an intrinsically disordered protein domain unique to mycobacteria. The clade-specific features of the mycobacteria RNAP provide clues to the profound instability of mycobacteria RPo compared with E. coli.« less

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.

Structure-related frustrated magnetism of nanosized polyoxometalates: aesthetics and properties in harmony.

PubMed

Kögerler, Paul; Tsukerblat, Boris; Müller, Achim

2010-01-07

The structural versatility characterizing polyoxometalate chemistry, in combination with the option to deliberately use well-defined building blocks, serves as the foundation for the generation of a large family of magnetic clusters, frequently comprising highly symmetric spin arrays. If the spin centers are coupled by antiferromagnetic exchange, some of these systems exhibit spin frustration, which can result in novel magnetic properties of purely molecular origins. We discuss here the magnetic properties of selected nanosized polyoxometalate clusters featuring spin triangles as their magnetic 'building blocks' or fragments. This includes unique porous Keplerate clusters of the type {(Mo)Mo(5)}(12)M(30) (M = Fe(III), Cr(III), V(IV)) with the spin centers defining a regular icosidodecahedron and the {V(15)As(6)}-type cluster sphere containing a single equilateral spin triangle; these species are widely discussed and studied in the literature for their role in materials science as molecular representations of Kagomé lattices and in relation to quantum computing, respectively. Exhibiting fascinating and unique structural features, these magnetic molecules allow the study of the implications of frustrated spin ordering. Furthermore, this perspective covers the impact of spin frustration on the degeneracy of the ground state and related problems, namely strong magnetic anisotropy and the interplay of antisymmetric exchange and structural Jahn-Teller effects.

Photovoltaic device

DOEpatents

Reese, Jason A.; Keenihan, James R.; Gaston, Ryan S.; Kauffmann, Keith L.; Langmaid, Joseph A.; Lopez, Leonardo C.; Maak, Kevin D.; Mills, Michael E.; Ramesh, Narayan; Teli, Samar R.

2015-06-02

The present invention is premised upon an improved photovoltaic device ("PV device"), more particularly to an improved photovoltaic device with a multilayered photovoltaic cell assembly and a body portion joined at an interface region and including an intermediate layer, at least one interconnecting structural member, relieving feature, unique component geometry, or any combination thereof.

Photovoltaic device

DOEpatents

Reese, Jason A; Keenihan, James R; Gaston, Ryan S; Kauffmann, Keith L; Langmaid, Joseph A; Lopez, Leonardo; Maak, Kevin D; Mills, Michael E; Ramesh, Narayan; Teli, Samar R

2017-03-21

The present invention is premised upon an improved photovoltaic device ("PV device"), more particularly to an improved photovoltaic device with a multilayered photovoltaic cell assembly and a body portion joined at an interface region and including an intermediate layer, at least one interconnecting structural member, relieving feature, unique component geometry, or any combination thereof.

HUMAN GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE-2 (GAPD2) GENE IS EXPRESSED SPECIFICALLY IN SPERMATOGENIC CELLS

EPA Science Inventory

Although the process of glycolysis is highly conserved in eukaryotes, several glycolytic enzymes have unique structural or functional features in spermatogenic cells. We previously identified and characterized the mouse complementary DNA (cDNA) and a gene for 1 of these enzymes, ...

Aerated Lagoons. Student Manual. Biological Treatment Process Control.

ERIC Educational Resources Information Center

Andersen, Lorri

This student manual contains the textual material for a unit which focuses on the structural and operationally unique features of aerated lagoons. Topic areas discussed include: (1) characteristics of completely mixed aerated lagoons; (2) facultative aerated lagoons; (3) aerated oxidation ponds; (4) effects of temperature on aerated lagoons; (5)…

Crystal structure of casein kinase-1, a phosphate-directed protein kinase.

PubMed Central

Xu, R M; Carmel, G; Sweet, R M; Kuret, J; Cheng, X

1995-01-01

The structure of a truncated variant of casein kinase-1 from Schizosaccharomyces pombe, has been determined in complex with MgATP at 2.0 A resolution. The model resembles the 'closed', ATP-bound conformations of the cyclin-dependent kinase 2 and the cAMP-dependent protein kinase, with clear differences in the structure of surface loops that impart unique features to casein kinase-1. The structure is of unphosphorylated, active conformation of casein kinase-1 and the peptide-binding site is fully accessible to substrate. Images PMID:7889932

Structure and Function of the First Full-Length Murein Peptide Ligase (Mpl) Cell Wall Recycling Protein

PubMed Central

Das, Debanu; Hervé, Mireille; Feuerhelm, Julie; Farr, Carol L.; Chiu, Hsiu-Ju; Elsliger, Marc-André; Knuth, Mark W.; Klock, Heath E.; Miller, Mitchell D.; Godzik, Adam; Lesley, Scott A.; Deacon, Ashley M.; Mengin-Lecreulx, Dominique; Wilson, Ian A.

2011-01-01

Bacterial cell walls contain peptidoglycan, an essential polymer made by enzymes in the Mur pathway. These proteins are specific to bacteria, which make them targets for drug discovery. MurC, MurD, MurE and MurF catalyze the synthesis of the peptidoglycan precursor UDP-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-meso-diaminopimelyl-D-alanyl-D-alanine by the sequential addition of amino acids onto UDP-N-acetylmuramic acid (UDP-MurNAc). MurC-F enzymes have been extensively studied by biochemistry and X-ray crystallography. In Gram-negative bacteria, ∼30–60% of the bacterial cell wall is recycled during each generation. Part of this recycling process involves the murein peptide ligase (Mpl), which attaches the breakdown product, the tripeptide L-alanyl-γ-D-glutamyl-meso-diaminopimelate, to UDP-MurNAc. We present the crystal structure at 1.65 Å resolution of a full-length Mpl from the permafrost bacterium Psychrobacter arcticus 273-4 (PaMpl). Although the Mpl structure has similarities to Mur enzymes, it has unique sequence and structure features that are likely related to its role in cell wall recycling, a function that differentiates it from the MurC-F enzymes. We have analyzed the sequence-structure relationships that are unique to Mpl proteins and compared them to MurC-F ligases. We have also characterized the biochemical properties of this enzyme (optimal temperature, pH and magnesium binding profiles and kinetic parameters). Although the structure does not contain any bound substrates, we have identified ∼30 residues that are likely to be important for recognition of the tripeptide and UDP-MurNAc substrates, as well as features that are unique to Psychrobacter Mpl proteins. These results provide the basis for future mutational studies for more extensive function characterization of the Mpl sequence-structure relationships. PMID:21445265

Structure and function of the first full-length murein peptide ligase (Mpl) cell wall recycling protein.

PubMed

Das, Debanu; Hervé, Mireille; Feuerhelm, Julie; Farr, Carol L; Chiu, Hsiu-Ju; Elsliger, Marc-André; Knuth, Mark W; Klock, Heath E; Miller, Mitchell D; Godzik, Adam; Lesley, Scott A; Deacon, Ashley M; Mengin-Lecreulx, Dominique; Wilson, Ian A

2011-03-18

Bacterial cell walls contain peptidoglycan, an essential polymer made by enzymes in the Mur pathway. These proteins are specific to bacteria, which make them targets for drug discovery. MurC, MurD, MurE and MurF catalyze the synthesis of the peptidoglycan precursor UDP-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-meso-diaminopimelyl-D-alanyl-D-alanine by the sequential addition of amino acids onto UDP-N-acetylmuramic acid (UDP-MurNAc). MurC-F enzymes have been extensively studied by biochemistry and X-ray crystallography. In gram-negative bacteria, ∼30-60% of the bacterial cell wall is recycled during each generation. Part of this recycling process involves the murein peptide ligase (Mpl), which attaches the breakdown product, the tripeptide L-alanyl-γ-D-glutamyl-meso-diaminopimelate, to UDP-MurNAc. We present the crystal structure at 1.65 Å resolution of a full-length Mpl from the permafrost bacterium Psychrobacter arcticus 273-4 (PaMpl). Although the Mpl structure has similarities to Mur enzymes, it has unique sequence and structure features that are likely related to its role in cell wall recycling, a function that differentiates it from the MurC-F enzymes. We have analyzed the sequence-structure relationships that are unique to Mpl proteins and compared them to MurC-F ligases. We have also characterized the biochemical properties of this enzyme (optimal temperature, pH and magnesium binding profiles and kinetic parameters). Although the structure does not contain any bound substrates, we have identified ∼30 residues that are likely to be important for recognition of the tripeptide and UDP-MurNAc substrates, as well as features that are unique to Psychrobacter Mpl proteins. These results provide the basis for future mutational studies for more extensive function characterization of the Mpl sequence-structure relationships.

Aromatic Structure in Simulates Titan Aerosol

NASA Technical Reports Server (NTRS)

Trainer, Melissa G.; Loeffler, M. J.; Anderson, C. M.; Hudson, R. L.; Samuelson, R. E.; Moore, M. A.

2011-01-01

Observations of Titan by the Cassini Composite Infrared Spectrometer (CIRS) between 560 and 20 per centimeter (approximately 18 to 500 micrometers) have been used to infer the vertical variations of Titan's ice abundances, as well as those of the aerosol from the surface to an altitude of 300 km [1]. The aerosol has a broad emission feature centered approximately at 140 per centimeter (71 micrometers). As seen in Figure 1, this feature cannot be reproduced using currently available optical constants from laboratory-generated Titan aerosol analogs [2]. The far-IR is uniquely qualified for investigating low-energy vibrational motions within the lattice structures of COITIDlex aerosol. The feature observed by CIRS is broad, and does not likely arise from individual molecules, but rather is representative of the skeletal movements of macromolecules. Since Cassini's arrival at Titan, benzene (C6H6) has been detected in the atmosphere at ppm levels as well as ions that may be polycyclic aromatic hydrocarbons (PAHs) [3]. We speculate that the feature may be a blended composite that can be identified with low-energy vibrations of two-dimensional lattice structures of large molecules, such as PAHs or nitrogenated aromatics. Such structures do not dominate the composition of analog materials generated from CH4 and N2 irradiation. We are performing studies forming aerosol analog via UV irradiation of aromatic precursors - specifically C6H6 - to understand how the unique chemical architecture of the products will influence the observable aerosol characteristics. The optical and chemical properties of the aromatic analog will be compared to those formed from CH4/N2 mixtures, with a focus on the as-yet unidentified far-IR absorbance feature. Preliminary results indicate that the photochemically-formed aromatic aerosol has distinct chemical composition, and may incorporate nitrogen either into the ring structure or adjoined chemical groups. These compositional differences are demonstrated in the aerosol mass spectra shown in Figure 2. The aromatic aerosol also demonstrates strong chemical reactivity when exposed to laboratory air, indicating substantial stored chemical potential. Oxidatoin and solubility studies wil be presented and implicatoins for prebiotic chemistry o nTitan will be discussed.

Suomi satellite brings to light a unique frontier of nighttime environmental sensing capabilities

PubMed Central

Miller, Steven D.; Mills, Stephen P.; Elvidge, Christopher D.; Lindsey, Daniel T.; Lee, Thomas F.; Hawkins, Jeffrey D.

2012-01-01

Most environmental satellite radiometers use solar reflectance information when it is available during the day but must resort at night to emission signals from infrared bands, which offer poor sensitivity to low-level clouds and surface features. A few sensors can take advantage of moonlight, but the inconsistent availability of the lunar source limits measurement utility. Here we show that the Day/Night Band (DNB) low-light visible sensor on the recently launched Suomi National Polar-orbiting Partnership (NPP) satellite has the unique ability to image cloud and surface features by way of reflected airglow, starlight, and zodiacal light illumination. Examples collected during new moon reveal not only meteorological and surface features, but also the direct emission of airglow structures in the mesosphere, including expansive regions of diffuse glow and wave patterns forced by tropospheric convection. The ability to leverage diffuse illumination sources for nocturnal environmental sensing applications extends the advantages of visible-light information to moonless nights. PMID:22984179

Unique Features of Halophilic Proteins.

PubMed

Arakawa, Tsutomu; Yamaguchi, Rui; Tokunaga, Hiroko; Tokunaga, Masao

2017-01-01

Proteins from moderate and extreme halophiles have unique characteristics. They are highly acidic and hydrophilic, similar to intrinsically disordered proteins. These characteristics make the halophilic proteins soluble in water and fold reversibly. In addition to reversible folding, the rate of refolding of halophilic proteins from denatured structure is generally slow, often taking several days, for example, for extremely halophilic proteins. This slow folding rate makes the halophilic proteins a novel model system for folding mechanism analysis. High solubility and reversible folding also make the halophilic proteins excellent fusion partners for soluble expression of recombinant proteins.

Acceleration Testing: A Better, Faster, Cheaper Alternative for Strength Qualification Testing

NASA Technical Reports Server (NTRS)

Mattiello, Carmine F.

1997-01-01

This paper addresses the advantages of utilizing a centrifuge test over the conventional static load test methods to structurally qualify aerospace structures. Three recent test cases are reviewed and used as examples to highlight these benefits. In addition, the overall capability of Goddard's High Capacity Centrifuge (HCC) is outlined along with some unique features that were designed specifically to reduce costs, test turn around time, and increase test item safety.

Intelligent Multi-scale Sensors for Damage Identification and Mitigation in Woven Composites for Aerospace Structural Applications

DTIC Science & Technology

2012-08-15

Bragg grating ( FBG ) sensors within these composite structures allows one to correlate sensor response features to “critical damage events” within the...material. The unique capabilities of this identification strategy are due to the detailed information obtained from the FBG sensors and the... FBG sensors relate to damage states not merely strain amplitudes. The research objectives of this project were therefore to:  demonstrate FBG

What are the structural features that drive partitioning of proteins in aqueous two-phase systems?

PubMed

Wu, Zhonghua; Hu, Gang; Wang, Kui; Zaslavsky, Boris Yu; Kurgan, Lukasz; Uversky, Vladimir N

2017-01-01

Protein partitioning in aqueous two-phase systems (ATPSs) represents a convenient, inexpensive, and easy to scale-up protein separation technique. Since partition behavior of a protein dramatically depends on an ATPS composition, it would be highly beneficial to have reliable means for (even qualitative) prediction of partitioning of a target protein under different conditions. Our aim was to understand which structural features of proteins contribute to partitioning of a query protein in a given ATPS. We undertook a systematic empirical analysis of relations between 57 numerical structural descriptors derived from the corresponding amino acid sequences and crystal structures of 10 well-characterized proteins and the partition behavior of these proteins in 29 different ATPSs. This analysis revealed that just a few structural characteristics of proteins can accurately determine behavior of these proteins in a given ATPS. However, partition behavior of proteins in different ATPSs relies on different structural features. In other words, we could not find a unique set of protein structural features derived from their crystal structures that could be used for the description of the protein partition behavior of all proteins in all ATPSs analyzed in this study. We likely need to gain better insight into relationships between protein-solvent interactions and protein structure peculiarities, in particular given limitations of the used here crystal structures, to be able to construct a model that accurately predicts protein partition behavior across all ATPSs. Copyright © 2016 Elsevier B.V. All rights reserved.

Organic-Inorganic Perovskites: Structural Versatility for Functional Materials Design.

PubMed

Saparov, Bayrammurad; Mitzi, David B

2016-04-13

Although known since the late 19th century, organic-inorganic perovskites have recently received extraordinary research community attention because of their unique physical properties, which make them promising candidates for application in photovoltaic (PV) and related optoelectronic devices. This review will explore beyond the current focus on three-dimensional (3-D) lead(II) halide perovskites, to highlight the great chemical flexibility and outstanding potential of the broader class of 3-D and lower dimensional organic-based perovskite family for electronic, optical, and energy-based applications as well as fundamental research. The concept of a multifunctional organic-inorganic hybrid, in which the organic and inorganic structural components provide intentional, unique, and hopefully synergistic features to the compound, represents an important contemporary target.

Glucose, Lactate, and Shuttling of Metabolites in Vertebrate Retinas

PubMed Central

Hurley, James B.; Lindsay, Kenneth J.; Du, Jianhai

2016-01-01

The vertebrate retina has specific functions and structures that give it a unique set of constraints on the way in which it can produce and use metabolic energy. The retina’s response to illumination influences its energy requirements, and the retina’s laminated structure influences the extent to which neurons and glia can access metabolic fuels. There are fundamental differences between energy metabolism in retina and that in brain. The retina relies on aerobic glycolysis much more than the brain does, and morphological differences between retina and brain limit the types of metabolic relationships that are possible between neurons and glia. This Mini-Review summarizes the unique metabolic features of the retina with a focus on the role of lactate shuttling. PMID:25801286

Data processing in neutron protein crystallography using positron-sensitive detectors

NASA Astrophysics Data System (ADS)

Schoenborn, B. P.

Neutrons provide a unique probe for localizing hydrogen atoms and for distinguishing hydrogen from deuterons. Hydrogen atoms largely determine the three dimensional structure of proteins and are responsible for many catalytic reactions. The study of hydrogen bonding and hydrogen exchange will therefore give insight into reaction mechanisms and conformational fluctuations. In addition, neutrons provide the ability to distinguish N from C and O and to allow correct orientation of groups such as histidine and glutamine. To take advantage of these unique features of neutron crystallography, one needs accurate Fourier maps depicting atomic structure to a high precision. Special attention is given to subtraction of the high background associated with hydrogen containing molecules, which produces a disproportionately large statistical error.

Similar Ring Structures on Mars and Tibetan Plateau confirm recent tectonism on Martian Northern polar region

NASA Astrophysics Data System (ADS)

Anglés, A.; Li, Y. L.

2017-10-01

The polar regions of Mars feature layered deposits, some of which exist as enclosed zoning structures. These deposits raised strong interest since their discovery and still remain one of the most controversial features on Mars. Zoning structures that are enclosed only appear in the Northern polar region, where the disappearance of water bodies may have left behind huge deposits of evaporate salts. The origin of the layered deposits has been widely debated. Here we propose that the enclosed nature of the zoning structures indicates the result of recent tectonism. We compared similar structures at an analogue site located in the western Qaidam Basin of Tibetan Plateau, a unique tectonic setting with abundant saline deposits. The enclosed structures, which we term Ring Structures, in both the analogue site and in the Northern polar region of Mars, were formed by uplift induced pressurization and buoyancy of salts as the result of recent tectonic activity.

The post-rigor structure of myosin VI and implications for the recovery stroke

PubMed Central

Ménétrey, Julie; Llinas, Paola; Cicolari, Jérome; Squires, Gaëlle; Liu, Xiaoyan; Li, Anna; Sweeney, H Lee; Houdusse, Anne

2008-01-01

Myosin VI has an unexpectedly large swing of its lever arm (powerstroke) that optimizes its unique reverse direction movement. The basis for this is an unprecedented rearrangement of the subdomain to which the lever arm is attached, referred to as the converter. It is unclear at what point(s) in the myosin VI ATPase cycle rearrangements in the converter occur, and how this would effect lever arm position. We solved the structure of myosin VI with an ATP analogue (ADP.BeF3) bound in its nucleotide-binding pocket. The structure reveals that no rearrangement in the converter occur upon ATP binding. Based on previously solved myosin structures, our structure suggests that no reversal of the powerstroke occurs during detachment of myosin VI from actin. The structure also reveals novel features of the myosin VI motor that may be important in maintaining the converter conformation during detachment from actin, and other features that may promote rapid rearrangements in the structure following actin detachment that enable hydrolysis of ATP. PMID:18046460

Unique Features of Metformin: A Combined Experimental, Theoretical, and Simulation Study of Its Structure, Dynamics, and Interaction Energetics with DNA Grooves.

PubMed

Mondal, Sayantan; Samajdar, Rudra N; Mukherjee, Saumyak; Bhattacharyya, Aninda J; Bagchi, Biman

2018-03-01

There are certain small molecules that exhibit extraordinarily diverse biological activities. Metformin is one of them. It is widely used as an antidiabetic drug for type-two diabetes. Recent lines of evidence of its role in antitumor activities and increasing the survival rates of cancer patients (namely, colorectal, breast, pancreas, and prostate cancer) are emerging. However, theoretical studies of the structure and dynamics of metformin have not yet been fully explored. In this work, we investigate the characteristic structural and dynamical features of three monoprotonated forms of metformin hydrochloride with the help of experiments, quantum chemical calculations, and atomistic molecular dynamics simulations. We validate our force field by comparing simulation results to those of the experimental findings. Energetics of proton transfer between two planar monoprotonated forms reveals a low energy barrier, which leads us to speculate a possible coexistence of them. Nevertheless, among the protonation states, we find that the nonplanar tautomeric form is the most stable. Our calculated values of the self-diffusion coefficient agree quantitatively with NMR results. Metformin forms strong hydrogen bonds with surrounding water molecules, and its solvation dynamics shows unique features. Because of an extended positive charge distribution, metformin possesses features of being a permanent cationic partner toward several targets. We study its interaction and binding ability with DNA using UV spectroscopy, circular dichroism, fluorimetry, and metadynamics simulation. We find a nonintercalative mode of interaction. Metformin feasibly forms a minor/major groove-bound state within a few tens of nanoseconds, preferably with AT-rich domains. A significant decrease in the free energy of binding is observed when it binds to a minor groove of DNA.

Photovoltaic device

DOEpatents

Reese, Jason A.; Keenihan, James R.; Gaston, Ryan S.; Kauffmann, Keith L.; Langmaid, Joseph A.; Lopez, Leonardo C.; Maak, Kevin D.; Mills, Michael E.; Ramesh, Narayan; Teli, Samar R.

2015-09-01

The present invention is premised upon an improved photovoltaic device ("PV device"), more particularly to an improved photovoltaic device (10) with a multilayered photovoltaic cell assembly (100) and a body portion (200) joined at an interface region (410) and including an intermediate layer (500), at least one interconnecting structural member (1500), relieving feature (2500), unique component geometry, or any combination thereof.

Anatomy and clinical significance of the uncinate process and uncovertebral joint: A comprehensive review.

PubMed

Hartman, Jeffrey

2014-04-01

The uncinate process and its associated uncovertebral articulation are features unique to the cervical spine. This review examines the morphology of these unique structures with particular emphasis on the regional anatomy, development and clinical significance. Five electronic databases were utilized in the literature search and additional relevant citations were retrieved from the references. A total of 74 citations were included for review. This literature review found that the uncinate processes and uncovertebral articulations are rudimentary at birth and develop and evolve with age. With degeneration they become clinically apparent with compression of related structures; most importantly affecting the spinal nerve root and vertebral artery. The articulations have also been found to precipitate torticollis when edematous and be acutely damaged in severe head and neck injuries. The uncinate processes are also important in providing stability and guiding the motion of the cervical spine. This review is intended to re-examine an often overlooked region of the cervical spine as not only an interesting anatomical feature but also a clinically relevant one. Copyright © 2014 Wiley Periodicals, Inc.

The Function of Embryonic Stem Cell-expressed RAS (E-RAS), a Unique RAS Family Member, Correlates with Its Additional Motifs and Its Structural Properties.

PubMed

Nakhaei-Rad, Saeideh; Nakhaeizadeh, Hossein; Kordes, Claus; Cirstea, Ion C; Schmick, Malte; Dvorsky, Radovan; Bastiaens, Philippe I H; Häussinger, Dieter; Ahmadian, Mohammad Reza

2015-06-19

E-RAS is a member of the RAS family specifically expressed in embryonic stem cells, gastric tumors, and hepatic stellate cells. Unlike classical RAS isoforms (H-, N-, and K-RAS4B), E-RAS has, in addition to striking and remarkable sequence deviations, an extended 38-amino acid-long unique N-terminal region with still unknown functions. We investigated the molecular mechanism of E-RAS regulation and function with respect to its sequence and structural features. We found that N-terminal extension of E-RAS is important for E-RAS signaling activity. E-RAS protein most remarkably revealed a different mode of effector interaction as compared with H-RAS, which correlates with deviations in the effector-binding site of E-RAS. Of all these residues, tryptophan 79 (arginine 41 in H-RAS), in the interswitch region, modulates the effector selectivity of RAS proteins from H-RAS to E-RAS features. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

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

Dolyniuk, Juli-Anna; Zaikina, Julia V.; Kaseman, Derrick C.

A new clathrate type has been discovered in the Ba/Cu/Zn/P system. The crystal structure of the Ba 8M 24P 28+δ (M=Cu/Zn) clathrate is composed of the pentagonal dodecahedra common to clathrates along with a unique 22-vertex polyhedron with two hexagonal faces capped by additional partially occupied phosphorus sites. This is the first example of a clathrate compound where the framework atoms are not in tetrahedral or trigonal-pyramidal coordination. In Ba 8M 24P 28+δ a majority of the framework atoms are five- and six-coordinated, a feature more common to electron-rich intermetallics. The crystal structure of this new clathrate was determined bymore » a combination of X-ray and neutron diffraction and was confirmed with solid-state 31P NMR spectroscopy. Based on chemical bonding analysis, the driving force for the formation of this new clathrate is the excess of electrons generated by a high concentration of Zn atoms in the framework. The rattling of guest atoms in the large cages results in a very low thermal conductivity, a unique feature of the clathrate family of compounds.« less

Amyloidogenesis of Natively Unfolded Proteins

PubMed Central

Uversky, Vladimir N.

2009-01-01

Aggregation and subsequent development of protein deposition diseases originate from conformational changes in corresponding amyloidogenic proteins. The accumulated data support the model where protein fibrillogenesis proceeds via the formation of a relatively unfolded amyloidogenic conformation, which shares many structural properties with the pre-molten globule state, a partially folded intermediate first found during the equilibrium and kinetic (un)folding studies of several globular proteins and later described as one of the structural forms of natively unfolded proteins. The flexibility of this structural form is essential for the conformational rearrangements driving the formation of the core cross-beta structure of the amyloid fibril. Obviously, molecular mechanisms describing amyloidogenesis of ordered and natively unfolded proteins are different. For ordered protein to fibrillate, its unique and rigid structure has to be destabilized and partially unfolded. On the other hand, fibrillogenesis of a natively unfolded protein involves the formation of partially folded conformation; i.e., partial folding rather than unfolding. In this review recent findings are surveyed to illustrate some unique features of the natively unfolded proteins amyloidogenesis. PMID:18537543

Structural Characterization of Proline-rich Tyrosine Kinase 2 (PYK2) Reveals a Unique (DFG-out) Conformation and Enables Inhibitor Design

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

Han, Seungil; Mistry, Anil; Chang, Jeanne S.

Proline-rich tyrosine kinase 2 (PYK2) is a cytoplasmic, non-receptor tyrosine kinase implicated in multiple signaling pathways. It is a negative regulator of osteogenesis and considered a viable drug target for osteoporosis treatment. The high-resolution structures of the human PYK2 kinase domain with different inhibitor complexes establish the conventional bilobal kinase architecture and show the conformational variability of the DFG loop. The basis for the lack of selectivity for the classical kinase inhibitor, PF-431396, within the FAK family is explained by our structural analyses. Importantly, the novel DFG-out conformation with two diarylurea inhibitors (BIRB796, PF-4618433) reveals a distinct subclass of non-receptormore » tyrosine kinases identifiable by the gatekeeper Met-502 and the unique hinge loop conformation of Leu-504. This is the first example of a leucine residue in the hinge loop that blocks the ATP binding site in the DFG-out conformation. Our structural, biophysical, and pharmacological studies suggest that the unique features of the DFG motif, including Leu-504 hinge-loop variability, can be exploited for the development of selective protein kinase inhibitors.« less

DSSR-enhanced visualization of nucleic acid structures in Jmol

PubMed Central

Hanson, Robert M.

2017-01-01

Abstract Sophisticated and interactive visualizations are essential for making sense of the intricate 3D structures of macromolecules. For proteins, secondary structural components are routinely featured in molecular graphics visualizations. However, the field of RNA structural bioinformatics is still lagging behind; for example, current molecular graphics tools lack built-in support even for base pairs, double helices, or hairpin loops. DSSR (Dissecting the Spatial Structure of RNA) is an integrated and automated command-line tool for the analysis and annotation of RNA tertiary structures. It calculates a comprehensive and unique set of features for characterizing RNA, as well as DNA structures. Jmol is a widely used, open-source Java viewer for 3D structures, with a powerful scripting language. JSmol, its reincarnation based on native JavaScript, has a predominant position in the post Java-applet era for web-based visualization of molecular structures. The DSSR-Jmol integration presented here makes salient features of DSSR readily accessible, either via the Java-based Jmol application itself, or its HTML5-based equivalent, JSmol. The DSSR web service accepts 3D coordinate files (in mmCIF or PDB format) initiated from a Jmol or JSmol session and returns DSSR-derived structural features in JSON format. This seamless combination of DSSR and Jmol/JSmol brings the molecular graphics of 3D RNA structures to a similar level as that for proteins, and enables a much deeper analysis of structural characteristics. It fills a gap in RNA structural bioinformatics, and is freely accessible (via the Jmol application or the JSmol-based website http://jmol.x3dna.org). PMID:28472503

Fiberprint: A subject fingerprint based on sparse code pooling for white matter fiber analysis.

PubMed

Kumar, Kuldeep; Desrosiers, Christian; Siddiqi, Kaleem; Colliot, Olivier; Toews, Matthew

2017-09-01

White matter characterization studies use the information provided by diffusion magnetic resonance imaging (dMRI) to draw cross-population inferences. However, the structure, function, and white matter geometry vary across individuals. Here, we propose a subject fingerprint, called Fiberprint, to quantify the individual uniqueness in white matter geometry using fiber trajectories. We learn a sparse coding representation for fiber trajectories by mapping them to a common space defined by a dictionary. A subject fingerprint is then generated by applying a pooling function for each bundle, thus providing a vector of bundle-wise features describing a particular subject's white matter geometry. These features encode unique properties of fiber trajectories, such as their density along prominent bundles. An analysis of data from 861 Human Connectome Project subjects reveals that a fingerprint based on approximately 3000 fiber trajectories can uniquely identify exemplars from the same individual. We also use fingerprints for twin/sibling identification, our observations consistent with the twin data studies of white matter integrity. Our results demonstrate that the proposed Fiberprint can effectively capture the variability in white matter fiber geometry across individuals, using a compact feature vector (dimension of 50), making this framework particularly attractive for handling large datasets. Copyright © 2017 Elsevier Inc. All rights reserved.

TRANSAT-- method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures.

PubMed

Wiebe, Nicholas J P; Meyer, Irmtraud M

2010-06-24

The prediction of functional RNA structures has attracted increased interest, as it allows us to study the potential functional roles of many genes. RNA structure prediction methods, however, assume that there is a unique functional RNA structure and also do not predict functional features required for in vivo folding. In order to understand how functional RNA structures form in vivo, we require sophisticated experiments or reliable prediction methods. So far, there exist only a few, experimentally validated transient RNA structures. On the computational side, there exist several computer programs which aim to predict the co-transcriptional folding pathway in vivo, but these make a range of simplifying assumptions and do not capture all features known to influence RNA folding in vivo. We want to investigate if evolutionarily related RNA genes fold in a similar way in vivo. To this end, we have developed a new computational method, Transat, which detects conserved helices of high statistical significance. We introduce the method, present a comprehensive performance evaluation and show that Transat is able to predict the structural features of known reference structures including pseudo-knotted ones as well as those of known alternative structural configurations. Transat can also identify unstructured sub-sequences bound by other molecules and provides evidence for new helices which may define folding pathways, supporting the notion that homologous RNA sequence not only assume a similar reference RNA structure, but also fold similarly. Finally, we show that the structural features predicted by Transat differ from those assuming thermodynamic equilibrium. Unlike the existing methods for predicting folding pathways, our method works in a comparative way. This has the disadvantage of not being able to predict features as function of time, but has the considerable advantage of highlighting conserved features and of not requiring a detailed knowledge of the cellular environment.

The crystal structure of NADPH:ferredoxin reductase from Azotobacter vinelandii.

PubMed Central

Sridhar Prasad, G.; Kresge, N.; Muhlberg, A. B.; Shaw, A.; Jung, Y. S.; Burgess, B. K.; Stout, C. D.

1998-01-01

NADPH:ferredoxin reductase (AvFPR) is involved in the response to oxidative stress in Azotobacter vinelandii. The crystal structure of AvFPR has been determined at 2.0 A resolution. The polypeptide fold is homologous with six other oxidoreductases whose structures have been solved including Escherichia coli flavodoxin reductase (EcFldR) and spinach, and Anabaena ferredoxin:NADP+ reductases (FNR). AvFPR is overall most homologous to EcFldR. The structure is comprised of a N-terminal six-stranded antiparallel beta-barrel domain, which binds FAD, and a C-terminal five-stranded parallel beta-sheet domain, which binds NADPH/NADP+ and has a classical nucleotide binding fold. The two domains associate to form a deep cleft where the NADPH and FAD binding sites are juxtaposed. The structure displays sequence conserved motifs in the region surrounding the two dinucleotide binding sites, which are characteristic of the homologous enzymes. The folded over conformation of FAD in AvFPR is similar to that in EcFldR due to stacking of Phe255 on the adenine ring of FAD, but it differs from that in the FNR enzymes, which lack a homologous aromatic residue. The structure of AvFPR displays three unique features in the environment of the bound FAD. Two features may affect the rate of reduction of FAD: the absence of an aromatic residue stacked on the isoalloxazine ring in the NADPH binding site; and the interaction of a carbonyl group with N10 of the flavin. Both of these features are due to the substitution of a conserved C-terminal tyrosine residue with alanine (Ala254) in AvFPR. An additional unique feature may affect the interaction of AvFPR with its redox partner ferredoxin I (FdI). This is the extension of the C-terminus by three residues relative to EcFldR and by four residues relative to FNR. The C-terminal residue, Lys258, interacts with the AMP phosphate of FAD. Consequently, both phosphate groups are paired with a basic group due to the simultaneous interaction of the FMN phosphate with Arg51 in a conserved FAD binding motif. The fourth feature, common to homologous oxidoreductases, is a concentration of 10 basic residues on the face of the protein surrounding the active site, in addition to Arg51 and Lys258. PMID:9865948

Self-assembled ultrathin nanotubes on diamond (100) surface

NASA Astrophysics Data System (ADS)

Lu, Shaohua; Wang, Yanchao; Liu, Hanyu; Miao, Mao-Sheng; Ma, Yanming

2014-04-01

Surfaces of semiconductors are crucially important for electronics, especially when the devices are reduced to the nanoscale. However, surface structures are often elusive, impeding greatly the engineering of devices. Here we develop an efficient method that can automatically explore the surface structures using structure swarm intelligence. Its application to a simple diamond (100) surface reveals an unexpected surface reconstruction featuring self-assembled carbon nanotubes arrays. Such a surface is energetically competitive with the known dimer structure under normal conditions, but it becomes more favourable under a small compressive strain or at high temperatures. The intriguing covalent bonding between neighbouring tubes creates a unique feature of carrier kinetics (that is, one dimensionality of hole states, while two dimensionality of electron states) that could lead to novel design of superior electronics. Our findings highlight that the surface plays vital roles in the fabrication of nanodevices by being a functional part of them.

Solid-State NMR Structure of a Pathogenic Fibril of Full-Length Human α-Synuclein

PubMed Central

Tuttle, Marcus D.; Comellas, Gemma; Nieuwkoop, Andrew J.; Covell, Dustin J.; Berthold, Deborah A.; Kloepper, Kathryn D.; Courtney, Joseph M.; Kim, Jae K.; Barclay, Alexander M.; Kendall, Amy; Wan, William; Stubbs, Gerald; Schwieters, Charles D.; Lee, Virginia M. Y.; George, Julia M.; Rienstra, Chad M.

2016-01-01

Misfolded α-synuclein amyloid fibrils are the principal components of Lewy bodies and neurites, hallmarks of Parkinson’s disease (PD). Here we present a high-resolution structure of an α-synuclein fibril, in a form that induces robust pathology in primary neuronal culture, determined by solid-state NMR spectroscopy and validated by electron microscopy and X-ray fiber diffraction. Over 200 unique long-range distance restraints define a consensus structure with common amyloid features including parallel in-register β-sheets and hydrophobic core residues, but also substantial complexity, arising from diverse structural features: an intermolecular salt bridge, a glutamine ladder, close backbone interactions involving small residues, and several steric zippers stabilizing a novel, orthogonal Greek-key topology. These characteristics contribute to the robust propagation of this fibril form, as evidenced by structural similarity of early-onset PD mutants. The structure provides a framework for understanding the interactions of α-synuclein with other proteins and small molecules to diagnose and treat PD. PMID:27018801

Phenylethynyl reactive diluents

NASA Technical Reports Server (NTRS)

Bryant, Robert G. (Inventor); Jensen, Brian J. (Inventor); Hergenrother, Paul M. (Inventor)

1995-01-01

A composition of matter having a specified general structure is employed to terminate a nucleophilic reagent, resulting in the exclusive production of phenylethynyl terminated reactive oligomers which display unique thermal characteristics. A reactive diluent having a specified general structure is employed to decrease the melt viscosity of a phenylethynyl terminated reactive oligomer and to subsequently react with to provide a thermosetting material of enhanced density. These materials have features which make them attractive candidates for use as composite matrices and adhesives.

A neuro-fuzzy architecture for real-time applications

NASA Technical Reports Server (NTRS)

Ramamoorthy, P. A.; Huang, Song

1992-01-01

Neural networks and fuzzy expert systems perform the same task of functional mapping using entirely different approaches. Each approach has certain unique features. The ability to learn specific input-output mappings from large input/output data possibly corrupted by noise and the ability to adapt or continue learning are some important features of neural networks. Fuzzy expert systems are known for their ability to deal with fuzzy information and incomplete/imprecise data in a structured, logical way. Since both of these techniques implement the same task (that of functional mapping--we regard 'inferencing' as one specific category under this class), a fusion of the two concepts that retains their unique features while overcoming their individual drawbacks will have excellent applications in the real world. In this paper, we arrive at a new architecture by fusing the two concepts. The architecture has the trainability/adaptibility (based on input/output observations) property of the neural networks and the architectural features that are unique to fuzzy expert systems. It also does not require specific information such as fuzzy rules, defuzzification procedure used, etc., though any such information can be integrated into the architecture. We show that this architecture can provide better performance than is possible from a single two or three layer feedforward neural network. Further, we show that this new architecture can be used as an efficient vehicle for hardware implementation of complex fuzzy expert systems for real-time applications. A numerical example is provided to show the potential of this approach.

The Rock Elm meteorite impact structure, Wisconsin: Geology and shock-metamorphic effects in quartz

USGS Publications Warehouse

French, B.M.; Cordua, W.S.; Plescia, J.B.

2004-01-01

The Rock Elm structure in southwest Wisconsin is an anomalous circular area of highly deformed rocks, ???6.5 km in diameter, located in a region of virtually horizontal undeformed sedimentary rocks. Shock-produced planar microstructures (PMs) have been identified in quartz grains in several lithologies associated with the structure: sandstones, quartzite pebbles, and breccia. Two distinct types of PMs are present: P1 features, which appear identical to planar fractures (PFs or cleavage), and P2 features, which are interpreted as possible incipient planar deformation features (PDFs). The latter are uniquely produced by the shock waves associated with meteorite impact events. Both types of PMs are oriented parallel to specific crystallographic planes in the quartz, most commonly to c(0001), ??112??2, and r/z101??1. The association of unusual, structurally deformed strata with distinct shock-produced microdeformation features in their quartz-bearing rocks establishes Rock Elm as a meteorite impact structure and supports the view that the presence of multiple parallel cleavages in quartz may be used independently as a criterion for meteorite impact. Preliminary paleontological studies indicate a minimum age of Middle Ordovician for the Rock Elm structure. A similar age estimate (450-400 Ma) is obtained independently by combining the results of studies of the general morphology of complex impact structures with estimated rates of sedimentation for the region. Such methods may be applicable to dating other old and deeply eroded impact structures formed in sedimentary target rocks.

Assessment of metal ion concentration in water with structured feature selection.

PubMed

Naula, Pekka; Airola, Antti; Pihlasalo, Sari; Montoya Perez, Ileana; Salakoski, Tapio; Pahikkala, Tapio

2017-10-01

We propose a cost-effective system for the determination of metal ion concentration in water, addressing a central issue in water resources management. The system combines novel luminometric label array technology with a machine learning algorithm that selects a minimal number of array reagents (modulators) and liquid sample dilutions, such that enable accurate quantification. The algorithm is able to identify the optimal modulators and sample dilutions leading to cost reductions since less manual labour and resources are needed. Inferring the ion detector involves a unique type of a structured feature selection problem, which we formalize in this paper. We propose a novel Cartesian greedy forward feature selection algorithm for solving the problem. The novel algorithm was evaluated in the concentration assessment of five metal ions and the performance was compared to two known feature selection approaches. The results demonstrate that the proposed system can assist in lowering the costs with minimal loss in accuracy. Copyright © 2017 Elsevier Ltd. All rights reserved.

Structural basis for precursor protein-directed ribosomal peptide macrocyclization

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

Li, Kunhua; Condurso, Heather L.; Li, Gengnan

Macrocyclization is a common feature of natural product biosynthetic pathways including the diverse family of ribosomal peptides. Microviridins are architecturally complex cyanobacterial ribosomal peptides that target proteases with potent reversible inhibition. The product structure is constructed via three macrocyclizations catalyzed sequentially by two members of the ATP-grasp family, a unique strategy for ribosomal peptide macrocyclization. Here we describe in detail the structural basis for the enzyme-catalyzed macrocyclizations in the microviridin J pathway of Microcystis aeruginosa. The macrocyclases MdnC and MdnB interact with a conserved α-helix of the precursor peptide using a novel precursor-peptide recognition mechanism. The results provide insight intomore » the unique protein–protein interactions that are key to the chemistry, suggest an origin for the natural combinatorial synthesis of microviridin peptides, and provide a framework for future engineering efforts to generate designed compounds.« less

Unique Chiral Interpenetrating d-f Heterometallic MOFs as Luminescent Sensors.

PubMed

Wu, Zhi-Lei; Dong, Jie; Ni, Wei-Yan; Zhang, Bo-Wen; Cui, Jian-Zhong; Zhao, Bin

2015-06-01

One novel three-dimensional (3D) 3d-4f metal-organic framework (MOF), [TbZn(L)(CO3)2(H2O)]n (1) [HL = 4'-(4-carboxyphenyl)-2,2':6',2″-terpyridine], has been successfully synthesized and structurally characterized. Structural analysis shows that compound 1 features a unique chiral interpenetrating 3D framework for the first time. The resulting crystals of 1 are composed of enantiomers 1a (P41) and 1b (P43), as was clearly confirmed by the crystal structure and the corresponding circular dichroism (CD) analyses of eight randomly selected crystals. The investigations on CD spectra based on every single crystal clearly assigned the Cotton effect signals. The powder X-ray diffraction measurement of 1 after being immersed in common solvents reveals that 1 possess excellent solvent stability. Furthermore, luminescent studies imply that 1 displays highly selective luminescent sensing of aldehydes, such as formol, acetaldehyde, and propanal.

Profiling of the Tox21 Chemical Collection for Mitochondrial ...

EPA Pesticide Factsheets

Mitochondrial dysfunction has been implicated in the pathogenesis of a variety of disorders including cancer, diabetes, and neurodegenerative and cardiovascular diseases. Understanding how different environmental chemicals and drug-like molecules impact mitochondrial function represents an initial step in predicting exposure-related toxic effects and defining a possible role for such compounds in the onset of various diseases. OBJECTIVES: To identify individual chemicals and general structural features associated with the disruption of mitochondrial membrane potential (MMP). METHODS: We used a multiplexed quantitative high throughput screening (qHTS) approach combined with informatics tools to screen the Tox21 10,000 compound library (~8300 unique chemicals) at 15 concentrations in triplicate to identify chemicals and structural features that are associated with changes in MMP in HepG2 cells. RESULTS: In the primary screening, approximately 11% of the compounds (913 unique compounds) decreased the MMP after 1 h of treatment without affecting cell viability. Additionally, 309 compounds decreased MMP over a concentration range that also produced measurable cytotoxicity [half maximal inhibitory concentration (IC50) in MMP assay/IC50 in viability assay) ≤ 3, p<0.05]. Over 11% of the structural clusters that constitute the Tox21 library (76 of 651 clusters) were significantly enriched for compounds that decreased the MMP. CONCLUSIONS: Our multiplexed qHTS approach

Biochemical Regulatory Features of Activation-Induced Cytidine Deaminase Remain Conserved from Lampreys to Humans

PubMed Central

King, Justin J.; Amemiya, Chris T.; Hsu, Ellen

2017-01-01

ABSTRACT Activation-induced cytidine deaminase (AID) is a genome-mutating enzyme that initiates class switch recombination and somatic hypermutation of antibodies in jawed vertebrates. We previously described the biochemical properties of human AID and found that it is an unusual enzyme in that it exhibits binding affinities for its substrate DNA and catalytic rates several orders of magnitude higher and lower, respectively, than a typical enzyme. Recently, we solved the functional structure of AID and demonstrated that these properties are due to nonspecific DNA binding on its surface, along with a catalytic pocket that predominantly assumes a closed conformation. Here we investigated the biochemical properties of AID from a sea lamprey, nurse shark, tetraodon, and coelacanth: representative species chosen because their lineages diverged at the earliest critical junctures in evolution of adaptive immunity. We found that these earliest-diverged AID orthologs are active cytidine deaminases that exhibit unique substrate specificities and thermosensitivities. Significant amino acid sequence divergence among these AID orthologs is predicted to manifest as notable structural differences. However, despite major differences in sequence specificities, thermosensitivities, and structural features, all orthologs share the unusually high DNA binding affinities and low catalytic rates. This absolute conservation is evidence for biological significance of these unique biochemical properties. PMID:28716949

Palm Vein Verification Using Multiple Features and Locality Preserving Projections

PubMed Central

Bu, Wei; Wu, Xiangqian; Zhao, Qiushi

2014-01-01

Biometrics is defined as identifying people by their physiological characteristic, such as iris pattern, fingerprint, and face, or by some aspects of their behavior, such as voice, signature, and gesture. Considerable attention has been drawn on these issues during the last several decades. And many biometric systems for commercial applications have been successfully developed. Recently, the vein pattern biometric becomes increasingly attractive for its uniqueness, stability, and noninvasiveness. A vein pattern is the physical distribution structure of the blood vessels underneath a person's skin. The palm vein pattern is very ganglion and it shows a huge number of vessels. The attitude of the palm vein vessels stays in the same location for the whole life and its pattern is definitely unique. In our work, the matching filter method is proposed for the palm vein image enhancement. New palm vein features extraction methods, global feature extracted based on wavelet coefficients and locality preserving projections (WLPP), and local feature based on local binary pattern variance and locality preserving projections (LBPV_LPP) have been proposed. Finally, the nearest neighbour matching method has been proposed that verified the test palm vein images. The experimental result shows that the EER to the proposed method is 0.1378%. PMID:24693230

Palm vein verification using multiple features and locality preserving projections.

PubMed

Al-Juboori, Ali Mohsin; Bu, Wei; Wu, Xiangqian; Zhao, Qiushi

2014-01-01

Biometrics is defined as identifying people by their physiological characteristic, such as iris pattern, fingerprint, and face, or by some aspects of their behavior, such as voice, signature, and gesture. Considerable attention has been drawn on these issues during the last several decades. And many biometric systems for commercial applications have been successfully developed. Recently, the vein pattern biometric becomes increasingly attractive for its uniqueness, stability, and noninvasiveness. A vein pattern is the physical distribution structure of the blood vessels underneath a person's skin. The palm vein pattern is very ganglion and it shows a huge number of vessels. The attitude of the palm vein vessels stays in the same location for the whole life and its pattern is definitely unique. In our work, the matching filter method is proposed for the palm vein image enhancement. New palm vein features extraction methods, global feature extracted based on wavelet coefficients and locality preserving projections (WLPP), and local feature based on local binary pattern variance and locality preserving projections (LBPV_LPP) have been proposed. Finally, the nearest neighbour matching method has been proposed that verified the test palm vein images. The experimental result shows that the EER to the proposed method is 0.1378%.

Inorganic and methane clathrates: Versatility of guest–host compounds for energy harvesting

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

Krishna, Lakshmi; Koh, Carolyn A.

ABSTRACT This review article evaluates the structure–property relations of inorganic clathrates and clathrate hydrates and their potential role in energy harvesting. There is potential cross-fertilization between the two research areas. Guest–host clathrate compounds exhibit unique structural and physical properties, which lead to their versatile roles in energy applications. Prominent classes of clathrate compounds are gas hydrates and inorganic clathrates. That said, there is limited cross-fertilization between the clathrate hydrate and inorganic clathrate communities, with researchers in the respective fields being less informed on the other field. Yet the structures and unique guest–host interactions in both these compounds are common importantmore » features of these clathrates. Common features and procedures can inspire and inform development between the compound classes, which may be important to the technological advancements for the different clathrate materials, e.g., structure characterization techniques and guest–host dynamics in which the “guest” tends to be imprisoned in the host structure, until external forces are applied. Conversely, the diversity in chemical compositions of these two classes of materials leads to the different applications from methane capture and storage to converting waste heat to electricity (thermoelectrics). This article highlights the structural and physical similarities and differences of inorganic and methane clathrates. The most promising state-of-the-art applications of the clathrates are highlighted for harvesting energy from methane (clathrate) hydrate deposits under the ocean and for inorganic clathrates as promising thermoelectric materials.« less

Inorganic and methane clathrates: Versatility of guest–host compounds for energy harvesting

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

Krishna, Lakshmi; Koh, Carolyn A.

2015-01-01

ABSTRACT This review article evaluates the structure–property relations of inorganic clathrates and clathrate hydrates and their potential role in energy harvesting. There is potential cross-fertilization between the two research areas. Guest–host clathrate compounds exhibit unique structural and physical properties, which lead to their versatile roles in energy applications. Prominent classes of clathrate compounds are gas hydrates and inorganic clathrates. That said, there is limited cross-fertilization between the clathrate hydrate and inorganic clathrate communities, with researchers in the respective fields being less informed on the other field. Yet the structures and unique guest–host interactions in both these compounds are common importantmore » features of these clathrates. Common features and procedures can inspire and inform development between the compound classes, which may be important to the technological advancements for the different clathrate materials, e.g., structure characterization techniques and guest–host dynamics in which the “guest” tends to be imprisoned in the host structure, until external forces are applied. Conversely, the diversity in chemical compositions of these two classes of materials leads to the different applications from methane capture and storage to converting waste heat to electricity (thermoelectrics). This article highlights the structural and physical similarities and differences of inorganic and methane clathrates. The most promising state-of-the-art applications of the clathrates are highlighted for harvesting energy from methane (clathrate) hydrate deposits under the ocean and for inorganic clathrates as promising thermoelectric materials.« less

Determining the Energetics of the Hydrogen Bond through FTIR: A Hands-On Physical Chemistry Lab Experiment

ERIC Educational Resources Information Center

Guerin, Abby C.; Riley, Kristi; Rupnik, Kresimir; Kuroda, Daniel G.

2016-01-01

Hydrogen bonds are very important chemical structures that are responsible for many unique and important properties of solvents, such as the solvation power of water. These distinctive features are directly related to the stabilization energy conferred by hydrogen bonds to the solvent. Thus, the characterization of hydrogen bond energetics has…

The design of a monopole radiator to investigate the effect of microwave radiation in biological systems.

PubMed

Bigu-del-Blanco, J; Romero-Sierra, C

1977-08-01

The design of a microwave monopole radiator, using a hollow hypodermic needle, is described. This radiator has two unique features. It allows both i) irradiation of deep biological structures by simple needle injection and ii) simultaneous chemotherapic treatment of tissue. The matching characteristics of the monopole in saline solutions are given.

Biophysical Adaptations of Prokaryotic Voltage-Gated Sodium Channels.

PubMed

Vien, T N; DeCaen, P G

2016-01-01

This chapter describes the adaptive features found in voltage-gated sodium channels (NaVs) of prokaryotes and eukaryotes. These two families are distinct, having diverged early in evolutionary history but maintain a surprising degree of convergence in function. While prokaryotic NaVs are required for growth and motility, eukaryotic NaVs selectively conduct fast electrical currents for short- and long-range signaling across cell membranes in mammalian organs. Current interest in prokaryotic NaVs is stoked by their resolved high-resolution structures and functional features which are reminiscent of eukaryotic NaVs. In this chapter, comparisons between eukaryotic and prokaryotic NaVs are made to highlight the shared and unique aspects of ion selectivity, voltage sensitivity, and pharmacology. Examples of prokaryotic and eukaryotic NaV convergent evolution will be discussed within the context of their structural features. Copyright © 2016 Elsevier Inc. All rights reserved.

Low floor mass transit vehicle

DOEpatents

Emmons, J Bruce [Beverly Hills, MI; Blessing, Leonard J [Rochester, MI

2004-02-03

A mass transit vehicle includes a frame structure that provides an efficient and economical approach to providing a low floor bus. The inventive frame includes a stiff roof panel and a stiff floor panel. A plurality of generally vertical pillars extend between the roof and floor panels. A unique bracket arrangement is disclosed for connecting the pillars to the panels. Side panels are secured to the pillars and carry the shear stresses on the frame. A unique seating assembly that can be advantageously incorporated into the vehicle taking advantage of the load distributing features of the inventive frame is also disclosed.

Enzymatic Inverse Opal Hydrogel Particles for Biocatalyst.

PubMed

Wang, Huan; Gu, Hongcheng; Chen, Zhuoyue; Shang, Luoran; Zhao, Ze; Gu, Zhongze; Zhao, Yuanjin

2017-04-19

Enzymatic carriers have a demonstrated value for chemical reactions and industrial applications. Here, we present a novel kind of inverse opal hydrogel particles as the enzymatic carriers. The particles were negatively replicated from spherical colloidal crystal templates by using magnetic nanoparticles tagged acrylamide hydrogel. Thus, they were endowed with the features of monodispersity, small volume, complete penetrating structure, and controllable motion, which are all beneficial for improving the efficiency of biocatalysis. In addition, due to the ordered porous nanostructure, the inverse opal hydrogel particles were imparted with unique photonic band gaps (PBGs) and vivid structural colors for encoding varieties of immobilized enzymes and for constructing a multienzymes biocatalysis system. These features of the inverse opal hydrogel particles indicate that they are ideal enzymatic carriers for biocatalysis.

Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features.

PubMed

Speranzini, Valentina; Rotili, Dante; Ciossani, Giuseppe; Pilotto, Simona; Marrocco, Biagina; Forgione, Mariantonietta; Lucidi, Alessia; Forneris, Federico; Mehdipour, Parinaz; Velankar, Sameer; Mai, Antonello; Mattevi, Andrea

2016-09-01

Because of its involvement in the progression of several malignant tumors, the histone lysine-specific demethylase 1 (LSD1) has become a prominent drug target in modern medicinal chemistry research. We report on the discovery of two classes of noncovalent inhibitors displaying unique structural features. The antibiotics polymyxins bind at the entrance of the substrate cleft, where their highly charged cyclic moiety interacts with a cluster of positively charged amino acids. The same site is occupied by quinazoline-based compounds, which were found to inhibit the enzyme through a most peculiar mode because they form a pile of five to seven molecules that obstruct access to the active center. These data significantly indicate unpredictable strategies for the development of epigenetic inhibitors.

Past, Present, and Future Capabilities of the Transonic Dynamics Tunnel from an Aeroelasticity Perspective

NASA Technical Reports Server (NTRS)

Cole, Stanley R.; Garcia, Jerry L.

2000-01-01

The NASA Langley Transonic Dynamics Tunnel (TDT) has provided a unique capability for aeroelastic testing for forty years. The facility has a rich history of significant contributions to the design of many United States commercial transports, military aircraft, launch vehicles, and spacecraft. The facility has many features that contribute to its uniqueness for aeroelasticity testing, perhaps the most important feature being the use of a heavy gas test medium to achieve higher test densities. Higher test medium densities substantially improve model-building requirements and therefore simplify the fabrication process for building aeroelastically scaled wind tunnel models. Aeroelastic scaling for the heavy gas results in lower model structural frequencies. Lower model frequencies tend to a make aeroelastic testing safer. This paper will describe major developments in the testing capabilities at the TDT throughout its history, the current status of the facility, and planned additions and improvements to its capabilities in the near future.

Recent advances in flexible low power cholesteric LCDs

NASA Astrophysics Data System (ADS)

Khan, Asad; Shiyanovskaya, Irina; Montbach, Erica; Schneider, Tod; Nicholson, Forrest; Miller, Nick; Marhefka, Duane; Ernst, Todd; Doane, J. W.

2006-05-01

Bistable reflective cholesteric displays are a liquid crystal display technology developed to fill a market need for very low power displays. Their unique look, high reflectivity, bistability, and simple structure make them an ideal flat panel display choice for handheld or other portable devices where small lightweight batteries with long lifetimes are important. Applications ranging from low resolution large signs to ultra high resolution electronic books can utilize cholesteric displays to not only benefit from the numerous features, but also create enabling features that other flat panel display technologies cannot. Flexible displays are the focus of attention of numerous research groups and corporations worldwide. Cholesteric displays have been demonstrated to be highly amenable to flexible substrates. This paper will review recent advances in flexible cholesteric displays including both phase separation and emulsification approaches to encapsulation. Both approaches provide unique benefits to various aspects of manufacturability, processes, flexibility, and conformability.

The flagellum of Trypanosoma brucei: new tricks from an old dog

PubMed Central

Ralston, Katherine S.; Hill, Kent L.

2010-01-01

African trypanosomes, i.e. Trypanosoma brucei and related sub-species, are devastating human and animal pathogens that cause significant human mortality and limit sustained economic development in sub-Saharan Africa. Trypanosoma brucei is a highly motile protozoan parasite and coordinated motility is central to both disease pathogenesis in the mammalian host and parasite development in the tsetse fly vector. Since motility is critical for parasite development and pathogenesis, understanding unique aspects of the T. brucei flagellum may uncover novel targets for therapeutic intervention in African sleeping sickness. Moreover, studies of conserved features of the T. brucei flagellum are directly relevant to understanding fundamental aspects of flagellum and cilium function in other eukaryotes, making T. brucei an important model system. The T. brucei flagellum contains a canonical 9 + 2 axoneme, together with additional features that are unique to kinetoplastids and a few closely-related organisms. Until recently, much of our knowledge of the structure and function of the trypanosome flagellum was based on analogy and inference from other organisms. There has been an explosion in functional studies in T. brucei in recent years, revealing conserved as well as novel and unexpected structural and functional features of the flagellum. Most notably, the flagellum has been found to be an essential organelle, with critical roles in parasite motility, morphogenesis, cell division and immune evasion. This review highlights recent discoveries on the T. brucei flagellum. PMID:18472102

Efficient enumeration of monocyclic chemical graphs with given path frequencies

PubMed Central

2014-01-01

Background The enumeration of chemical graphs (molecular graphs) satisfying given constraints is one of the fundamental problems in chemoinformatics and bioinformatics because it leads to a variety of useful applications including structure determination and development of novel chemical compounds. Results We consider the problem of enumerating chemical graphs with monocyclic structure (a graph structure that contains exactly one cycle) from a given set of feature vectors, where a feature vector represents the frequency of the prescribed paths in a chemical compound to be constructed and the set is specified by a pair of upper and lower feature vectors. To enumerate all tree-like (acyclic) chemical graphs from a given set of feature vectors, Shimizu et al. and Suzuki et al. proposed efficient branch-and-bound algorithms based on a fast tree enumeration algorithm. In this study, we devise a novel method for extending these algorithms to enumeration of chemical graphs with monocyclic structure by designing a fast algorithm for testing uniqueness. The results of computational experiments reveal that the computational efficiency of the new algorithm is as good as those for enumeration of tree-like chemical compounds. Conclusions We succeed in expanding the class of chemical graphs that are able to be enumerated efficiently. PMID:24955135

Origami-based mechanical metamaterials with tunable frequency band structures (Conference Presentation)

NASA Astrophysics Data System (ADS)

Yasuda, Hiromi; Pratt, Riley; Yang, Jinkyu

2017-04-01

We investigate wave dynamics in origami-based mechanical metamaterials composed of bellows-like origami structures, specifically the Tachi-Miura Polyhedron (TMP). One of the unique features of the TMP is that its structural deformations take place only along the crease lines, therefore the structure can be made of rigid plates and hinges. By utilizing this feature, we introduce linear torsional springs to model the crease lines and derive the force and displacement relationship of the TMP structure along the longitudinal direction. Our analysis shows strain softening/hardening behaviors in compression/tensile regions respectively, and the force-displacement curve can be manipulated by altering the initial configuration of the TMP (e.g., the initial folding angle). We also fabricate physical prototypes and measure the force-displacement behavior to verify our analytical model. Based on this static analysis on the TMP, we simplify the TMP structure into a linkage model, preserving the tunable strain softening/hardening behaviors. Dynamic analysis is also conducted numerically to analyze the frequency response of the simplified TMP unit cell under harmonic excitations. The simplified TMP exhibits a transition between linear and nonlinear behaviors, which depends on the amplitude of the excitation and the initial configuration. In addition, we design a 1D system composed of simplified TMP unit cells and analyze the relationship between frequency and wave number. If two different configurations of the unit cell (e.g., different initial folding angles) are connected in an alternating arrangement, the system develops frequency bandgaps. These unique static/dynamic behaviors can be exploited to design engineering devices which can handle vibrations and impact in an efficient manner.

Benzimidazole-core as an antimycobacterial agent.

PubMed

Keri, Rangappa S; Rajappa, Chethana Kolambae; Patil, Siddappa A; Nagaraja, Bhari Mallanna

2016-12-01

Mycobacterium tuberculosis (Mtb) is considered as one of the precarious bacterial infections around the world. Through a projected 8.7 million new tuberculosis (TB) cases and 1.4 million mortalities per annum, this deadly infection resulted insubstantial amount of human deaths than any other single organism bacterial infections. TB is one of India's most threatening human health problems and it accounts for approximately 33% of the global health issues. Subsequently, for TB there is an imperative need for the improvement of existing drug candidates with newer targets and specified mechanism of action. Within the wide spectra of heterocycles, benzimidazole and its substituted analogues were evidenced promising biological efficacies enabling them to perform as new drug or prodrug candidates. Exceptional structural features of this class of heterocycle and versatile biological applications made it a privileged structural backbone in new drug design and discovery. Majorly, 2,5- and 2,6-disubstituted benzimidazole derivatives shown to induce significant antiTB potential. To seek more insights on this unique feature of benzimidazole candidates, there is an urgency to assemble the recent advances in this promising area. This review presents an overview of the recent advancements and focuses on the structural features responsible for unique antiTB applications and compiled published reports on benzimidazole derivatives emphasizing on different approaches employed for their syntheses in order to help medicinal and clinical chemists in designing next generation, yet effective and safer antiTB candidates. Copyright © 2016 Institute of Pharmacology, Polish Academy of Sciences. Published by Elsevier Urban & Partner Sp. z o.o. All rights reserved.

DSSR-enhanced visualization of nucleic acid structures in Jmol.

PubMed

Hanson, Robert M; Lu, Xiang-Jun

2017-07-03

Sophisticated and interactive visualizations are essential for making sense of the intricate 3D structures of macromolecules. For proteins, secondary structural components are routinely featured in molecular graphics visualizations. However, the field of RNA structural bioinformatics is still lagging behind; for example, current molecular graphics tools lack built-in support even for base pairs, double helices, or hairpin loops. DSSR (Dissecting the Spatial Structure of RNA) is an integrated and automated command-line tool for the analysis and annotation of RNA tertiary structures. It calculates a comprehensive and unique set of features for characterizing RNA, as well as DNA structures. Jmol is a widely used, open-source Java viewer for 3D structures, with a powerful scripting language. JSmol, its reincarnation based on native JavaScript, has a predominant position in the post Java-applet era for web-based visualization of molecular structures. The DSSR-Jmol integration presented here makes salient features of DSSR readily accessible, either via the Java-based Jmol application itself, or its HTML5-based equivalent, JSmol. The DSSR web service accepts 3D coordinate files (in mmCIF or PDB format) initiated from a Jmol or JSmol session and returns DSSR-derived structural features in JSON format. This seamless combination of DSSR and Jmol/JSmol brings the molecular graphics of 3D RNA structures to a similar level as that for proteins, and enables a much deeper analysis of structural characteristics. It fills a gap in RNA structural bioinformatics, and is freely accessible (via the Jmol application or the JSmol-based website http://jmol.x3dna.org). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Human HDAC isoform selectivity achieved via exploitation of the acetate release channel with structurally unique small molecule inhibitors

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

Whitehead, Lewis; Dobler, Markus R.; Radetich, Branko

2013-11-20

Herein we report the discovery of a family of novel yet simple, amino-acid derived class I HDAC inhibitors that demonstrate isoform selectivity via access to the internal acetate release channel. Isoform selectivity criteria is discussed on the basis of X-ray crystallography and molecular modeling of these novel inhibitors bound to HDAC8, potentially revealing insights into the mechanism of enzymatic function through novel structural features revealed at the atomic level.

Study of Comets Composition and Structure

NASA Astrophysics Data System (ADS)

Khalaf, S. Z.; Selman, A. A.; Ali, H. S.

2008-12-01

The present paper focuses on the nature of the different interactions between cometary nucleus and tail with solar wind. The dynamics of the comet will impose many features that provide unique behavior of the comet when entering the solar system. These features are reviewed in this paper and few investigations are made. The calculations made in this work represent the analysis and interpretation of the different features of the comet, such as perihelion and eccentricity dependence on the gas production rate, and the dependence of the latter on the composition of the comet nucleus. The dependences of the heliocentric, bow shock, contact surface, and stand-off distances with gas production rate for many types of comets that cover linear and non-linear types are studied in this work. Important results are obtained which indicated the different physical interactions between cometary ions and solar wind. Furthermore, the important relation between mean molecular weight and gas production rate are analyzed and studied in this work and a conclusion is made that, as the gas production rate increases, the mean molecular weight will decrease exponentially. A detailed discussion for this unique relation is given.

Grid point extraction and coding for structured light system

NASA Astrophysics Data System (ADS)

Song, Zhan; Chung, Ronald

2011-09-01

A structured light system simplifies three-dimensional reconstruction by illuminating a specially designed pattern to the target object, thereby generating a distinct texture on it for imaging and further processing. Success of the system hinges upon what features are to be coded in the projected pattern, extracted in the captured image, and matched between the projector's display panel and the camera's image plane. The codes have to be such that they are largely preserved in the image data upon illumination from the projector, reflection from the target object, and projective distortion in the imaging process. The features also need to be reliably extracted in the image domain. In this article, a two-dimensional pseudorandom pattern consisting of rhombic color elements is proposed, and the grid points between the pattern elements are chosen as the feature points. We describe how a type classification of the grid points plus the pseudorandomness of the projected pattern can equip each grid point with a unique label that is preserved in the captured image. We also present a grid point detector that extracts the grid points without the need of segmenting the pattern elements, and that localizes the grid points in subpixel accuracy. Extensive experiments are presented to illustrate that, with the proposed pattern feature definition and feature detector, more features points in higher accuracy can be reconstructed in comparison with the existing pseudorandomly encoded structured light systems.

A unique GCN5-related glucosamine N-acetyltransferase region exist in the fungal multi-domain glycoside hydrolase family 3 β-N-acetylglucosaminidase

PubMed Central

Qin, Zhen; Xiao, Yibei; Yang, Xinbin; Mesters, Jeroen R.; Yang, Shaoqing; Jiang, Zhengqiang

2015-01-01

Glycoside hydrolase (GH) family 3 β-N-acetylglucosaminidases widely exist in the filamentous fungi, which may play a key role in chitin metabolism of fungi. A multi-domain GH family 3 β-N-acetylglucosaminidase from Rhizomucor miehei (RmNag), exhibiting a potential N-acetyltransferase region, has been recently reported to show great potential in industrial applications. In this study, the crystal structure of RmNag was determined at 2.80 Å resolution. The three-dimensional structure of RmNag showed four distinctive domains, which belong to two distinguishable functional regions — a GH family 3 β-N-acetylglucosaminidase region (N-terminal) and a N-acetyltransferase region (C-terminal). From structural and functional analysis, the C-terminal region of RmNag was identified as a unique tandem array linking general control non-derepressible 5 (GCN5)-related N-acetyltransferase (GNAT), which displayed glucosamine N-acetyltransferase activity. Structural analysis of this glucosamine N-acetyltransferase region revealed that a unique glucosamine binding pocket is located in the pantetheine arm binding terminal region of the conserved CoA binding pocket, which is different from all known GNAT members. This is the first structural report of a glucosamine N-acetyltransferase, which provides novel structural information about substrate specificity of GNATs. The structural and functional features of this multi-domain β-N-acetylglucosaminidase could be useful in studying the catalytic mechanism of GH family 3 proteins. PMID:26669854

A unique GCN5-related glucosamine N-acetyltransferase region exist in the fungal multi-domain glycoside hydrolase family 3 β-N-acetylglucosaminidase.

PubMed

Qin, Zhen; Xiao, Yibei; Yang, Xinbin; Mesters, Jeroen R; Yang, Shaoqing; Jiang, Zhengqiang

2015-12-16

Glycoside hydrolase (GH) family 3 β-N-acetylglucosaminidases widely exist in the filamentous fungi, which may play a key role in chitin metabolism of fungi. A multi-domain GH family 3 β-N-acetylglucosaminidase from Rhizomucor miehei (RmNag), exhibiting a potential N-acetyltransferase region, has been recently reported to show great potential in industrial applications. In this study, the crystal structure of RmNag was determined at 2.80 Å resolution. The three-dimensional structure of RmNag showed four distinctive domains, which belong to two distinguishable functional regions--a GH family 3 β-N-acetylglucosaminidase region (N-terminal) and a N-acetyltransferase region (C-terminal). From structural and functional analysis, the C-terminal region of RmNag was identified as a unique tandem array linking general control non-derepressible 5 (GCN5)-related N-acetyltransferase (GNAT), which displayed glucosamine N-acetyltransferase activity. Structural analysis of this glucosamine N-acetyltransferase region revealed that a unique glucosamine binding pocket is located in the pantetheine arm binding terminal region of the conserved CoA binding pocket, which is different from all known GNAT members. This is the first structural report of a glucosamine N-acetyltransferase, which provides novel structural information about substrate specificity of GNATs. The structural and functional features of this multi-domain β-N-acetylglucosaminidase could be useful in studying the catalytic mechanism of GH family 3 proteins.

Total synthesis of (+)-antroquinonol and (+)-antroquinonol D.

PubMed

Sulake, Rohidas S; Chen, Chinpiao

2015-03-06

The first total synthesis of (+)-antroquinonol and (+)-antroquinonol D, two structurally unique quinonols with a sesquiterpene side chain, is described. The route features an iridium-catalyzed olefin isomerization-Claisen rearrangement reaction (ICR), lactonization, and Grubbs olefin metathesis. The requisite α,β-unsaturation was achieved via the selenylation/oxidation protocol and elimination of β-methoxy group to provide two natural products from a common intermediate.

The XFV-12A Thrust-Augmented Wing (TAW) prototype aircraft

NASA Technical Reports Server (NTRS)

Murphy, R.; Lewis, E. L.

1979-01-01

The XFV-12A, a unique V/STOL technology prototype aircraft being developed for the Navy, is described. The innovative design features a thrust augmented wing and a canard ejector. Structural, functional, and control test performances are discussed. Static tether test results are also discussed. Assessment of test results are given along with projections for future modification areas.

Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion

Treesearch

Diego Martinez; Jean Challacombe; Ingo Morgenstern; David Hibbett; Monika Schmoll; Christian P. Kubicek; Patricia Ferreira; Francisco J. Ruiz-Duenas; Angel T. Martinez; Philip J. Kersten; Kenneth E. Hammel; Jill A. Gaskell; Daniel Cullen

2009-01-01

Brown-rot fungi such as Postia placenta are common inhabitants of forest ecosystems and are also largely responsible for the destructive decay of wooden structures. Rapid depolymerization of cellulose is a distinguishing feature of brown-rot, but the biochemical mechanisms and underlying genetics are poorly understood. Systematic examination of the P. placenta genome,...

The elastase-PK101 structure: Mechanism of an ultrasensitive activity-based probe revealed

DOE PAGES

Lechtenberg, Bernhard C.; Robinson, Howard R.; Kasperkiewicz, Paulina; ...

2015-01-22

Human neutrophil elastase (HNE) plays a central role in neutrophil host defense, but its broad specificity makes HNE a difficult target for both inhibitor and probe development. Recently, we identified the unnatural amino acid containing activity-based probe PK101, which exhibits astounding sensitivity and selectivity for HNE, yet completely lacks mechanistic explanation for its unique characteristics. Here, we present the crystal structure of the HNE-PK101 complex which not only reveals the basis for PK101 ultrasensitivity but also uncovers so far unrecognized HNE features. Strikingly, the Nle( O-Bzl) function in the P4 position of PK101 reveals and leverages an “exo-pocket” on HNEmore » as a critical factor for selectivity. Furthermore, the PK101 P3 position harbors a methionine dioxide function, which mimics a post-translationally oxidized methionine residue and forms a critical hydrogen bond to the backbone amide of Gly219 of HNE. Gly219 resides in a Gly–Gly motif that is unique to HNE, yet compulsory for this interaction. Consequently, this feature enables HNE to accommodate substrates that have undergone methionine oxidation, which constitutes a hallmark post-translational modification of neutrophil signaling.« less

Enhanced Imaging of Corrosion in Aircraft Structures with Reverse Geometry X-ray(registered tm)

NASA Technical Reports Server (NTRS)

Winfree, William P.; Cmar-Mascis, Noreen A.; Parker, F. Raymond

2000-01-01

The application of Reverse Geometry X-ray to the detection and characterization of corrosion in aircraft structures is presented. Reverse Geometry X-ray is a unique system that utilizes an electronically scanned x-ray source and a discrete detector for real time radiographic imaging of a structure. The scanned source system has several advantages when compared to conventional radiography. First, the discrete x-ray detector can be miniaturized and easily positioned inside a complex structure (such as an aircraft wing) enabling images of each surface of the structure to be obtained separately. Second, using a measurement configuration with multiple detectors enables the simultaneous acquisition of data from several different perspectives without moving the structure or the measurement system. This provides a means for locating the position of flaws and enhances separation of features at the surface from features inside the structure. Data is presented on aircraft specimens with corrosion in the lap joint. Advanced laminographic imaging techniques utilizing data from multiple detectors are demonstrated to be capable of separating surface features from corrosion in the lap joint and locating the corrosion in multilayer structures. Results of this technique are compared to computed tomography cross sections obtained from a microfocus x-ray tomography system. A method is presented for calibration of the detectors of the Reverse Geometry X-ray system to enable quantification of the corrosion to within 2%.

Structure–Function Studies of DNA Polymerase λ

PubMed Central

2015-01-01

DNA polymerase λ (pol λ) functions in DNA repair with its main roles considered to be filling short gaps during repair of double-strand breaks by nonhomologous end joining and during base excision repair. As indicated by structural and biochemical studies over the past 10 years, pol λ shares many common properties with other family X siblings (pol β, pol μ, and terminal deoxynucleotidyl transferase) but also has unique structural features that determine its specific functions. In this review, we consider how structural studies over the past decade furthered our understanding of the behavior and biological roles of pol λ. PMID:24716527

Music and movement share a dynamic structure that supports universal expressions of emotion

PubMed Central

Sievers, Beau; Polansky, Larry; Casey, Michael; Wheatley, Thalia

2013-01-01

Music moves us. Its kinetic power is the foundation of human behaviors as diverse as dance, romance, lullabies, and the military march. Despite its significance, the music-movement relationship is poorly understood. We present an empirical method for testing whether music and movement share a common structure that affords equivalent and universal emotional expressions. Our method uses a computer program that can generate matching examples of music and movement from a single set of features: rate, jitter (regularity of rate), direction, step size, and dissonance/visual spikiness. We applied our method in two experiments, one in the United States and another in an isolated tribal village in Cambodia. These experiments revealed three things: (i) each emotion was represented by a unique combination of features, (ii) each combination expressed the same emotion in both music and movement, and (iii) this common structure between music and movement was evident within and across cultures. PMID:23248314

The puzzling Venusian polar atmospheric structure reproduced by a general circulation model

PubMed Central

Ando, Hiroki; Sugimoto, Norihiko; Takagi, Masahiro; Kashimura, Hiroki; Imamura, Takeshi; Matsuda, Yoshihisa

2016-01-01

Unlike the polar vortices observed in the Earth, Mars and Titan atmospheres, the observed Venus polar vortex is warmer than the midlatitudes at cloud-top levels (∼65 km). This warm polar vortex is zonally surrounded by a cold latitude band located at ∼60° latitude, which is a unique feature called ‘cold collar' in the Venus atmosphere. Although these structures have been observed in numerous previous observations, the formation mechanism is still unknown. Here we perform numerical simulations of the Venus atmospheric circulation using a general circulation model, and succeed in reproducing these puzzling features in close agreement with the observations. The cold collar and warm polar region are attributed to the residual mean meridional circulation enhanced by the thermal tide. The present results strongly suggest that the thermal tide is crucial for the structure of the Venus upper polar atmosphere at and above cloud levels. PMID:26832195

Unique Zigzag-Shaped Buckling Zn2C Monolayer with Strain-Tunable Band Gap and Negative Poisson Ratio.

PubMed

Meng, Lingbiao; Zhang, Yingjuan; Zhou, Minjie; Zhang, Jicheng; Zhou, Xiuwen; Ni, Shuang; Wu, Weidong

2018-02-19

Designing new materials with reduced dimensionality and distinguished properties has continuously attracted intense interest for materials innovation. Here we report a novel two-dimensional (2D) Zn 2 C monolayer nanomaterial with exceptional structure and properties by means of first-principles calculations. This new Zn 2 C monolayer is composed of quasi-tetrahedral tetracoordinate carbon and quasi-linear bicoordinate zinc, featuring a peculiar zigzag-shaped buckling configuration. The unique coordinate topology endows this natural 2D semiconducting monolayer with strongly strain tunable band gap and unusual negative Poisson ratios. The monolayer has good dynamic and thermal stabilities and is also the lowest-energy structure of 2D space indicated by the particle-swarm optimization (PSO) method, implying its synthetic feasibility. With these intriguing properties the material may find applications in nanoelectronics and micromechanics.

Facial Structure Predicts Sexual Orientation in Both Men and Women.

PubMed

Skorska, Malvina N; Geniole, Shawn N; Vrysen, Brandon M; McCormick, Cheryl M; Bogaert, Anthony F

2015-07-01

Biological models have typically framed sexual orientation in terms of effects of variation in fetal androgen signaling on sexual differentiation, although other biological models exist. Despite marked sex differences in facial structure, the relationship between sexual orientation and facial structure is understudied. A total of 52 lesbian women, 134 heterosexual women, 77 gay men, and 127 heterosexual men were recruited at a Canadian campus and various Canadian Pride and sexuality events. We found that facial structure differed depending on sexual orientation; substantial variation in sexual orientation was predicted using facial metrics computed by a facial modelling program from photographs of White faces. At the univariate level, lesbian and heterosexual women differed in 17 facial features (out of 63) and four were unique multivariate predictors in logistic regression. Gay and heterosexual men differed in 11 facial features at the univariate level, of which three were unique multivariate predictors. Some, but not all, of the facial metrics differed between the sexes. Lesbian women had noses that were more turned up (also more turned up in heterosexual men), mouths that were more puckered, smaller foreheads, and marginally more masculine face shapes (also in heterosexual men) than heterosexual women. Gay men had more convex cheeks, shorter noses (also in heterosexual women), and foreheads that were more tilted back relative to heterosexual men. Principal components analysis and discriminant functions analysis generally corroborated these results. The mechanisms underlying variation in craniofacial structure--both related and unrelated to sexual differentiation--may thus be important in understanding the development of sexual orientation.

The new applications of sputtering and ion plating

NASA Technical Reports Server (NTRS)

Spalvins, T.

1977-01-01

The potential industrial applications of sputtering and ion plating are strictly governed by the unique features these methods possess. The outstanding features of each method, the resultant coating characteristics and the various sputtering modes and configurations are discussed. New, more complex coatings and deposits can be developed such as graded composition structures (metal-ceramic seals), laminated and dispersion strengthened composites which improve the mechanical properties and high temperature stability. Specific industrial areas where future effort of sputtering and ion plating will concentrate to develop intricate alloy or compound coatings and solve difficult problem areas are discussed.

Placenta and Placental Derivatives in Regenerative Therapies: Experimental Studies, History, and Prospects

PubMed Central

Prokopyuk, Volodymyr; Pogozhykh, Denys

2018-01-01

Placental structures, capable to persist in a genetically foreign organism, are a natural model of allogeneic engraftment carrying a number of distinctive properties. In this review, the main features of the placenta and its derivatives such as structure, cellular composition, immunological and endocrine aspects, and the ability to invasion and deportation are discussed. These features are considered from a perspective that determines the placental material as a unique source for regenerative cell therapies and a lesson for immunological tolerance. A historical overview of clinical applications of placental extracts, cells, and tissue components is described. Empirically accumulated data are summarized and compared with modern research. Furthermore, we define scopes and outlooks of application of placental cells and tissues in the rapidly progressing field of regenerative medicine. PMID:29535770

Distribution and Features of the Six Classes of Peroxiredoxins

PubMed Central

Poole, Leslie B.; Nelson, Kimberly J.

2016-01-01

Peroxiredoxins are cysteine-dependent peroxide reductases that group into 6 different, structurally discernable classes. In 2011, our research team reported the application of a bioinformatic approach called active site profiling to extract active site-proximal sequence segments from the 29 distinct, structurally-characterized peroxiredoxins available at the time. These extracted sequences were then used to create unique profiles for the six groups which were subsequently used to search GenBank(nr), allowing identification of ∼3500 peroxiredoxin sequences and their respective subgroups. Summarized in this minireview are the features and phylogenetic distributions of each of these peroxiredoxin subgroups; an example is also provided illustrating the use of the web accessible, searchable database known as PREX to identify subfamily-specific peroxiredoxin sequences for the organism Vitis vinifera (grape). PMID:26810075

Ultrasonic Fingerprinting of Structural Materials: Spent Nuclear Fuel Containers Case-Study

NASA Astrophysics Data System (ADS)

Sednev, D.; Lider, A.; Demyanuk, D.; Kroening, M.; Salchak, Y.

Nowadays, NDT is mainly focused on safety purposes, but it seems possible to apply those methods to provide national and IAEA safeguards. The containment of spent fuel in storage casks could be dramatically improved in case of development of so-called "smart" spent fuel storage and transfer casks. Such casks would have tamper indicating and monitoring/tracking features integrated directly into the cask design. The microstructure of the containers material as well as of the dedicated weld seam is applied to the lid and the cask body and provides a unique fingerprint of the full container, which can be reproducibly scanned by using an appropriate technique. The echo-sounder technique, which is the most commonly used method for material inspection, was chosen for this project. The main measuring parameter is acoustic noise, reflected from material's artefacts. The purpose is to obtain structural fingerprinting. Reference measurement and additional measurement results were compared. Obtained results have verified the appliance of structural fingerprint and the chosen control method. The successful authentication demonstrates the levels of the feature points' compliance exceeding the given threshold which differs considerably from the percentage of the concurrent points during authentication from other points. Since reproduction or doubling of the proposed unique identification characteristics is impossible at the current state science and technology, application of this technique is considered to identify the interference into the nuclear materials displacement with high accuracy.

Band Structure Engineering and Thermoelectric Properties of Charge-Compensated Filled Skutterudites

PubMed Central

Shi, Xiaoya; Yang, Jiong; Wu, Lijun; Salvador, James R.; Zhang, Cheng; Villaire, William L.; Haddad, Daad; Yang, Jihui; Zhu, Yimei; Li, Qiang

2015-01-01

Thermoelectric properties of semiconductors are intimately related to their electronic band structure, which can be engineered via chemical doping. Dopant Ga in the cage-structured skutterudite Co4Sb12 substitutes Sb sites while occupying the void sites. Combining quantitative scanning transmission electron microscopy and first-principles calculations, we show that Ga dual-site occupancy breaks the symmetry of the Sb-Sb network, splits the deep triply-degenerate conduction bands, and drives them downward to the band edge. The charge-compensating nature of the dual occupancy Ga increases overall filling fraction limit. By imparting this unique band structure feature, and judiciously doping the materials by increasing the Yb content, we promote the Fermi level to a point where carriers are in energetic proximity to these features. Increased participation of these heavier bands in electronic transport leads to increased thermopower and effective mass. Further, the localized distortion from Ga/Sb substitution enhances the phonon scattering to reduce the thermal conductivity effectively. PMID:26456013

Band structure engineering and thermoelectric properties of charge-compensated filled skutterudites

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

Shi, Xiaoya; Yang, Jiong; Wu, Lijun

2015-10-12

Thermoelectric properties of semiconductors are intimately related to their electronic band structure, which can be engineered via chemical doping. Dopant Ga in the cage-structured skutterudite Co 4Sb 12 substitutes Sb sites while occupying the void sites. Combining quantitative scanning transmission electron microscopy and first-principles calculations, we show that Ga dual-site occupancy breaks the symmetry of the Sb-Sb network, splits the deep triply-degenerate conduction bands, and drives them downward to the band edge. The charge-compensating nature of the dual occupancy Ga increases overall filling fraction limit. By imparting this unique band structure feature, and judiciously doping the materials by increasing themore » Yb content, we promote the Fermi level to a point where carriers are in energetic proximity to these features. Increased participation of these heavier bands in electronic transport leads to increased thermopower and effective mass. Further, the localized distortion from Ga/Sb substitution enhances the phonon scattering to reduce the thermal conductivity effectively.« less

Band Structure Engineering and Thermoelectric Properties of Charge-Compensated Filled Skutterudites

NASA Astrophysics Data System (ADS)

Shi, Xiaoya; Yang, Jiong; Wu, Lijun; Salvador, James R.; Zhang, Cheng; Villaire, William L.; Haddad, Daad; Yang, Jihui; Zhu, Yimei; Li, Qiang

2015-10-01

Thermoelectric properties of semiconductors are intimately related to their electronic band structure, which can be engineered via chemical doping. Dopant Ga in the cage-structured skutterudite Co4Sb12 substitutes Sb sites while occupying the void sites. Combining quantitative scanning transmission electron microscopy and first-principles calculations, we show that Ga dual-site occupancy breaks the symmetry of the Sb-Sb network, splits the deep triply-degenerate conduction bands, and drives them downward to the band edge. The charge-compensating nature of the dual occupancy Ga increases overall filling fraction limit. By imparting this unique band structure feature, and judiciously doping the materials by increasing the Yb content, we promote the Fermi level to a point where carriers are in energetic proximity to these features. Increased participation of these heavier bands in electronic transport leads to increased thermopower and effective mass. Further, the localized distortion from Ga/Sb substitution enhances the phonon scattering to reduce the thermal conductivity effectively.

Distributed cable sensors with memory feature for post-disaster damage assessment

NASA Astrophysics Data System (ADS)

Chen, Genda; McDaniel, Ryan D.; Pommerenke, David J.; Sun, Shishuang

2005-05-01

A new design of distributed crack sensors is presented for the condition assessment of reinforced concrete (RC) structures during and immediately after an earthquake event. This study is mainly focused on the performance of cable sensors under dynamic loading, particularly their ability to memorize the crack history of an RC member. This unique memory feature enables the post-earthquake condition assessment of structural members such as RC columns, in which the earthquake-induced cracks are closed immediately after an earthquake event due to gravity loads and they are visually undetectable. Factors affecting the onset of the memory feature were investigated experimentally with small-scale RC beams under cyclic loading. Test results indicated that both crack width and the number of loading cycles were instrumental in the onset of the memory feature of cable sensors. Practical issues related to dynamic acquisition with the sensors were discussed. The sensors were proven to be fatigue resistant from the shake table tests of RC columns. They continued to show useful signal after the columns can no longer support additional loads.

Where and what is the paralaminar nucleus? A review on a unique and frequently overlooked area of the primate amygdala

PubMed Central

deCampo, Danielle; Fudge, Julie

2011-01-01

The primate amygdala is composed of multiple subnuclei that play distinct roles in amygdala function. While some nuclei have been areas of focused investigation, others remain virtually unknown. One of the more obscure regions of the amygdala is the paralaminar nucleus (PL). The PL in humans and non-human primates is relatively expanded compared to lower species. Long considered to be part of the basal nucleus, the PL has several interesting features that make it unique. These features include a dense concentration of small cells, high concentrations of receptors for corticotropin releasing hormone and benzodiazepines, and dense innervation of serotonergic fibers. More recently, high concentrations of immature-appearing cells have been noted in the primate PL, suggesting special mechanisms of neural plasticity. Following a brief overview of amygdala structure and function, this review will provide an introduction to the history, embryology, anatomical connectivity, immunohistochemical and cytoarchitectural properties of the PL. Our conclusion based on the following information, is that the PL is a unique subregion of the amygdala that may yield important clues about the normal growth and function of the amygdala, particularly in higher species. PMID:21906624

Molecular Biology of Archaebacteria

DTIC Science & Technology

1988-03-31

Biology of Archaebacteria i2 PERSONAL AUTHOR(S) Patrick P. Dennis 13a. TYPE OF REPORT 13b- TIME COVERED 114. DATE OF REPORT (Year, Month, Day) 15. PAGE...elucidate at the molecular level some of the features that make archaebacteria unique and distinguish them from eubacteria and eucaryotes. Three types...of genes, encoding rRNAs, ribosomal proteins and superoxide dismutase are phylogenetically conserved in all three kingdoms . The structure, organization

Synthesis of the C(18) -norditerpenoid alkaloid neofinaconitine: a lesson in convergent synthesis planning.

PubMed

Liu, Xiao-Yu; Chen, David Y-K

2014-01-20

Hexacyclic framework: The total synthesis of the complex C18 -norditerpenoid alkaloid neofinaconitine has been achieved by a convergent approach. This remarkable synthesis featured two Diels-Alder cycloadditions and subsequent Mannich-type N-acyliminium and radical cyclizations to establish the unique hexacyclic core structure of the target molecule. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Coherent perfect rotation theory: connections with, and consequences beyond, the anti-laser

NASA Astrophysics Data System (ADS)

Crescimanno, Michael; Andrews, James; Zhou, Chuanhong; Baker, Michael

2014-05-01

Coherent Perfect Rotation (CPR) phenomena are a reversible generalization of the anti-laser. By evaluating CPR in a broad variety of common optical systems, including optical cavities and DFB and DBR structures, we illustrate its unique threshold and resonance features. This study builds intuition critical to assessing the utility of CPR in optical devices, and we detail it in a concrete application.

A Pencil Rescues Impaired Performance on a Visual Discrimination Task in Patients with Medial Temporal Lobe Lesions

ERIC Educational Resources Information Center

Knutson, Ashley R.; Hopkins, Ramona O.; Squire, Larry R.

2013-01-01

We tested proposals that medial temporal lobe (MTL) structures support not just memory but certain kinds of visual perception as well. Patients with hippocampal lesions or larger MTL lesions attempted to identify the unique object among twin pairs of objects that had a high degree of feature overlap. Patients were markedly impaired under the more…

A review on the synthesis, crystal growth, structure and physical properties of rare earth based quaternary intermetallic compounds

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

Mumbaraddi, Dundappa; Sarkar, Sumanta; Peter, Sebastian C., E-mail: sebastiancp@jncasr.ac.in

2016-04-15

This review highlights the synthesis and crystal growth of quaternary intermetallic compounds based on rare earth metals. In the first part of this review, we highlight briefly about intermetallics and their versatile properties in comparison to the constituent elements. In the next part, we have discussed about various synthesis techniques with more focus on the metal flux technique towards the well shaped crystal growth of novel compounds. In the subsequent parts, several disordered quaternary compounds have been reviewed and then outlined most known ordered quaternary compounds with their complex structure. A special attention has been given to the ordered compoundsmore » with structural description and relation to the parent binary and ternary compounds. The importance of electronic and structural feature is highlighted as the key roles in designing these materials for emerging applications. - Graphical abstract: Rare earth based quaternary intermetallic compounds crystallize in complex novel crystal structures. The diversity in the crystal structure may induce unique properties and can be considered them as future materials. - Highlights: • Crystal growth and crystal structure of quaternary rare earth based intermetallics. • Structural complexity of quaternary compounds in comparison to the parent compounds. • Novel quaternary compounds display unique crystal structure.« less

Distinct Morphology of Human T-Cell Leukemia Virus Type 1-Like Particles

PubMed Central

Maldonado, José O.; Cao, Sheng; Zhang, Wei; Mansky, Louis M.

2016-01-01

The Gag polyprotein is the main retroviral structural protein and is essential for the assembly and release of virus particles. In this study, we have analyzed the morphology and Gag stoichiometry of human T-cell leukemia virus type 1 (HTLV-1)-like particles and authentic, mature HTLV-1 particles by using cryogenic transmission electron microscopy (cryo-TEM) and scanning transmission electron microscopy (STEM). HTLV-1-like particles mimicked the morphology of immature authentic HTLV-1 virions. Importantly, we have observed for the first time that the morphology of these virus-like particles (VLPs) has the unique local feature of a flat Gag lattice that does not follow the curvature of the viral membrane, resulting in an enlarged distance between the Gag lattice and the viral membrane. Other morphological features that have been previously observed with other retroviruses include: (1) a Gag lattice with multiple discontinuities; (2) membrane regions associated with the Gag lattice that exhibited a string of bead-like densities at the inner leaflet; and (3) an arrangement of the Gag lattice resembling a railroad track. Measurement of the average size and mass of VLPs and authentic HTLV-1 particles suggested a consistent range of size and Gag copy numbers in these two groups of particles. The unique local flat Gag lattice morphological feature observed suggests that HTLV-1 Gag could be arranged in a lattice structure that is distinct from that of other retroviruses characterized to date. PMID:27187442

Co-Conserved MAPK Features Couple D-Domain Docking Groove to Distal Allosteric Sites via the C-Terminal Flanking Tail

PubMed Central

Nguyen, Tuan; Ruan, Zheng; Oruganty, Krishnadev; Kannan, Natarajan

2015-01-01

Mitogen activated protein kinases (MAPKs) form a closely related family of kinases that control critical pathways associated with cell growth and survival. Although MAPKs have been extensively characterized at the biochemical, cellular, and structural level, an integrated evolutionary understanding of how MAPKs differ from other closely related protein kinases is currently lacking. Here, we perform statistical sequence comparisons of MAPKs and related protein kinases to identify sequence and structural features associated with MAPK functional divergence. We show, for the first time, that virtually all MAPK-distinguishing sequence features, including an unappreciated short insert segment in the β4-β5 loop, physically couple distal functional sites in the kinase domain to the D-domain peptide docking groove via the C-terminal flanking tail (C-tail). The coupling mediated by MAPK-specific residues confers an allosteric regulatory mechanism unique to MAPKs. In particular, the regulatory αC-helix conformation is controlled by a MAPK-conserved salt bridge interaction between an arginine in the αC-helix and an acidic residue in the C-tail. The salt-bridge interaction is modulated in unique ways in individual sub-families to achieve regulatory specificity. Our study is consistent with a model in which the C-tail co-evolved with the D-domain docking site to allosterically control MAPK activity. Our study provides testable mechanistic hypotheses for biochemical characterization of MAPK-conserved residues and new avenues for the design of allosteric MAPK inhibitors. PMID:25799139

Raman Spectral Signatures as Conformational Probes of Biomolecules

NASA Astrophysics Data System (ADS)

Golan, Amir; Mayorkas, Nitzan; Rosenwaks, Salman; Bar, Ilana

2009-06-01

A first application of ionization-loss stimulated Raman spectroscopy (ILSRS) for monitoring the spectral features of four conformers of a gas phase neurotransmitter (2-phenylethylamine) is reported. The Raman spectra of the conformers show bands that uniquely identify the conformational structure of the molecule and are well matched by density functional theory calculations. The measurement of spectral signatures by ILSRS in an extended spectral range, with a relatively convenient laser source, is extremely important, allowing enhanced accessibility to intra- and inter-molecular forces, which are significant in biological structure and activity.

Raman Spectral Signatures as Conformational Probes of Biomolecules

NASA Astrophysics Data System (ADS)

Bar, Ilana; Golan, Amir; Mayorkas, Nitzan; Rosenwaks, Salman

2009-03-01

A first application of ionization-loss stimulated Raman spectroscopy (ILSRS) monitoring the spectral features of four conformers of a gas phase neurotransmitter (2-phenylethylamine) is reported. The Raman spectra of the conformers show bands that uniquely identify the conformational structure of the molecule and are well matched by density functional theory calculations. The measurement of spectral signatures by ILSRS in an extended spectral range, with a relatively convenient laser source, is extremely important, allowing enhanced accessibility to intra- and inter-molecular forces, which are significant in biological structure and activity.

Raman spectral signatures as conformational probes of gas phase flexible molecules

NASA Astrophysics Data System (ADS)

Golan, Amir; Mayorkas, Nitzan; Rosenwaks, Salman; Bar, Ilana

2009-07-01

A novel application of ionization-loss stimulated Raman spectroscopy (ILSRS) for monitoring the spectral features of four conformers of a gas phase flexible molecule is reported. The Raman spectral signatures of four conformers of 2-phenylethylamine are well matched by the results of density functional theory calculations, showing bands uniquely identifying the structures. The measurement of spectral signatures by ILSRS in an extended spectral range, with a conventional laser source, is instrumental in facilitating the unraveling of intra- and intermolecular interactions that are significant in biological structure and activity.

Synthesis, Crystal Structures and Properties of Ferrocenyl Bis-Amide Derivatives Yielded via the Ugi Four-Component Reaction.

PubMed

Zhao, Mei; Shao, Guang-Kui; Huang, Dan-Dan; Lv, Xue-Xin; Guo, Dian-Shun

2017-05-04

Ten ferrocenyl bis-amide derivatives were successfully synthesized via the Ugi four-component reaction by treating ferrocenecarboxylic acid with diverse aldehydes, amines, and isocyanides in methanol solution. Their chemical structures were fully characterized by IR, NMR, HR-MS, and X-ray diffraction analyses. They feature unique molecular morphologies and create a 14-membered ring motif in the centro-symmetric dimers generated in the solid state. Moreover, the electrochemical behavior of these ferrocenyl bis-amides was assessed by cyclic voltammetry.

Bonding thermoplastic polymers

DOEpatents

Wallow, Thomas I [Fremont, CA; Hunter, Marion C [Livermore, CA; Krafcik, Karen Lee [Livermore, CA; Morales, Alfredo M [Livermore, CA; Simmons, Blake A [San Francisco, CA; Domeier, Linda A [Danville, CA

2008-06-24

We demonstrate a new method for joining patterned thermoplastic parts into layered structures. The method takes advantage of case-II permeant diffusion to generate dimensionally controlled, activated bonding layers at the surfaces being joined. It is capable of producing bonds characterized by cohesive failure while preserving the fidelity of patterned features in the bonding surfaces. This approach is uniquely suited to production of microfluidic multilayer structures, as it allows the bond-forming interface between plastic parts to be precisely manipulated at micrometer length scales. The bond enhancing procedure is easily integrated in standard process flows and requires no specialized equipment.

Carbonate Biogenic Structures in Storrs Lake, Bahamas

NASA Technical Reports Server (NTRS)

Byrne, Monica; Morris, Penny A.; Wentworth, Susan J.; Brigmon, Robin L.; McKay, David S.

2001-01-01

Storr's Lake, an inland hypersaline lake on San Salvador Island, Bahamas, contains calcium carbonate-rich lithified mats of filamentous microorganisms, diatoms, associated photosynthetic and chemotrophic bacteria, and trapped sediment. In addition, 16S rRNA analysis indicates the presence of five sulfur-reducing genera of bacteria. These microbes are potential modern-day analogs to some ancient stromatolitic structures. The goals of this study are to identify unique compositional and biogenic features, possibly correlating some of these with some of the sulfate-reducing bacteria. Additional information is contained in the original extended abstract.

The microscopic anatomy of the esophagus including the individual layers, specialized tissues, and unique components and their responses to injury.

PubMed

Zhang, Xuchen; Patil, Deepa; Odze, Robert D; Zhao, Lei; Lisovsky, Mikhail; Guindi, Maha; Riddell, Robert; Bellizzi, Andrew; Yantiss, Rhonda K; Nalbantoglu, Ilke; Appelman, Henry D

2018-05-15

The esophagus, a straight tube that connects the pharynx to the stomach, has the complex architecture common to the rest of the gastrointestinal tract with special differences that relate to its function as a conduit of ingested substances. For instance, it has submucosal glands that are unique and have a specific protective function. It has a squamous lining that exists nowhere else in the gut except the anus and it has a different submucosal nerve plexus when compared to the stomach and intestines. All of the layers of the esophageal wall and the specialized structures including blood and lymphatic vessels and nerves have specific responses to injury. The esophagus also has unique features such as patches of gastric mucosa called inlet patches at the very proximal part and it has a special sphincter mechanism at the most distal aspect. This review covers the normal microscopic anatomy of the esophagus and the patterns of reaction to stress and injury of each layer and each special structure. © 2018 New York Academy of Sciences.

Citation Sentiment Analysis in Clinical Trial Papers

PubMed Central

Xu, Jun; Zhang, Yaoyun; Wu, Yonghui; Wang, Jingqi; Dong, Xiao; Xu, Hua

2015-01-01

In scientific writing, positive credits and negative criticisms can often be seen in the text mentioning the cited papers, providing useful information about whether a study can be reproduced or not. In this study, we focus on citation sentiment analysis, which aims to determine the sentiment polarity that the citation context carries towards the cited paper. A citation sentiment corpus was annotated first on clinical trial papers. The effectiveness of n-gram and sentiment lexicon features, and problem-specified structure features for citation sentiment analysis were then examined using the annotated corpus. The combined features from the word n-grams, the sentiment lexicons and the structure information achieved the highest Micro F-score of 0.860 and Macro-F score of 0.719, indicating that it is feasible to use machine learning methods for citation sentiment analysis in biomedical publications. A comprehensive comparison between citation sentiment analysis of clinical trial papers and other general domains were conducted, which additionally highlights the unique challenges within this domain. PMID:26958274

Structure of Radical-Induced Cell Death1 Hub Domain Reveals a Common αα-Scaffold for Disorder in Transcriptional Networks.

PubMed

Bugge, Katrine; Staby, Lasse; Kemplen, Katherine R; O'Shea, Charlotte; Bendsen, Sidsel K; Jensen, Mikael K; Olsen, Johan G; Skriver, Karen; Kragelund, Birthe B

2018-05-01

Communication within cells relies on a few protein nodes called hubs, which organize vast interactomes with many partners. Frequently, hub proteins are intrinsically disordered conferring multi-specificity and dynamic communication. Conversely, folded hub proteins may organize networks using disordered partners. In this work, the structure of the RST domain, a unique folded hub, is solved by nuclear magnetic resonance spectroscopy and small-angle X-ray scattering, and its complex with a region of the transcription factor DREB2A is provided through data-driven HADDOCK modeling and mutagenesis analysis. The RST fold is unique, but similar structures are identified in the PAH (paired amphipathic helix), TAFH (TATA-box-associated factor homology), and NCBD (nuclear coactivator binding domain) domains. We designate them as a group the αα hubs, as they share an αα-hairpin super-secondary motif, which serves as an organizing platform for malleable helices of varying topology. This allows for partner adaptation, exclusion, and selection. Our findings provide valuable insights into structural features enabling signaling fidelity. Copyright © 2018 Elsevier Ltd. All rights reserved.

Bowl Inversion and Electronic Switching of Buckybowls on Gold.

PubMed

Fujii, Shintaro; Ziatdinov, Maxim; Higashibayashi, Shuhei; Sakurai, Hidehiro; Kiguchi, Manabu

2016-09-21

Bowl-shaped π-conjugated compounds, or buckybowls, are a novel class of sp(2)-hybridized nanocarbon materials. In contrast to tubular carbon nanotubes and ball-shaped fullerenes, the buckybowls feature structural flexibility. Bowl-to-bowl structural inversion is one of the unique properties of the buckybowls in solutions. Bowl inversion on a surface modifies the metal-molecule interactions through bistable switching between bowl-up and bowl-down states on the surface, which makes surface-adsorbed buckybowls a relevant model system for elucidation of the mechano-electronic properties of nanocarbon materials. Here, we report a combination of scanning tunneling microscopy (STM) measurements and ab initio atomistic simulations to identify the adlayer structure of the sumanene buckybowl on Au(111) and reveal its unique bowl inversion behavior. We demonstrate that the bowl inversion can be induced by approaching the STM tip toward the molecule. By tuning the local metal-molecule interaction using the STM tip, the sumanene buckybowl exhibits structural bistability with a switching rate that is two orders of magnitude faster than that of the stochastic inversion process.

Crystal Structure of Cockroach Allergen Bla g 2, an Unusual Zinc Binding Aspartic Protease with a Novel Mode of Self-inhibition

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

Gustchina, Alla; Li, Mi; Wunschmann, Sabina

2010-07-19

The crystal structure of Bla g 2 was solved in order to investigate the structural basis for the allergenic properties of this unusual protein. This is the first structure of an aspartic protease in which conserved glycine residues, in two canonical DTG triads, are substituted by different amino acid residues. Another unprecedented feature revealed by the structure is the single phenylalanine residue insertion on the tip of the flap, with the side-chain occupying the S1 binding pocket. This and other important amino acid substitutions in the active site region of Bla g 2 modify the interactions in the vicinity ofmore » the catalytic aspartate residues, increasing the distance between them to {approx}4 {angstrom} and establishing unique direct contacts between the flap and the catalytic residues. We attribute the absence of substantial catalytic activity in Bla g 2 to these unusual features of the active site. Five disulfide bridges and a Zn-binding site confer stability to the protein, which may contribute to sensitization at lower levels of exposure than other allergens.« less

Systems-Level Annotation of a Metabolomics Data Set Reduces 25 000 Features to Fewer than 1000 Unique Metabolites.

PubMed

Mahieu, Nathaniel G; Patti, Gary J

2017-10-03

When using liquid chromatography/mass spectrometry (LC/MS) to perform untargeted metabolomics, it is now routine to detect tens of thousands of features from biological samples. Poor understanding of the data, however, has complicated interpretation and masked the number of unique metabolites actually being measured in an experiment. Here we place an upper bound on the number of unique metabolites detected in Escherichia coli samples analyzed with one untargeted metabolomics method. We first group multiple features arising from the same analyte, which we call "degenerate features", using a context-driven annotation approach. Surprisingly, this analysis revealed thousands of previously unreported degeneracies that reduced the number of unique analytes to ∼2961. We then applied an orthogonal approach to remove nonbiological features from the data using the 13 C-based credentialing technology. This further reduced the number of unique analytes to less than 1000. Our 90% reduction in data is 5-fold greater than previously published studies. On the basis of the results, we propose an alternative approach to untargeted metabolomics that relies on thoroughly annotated reference data sets. To this end, we introduce the creDBle database ( http://creDBle.wustl.edu ), which contains accurate mass, retention time, and MS/MS fragmentation data as well as annotations of all credentialed features.

A hydrodynamic microchip for formation of continuous cell chains

NASA Astrophysics Data System (ADS)

Khoshmanesh, Khashayar; Zhang, Wei; Tang, Shi-Yang; Nasabi, Mahyar; Soffe, Rebecca; Tovar-Lopez, Francisco J.; Rajadas, Jayakumar; Mitchell, Arnan

2014-05-01

Here, we demonstrate the unique features of a hydrodynamic based microchip for creating continuous chains of model yeast cells. The system consists of a disk shaped microfluidic structure, containing narrow orifices that connect the main channel to an array of spoke channels. Negative pressure provided by a syringe pump draws fluid from the main channel through the narrow orifices. After cleaning process, a thin layer of water is left between the glass substrate and the polydimethylsiloxane microchip, enabling leakage beneath the channel walls. A mechanical clamp is used to adjust the operation of the microchip. Relaxing the clamp allows leakage of liquid beneath the walls in a controllable fashion, leading to formation of a long cell chain evenly distributed along the channel wall. The unique features of the microchip are demonstrated by creating long chains of yeast cells and model 15 μm polystyrene particles along the side wall and analysing the hydrogen peroxide induced death of patterned cells.

Micro- and nanofluidic systems in devices for biological, medical and environmental research

NASA Astrophysics Data System (ADS)

Evstrapov, A. A.

2017-11-01

The use of micro- and nanofluidic systems in modern analytical instruments allow you to implement a number of unique opportunities and achieve ultra-high measurement sensitivity. The possibility of manipulation of the individual biological objects (cells, bacteria, viruses, proteins, nucleic acids) in a liquid medium caused the development of devices on microchip platform for methods: chromatographic and electrophoretic analyzes; polymerase chain reaction; sequencing of nucleic acids; immunoassay; cytometric studies. Development of micro and nano fabrication technologies, materials science, surface chemistry, analytical chemistry, cell engineering have led to the creation of a unique systems such as “lab-on-a-chip”, “human-on-a-chip” and other. This article discusses common in microfluidics materials and methods of making functional structures. Examples of integration of nanoscale structures in microfluidic devices for the implementation of new features and improve the technical characteristics of devices and systems are shown.

O2 reduction to H2O by the multicopper oxidases.

PubMed

Solomon, Edward I; Augustine, Anthony J; Yoon, Jungjoo

2008-08-14

In nature the four electron reduction of O2 to H2O is carried out by Cytochrome c oxidase (CcO) and the multicopper oxidases (MCOs). In the former, Cytochrome c provides electrons for pumping protons to produce a gradient for ATP synthesis, while in the MCOs the function is the oxidation of substrates, either organic or metal ions. In the MCOs the reduction of O2 is carried out at a trinuclear Cu cluster (TNC). Oxygen intermediates have been trapped which exhibit unique spectroscopic features that reflect novel geometric and electronic structures. These intermediates have both intact and cleaved O-O bonds, allowing the reductive cleavage of the O-O bond to be studied in detail both experimentally and computationally. These studies show that the topology of the TNC provides a unique geometric and electronic structure particularly suited to carry out this key reaction in nature.

O2 Reduction to H2O by the Multicopper Oxidases

PubMed Central

Solomon, Edward I.; Augustine, Anthony J.; Yoon, Jungjoo

2010-01-01

In nature the four electron reduction of O2 to H2O is carried out by Cytochrome c Oxidase (CcO) and the multicopper oxidases (MCOs). In the former, Cytochrome c provides electrons for pumping protons to produce a gradient for ATP synthesis, while in the MCOs the function is the oxidation of substrates, either organic or metal ions. In the MCOs the reduction of O2 is carried out at a trinuclear Cu cluster (TNC). Oxygen intermediates have been trapped which exhibit unique spectroscopic features that reflect novel geometric and electronic structures. These intermediates have both intact and cleaved O-O bonds, allowing the reductive cleavage of the O-O bond to be studied in detail both experimentally and computationally. These studies show that the topology of the TNC provides a unique geometric and electronic structure particularly suited to carry out this key reaction in Nature. PMID:18648693

Combining unique properties of dendrimers and magnetic nanoparticles towards cancer theranostics.

PubMed

Chandra, Sudeshna; Nigam, Saumya; Bahadur, Dhirendra

2014-01-01

Magnetic nanoparticles (MNPs) are a well explored class of nanomaterials, known for their high magnetization and biocompatibility thus finding their way in several biomedical applications viz., drug delivery, magnetic resonance imaging contrast agent, immunoassay, detoxification of biological fluids and cell separation, biosensing and hyperthermia. On other hand, dendrimers are a class of hyperbranched, mostly symmetrical polymers that originate from a central core with repetitive branching units, called monomers, thus forming a globular structure. Due to their structural properties and controlled size, dendrimers have emerged as an attractive material for biomedical applications particularly as carriers for therapeutic cargo. Of late, researchers have started attempting to combine the unique features of dendrimer chemistry with the versatile magnetic nanoparticles to provide a facile platform for enhanced therapeutics and biomedical applications. This review intends to present the advances made towards fabrication of dendrimer based magnetic nanoparticles with varied surface architecture and their contribution towards theranostics, particularly for cancer.

The fast filling of nano-SnO2 in CNTs by vacuum absorption: a new approach to realize cyclic durable anodes for lithium ion batteries.

PubMed

Hu, Renzong; Sun, Wei; Liu, Hui; Zeng, Meiqin; Zhu, Min

2013-12-07

CNTs filled with amorphous-nanocrystalline SnO2, as a unique SnO2-based nanocomposite structure, were synthesized by a rapid vacuum absorption followed by calcination. The SnO2/CNT nanocomposite anodes had a much higher Li storage capacity than the pristine CNTs, as well as a markedly improved cyclic performance (430 mA h g(-1) after 300 cycles at 0.1 A g(-1)). These superior electrode properties resulted from the unique feature of the amorphous-nanocrystalline mixture of tin oxides stored in the CNT tubes of this nanocomposite, because this structure accommodated the stress and confined the volume change of Li(+) insertion/desertion in Sn. Although the nanocomposites had a large initial irreversible capacity loss due to SEI formation, it could be dramatically reduced by prelithiation treatment of the nanocomposite electrode.

In situ template synthesis of hollow nanospheres assembled from NiCo2S4@C ultrathin nanosheets with high electrochemical activities for lithium storage and ORR catalysis.

PubMed

Wu, Xiaoyu; Li, Songmei; Wang, Bo; Liu, Jianhua; Yu, Mei

2017-05-10

Transition-metal sulfide hollow nanostructures have received intensive attention in energy-related applications due to their unique structural features and high electrochemical activities. Here, a well-designed composite of NiCo 2 S 4 @C is successfully fabricated using a facile in situ template removal method. The obtained composite shows unique microstructures of hollow nanospheres (∼650 nm in diameter) assembled from ultrathin NiCo 2 S 4 @C nanosheets, in which numerous scattered NiCo 2 S 4 nanoparticles are embedded in ultrathin carbon nanosheets, exhibiting mesoporous features with a high surface area of 247.25 m 2 g -1 . When used as anode materials for LIBs, NiCo 2 S 4 @C hollow nanospheres exhibit a high reversible capacity of 1592 mA h g -1 at a current density of 500 mA g -1 , enhanced cycling performance maintaining a capacity of 1178 mA h g -1 after 200 cycles, and a remarkable rate capability. Meanwhile, the hollow nanospheres display excellent catalytic activity as ORR catalysts with a four-electron pathway and superior durability to that of commercial Pt/C catalysts. Their excellent lithium storage and ORR catalysis performance can be attributed to the rational incorporation of high-activity NiCo 2 S 4 and ultrathin carbon nanosheets, as well as unique hollow microstructures, which offer efficient electron/ion transport, an enhanced electroactive material/electrolyte contact area, numerous active sites, and excellent structural stability.

Structure and function of the hearts of lizards and snakes.

PubMed

Jensen, Bjarke; Moorman, Antoon F M; Wang, Tobias

2014-05-01

With approximately 7000 species, snakes and lizards, collectively known as squamates, are by far the most species-rich group of reptiles. It was from reptile-like ancestors that mammals and birds evolved and squamates can be viewed as phylogenetically positioned between them and fishes. Hence, their hearts have been studied for more than a century yielding insights into the group itself and into the independent evolution of the fully divided four-chambered hearts of mammals and birds. Structurally the heart is complex and debates persist on rudimentary issues such as identifying structures critical to understanding ventricle function. In seeking to resolve these controversies we have generated three-dimensional (3D) models in portable digital format (pdf) of the anaconda and anole lizard hearts ('typical' squamate hearts) and the uniquely specialized python heart with comprehensive annotations of structures and cavities. We review the anatomy and physiology of squamate hearts in general and emphasize the unique features of pythonid and varanid lizard hearts that endow them with mammal-like blood pressures. Excluding pythons and varanid lizards it is concluded that the squamate heart has a highly consistent design including a disproportionately large right side (systemic venous) probably due to prevailing pulmonary bypass (intraventricular shunting). Unfortunately, investigations on rudimentary features are sparse. We therefore point out gaps in our knowledge, such as the size and functional importance of the coronary vasculature and of the first cardiac chamber, the sinus venosus, and highlight areas with implications for vertebrate cardiac evolution. © 2013 The Authors. Biological Reviews © 2013 Cambridge Philosophical Society.

Structure–property characterization of the crinkle-leaf peach wood phenotype: a future model system for wood properties research?

Treesearch

Alex C. Wiedenhoeft; Rafael Arévalo; Craig Ledbetter; Joseph E. Jakes

2016-01-01

Nearly 400 million years of evolution and field-testing by the natural world has given humans thousands of wood types, each with unique structure– property relationships to study, exploit, and ideally, to manipulate, but the slow growth of trees makes them a recalcitrant experimental system. Variations in wood features of two genotypes of peach (Prunus persica L.)...

[Buying and distribution of drugs: perceptions of officers of a network of primary health care in the interior of the state of Sao Paulo].

PubMed

Juliani, C M

1995-12-01

The study present analyse the process to buy and distribution of medicaments for the Basic Unit of Health in municipal district of state São Paulo. To achieve some general considerations about the National Politic of Medicaments in Brazil, to emphasize feature relative the its structuration in the Unique System of Health.

Aging Differences in Ethnic Skin

PubMed Central

Buainain De Castro Maymone, Mayra; Kundu, Roopal V.

2016-01-01

Aging is an inevitable and complex process that can be described clinically as features of wrinkles, sunspots, uneven skin color, and sagging skin. These cutaneous effects are influenced by both intrinsic and extrinsic factors and often are varied based on ethnic origin given underlying structural and functional differences. The authors sought to provide updated information on facets of aging and how it relates to ethnic variation given innate differences in skin structure and function. Publications describing structural and functional principles of ethnic and aging skin were primarily found through a PubMed literature search and supplemented with a review of textbook chapters. The most common signs of skin aging despite skin type are dark spots, loss of elasticity, loss of volume, and rhytides. Skin of color has many characteristics that make its aging process unique. Those of Asian, Hispanic, and African American descent have distinct facial structures. Differences in the concentration of epidermal melanin makes darkly pigmented persons more vulnerable to dyspigmentation, while a thicker and more compact dermis makes facial lines less noticeable. Ethnic skin comprises a large portion of the world population. Therefore, it is important to understand the unique structural and functional differences among ethnicities to adequately treat the signs of aging. PMID:26962390

Texture analysis of radiometric signatures of new sea ice forming in Arctic leads

NASA Technical Reports Server (NTRS)

Eppler, Duane T.; Farmer, L. Dennis

1991-01-01

Analysis of 33.6-GHz, high-resolution, passive microwave images suggests that new sea ice accumulating in open leads is characterized by a unique textural signature which can be used to discriminate new ice forming in this environment from adjacent surfaces of similar radiometric temperature. Ten training areas were selected from the data set, three of which consisted entirely of first-year ice, four entirely of multilayer ice, and three of new ice in open leads in the process of freezing. A simple gradient operator was used to characterize the radiometric texture in each training region in terms of the degree to which radiometric gradients are oriented. New ice in leads has a sufficiently high proportion of well-oriented features to distinguish it uniquely from first-year ice and multiyear ice. The predominance of well-oriented features probably reflects physical processes by which new ice accumulates in open leads. Banded structures, which are evident in aerial photographs of new ice, apparently give rise to the radiometric signature observed, in which the trend of brightness temperature gradients is aligned parallel to lead trends. First-year ice and multiyear ice, which have been subjected to a more random growth and process history, lack this banded structure and therefore are characterized by signatures in which well-aligned elements are less dominant.

A discrete polar Stockwell transform for enhanced characterization of tissue structure using MRI.

PubMed

Pridham, Glen; Steenwijk, Martijn D; Geurts, Jeroen J G; Zhang, Yunyan

2018-05-02

The purpose of this study was to present an effective algorithm for computing the discrete polar Stockwell transform (PST), investigate its unique multiscale and multi-orientation features, and explore potentially new applications including denoising and tissue segmentation. We investigated PST responses using both synthetic and MR images. Moreover, we compared the features of PST with both Gabor and Morlet wavelet transforms, and compared the PST with two wavelet approaches for denoising using MRI. Using a synthetic image, we also tested the edge effect of PST through signal-padding. Then, we constructed a partially supervised classifier using radial, marginal PST spectra of T2-weighted MRI, acquired from postmortem brains with multiple sclerosis. The classification involved three histology-verified tissue types: normal appearing white matter (NAWM), lesion, or other, along with 5-fold cross-validation. The PST generated a series of images with varying orientations or rotation-invariant scales. Radial frequencies highlighted image structures of different size, and angular frequencies enhanced structures by orientation. Signal-padding helped suppress boundary artifacts but required attention to incidental artifacts. In comparison, the Gabor transform produced more redundant images and the wavelet spectra appeared less spatially smooth than the PST. In addition, the PST demonstrated lower root-mean-square errors than other transforms in denoising and achieved a 93% accuracy for NAWM pixels (296/317), and 88% accuracy for lesion pixels (165/188) in MRI segmentation. The PST is a unique local spectral density-assessing tool which is sensitive to both structure orientations and scales. This may facilitate multiple new applications including advanced characterization of tissue structure in standard MRI. © 2018 International Society for Magnetic Resonance in Medicine.

AiResearch QCGAT engine, airplane, and nacelle design features

NASA Technical Reports Server (NTRS)

Heldenbrand, R. W.

1980-01-01

The quiet, clean, general aviation turbofan engine and nacelle system was designed and tested. The engine utilized the core of the AiResearch model TFE731-3 engine and incorporated several unique noise- and emissions-reduction features. Components that were successfully adapted to this core include the fan, gearbox, combustor, low-pressure turbine, and associated structure. A highly versatile workhorse nacelle incorporating interchangeable acoustic and hardwall duct liners, showed that large-engine attenuation technology could be applied to small propulsion engines. The application of the mixer compound nozzle demonstrated both performance and noise advantages on the engine. Major performance, emissions, and noise goals were demonstrated.

A new ultrasonic real-time scanner featuring a servo-controlled transducer displaying a sector image.

PubMed

Skolnick, M L; Matzuk, T

1978-08-01

This paper describes a new real-time servo-controlled sector scanner that produces high-resolution images similar to phased-array systems, but possesses the simplicity of design and low cost best achievable in a mechanical sector scanner. Its unique feature is the transducer head which contains a single moving part--the transducer. Frame rates vary from 0 to 30 degrees and the sector angle from 0 to 60 degrees. Abdominal applications include: differentiation of vascular structures, detection of small masses, imaging of diagonally oriented organs. Survey scanning, and demonstration of regions difficult to image with contact scanners. Cardiac uses are also described.

Salvage of failed protein targets by reductive alkylation.

PubMed

Tan, Kemin; Kim, Youngchang; Hatzos-Skintges, Catherine; Chang, Changsoo; Cuff, Marianne; Chhor, Gekleng; Osipiuk, Jerzy; Michalska, Karolina; Nocek, Boguslaw; An, Hao; Babnigg, Gyorgy; Bigelow, Lance; Joachimiak, Grazyna; Li, Hui; Mack, Jamey; Makowska-Grzyska, Magdalena; Maltseva, Natalia; Mulligan, Rory; Tesar, Christine; Zhou, Min; Joachimiak, Andrzej

2014-01-01

The growth of diffraction-quality single crystals is of primary importance in protein X-ray crystallography. Chemical modification of proteins can alter their surface properties and crystallization behavior. The Midwest Center for Structural Genomics (MCSG) has previously reported how reductive methylation of lysine residues in proteins can improve crystallization of unique proteins that initially failed to produce diffraction-quality crystals. Recently, this approach has been expanded to include ethylation and isopropylation in the MCSG protein crystallization pipeline. Applying standard methods, 180 unique proteins were alkylated and screened using standard crystallization procedures. Crystal structures of 12 new proteins were determined, including the first ethylated and the first isopropylated protein structures. In a few cases, the structures of native and methylated or ethylated states were obtained and the impact of reductive alkylation of lysine residues was assessed. Reductive methylation tends to be more efficient and produces the most alkylated protein structures. Structures of methylated proteins typically have higher resolution limits. A number of well-ordered alkylated lysine residues have been identified, which make both intermolecular and intramolecular contacts. The previous report is updated and complemented with the following new data; a description of a detailed alkylation protocol with results, structural features, and roles of alkylated lysine residues in protein crystals. These contribute to improved crystallization properties of some proteins.

Salvage of Failed Protein Targets by Reductive Alkylation

PubMed Central

Tan, Kemin; Kim, Youngchang; Hatzos-Skintges, Catherine; Chang, Changsoo; Cuff, Marianne; Chhor, Gekleng; Osipiuk, Jerzy; Michalska, Karolina; Nocek, Boguslaw; An, Hao; Babnigg, Gyorgy; Bigelow, Lance; Joachimiak, Grazyna; Li, Hui; Mack, Jamey; Makowska-Grzyska, Magdalena; Maltseva, Natalia; Mulligan, Rory; Tesar, Christine; Zhou, Min; Joachimiak, Andrzej

2014-01-01

The growth of diffraction-quality single crystals is of primary importance in protein X-ray crystallography. Chemical modification of proteins can alter their surface properties and crystallization behavior. The Midwest Center for Structural Genomics (MCSG) has previously reported how reductive methylation of lysine residues in proteins can improve crystallization of unique proteins that initially failed to produce diffraction-quality crystals. Recently, this approach has been expanded to include ethylation and isopropylation in the MCSG protein crystallization pipeline. Applying standard methods, 180 unique proteins were alkylated and screened using standard crystallization procedures. Crystal structures of 12 new proteins were determined, including the first ethylated and the first isopropylated protein structures. In a few cases, the structures of native and methylated or ethylated states were obtained and the impact of reductive alkylation of lysine residues was assessed. Reductive methylation tends to be more efficient and produces the most alkylated protein structures. Structures of methylated proteins typically have higher resolution limits. A number of well-ordered alkylated lysine residues have been identified, which make both intermolecular and intramolecular contacts. The previous report is updated and complemented with the following new data; a description of a detailed alkylation protocol with results, structural features, and roles of alkylated lysine residues in protein crystals. These contribute to improved crystallization properties of some proteins. PMID:24590719

Multiscale Feature Analysis of Salivary Gland Branching Morphogenesis

PubMed Central

Baydil, Banu; Daley, William P.; Larsen, Melinda; Yener, Bülent

2012-01-01

Pattern formation in developing tissues involves dynamic spatio-temporal changes in cellular organization and subsequent evolution of functional adult structures. Branching morphogenesis is a developmental mechanism by which patterns are generated in many developing organs, which is controlled by underlying molecular pathways. Understanding the relationship between molecular signaling, cellular behavior and resulting morphological change requires quantification and categorization of the cellular behavior. In this study, tissue-level and cellular changes in developing salivary gland in response to disruption of ROCK-mediated signaling by are modeled by building cell-graphs to compute mathematical features capturing structural properties at multiple scales. These features were used to generate multiscale cell-graph signatures of untreated and ROCK signaling disrupted salivary gland organ explants. From confocal images of mouse submandibular salivary gland organ explants in which epithelial and mesenchymal nuclei were marked, a multiscale feature set capturing global structural properties, local structural properties, spectral, and morphological properties of the tissues was derived. Six feature selection algorithms and multiway modeling of the data was performed to identify distinct subsets of cell graph features that can uniquely classify and differentiate between different cell populations. Multiscale cell-graph analysis was most effective in classification of the tissue state. Cellular and tissue organization, as defined by a multiscale subset of cell-graph features, are both quantitatively distinct in epithelial and mesenchymal cell types both in the presence and absence of ROCK inhibitors. Whereas tensor analysis demonstrate that epithelial tissue was affected the most by inhibition of ROCK signaling, significant multiscale changes in mesenchymal tissue organization were identified with this analysis that were not identified in previous biological studies. We here show how to define and calculate a multiscale feature set as an effective computational approach to identify and quantify changes at multiple biological scales and to distinguish between different states in developing tissues. PMID:22403724

Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus

PubMed Central

Eyal, Zohar; Matzov, Donna; Krupkin, Miri; Wekselman, Itai; Paukner, Susanne; Zimmerman, Ella; Rozenberg, Haim; Bashan, Anat; Yonath, Ada

2015-01-01

The emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. Here we present the crystal structure of the large ribosomal subunit from Staphylococcus aureus, a versatile Gram-positive aggressive pathogen, and its complexes with the known antibiotics linezolid and telithromycin, as well as with a new, highly potent pleuromutilin derivative, BC-3205. These crystal structures shed light on specific structural motifs of the S. aureus ribosome and the binding modes of the aforementioned antibiotics. Moreover, by analyzing the ribosome structure and comparing it with those of nonpathogenic bacterial models, we identified some unique internal and peripheral structural motifs that may be potential candidates for improving known antibiotics and for use in the design of selective antibiotic drugs against S. aureus. PMID:26464510

A Sieving ANN for Emotion-Based Movie Clip Classification

NASA Astrophysics Data System (ADS)

Watanapa, Saowaluk C.; Thipakorn, Bundit; Charoenkitkarn, Nipon

Effective classification and analysis of semantic contents are very important for the content-based indexing and retrieval of video database. Our research attempts to classify movie clips into three groups of commonly elicited emotions, namely excitement, joy and sadness, based on a set of abstract-level semantic features extracted from the film sequence. In particular, these features consist of six visual and audio measures grounded on the artistic film theories. A unique sieving-structured neural network is proposed to be the classifying model due to its robustness. The performance of the proposed model is tested with 101 movie clips excerpted from 24 award-winning and well-known Hollywood feature films. The experimental result of 97.8% correct classification rate, measured against the collected human-judges, indicates the great potential of using abstract-level semantic features as an engineered tool for the application of video-content retrieval/indexing.

Williams syndrome-specific neuroanatomical profile and its associations with behavioral features.

PubMed

Fan, Chun Chieh; Brown, Timothy T; Bartsch, Hauke; Kuperman, Joshua M; Hagler, Donald J; Schork, Andrew; Searcy, Yvonne; Bellugi, Ursula; Halgren, Eric; Dale, Anders M

2017-01-01

Williams Syndrome (WS) is a rare genetic disorder with unique behavioral features. Yet the rareness of WS has limited the number and type of studies that can be conducted in which inferences are made about how neuroanatomical abnormalities mediate behaviors. In this study, we extracted a WS-specific neuroanatomical profile from structural magnetic resonance imaging (MRI) measurements and tested its association with behavioral features of WS. Using a WS adult cohort (22 WS, 16 healthy controls), we modeled a sparse representation of a WS-specific neuroanatomical profile. The predictive performances are robust within the training cohort (10-fold cross-validation, AUC = 1.0) and accurately identify all WS individuals in an independent child WS cohort (seven WS, 59 children with diverse developmental status, AUC = 1.0). The WS-specific neuroanatomical profile includes measurements in the orbitofrontal cortex, superior parietal cortex, Sylvian fissures, and basal ganglia, and variability within these areas related to the underlying size of hemizygous deletion in patients with partial deletions. The profile intensity mediated the overall cognitive impairment as well as personality features related to hypersociability. Our results imply that the unique behaviors in WS were mediated through the constellation of abnormalities in cortical-subcortical circuitry consistent in child WS and adult WS. The robustness of the derived WS-specific neuroanatomical profile also demonstrates the potential utility of our approach in both clinical and research applications.

Performance and Design Considerations of a Novel Dual-Material Gate Carbon Nanotube Field-Effect Transistors: Nonequilibrium Green's Function Approach

NASA Astrophysics Data System (ADS)

Arefinia, Zahra; Orouji, Ali A.

2009-02-01

The concept of dual-material gate (DMG) is applied to the carbon nanotube field-effect transistor (CNTFET) with doped source and drain extensions, and the features exhibited by the resulting new structure, i.e., the DMG-CNTFET structure, have been examined for the first time by developing a two-dimensional (2D) full quantum simulation. The simulations have been done by the self-consistent solution of 2D Poisson-Schrödinger equations, within the nonequilibrium Green's function (NEGF) formalism. The results show DMG-CNTFET decreases significantly leakage current and drain conductance and increases on-off current ratio and voltage gain as compared to the single material gate counterparts CNTFET. It is seen that short channel effects in this structure are suppressed because of the perceivable step in the surface potential profile, which screens the drain potential. Moreover, these unique features can be controlled by engineering the workfunction and length of the gate metals. Therefore, this work provides an incentive for further experimental exploration.

A framework for solving ill-structured community problems

NASA Astrophysics Data System (ADS)

Keller, William Cotesworth

A multifaceted protocol for solving ill-structured community problems has been developed. It embodies the lessons learned from the past by refining and extending features of previous models from the systems thinkers, and the fields of behavioral decision making and creative problem solving. The protocol also embraces additional features needed to address the unique aspects of community decision situations. The essential elements of the protocol are participants from the community, a problem-solving process, a systems picture, a facilitator, a modified Delphi method of communications, and technical expertise. This interdisciplinary framework has been tested by a quasi experiment with a real world community problem (the high cost of electrical power on Long Island, NY). Results indicate the protocol can enable members of the community to understand a complicated, ill-structured problem and guide them to action to solve the issue. However, the framework takes time (over one year in the test case) and will be inappropriate for crises where quick action is needed.

A Novel Characterization of Amalgamated Networks in Natural Systems

PubMed Central

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

2015-01-01

Densely-connected networks are prominent among natural systems, exhibiting structural characteristics often optimized for biological function. To reveal such features in highly-connected networks, we introduce a new network characterization determined by a decomposition of network-connectivity into low-rank and sparse components. Based on these components, we discover a new class of networks we define as amalgamated networks, which exhibit large functional groups and dense connectivity. Analyzing recent experimental findings on cerebral cortex, food-web, and gene regulatory networks, we establish the unique importance of amalgamated networks in fostering biologically advantageous properties, including rapid communication among nodes, structural stability under attacks, and separation of network activity into distinct functional modules. We further observe that our network characterization is scalable with network size and connectivity, thereby identifying robust features significant to diverse physical systems, which are typically undetectable by conventional characterizations of connectivity. We expect that studying the amalgamation properties of biological networks may offer new insights into understanding their structure-function relationships. PMID:26035066

An overview of inverted colloidal crystal systems for tissue engineering.

PubMed

João, Carlos Filipe C; Vasconcelos, Joana Marta; Silva, Jorge Carvalho; Borges, João Paulo

2014-10-01

Scaffolding is at the heart of tissue engineering but the number of techniques available for turning biomaterials into scaffolds displaying the features required for a tissue engineering application is somewhat limited. Inverted colloidal crystals (ICCs) are inverse replicas of an ordered array of monodisperse colloidal particles, which organize themselves in packed long-range crystals. The literature on ICC systems has grown enormously in the past 20 years, driven by the need to find organized macroporous structures. Although replicating the structure of packed colloidal crystals (CCs) into solid structures has produced a wide range of advanced materials (e.g., photonic crystals, catalysts, and membranes) only in recent years have ICCs been evaluated as devices for medical/pharmaceutical and tissue engineering applications. The geometry, size, pore density, and interconnectivity are features of the scaffold that strongly affect the cell environment with consequences on cell adhesion, proliferation, and differentiation. ICC scaffolds are highly geometrically ordered structures with increased porosity and connectivity, which enhances oxygen and nutrient diffusion, providing optimum cellular development. In comparison to other types of scaffolds, ICCs have three major unique features: the isotropic three-dimensional environment, comprising highly uniform and size-controllable pores, and the presence of windows connecting adjacent pores. Thus far, this is the only technique that guarantees these features with a long-range order, between a few nanometers and thousands of micrometers. In this review, we present the current development status of ICC scaffolds for tissue engineering applications.

Quantitative profiling of immune repertoires for minor lymphocyte counts using unique molecular identifiers.

PubMed

Egorov, Evgeny S; Merzlyak, Ekaterina M; Shelenkov, Andrew A; Britanova, Olga V; Sharonov, George V; Staroverov, Dmitriy B; Bolotin, Dmitriy A; Davydov, Alexey N; Barsova, Ekaterina; Lebedev, Yuriy B; Shugay, Mikhail; Chudakov, Dmitriy M

2015-06-15

Emerging high-throughput sequencing methods for the analyses of complex structure of TCR and BCR repertoires give a powerful impulse to adaptive immunity studies. However, there are still essential technical obstacles for performing a truly quantitative analysis. Specifically, it remains challenging to obtain comprehensive information on the clonal composition of small lymphocyte populations, such as Ag-specific, functional, or tissue-resident cell subsets isolated by sorting, microdissection, or fine needle aspirates. In this study, we report a robust approach based on unique molecular identifiers that allows profiling Ag receptors for several hundred to thousand lymphocytes while preserving qualitative and quantitative information on clonal composition of the sample. We also describe several general features regarding the data analysis with unique molecular identifiers that are critical for accurate counting of starting molecules in high-throughput sequencing applications. Copyright © 2015 by The American Association of Immunologists, Inc.

Regional shape-based feature space for segmenting biomedical images using neural networks

NASA Astrophysics Data System (ADS)

Sundaramoorthy, Gopal; Hoford, John D.; Hoffman, Eric A.

1993-07-01

In biomedical images, structure of interest, particularly the soft tissue structures, such as the heart, airways, bronchial and arterial trees often have grey-scale and textural characteristics similar to other structures in the image, making it difficult to segment them using only gray- scale and texture information. However, these objects can be visually recognized by their unique shapes and sizes. In this paper we discuss, what we believe to be, a novel, simple scheme for extracting features based on regional shapes. To test the effectiveness of these features for image segmentation (classification), we use an artificial neural network and a statistical cluster analysis technique. The proposed shape-based feature extraction algorithm computes regional shape vectors (RSVs) for all pixels that meet a certain threshold criteria. The distance from each such pixel to a boundary is computed in 8 directions (or in 26 directions for a 3-D image). Together, these 8 (or 26) values represent the pixel's (or voxel's) RSV. All RSVs from an image are used to train a multi-layered perceptron neural network which uses these features to 'learn' a suitable classification strategy. To clearly distinguish the desired object from other objects within an image, several examples from inside and outside the desired object are used for training. Several examples are presented to illustrate the strengths and weaknesses of our algorithm. Both synthetic and actual biomedical images are considered. Future extensions to this algorithm are also discussed.

Distinct contributions of functional and deep neural network features to representational similarity of scenes in human brain and behavior

PubMed Central

Greene, Michelle R; Baldassano, Christopher; Fei-Fei, Li; Beck, Diane M; Baker, Chris I

2018-01-01

Inherent correlations between visual and semantic features in real-world scenes make it difficult to determine how different scene properties contribute to neural representations. Here, we assessed the contributions of multiple properties to scene representation by partitioning the variance explained in human behavioral and brain measurements by three feature models whose inter-correlations were minimized a priori through stimulus preselection. Behavioral assessments of scene similarity reflected unique contributions from a functional feature model indicating potential actions in scenes as well as high-level visual features from a deep neural network (DNN). In contrast, similarity of cortical responses in scene-selective areas was uniquely explained by mid- and high-level DNN features only, while an object label model did not contribute uniquely to either domain. The striking dissociation between functional and DNN features in their contribution to behavioral and brain representations of scenes indicates that scene-selective cortex represents only a subset of behaviorally relevant scene information. PMID:29513219

Distinct contributions of functional and deep neural network features to representational similarity of scenes in human brain and behavior.

PubMed

Groen, Iris Ia; Greene, Michelle R; Baldassano, Christopher; Fei-Fei, Li; Beck, Diane M; Baker, Chris I

2018-03-07

Inherent correlations between visual and semantic features in real-world scenes make it difficult to determine how different scene properties contribute to neural representations. Here, we assessed the contributions of multiple properties to scene representation by partitioning the variance explained in human behavioral and brain measurements by three feature models whose inter-correlations were minimized a priori through stimulus preselection. Behavioral assessments of scene similarity reflected unique contributions from a functional feature model indicating potential actions in scenes as well as high-level visual features from a deep neural network (DNN). In contrast, similarity of cortical responses in scene-selective areas was uniquely explained by mid- and high-level DNN features only, while an object label model did not contribute uniquely to either domain. The striking dissociation between functional and DNN features in their contribution to behavioral and brain representations of scenes indicates that scene-selective cortex represents only a subset of behaviorally relevant scene information.

From the Cover: Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features

NASA Astrophysics Data System (ADS)

Derelle, Evelyne; Ferraz, Conchita; Rombauts, Stephane; Rouzé, Pierre; Worden, Alexandra Z.; Robbens, Steven; Partensky, Frédéric; Degroeve, Sven; Echeynié, Sophie; Cooke, Richard; Saeys, Yvan; Wuyts, Jan; Jabbari, Kamel; Bowler, Chris; Panaud, Olivier; Piégu, Benoît; Ball, Steven G.; Ral, Jean-Philippe; Bouget, François-Yves; Piganeau, Gwenael; de Baets, Bernard; Picard, André; Delseny, Michel; Demaille, Jacques; van de Peer, Yves; Moreau, Hervé

2006-08-01

The green lineage is reportedly 1,500 million years old, evolving shortly after the endosymbiosis event that gave rise to early photosynthetic eukaryotes. In this study, we unveil the complete genome sequence of an ancient member of this lineage, the unicellular green alga Ostreococcus tauri (Prasinophyceae). This cosmopolitan marine primary producer is the world's smallest free-living eukaryote known to date. Features likely reflecting optimization of environmentally relevant pathways, including resource acquisition, unusual photosynthesis apparatus, and genes potentially involved in C4 photosynthesis, were observed, as was downsizing of many gene families. Overall, the 12.56-Mb nuclear genome has an extremely high gene density, in part because of extensive reduction of intergenic regions and other forms of compaction such as gene fusion. However, the genome is structurally complex. It exhibits previously unobserved levels of heterogeneity for a eukaryote. Two chromosomes differ structurally from the other eighteen. Both have a significantly biased G+C content, and, remarkably, they contain the majority of transposable elements. Many chromosome 2 genes also have unique codon usage and splicing, but phylogenetic analysis and composition do not support alien gene origin. In contrast, most chromosome 19 genes show no similarity to green lineage genes and a large number of them are specialized in cell surface processes. Taken together, the complete genome sequence, unusual features, and downsized gene families, make O. tauri an ideal model system for research on eukaryotic genome evolution, including chromosome specialization and green lineage ancestry. genome heterogeneity | genome sequence | green alga | Prasinophyceae | gene prediction

Structural analysis of hierarchically organized zeolites

PubMed Central

Mitchell, Sharon; Pinar, Ana B.; Kenvin, Jeffrey; Crivelli, Paolo; Kärger, Jörg; Pérez-Ramírez, Javier

2015-01-01

Advances in materials synthesis bring about many opportunities for technological applications, but are often accompanied by unprecedented complexity. This is clearly illustrated by the case of hierarchically organized zeolite catalysts, a class of crystalline microporous solids that has been revolutionized by the engineering of multilevel pore architectures, which combine unique chemical functionality with efficient molecular transport. Three key attributes, the crystal, the pore and the active site structure, can be expected to dominate the design process. This review examines the adequacy of the palette of techniques applied to characterize these distinguishing features and their catalytic impact. PMID:26482337

A VHDL Core for Intrinsic Evolution of Discrete Time Filters with Signal Feedback

NASA Technical Reports Server (NTRS)

Gwaltney, David A.; Dutton, Kenneth

2005-01-01

The design of an Evolvable Machine VHDL Core is presented, representing a discrete-time processing structure capable of supporting control system applications. This VHDL Core is implemented in an FPGA and is interfaced with an evolutionary algorithm implemented in firmware on a Digital Signal Processor (DSP) to create an evolvable system platform. The salient features of this architecture are presented. The capability to implement IIR filter structures is presented along with the results of the intrinsic evolution of a filter. The robustness of the evolved filter design is tested and its unique characteristics are described.

Dynamical Structure of Madden-Julian Oscillation over Malay Peninsula

NASA Astrophysics Data System (ADS)

Djamil, Y. S.; Koh, T. Y.; Chandimala, J.; Teo, C. K.

2014-12-01

Madden-Julian Oscillation (MJO) is the dominant weather event in the intraseasonal time scale over Malay Peninsula region. The MJO signals are represented by the first two modes of radiosonde records extracted using Extended Empirical Orthogonal Function (EEOF) analyses which we label as Local Multivariate MJO (LMM). LMM is able to capture the spatio-temporal profile of MJO along the global tropics in all seasons. With the help of LMM, we clarify the dynamical and thermodynamical structure of the MJO over Malay Peninsula, including the unique "boomerang-shaped" feature in the time-height temperature profile identified in previous literature.

Bimodal pair f-KdV dynamics in star-forming clouds

NASA Astrophysics Data System (ADS)

Karmakar, Pralay Kumar; Haloi, Archana; Roy, Supriya

2018-04-01

A theoretical formalism for investigating the bimodal conjugational mode dynamics of hybrid source, dictated by a unique pair of forced Korteweg-de Vries (f-KdV) equations in a complex turbo-magnetized star-forming cloud, is reported. It uses a standard multi-scale analysis executed over the cloud-governing equations in a closure form to derive the conjugated pair f-KdV system. We numerically see the structural features of two distinctive classes of eigenmode patterns stemming from the conjoint gravito-electrostatic interplay. The electrostatic compressive monotonic aperiodic shock-like patterns and gravitational compressive non-monotonic oscillatory shock-like structures are excitable. It is specifically revealed that the constitutive grain-charge (grain-mass) acts as electrostatic stabilizer (gravitational destabilizer) against the global cloud collapse dynamics. The basic features of the nonlinear coherent structures are confirmed in systematic phase-plane landscapes, indicating electrostatic irregular non-homoclinic open trajectories and gravitational atypical non-chaotic homoclinic fixed-point attractors. The relevance in the real astro-cosmic scenarios of the early phases of structure formation via wave-driven fluid-accretive transport processes is summarily emphasized.

Three-dimensionally networked graphene hydroxide with giant pores and its application in supercapacitors

PubMed Central

Lee, Dongwook; Seo, Jiwon

2014-01-01

The three-dimensionally networked and layered structure of graphene hydroxide (GH) was investigated. After lengthy immersion in a NaOH solution, most of the epoxy groups in the graphene oxide were destroyed, and more hydroxyl groups were generated, transforming the graphene oxide into graphene hydroxide. Additionally, benzoic acid groups were formed, and the ether groups link the neighboring layers, creating a near-3D structure in the GH. To utilize these unique structural features, electrodes with large pores for use in supercapacitors were fabricated using thermal reduction in vacuum. The reduced GH maintained its layered structure and developed a lot of large of pores between/inside the layers. The GH electrodes exhibited high gravimetric as well as high volumetric capacitance. PMID:25492227

Three-dimensionally networked graphene hydroxide with giant pores and its application in supercapacitors

NASA Astrophysics Data System (ADS)

Lee, Dongwook; Seo, Jiwon

2014-12-01

The three-dimensionally networked and layered structure of graphene hydroxide (GH) was investigated. After lengthy immersion in a NaOH solution, most of the epoxy groups in the graphene oxide were destroyed, and more hydroxyl groups were generated, transforming the graphene oxide into graphene hydroxide. Additionally, benzoic acid groups were formed, and the ether groups link the neighboring layers, creating a near-3D structure in the GH. To utilize these unique structural features, electrodes with large pores for use in supercapacitors were fabricated using thermal reduction in vacuum. The reduced GH maintained its layered structure and developed a lot of large of pores between/inside the layers. The GH electrodes exhibited high gravimetric as well as high volumetric capacitance.

Three-dimensionally networked graphene hydroxide with giant pores and its application in supercapacitors.

PubMed

Lee, Dongwook; Seo, Jiwon

2014-12-10

The three-dimensionally networked and layered structure of graphene hydroxide (GH) was investigated. After lengthy immersion in a NaOH solution, most of the epoxy groups in the graphene oxide were destroyed, and more hydroxyl groups were generated, transforming the graphene oxide into graphene hydroxide. Additionally, benzoic acid groups were formed, and the ether groups link the neighboring layers, creating a near-3D structure in the GH. To utilize these unique structural features, electrodes with large pores for use in supercapacitors were fabricated using thermal reduction in vacuum. The reduced GH maintained its layered structure and developed a lot of large of pores between/inside the layers. The GH electrodes exhibited high gravimetric as well as high volumetric capacitance.

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

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.

Structural Analysis of PTM Hotspots (SAPH-ire) – A Quantitative Informatics Method Enabling the Discovery of Novel Regulatory Elements in Protein Families*

PubMed Central

Dewhurst, Henry M.; Choudhury, Shilpa; Torres, Matthew P.

2015-01-01

Predicting the biological function potential of post-translational modifications (PTMs) is becoming increasingly important in light of the exponential increase in available PTM data from high-throughput proteomics. We developed structural analysis of PTM hotspots (SAPH-ire)—a quantitative PTM ranking method that integrates experimental PTM observations, sequence conservation, protein structure, and interaction data to allow rank order comparisons within or between protein families. Here, we applied SAPH-ire to the study of PTMs in diverse G protein families, a conserved and ubiquitous class of proteins essential for maintenance of intracellular structure (tubulins) and signal transduction (large and small Ras-like G proteins). A total of 1728 experimentally verified PTMs from eight unique G protein families were clustered into 451 unique hotspots, 51 of which have a known and cited biological function or response. Using customized software, the hotspots were analyzed in the context of 598 unique protein structures. By comparing distributions of hotspots with known versus unknown function, we show that SAPH-ire analysis is predictive for PTM biological function. Notably, SAPH-ire revealed high-ranking hotspots for which a functional impact has not yet been determined, including phosphorylation hotspots in the N-terminal tails of G protein gamma subunits—conserved protein structures never before reported as regulators of G protein coupled receptor signaling. To validate this prediction we used the yeast model system for G protein coupled receptor signaling, revealing that gamma subunit–N-terminal tail phosphorylation is activated in response to G protein coupled receptor stimulation and regulates protein stability in vivo. These results demonstrate the utility of integrating protein structural and sequence features into PTM prioritization schemes that can improve the analysis and functional power of modification-specific proteomics data. PMID:26070665

Structure, proteome and genome of Sinorhizobium meliloti phage ΦM5: A virus with LUZ24-like morphology and a highly mosaic genome.

PubMed

Johnson, Matthew C; Sena-Velez, Marta; Washburn, Brian K; Platt, Georgia N; Lu, Stephen; Brewer, Tess E; Lynn, Jason S; Stroupe, M Elizabeth; Jones, Kathryn M

2017-12-01

Bacteriophages of nitrogen-fixing rhizobial bacteria are revealing a wealth of novel structures, diverse enzyme combinations and genomic features. Here we report the cryo-EM structure of the phage capsid at 4.9-5.7Å-resolution, the phage particle proteome, and the genome of the Sinorhizobium meliloti-infecting Podovirus ΦM5. This is the first structure of a phage with a capsid and capsid-associated structural proteins related to those of the LUZ24-like viruses that infect Pseudomonas aeruginosa. Like many other Podoviruses, ΦM5 is a T=7 icosahedron with a smooth capsid and short, relatively featureless tail. Nonetheless, this group is phylogenetically quite distinct from Podoviruses of the well-characterized T7, P22, and epsilon 15 supergroups. Structurally, a distinct bridge of density that appears unique to ΦM5 reaches down the body of the coat protein to the extended loop that interacts with the next monomer in a hexamer, perhaps stabilizing the mature capsid. Further, the predicted tail fibers of ΦM5 are quite different from those of enteric bacteria phages, but have domains in common with other rhizophages. Genomically, ΦM5 is highly mosaic. The ΦM5 genome is 44,005bp with 357bp direct terminal repeats (DTRs) and 58 unique ORFs. Surprisingly, the capsid structural module, the tail module, the DNA-packaging terminase, the DNA replication module and the integrase each appear to be from a different lineage. One of the most unusual features of ΦM5 is its terminase whose large subunit is quite different from previously-described short-DTR-generating packaging machines and does not fit into any of the established phylogenetic groups. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

The management of nonunion and malunion of the distal humerus--a 30-year experience.

PubMed

Jupiter, Jesse B

2008-01-01

This personal series of nonunions of the distal humerus reviews unique features of this problem, categorizes them according to unique anatomic features, and presents pitfalls and pearls in the management of these complex reconstructive problems.

The synthesis of monomers with pendent ethynyl groups for modified high performance thermoplastics

NASA Technical Reports Server (NTRS)

Nwokogu, Godson C.; Antoine, Miquel D.; Ansong, Omari

1994-01-01

Synthetic schemes were developed and optimized for twelve new monomers possessing unique structural features and one aspartimide. Two synthetic pathways were compared for preparation of the triarylethane monomers with pendent ethynyl groups. The results show that one of these pathways can be generally applied. The alternative pathway was applicable to the preparation of only one of the twelve compounds, the problem being secondary reactions of the initially formed desired product.

Small-molecule WNK inhibition regulates cardiovascular and renal function

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

Yamada, Ken; Park, Hyi-Man; Rigel, Dean F.

The With-No-Lysine (K) (WNK) kinases play a critical role in blood pressure regulation and body fluid and electrolyte homeostasis. Herein, we introduce the first orally bioavailable pan-WNK-kinase inhibitor, WNK463, that exploits unique structural features of the WNK kinases for both affinity and kinase selectivity. In rodent models of hypertension, WNK463 affects blood pressure and body fluid and electro-lyte homeostasis, consistent with WNK-kinase-associated physiology and pathophysiology.

Building Structure Feature-based Models for Predicting Isoform-specific Human Cytochrome P-450 (hCYP 3A4, 2D6 and 2C9) Inhibition Assay Results in ToxCast

EPA Science Inventory

EPA’s ToxCast project is using high-throughput screening (HTS) to profile and prioritize chemicals for further testing. ToxCast Phase I evaluated 309 unique chemicals, the majority pesticide actives, in over 500 HTS assays. These included 3 human cytochrome P450 (hCYP3A4, hCYP2...

A Comparison of Hyporheic Transport at a Cross-Vane Structure and Natural Riffle.

PubMed

Smidt, Samuel J; Cullin, Joseph A; Ward, Adam S; Robinson, Jesse; Zimmer, Margaret A; Lautz, Laura K; Endreny, Theodore A

2015-01-01

While restoring hyporheic flowpaths has been cited as a benefit to stream restoration structures, little documentation exists confirming that constructed restoration structures induce comparable hyporheic exchange to natural stream features. This study compares a stream restoration structure (cross-vane) to a natural feature (riffle) concurrently in the same stream reach using time-lapsed electrical resistivity (ER) tomography. Using this hydrogeophysical approach, we were able to quantify hyporheic extent and transport beneath the cross-vane structure and the riffle. We interpret from the geophysical data that the cross-vane and the natural riffle induced spatially and temporally unique hyporheic extent and transport, and the cross-vane created both spatially larger and temporally longer hyporheic flowpaths than the natural riffle. Tracer from the 4.67-h injection was detected along flowpaths for 4.6 h at the cross-vane and 4.2 h at the riffle. The spatial extent of the hyporheic zone at the cross-vane was 12% larger than that at the riffle. We compare ER results of this study to vertical fluxes calculated from temperature profiles and conclude significant differences in the interpretation of hyporheic transport from these different field techniques. Results of this study demonstrate a high degree of heterogeneity in transport metrics at both the cross-vane and the riffle and differences between the hyporheic flowpath networks at the two different features. Our results suggest that restoration structures may be capable of creating sufficient exchange flux and timescales of transport to achieve the same ecological functions as natural features, but engineering of the physical and biogeochemical environment may be necessary to realize these benefits. © 2014, National Ground Water Association.

Differential role of molten globule and protein folding in distinguishing unique features of botulinum neurotoxin.

PubMed

Kumar, Raj; Kukreja, Roshan V; Cai, Shuowei; Singh, Bal R

2014-06-01

Botulinum neurotoxins (BoNTs) are proteins of great interest not only because of their extreme toxicity but also paradoxically for their therapeutic applications. All the known serotypes (A-G) have varying degrees of longevity and potency inside the neuronal cell. Differential chemical modifications such as phosphorylation and ubiquitination have been suggested as possible mechanisms for their longevity, but the molecular basis of the longevity remains unclear. Since the endopeptidase domain (light chain; LC) of toxin apparently survives inside the neuronal cells for months, it is important to examine the structural features of this domain to understand its resistance to intracellular degradation. Published crystal structures (both botulinum neurotoxins and endopeptidase domain) have not provided adequate explanation for the intracellular longevity of the domain. Structural features obtained from spectroscopic analysis of LCA and LCB were similar, and a PRIME (PReImminent Molten Globule Enzyme) conformation appears to be responsible for their optimal enzymatic activity at 37°C. LCE, on the other hand, was although optimally active at 37°C, but its active conformation differed from the PRIME conformation of LCA and LCB. This study establishes and confirms our earlier finding that an optimally active conformation of these proteins in the form of PRIME exists for the most poisonous poison, botulinum neurotoxin. There are substantial variations in the structural and functional characteristics of these active molten globule related structures among the three BoNT endopeptidases examined. These differential conformations of LCs are important in understanding the fundamental structural features of proteins, and their possible connection to intracellular longevity could provide significant clues for devising new countermeasures and effective therapeutics. Copyright © 2014 Elsevier B.V. All rights reserved.

Giant surfactants provide a versatile platform for sub-10-nm nanostructure engineering

PubMed Central

Yu, Xinfei; Yue, Kan; Hsieh, I-Fan; Li, Yiwen; Dong, Xue-Hui; Liu, Chang; Xin, Yu; Wang, Hsiao-Fang; Shi, An-Chang; Newkome, George R.; Chen, Er-Qiang; Zhang, Wen-Bin; Cheng, Stephen Z. D.

2013-01-01

The engineering of structures across different length scales is central to the design of novel materials with controlled macroscopic properties. Herein, we introduce a unique class of self-assembling materials, which are built upon shape- and volume-persistent molecular nanoparticles and other structural motifs, such as polymers, and can be viewed as a size-amplified version of the corresponding small-molecule counterparts. Among them, “giant surfactants” with precise molecular structures have been synthesized by “clicking” compact and polar molecular nanoparticles to flexible polymer tails of various composition and architecture at specific sites. Capturing the structural features of small-molecule surfactants but possessing much larger sizes, giant surfactants bridge the gap between small-molecule surfactants and block copolymers and demonstrate a duality of both materials in terms of their self-assembly behaviors. The controlled structural variations of these giant surfactants through precision synthesis further reveal that their self-assemblies are remarkably sensitive to primary chemical structures, leading to highly diverse, thermodynamically stable nanostructures with feature sizes around 10 nm or smaller in the bulk, thin-film, and solution states, as dictated by the collective physical interactions and geometric constraints. The results suggest that this class of materials provides a versatile platform for engineering nanostructures with sub-10-nm feature sizes. These findings are not only scientifically intriguing in understanding the chemical and physical principles of the self-assembly, but also technologically relevant, such as in nanopatterning technology and microelectronics. PMID:23716680

Chemically Patterned Inverse Opal Created by a Selective Photolysis Modification Process.

PubMed

Tian, Tian; Gao, Ning; Gu, Chen; Li, Jian; Wang, Hui; Lan, Yue; Yin, Xianpeng; Li, Guangtao

2015-09-02

Anisotropic photonic crystal materials have long been pursued for their broad applications. A novel method for creating chemically patterned inverse opals is proposed here. The patterning technique is based on selective photolysis of a photolabile polymer together with postmodification on released amine groups. The patterning method allows regioselective modification within an inverse opal structure, taking advantage of selective chemical reaction. Moreover, combined with the unique signal self-reporting feature of the photonic crystal, the fabricated structure is capable of various applications, including gradient photonic bandgap and dynamic chemical patterns. The proposed method provides the ability to extend the structural and chemical complexity of the photonic crystal, as well as its potential applications.

A novel snowflake-like SnO2 hierarchical architecture with superior gas sensing properties

NASA Astrophysics Data System (ADS)

Li, Yanqiong

2018-02-01

Snowflake-like SnO2 hierarchical architecture has been synthesized via a facile hydrothermal method and followed by calcination. The SnO2 hierarchical structures are assembled with thin nanoflakes blocks, which look like snowflake shape. A possible mechanism for the formation of the SnO2 hierarchical structures is speculated. Moreover, gas sensing tests show that the sensor based on snowflake-like SnO2 architectures exhibited excellent gas sensing properties. The enhancement may be attributed to its unique structures, in which the porous feature on the snowflake surface could further increase the active surface area of the materials and provide facile pathways for the target gas.

The dielectric signature of glass density

NASA Astrophysics Data System (ADS)

Rams-Baron, M.; Wojnarowska, Z.; Knapik-Kowalczuk, J.; Jurkiewicz, K.; Burian, A.; Wojtyniak, M.; Pionteck, J.; Jaworska, M.; Rodríguez-Tinoco, C.; Paluch, M.

2017-09-01

At present, we are witnessing a renewed interest in the properties of densified glasses prepared by isobaric cooling of a liquid at elevated pressure. As high-pressure densification emerges as a promising approach in the development of glasses with customized features, understanding and controlling their unique properties represent a contemporary scientific and technological goal. The results presented herein indicate that the applied high-pressure preparation route leads to a glassy state with higher density (˜1%) and a reduced free volume of about 7%. We show that these subtle structural changes remarkably influence the dielectric response and spectral features of β-relaxation in etoricoxib glass. Our study, combining dynamical and structural techniques, reveal that β-relaxation in etoricoxib is extremely sensitive to the variations in molecular packing and can be used to probe the changes in glass density. Such connection is technologically relevant and may advance further progress in the field.

Conformational Effects through Hydrogen Bonding in a Constrained γ-Peptide Template: From Intraresidue Seven-Membered Rings to a Gel-Forming Sheet Structure.

PubMed

Awada, Hawraà; Grison, Claire M; Charnay-Pouget, Florence; Baltaze, Jean-Pierre; Brisset, François; Guillot, Régis; Robin, Sylvie; Hachem, Ali; Jaber, Nada; Naoufal, Daoud; Yazbeck, Ogaritte; Aitken, David J

2017-05-05

A series of three short oligomers (di-, tri-, and tetramers) of cis-2-(aminomethyl)cyclobutane carboxylic acid, a γ-amino acid featuring a cyclobutane ring constraint, were prepared, and their conformational behavior was examined spectroscopically and by molecular modeling. In dilute solutions, these peptides showed a number of low-energy conformers, including ribbonlike structures pleated around a rarely observed series of intramolecular seven-membered hydrogen bonds. In more concentrated solutions, these interactions defer to an organized supramolecular assembly, leading to thermoreversible organogel formation notably for the tripeptide, which produced fibrillar xerogels. In the solid state, the dipeptide adopted a fully extended conformation featuring a one-dimensional network of intermolecularly H-bonded molecules stacked in an antiparallel sheet alignment. This work provides unique insight into the interplay between inter- and intramolecular H-bonded conformer topologies for the same peptide template.

Selective binding of choline by a phosphate-coordination-based triple helicate featuring an aromatic box

DOE PAGES

Jia, Chuandong; Zuo, Wei; Yang, Dong; ...

2017-10-16

In nature, proteins have evolved sophisticated cavities tailored for capturing target guests selectively among competitors of similar size, shape, and charge. The fundamental principles guiding the molecular recognition, such as self-assembly and complementarity, have inspired the development of biomimetic receptors. In the current work, we report a self-assembled triple anion helicate (host 2) featuring a cavity resembling that of the choline-binding protein ChoX, as revealed by crystal and density functional theory (DFT)-optimized structures, which binds choline in a unique dual-site-binding mode. Here, this similarity in structure leads to a similarly high selectivity of host 2 for choline over its derivatives,more » as demonstrated by the NMR and fluorescence competition experiments. Furthermore, host 2 is able to act as a fluorescence displacement sensor for discriminating choline, acetylcholine, l-carnitine, and glycine betaine effectively.« less

Astragalar Morphology of Selected Giraffidae.

PubMed

Solounias, Nikos; Danowitz, Melinda

2016-01-01

The artiodactyl astragalus has been modified to exhibit two trochleae, creating a double pullied structure allowing for significant dorso-plantar motion, and limited mediolateral motion. The astragalus structure is partly influenced by environmental substrates, and correspondingly, morphometric studies can yield paleohabitat information. The present study establishes terminology and describes detailed morphological features on giraffid astragali. Each giraffid astragalus exhibits a unique combination of anatomical characteristics. The giraffid astragalar morphologies reinforce previously established phylogenetic relationships. We find that the enlargement of the navicular head is a feature shared by all giraffids, and that the primitive giraffids possess exceptionally tall astragalar heads in relation to the total astragalar height. The sivatheres and the okapi share a reduced notch on the lateral edge of the astragalus. We find that Samotherium is more primitive in astragalar morphologies than Palaeotragus, which is reinforced by tooth characteristics and ossicone position. Diagnostic anatomical characters on the astragalus allow for giraffid species identifications and a better understanding of Giraffidae.

Upheaval Dome, Utah, USA: Impact origin confirmed

NASA Astrophysics Data System (ADS)

Buchner, Elmar; Kenkmann, Thomas

2008-03-01

Upheaval Dome is a unique circular structure on the ColoradoPlateau in SE Utah, the origin of which has been controversiallydiscussed for decades. It has been interpreted as a crypto volcanicfeature, a salt diapir, a pinched-off salt diapir, and an erodedimpact crater. While recent structural mapping, modeling, andanalyses of deformation mechanisms strongly support an impactorigin, ultimate proof, namely the documentation of unambiguousshock features, has yet to be successfully provided. In thisstudy, we document, for the first time, shocked quartz grainsfrom this crater in sandstones of the Jurassic Kayenta Formation.The investigated grains contain multiple sets of decorated planardeformation features. Transmission electron microscopy (TEM)reveals that the amorphous lamellae are annealed and exhibitdense tangles of dislocations as well as trails of fluid inclusions.The shocked quartz grains were found in the periphery of thecentral uplift in the northeastern sector of the crater, whichmost likely represents the cross range crater sector.

Unique Aspects of Cryptochrome in Chronobiology and Metabolism, Pancreatic β-Cell Dysfunction, and Regeneration: Research into Cysteine414-Alanine Mutant CRY1.

PubMed

Okano, Satoshi

2016-01-01

Cryptochrome proteins (CRYs), which can bind noncovalently to cofactor (chromophore) flavin adenine dinucleotide (FAD), occur widely among organisms. CRYs play indispensable roles in the generation of circadian rhythm in mammals. Transgenic mice (Tg mice), ubiquitously expressing mouse CRY1 having a mutation in which cysteine414 (the zinc-binding site of CRY1) being replaced with alanine, display unique phenotypes in their circadian rhythms. Moreover, male Tg mice exhibit symptoms of diabetes characterized by beta-cell dysfunction, resembling human maturity onset diabetes of the young (MODY). The lowered proliferation of β -cells is a primary cause of age-dependent β -cell loss. Furthermore, unusually enlarged duct-like structures developed prominently in the Tg mice pancreases. The duct-like structures contained insulin-positive cells, suggesting neogenesis of β -cells in the Tg mice. This review, based mainly on the author's investigation of the unique features of Tg mice, presents reported results and recent findings related to molecular processes associated with mammalian cryptochromes, especially their involvement in the regulation of metabolism. New information is described with emphasis on the aspects of islet architecture, pancreatic β -cell dysfunction, and regeneration.

Highly Luminescent 2D-Type Slab Crystals Based on a Molecular Charge-Transfer Complex as Promising Organic Light-Emitting Transistor Materials.

PubMed

Park, Sang Kyu; Kim, Jin Hong; Ohto, Tatsuhiko; Yamada, Ryo; Jones, Andrew O F; Whang, Dong Ryeol; Cho, Illhun; Oh, Sangyoon; Hong, Seung Hwa; Kwon, Ji Eon; Kim, Jong H; Olivier, Yoann; Fischer, Roland; Resel, Roland; Gierschner, Johannes; Tada, Hirokazu; Park, Soo Young

2017-09-01

A new 2:1 donor (D):acceptor (A) mixed-stacked charge-transfer (CT) cocrystal comprising isometrically structured dicyanodistyrylbenzene-based D and A molecules is designed and synthesized. Uniform 2D-type morphology is manifested by the exquisite interplay of intermolecular interactions. In addition to its appealing structural features, unique optoelectronic properties are unveiled. Exceptionally high photoluminescence quantum yield (Φ F ≈ 60%) is realized by non-negligible oscillator strength of the S 1 transition, and rigidified 2D-type structure. Moreover, this luminescent 2D-type CT crystal exhibits balanced ambipolar transport (µ h and µ e of ≈10 -4 cm 2 V -1 s -1 ). As a consequence of such unique optoelectronic characteristics, the first CT electroluminescence is demonstrated in a single active-layered organic light-emitting transistor (OLET) device. The external quantum efficiency of this OLET is as high as 1.5% to suggest a promising potential of luminescent mixed-stacked CT cocrystals in OLET applications. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Voyager 1 imaging and IRIS observations of Jovian methane absorption and thermal emission: Implications for cloud structure

NASA Technical Reports Server (NTRS)

West, R. A.; Kupferman, P. N.; Hart, H.

1984-01-01

Images from three filters of the Voyager 1 wide angle camera are used to measure the continuum reflectivity and spectral gradient near 6000 A and the 6190 A band methane/continuum ratio for a variety of cloud features in Jupiter's atmosphere. The dark barge features in the North Equatorial Belt have anomalously strong positive continuum spectral gradients suggesting unique composition. Methane absorption is shown at unprecedented spatial scales for the Great Red Spot and its immediate environment, for a dark barge feature in the North Equatorial Belt, and for two hot spot and plume regions in the North Equatorial Belt. Methane absorption and five micrometer emission are correlated in the vicinity of the Great Red Spot but are anticorrelated in one of the plume hot spot regions. Methane absorption and simultaneous maps of five micrometer brightness temperature is quantitatively compared to realistic cloud structure models which include multiple scattering at five micrometer as well as in the visible. Variability in H2 quadrupole lines are also investigated.

Structural biology at the European X-ray free-electron laser facility

PubMed Central

Altarelli, Massimo; Mancuso, Adrian P.

2014-01-01

The European X-ray free-electron laser (XFEL) facility, under construction in the Hamburg region, will provide high-peak brilliance (greater than 1033 photons s−1 mm−2 mrad−2 per 0.1% BW), ultrashort pulses (approx. 10 fs) of X-rays, with a high repetition rate (up to 27 000 pulses s−1) from 2016 onwards. The main features of this exceptional X-ray source, and the instrumentation developments necessary to exploit them fully, for application to a variety of scientific disciplines, are briefly summarized. In the case of structural biology, that has a central role in the scientific case of this new facility, the instruments and ancillary laboratories that are being planned and built within the baseline programme of the European XFEL and by consortia of users are also discussed. It is expected that the unique features of the source and the advanced features of the instrumentation will allow operation modes with more efficient use of sample materials, faster acquisition times, and conditions better approaching feasibility of single molecule imaging. PMID:24914145

Structural biology at the European X-ray free-electron laser facility.

PubMed

Altarelli, Massimo; Mancuso, Adrian P

2014-07-17

The European X-ray free-electron laser (XFEL) facility, under construction in the Hamburg region, will provide high-peak brilliance (greater than 10(33) photons s(-1) mm(-2) mrad(-2) per 0.1% BW), ultrashort pulses (approx. 10 fs) of X-rays, with a high repetition rate (up to 27 000 pulses s(-1)) from 2016 onwards. The main features of this exceptional X-ray source, and the instrumentation developments necessary to exploit them fully, for application to a variety of scientific disciplines, are briefly summarized. In the case of structural biology, that has a central role in the scientific case of this new facility, the instruments and ancillary laboratories that are being planned and built within the baseline programme of the European XFEL and by consortia of users are also discussed. It is expected that the unique features of the source and the advanced features of the instrumentation will allow operation modes with more efficient use of sample materials, faster acquisition times, and conditions better approaching feasibility of single molecule imaging. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Voyager 1 imaging and IRIS observations of Jovian methane absorption and thermal emission - Implications for cloud structure

NASA Technical Reports Server (NTRS)

West, R. A.; Kupferman, P. N.; Hart, H.

1985-01-01

Images from three filters of the Voyager 1 wide angle camera are used to measure the continuum reflectivity and spectral gradient near 6000 A and the 6190 A band methane/continuum ratio for a variety of cloud features in Jupiter's atmosphere. The dark barge features in the North Equatorial Belt have anomalously strong positive continuum spectral gradients suggesting unique composition. Methane absorption is shown at unprecedented spatial scales for the Great Red Spot and its immediate environment, for a dark barge feature in the North Equatorial Belt, and for two hot spot and plume regions in the North Equatorial Belt. Methane absorption and five micrometer emission are correlated in the vicinity of the Great Red Spot but are anticorrelated in one of the plume hot spot regions. Methane absorption and simultaneous maps of five micrometer brightness temperature are quantitatively compared to realistic cloud structure models which include multiple scattering at five micrometer as well as in the visible. Variability in H2 quadrupole lines are also investigated.

Morphology control, defect engineering and photoactivity tuning of ZnO crystals by graphene oxide--a unique 2D macromolecular surfactant.

PubMed

Pan, Xiaoyang; Yang, Min-Quan; Xu, Yi-Jun

2014-03-28

Zinc oxide (ZnO) nanostructured materials have received significant attention because of their unique physicochemical and electronic properties. In particular, the functional properties of ZnO are strongly dependent on its morphology and defect structure, particularly for a semiconductor ZnO-based photocatalyst. Here, we demonstrate a simple strategy for simultaneous morphology control, defect engineering and photoactivity tuning of semiconductor ZnO by utilizing the unique surfactant properties of graphene oxide (GO) in a liquid phase. By varying the amount of GO added during the synthesis process, the morphology of ZnO gradually evolves from a one dimensional prismatic rod to a hexagonal tube-like architecture while GO is converted into reduced GO (RGO). In addition, the introduction of GO can create oxygen vacancies in the lattice of ZnO crystals. As a result, the absorption edge of the wide band gap semiconductor ZnO is effectively extended to the visible light region, which thus endows the RGO-ZnO nanocomposites with visible light photoactivity; in contrast, the bare ZnO nanorod is only UV light photoactive. The synergistic integration of the unique morphology and the presence of oxygen vacancies imparts the RGO-ZnO nanocomposite with remarkably enhanced visible light photoactivity as compared to bare ZnO and its counterpart featuring different structural morphologies and the absence of oxygen vacancies. Our promising results highlight the versatility of the 2D GO as a solution-processable macromolecular surfactant to fabricate RGO-semiconductor nanocomposites with tunable morphology, defect structure and photocatalytic performance in a system-materials-engineering way.

Beyond lognormal inequality: The Lorenz Flow Structure

NASA Astrophysics Data System (ADS)

Eliazar, Iddo

2016-11-01

Observed from a socioeconomic perspective, the intrinsic inequality of the lognormal law happens to manifest a flow generated by an underlying ordinary differential equation. In this paper we extend this feature of the lognormal law to a general ;Lorenz Flow Structure; of Lorenz curves-objects that quantify socioeconomic inequality. The Lorenz Flow Structure establishes a general framework of size distributions that span continuous spectra of socioeconomic states ranging from the pure-communism extreme to the absolute-monarchy extreme. This study introduces and explores the Lorenz Flow Structure, analyzes its statistical properties and its inequality properties, unveils the unique role of the lognormal law within this general structure, and presents various examples of this general structure. Beyond the lognormal law, the examples include the inverse-Pareto and Pareto laws-which often govern the tails of composite size distributions.

An Analysis of Cassini Observations Regarding the Structure of Jupiter's Equatorial Atmosphere

NASA Technical Reports Server (NTRS)

Choi, David S.; Simon-Miller, Amy A.

2012-01-01

A variety of intriguing atmospheric phenomena reside on both sides of Jupiter's equator. 5-micron bright hot spots and opaque plumes prominently exhibit dynamic behavior to the north, whereas compact, dark chevron-shaped features and isolated anticyclonic disturbances periodically occupy the southern equatorial latitudes. All of these phenomena are associated with the vertical and meridional perturbations of Rossby waves disturbing the mean atmospheric state. As previous observational analysis and numerical simulations have investigated the dynamics of the region, an examination of the atmosphere's vertical structure though radiative transfer analysis is necessary for improved understanding of this unique environment. Here we present preliminary analysis of a multispectral Cassini imaging data set acquired during the spacecraft's flyby of Jupiter in 2000. We evaluated multiple methane and continuum spectral channels at available viewing angles to improve constraints on the vertical structure of the haze and cloud layers comprising these interesting features. Our preliminary results indicate distinct differences in the structure for both hemispheres. Upper troposphere hazes and cloud layers are prevalent in the northern equatorial latitudes, but are not present in corresponding southern latitudes. Continued analysis will further constrain the precise structure present in these phenomena and the differences between them.

Application of Wavelet Transform for PDZ Domain Classification

PubMed Central

Daqrouq, Khaled; Alhmouz, Rami; Balamesh, Ahmed; Memic, Adnan

2015-01-01

PDZ domains have been identified as part of an array of signaling proteins that are often unrelated, except for the well-conserved structural PDZ domain they contain. These domains have been linked to many disease processes including common Avian influenza, as well as very rare conditions such as Fraser and Usher syndromes. Historically, based on the interactions and the nature of bonds they form, PDZ domains have most often been classified into one of three classes (class I, class II and others - class III), that is directly dependent on their binding partner. In this study, we report on three unique feature extraction approaches based on the bigram and trigram occurrence and existence rearrangements within the domain's primary amino acid sequences in assisting PDZ domain classification. Wavelet packet transform (WPT) and Shannon entropy denoted by wavelet entropy (WE) feature extraction methods were proposed. Using 115 unique human and mouse PDZ domains, the existence rearrangement approach yielded a high recognition rate (78.34%), which outperformed our occurrence rearrangements based method. The recognition rate was (81.41%) with validation technique. The method reported for PDZ domain classification from primary sequences proved to be an encouraging approach for obtaining consistent classification results. We anticipate that by increasing the database size, we can further improve feature extraction and correct classification. PMID:25860375

From Sequence and Forces to Structure, Function and Evolution of Intrinsically Disordered Proteins

PubMed Central

Forman-Kay, Julie D.; Mittag, Tanja

2015-01-01

Intrinsically disordered proteins (IDPs), which lack persistent structure, are a challenge to structural biology due to the inapplicability of standard methods for characterization of folded proteins as well as their deviation from the dominant structure/function paradigm. Their widespread presence and involvement in biological function, however, has spurred the growing acceptance of the importance of IDPs and the development of new tools for studying their structure, dynamics and function. The interplay of folded and disordered domains or regions for function and the existence of a continuum of protein states with respect to conformational energetics, motional timescales and compactness is shaping a unified understanding of structure-dynamics-disorder/function relationships. On the 20th anniversary of this journal, Structure, we provide a historical perspective on the investigation of IDPs and summarize the sequence features and physical forces that underlie their unique structural, functional and evolutionary properties. PMID:24010708

From sequence and forces to structure, function, and evolution of intrinsically disordered proteins.

PubMed

Forman-Kay, Julie D; Mittag, Tanja

2013-09-03

Intrinsically disordered proteins (IDPs), which lack persistent structure, are a challenge to structural biology due to the inapplicability of standard methods for characterization of folded proteins as well as their deviation from the dominant structure/function paradigm. Their widespread presence and involvement in biological function, however, has spurred the growing acceptance of the importance of IDPs and the development of new tools for studying their structure, dynamics, and function. The interplay of folded and disordered domains or regions for function and the existence of a continuum of protein states with respect to conformational energetics, motional timescales, and compactness are shaping a unified understanding of structure-dynamics-disorder/function relationships. In the 20(th) anniversary of Structure, we provide a historical perspective on the investigation of IDPs and summarize the sequence features and physical forces that underlie their unique structural, functional, and evolutionary properties. Copyright © 2013 Elsevier Ltd. All rights reserved.

Liquid crystalline polymers

NASA Technical Reports Server (NTRS)

1990-01-01

The remarkable mechanical properties and thermal stability of fibers fabricated from liquid crystalline polymers (LCPs) have led to the use of these materials in structural applications where weight savings are critical. Advances in processing of LCPs could permit the incorporation of these polymers into other than uniaxial designs and extend their utility into new areas such as nonlinear optical devices. However, the unique feature of LCPs (intrinsic orientation order) is itself problematic, and current understanding of processing with control of orientation falls short of allowing manipulation of macroscopic orientation (except for the case of uniaxial fibers). The current and desirable characteristics of LCPs are reviewed and specific problems are identified along with issues that must be addressed so that advances in the use of these unique polymers can be expedited.

Cell–cell adhesion in metazoans relies on evolutionarily conserved features of the α-catenin·β-catenin–binding interface

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

Shao, Xiangqiang; Kang, Hyunook; Loveless, Timothy

Stable tissue integrity during embryonic development relies on the function of the cadherin·catenin complex (CCC). The Caenorhabditis elegans CCC is a useful paradigm for analyzing in vivo requirements for specific interactions among the core components of the CCC, and it provides a unique opportunity to examine evolutionarily conserved mechanisms that govern the interaction between α- and β-catenin. HMP-1, unlike its mammalian homolog α-catenin, is constitutively monomeric, and its binding affinity for HMP-2/β-catenin is higher than that of α-catenin for β-catenin. A crystal structure shows that the HMP-1·HMP-2 complex forms a five-helical bundle structure distinct from the structure of the mammalianmore » α-catenin·β-catenin complex. Deletion analysis based on the crystal structure shows that the first helix of HMP-1 is necessary for binding HMP-2 avidly in vitro and for efficient recruitment of HMP-1 to adherens junctions in embryos. HMP-2 Ser-47 and Tyr-69 flank its binding interface with HMP-1, and we show that phosphomimetic mutations at these two sites decrease binding affinity of HMP-1 to HMP-2 by 40–100-fold in vitro. In vivo experiments using HMP-2 S47E and Y69E mutants showed that they are unable to rescue hmp-2(zu364) mutants, suggesting that phosphorylation of HMP-2 on Ser-47 and Tyr-69 could be important for regulating CCC formation in C. elegans. Our data provide novel insights into how cadherin-dependent cell–cell adhesion is modulated in metazoans by conserved elements as well as features unique to specific organisms.« less

Cell–cell adhesion in metazoans relies on evolutionarily conserved features of the α-catenin·β-catenin–binding interface

DOE PAGES

Shao, Xiangqiang; Kang, Hyunook; Loveless, Timothy; ...

2017-08-25

Stable tissue integrity during embryonic development relies on the function of the cadherin·catenin complex (CCC). The Caenorhabditis elegans CCC is a useful paradigm for analyzing in vivo requirements for specific interactions among the core components of the CCC, and it provides a unique opportunity to examine evolutionarily conserved mechanisms that govern the interaction between α- and β-catenin. HMP-1, unlike its mammalian homolog α-catenin, is constitutively monomeric, and its binding affinity for HMP-2/β-catenin is higher than that of α-catenin for β-catenin. A crystal structure shows that the HMP-1·HMP-2 complex forms a five-helical bundle structure distinct from the structure of the mammalianmore » α-catenin·β-catenin complex. Deletion analysis based on the crystal structure shows that the first helix of HMP-1 is necessary for binding HMP-2 avidly in vitro and for efficient recruitment of HMP-1 to adherens junctions in embryos. HMP-2 Ser-47 and Tyr-69 flank its binding interface with HMP-1, and we show that phosphomimetic mutations at these two sites decrease binding affinity of HMP-1 to HMP-2 by 40–100-fold in vitro. In vivo experiments using HMP-2 S47E and Y69E mutants showed that they are unable to rescue hmp-2(zu364) mutants, suggesting that phosphorylation of HMP-2 on Ser-47 and Tyr-69 could be important for regulating CCC formation in C. elegans. Our data provide novel insights into how cadherin-dependent cell–cell adhesion is modulated in metazoans by conserved elements as well as features unique to specific organisms.« less

Using non-invasive molecular spectroscopic techniques to detect unique aspects of protein Amide functional groups and chemical properties of modeled forage from different sourced-origins

NASA Astrophysics Data System (ADS)

Ji, Cuiying; Zhang, Xuewei; Yu, Peiqiang

2016-03-01

The non-invasive molecular spectroscopic technique-FT/IR is capable to detect the molecular structure spectral features that are associated with biological, nutritional and biodegradation functions. However, to date, few researches have been conducted to use these non-invasive molecular spectroscopic techniques to study forage internal protein structures associated with biodegradation and biological functions. The objectives of this study were to detect unique aspects and association of protein Amide functional groups in terms of protein Amide I and II spectral profiles and chemical properties in the alfalfa forage (Medicago sativa L.) from different sourced-origins. In this study, alfalfa hay with two different origins was used as modeled forage for molecular structure and chemical property study. In each forage origin, five to seven sources were analyzed. The molecular spectral profiles were determined using FT/IR non-invasive molecular spectroscopy. The parameters of protein spectral profiles included functional groups of Amide I, Amide II and Amide I to II ratio. The results show that the modeled forage Amide I and Amide II were centered at 1653 cm- 1 and 1545 cm- 1, respectively. The Amide I spectral height and area intensities were from 0.02 to 0.03 and 2.67 to 3.36 AI, respectively. The Amide II spectral height and area intensities were from 0.01 to 0.02 and 0.71 to 0.93 AI, respectively. The Amide I to II spectral peak height and area ratios were from 1.86 to 1.88 and 3.68 to 3.79, respectively. Our results show that the non-invasive molecular spectroscopic techniques are capable to detect forage internal protein structure features which are associated with forage chemical properties.

Evaluating Sensory Processing in Fragile X Syndrome: Psychometric Analysis of the Brain Body Center Sensory Scales (BBCSS).

PubMed

Kolacz, Jacek; Raspa, Melissa; Heilman, Keri J; Porges, Stephen W

2018-06-01

Individuals with fragile X syndrome (FXS), especially those co-diagnosed with autism spectrum disorder (ASD), face many sensory processing challenges. However, sensory processing measures informed by neurophysiology are lacking. This paper describes the development and psychometric properties of a parent/caregiver report, the Brain-Body Center Sensory Scales (BBCSS), based on Polyvagal Theory. Parents/guardians reported on 333 individuals with FXS, 41% with ASD features. Factor structure using a split-sample exploratory-confirmatory design conformed to neurophysiological predictions. Internal consistency, test-retest, and inter-rater reliability were good to excellent. BBCSS subscales converged with the Sensory Profile and Sensory Experiences Questionnaire. However, data also suggest that BBCSS subscales reflect unique features related to sensory processing. Individuals with FXS and ASD features displayed more sensory challenges on most subscales.

The role of nonconserved residues of Archaeoglobus fulgidus ferritin on its unique structure and biophysical properties.

PubMed

Sana, Barindra; Johnson, Eric; Le Magueres, Pierre; Criswell, Angela; Cascio, Duilio; Lim, Sierin

2013-11-08

Archaeoglobus fulgidus ferritin (AfFtn) is the only tetracosameric ferritin known to form a tetrahedral cage, a structure that remains unique in structural biology. As a result of the tetrahedral (2-3) symmetry, four openings (∼45 Å in diameter) are formed in the cage. This open tetrahedral assembly contradicts the paradigm of a typical ferritin cage: a closed assembly having octahedral (4-3-2) symmetry. To investigate the molecular mechanism affecting this atypical assembly, amino acid residues Lys-150 and Arg-151 were replaced by alanine. The data presented here shed light on the role that these residues play in shaping the unique structural features and biophysical properties of the AfFtn. The x-ray crystal structure of the K150A/R151A mutant, solved at 2.1 Å resolution, indicates that replacement of these key residues flips a "symmetry switch." The engineered molecule no longer assembles with tetrahedral symmetry but forms a typical closed octahedral ferritin cage. Small angle x-ray scattering reveals that the overall shape and size of AfFtn and AfFtn-AA in solution are consistent with those observed in their respective crystal structures. Iron binding and release kinetics of the AfFtn and AfFtn-AA were investigated to assess the contribution of cage openings to the kinetics of iron oxidation, mineralization, or reductive iron release. Identical iron binding kinetics for AfFtn and AfFtn-AA suggest that Fe(2+) ions do not utilize the triangular pores for access to the catalytic site. In contrast, relatively slow reductive iron release was observed for the closed AfFtn-AA, demonstrating involvement of the large pores in the pathway for iron release.

Geologic map of the Lakshmi Planum quadrangle (V-7), Venus

USGS Publications Warehouse

Ivanov, Mikhail A.; Head, James W.

2010-01-01

The Lakshmi Planum quadrangle is in the northern hemisphere of Venus and extends from lat 50 degrees to 75 degrees N., and from long 300 degrees to 360 degrees E. The elevated volcanic plateau of Lakshmi Planum, which represents a very specific and unique class of highlands on Venus, dominates the northern half of the quadrangle. The surface of the planum stands 3-4 km above mean planetary radius and the plateau is surrounded by the highest Venusian mountain ranges, 7-10 km high. Before the Magellan mission, the geology of the Lakshmi Planum quadrangle was known on the basis of topographic data acquired by the Pioneer-Venus and Venera-15/16 altimeter and radar images received by the Arecibo telescope and Venera-15/16 spacecraft. These data showed unique topographic and morphologic structures of the mountain belts, which have no counterparts elsewhere on Venus, and the interior volcanic plateau with two large and low volcanic centers and large blocks of tessera-like terrain. From the outside, Lakshmi Planum is outlined by a zone of complexly deformed terrains that occur on the regional outer slope of Lakshmi. Vast low-lying plains surround this zone. After acquisition of the Venera-15/16 data, two classes of hypotheses were formulated to explain the unique structure of Lakshmi Planum and its surrounding. The first proposed that the western portion of Ishtar Terra, dominated by Lakshmi Planum, was a site of large-scale upwelling while the alternative hypothesis considered this region as a site of large-scale downwelling and underthrusting. Early Magellan results showed important details of the general geology of this area displayed in the Venera-15/16 images. Swarms of extensional structures and massifs of tesserae populate the southern slope of Lakshmi. The zone of fractures and grabens form a giant arc thousands of kilometers long and hundreds of kilometers wide around the southern flank of Lakshmi Planum. From the north, the deformational zones consist mostly of contractional structures such as ridges. Corona and corona-like structures are not typical features of this zone but occur within separate branches of extensional structures oriented radial to the edge of Lakshmi. The southeastern edge of Lakshmi appears to be the source of large volcanic flows that extend to the south toward the lowland areas of Sedna Planitia. Colette and Sacajawea Paterae in the interior of Lakshmi are low volcanic centers with very deep central depressions. Lava flows sourced by Colette and Sacajawea form distinctive radial patterns around these volcanoes. Magellan gravity data show that the northern and northeastern portions of the quadrangle, which correspond to Lakshmi Planum, represent a significant geoid anomaly with the peak value of about 90 m over Maxwell Montes at the eastern edge of the map area. Maxwell is characterized also by very high vertical gravity acceleration values (as much as 268 mGal). The lowland of Sedna Planitia to the south of Lakshmi has mostly negative geoid values (down to -40 m). The key geological structure of the quadrangle is Lakshmi Planum, the mode of formation of which is still a major unresolved problem. The topographic configuration, gravity signature, and pattern of deformation inside Lakshmi and along its boundaries make this feature unique on Venus. Thus, geological mapping of this region allows addressing several important questions that should help to put some constraints on the existing models of Lakshmi formation. What is the sequence of events in the formation and evolution of such a unique morphologic and topographic feature? What are the characteristics of the marginal areas of Lakshmi: the compact mountain belts and broad zones of deformation in the transition zone between Lakshmi and surrounding lowlands? How do the units in Lakshmi Planum quadrangle compare with the units mapped in neighboring and distant regions of Venus and what information do they provide concerning models for Venus

The crystal structure of the Leishmania infantum Silent Information Regulator 2 related protein 1: Implications to protein function and drug design.

PubMed

Ronin, Céline; Costa, David Mendes; Tavares, Joana; Faria, Joana; Ciesielski, Fabrice; Ciapetti, Paola; Smith, Terry K; MacDougall, Jane; Cordeiro-da-Silva, Anabela; Pemberton, Iain K

2018-01-01

The de novo crystal structure of the Leishmania infantum Silent Information Regulator 2 related protein 1 (LiSir2rp1) has been solved at 1.99Å in complex with an acetyl-lysine peptide substrate. The structure is broadly commensurate with Hst2/SIRT2 proteins of yeast and human origin, reproducing many of the structural features common to these sirtuin deacetylases, including the characteristic small zinc-binding domain, and the larger Rossmann-fold domain involved in NAD+-binding interactions. The two domains are linked via a cofactor binding loop ordered in open conformation. The peptide substrate binds to the LiSir2rp1 protein via a cleft formed between the small and large domains, with the acetyl-lysine side chain inserting further into the resultant hydrophobic tunnel. Crystals were obtained only with recombinant LiSir2rp1 possessing an extensive internal deletion of a proteolytically-sensitive region unique to the sirtuins of kinetoplastid origin. Deletion of 51 internal amino acids (P253-E303) from LiSir2rp1 did not appear to alter peptide substrate interactions in deacetylation assays, but was indispensable to obtain crystals. Removal of this potentially flexible region, that otherwise extends from the classical structural elements of the Rossmann-fold, specifically the β8-β9 connector, appears to result in lower accumulation of the protein when expressed from episomal vectors in L. infantum SIR2rp1 single knockout promastigotes. The biological function of the large serine-rich insertion in kinetoplastid/trypanosomatid sirtuins, highlighted as a disordered region with strong potential for post-translational modification, remains unknown but may confer additional cellular functions that are distinct from their human counterparts. These unique molecular features, along with the resolution of the first kinetoplastid sirtuin deacetylase structure, present novel opportunities for drug design against a protein target previously established as essential to parasite survival and proliferation.

Conservation and divergence of C-terminal domain structure in the retinoblastoma protein family

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

Liban, Tyler J.; Medina, Edgar M.; Tripathi, Sarvind

The retinoblastoma protein (Rb) and the homologous pocket proteins p107 and p130 negatively regulate cell proliferation by binding and inhibiting members of the E2F transcription factor family. The structural features that distinguish Rb from other pocket proteins have been unclear but are critical for understanding their functional diversity and determining why Rb has unique tumor suppressor activities. We describe here important differences in how the Rb and p107 C-terminal domains (CTDs) associate with the coiled-coil and marked-box domains (CMs) of E2Fs. We find that although CTD–CM binding is conserved across protein families, Rb and p107 CTDs show clear preferences formore » different E2Fs. A crystal structure of the p107 CTD bound to E2F5 and its dimer partner DP1 reveals the molecular basis for pocket protein–E2F binding specificity and how cyclin-dependent kinases differentially regulate pocket proteins through CTD phosphorylation. Our structural and biochemical data together with phylogenetic analyses of Rb and E2F proteins support the conclusion that Rb evolved specific structural motifs that confer its unique capacity to bind with high affinity those E2Fs that are the most potent activators of the cell cycle.« less

Mitochondrial ADCK3 employs an atypical protein kinase-like fold to enable coenzyme Q biosynthesis

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

Stefely, Jonathan A.; Reidenbach, Andrew G.; Ulbrich, Arne

The ancient UbiB protein kinase-like family is involved in isoprenoid lipid biosynthesis and is implicated in human diseases, but demonstration of UbiB kinase activity has remained elusive for unknown reasons. In this paper, we quantitatively define UbiB-specific sequence motifs and reveal their positions within the crystal structure of a UbiB protein, ADCK3. We find that multiple UbiB-specific features are poised to inhibit protein kinase activity, including an N-terminal domain that occupies the typical substrate binding pocket and a unique A-rich loop that limits ATP binding by establishing an unusual selectivity for ADP. A single alanine-to-glycine mutation of this loop flipsmore » this coenzyme selectivity and enables autophosphorylation but inhibits coenzyme Q biosynthesis in vivo, demonstrating functional relevance for this unique feature. Finally, our work provides mechanistic insight into UbiB enzyme activity and establishes a molecular foundation for further investigation of how UbiB family proteins affect diseases and diverse biological pathways.« less

Mitochondrial ADCK3 employs an atypical protein kinase-like fold to enable coenzyme Q biosynthesis

DOE PAGES

Stefely, Jonathan A.; Reidenbach, Andrew G.; Ulbrich, Arne; ...

2014-12-11

The ancient UbiB protein kinase-like family is involved in isoprenoid lipid biosynthesis and is implicated in human diseases, but demonstration of UbiB kinase activity has remained elusive for unknown reasons. In this paper, we quantitatively define UbiB-specific sequence motifs and reveal their positions within the crystal structure of a UbiB protein, ADCK3. We find that multiple UbiB-specific features are poised to inhibit protein kinase activity, including an N-terminal domain that occupies the typical substrate binding pocket and a unique A-rich loop that limits ATP binding by establishing an unusual selectivity for ADP. A single alanine-to-glycine mutation of this loop flipsmore » this coenzyme selectivity and enables autophosphorylation but inhibits coenzyme Q biosynthesis in vivo, demonstrating functional relevance for this unique feature. Finally, our work provides mechanistic insight into UbiB enzyme activity and establishes a molecular foundation for further investigation of how UbiB family proteins affect diseases and diverse biological pathways.« less

Eye development in the four-eyed fish Anableps anableps: cranial and retinal adaptations to simultaneous aerial and aquatic vision

PubMed Central

Perez, Louise N.; Lorena, Jamily; Costa, Carinne M.; Araujo, Maysa S.; Frota-Lima, Gabriela N.; Matos-Rodrigues, Gabriel E.; Martins, Rodrigo A. P.; Mattox, George M. T.

2017-01-01

The unique eyes of the four-eyed fish Anableps anableps have long intrigued biologists. Key features associated with the bulging eye of Anableps include the expanded frontal bone and the duplicated pupils and cornea. Furthermore, the Anableps retina expresses different photoreceptor genes in dorsal and ventral regions, potentially associated with distinct aerial and aquatic stimuli. To gain insight into the developmental basis of the Anableps unique eye, we examined neurocranium and eye ontogeny, as well as photoreceptor gene expression during larval stages. First, we described six larval stages during which duplication of eye structures occurs. Our osteological analysis of neurocranium ontogeny revealed another distinctive Anablepid feature: an ossified interorbital septum partially separating the orbital cavities. Furthermore, we identified the onset of differences in cell proliferation and cell layer density between dorsal and ventral regions of the retina. Finally, we show that differential photoreceptor gene expression in the retina initiates during development, suggesting that it is inherited and not environmentally determined. In sum, our results shed light on the ontogenetic steps leading to the highly derived Anableps eye. PMID:28381624

A rigid and thermally stable all ceramic optical support bench assembly for the LSST Camera

NASA Astrophysics Data System (ADS)

Kroedel, Matthias; Langton, J. Brian; Wahl, Bill

2017-09-01

This paper will present the ceramic design, fabrication and metrology results and assembly plan of the LSST camera optical bench structure which is using the unique manufacturing features of the HB-Cesic technology. The optical bench assembly consists of a rigid "Grid" fabrication supporting individual raft plates mounting sensor assemblies by way of a rigid kinematic support system to meet extreme stringent requirements for focal plane planarity and stability.

Group therapy techniques for sexually abused preteen girls.

PubMed

Berman, P

1990-01-01

This article describes an open-ended, structured, highly intensive therapy group for sexually abused preteen girls that was the primary mode of treatment for 11 girls from multiproblem, low-income, rural, white families. The active support of Child Protective Service workers was important in maintaining the girls in treatment in the face of strong parental opposition. Unique features of the group included simultaneous group goals and individualized goals. A case description illustrates the makeup and functioning of the program.

Western Pacific Tropical Cyclone Adaptive Observing of Inner Core Life-cycle Structure and Intensity Change

DTIC Science & Technology

2009-09-30

airborne radar images; develop an analysis scheme for the monsoon and storm- scale circulation features that would: a. Define large-scale context...Doppler radar observations of TC mesoscale observations. The TCS-08 field program provided unique aircraft reconnaissance (recon) data that will be...system for WC-130J, as well as developed new system for recording airborne radar video for the first time. 3. Created an archive of all WC-130J

Voltage-sensing phosphatase: its molecular relationship with PTEN.

PubMed

Okamura, Yasushi; Dixon, Jack E

2011-02-01

Voltage-sensing phosphoinositide phosphatase (VSP) contains voltage sensor and cytoplasmic phosphatase domains. A unique feature of this protein is that depolarization-induced motions of the voltage sensor activate PtdIns(3,4,5)P(3) and PtdIns(4,5)P(2) phosphatase activities. VSP exhibits remarkable structural similarities with PTEN, the phosphatase and tensin homolog deleted on chromosome 10. These similarities include the cytoplasmic phosphatase region, the phosphoinositide binding region, and the putative membrane interacting C2 domain.

Functional conjugated pyridines via main-group element tuning.

PubMed

Stolar, Monika; Baumgartner, Thomas

2018-03-29

Pyridine-based materials have seen widespread attention for the development of n-type organic materials. In recent years, the incorporation of main-group elements has also explored significant advantages for the development and tunability of organic conjugated materials. The unique chemical and electronic structure of main-group elements has led to several enhancements in conventional organic materials. This Feature article highlights recent main-group based pyridine materials by discussing property enhancements and application in organic electronics.

Animal Toxins Providing Insights into TRPV1 Activation Mechanism

PubMed Central

Geron, Matan; Hazan, Adina

2017-01-01

Beyond providing evolutionary advantages, venoms offer unique research tools, as they were developed to target functionally important proteins and pathways. As a key pain receptor in the nociceptive pathway, transient receptor potential vanilloid 1 (TRPV1) of the TRP superfamily has been shown to be a target for several toxins, as a way of producing pain to deter predators. Importantly, TRPV1 is involved in thermoregulation, inflammation, and acute nociception. As such, toxins provide tools to understand TRPV1 activation and modulation, a critical step in advancing pain research and the development of novel analgesics. Indeed, the phytotoxin capsaicin, which is the spicy chemical in chili peppers, was invaluable in the original cloning and characterization of TRPV1. The unique properties of each subsequently characterized toxin have continued to advance our understanding of functional, structural, and biophysical characteristics of TRPV1. By building on previous reviews, this work aims to provide a comprehensive summary of the advancements made in TRPV1 research in recent years by employing animal toxins, in particular DkTx, RhTx, BmP01, Echis coloratus toxins, APHCs and HCRG21. We examine each toxin’s functional aspects, behavioral effects, and structural features, all of which have contributed to our current knowledge of TRPV1. We additionally discuss the key features of TRPV1’s outer pore domain, which proves to be the target of the currently discussed toxins. PMID:29035314

Intrahaplotypic Variants Differentiate Complex Linkage Disequilibrium within Human MHC Haplotypes

PubMed Central

Lam, Tze Hau; Tay, Matthew Zirui; Wang, Bei; Xiao, Ziwei; Ren, Ee Chee

2015-01-01

Distinct regions of long-range genetic fixation in the human MHC region, known as conserved extended haplotypes (CEHs), possess unique genomic characteristics and are strongly associated with numerous diseases. While CEHs appear to be homogeneous by SNP analysis, the nature of fine variations within their genomic structure is unknown. Using multiple, MHC-homozygous cell lines, we demonstrate extensive sequence conservation in two common Asian MHC haplotypes: A33-B58-DR3 and A2-B46-DR9. However, characterization of phase-resolved MHC haplotypes revealed unique intra-CEH patterns of variation and uncovered 127 single nucleotide variants (SNVs) which are missing from public databases. We further show that the strong linkage disequilibrium structure within the human MHC that typically confounds precise identification of genetic features can be resolved using intra-CEH variants, as evidenced by rs3129063 and rs448489, which affect expression of ZFP57, a gene important in methylation and epigenetic regulation. This study demonstrates an improved strategy that can be used towards genetic dissection of diseases. PMID:26593880

The structure and organization of lanceolate mechanosensory complexes at mouse hair follicles

PubMed Central

Li, Lishi; Ginty, David D

2014-01-01

In mouse hairy skin, lanceolate complexes associated with three types of hair follicles, guard, awl/auchene and zigzag, serve as mechanosensory end organs. These structures are formed by unique combinations of low-threshold mechanoreceptors (LTMRs), Aβ RA-LTMRs, Aδ-LTMRs, and C-LTMRs, and their associated terminal Schwann cells (TSCs). In this study, we investigated the organization, ultrastructure, and maintenance of longitudinal lanceolate complexes at each hair follicle subtype. We found that TSC processes at hair follicles are tiled and that individual TSCs host axonal endings of more than one LTMR subtype. Electron microscopic analyses revealed unique ultrastructural features of lanceolate complexes that are proposed to underlie mechanotransduction. Moreover, Schwann cell ablation leads to loss of LTMR terminals at hair follicles while, in contrast, TSCs remain associated with hair follicles following skin denervation in adult mice and, remarkably, become re-associated with newly formed axons, indicating a TSC-dependence of lanceolate complex maintenance and regeneration in adults. DOI: http://dx.doi.org/10.7554/eLife.01901.001 PMID:24569481

The structure and organization of lanceolate mechanosensory complexes at mouse hair follicles.

PubMed

Li, Lishi; Ginty, David D

2014-02-25

In mouse hairy skin, lanceolate complexes associated with three types of hair follicles, guard, awl/auchene and zigzag, serve as mechanosensory end organs. These structures are formed by unique combinations of low-threshold mechanoreceptors (LTMRs), Aβ RA-LTMRs, Aδ-LTMRs, and C-LTMRs, and their associated terminal Schwann cells (TSCs). In this study, we investigated the organization, ultrastructure, and maintenance of longitudinal lanceolate complexes at each hair follicle subtype. We found that TSC processes at hair follicles are tiled and that individual TSCs host axonal endings of more than one LTMR subtype. Electron microscopic analyses revealed unique ultrastructural features of lanceolate complexes that are proposed to underlie mechanotransduction. Moreover, Schwann cell ablation leads to loss of LTMR terminals at hair follicles while, in contrast, TSCs remain associated with hair follicles following skin denervation in adult mice and, remarkably, become re-associated with newly formed axons, indicating a TSC-dependence of lanceolate complex maintenance and regeneration in adults. DOI: http://dx.doi.org/10.7554/eLife.01901.001.

Optically pumped VECSELs: review of technology and progress

NASA Astrophysics Data System (ADS)

Guina, M.; Rantamäki, A.; Härkönen, A.

2017-09-01

Vertical-external-cavity surface-emitting lasers (VECSELs) are the most versatile laser sources, combining unique features such as wide spectral coverage, ultrashort pulse operation, low noise properties, high output power, high brightness and compact form-factor. This paper reviews the recent technological developments of VECSELs in connection with the new milestones that continue to pave the way towards their use in numerous applications. Significant attention is devoted to the fabrication of VECSEL gain mirrors in challenging wavelength regions, especially at the yellow and red wavelengths. The reviewed fabrication approaches address wafer-bonded VECSEL structures as well as the use of hybrid mirror structures. Moreover, a comprehensive summary of VECSEL characterization methods is presented; the discussion covers different stages of VECSEL development and different operation regimes, pointing out specific characterization techniques for each of them. Finally, several emerging applications are discussed, with emphasis on the unique application objectives that VECSELs render possible, for example in atom and molecular physics, dermatology and spectroscopy.

Biomechanical and Structural Features of CS2 Fimbriae of Enterotoxigenic Escherichia coli

PubMed Central

Mortezaei, Narges; Singh, Bhupender; Zakrisson, Johan; Bullitt, Esther; Andersson, Magnus

2015-01-01

Enterotoxigenic Escherichia coli (ETEC) are a major cause of diarrhea worldwide, and infection of children in under-developed countries often leads to high mortality rates. Isolated ETEC expresses a plethora of colonization factors (fimbriae/pili), of which CFA/I and CFA/II, which are assembled via the alternate chaperone pathway (ACP), are among the most common. Fimbriae are filamentous structures whose shafts are primarily composed of helically arranged single pilin-protein subunits, with a unique biomechanical ability to unwind and rewind. A sustained ETEC infection, under adverse conditions of dynamic shear forces, is primarily attributed to this biomechanical feature of ETEC fimbriae. Recent understanding about the role of fimbriae as virulence factors points to an evolutionary adaptation of their structural and biomechanical features. In this work, we investigated the biophysical properties of CS2 fimbriae from the CFA/II group. Homology modeling of its major structural subunit, CotA, reveals structural clues related to the niche in which they are expressed. Using optical-tweezers force spectroscopy, we found that CS2 fimbriae unwind at a constant force of 10 pN and have a corner velocity (i.e., the velocity at which the force required for unwinding rises exponentially with increased speed) of 1300 nm/s. The biophysical properties of CS2 fimbriae assessed in this work classify them into a low-force unwinding group of fimbriae together with the CFA/I and CS20 fimbriae expressed by ETEC strains. The three fimbriae are expressed by ETEC, colonize in similar gut environments, and exhibit similar biophysical features, but differ in their biogenesis. Our observation suggests that the environment has a strong impact on the biophysical characteristics of fimbriae expressed by ETEC. PMID:26153701

The molecular biology of the group VIA Ca2+-independent phospholipase A2.

PubMed

Ma, Z; Turk, J

2001-01-01

The group VIA PLA2 is a member of the PLA2 superfamily. This enzyme, which is cytosolic and Ca2+-independent, has been designated iPLA2beta to distinguish it from another recently cloned Ca2+-independent PLA2. Features of iPLA2beta molecular structure offer some insight into possible cellular functions of the enzyme. At least two catalytically active iPLA2beta isoforms and additionalsplicing variants are derived from a single gene that consists of at least 17 exons located on human chromosome 22q13.1. Potential tumor suppressor genes also reside at or near this locus. Structural analyses reveal that iPLA2beta contains unique structural features that include a serine lipase consensus motif (GXSXG), a putative ATP-binding domain, an ankyrin-repeat domain, a caspase-3 cleavage motif DVTD138Y/N, a bipartite nuclear localization signal sequence, and a proline-rich region in the human long isoform. iPLA2beta is widely expressed among mammalian tissues, with highest expression in testis and brain. iPLA2beta prefers to hydrolyze fatty acid at the sn-2 fatty acid substituent but also exhibits phospholipase A1, lysophospholipase, PAF acetylhydrolase, and transacylase activities. iPLA2beta may participate in signaling, apoptosis, membrane phospholipid remodeling, membrane homeostasis, arachidonate release, and exocytotic membrane fusion. Structural features and the existence of multiple splicing variants of iPLA2beta suggest that iPLA2beta may be subject to complex regulatory mechanisms that differ among cell types. Further study of its regulation and interaction with other proteins may yield insight into how its structural features are related to its function.

A General-Purpose Optimization Engine for Multi-Disciplinary Design Applications

NASA Technical Reports Server (NTRS)

Patnaik, Surya N.; Hopkins, Dale A.; Berke, Laszlo

1996-01-01

A general purpose optimization tool for multidisciplinary applications, which in the literature is known as COMETBOARDS, is being developed at NASA Lewis Research Center. The modular organization of COMETBOARDS includes several analyzers and state-of-the-art optimization algorithms along with their cascading strategy. The code structure allows quick integration of new analyzers and optimizers. The COMETBOARDS code reads input information from a number of data files, formulates a design as a set of multidisciplinary nonlinear programming problems, and then solves the resulting problems. COMETBOARDS can be used to solve a large problem which can be defined through multiple disciplines, each of which can be further broken down into several subproblems. Alternatively, a small portion of a large problem can be optimized in an effort to improve an existing system. Some of the other unique features of COMETBOARDS include design variable formulation, constraint formulation, subproblem coupling strategy, global scaling technique, analysis approximation, use of either sequential or parallel computational modes, and so forth. The special features and unique strengths of COMETBOARDS assist convergence and reduce the amount of CPU time used to solve the difficult optimization problems of aerospace industries. COMETBOARDS has been successfully used to solve a number of problems, including structural design of space station components, design of nozzle components of an air-breathing engine, configuration design of subsonic and supersonic aircraft, mixed flow turbofan engines, wave rotor topped engines, and so forth. This paper introduces the COMETBOARDS design tool and its versatility, which is illustrated by citing examples from structures, aircraft design, and air-breathing propulsion engine design.

Anterior lens epithelium in intumescent white cataracts - scanning and transmission electron microscopy study.

PubMed

Andjelic, Sofija; Drašlar, Kazimir; Hvala, Anastazija; Hawlina, Marko

2016-02-01

Our purpose was to study the structure of the lens epithelial cells (LECs) of intumescent white cataracts (IC) in comparison with nuclear cataracts (NC) in order to investigate possible structural reasons for development of IC. The anterior lens capsule (aLC: basement membrane and associated LECs) were obtained from cataract surgery and prepared for scanning electron microscopy (SEM) and transmission electron microscopy (TEM). We observed by SEM that in IC, LEC swelling was pronounced with the clefts surrounding the groups of LECs. Another structural feature was spherical formations, that were observed on the apical side of LEC's, towards the fibre cell layer, both by SEM and TEM. Development of these structures, bulging out from the apical cell membrane of the LEC's and disrupting it, could be followed in steps towards the sphere formation. The degeneration of the lens epithelium and the structures of the aLC in IC similar to Morgagnian globules were also observed. None of these structural changes were observed in NC. We show by SEM and TEM that, in IC, LECs have pronounced structural features not observed in NC. This supports the hypothesis that the disturbed structure of LECs plays a role in water accumulation in the IC lens. We also suggest that, in IC, LECs produce bulging spheres that represent unique structures of degenerated material, extruded from the LEC.

Modeling photoacoustic spectral features of micron-sized particles

NASA Astrophysics Data System (ADS)

Strohm, Eric M.; Gorelikov, Ivan; Matsuura, Naomi; Kolios, Michael C.

2014-10-01

The photoacoustic signal generated from particles when irradiated by light is determined by attributes of the particle such as the size, speed of sound, morphology and the optical absorption coefficient. Unique features such as periodically varying minima and maxima are observed throughout the photoacoustic signal power spectrum, where the periodicity depends on these physical attributes. The frequency content of the photoacoustic signals can be used to obtain the physical attributes of unknown particles by comparison to analytical solutions of homogeneous symmetric geometric structures, such as spheres. However, analytical solutions do not exist for irregularly shaped particles, inhomogeneous particles or particles near structures. A finite element model (FEM) was used to simulate photoacoustic wave propagation from four different particle configurations: a homogeneous particle suspended in water, a homogeneous particle on a reflecting boundary, an inhomogeneous particle with an absorbing shell and non-absorbing core, and an irregularly shaped particle such as a red blood cell. Biocompatible perfluorocarbon droplets, 3-5 μm in diameter containing optically absorbing nanoparticles were used as the representative ideal particles, as they are spherical, homogeneous, optically translucent, and have known physical properties. The photoacoustic spectrum of micron-sized single droplets in suspension and on a reflecting boundary were measured over the frequency range of 100-500 MHz and compared directly to analytical models and the FEM. Good agreement between the analytical model, FEM and measured values were observed for a droplet in suspension, where the spectral minima agreed to within a 3.3 MHz standard deviation. For a droplet on a reflecting boundary, spectral features were correctly reproduced using the FEM but not the analytical model. The photoacoustic spectra from other common particle configurations such as particle with an absorbing shell and a biconcave-shaped red blood cell were also investigated, where unique features in the power spectrum could be used to identify them.

Aerogel materials with periodic structures imprinted with cellulose nanocrystals.

PubMed

Xu, Yi-Tao; Dai, Yiling; Nguyen, Thanh-Dinh; Hamad, Wadood Y; MacLachlan, Mark J

2018-02-22

Novel aerogel materials with periodic structures derived from chiral nematic liquid crystalline cellulose nanocrystals (CNCs) are reported. The liquid crystalline structure of phase-separated CNCs is locked by a simple solvent exchange method or silica condensation. Both cellulose and silica/cellulose aerogel materials were obtained after critical point drying, and subsequent calcination of the silica/cellulose composite afforded a silica aerogel with periodic order. Gas adsorption and electron microscopy studies revealed that these materials have high surface areas and a unique chiral nematic structure imparted from the helicoidal CNC template. This is a new, scalable approach to aerogel materials with highly anisotropic structures. The high porosity and periodic, chiral features of these new materials may make them suitable for applications that require anisotropic properties or as hard templates for the construction of other ordered aerogels.

A flexible pressure responsive device based on the interaction between silver nanoparticles and an aluminum reflector

NASA Astrophysics Data System (ADS)

Rankin, Alasdair; McGarry, Steven

2018-01-01

The unique and tunable optical properties of metal nanoparticles have attracted intense and sustained academic attention in recent years. In tandem with the demand for low-cost responsive materials, one particular topic of interest is the development of mechanically responsive device structures. This work describes the design, fabrication, and testing of a mechanically responsive plasmonic device structure that has been integrated onto a standard commercial plastic substrate. With a low actuation force and a visually perceivable color shift, this device would be attractive for applications requiring responsive features that can be activated by the human hand.

Phenylethynyl terminated reactive oligomer

NASA Technical Reports Server (NTRS)

Bryant, Robert G. (Inventor); Jensen, Brian J. (Inventor); Hergenrother, Paul M. (Inventor)

1995-01-01

A composition of matter having the general structure: ##STR1## (wherein X is F, Cl, or NO.sub.2, and Y is CO, SO.sub.2 or C(CF.sub.3).sub.2) is employed to terminate a nucleophilic reagent, resulting in the exclusive production of phenylethynyl terminated reactive oligomers which display unique thermal characteristics. A reactive diluent having the general structure: ##STR2## (wherein R is any aliphatic or aromatic moiety) is employed to decrease the melt viscosity of a phenylethynyl terminated reactive oligomer and to subsequently react therewith to provide a thermosetting material of enhanced density. These materials have features which make them attractive candidates for use as composite matrices and adhesives.

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.

Vibronic structure and coupling of higher excited electronic states in carotenoids

NASA Astrophysics Data System (ADS)

Krawczyk, Stanisław; Luchowski, Rafał

2013-03-01

Absorption spectra of all-trans carotenoids (lycopene, violaxanthin, ζ-carotene) at low temperature exhibit peculiar features in the UV range. The transition to the 11Ag+ state ('cis-band') weakens on cooling, indicating that it is induced by thermal deformations of the conjugated chain. The higher energy band has unique vibrational structure indicating the vibronic coupling of nBu with another electronic state. The electroabsorption spectra point to the electric field-induced mixing of the nBu state with the vibrational continuum of a lower-lying excited state (Fano effect). These observations widen the basis for elucidation of the vibronic coupling effects in the lower excited states.

Chemical property based sequence characterization of PpcA and its homolog proteins PpcB-E: A mathematical approach

PubMed Central

Pal Choudhury, Pabitra

2017-01-01

Periplasmic c7 type cytochrome A (PpcA) protein is determined in Geobacter sulfurreducens along with its other four homologs (PpcB-E). From the crystal structure viewpoint the observation emerges that PpcA protein can bind with Deoxycholate (DXCA), while its other homologs do not. But it is yet to be established with certainty the reason behind this from primary protein sequence information. This study is primarily based on primary protein sequence analysis through the chemical basis of embedded amino acids. Firstly, we look for the chemical group specific score of amino acids. Along with this, we have developed a new methodology for the phylogenetic analysis based on chemical group dissimilarities of amino acids. This new methodology is applied to the cytochrome c7 family members and pinpoint how a particular sequence is differing with others. Secondly, we build a graph theoretic model on using amino acid sequences which is also applied to the cytochrome c7 family members and some unique characteristics and their domains are highlighted. Thirdly, we search for unique patterns as subsequences which are common among the group or specific individual member. In all the cases, we are able to show some distinct features of PpcA that emerges PpcA as an outstanding protein compared to its other homologs, resulting towards its binding with deoxycholate. Similarly, some notable features for the structurally dissimilar protein PpcD compared to the other homologs are also brought out. Further, the five members of cytochrome family being homolog proteins, they must have some common significant features which are also enumerated in this study. PMID:28362850

Profiling of the Tox21 Chemical Collection for Mitochondrial Function to Identify Compounds that Acutely Decrease Mitochondrial Membrane Potential

PubMed Central

Attene-Ramos, Matias S.; Huang, Ruili; Michael, Sam; Witt, Kristine L.; Richard, Ann; Tice, Raymond R.; Simeonov, Anton; Austin, Christopher P.

2014-01-01

Background: Mitochondrial dysfunction has been implicated in the pathogenesis of a variety of disorders including cancer, diabetes, and neurodegenerative and cardiovascular diseases. Understanding whether different environmental chemicals and druglike molecules impact mitochondrial function represents an initial step in predicting exposure-related toxicity and defining a possible role for such compounds in the onset of various diseases. Objectives: We sought to identify individual chemicals and general structural features associated with changes in mitochondrial membrane potential (MMP). Methods: We used a multiplexed [two end points in one screen; MMP and adenosine triphosphate (ATP) content] quantitative high throughput screening (qHTS) approach combined with informatics tools to screen the Tox21 library of 10,000 compounds (~ 8,300 unique chemicals) at 15 concentrations each in triplicate to identify chemicals and structural features that are associated with changes in MMP in HepG2 cells. Results: Approximately 11% of the compounds (913 unique compounds) decreased MMP after 1 hr of treatment without affecting cell viability (ATP content). In addition, 309 compounds decreased MMP over a concentration range that also produced measurable cytotoxicity [half maximal inhibitory concentration (IC50) in MMP assay/IC50 in viability assay ≤ 3; p < 0.05]. More than 11% of the structural clusters that constitute the Tox21 library (76 of 651 clusters) were significantly enriched for compounds that decreased the MMP. Conclusions: Our multiplexed qHTS approach allowed us to generate a robust and reliable data set to evaluate the ability of thousands of drugs and environmental compounds to decrease MMP. The use of structure-based clustering analysis allowed us to identify molecular features that are likely responsible for the observed activity. Citation: Attene-Ramos MS, Huang R, Michael S, Witt KL, Richard A, Tice RR, Simeonov A, Austin CP, Xia M. 2015. Profiling of the Tox21 chemical collection for mitochondrial function to identify compounds that acutely decrease mitochondrial membrane potential. Environ Health Perspect 123:49–56; http://dx.doi.org/10.1289/ehp.1408642 PMID:25302578

Chromophoric Nucleoside Analogues: Synthesis and Characterization of 6-Aminouracil-Based Nucleodyes.

PubMed

Freeman, Noam S; Moore, Curtis E; Wilhelmsson, L Marcus; Tor, Yitzhak

2016-06-03

Nucleodyes, visibly colored chromophoric nucleoside analogues, are reported. Design criteria are outlined and the syntheses of cytidine and uridine azo dye analogues derived from 6-aminouracil are described. Structural analysis shows that the nucleodyes are sound structural analogues of their native nucleoside counterparts, and photophysical studies demonstrate that the nucleodyes are sensitive to microenvironmental changes. Quantum chemical calculations are presented as a valuable complementary tool for the design of strongly absorbing nucleodyes, which overlap with the emission of known fluorophores. Förster critical distance (R0) calculations determine that the nucleodyes make good FRET pairs with both 2-aminopurine (2AP) and pyrrolocytosine (PyC). Additionally, unique tautomerization features exhibited by 5-(4-nitrophenylazo)-6-oxocytidine (8) are visualized by an extraordinary crystal structure.

Liquid crystals from mesogens containing gold nanoparticles

NASA Astrophysics Data System (ADS)

Lewandowski, Wiktor; Gorecka, Ewa

Long-range ordered structures made of nanoparticles are perspective materials for future optical, electronic and sensing technologies. Conspicuous physicochemical features of nanoparticle aggregates originate from distant-dependent collective interactions, therefore lately a lot of attention was put to the development of assembly strategies allowing control over nanoparticle spatial distribution. In this chapter we will focus on the assembly process based on using thermotropic liquid-crystalline molecules as surface nanoparticle ligands. First, we discuss architectural parameters that inuence structure and thermal properties of the aggregates. Then, we show that this approach enables formation of assemblies with metamaterial characteristic, gives access to dynamic materials with light-, magneto- and thermo-responsive behavior and allows formation of aggregates with unique structures, which all make this strategy an attractive object of research.

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels.

PubMed

Jossinet, Fabrice; Ludwig, Thomas E; Westhof, Eric

2010-08-15

Assemble is an intuitive graphical interface to analyze, manipulate and build complex 3D RNA architectures. It provides several advanced and unique features within the framework of a semi-automated modeling process that can be performed by homology and ab initio with or without electron density maps. Those include the interactive editing of a secondary structure and a searchable, embedded library of annotated tertiary structures. Assemble helps users with performing recurrent and otherwise tedious tasks in structural RNA research. Assemble is released under an open-source license (MIT license) and is freely available at http://bioinformatics.org/assemble. It is implemented in the Java language and runs on MacOSX, Linux and Windows operating systems.

Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences.

PubMed

Mizianty, Marcin J; Kurgan, Lukasz

2009-12-13

Knowledge of structural class is used by numerous methods for identification of structural/functional characteristics of proteins and could be used for the detection of remote homologues, particularly for chains that share twilight-zone similarity. In contrast to existing sequence-based structural class predictors, which target four major classes and which are designed for high identity sequences, we predict seven classes from sequences that share twilight-zone identity with the training sequences. The proposed MODular Approach to Structural class prediction (MODAS) method is unique as it allows for selection of any subset of the classes. MODAS is also the first to utilize a novel, custom-built feature-based sequence representation that combines evolutionary profiles and predicted secondary structure. The features quantify information relevant to the definition of the classes including conservation of residues and arrangement and number of helix/strand segments. Our comprehensive design considers 8 feature selection methods and 4 classifiers to develop Support Vector Machine-based classifiers that are tailored for each of the seven classes. Tests on 5 twilight-zone and 1 high-similarity benchmark datasets and comparison with over two dozens of modern competing predictors show that MODAS provides the best overall accuracy that ranges between 80% and 96.7% (83.5% for the twilight-zone datasets), depending on the dataset. This translates into 19% and 8% error rate reduction when compared against the best performing competing method on two largest datasets. The proposed predictor provides accurate predictions at 58% accuracy for membrane proteins class, which is not considered by majority of existing methods, in spite that this class accounts for only 2% of the data. Our predictive model is analyzed to demonstrate how and why the input features are associated with the corresponding classes. The improved predictions stem from the novel features that express collocation of the secondary structure segments in the protein sequence and that combine evolutionary and secondary structure information. Our work demonstrates that conservation and arrangement of the secondary structure segments predicted along the protein chain can successfully predict structural classes which are defined based on the spatial arrangement of the secondary structures. A web server is available at http://biomine.ece.ualberta.ca/MODAS/.

Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences

PubMed Central

2009-01-01

Background Knowledge of structural class is used by numerous methods for identification of structural/functional characteristics of proteins and could be used for the detection of remote homologues, particularly for chains that share twilight-zone similarity. In contrast to existing sequence-based structural class predictors, which target four major classes and which are designed for high identity sequences, we predict seven classes from sequences that share twilight-zone identity with the training sequences. Results The proposed MODular Approach to Structural class prediction (MODAS) method is unique as it allows for selection of any subset of the classes. MODAS is also the first to utilize a novel, custom-built feature-based sequence representation that combines evolutionary profiles and predicted secondary structure. The features quantify information relevant to the definition of the classes including conservation of residues and arrangement and number of helix/strand segments. Our comprehensive design considers 8 feature selection methods and 4 classifiers to develop Support Vector Machine-based classifiers that are tailored for each of the seven classes. Tests on 5 twilight-zone and 1 high-similarity benchmark datasets and comparison with over two dozens of modern competing predictors show that MODAS provides the best overall accuracy that ranges between 80% and 96.7% (83.5% for the twilight-zone datasets), depending on the dataset. This translates into 19% and 8% error rate reduction when compared against the best performing competing method on two largest datasets. The proposed predictor provides accurate predictions at 58% accuracy for membrane proteins class, which is not considered by majority of existing methods, in spite that this class accounts for only 2% of the data. Our predictive model is analyzed to demonstrate how and why the input features are associated with the corresponding classes. Conclusions The improved predictions stem from the novel features that express collocation of the secondary structure segments in the protein sequence and that combine evolutionary and secondary structure information. Our work demonstrates that conservation and arrangement of the secondary structure segments predicted along the protein chain can successfully predict structural classes which are defined based on the spatial arrangement of the secondary structures. A web server is available at http://biomine.ece.ualberta.ca/MODAS/. PMID:20003388

Advanced understanding on electronic structure of molecular semiconductors and their interfaces

NASA Astrophysics Data System (ADS)

Akaike, Kouki

2018-03-01

Understanding the electronic structure of organic semiconductors and their interfaces is critical to optimizing functionalities for electronics applications, by rational chemical design and appropriate combination of device constituents. The unique electronic structure of a molecular solid is characterized as (i) anisotropic electrostatic fields that originate from molecular quadrupoles, (ii) interfacial energy-level lineup governed by simple electrostatics, and (iii) weak intermolecular interactions that make not only structural order but also energy distributions of the frontier orbitals sensitive to atmosphere and interface growth. This article shows an overview on these features with reference to the improved understanding of the orientation-dependent electronic structure, comprehensive mechanisms of molecular doping, and energy-level alignment. Furthermore, the engineering of ionization energy by the control of the electrostatic fields and work function of practical electrodes by contact-induced doping is briefly described for the purpose of highlighting how the electronic structure impacts the performance of organic devices.

Influence of landscape structure on reef fish assemblages

USGS Publications Warehouse

Grober-Dunsmore, R.; Frazer, T.K.; Beets, J.P.; Lindberg, W.J.; Zwick, P.; Funicelli, N.A.

2008-01-01

Management of tropical marine environments calls for interdisciplinary studies and innovative methodologies that consider processes occurring over broad spatial scales. We investigated relationships between landscape structure and reef fish assemblage structure in the US Virgin Islands. Measures of landscape structure were transformed into a reduced set of composite indices using principal component analyses (PCA) to synthesize data on the spatial patterning of the landscape structure of the study reefs. However, composite indices (e.g., habitat diversity) were not particularly informative for predicting reef fish assemblage structure. Rather, relationships were interpreted more easily when functional groups of fishes were related to individual habitat features. In particular, multiple reef fish parameters were strongly associated with reef context. Fishes responded to benthic habitat structure at multiple spatial scales, with various groups of fishes each correlated to a unique suite of variables. Accordingly, future experiments should be designed to test functional relationships based on the ecology of the organisms of interest. Our study demonstrates that landscape-scale habitat features influence reef fish communities, illustrating promise in applying a landscape ecology approach to better understand factors that structure coral reef ecosystems. Furthermore, our findings may prove useful in design of spatially-based conservation approaches such as marine protected areas (MPAs), because landscape-scale metrics may serve as proxies for areas with high species diversity and abundance within the coral reef landscape. ?? 2007 Springer Science+Business Media B.V.

Occurrence and structure of epipharyngeal pouches in bears (Ursidae)

PubMed Central

WEISSENGRUBER, G. E.; FORSTENPOINTNER, G.; KÜBBER-HEISS, A.; RIEDELBERGER, K.; SCHWAMMER, H.; GANZBERGER, K.

2001-01-01

The infrequent mention of epipharyngeal pouches occurring in some species of bears indicates the scarcity of morphological and functional knowledge about these structures. In order to provide precise morphological data on the structure of these remarkable formations and to verify their taxonomic utility, the pharyngeal regions of 1 spectacled bear and 3 brown bears were examined. All these individuals possessed epipharyngeal pouches, which are tubular, blind-ending outpouchings of the caudodorsal pharyngeal wall equipped with respiratory epithelium and a thick layer of elastic fibres. While the spectacled bear and Ursus arctos syriacus possessed a single pouch on the caudodorsal wall of the nasopharynx, in Ursus arctos and Ursus arctos beringianus 2 unequally sized pouches were present. Two additional sacs of smaller size, representing outpouchings of the lateral pharyngeal wall, occurred in the spectacled bear. These findings prove epipharyngeal pouches to be constant and unique morphological features of the family Ursidae, the anatomical features suggesting involvement in the respiratory system most probably in important aspects of ursid phonation. This is the first description of epipharyngeal pouches in the spectacled bear. PMID:11322723

Selective binding of choline by a phosphate-coordination-based triple helicate featuring an aromatic box.

PubMed

Jia, Chuandong; Zuo, Wei; Yang, Dong; Chen, Yanming; Cao, Liping; Custelcean, Radu; Hostaš, Jiří; Hobza, Pavel; Glaser, Robert; Wang, Yao-Yu; Yang, Xiao-Juan; Wu, Biao

2017-10-16

In nature, proteins have evolved sophisticated cavities tailored for capturing target guests selectively among competitors of similar size, shape, and charge. The fundamental principles guiding the molecular recognition, such as self-assembly and complementarity, have inspired the development of biomimetic receptors. In the current work, we report a self-assembled triple anion helicate (host 2) featuring a cavity resembling that of the choline-binding protein ChoX, as revealed by crystal and density functional theory (DFT)-optimized structures, which binds choline in a unique dual-site-binding mode. This similarity in structure leads to a similarly high selectivity of host 2 for choline over its derivatives, as demonstrated by the NMR and fluorescence competition experiments. Furthermore, host 2 is able to act as a fluorescence displacement sensor for discriminating choline, acetylcholine, L-carnitine, and glycine betaine effectively.The choline-binding protein ChoX exhibits a synergistic dual-site binding mode that allows it to discriminate choline over structural analogues. Here, the authors design a biomimetic triple anion helicate receptor whose selectivity for choline arises from a similar binding mechanism.

Plasmonic nanostructures through DNA-assisted lithography

PubMed Central

Shen, Boxuan; Linko, Veikko; Tapio, Kosti; Pikker, Siim; Lemma, Tibebe; Gopinath, Ashwin; Gothelf, Kurt V.; Kostiainen, Mauri A.; Toppari, J. Jussi

2018-01-01

Programmable self-assembly of nucleic acids enables the fabrication of custom, precise objects with nanoscale dimensions. These structures can be further harnessed as templates to build novel materials such as metallic nanostructures, which are widely used and explored because of their unique optical properties and their potency to serve as components of novel metamaterials. However, approaches to transfer the spatial information of DNA constructions to metal nanostructures remain a challenge. We report a DNA-assisted lithography (DALI) method that combines the structural versatility of DNA origami with conventional lithography techniques to create discrete, well-defined, and entirely metallic nanostructures with designed plasmonic properties. DALI is a parallel, high-throughput fabrication method compatible with transparent substrates, thus providing an additional advantage for optical measurements, and yields structures with a feature size of ~10 nm. We demonstrate its feasibility by producing metal nanostructures with a chiral plasmonic response and bowtie-shaped nanoantennas for surface-enhanced Raman spectroscopy. We envisage that DALI can be generalized to large substrates, which would subsequently enable scale-up production of diverse metallic nanostructures with tailored plasmonic features. PMID:29423446

In vitro developmental model of the gastrointestinal tract from mouse embryonic stem cells.

PubMed

Torihashi, Shigeko; Kuwahara, Masaki; Kurahashi, Masaaki

2007-10-01

Mouse embryonic stem (ES) cells are pluripotent and retain their potential to form cells, tissues and organs originated from three embryonic germ layers. Recently, we developed in vitro organ--gut-like structures--from mouse ES cells. They had basically similar morphological features to a mouse gastrointestinal tract in vivo composed of three distinct layers (i.e., epithelium, connective tissue and musculature). Gut-like structures showed spontaneous contractions derived from pacemaker cells (interstitial cells of Cajal) in the musculature. We also examined their formation process and expression pattern of transcription factors crucial for gut organogenesis such as Id2, Sox17, HNF3beta/Foxa2 and GATA4. We found that they mimic the development of embryonic gut in vivo and showed a similar expression pattern of common transcription factors. They also maintain their developmental potential after transplantation to a renal capsule. Therefore, gut-like structures are suitable for in vitro models of gastrointestinal tracts and their development. In addition, we pointed out several unique features different from gut in vivo that provide useful and advantageous tools to investigate the developmental mechanism of the gastrointestinal tract.

Methods, systems and devices for detecting threatening objects and for classifying magnetic data

DOEpatents

Kotter, Dale K [Shelley, ID; Roybal, Lyle G [Idaho Falls, ID; Rohrbaugh, David T [Idaho Falls, ID; Spencer, David F [Idaho Falls, ID

2012-01-24

A method for detecting threatening objects in a security screening system. The method includes a step of classifying unique features of magnetic data as representing a threatening object. Another step includes acquiring magnetic data. Another step includes determining if the acquired magnetic data comprises a unique feature.

Family-based risk factors for non-suicidal self-injury: Considering influences of maltreatment, adverse family-life experiences, and parent-child relational risk.

PubMed

Martin, Jodi; Bureau, Jean-François; Yurkowski, Kim; Fournier, Tania Renaud; Lafontaine, Marie-France; Cloutier, Paula

2016-06-01

The current investigation addressed the potential for unique influences of perceived childhood maltreatment, adverse family-life events, and parent-child relational trauma on the lifetime occurrence and addictive features of non-suicidal self-injury (NSSI). Participants included 957 undergraduate students (747 females; M = 20.14 years, SD = 3.88) who completed online questionnaires regarding the key variables under study. Although self-injuring youth reported more experiences with each family-based risk factor, different patterns of association were found when lifetime engagement in NSSI or its addictive features were under study. Perceived parent-child relational trauma was uniquely linked with NSSI behavior after accounting for perceived childhood maltreatment; adverse family-life events had an additional unique association. In contrast, perceived paternal maltreatment was uniquely related with NSSI's addictive features. Findings underline the importance of studying inter-related family-based risk factors of NSSI simultaneously for a comprehensive understanding of familial correlates of NSSI behavior and its underlying features. Copyright © 2016 The Foundation for Professionals in Services for Adolescents. Published by Elsevier Ltd. All rights reserved.

Asymmetric hindwing foldings in rove beetles.

PubMed

Saito, Kazuya; Yamamoto, Shuhei; Maruyama, Munetoshi; Okabe, Yoji

2014-11-18

Foldable wings of insects are the ultimate deployable structures and have attracted the interest of aerospace engineering scientists as well as entomologists. Rove beetles are known to fold their wings in the most sophisticated ways that have right-left asymmetric patterns. However, the specific folding process and the reason for this asymmetry remain unclear. This study reveals how these asymmetric patterns emerge as a result of the folding process of rove beetles. A high-speed camera was used to reveal the details of the wing-folding movement. The results show that these characteristic asymmetrical patterns emerge as a result of simultaneous folding of overlapped wings. The revealed folding mechanisms can achieve not only highly compact wing storage but also immediate deployment. In addition, the right and left crease patterns are interchangeable, and thus each wing internalizes two crease patterns and can be folded in two different ways. This two-way folding gives freedom of choice for the folding direction to a rove beetle. The use of asymmetric patterns and the capability of two-way folding are unique features not found in artificial structures. These features have great potential to extend the design possibilities for all deployable structures, from space structures to articles of daily use.

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.

Generation of the first structure-based pharmacophore model containing a selective "zinc binding group" feature to identify potential glyoxalase-1 inhibitors.

PubMed

Al-Balas, Qosay; Hassan, Mohammad; Al-Oudat, Buthina; Alzoubi, Hassan; Mhaidat, Nizar; Almaaytah, Ammar

2012-11-22

Within this study, a unique 3D structure-based pharmacophore model of the enzyme glyoxalase-1 (Glo-1) has been revealed. Glo-1 is considered a zinc metalloenzyme in which the inhibitor binding with zinc atom at the active site is crucial. To our knowledge, this is the first pharmacophore model that has a selective feature for a "zinc binding group" which has been customized within the structure-based pharmacophore model of Glo-1 to extract ligands that possess functional groups able to bind zinc atom solely from database screening. In addition, an extensive 2D similarity search using three diverse similarity techniques (Tanimoto, Dice, Cosine) has been performed over the commercially available "Zinc Clean Drug-Like Database" that contains around 10 million compounds to help find suitable inhibitors for this enzyme based on known inhibitors from the literature. The resultant hits were mapped over the structure based pharmacophore and the successful hits were further docked using three docking programs with different pose fitting and scoring techniques (GOLD, LibDock, CDOCKER). Nine candidates were suggested to be novel Glo-1 inhibitors containing the "zinc binding group" with the highest consensus scoring from docking.

Perovskites: transforming photovoltaics, a mini-review

DOE PAGES

Chilvery, Ashwith Kumar; Batra, Ashok K.; Yang, Bin; ...

2015-01-06

The recent power-packed advent of perovskite solar cells is transforming photovoltaics (PV) with their superior efficiencies, ease of fabrication, and cost. This perovskite solar cell further boasts of many unexplored features that can further enhance its PV properties and lead to it being branded as a successful commercial product. This paper provides a detailed insight of the organometal halide based perovskite structure, its unique stoichiometric design, and its underlying principles for PV applications. Finally, the compatibility of various PV layers and its fabrication methods is also discussed.

Pediatric Thoracic Trauma: Recognition and Management.

PubMed

Reynolds, Stacy L

2018-05-01

Thoracic injuries account for less than one-tenth of all pediatric trauma-related injuries but comprise 14% of pediatric trauma-related deaths. Thoracic trauma includes injuries to the lungs, heart, aorta and great vessels, esophagus, tracheobronchial tree, and structures of the chest wall. Children have unique anatomic features that change the patterns of observed injury compared with adults. This review article outlines the clinical presentation, diagnostic testing, and management principles required to successfully manage injured children with thoracic trauma. Copyright © 2018 Elsevier Inc. All rights reserved.

[Biotechnological potential of methylotrophic bacteria: a review of current status and future prospects].

PubMed

Trotsenko, Iu A; Doronina, N V; Khmelenina, V N

2005-01-01

Major results of the authors' findings on the implementation of biotechnological potential of aerobic methylobacteria and methanotrophs for obtaining forage proteins, biopolymers (polybutyrate and polysaccharides), enzymes (oxidoreductases), and bioprotectors (ectoin), as well as for degrading toxic C1 and Cn compounds have been reviewed. Unique features of the structural and functional organization of the metabolism of extremophilic (tolerant) methylotrophs are discussed, with a view for their prospective use in various fields of modern biotechnology, including biocatalysis and nanotechnology.

Evaluation of feature selection algorithms for classification in temporal lobe epilepsy based on MR images

NASA Astrophysics Data System (ADS)

Lai, Chunren; Guo, Shengwen; Cheng, Lina; Wang, Wensheng; Wu, Kai

2017-02-01

It's very important to differentiate the temporal lobe epilepsy (TLE) patients from healthy people and localize the abnormal brain regions of the TLE patients. The cortical features and changes can reveal the unique anatomical patterns of brain regions from the structural MR images. In this study, structural MR images from 28 normal controls (NC), 18 left TLE (LTLE), and 21 right TLE (RTLE) were acquired, and four types of cortical feature, namely cortical thickness (CTh), cortical surface area (CSA), gray matter volume (GMV), and mean curvature (MCu), were explored for discriminative analysis. Three feature selection methods, the independent sample t-test filtering, the sparse-constrained dimensionality reduction model (SCDRM), and the support vector machine-recursive feature elimination (SVM-RFE), were investigated to extract dominant regions with significant differences among the compared groups for classification using the SVM classifier. The results showed that the SVM-REF achieved the highest performance (most classifications with more than 92% accuracy), followed by the SCDRM, and the t-test. Especially, the surface area and gray volume matter exhibited prominent discriminative ability, and the performance of the SVM was improved significantly when the four cortical features were combined. Additionally, the dominant regions with higher classification weights were mainly located in temporal and frontal lobe, including the inferior temporal, entorhinal cortex, fusiform, parahippocampal cortex, middle frontal and frontal pole. It was demonstrated that the cortical features provided effective information to determine the abnormal anatomical pattern and the proposed method has the potential to improve the clinical diagnosis of the TLE.

What causes Mars' annular polar vortices?

NASA Astrophysics Data System (ADS)

Toigo, A. D.; Waugh, D. W.; Guzewich, S. D.

2017-01-01

A distinctive feature of the Martian atmosphere is that the winter polar vortices exhibit annuli of high potential vorticity (PV) with a local minimum near the pole. These annuli are seen in observations, reanalyses, and free-running general circulation model simulations of Mars, but are not generally a feature of Earth's polar vortices, where there is a monotonic increase in magnitude of PV with latitude. The creation and maintenance of the annular polar vortices on Mars are not well understood. Here we use simulations with a Martian general circulation model to the show that annular vortices are related to another distinctive, and possibly unique in the solar system, feature of the Martian atmosphere: the condensation of the predominant atmospheric gas species (CO2) in polar winter regions. The latent heat associated with CO2 condensation leads to destruction of PV in the polar lower atmosphere, inducing the formation of an annular PV structure.

Molecular reorientation of a nematic liquid crystal by thermal expansion

PubMed Central

Kim, Young-Ki; Senyuk, Bohdan; Lavrentovich, Oleg D.

2012-01-01

A unique feature of nematic liquid crystals is orientational order of molecules that can be controlled by electromagnetic fields, surface modifications and pressure gradients. Here we demonstrate a new effect in which the orientation of nematic liquid crystal molecules is altered by thermal expansion. Thermal expansion (or contraction) causes the nematic liquid crystal to flow; the flow imposes a realigning torque on the nematic liquid crystal molecules and the optic axis. The optical and mechanical responses activated by a simple temperature change can be used in sensing, photonics, microfluidic, optofluidic and lab-on-a-chip applications as they do not require externally imposed gradients of temperature, pressure, surface realignment, nor electromagnetic fields. The effect has important ramifications for the current search of the biaxial nematic phase as the optical features of thermally induced structural changes in the uniaxial nematic liquid crystal mimic the features expected of the biaxial nematic liquid crystal. PMID:23072803

Bacterial CRISPR Regions: General Features and their Potential for Epidemiological Molecular Typing Studies.

PubMed

Karimi, Zahra; Ahmadi, Ali; Najafi, Ali; Ranjbar, Reza

2018-01-01

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci as novel and applicable regions in prokaryotic genomes have gained great attraction in the post genomics era. These unique regions are diverse in number and sequence composition in different pathogenic bacteria and thereby can be a suitable candidate for molecular epidemiology and genotyping studies. Results:Furthermore, the arrayed structure of CRISPR loci (several unique repeats spaced with the variable sequence) and associated cas genes act as an active prokaryotic immune system against viral replication and conjugative elements. This property can be used as a tool for RNA editing in bioengineering studies. The aim of this review was to survey some details about the history, nature, and potential applications of CRISPR arrays in both genetic engineering and bacterial genotyping studies.

Thermal Decoherence of a Nonequilibrium Polariton Fluid

NASA Astrophysics Data System (ADS)

Klembt, Sebastian; Stepanov, Petr; Klein, Thorsten; Minguzzi, Anna; Richard, Maxime

2018-01-01

Exciton polaritons constitute a unique realization of a quantum fluid interacting with its environment. Using selenide-based microcavities, we exploit this feature to warm up a polariton condensate in a controlled way and monitor its spatial coherence. We determine directly the amount of heat picked up by the condensate by measuring the phonon-polariton scattering rate and comparing it with the loss rate. We find that, upon increasing the heating rate, the spatial coherence length decreases markedly, while localized phase structures vanish, in good agreement with a stochastic mean-field theory. From the thermodynamical point of view, this regime is unique, as it involves a nonequilibrium quantum fluid with no well-defined temperature but which is nevertheless able to pick up heat with dramatic effects on the order parameter.

Structural Similarities and Differences between Two Functionally Distinct SecA Proteins, Mycobacterium tuberculosis SecA1 and SecA2

PubMed Central

Swanson, Stephanie; Ioerger, Thomas R.; Rigel, Nathan W.; Miller, Brittany K.; Braunstein, Miriam

2015-01-01

ABSTRACT While SecA is the ATPase component of the major bacterial secretory (Sec) system, mycobacteria and some Gram-positive pathogens have a second paralog, SecA2. In bacteria with two SecA paralogs, each SecA is functionally distinct, and they cannot compensate for one another. Compared to SecA1, SecA2 exports a distinct and smaller set of substrates, some of which have roles in virulence. In the mycobacterial system, some SecA2-dependent substrates lack a signal peptide, while others contain a signal peptide but possess features in the mature protein that necessitate a role for SecA2 in their export. It is unclear how SecA2 functions in protein export, and one open question is whether SecA2 works with the canonical SecYEG channel to export proteins. In this study, we report the structure of Mycobacterium tuberculosis SecA2 (MtbSecA2), which is the first structure of any SecA2 protein. A high level of structural similarity is observed between SecA2 and SecA1. The major structural difference is the absence of the helical wing domain, which is likely to play a role in how MtbSecA2 recognizes its unique substrates. Importantly, structural features critical to the interaction between SecA1 and SecYEG are preserved in SecA2. Furthermore, suppressor mutations of a dominant-negative secA2 mutant map to the surface of SecA2 and help identify functional regions of SecA2 that may promote interactions with SecYEG or the translocating polypeptide substrate. These results support a model in which the mycobacterial SecA2 works with SecYEG. IMPORTANCE SecA2 is a paralog of SecA1, which is the ATPase of the canonical bacterial Sec secretion system. SecA2 has a nonredundant function with SecA1, and SecA2 exports a distinct and smaller set of substrates than SecA1. This work reports the crystal structure of SecA2 of Mycobacterium tuberculosis (the first SecA2 structure reported for any organism). Many of the structural features of SecA1 are conserved in the SecA2 structure, including putative contacts with the SecYEG channel. Several structural differences are also identified that could relate to the unique function and selectivity of SecA2. Suppressor mutations of a secA2 mutant map to the surface of SecA2 and help identify functional regions of SecA2 that may promote interactions with SecYEG. PMID:26668263

Intricate Hollow Structures: Controlled Synthesis and Applications in Energy Storage and Conversion.

PubMed

Zhou, Liang; Zhuang, Zechao; Zhao, Huihui; Lin, Mengting; Zhao, Dongyuan; Mai, Liqiang

2017-05-01

Intricate hollow structures garner tremendous interest due to their aesthetic beauty, unique structural features, fascinating physicochemical properties, and widespread applications. Here, the recent advances in the controlled synthesis are discussed, as well as applications of intricate hollow structures with regard to energy storage and conversion. The synthetic strategies toward complex multishelled hollow structures are classified into six categories, including well-established hard- and soft-templating methods, as well as newly emerging approaches based on selective etching of "soft@hard" particles, Ostwald ripening, ion exchange, and thermally induced mass relocation. Strategies for constructing structures beyond multishelled hollow structures, such as bubble-within-bubble, tube-in-tube, and wire-in-tube structures, are also covered. Niche applications of intricate hollow structures in lithium-ion batteries, Li-S batteries, supercapacitors, Li-O 2 batteries, dye-sensitized solar cells, photocatalysis, and fuel cells are discussed in detail. Some perspectives on the future research and development of intricate hollow structures are also provided. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ligand and coactivator identity determines the requirement of the charge clamp for coactivation of the peroxisome proliferator-activated receptor gamma.

PubMed

Wu, Yifei; Chin, William W; Wang, Yong; Burris, Thomas P

2003-03-07

The activation function 2 (AF-2)-dependent recruitment of coactivator is essential for gene activation by nuclear receptors. We show that the peroxisome proliferator-activated receptor gamma (PPARgamma) (NR1C3) coactivator-1 (PGC-1) requires both the intact AF-2 domain of PPARgamma and the LXXLL domain of PGC-1 for ligand-dependent and ligand-independent interaction and coactivation. Although the AF-2 domain of PPARgamma is absolutely required for PGC-1-mediated coactivation, this coactivator displayed a unique lack of requirement for the charge clamp of the ligand-binding domain of the receptor that is thought to be essential for LXXLL motif recognition. The mutation of a single serine residue adjacent to the core LXXLL motif of PGC-1 led to restoration of the typical charge clamp requirement. Thus, the unique structural features of the PGC-1 LXXLL motif appear to mediate an atypical mode of interaction with PPARgamma. Unexpectedly, we discovered that various ligands display variability in terms of their requirement for the charge clamp of PPARgamma for coactivation by PGC-1. This ligand-selective variable requirement for the charge clamp was coactivator-specific. Thus, distinct structural determinants, which may be unique for a particular ligand, are utilized by the receptor to recognize the coactivator. Our data suggest that even subtle differences in ligand structure are perceived by the receptor and translated into a unique display of the coactivator-binding surface of the ligand-binding domain, allowing for differential recognition of coactivators that may underlie distinct pharmacological profiles observed for ligands of a particular nuclear receptor.

A survey of advancements in nucleic acid-based logic gates and computing for applications in biotechnology and biomedicine.

PubMed

Wu, Cuichen; Wan, Shuo; Hou, Weijia; Zhang, Liqin; Xu, Jiehua; Cui, Cheng; Wang, Yanyue; Hu, Jun; Tan, Weihong

2015-03-04

Nucleic acid-based logic devices were first introduced in 1994. Since then, science has seen the emergence of new logic systems for mimicking mathematical functions, diagnosing disease and even imitating biological systems. The unique features of nucleic acids, such as facile and high-throughput synthesis, Watson-Crick complementary base pairing, and predictable structures, together with the aid of programming design, have led to the widespread applications of nucleic acids (NA) for logic gate and computing in biotechnology and biomedicine. In this feature article, the development of in vitro NA logic systems will be discussed, as well as the expansion of such systems using various input molecules for potential cellular, or even in vivo, applications.

A Survey of Advancements in Nucleic Acid-based Logic Gates and Computing for Applications in Biotechnology and biomedicine

PubMed Central

Wu, Cuichen; Wan, Shuo; Hou, Weijia; Zhang, Liqin; Xu, Jiehua; Cui, Cheng; Wang, Yanyue; Hu, Jun

2015-01-01

Nucleic acid-based logic devices were first introduced in 1994. Since then, science has seen the emergence of new logic systems for mimicking mathematical functions, diagnosing disease and even imitating biological systems. The unique features of nucleic acids, such as facile and high-throughput synthesis, Watson-Crick complementary base pairing, and predictable structures, together with the aid of programming design, have led to the widespread applications of nucleic acids (NA) for logic gating and computing in biotechnology and biomedicine. In this feature article, the development of in vitro NA logic systems will be discussed, as well as the expansion of such systems using various input molecules for potential cellular, or even in vivo, applications. PMID:25597946

Babinet-Inverted Optical Yagi-Uda Antenna for Unidirectional Radiation to Free Space

NASA Astrophysics Data System (ADS)

Kim, Jineun; Roh, Young-Geun; Cheon, Sangmo; Choe, Jong-Ho; Lee, Jongcheon; Lee, Jaesoong; Jeong, Heejeong; Kim, Un Jeong; Park, Yeonsang; Song, In Yong; Park, Q.-Han; Hwang, Sung Woo; Kim, Kinam; Lee, Chang-Won

2014-06-01

Plasmonic nanoantennas are key elements in nanophotonics capable of directing radiation or enhancing the transition rate of a quantum emitter. Slot-type magnetic-dipole nanoantennas, which are complementary structures of typical electric-dipole-type antennas, have received little attention, leaving their antenna properties largely unexplored. Here we present a novel magnetic-dipole-fed multi-slot optical Yagi-Uda antenna. By engineering the relative phase of the interacting surface plasmon polaritons between the slot elements, we demonstrate that the optical antenna exhibits highly unidirectional radiation to free space. The unique features of the slot-based magnetic nanoantenna provide a new possibility of achieving integrated features such as energy transfer from one waveguide to another by working as a future optical via.

Typomorphic Characteristics of Molybdenite from the Bystrinsky Cu-Au Porphyry-Skarn Deposit, Eastern Transbaikal Region, Russia

NASA Astrophysics Data System (ADS)

Kovalenker, V. A.; Trubkin, N. V.; Abramova, V. D.; Plotinskaya, O. Yu.; Kiseleva, G. D.; Borisovskii, S. E.; Yazykova, Yu. I.

2018-01-01

The paper presents pioneering data on the composition, texture, and crystal structure of molybdenite from various types of molybdenum mineralization at the Bystrinsky Cu-Au-Fe porphyry-skarn deposit in the eastern Transbaikal region, Russia. The data were obtained using electron microprobe analysis (EMPA), laser ablation-inductively coupled plasma mass spectrometry (LA-ICP-MS), and high-resolution transmission electron microscopy (HRTEM). Molybdenite found at the deposit in skarn, sulfide-poor quartz veins, and quartz-feldspar alteration markedly differs in the concentrations of trace elements determined by their species in the mineral, as well as in its structural features. Molybdenite-2H from skarn associated with phyllosilicates occurs as ultrafine crystals with uniform shape and texture; no dislocations or inclusions were found but amorphous silica was. The molybdenite composition is highly contrasting in the content and distribution of both structure-related (Re, W, and Se) and other (Mn, Co, Ni, Cu, Zn, As, Ag, Cd, Sb, Te, Ag, Pd, Au, Hg, Pb, and Bi) metals. In the sulfide-poor quartz veins, highly structurally heterogeneous (2H + 3R) molybdenite microcrystals with abundant defects (dislocations and volumetrically distributed inclusions) are associated with illite, goethite, and barite. Some single crystals are unique three-phase (2H + 3R polytypes + amorphous MoS2). The mineral has a low concentration of all trace elements, which are uniformly distributed. However, individual domains with uniquely high Pd, Te, Ni, Hg, and W concentrations caused by mineral inclusions are found in some grains. Molybdenite from quartz-feldspar alteration is characterized by low concentrations of all trace elements except for Re and Se, which enrich some domains of the grains. Our data indicate that the compositional and structural heterogeneity of molybdenite from the Bystrinsky deposit are its crucial features, which obviously correlate with the types of Mo mineralization.

Seismic imaging of the upper mantle beneath the northern Central Andean Plateau: Implications for surface topography

NASA Astrophysics Data System (ADS)

Ward, K. M.; Zandt, G.; Beck, S. L.; Wagner, L. S.

2015-12-01

Extending over 1,800 km along the active South American Cordilleran margin, the Central Andean Plateau (CAP) as defined by the 3 km elevation contour is second only to the Tibetan Plateau in geographic extent. The uplift history of the 4 km high Plateau remains uncertain with paleoelevation studies along the CAP suggesting a complex, non-uniform uplift history. As part of the Central Andean Uplift and the Geodynamics of High Topography (CAUGHT) project, we use surface waves measured from ambient noise and two-plane wave tomography to image the S-wave velocity structure of the crust and upper mantle to investigate the upper mantle component of plateau uplift. We observe three main features in our S-wave velocity model including (1), a high velocity slab (2), a low velocity anomaly above the slab where the slab changes dip from near horizontal to a normal dip, and (3), a high-velocity feature in the mantle above the slab that extends along the length of the Altiplano from the base of the Moho to a depth of ~120 km with the highest velocities observed under Lake Titicaca. A strong spatial correlation exists between the lateral extent of this high-velocity feature beneath the Altiplano and the lower elevations of the Altiplano basin suggesting a potential relationship. Non-uniqueness in our seismic models preclude uniquely constraining this feature as an uppermost mantle feature bellow the Moho or as a connected eastward dipping feature extending up to 300 km in the mantle as seen in deeper mantle tomography studies. Determining if the high velocity feature represents a small lithospheric root or a delaminating lithospheric root extending ~300 km into the mantle requires more integration of observations, but either interpretation shows a strong geodynamic connection with the uppermost mantle and the current topography of the northern CAP.

Sleep Benefits Memory for Semantic Category Structure While Preserving Exemplar-Specific Information.

PubMed

Schapiro, Anna C; McDevitt, Elizabeth A; Chen, Lang; Norman, Kenneth A; Mednick, Sara C; Rogers, Timothy T

2017-11-01

Semantic memory encompasses knowledge about both the properties that typify concepts (e.g. robins, like all birds, have wings) as well as the properties that individuate conceptually related items (e.g. robins, in particular, have red breasts). We investigate the impact of sleep on new semantic learning using a property inference task in which both kinds of information are initially acquired equally well. Participants learned about three categories of novel objects possessing some properties that were shared among category exemplars and others that were unique to an exemplar, with exposure frequency varying across categories. In Experiment 1, memory for shared properties improved and memory for unique properties was preserved across a night of sleep, while memory for both feature types declined over a day awake. In Experiment 2, memory for shared properties improved across a nap, but only for the lower-frequency category, suggesting a prioritization of weakly learned information early in a sleep period. The increase was significantly correlated with amount of REM, but was also observed in participants who did not enter REM, suggesting involvement of both REM and NREM sleep. The results provide the first evidence that sleep improves memory for the shared structure of object categories, while simultaneously preserving object-unique information.

Multiple conformations of the cytidine repressor DNA-binding domain coalesce to one upon recognition of a specific DNA surface.

PubMed

Moody, Colleen L; Tretyachenko-Ladokhina, Vira; Laue, Thomas M; Senear, Donald F; Cocco, Melanie J

2011-08-09

The cytidine repressor (CytR) is a member of the LacR family of bacterial repressors with distinct functional features. The Escherichia coli CytR regulon comprises nine operons whose palindromic operators vary in both sequence and, most significantly, spacing between the recognition half-sites. This suggests a strong likelihood that protein folding would be coupled to DNA binding as a mechanism to accommodate the variety of different operator architectures to which CytR is targeted. Such coupling is a common feature of sequence-specific DNA-binding proteins, including the LacR family repressors; however, there are no significant structural rearrangements upon DNA binding within the three-helix DNA-binding domains (DBDs) studied to date. We used nuclear magnetic resonance (NMR) spectroscopy to characterize the CytR DBD free in solution and to determine the high-resolution structure of a CytR DBD monomer bound specifically to one DNA half-site of the uridine phosphorylase (udp) operator. We find that the free DBD populates multiple distinct conformations distinguished by up to four sets of NMR peaks per residue. This structural heterogeneity is previously unknown in the LacR family. These stable structures coalesce into a single, more stable udp-bound form that features a three-helix bundle containing a canonical helix-turn-helix motif. However, this structure differs from all other LacR family members whose structures are known with regard to the packing of the helices and consequently their relative orientations. Aspects of CytR activity are unique among repressors; we identify here structural properties that are also distinct and that might underlie the different functional properties. © 2011 American Chemical Society

Unique Action of Interleukin-18 on T Cells and Other Immune Cells.

PubMed

Nakanishi, Kenji

2018-01-01

Interleukin (IL)-18 was originally discovered as a factor that enhances interferon (IFN)-γ production by anti-CD3-stimulated Th1 cells, particularly in association with IL-12. IL-12 is a cytokine that induces development of Th1 cells. IL-18 cannot induce Th1 cell development, but has the capacity to activate established Th1 cells to produce IFN-γ in the presence of IL-12. Thus, IL-18 is regarded as a proinflammatory cytokine that facilitates type 1 responses. However, in the absence of IL-12 but presence of IL-2, IL-18 stimulates natural killer cells, NKT cells, and even established Th1 cells to produce IL-3, IL-9, and IL-13. Thus, IL-18 also facilitates type 2 responses. This unique function of IL-18 contributes to infection-associated allergic diseases. Together with IL-3, IL-18 stimulates mast cells and basophils to produce IL-4, IL-13, and chemical mediators such as histamine. Thus, IL-18 also induces innate-type allergic inflammation. IL-18 belongs to the IL-1 family of cytokines, which share similar molecular structures, receptors structures, and signal transduction pathways. Nevertheless, IL-18 shows a unique function by binding to a specific receptor expressed on distinct types of cells. In this review article, I will focus on the unique features of IL-18 in lymphocytes, basophils, and mast cells, particularly in comparison with IL-33.

Crystal structure of the zymogen form of the group A Streptococcus virulence factor SpeB: an integrin-binding cysteine protease.

PubMed

Kagawa, T F; Cooney, J C; Baker, H M; McSweeney, S; Liu, M; Gubba, S; Musser, J M; Baker, E N

2000-02-29

Pathogenic bacteria secrete protein toxins that weaken or disable their host, and thereby act as virulence factors. We have determined the crystal structure of streptococcal pyrogenic exotoxin B (SpeB), a cysteine protease that is a major virulence factor of the human pathogen Streptococcus pyogenes and participates in invasive disease episodes, including necrotizing fasciitis. The structure, determined for the 40-kDa precursor form of SpeB at 1.6-A resolution, reveals that the protein is a distant homologue of the papain superfamily that includes the mammalian cathepsins B, K, L, and S. Despite negligible sequence identity, the protease portion has the canonical papain fold, albeit with major loop insertions and deletions. The catalytic site differs from most other cysteine proteases in that it lacks the Asn residue of the Cys-His-Asn triad. The prosegment has a unique fold and inactivation mechanism that involves displacement of the catalytically essential His residue by a loop inserted into the active site. The structure also reveals the surface location of an integrin-binding Arg-Gly-Asp (RGD) motif that is a feature unique to SpeB among cysteine proteases and is linked to the pathogenesis of the most invasive strains of S. pyogenes.

Statistical inference of seabed sound-speed structure in the Gulf of Oman Basin.

PubMed

Sagers, Jason D; Knobles, David P

2014-06-01

Addressed is the statistical inference of the sound-speed depth profile of a thick soft seabed from broadband sound propagation data recorded in the Gulf of Oman Basin in 1977. The acoustic data are in the form of time series signals recorded on a sparse vertical line array and generated by explosive sources deployed along a 280 km track. The acoustic data offer a unique opportunity to study a deep-water bottom-limited thickly sedimented environment because of the large number of time series measurements, very low seabed attenuation, and auxiliary measurements. A maximum entropy method is employed to obtain a conditional posterior probability distribution (PPD) for the sound-speed ratio and the near-surface sound-speed gradient. The multiple data samples allow for a determination of the average error constraint value required to uniquely specify the PPD for each data sample. Two complicating features of the statistical inference study are addressed: (1) the need to develop an error function that can both utilize the measured multipath arrival structure and mitigate the effects of data errors and (2) the effect of small bathymetric slopes on the structure of the bottom interacting arrivals.

TCRmodel: high resolution modeling of T cell receptors from sequence.

PubMed

Gowthaman, Ragul; Pierce, Brian G

2018-05-22

T cell receptors (TCRs), along with antibodies, are responsible for specific antigen recognition in the adaptive immune response, and millions of unique TCRs are estimated to be present in each individual. Understanding the structural basis of TCR targeting has implications in vaccine design, autoimmunity, as well as T cell therapies for cancer. Given advances in deep sequencing leading to immune repertoire-level TCR sequence data, fast and accurate modeling methods are needed to elucidate shared and unique 3D structural features of these molecules which lead to their antigen targeting and cross-reactivity. We developed a new algorithm in the program Rosetta to model TCRs from sequence, and implemented this functionality in a web server, TCRmodel. This web server provides an easy to use interface, and models are generated quickly that users can investigate in the browser and download. Benchmarking of this method using a set of nonredundant recently released TCR crystal structures shows that models are accurate and compare favorably to models from another available modeling method. This server enables the community to obtain insights into TCRs of interest, and can be combined with methods to model and design TCR recognition of antigens. The TCRmodel server is available at: http://tcrmodel.ibbr.umd.edu/.

Signature properties of water: Their molecular electronic origins

PubMed Central

Jones, Andrew P.; Cipcigan, Flaviu S.; Crain, Jason; Martyna, Glenn J.

2015-01-01

Water challenges our fundamental understanding of emergent materials properties from a molecular perspective. It exhibits a uniquely rich phenomenology including dramatic variations in behavior over the wide temperature range of the liquid into water’s crystalline phases and amorphous states. We show that many-body responses arising from water’s electronic structure are essential mechanisms harnessed by the molecule to encode for the distinguishing features of its condensed states. We treat the complete set of these many-body responses nonperturbatively within a coarse-grained electronic structure derived exclusively from single-molecule properties. Such a “strong coupling” approach generates interaction terms of all symmetries to all orders, thereby enabling unique transferability to diverse local environments such as those encountered along the coexistence curve. The symmetries of local motifs that can potentially emerge are not known a priori. Consequently, electronic responses unfiltered by artificial truncation are then required to embody the terms that tip the balance to the correct set of structures. Therefore, our fully responsive molecular model produces, a simple, accurate, and intuitive picture of water’s complexity and its molecular origin, predicting water’s signature physical properties from ice, through liquid–vapor coexistence, to the critical point. PMID:25941394

Neurocomputational Consequences of Evolutionary Connectivity Changes in Perisylvian Language Cortex.

PubMed

Schomers, Malte R; Garagnani, Max; Pulvermüller, Friedemann

2017-03-15

The human brain sets itself apart from that of its primate relatives by specific neuroanatomical features, especially the strong linkage of left perisylvian language areas (frontal and temporal cortex) by way of the arcuate fasciculus (AF). AF connectivity has been shown to correlate with verbal working memory-a specifically human trait providing the foundation for language abilities-but a mechanistic explanation of any related causal link between anatomical structure and cognitive function is still missing. Here, we provide a possible explanation and link, by using neurocomputational simulations in neuroanatomically structured models of the perisylvian language cortex. We compare networks mimicking key features of cortical connectivity in monkeys and humans, specifically the presence of relatively stronger higher-order "jumping links" between nonadjacent perisylvian cortical areas in the latter, and demonstrate that the emergence of working memory for syllables and word forms is a functional consequence of this structural evolutionary change. We also show that a mere increase of learning time is not sufficient, but that this specific structural feature, which entails higher connectivity degree of relevant areas and shorter sensorimotor path length, is crucial. These results offer a better understanding of specifically human anatomical features underlying the language faculty and their evolutionary selection advantage. SIGNIFICANCE STATEMENT Why do humans have superior language abilities compared to primates? Recently, a uniquely human neuroanatomical feature has been demonstrated in the strength of the arcuate fasciculus (AF), a fiber pathway interlinking the left-hemispheric language areas. Although AF anatomy has been related to linguistic skills, an explanation of how this fiber bundle may support language abilities is still missing. We use neuroanatomically structured computational models to investigate the consequences of evolutionary changes in language area connectivity and demonstrate that the human-specific higher connectivity degree and comparatively shorter sensorimotor path length implicated by the AF entail emergence of verbal working memory, a prerequisite for language learning. These results offer a better understanding of specifically human anatomical features for language and their evolutionary selection advantage. Copyright © 2017 Schomers et al.

Linking high resolution mass spectrometry data with exposure ...

EPA Pesticide Factsheets

There is a growing need in the field of exposure science for monitoring methods that rapidly screen environmental media for suspect contaminants. Measurement and analysis platforms, based on high resolution mass spectrometry (HRMS), now exist to meet this need. Here we describe results of a study that links HRMS data with exposure predictions from the U.S. EPA's ExpoCast™ program and in vitro bioassay data from the U.S. interagency Tox21 consortium. Vacuum dust samples were collected from 56 households across the U.S. as part of the American Healthy Homes Survey (AHHS). Sample extracts were analyzed using liquid chromatography time-of-flight mass spectrometry (LC–TOF/MS) with electrospray ionization. On average, approximately 2000 molecular features were identified per sample (based on accurate mass) in negative ion mode, and 3000 in positive ion mode. Exact mass, isotope distribution, and isotope spacing were used to match molecular features with a unique listing of chemical formulas extracted from EPA's Distributed Structure-Searchable Toxicity (DSSTox) database. A total of 978 DSSTox formulas were consistent with the dust LC–TOF/molecular feature data (match score ≥ 90); these formulas mapped to 3228 possible chemicals in the database. Correct assignment of a unique chemical to a given formula required additional validation steps. Each suspect chemical was prioritized for follow-up confirmation using abundance and detection frequency results, along wi

Hitherto unknown shear rupture mechanism as a source of instability in intact hard rocks at highly confined compression

NASA Astrophysics Data System (ADS)

Tarasov, Boris G.

2014-05-01

Today, frictional shear resistance along pre-existing faults is considered to be the lower limit on rock shear strength for confined conditions corresponding to the seismogenic layer. This paper introduces a recently identified shear rupture mechanism providing a paradoxical feature of hard rocks - the possibility of shear rupture propagation through the highly confined intact rock mass at shear stress levels significantly less than frictional strength. In the new mechanism, the rock failure associated with consecutive creation of small slabs (known as ‘domino-blocks') from the intact rock in the rupture tip is driven by a fan-shaped domino structure representing the rupture head. The fan-head combines such unique features as: extremely low shear resistance, self-sustaining stress intensification, and self-unbalancing conditions. Due to this the failure process caused by the mechanism is very dynamic and violent. This makes it impossible to directly observe and study the mechanism and can explain why the mechanism has not been detected before. This paper provides physical motivation for the mechanism, based upon side effects accompanying the failure process. Physical and mathematical models of the mechanism presented in the paper explain unique and paradoxical features of the mechanism. The new shear rupture mechanism allows a novel point of view for understanding the nature of spontaneous failure processes in hard rocks including earthquakes.

Linking high resolution mass spectrometry data with exposure and toxicity forecasts to advance high-throughput environmental monitoring

EPA Pesticide Factsheets

There is a growing need in the field of exposure science for monitoring methods that rapidly screen environmental media for suspect contaminants. Measurement and analysis platforms, based on high resolution mass spectrometry (HRMS), now exist to meet this need. Here we describe results of a study that links HRMS data with exposure predictions from the U.S. EPA's ExpoCast? program and in vitro bioassay data from the U.S. interagency Tox21 consortium. Vacuum dust samples were collected from 56 households across the U.S. as part of the American Healthy Homes Survey (AHHS). Sample extracts were analyzed using liquid chromatography time-of-flight mass spectrometry (LC??TOF/MS) with electrospray ionization. On average, approximately 2000 molecular features were identified per sample (based on accurate mass) in negative ion mode, and 3000 in positive ion mode. Exact mass, isotope distribution, and isotope spacing were used to match molecular features with a unique listing of chemical formulas extracted from EPA's Distributed Structure-Searchable Toxicity (DSSTox) database. A total of 978 DSSTox formulas were consistent with the dust LC??TOF/molecular feature data (match score ? 90); these formulas mapped to 3228 possible chemicals in the database. Correct assignment of a unique chemical to a given formula required additional validation steps. Each suspect chemical was prioritized for follow-up confirmation using abundance and detection frequency results, along with exp

Aggrecan-based extracellular matrix shows unique cortical features and conserved subcortical principles of mammalian brain organization in the Madagascan lesser hedgehog tenrec (Echinops telfairi Martin, 1838).

PubMed

Morawski, M; Brückner, G; Jäger, C; Seeger, G; Künzle, H; Arendt, T

2010-02-03

The Madagascan tenrecs (Afrotheria), an ancient mammalian clade, are characterized by unique brain anatomy. Striking features are an expanded paleocortex but a small and poorly differentiated neocortex devoid of a distinct granular layer IV. To investigate the organization of cortical areas we analyzed extracellular matrix components in perineuronal nets (PNs) using antibodies to aggrecan, lectin staining and hyaluronan-binding protein. Selected subcortical regions were studied to correlate the cortical patterns with features in evolutionary conserved systems. In the neocortex, paleocortex and hippocampus PNs were associated with nonpyramidal neurons. Quantitative analysis in the cerebral cortex revealed area-specific proportions and laminar distribution patterns of neurons ensheathed by PNs. Cortical PNs showed divergent structural phenotypes. Diffuse PNs forming a cotton wool-like perisomatic rim were characteristic of the paleocortex. These PNs were associated with a dense pericellular plexus of calretinin-immunoreactive fibres. Clearly contoured PNs were devoid of a calretinin-positive plexus and predominated in the neocortex and hippocampus. The organization of the extracellular matrix in subcortical nuclei followed the widely distributed mammalian type. We conclude that molecular properties of the aggrecan-based extracellular matrix are conserved during evolution of mammals; however, the matrix scaffold is adapted to specific wiring patterns of cortical and subcortical neuronal networks. Copyright 2010 IBRO. Published by Elsevier Ltd. All rights reserved.

Computational and Statistical Analyses of Amino Acid Usage and Physico-Chemical Properties of the Twelve Late Embryogenesis Abundant Protein Classes

PubMed Central

Jaspard, Emmanuel; Macherel, David; Hunault, Gilles

2012-01-01

Late Embryogenesis Abundant Proteins (LEAPs) are ubiquitous proteins expected to play major roles in desiccation tolerance. Little is known about their structure - function relationships because of the scarcity of 3-D structures for LEAPs. The previous building of LEAPdb, a database dedicated to LEAPs from plants and other organisms, led to the classification of 710 LEAPs into 12 non-overlapping classes with distinct properties. Using this resource, numerous physico-chemical properties of LEAPs and amino acid usage by LEAPs have been computed and statistically analyzed, revealing distinctive features for each class. This unprecedented analysis allowed a rigorous characterization of the 12 LEAP classes, which differed also in multiple structural and physico-chemical features. Although most LEAPs can be predicted as intrinsically disordered proteins, the analysis indicates that LEAP class 7 (PF03168) and probably LEAP class 11 (PF04927) are natively folded proteins. This study thus provides a detailed description of the structural properties of this protein family opening the path toward further LEAP structure - function analysis. Finally, since each LEAP class can be clearly characterized by a unique set of physico-chemical properties, this will allow development of software to predict proteins as LEAPs. PMID:22615859

Vibration reduction for smart periodic structures via periodic piezoelectric arrays with nonlinear interleaved-switched electronic networks

NASA Astrophysics Data System (ADS)

Bao, Bin; Guyomar, Daniel; Lallart, Mickaël

2017-01-01

Smart periodic structures covered by periodically distributed piezoelectric patches have drawn more and more attention in recent years for wave propagation attenuation and corresponding structural vibration suppression. Since piezoelectric materials are special type of energy conversion materials that link mechanical characteristics with electrical characteristics, shunt circuits coupled with such materials play a key role in the wave propagation and/or vibration control performance in smart periodic structures. Conventional shunt circuit designs utilize resistive shunt (R-shunt) and resonant shunt (RL-shunt). More recently, semi-passive nonlinear approaches have also been developed for efficiently controlling the vibrations of such structures. In this paper, an innovative smart periodic beam structure with nonlinear interleaved-switched electric networks based on synchronized switching damping on inductor (SSDI) is proposed and investigated for vibration reduction and wave propagation attenuation. Different from locally resonant band gap mechanism forming narrow band gaps around the desired resonant frequencies, the proposed interleaved electrical networks can induce new broadly low-frequency stop bands and broaden primitive Bragg stop bands by virtue of unique interleaved electrical configurations and the SSDI technique which has the unique feature of realizing automatic impedance adaptation with a small inductance. Finite element modeling of a Timoshenko electromechanical beam structure is also presented for validating dispersion properties of the structure. Both theoretical and experimental results demonstrate that the proposed beam structure not only shows better vibration and wave propagation attenuation than the smart beam structure with independent switched networks, but also has technical simplicity of requiring only half of the number of switches than the independent switched network needs.

IR spectroscopy of protonation in benzene-water nanoclusters: hydronium, zundel, and eigen at a hydrophobic interface.

PubMed

Cheng, Timothy C; Bandyopadhyay, Biswajit; Mosley, Jonathan D; Duncan, Michael A

2012-08-08

The structure of ions in water at a hydrophobic interface influences important processes throughout chemistry and biology. However, experiments to measure these structures are limited by the distribution of configurations present and the inability to selectively probe the interfacial region. Here, protonated nanoclusters containing benzene and water are produced in the gas phase, size-selected, and investigated with infrared laser spectroscopy. Proton stretch, free OH, and hydrogen-bonding vibrations uniquely define protonation sites and hydrogen-bonding networks. The structures consist of protonated water clusters binding to the hydrophobic interface of neutral benzene via one or more π-hydrogen bonds. Comparison to the spectra of isolated hydronium, zundel, or eigen ions reveals the inductive effects and local ordering induced by the interface. The structures and interactions revealed here represent key features expected for aqueous hydrophobic interfaces.

The possible importance of synchrotron/inverse Compton losses to explain fast MM-wave and hard X-ray emission of a solar event

NASA Technical Reports Server (NTRS)

Correia, E.; Kaufmann, P.; Costa, J. E. R.; Vaz, A. M. Z.; Dennis, B. R.

1986-01-01

The solar burst of 21 May 1984 presented a number of unique features. The time profile consisted of seven major structures (seconds), with a turnover frequency or approx. 90 GHz, well correlated in time to hard X-ray emission. Each structure consisted of multiple fast pulses (.1 seconds), which were analyzed in detail. A proportionality between the repetition rate of the pulses and the burst fluxes at 90 GHz and or approx. 100 keV hard X-rays, and an inverse proportionality between repetition rates and hard X-rays power law indices have been found. A synchrotron/inverse Compton model has been applied to explain the emission of the fast burst structures, which appear to be possible for the first three or four structures.

The possible importance of synchrotron/inverse Compton losses to explain fast mm-wave and hard X-ray emission of a solar event

NASA Technical Reports Server (NTRS)

Correia, E.; Kaufmann, P.; Costa, J. E. R.; Zodivaz, A. M.; Dennis, B. R.

1986-01-01

The solar burst of 21 May 1984, presented a number of unique features. The time profile consisted of seven major structures (seconds), with a turnover frequency of greater than or approximately 90 GHz, well correlated in time to hard X-ray emission. Each structure consisted of multiple fast pulses (0.1 seconds), which were analyzed in detail. A proportionality between the repetition rate of the pulses and the burst fluxes at 90 GHz and greater than or approximately 100 keV hard X-rays, and an inverse proportionality between repetition rates and hard X-ray power law indices were found. A synchrotron/inverse Compton model was applied to explain the emission of the fast burst structures, which appear to be possible for the first three or four structures.

Spirulina-Templated Metal Microcoils with Controlled Helical Structures for THz Electromagnetic Responses

PubMed Central

Kamata, Kaori; Piao, Zhenzi; Suzuki, Soichiro; Fujimori, Takahiro; Tajiri, Wataru; Nagai, Keiji; Iyoda, Tomokazu; Yamada, Atsushi; Hayakawa, Toshiaki; Ishiwara, Mitsuteru; Horaguchi, Satoshi; Belay, Amha; Tanaka, Takuo; Takano, Keisuke; Hangyo, Masanori

2014-01-01

Microstructures in nature are ultrafine and ordered in biological roles, which have attracted material scientists. Spirulina forms three-dimensional helical microstructure, one of remarkable features in nature beyond our current processing technology such as lithography in terms of mass-productivity and structural multiplicity. Spirulina varies its diameter, helical pitch, and/or length against growing environment. This unique helix is suggestive of a tiny electromagnetic coil, if composed of electro-conductive metal, which brought us main concept of this work. Here, we describe the biotemplating process onto Spirulina surface to fabricate metal microcoils. Structural parameters of the microcoil can be controlled by the cultivation conditions of Spirulina template and also purely one-handed microcoil can be fabricated. A microcoil dispersion sheet exhibited optically active response attributed to structural resonance in terahertz-wave region. PMID:24815190

Self-ordered, controlled structure nanoporous membranes using constant current anodization.

PubMed

Lee, Kwan; Tang, Yun; Ouyang, Min

2008-12-01

We report a constant current (CC) based anodization technique to fabricate and control structure of mechanically stable anodic aluminum oxide (AAO) membranes with a long-range ordered hexagonal nanopore pattern. For the first time we show that interpore distance (Dint) of a self-ordered nanopore feature can be continuously tuned over a broad range with CC anodization and is uniquely defined by the conductivity of sulfuric acid as electrolyte. We further demonstrate that this technique can offer new degrees of freedom for engineering planar nanopore structures by fine tailoring the CC based anodization process. Our results not only facilitate further understanding of self-ordering mechanism of alumina membranes but also provide a fast, simple (without requirement of prepatterning or preoxide layer), and flexible methodology for controlling complex nanoporous structures, thus offering promising practical applications in nanotechnology.

Sequence-dependent effects in drug-DNA interaction: the crystal structure of Hoechst 33258 bound to the d(CGCAAATTTGCG)2 duplex.

PubMed Central

Spink, N; Brown, D G; Skelly, J V; Neidle, S

1994-01-01

The bis-benzimidazole drug Hoechst 33258 has been co-crystallized with the dodecanucleotide sequence d(CGCAAATTTGCG)2. The structure has been solved by molecular replacement and refined to an R factor of 18.5% for 2125 reflections collected on a Xentronics area detector. The drug is bound in the minor groove, at the five base-pair site 5'-ATTTG and is in a unique orientation. This is displaced by one base pair in the 5' direction compared to previously-determined structures of this drug with the sequence d(CGCGAATTCGCG)2. Reasons for this difference in behaviour are discussed in terms of several sequence-dependent structural features of the DNA, with particular reference to differences in propeller twist and minor-groove width. Images PMID:7515488

Design of plate directional heat transmission structure based on layered thermal metamaterials

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

Sun, L. K.; Yu, Z. F.; Huang, J., E-mail: slk-0-1999@163.com

2016-02-15

Invisibility cloaks based on transformation optics are often closed structures; however, such a structure limits the kinds of objects that can be placed in the cloak. In this work, we adopt a transformation thermodynamics approach to design an “open cloak”, called a plate directional heat transmission structure, which is capable of guiding heat fluxes to the flank region of the metamaterial device. The most fascinating and unique feature of the device is that the lower surface can remain at a lower temperature compared with the SiO{sub 2} aerogel thermal insulation material. Our results are expected to markedly enhance capabilities inmore » thermal protection, thermal-energy utilization, and domains beyond. In addition to the theoretical analysis, the present design is demonstrated in numerical simulations based on finite element calculations.« less

Single-shot mega-electronvolt ultrafast electron diffraction for structure dynamic studies of warm dense matter

NASA Astrophysics Data System (ADS)

Mo, M. Z.; Shen, X.; Chen, Z.; Li, R. K.; Dunning, M.; Sokolowski-Tinten, K.; Zheng, Q.; Weathersby, S. P.; Reid, A. H.; Coffee, R.; Makasyuk, I.; Edstrom, S.; McCormick, D.; Jobe, K.; Hast, C.; Glenzer, S. H.; Wang, X.

2016-11-01

We have developed a single-shot mega-electronvolt ultrafast-electron-diffraction system to measure the structural dynamics of warm dense matter. The electron probe in this system is featured by a kinetic energy of 3.2 MeV and a total charge of 20 fC, with the FWHM pulse duration and spot size at sample of 350 fs and 120 μm respectively. We demonstrate its unique capability by visualizing the atomic structural changes of warm dense gold formed from a laser-excited 35-nm freestanding single-crystal gold foil. The temporal evolution of the Bragg peak intensity and of the liquid signal during solid-liquid phase transition are quantitatively determined. This experimental capability opens up an exciting opportunity to unravel the atomic dynamics of structural phase transitions in warm dense matter regime.

Multiplex congruence network of natural numbers.

PubMed

Yan, Xiao-Yong; Wang, Wen-Xu; Chen, Guan-Rong; Shi, Ding-Hua

2016-03-31

Congruence theory has many applications in physical, social, biological and technological systems. Congruence arithmetic has been a fundamental tool for data security and computer algebra. However, much less attention was devoted to the topological features of congruence relations among natural numbers. Here, we explore the congruence relations in the setting of a multiplex network and unveil some unique and outstanding properties of the multiplex congruence network. Analytical results show that every layer therein is a sparse and heterogeneous subnetwork with a scale-free topology. Counterintuitively, every layer has an extremely strong controllability in spite of its scale-free structure that is usually difficult to control. Another amazing feature is that the controllability is robust against targeted attacks to critical nodes but vulnerable to random failures, which also differs from ordinary scale-free networks. The multi-chain structure with a small number of chain roots arising from each layer accounts for the strong controllability and the abnormal feature. The multiplex congruence network offers a graphical solution to the simultaneous congruences problem, which may have implication in cryptography based on simultaneous congruences. Our work also gains insight into the design of networks integrating advantages of both heterogeneous and homogeneous networks without inheriting their limitations.

Multiplex congruence network of natural numbers

NASA Astrophysics Data System (ADS)

Yan, Xiao-Yong; Wang, Wen-Xu; Chen, Guan-Rong; Shi, Ding-Hua

2016-03-01

Congruence theory has many applications in physical, social, biological and technological systems. Congruence arithmetic has been a fundamental tool for data security and computer algebra. However, much less attention was devoted to the topological features of congruence relations among natural numbers. Here, we explore the congruence relations in the setting of a multiplex network and unveil some unique and outstanding properties of the multiplex congruence network. Analytical results show that every layer therein is a sparse and heterogeneous subnetwork with a scale-free topology. Counterintuitively, every layer has an extremely strong controllability in spite of its scale-free structure that is usually difficult to control. Another amazing feature is that the controllability is robust against targeted attacks to critical nodes but vulnerable to random failures, which also differs from ordinary scale-free networks. The multi-chain structure with a small number of chain roots arising from each layer accounts for the strong controllability and the abnormal feature. The multiplex congruence network offers a graphical solution to the simultaneous congruences problem, which may have implication in cryptography based on simultaneous congruences. Our work also gains insight into the design of networks integrating advantages of both heterogeneous and homogeneous networks without inheriting their limitations.

Characterising the Architecture of New Zealand's Geothermal Structural Fluid Flow Networks Using Borehole Images

NASA Astrophysics Data System (ADS)

McNamara, David; Milicich, Sarah; Massiot, Cécile

2017-04-01

Borehole imaging has been used worldwide since the 1950's to capture vital geological information on the lithology, structure, and stress conditions of the Earth's subsurface. In New Zealand both acoustic and resistivity based borehole image logs are utilised to explore the geological nature of the basement and volcanic rocks that contain the country's unique geothermal reservoirs. Borehole image logs in wells from three geothermal fields in the Taupo Volcanic Zone (TVZ) provide the first, direct, subsurface, structural orientation measurements in New Zealand geothermal reservoir lithologies. While showing an overall structural pattern aligned to the regional tectonic trend, heterogeneities are observed that provide insight into the complexity of the structurally controlled, geothermal, fluid flow pathways. Analysis of imaged stress induced features informs us that the stress field orientation in the TVZ is also not homogenous, but is variable at a local scale.

Nonlinear analysis for high-temperature multilayered fiber composite structures. M.S. Thesis; [turbine blades

NASA Technical Reports Server (NTRS)

Hopkins, D. A.

1984-01-01

A unique upward-integrated top-down-structured approach is presented for nonlinear analysis of high-temperature multilayered fiber composite structures. Based on this approach, a special purpose computer code was developed (nonlinear COBSTRAN) which is specifically tailored for the nonlinear analysis of tungsten-fiber-reinforced superalloy (TFRS) composite turbine blade/vane components of gas turbine engines. Special features of this computational capability include accounting of; micro- and macro-heterogeneity, nonlinear (stess-temperature-time dependent) and anisotropic material behavior, and fiber degradation. A demonstration problem is presented to mainfest the utility of the upward-integrated top-down-structured approach, in general, and to illustrate the present capability represented by the nonlinear COBSTRAN code. Preliminary results indicate that nonlinear COBSTRAN provides the means for relating the local nonlinear and anisotropic material behavior of the composite constituents to the global response of the turbine blade/vane structure.

Insights into the structural features and stability of peptide nucleic acid with a D-prolyl-2-aminocyclopentane carboxylic acid backbone that binds to DNA and RNA.

PubMed

Poomsuk, Nattawee; Vilaivan, Tirayut; Siriwong, Khatcharin

2018-06-12

Peptide nucleic acid (PNA) is a powerful biomolecule with a wide variety of important applications. In this work, the molecular structures and binding affinity of PNA with a D-prolyl-2-aminocyclopentane carboxylic acid backbone (acpcPNA) that binds to both DNA and RNA were studied using molecular dynamics simulations. The simulated structures of acpcPNA-DNA and acpcPNA-RNA duplexes more closely resembled the typical structures of B-DNA and A-RNA than the corresponding duplexes of aegPNA. The calculated binding free energies are in good agreement with the experimental results that the acpcPNA-DNA duplex is more stable than the acpcPNA-RNA duplex regardless of the base sequences. The results provide further insights in the relationship between structure and stability of this unique PNA system. Copyright © 2018 Elsevier Inc. All rights reserved.

Laryngeal Features Are Phonetically Abstract: Mismatch Negativity Evidence from Arabic, English, and Russian

PubMed Central

Schluter, Kevin T.; Politzer-Ahles, Stephen; Al Kaabi, Meera; Almeida, Diogo

2017-01-01

Many theories of phonology assume that the sound structure of language is made up of distinctive features, but there is considerable debate about how much articulatory detail distinctive features encode in long-term memory. Laryngeal features such as voicing provide a unique window into this question: while many languages have two-way contrasts that can be given a simple binary feature account [±VOICE], the precise articulatory details underlying these contrasts can vary significantly across languages. Here, we investigate a series of two-way voicing contrasts in English, Arabic, and Russian, three languages that implement their voicing contrasts very differently at the articulatory-phonetic level. In three event-related potential experiments contrasting English, Arabic, and Russian fricatives along with Russian stops, we observe a consistent pattern of asymmetric mismatch negativity (MMN) effects that is compatible with an articulatorily abstract and cross-linguistically uniform way of marking two-way voicing contrasts, as opposed to an articulatorily precise and cross-linguistically diverse way of encoding them. Regardless of whether a language is theorized to encode [VOICE] over [SPREAD GLOTTIS], the data is consistent with a universal marking of the [SPREAD GLOTTIS] feature. PMID:28555118

Direct Evidence of Intrinsic Blue Fluorescence from Oligomeric Interfaces of Human Serum Albumin.

PubMed

Bhattacharya, Arpan; Bhowmik, Soumitra; Singh, Amit K; Kodgire, Prashant; Das, Apurba K; Mukherjee, Tushar Kanti

2017-10-10

The molecular origin behind the concentration-dependent intrinsic blue fluorescence of human serum albumin (HSA) is not known yet. This unusual blue fluorescence is believed to be a characteristic feature of amyloid-like fibrils of protein/peptide and originates due to the delocalization of peptide bond electrons through the extended hydrogen bond networks of cross-β-sheet structure. Herein, by combining the results of spectroscopy, size exclusion chromatography, native gel electrophoresis, and confocal microscopy, we have shown that the intrinsic blue fluorescence of HSA exclusively originates from oligomeric interfaces devoid of any amyloid-like fibrillar structure. Our study suggests that this low energy fluorescence band is not due to any particular residue/sequence, but rather it is a common feature of self-assembled peptide bonds. The present findings of intrinsic blue fluorescence from oligomeric interfaces pave the way for future applications of this unique visual phenomenon for early stage detection of various protein aggregation related human diseases.

Olefinic Thermoplastic Elastomer Gels: Combining Polymer Crystallization and Microphase Separation in a Selective Solvent

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

Armstrong, Daniel P.; Mineart, Kenneth P.; Lee, Byeongdu

Since selectively swollen thermoplastic elastomer gels (TPEGs) afford a wide range of beneficial properties that open new doors to developing elastomer-based technologies, in this study we examine the unique structure-property behavior of TPEGs composed of olefinic block copolymers (OBCs). Unlike their styrenic counterparts typically possessing two chemically different blocks, this class of multiblock copolymers consists of linear polyethylene hard blocks and poly(ethylene-co-α-octene) soft blocks, in which case, microphase separation between the hard and the soft blocks is accompanied by crystallization of the hard blocks. We prepare olefinic TPEGs (OTPEGs) through the incorporation of a primarily aliphatic oil that selectively swellsmore » the soft block and investigate the resultant morphological features through the use of polarized light microscopy and small-/wideangle X-ray scattering. These features are correlated with thermal and mechanical property measurements from calorimetry, rheology, and extensiometry to elucidate the roles of crystallization and self-assembly on gel characteristics and establish useful structure-property relationships.« less

Astragalar Morphology of Selected Giraffidae

PubMed Central

2016-01-01

The artiodactyl astragalus has been modified to exhibit two trochleae, creating a double pullied structure allowing for significant dorso-plantar motion, and limited mediolateral motion. The astragalus structure is partly influenced by environmental substrates, and correspondingly, morphometric studies can yield paleohabitat information. The present study establishes terminology and describes detailed morphological features on giraffid astragali. Each giraffid astragalus exhibits a unique combination of anatomical characteristics. The giraffid astragalar morphologies reinforce previously established phylogenetic relationships. We find that the enlargement of the navicular head is a feature shared by all giraffids, and that the primitive giraffids possess exceptionally tall astragalar heads in relation to the total astragalar height. The sivatheres and the okapi share a reduced notch on the lateral edge of the astragalus. We find that Samotherium is more primitive in astragalar morphologies than Palaeotragus, which is reinforced by tooth characteristics and ossicone position. Diagnostic anatomical characters on the astragalus allow for giraffid species identifications and a better understanding of Giraffidae. PMID:27028515

Predominant information quality scheme for the essential amino acids: an information-theoretical analysis.

PubMed

Esquivel, Rodolfo O; Molina-Espíritu, Moyocoyani; López-Rosa, Sheila; Soriano-Correa, Catalina; Barrientos-Salcedo, Carolina; Kohout, Miroslav; Dehesa, Jesús S

2015-08-24

In this work we undertake a pioneer information-theoretical analysis of 18 selected amino acids extracted from a natural protein, bacteriorhodopsin (1C3W). The conformational structures of each amino acid are analyzed by use of various quantum chemistry methodologies at high levels of theory: HF, M062X and CISD(Full). The Shannon entropy, Fisher information and disequilibrium are determined to grasp the spatial spreading features of delocalizability, order and uniformity of the optimized structures. These three entropic measures uniquely characterize all amino acids through a predominant information-theoretic quality scheme (PIQS), which gathers all chemical families by means of three major spreading features: delocalization, narrowness and uniformity. This scheme recognizes four major chemical families: aliphatic (delocalized), aromatic (delocalized), electro-attractive (narrowed) and tiny (uniform). All chemical families recognized by the existing energy-based classifications are embraced by this entropic scheme. Finally, novel chemical patterns are shown in the information planes associated with the PIQS entropic measures. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Olefinic Thermoplastic Elastomer Gels: Combining Polymer Crystallization and Microphase Separation in a Selective Solvent

DOE PAGES

Armstrong, Daniel P.; Mineart, Kenneth P.; Lee, Byeongdu; ...

2016-11-01

Since selectively swollen thermoplastic elastomer gels (TPEGs) afford a wide range of beneficial properties that open new doors to developing elastomer-based technologies, in this study we examine the unique structure-property behavior of TPEGs composed of olefinic block copolymers (OBCs). Unlike their styrenic counterparts typically possessing two chemically different blocks, this class of multiblock copolymers consists of linear polyethylene hard blocks and poly(ethylene-co-α-octene) soft blocks, in which case, microphase separation between the hard and the soft blocks is accompanied by crystallization of the hard blocks. We prepare olefinic TPEGs (OTPEGs) through the incorporation of a primarily aliphatic oil that selectively swellsmore » the soft block and investigate the resultant morphological features through the use of polarized light microscopy and small-/wideangle X-ray scattering. These features are correlated with thermal and mechanical property measurements from calorimetry, rheology, and extensiometry to elucidate the roles of crystallization and self-assembly on gel characteristics and establish useful structure-property relationships.« less

Structural Analysis of PTM Hotspots (SAPH-ire)--A Quantitative Informatics Method Enabling the Discovery of Novel Regulatory Elements in Protein Families.

PubMed

Dewhurst, Henry M; Choudhury, Shilpa; Torres, Matthew P

2015-08-01

Predicting the biological function potential of post-translational modifications (PTMs) is becoming increasingly important in light of the exponential increase in available PTM data from high-throughput proteomics. We developed structural analysis of PTM hotspots (SAPH-ire)--a quantitative PTM ranking method that integrates experimental PTM observations, sequence conservation, protein structure, and interaction data to allow rank order comparisons within or between protein families. Here, we applied SAPH-ire to the study of PTMs in diverse G protein families, a conserved and ubiquitous class of proteins essential for maintenance of intracellular structure (tubulins) and signal transduction (large and small Ras-like G proteins). A total of 1728 experimentally verified PTMs from eight unique G protein families were clustered into 451 unique hotspots, 51 of which have a known and cited biological function or response. Using customized software, the hotspots were analyzed in the context of 598 unique protein structures. By comparing distributions of hotspots with known versus unknown function, we show that SAPH-ire analysis is predictive for PTM biological function. Notably, SAPH-ire revealed high-ranking hotspots for which a functional impact has not yet been determined, including phosphorylation hotspots in the N-terminal tails of G protein gamma subunits--conserved protein structures never before reported as regulators of G protein coupled receptor signaling. To validate this prediction we used the yeast model system for G protein coupled receptor signaling, revealing that gamma subunit-N-terminal tail phosphorylation is activated in response to G protein coupled receptor stimulation and regulates protein stability in vivo. These results demonstrate the utility of integrating protein structural and sequence features into PTM prioritization schemes that can improve the analysis and functional power of modification-specific proteomics data. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Fine-Scale Analysis Reveals Cryptic Landscape Genetic Structure in Desert Tortoises

PubMed Central

Latch, Emily K.; Boarman, William I.; Walde, Andrew; Fleischer, Robert C.

2011-01-01

Characterizing the effects of landscape features on genetic variation is essential for understanding how landscapes shape patterns of gene flow and spatial genetic structure of populations. Most landscape genetics studies have focused on patterns of gene flow at a regional scale. However, the genetic structure of populations at a local scale may be influenced by a unique suite of landscape variables that have little bearing on connectivity patterns observed at broader spatial scales. We investigated fine-scale spatial patterns of genetic variation and gene flow in relation to features of the landscape in desert tortoise (Gopherus agassizii), using 859 tortoises genotyped at 16 microsatellite loci with associated data on geographic location, sex, elevation, slope, and soil type, and spatial relationship to putative barriers (power lines, roads). We used spatially explicit and non-explicit Bayesian clustering algorithms to partition the sample into discrete clusters, and characterize the relationships between genetic distance and ecological variables to identify factors with the greatest influence on gene flow at a local scale. Desert tortoises exhibit weak genetic structure at a local scale, and we identified two subpopulations across the study area. Although genetic differentiation between the subpopulations was low, our landscape genetic analysis identified both natural (slope) and anthropogenic (roads) landscape variables that have significantly influenced gene flow within this local population. We show that desert tortoise movements at a local scale are influenced by features of the landscape, and that these features are different than those that influence gene flow at larger scales. Our findings are important for desert tortoise conservation and management, particularly in light of recent translocation efforts in the region. More generally, our results indicate that recent landscape changes can affect gene flow at a local scale and that their effects can be detected almost immediately. PMID:22132143

Fine-scale analysis reveals cryptic landscape genetic structure in desert tortoises.

PubMed

Latch, Emily K; Boarman, William I; Walde, Andrew; Fleischer, Robert C

2011-01-01

Characterizing the effects of landscape features on genetic variation is essential for understanding how landscapes shape patterns of gene flow and spatial genetic structure of populations. Most landscape genetics studies have focused on patterns of gene flow at a regional scale. However, the genetic structure of populations at a local scale may be influenced by a unique suite of landscape variables that have little bearing on connectivity patterns observed at broader spatial scales. We investigated fine-scale spatial patterns of genetic variation and gene flow in relation to features of the landscape in desert tortoise (Gopherus agassizii), using 859 tortoises genotyped at 16 microsatellite loci with associated data on geographic location, sex, elevation, slope, and soil type, and spatial relationship to putative barriers (power lines, roads). We used spatially explicit and non-explicit Bayesian clustering algorithms to partition the sample into discrete clusters, and characterize the relationships between genetic distance and ecological variables to identify factors with the greatest influence on gene flow at a local scale. Desert tortoises exhibit weak genetic structure at a local scale, and we identified two subpopulations across the study area. Although genetic differentiation between the subpopulations was low, our landscape genetic analysis identified both natural (slope) and anthropogenic (roads) landscape variables that have significantly influenced gene flow within this local population. We show that desert tortoise movements at a local scale are influenced by features of the landscape, and that these features are different than those that influence gene flow at larger scales. Our findings are important for desert tortoise conservation and management, particularly in light of recent translocation efforts in the region. More generally, our results indicate that recent landscape changes can affect gene flow at a local scale and that their effects can be detected almost immediately.

Two new phases in the ternary RE-Ga-S systems with the unique interlinkage of GaS4 building units: synthesis, structure, and properties.

PubMed

Lin, Hua; Shen, Jin-Ni; Zhu, Wei-Wei; Liu, Yi; Wu, Xin-Tao; Zhu, Qi-Long; Wu, Li-Ming

2017-10-17

Two novel ternary rare-earth chalcogenides, Yb 6 Ga 4 S 15 and Lu 5 GaS 9 , have been prepared by solid-state reactions of an elemental mixture at high temperatures. Their structures were determined on the basis of single-crystal X-ray diffraction. Yb 6 Ga 4 S 15 crystallizes in the monoclinic space group C2/m (no.12) [a = 23.557(2) Å, b = 3.7664(4) Å, c = 12.466(1) Å, β = 90.915(9)°, V = 1105.9(2) Å 3 and Z = 2], whereas Lu 5 GaS 9 crystallizes in the triclinic space group P1[combining macron] (no.2) [a = 7.735(3) Å, b = 10.033(4) Å, c = 10.120(4) Å, α = 106.296(4)°, β = 100.178(5)°, γ = 101.946(3)°, V = 714.1(5) Å 3 and Z = 2]. Both the structures feature complicated three dimensional frameworks with the unique interlinkages of GaS 4 as basic building units. Significantly, photo-electrochemical measurements indicated that title compounds were photoresponsive under visible-light illumination. Furthermore, the UV-visible-near IR diffuse reflectance spectra, thermal stabilities, electronic structures, physical properties as well as a structure change trend of the ternary rare-earth/gallium/sulfur compounds have been evaluated.

A longitudinal study of women's depression symptom profiles during and after the postpartum phase.

PubMed

Fox, Molly; Sandman, Curt A; Davis, Elysia Poggi; Glynn, Laura M

2018-04-01

An issue of critical importance for psychiatry and women's health is whether postpartum depression (PPD) represents a unique condition. The Diagnostic and Statistical Manual of Mental Disorders asserts that major depressive disorder (MDD) may present with peripartum onset, without suggesting any other differences between MDD and PPD. The absence of any distinct features calls into question the nosologic validity of PPD as a diagnostic category. The present study investigates whether symptom profiles differ between PPD and depression occurring outside the postpartum phase. In a prospective, longitudinal study of parturient women (N = 239), we examine the manifestation of depression symptoms. We assess factor structure of symptom profiles, and whether factors are differentially pronounced during and after the postpartum period. Factors were revealed representing: Worry, Emotional/Circadian/Energetic Dysregulation, Somatic/Cognitive, Appetite, Distress Display, and Anger symptoms. The factor structure was validated at postpartum and after-postpartum timepoints. Interestingly, the Worry factor, comprising anxiety and guilt, was significantly more pronounced during the postpartum timepoint, and the Emotional/Circadian/Energetic Dysregulation factor, which contained sadness and anhedonia, was significantly less pronounced during the postpartum period. These results suggest that PPD may be a unique syndrome, necessitating research, diagnosis, and treatment strategies distinct from those for MDD. Results indicate the possibility that Worry is an enhanced feature of PPD compared to depression outside the postpartum period, and the crucial role of sadness/anhedonia in MDD diagnosis may be less applicable to PPD diagnosis. © 2018 Wiley Periodicals, Inc.

Electron Microscopy and Analytical X-ray Characterization of Compositional and Nanoscale Structural Changes in Fossil Bone

NASA Astrophysics Data System (ADS)

Boatman, Elizabeth Marie

The nanoscale structure of compact bone contains several features that are direct indicators of bulk tissue mechanical properties. Fossil bone tissues represent unique opportunities to understand the compact bone structure/property relationships from a deep time perspective, offering a possible array of new insights into bone diseases, biomimicry of composite materials, and basic knowledge of bioapatite composition and nanoscale bone structure. To date, most work with fossil bone has employed microscale techniques and has counter-indicated the survival of bioapatite and other nanoscale structural features. The obvious disconnect between the use of microscale techniques and the discernment of nanoscale structure has prompted this work. The goal of this study was to characterize the nanoscale constituents of fossil compact bone by applying a suite of diffraction, microscopy, and spectrometry techniques, representing the highest levels of spatial and energy resolution available today, and capable of complementary structural and compositional characterization from the micro- to the nanoscale. Fossil dinosaur and crocodile long bone specimens, as well as modern ratite and crocodile femurs, were acquired from the UC Museum of Paleontology. Preserved physiological features of significance were documented with scanning electron microscopy back-scattered imaging. Electron microprobe wavelength-dispersive X-ray spectroscopy (WDS) revealed fossil bone compositions enriched in fluorine with a complementary loss of oxygen. X-ray diffraction analyses demonstrated that all specimens were composed of apatite. Transmission electron microscopy (TEM) imaging revealed preserved nanocrystallinity in the fossil bones and electron diffraction studies further identified these nanocrystallites as apatite. Tomographic analyses of nanoscale elements imaged by TEM and small angle X-ray scattering were performed, with the results of each analysis further indicating that nanoscale structure is highly conserved in these four fossil specimens. Finally, the results of this study indicate that bioapatite can be preserved in even the most ancient vertebrate specimens, further supporting the idea that fossilization is a preservational process. This work also underlines the importance of using appropriately selected characterization and analytical techniques for the study of fossil bone, especially from the perspective of spatial resolution and the scale of the bone structural features in question.

Feature and Statistical Model Development in Structural Health Monitoring

NASA Astrophysics Data System (ADS)

Kim, Inho

All structures suffer wear and tear because of impact, excessive load, fatigue, corrosion, etc. in addition to inherent defects during their manufacturing processes and their exposure to various environmental effects. These structural degradations are often imperceptible, but they can severely affect the structural performance of a component, thereby severely decreasing its service life. Although previous studies of Structural Health Monitoring (SHM) have revealed extensive prior knowledge on the parts of SHM processes, such as the operational evaluation, data processing, and feature extraction, few studies have been conducted from a systematical perspective, the statistical model development. The first part of this dissertation, the characteristics of inverse scattering problems, such as ill-posedness and nonlinearity, reviews ultrasonic guided wave-based structural health monitoring problems. The distinctive features and the selection of the domain analysis are investigated by analytically searching the conditions of the uniqueness solutions for ill-posedness and are validated experimentally. Based on the distinctive features, a novel wave packet tracing (WPT) method for damage localization and size quantification is presented. This method involves creating time-space representations of the guided Lamb waves (GLWs), collected at a series of locations, with a spatially dense distribution along paths at pre-selected angles with respect to the direction, normal to the direction of wave propagation. The fringe patterns due to wave dispersion, which depends on the phase velocity, are selected as the primary features that carry information, regarding the wave propagation and scattering. The following part of this dissertation presents a novel damage-localization framework, using a fully automated process. In order to construct the statistical model for autonomous damage localization deep-learning techniques, such as restricted Boltzmann machine and deep belief network, are trained and utilized to interpret nonlinear far-field wave patterns. Next, a novel bridge scour estimation approach that comprises advantages of both empirical and data-driven models is developed. Two field datasets from the literature are used, and a Support Vector Machine (SVM), a machine-learning algorithm, is used to fuse the field data samples and classify the data with physical phenomena. The Fast Non-dominated Sorting Genetic Algorithm (NSGA-II) is evaluated on the model performance objective functions to search for Pareto optimal fronts.

Crystal structure of the human 4-1BB/4-1BBL complex.

PubMed

Gilbreth, Ryan N; Oganesyan, Vaheh Y; Amdouni, Hamza; Novarra, Shabazz; Grinberg, Luba; Barnes, Arnita; Baca, Manuel

2018-05-02

4-1BBL is a member of the TNF superfamily and is the ligand for the TNFRsuperfamily receptor, 4-1BB. 4-1BB plays an immunomodulatory role in T cells and NK cells and agonists of this receptor have garnered strong attention as potentialimmunotherapy agents. Broadly speaking, the structural features of TNF superfamilymembers, their receptors and ligand/receptor complexes are similar. However, apublished crystal structure of human 4-1BBL suggests that it may be unique in thisregard, exhibiting a three-bladed propeller-like trimer assembly that is distinctly different from that observed in other family members. This unusual structure also suggests that the human 4-1BB/4-1BBL complex may be structurally unique within the TNF/TNFR superfamily, but to date no structural data have been reported. Here we report the crystal structure of the human 4-1BB/4-1BBL complex at 2.4 Å resolution. In this structure, 4-1BBL does not adopt the unusual trimer assembly previously reported, but instead forms a canonical bell-shaped trimer typical of other TNF superfamily members. The structure of 4-1BB is also largely canonical as is the 4-1BB/4-1BBL complex. Mutational data support the 4-1BBL structure reported here as being biologically relevant, suggesting that the previously reported structure is not. Together, the data presented here offer insight into structure/function relationships in the 4-1BB/4-1BBL system and improve our structural understanding of the TNF/TNFR superfamily more broadly. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Structure and Dynamic Regulation of Abl Kinases*

PubMed Central

Panjarian, Shoghag; Iacob, Roxana E.; Chen, Shugui; Engen, John R.; Smithgall, Thomas E.

2013-01-01

The c-abl proto-oncogene encodes a unique protein-tyrosine kinase (Abl) distinct from c-Src, c-Fes, and other cytoplasmic tyrosine kinases. In normal cells, Abl plays prominent roles in cellular responses to genotoxic stress as well as in the regulation of the actin cytoskeleton. Abl is also well known in the context of Bcr-Abl, the oncogenic fusion protein characteristic of chronic myelogenous leukemia. Selective inhibitors of Bcr-Abl, of which imatinib is the prototype, have had a tremendous impact on clinical outcomes in chronic myelogenous leukemia and revolutionized the field of targeted cancer therapy. In this minireview, we focus on the structural organization and dynamics of Abl kinases and how these features influence inhibitor sensitivity. PMID:23316053

Using the NASTRAN Thermal Analyzer to simulate a flight scientific instrument package

NASA Technical Reports Server (NTRS)

Lee, H.-P.; Jackson, C. E., Jr.

1974-01-01

The NASTRAN Thermal Analyzer has proven to be a unique and useful tool for thermal analyses involving large and complex structures where small, thermally induced deformations are critical. Among its major advantages are direct grid point-to-grid point compatibility with large structural models; plots of the model that may be generated for both conduction and boundary elements; versatility of applying transient thermal loads especially to repeat orbital cycles; on-line printer plotting of temperatures and rate of temperature changes as a function of time; and direct matrix input to solve linear differential equations on-line. These features provide a flexibility far beyond that available in most finite-difference thermal analysis computer programs.

Navigating at Will on the Water Phase Diagram

NASA Astrophysics Data System (ADS)

Pipolo, S.; Salanne, M.; Ferlat, G.; Klotz, S.; Saitta, A. M.; Pietrucci, F.

2017-12-01

Despite the simplicity of its molecular unit, water is a challenging system because of its uniquely rich polymorphism and predicted but yet unconfirmed features. Introducing a novel space of generalized coordinates that capture changes in the topology of the interatomic network, we are able to systematically track transitions among liquid, amorphous, and crystalline forms throughout the whole phase diagram of water, including the nucleation of crystals above and below the melting point. Our approach, based on molecular dynamics and enhanced sampling or free energy calculation techniques, is not specific to water and could be applied to very different structural phase transitions, paving the way towards the prediction of kinetic routes connecting polymorphic structures in a range of materials.

Magnetic ionic liquids in analytical chemistry: A review.

PubMed

Clark, Kevin D; Nacham, Omprakash; Purslow, Jeffrey A; Pierson, Stephen A; Anderson, Jared L

2016-08-31

Magnetic ionic liquids (MILs) have recently generated a cascade of innovative applications in numerous areas of analytical chemistry. By incorporating a paramagnetic component within the cation or anion, MILs exhibit a strong response toward external magnetic fields. Careful design of the MIL structure has yielded magnetoactive compounds with unique physicochemical properties including high magnetic moments, enhanced hydrophobicity, and the ability to solvate a broad range of molecules. The structural tunability and paramagnetic properties of MILs have enabled magnet-based technologies that can easily be added to the analytical method workflow, complement needed extraction requirements, or target specific analytes. This review highlights the application of MILs in analytical chemistry and examines the important structural features of MILs that largely influence their physicochemical and magnetic properties. Copyright © 2016 Elsevier B.V. All rights reserved.

Evolution of plant cell wall: Arabinogalactan-proteins from three moss genera show structural differences compared to seed plants.

PubMed

Bartels, Desirée; Baumann, Alexander; Maeder, Malte; Geske, Thomas; Heise, Esther Marie; von Schwartzenberg, Klaus; Classen, Birgit

2017-05-01

Arabinogalactan-proteins (AGPs) are important proteoglycans of plant cell walls. They seem to be present in most, if not all seed plants, but their occurrence and structure in bryophytes is widely unknown and actually the focus of AGP research. With regard to evolution of plant cell wall, we isolated AGPs from the three mosses Sphagnum sp., Physcomitrella patens and Polytrichastrum formosum. The moss AGPs show structural characteristics common for AGPs of seed plants, but also unique features, especially 3-O-methyl-rhamnose (trivial name acofriose) as terminal monosaccharide not found in arabinogalactan-proteins of angiosperms and 1,2,3-linked galactose as branching point never found in arabinogalactan-proteins before. Copyright © 2017 Elsevier Ltd. All rights reserved.

A natural language processing pipeline for pairing measurements uniquely across free-text CT reports.

PubMed

Sevenster, Merlijn; Bozeman, Jeffrey; Cowhy, Andrea; Trost, William

2015-02-01

To standardize and objectivize treatment response assessment in oncology, guidelines have been proposed that are driven by radiological measurements, which are typically communicated in free-text reports defying automated processing. We study through inter-annotator agreement and natural language processing (NLP) algorithm development the task of pairing measurements that quantify the same finding across consecutive radiology reports, such that each measurement is paired with at most one other ("partial uniqueness"). Ground truth is created based on 283 abdomen and 311 chest CT reports of 50 patients each. A pre-processing engine segments reports and extracts measurements. Thirteen features are developed based on volumetric similarity between measurements, semantic similarity between their respective narrative contexts and structural properties of their report positions. A Random Forest classifier (RF) integrates all features. A "mutual best match" (MBM) post-processor ensures partial uniqueness. In an end-to-end evaluation, RF has precision 0.841, recall 0.807, F-measure 0.824 and AUC 0.971; with MBM, which performs above chance level (P<0.001), it has precision 0.899, recall 0.776, F-measure 0.833 and AUC 0.935. RF (RF+MBM) has error-free performance on 52.7% (57.4%) of report pairs. Inter-annotator agreement of three domain specialists with the ground truth (κ>0.960) indicates that the task is well defined. Domain properties and inter-section differences are discussed to explain superior performance in abdomen. Enforcing partial uniqueness has mixed but minor effects on performance. A combined machine learning-filtering approach is proposed for pairing measurements, which can support prospective (supporting treatment response assessment) and retrospective purposes (data mining). Copyright © 2014 Elsevier Inc. All rights reserved.

Ultrastructural dynamics of human reproduction, from ovulation to fertilization and early embryo development.

PubMed

Familiari, Giuseppe; Heyn, Rosemarie; Relucenti, Michela; Nottola, Stefania A; Sathananthan, A Henry

2006-01-01

This study describes the updated, fine structure of human gametes, the human fertilization process, and human embryos, mainly derived from assisted reproductive technology (ART). As clearly shown, the ultrastructure of human reproduction is a peculiar multistep process, which differs in part from that of other mammalian models, having some unique features. Particular attention has been devoted to the (1) sperm ultrastructure, likely "Tygerberg (Kruger) strict morphology criteria"; (2) mature oocyte, in which the MII spindle is barrel shaped, anastral, and lacking centrioles; (3) three-dimensional microarchitecture of the zona pellucida with its unique supramolecular filamentous organization; (4) sperm-egg interactions with the peculiarity of the sperm centrosome that activates the egg and organizes the sperm aster and mitotic spindles of the embryo; and (5) presence of viable cumulus cells whose metabolic activity is closely related to egg and embryo behavior in in vitro as well as in vivo conditions, in a sort of extraovarian "microfollicular unit." Even if the ultrastructural morphodynamic features of human fertilization are well understood, our knowledge about in vivo fertilization is still very limited and the complex sequence of in vivo biological steps involved in human reproduction is only partially reproduced in current ART procedures.

EPA/NIEHS Children's Environmental Health and Disease ...

EPA Pesticide Factsheets

Powerpoint presentation - 32 slides. Introductory slides (4-5 slides); Unique Features such as the multidisciplinary Center structure, with community engagement as an integral element through the Community Outreach and Translation Cores (COTCs) (4 slides); Recent findings (Health effects of flame retardants (PBDEs)Health effects from near-road exposures, Asthma, Autism Spectrum Disorder (ASD))(4-5 slides); Impact from the work of the Centers (approx 10 Slides); Conclusion/looking forward/future activities (5 slides); A 3 minute video from one of the Children's Centers summarizing their work in the field will be shared at the end of the presentation. Dr. Johnson will be presenting the work of the EPA/NIEHS Children's Centers to Children’s Health Protection Advisory Committee (CHPAC). The Children's Health Protection Advisory Committee is a body of researchers, academicians, health care providers, environmentalists, state and tribal government employees, and members of the public who advise EPA on regulations, research, and communication issues relevant to the environmental precipitants of health in children. Members serve voluntarily and the CHPAC meets about three times per year to provide specific recommendations to the EPA Administrator. Dr. Johnson will be presenting on unique features of the Children's Centers, findings and impact from the work of the Children's Centers.

Molecular Characterization of LubX: Functional Divergence of the U-Box Fold by Legionella pneumophila.

PubMed

Quaile, Andrew T; Urbanus, Malene L; Stogios, Peter J; Nocek, Boguslaw; Skarina, Tatiana; Ensminger, Alexander W; Savchenko, Alexei

2015-08-04

LubX is part of the large arsenal of effectors in Legionella pneumophila that are translocated into the host cytosol during infection. Despite such unique features as the presence of two U-box motifs and its targeting of another effector SidH, the molecular basis of LubX activity remains poorly understood. Here we show that the N terminus of LubX is able to activate an extended number of ubiquitin-conjugating (E2) enzymes including UBE2W, UBEL6, and all tested members of UBE2D and UBE2E families. Crystal structures of LubX alone and in complex with UBE2D2 revealed drastic molecular diversification between the two U-box domains, with only the N-terminal U-box retaining E2 recognition features typical for its eukaryotic counterparts. Extensive mutagenesis followed by functional screening in a yeast model system captured functionally important LubX residues including Arg121, critical for interactions with SidH. Combined, these data provide a new molecular insight into the function of this unique pathogenic factor. Copyright © 2015 Elsevier Ltd. All rights reserved.

Eye development in the four-eyed fish Anableps anableps: cranial and retinal adaptations to simultaneous aerial and aquatic vision.

PubMed

Perez, Louise N; Lorena, Jamily; Costa, Carinne M; Araujo, Maysa S; Frota-Lima, Gabriela N; Matos-Rodrigues, Gabriel E; Martins, Rodrigo A P; Mattox, George M T; Schneider, Patricia N

2017-04-12

The unique eyes of the four-eyed fish Anableps anableps have long intrigued biologists. Key features associated with the bulging eye of Anableps include the expanded frontal bone and the duplicated pupils and cornea. Furthermore, the Anableps retina expresses different photoreceptor genes in dorsal and ventral regions, potentially associated with distinct aerial and aquatic stimuli. To gain insight into the developmental basis of the Anableps unique eye, we examined neurocranium and eye ontogeny, as well as photoreceptor gene expression during larval stages. First, we described six larval stages during which duplication of eye structures occurs. Our osteological analysis of neurocranium ontogeny revealed another distinctive Anablepid feature: an ossified interorbital septum partially separating the orbital cavities. Furthermore, we identified the onset of differences in cell proliferation and cell layer density between dorsal and ventral regions of the retina. Finally, we show that differential photoreceptor gene expression in the retina initiates during development, suggesting that it is inherited and not environmentally determined. In sum, our results shed light on the ontogenetic steps leading to the highly derived Anableps eye. © 2017 The Author(s).

Laser processing for manufacturing nanocarbon materials

NASA Astrophysics Data System (ADS)

Van, Hai Hoang

CNTs have been considered as the excellent candidate to revolutionize a broad range of applications. There have been many method developed to manipulate the chemistry and the structure of CNTs. Laser with non-contact treatment capability exhibits many processing advantages, including solid-state treatment, extremely fast processing rate, and high processing resolution. In addition, the outstanding monochromatic, coherent, and directional beam generates the powerful energy absorption and the resultant extreme processing conditions. In my research, a unique laser scanning method was developed to process CNTs, controlling the oxidation and the graphitization. The achieved controllability of this method was applied to address the important issues of the current CNT processing methods for three applications. The controllable oxidation of CNTs by laser scanning method was applied to cut CNT films to produce high-performance cathodes for FE devices. The production method includes two important self-developed techniques to produce the cold cathodes: the production of highly oriented and uniformly distributed CNT sheets and the precise laser trimming process. Laser cutting is the unique method to produce the cathodes with remarkable features, including ultrathin freestanding structure (~200 nm), greatly high aspect ratio, hybrid CNT-GNR emitter arrays, even emitter separation, and directional emitter alignment. This unique cathode structure was unachievable by other methods. The developed FE devices successfully solved the screening effect issue encounter by current FE devices. The laser-control oxidation method was further developed to sequentially remove graphitic walls of CNTs. The laser oxidation process was directed to occur along the CNT axes by the laser scanning direction. Additionally, the oxidation was further assisted by the curvature stress and the thermal expansion of the graphitic nanotubes, ultimately opening (namely unzipping) the tubular structure to produce GNRs. Therefore the developed laser scanning method optimally exploited the thermal laser-CNT interaction, successfully transforming CNTs into 2D GNRs. The solid-state laser unzipping process effectively addressed the issues of contamination and scalability encountered by the current unzipping methods. Additionally, the produced GNRs were uniquely featured with the freestanding structure and the smooth surfaces. If the scanning process was performed in an inert environment without the appearance of oxygen, the oxidation of CNTs would not happen. Instead, the greatly mobile carbon atoms of the heated CNTs would reorganize the crystal structure, inducing the graphitization process to improve the crystallinity. Many observations showing the structural improvement of CNTs under laser irradiation has been reported, confirming the capability of laser to heal graphitic defects. Laser methods were more time-efficient and energy-efficient than other annealing methods because laser can quickly heat CNTs to generate graphitization in less than one second. This subsecond heating process of laser irradiation was more effective than other heating methods because it avoided the undesired coalescence of CNTs. In my research, the laser scanning method was applied to generate the graphitization, healing the structural defects of CNTs. Different from the reported laser methods, the laser scanning directed the locally annealed areas to move along the CNT axes, migrating and coalescencing the graphitic defects to achieve better healing results. The critical information describing the CNT structural transformation caused by the moving laser irradiation was explored from the successful applications of the developed laser method. This knowledge inspires an important method to modifiy the general graphitic structure for important applications, such as carbon fiber production, CNT self-assembly process and CNT welding. This method will be effective, facile, versatile, and adaptable for laboratory and industrial facilities.

Reconstruction of biofilm images: combining local and global structural parameters

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

Resat, Haluk; Renslow, Ryan S.; Beyenal, Haluk

2014-10-20

Digitized images can be used for quantitative comparison of biofilms grown under different conditions. Using biofilm image reconstruction, it was previously found that biofilms with a completely different look can have nearly identical structural parameters and that the most commonly utilized global structural parameters were not sufficient to uniquely define these biofilms. Here, additional local and global parameters are introduced to show that these parameters considerably increase the reliability of the image reconstruction process. Assessment using human evaluators indicated that the correct identification rate of the reconstructed images increased from 50% to 72% with the introduction of the new parametersmore » into the reconstruction procedure. An expanded set of parameters especially improved the identification of biofilm structures with internal orientational features and of structures in which colony sizes and spatial locations varied. Hence, the newly introduced structural parameter sets helped to better classify the biofilms by incorporating finer local structural details into the reconstruction process.« less

Development and applications of two computational procedures for determining the vibration modes of structural systems. [aircraft structures - aerospaceplanes

NASA Technical Reports Server (NTRS)

Kvaternik, R. G.

1975-01-01

Two computational procedures for analyzing complex structural systems for their natural modes and frequencies of vibration are presented. Both procedures are based on a substructures methodology and both employ the finite-element stiffness method to model the constituent substructures. The first procedure is a direct method based on solving the eigenvalue problem associated with a finite-element representation of the complete structure. The second procedure is a component-mode synthesis scheme in which the vibration modes of the complete structure are synthesized from modes of substructures into which the structure is divided. The analytical basis of the methods contains a combination of features which enhance the generality of the procedures. The computational procedures exhibit a unique utilitarian character with respect to the versatility, computational convenience, and ease of computer implementation. The computational procedures were implemented in two special-purpose computer programs. The results of the application of these programs to several structural configurations are shown and comparisons are made with experiment.

Nakhla: a Martian Meteorite with Indigenous Organic Carbonaceous Features

NASA Technical Reports Server (NTRS)

McKay, D. S.; Gibson, E. K.; Thomas-Keprta, K. L.; Clemett, S. J.; Le, L.; Rahman, Z.; Wentworth, S. J.

2011-01-01

The Nakhla meteorite possesses discrete, well defined, structurally coherent morphologies of carbonaceous phases present within iddingsite alteration zones. Based upon both isotopic measurements and analysis of organic phases the presence of pre-terrestrial organics is now recognized. Within the microcrystalline layers of Nakhla s iddingsite, discrete clusters of salt crystals are present. These salts are predominantly halite (NaCl) with minor MgCl2 crystals. Some CaSO4, likely gypsum, appears to be partially intergrown with some of the halite. EDX mapping shows discrete C-rich features are interspersed among these crystals. A hollow semi-spherical bowl structure ( 3 m ) has been identified and analyzed after using a focused ion beam (FIB) to cut a transverse TEM thin section of the feature and the underlying iddingsite. TEM/EDX analysis reveals that the feature is primarily carbonaceous containing C with lesser amounts of Si, S, Ca, Cl, F, Na, and minor Mn and Fe; additionally a small peak consistent with N, which has been previously seen in Nakhla carbonaceous matter, is also present. Selected area electron diffraction (SAED) shows that this C-rich material is amorphous (lacking any long-range crystallographic order) and is not graphite or carbonate. Micro-Raman spectra acquired from the same surface from which the FIB section was extracted demonstrate a typical kerogen-like D and G band structure with a weak absorption peak at 1350 and a stronger peak at 1600/cm. The C-rich feature is intimately associated with both the surrounding halite and underlying iddingsite matrix. Both iddingsite and salts are interpreted as having formed as evaporate assemblages from progressive evaporation of water bodies on Mars. This assemblage, sans the carbonaceous moieties, closely resembles iddingsite alteration features previously described which were interpreted as indigenous Martian assemblages. These distinctive macromolecular carbonaceous structures in Nakhla may represent one of the sources of the high molecular weight organic material previously identified in Nakhla. While we do not speculate on the origin of these unique carbonaceous structures, we note that the significance of such observations is that it may allow us to construct a C-cycle for Mars based on the C chemistry of the Martian meteorites with obvious implications for astrobiology and the prebiotic evolution of Mars. In any case, our observations strongly suggest that organic C exists as micrometersize, discrete structures on Mars.

A decade and a half of protein intrinsic disorder: Biology still waits for physics

PubMed Central

Uversky, Vladimir N

2013-01-01

The abundant existence of proteins and regions that possess specific functions without being uniquely folded into unique 3D structures has become accepted by a significant number of protein scientists. Sequences of these intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) are characterized by a number of specific features, such as low overall hydrophobicity and high net charge which makes these proteins predictable. IDPs/IDPRs possess large hydrodynamic volumes, low contents of ordered secondary structure, and are characterized by high structural heterogeneity. They are very flexible, but some may undergo disorder to order transitions in the presence of natural ligands. The degree of these structural rearrangements varies over a very wide range. IDPs/IDPRs are tightly controlled under the normal conditions and have numerous specific functions that complement functions of ordered proteins and domains. When lacking proper control, they have multiple roles in pathogenesis of various human diseases. Gaining structural and functional information about these proteins is a challenge, since they do not typically “freeze” while their “pictures are taken.” However, despite or perhaps because of the experimental challenges, these fuzzy objects with fuzzy structures and fuzzy functions are among the most interesting targets for modern protein research. This review briefly summarizes some of the recent advances in this exciting field and considers some of the basic lessons learned from the analysis of physics, chemistry, and biology of IDPs. PMID:23553817

Modeling Hierarchical Non-Precious Metal Catalyst Cathodes for PEFCs Using Multi-Scale X-ray CT Imaging

DOE PAGES

Komini Babu, S.; Chung, H. T.; Wu, G.; ...

2014-08-18

This paper reports the development of a model for simulating polymer electrolyte fuel cells (PEFCs) with non-precious metal catalyst (NPMC) cathodes. NPMCs present an opportunity to dramatically reduce the cost of PEFC electrodes by removing the costly Pt catalyst. To address the significant transport losses in thick NPMC cathodes (ca. >60 µm), we developed a hierarchical electrode model that resolves the unique structure of the NPMCs we studied. A unique feature of the approach is the integration of the model with morphology data extracted from nano-scale resolution X-ray computed tomography (nano-CT) imaging of the electrodes. A notable finding is themore » impact of the liquid water accumulation in the electrode and the significant performance improvement possible if electrode flooding is mitigated.« less

Heliophysics Science and the Moon: Potential Solar and Space Physics Science for Lunar Exploration

NASA Technical Reports Server (NTRS)

2007-01-01

This report addresses both these features new science enabled by NASAs exploration initiative and enabling science that is critical to ensuring a safe return to the Moon and onward to Mars. The areas of interest are structured into four main themes: Theme 1: Heliophysics Science of the Moon Studies of the Moons unique magnetodynamic plasma environment. Theme 2: Space Weather, Safeguarding the Journey Studies aimed at developing a predictive capability for space weather hazards. Theme 3: The Moon as a Historical Record Studies of the variation of the lunar regolith to uncover the history of the Sun, solar system, local interstellar medium, galaxy, and universe. Theme 4: The Moon as a Heliophysics Science Platform Using the unique environment of the lunar surface as a platform to provide observations beneficial to advancing heliophysics science.

Unique Kinase Catalytic Mechanism of AceK with a Single Magnesium Ion

PubMed Central

Li, Quanjie; Zheng, Jimin; Tan, Hongwei; Li, Xichen; Chen, Guangju; Jia, Zongchao

2013-01-01

Isocitrate dehydrogenase kinase/phosphatase (AceK) is the founding member of the protein phosphorylation system in prokaryotes. Based on the novel and unique structural characteristics of AceK recently uncovered, we sought to understand its kinase reaction mechanism, along with other features involved in the phosphotransfer process. Herein we report density functional theory QM calculations of the mechanism of the phosphotransfer reaction catalysed by AceK. The transition states located by the QM calculations indicate that the phosphorylation reaction, catalysed by AceK, follows a dissociative mechanism with Asp457 serving as the catalytic base to accept the proton delivered by the substrate. Our results also revealed that AceK prefers a single Mg2+-containing active site in the phosphotransfer reaction. The catalytic roles of conserved residues in the active site are discussed. PMID:23977203

Bacterial CRISPR Regions: General Features and their Potential for Epidemiological Molecular Typing Studies

PubMed Central

Karimi, Zahra; Ahmadi, Ali; Najafi, Ali; Ranjbar, Reza

2018-01-01

Introduction: CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci as novel and applicable regions in prokaryotic genomes have gained great attraction in the post genomics era. Methods: These unique regions are diverse in number and sequence composition in different pathogenic bacteria and thereby can be a suitable candidate for molecular epidemiology and genotyping studies. Results:Furthermore, the arrayed structure of CRISPR loci (several unique repeats spaced with the variable sequence) and associated cas genes act as an active prokaryotic immune system against viral replication and conjugative elements. This property can be used as a tool for RNA editing in bioengineering studies. Conclusion: The aim of this review was to survey some details about the history, nature, and potential applications of CRISPR arrays in both genetic engineering and bacterial genotyping studies. PMID:29755603

The MB2 gene family of Plasmodium species has a unique combination of S1 and GTP-binding domains

PubMed Central

Romero, Lisa C; Nguyen, Thanh V; Deville, Benoit; Ogunjumo, Oluwasanmi; James, Anthony A

2004-01-01

Background Identification and characterization of novel Plasmodium gene families is necessary for developing new anti-malarial therapeutics. The products of the Plasmodium falciparum gene, MB2, were shown previously to have a stage-specific pattern of subcellular localization and proteolytic processing. Results Genes homologous to MB2 were identified in five additional parasite species, P. knowlesi, P. gallinaceum, P. berghei, P. yoelii, and P. chabaudi. Sequence comparisons among the MB2 gene products reveal amino acid conservation of structural features, including putative S1 and GTP-binding domains, and putative signal peptides and nuclear localization signals. Conclusions The combination of domains is unique to this gene family and indicates that MB2 genes comprise a novel family and therefore may be a good target for drug development. PMID:15222903

Embodied history. Uniqueness and exemplarity of South African AIDS.

PubMed

Fassin, Didier

2002-01-01

The exceptionality of AIDS in South Africa, both for its epidemiological features and public controversies, seems to have its correspondence in the exceptionalism of South African history, with its unprecedented regime of apartheid and its unexpected turn to democracy. The article shows that AIDS in this country can simultaneously be seen as unique (because of the historical context in which it is inscribed) and exemplar (of social determinants observed in other countries characterised by similar past or present of domination). As an alternative to cultural and behavioural models of the epidemic which have been widely spread on the African continent, the concept of embodiment of history is proposed in order to account for both the structural facts underlying the epidemic (inequality, violence, migration) and the construction of collective as well as individual narratives of the disease (including victimisation and accusation).

Continuous and embedded solutions for SHM of concrete structures using changing electrical potential in self-sensing cement-based composites

NASA Astrophysics Data System (ADS)

Downey, Austin; Garcia-Macias, Enrique; D'Alessandro, Antonella; Laflamme, Simon; Castro-Triguero, Rafael; Ubertini, Filippo

2017-04-01

Interest in the concept of self-sensing structural materials has grown in recent years due to its potential to enable continuous low-cost monitoring of next-generation smart-structures. The development of cement-based smart sensors appears particularly well suited for monitoring applications due to their numerous possible field applications, their ease of use and long-term stability. Additionally, cement-based sensors offer a unique opportunity for structural health monitoring of civil structures because of their compatibility with new or existing infrastructure. Particularly, the addition of conductive carbon nanofillers into a cementitious matrix provides a self-sensing structural material with piezoresistive characteristics sensitive to deformations. The strain-sensing ability is achieved by correlating the external loads with the variation of specific electrical parameters, such as the electrical resistance or impedance. Selection of the correct electrical parameter for measurement to correlate with features of interest is required for the condition assessment task. In this paper, we investigate the potential of using altering electrical potential in cement-based materials doped with carbon nanotubes to measure strain and detect damage in concrete structures. Experimental validation is conducted on small-scale specimens including a steel-reinforced beam of conductive cement paste. Comparisons are made with constant electrical potential and current methods commonly found in the literature. Experimental results demonstrate the ability of the changing electrical potential at detecting features important for assessing the condition of a structure.

A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure.

PubMed

Steckelberg, Anna-Lena; Akiyama, Benjamin M; Costantino, David A; Sit, Tim L; Nix, Jay C; Kieft, Jeffrey S

2018-06-19

Folded RNA elements that block processive 5' → 3' cellular exoribonucleases (xrRNAs) to produce biologically active viral noncoding RNAs have been discovered in flaviviruses, potentially revealing a new mode of RNA maturation. However, whether this RNA structure-dependent mechanism exists elsewhere and, if so, whether a singular RNA fold is required, have been unclear. Here we demonstrate the existence of authentic RNA structure-dependent xrRNAs in dianthoviruses, plant-infecting viruses unrelated to animal-infecting flaviviruses. These xrRNAs have no sequence similarity to known xrRNAs; thus, we used a combination of biochemistry and virology to characterize their sequence requirements and mechanism of stopping exoribonucleases. By solving the structure of a dianthovirus xrRNA by X-ray crystallography, we reveal a complex fold that is very different from that of the flavivirus xrRNAs. However, both versions of xrRNAs contain a unique topological feature, a pseudoknot that creates a protective ring around the 5' end of the RNA structure; this may be a defining structural feature of xrRNAs. Single-molecule FRET experiments reveal that the dianthovirus xrRNAs undergo conformational changes and can use "codegradational remodeling," exploiting the exoribonucleases' degradation-linked helicase activity to help form their resistant structure; such a mechanism has not previously been reported. Convergent evolution has created RNA structure-dependent exoribonuclease resistance in different contexts, which establishes it as a general RNA maturation mechanism and defines xrRNAs as an authentic functional class of RNAs.

Nanostructured core-shell electrode materials for electrochemical capacitors

NASA Astrophysics Data System (ADS)

Jiang, Long-bo; Yuan, Xing-zhong; Liang, Jie; Zhang, Jin; Wang, Hou; Zeng, Guang-ming

2016-11-01

Core-shell nanostructure represents a unique system for applications in electrochemical energy storage devices. Owing to the unique characteristics featuring high power delivery and long-term cycling stability, electrochemical capacitors (ECs) have emerged as one of the most attractive electrochemical storage systems since they can complement or even replace batteries in the energy storage field, especially when high power delivery or uptake is needed. This review aims to summarize recent progress on core-shell nanostructures for advanced supercapacitor applications in view of their hierarchical architecture which not only create the desired hierarchical porous channels, but also possess higher electrical conductivity and better structural mechanical stability. The core-shell nanostructures include carbon/carbon, carbon/metal oxide, carbon/conducting polymer, metal oxide/metal oxide, metal oxide/conducting polymer, conducting polymer/conducting polymer, and even more complex ternary core-shell nanoparticles. The preparation strategies, electrochemical performances, and structural stabilities of core-shell materials for ECs are summarized. The relationship between core-shell nanostructure and electrochemical performance is discussed in detail. In addition, the challenges and new trends in core-shell nanomaterials development have also been proposed.

Japanese encephalitis virus NS1' protein depends on pseudoknot secondary structure and is cleaved by caspase during virus infection and cell apoptosis.

PubMed

Sun, Jin; Yu, Yongxin; Deubel, Vincent

2012-09-01

Japanese encephalitis virus (JEV) is a flavivirus with a complex life cycle involving mosquito vectors that mainly target birds and pigs, and causes severe encephalitis in children in Asia. Neurotropic flaviviruses of the JEV serogroup have a particular characteristic of expressing a unique nonstructural NS1' protein, which is a prolongation of NS1 at the C terminus by 52 amino acids derived from a pseudoknot-driven-1 translation frameshift. Protein NS1' is associated with virus neuro-invasiveness. In this study, the need of the pseudoknot structure for NS1' synthesis was confirmed. By using a specific antibody against the prolonged peptide, NS1' was found to be absent from the JEV SA14-14-2 vaccine strain, resulting from a single nucleotide silent mutation in the pseudoknot. A partial cleavage of NS1' at a specific site of its C-terminal appendix recognized by caspases and inhibited by caspase inhibitors suggests a unique feature of intracellular NS1'. Copyright © 2012 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Impact origin of sediments at the Opportunity landing site on Mars.

PubMed

Knauth, L Paul; Burt, Donald M; Wohletz, Kenneth H

2005-12-22

Mars Exploration Rover Opportunity discovered sediments with layered structures thought to be unique to aqueous deposition and with minerals attributed to evaporation of an acidic salty sea. Remarkable iron-rich spherules were ascribed to later groundwater alteration, and the inferred abundance of water reinforced optimism that Mars was once habitable. The layered structures, however, are not unique to water deposition, and the scenario encounters difficulties in accounting for highly soluble salts admixed with less soluble salts, the lack of clay minerals from acid-rock reactions, high sphericity and near-uniform sizes of the spherules and the absence of a basin boundary. Here we present a simple alternative explanation involving deposition from a ground-hugging turbulent flow of rock fragments, salts, sulphides, brines and ice produced by meteorite impact. Subsequent weathering by intergranular water films can account for all of the features observed without invoking shallow seas, lakes or near-surface aquifers. Layered sequences observed elsewhere on heavily cratered Mars and attributed to wind, water or volcanism may well have formed similarly. If so, the search for past life on Mars should be reassessed accordingly.

Covalent Organic Frameworks: From Materials Design to Biomedical Application

PubMed Central

Zhao, Fuli; Liu, Huiming; Mathe, Salva D. R.; Dong, Anjie

2017-01-01

Covalent organic frameworks (COFs) are newly emerged crystalline porous polymers with well-defined skeletons and nanopores mainly consisted of light-weight elements (H, B, C, N and O) linked by dynamic covalent bonds. Compared with conventional materials, COFs possess some unique and attractive features, such as large surface area, pre-designable pore geometry, excellent crystallinity, inherent adaptability and high flexibility in structural and functional design, thus exhibiting great potential for various applications. Especially, their large surface area and tunable porosity and π conjugation with unique photoelectric properties will enable COFs to serve as a promising platform for drug delivery, bioimaging, biosensing and theranostic applications. In this review, we trace the evolution of COFs in terms of linkages and highlight the important issues on synthetic method, structural design, morphological control and functionalization. And then we summarize the recent advances of COFs in the biomedical and pharmaceutical sectors and conclude with a discussion of the challenges and opportunities of COFs for biomedical purposes. Although currently still at its infancy stage, COFs as an innovative source have paved a new way to meet future challenges in human healthcare and disease theranostic. PMID:29283423

The Phe105 loop of Alix Bro1 domain plays a key role in HIV-1 release

PubMed Central

Sette, Paola; Mu, Ruiling; Dussupt, Vincent; Jiang, Jiansheng; Snyder, Greg; Smith, Patrick; Xiao, Tsan. Sam; Bouamr, Fadila

2011-01-01

Summary Alix and cellular paralogs HD-PTP and Brox contain N-terminal Bro1 domains that bind ESCRT-III CHMP4. In contrast to HD-PTP and Brox, expression of the Bro1 domain of Alix alleviates HIV-1 release defects due to interrupted access to ESCRT. In an attempt to elucidate this functional discrepancy, we solved the crystal structures of the Bro1 domains of HD-PTP and Brox. They revealed typical “boomerang” folds they share with the Bro1 Alix domain. However, they each contain unique structural features that may be relevant to their specific function(s). In particular, phenylalanine residue in position 105 (Phe105) of Alix belongs to a long loop that is unique to its Bro1 domain. Concurrently mutation of Phe105 and surrounding residues at the tip of the loop compromises the function of Alix in HIV-1 budding without affecting its interactions with Gag or CHMP4. These studies identify a new functional determinant in the Bro1 domain of Alix. PMID:21889351

Decoy Strategies: The Structure of TL1A:DcR3 Complex

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

C Zhan; Y Patskovsky; Q Yan

2011-12-31

Decoy Receptor 3 (DcR3), a secreted member of the Tumor Necrosis Factor (TNF) receptor superfamily, neutralizes three different TNF ligands: FasL, LIGHT, and TL1A. Each of these ligands engages unique signaling receptors which direct distinct and critical immune responses. We report the crystal structures of the unliganded DcR3 ectodomain and its complex with TL1A, as well as complementary mutagenesis and biochemical studies. These analyses demonstrate that DcR3 interacts with invariant backbone and side-chain atoms in the membrane-proximal half of TL1A which supports recognition of its three distinct TNF ligands. Additional features serve as antideterminants that preclude interaction with other membersmore » of the TNF superfamily. This mode of interaction is unique among characterized TNF:TNFR family members and provides a mechanistic basis for the broadened specificity required to support the decoy function of DcR3, as well as for the rational manipulation of specificity and affinity of DcR3 and its ligands.« less

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

Peterson, T. J.; Weisend, II, J. G.

The TESLA collaboration developed a unique variant of SRF cryomodule designs, the chief feature being use of the large, low pressure helium vapor return pipe as the structural support backbone of the cryomodule. Additional innovative features include all cryogenic piping within the cryomodule (no parallel external cryogenic transfer line), long strings of RF cavities within a single cryomodule, and cryomodules connected in series. Several projects, including FLASH and XFEL at DESY, LCLS-II at SLAC, and the ILC technical design have adopted this general design concept. Advantages include saving space by eliminating the external transfer line, relatively tight packing of RFmore » cavities along the beamline due to fewer warm-cold transitions, and potentially lower costs. However, a primary disadvantage is the relative lack of independence for warm-up, replacement, and cool-down of individual cryomodules.« less

Colonize, evade, flourish

PubMed Central

Rubin, Erica J; Trent, M Stephen

2013-01-01

Helicobacter pylori is an adapted gastric pathogen that colonizes the human stomach, causing severe gastritis and gastric cancer. A hallmark of infection is the ability of this organism to evade detection by the human immune system. H. pylori has evolved a number of features to achieve this, many of which involve glyco-conjugates including the lipopolysaccharide, peptidoglycan layer, glycoproteins, and glucosylated cholesterol. These major bacterial components possess unique features from those of other gram-negative organisms, including differences in structure, assembly, and modification. These defining characteristics of H. pylori glycobiology help the pathogen establish a long-lived infection by providing camouflage, modulating the host immune response, and promoting virulence mechanisms. In this way, glyco-conjugates are essential for H. pylori pathogenicity and survival, allowing it to carve out a niche in the formidable environment of the human stomach. PMID:23859890

Nanofabrication of ultra-low reflectivity black silicon surfaces and devices (Presentation Recording)

NASA Astrophysics Data System (ADS)

White, Victor E.; Yee, Karl Y.; Balasubramanian, Kunjithapatham; Echternach, Pierre M.; Muller, Richard E.; Dickie, Matthew R.; Cady, Eric; Ryan, Daniel J.; Eastwood, Michael; van Gorp, Byron; Riggs, A. J. Eldorado; Zimmerman, Niel; Kasdin, N. Jeremy

2015-08-01

Optical devices with features exhibiting ultra low reflectivity on the order of 10-7 specular reflectance in the visible spectrum are required for coronagraph instruments and some spectrometers employed in space research. Nanofabrication technologies have been developed to produce such devices with various shapes and feature dimensions to meet these requirements. Infrared reflection is also suppressed significantly with chosen wafers and processes. Particularly, devices with very high (>0.9) and very low reflectivity (<10-7) on adjacent areas have been fabricated and characterized. Significantly increased surface area due to the long needle like nano structures also provides some unique applications in other technology areas. We present some of the approaches, challenges and achieved results in producing and characterizing such devices currently employed in laboratory testbeds and instruments.

Toward a low-cost, low-power, low-complexity DAC-based multilevel (M-ary QAM) coherent transmitter using compact linear optical field modulator

NASA Astrophysics Data System (ADS)

Dingel, Benjamin

2017-01-01

In this invited paper, we summarize the current developments in linear optical field modulators (LOFMs) for coherent multilevel optical transmitters. Our focus is the presentation of a new, novel LOFM design that provides beneficial and necessary features such as lowest hardware component counts, lowered insertion loss, smaller RF power consumption, smaller footprint, simple structure, and lowered cost. We refer to this modulator as called Double-Pass LOFM (DP-LOFM) that becomes the building block for high-performance, linear Dual-Polarization, In-Phase- Quadrature-Phase (DP-IQ) modulator. We analyze its performance in term of slope linearity, and present one of its unique feature -- a built-in compensation functionality that no other linear modulators possessed till now.

Overview of smartphone applications for sleep analysis.

PubMed

Ong, Adrian A; Gillespie, M Boyd

2016-03-01

To review and assess the current selection of sleep analysis smartphone applications (apps) available for download. The iOS and Google Play mobile app store were searched for sleep analysis apps targeted for consumer use. Alarm clock, sleep-aid, snoring and sleep-talking recorder, fitness tracker apps, and apps geared towards health professionals were excluded. App information and features were obtained from in-store descriptions, and the app developer website. A total of 51 unique sleep apps in both iOS and Google Play stores were included. The apps were rated 3.8/5 in both stores, and had an average price of $1.12 in the iOS store and $0.58 in the Google Play store. >65% of sleep apps report on sleep structure, including duration, time awake, and time in light/deep sleep, while reporting of REM was limited. The availability of extra features was variable, ranging from 4% to 73% of apps. There are a variety of sleep analysis apps with a range of functionality. The apps with the most reviews from the each store are featured. Many apps provide data on sleep structure; however the algorithms are not validated by scientific literature or studies. Since patients may inquire about their sleep habits from these apps, it is necessary for physicians to be aware of the most common apps and the features offered and their limitations in order to properly counsel patients.

Summary of the Normal-Conducting Accelerating Structures for LEDA and APT

NASA Astrophysics Data System (ADS)

Schneider, J. David

1998-04-01

The accelerator production of tritium (APT) plant requires a continuous (100% duty-factor), 100-mA, 1000--1700-MeV proton beam. Superconducting structures will accelerate protons above about 200 MeV, but room-temperature, normal-conducting (NC) copper structures will be used for lower energies. We will assemble the front 11-MeV portion of this NC accelerator as the low-energy demonstration accelerator (LEDA). This presentation will cover the demonstated operation of the proton injector, the design, fabrication, and tuning status of the 6.7-MeV RFQ, and the design features of the CCDTL (coupled-cavity drift-tube linac) that will accelerate protons to 100 MeV, before use of a conventional CCL (coupled-cavity linac). Several innovative features result in improved performance, ease of use, and improved reliabiltiy. The75-keV injector features a microwave ion source, dual-solenoid transport, and has no electronics at high potential. Its demonstrated high efficiency (less than 800 Watts), excellent proton fraction (>90%), high current (>110 mA), and reliability make it attractive for several other high-current applications. The 6.7-MeV, 350-MHz RFQ is an 8-meter-long, brazed-copper structure with hundreds of cooling channels that carry away the 1.3 MW of waste heat. During beam operation, only the cooling-water temperature is adjustable to maintain structure resonance. LEDA's 700-MHz CCDTL structure is new, combining features of the conventional DTL and CCL structures. All focus magnets are external to the copper accelerating cavities, each of which contains either one or two drift tubes. A `hot model' will validate fabrication, cooling, tuning, and coupling techniques. The LEDA facility is being upgraded with 15 MW of power and cooling utiliites, to support seven 1-MW cw RF systems needed to power all structures. The first few of these 1.3 MW 350-MHz systems are operational, and extensive testing was completed on the critical RF windows. Updates will be given on the development of vacuum, diagnostic, control, and cooling systems, as well as transport lines and beam stops. The unique and very compact, thin-walled beam stop is surrounded by an integral water shield for the prompt neutrons.

Multifunctional Nanostructured Conductive Polymer Gels: Synthesis, Properties, and Applications

DOE PAGES

Zhao, Fei; Shi, Ye; Pan, Lijia; ...

2017-06-26

Conductive polymers have attracted significant interest over the past few decades because they synergize the advantageous features of conventional polymeric materials and organic conductors. With rationally designed nanostructures, conductive polymers can further exhibit exceptional mechanical, electrical, and optical properties because of their confined dimensions at the nanoscale level. Among various nanostructured conductive polymers, conductive polymer gels (CPGs) with synthetically tunable hierarchical 3D network structures show great potential for a wide range of applications, such as bioelectronics, and energy storage/conversion devices owing to their structural features. CPGs retain the properties of nanosized conductive polymers during the assembly of the nanobuilding blocksmore » into a monolithic macroscopic structure while generating structure-derived features from the highly cross-linked network. In this Account, we review our recent progress on the synthesis, properties, and novel applications of dopant cross-linked CPGs. We first describe the synthetic strategies, in which molecules with multiple functional groups are adopted as cross-linkers to cross-link conductive polymer chains into a 3D molecular network. These cross-linking molecules also act as dopants to improve the electrical conductivity of the gel network. The microstructure and physical/chemical properties of CPGs can be tuned by controlling the synthetic conditions such as species of monomers and cross-linkers, reaction temperature, and solvents. By incorporating other functional polymers or particles into the CPG matrix, hybrid gels have been synthesized with tailored structures. These hybrid gel materials retain the functionalities from each component, as well as enable synergic effects to improve mechanical and electrical properties of CPGs. We then introduce the unique structure-derived properties of the CPGs. The network facilitates both electronic and ionic transport owing to the continuous pathways for electrons and hierarchical pores for ion diffusion. CPGs also provide high surface area and solvent compatibility, similar to natural gels. With these improved properties, CPGs have been explored to enable novel conceptual devices in diverse applications from smart electronics and ultrasensitive biosensors, to energy storage and conversion devices. CPGs have also been adopted for developing hybrid materials with multifunctionalities, such as stimuli responsiveness, self-healing properties, and super-repellency to liquid. With synthetically tunable physical/chemical properties, CPGs emerge as a unique material platform to develop novel multifunctional materials that have the potential to impact electronics, energy, and environmental technologies. Our hope is that this Account promotes further efforts toward synthetic control, fundamental investigation, and application exploration of CPGs.« less

Multifunctional Nanostructured Conductive Polymer Gels: Synthesis, Properties, and Applications

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

Zhao, Fei; Shi, Ye; Pan, Lijia

Conductive polymers have attracted significant interest over the past few decades because they synergize the advantageous features of conventional polymeric materials and organic conductors. With rationally designed nanostructures, conductive polymers can further exhibit exceptional mechanical, electrical, and optical properties because of their confined dimensions at the nanoscale level. Among various nanostructured conductive polymers, conductive polymer gels (CPGs) with synthetically tunable hierarchical 3D network structures show great potential for a wide range of applications, such as bioelectronics, and energy storage/conversion devices owing to their structural features. CPGs retain the properties of nanosized conductive polymers during the assembly of the nanobuilding blocksmore » into a monolithic macroscopic structure while generating structure-derived features from the highly cross-linked network. In this Account, we review our recent progress on the synthesis, properties, and novel applications of dopant cross-linked CPGs. We first describe the synthetic strategies, in which molecules with multiple functional groups are adopted as cross-linkers to cross-link conductive polymer chains into a 3D molecular network. These cross-linking molecules also act as dopants to improve the electrical conductivity of the gel network. The microstructure and physical/chemical properties of CPGs can be tuned by controlling the synthetic conditions such as species of monomers and cross-linkers, reaction temperature, and solvents. By incorporating other functional polymers or particles into the CPG matrix, hybrid gels have been synthesized with tailored structures. These hybrid gel materials retain the functionalities from each component, as well as enable synergic effects to improve mechanical and electrical properties of CPGs. We then introduce the unique structure-derived properties of the CPGs. The network facilitates both electronic and ionic transport owing to the continuous pathways for electrons and hierarchical pores for ion diffusion. CPGs also provide high surface area and solvent compatibility, similar to natural gels. With these improved properties, CPGs have been explored to enable novel conceptual devices in diverse applications from smart electronics and ultrasensitive biosensors, to energy storage and conversion devices. CPGs have also been adopted for developing hybrid materials with multifunctionalities, such as stimuli responsiveness, self-healing properties, and super-repellency to liquid. With synthetically tunable physical/chemical properties, CPGs emerge as a unique material platform to develop novel multifunctional materials that have the potential to impact electronics, energy, and environmental technologies. Our hope is that this Account promotes further efforts toward synthetic control, fundamental investigation, and application exploration of CPGs.« less

Multifunctional Nanostructured Conductive Polymer Gels: Synthesis, Properties, and Applications.

PubMed

Zhao, Fei; Shi, Ye; Pan, Lijia; Yu, Guihua

2017-07-18

Conductive polymers have attracted significant interest over the past few decades because they synergize the advantageous features of conventional polymeric materials and organic conductors. With rationally designed nanostructures, conductive polymers can further exhibit exceptional mechanical, electrical, and optical properties because of their confined dimensions at the nanoscale level. Among various nanostructured conductive polymers, conductive polymer gels (CPGs) with synthetically tunable hierarchical 3D network structures show great potential for a wide range of applications, such as bioelectronics, and energy storage/conversion devices owing to their structural features. CPGs retain the properties of nanosized conductive polymers during the assembly of the nanobuilding blocks into a monolithic macroscopic structure while generating structure-derived features from the highly cross-linked network. In this Account, we review our recent progress on the synthesis, properties, and novel applications of dopant cross-linked CPGs. We first describe the synthetic strategies, in which molecules with multiple functional groups are adopted as cross-linkers to cross-link conductive polymer chains into a 3D molecular network. These cross-linking molecules also act as dopants to improve the electrical conductivity of the gel network. The microstructure and physical/chemical properties of CPGs can be tuned by controlling the synthetic conditions such as species of monomers and cross-linkers, reaction temperature, and solvents. By incorporating other functional polymers or particles into the CPG matrix, hybrid gels have been synthesized with tailored structures. These hybrid gel materials retain the functionalities from each component, as well as enable synergic effects to improve mechanical and electrical properties of CPGs. We then introduce the unique structure-derived properties of the CPGs. The network facilitates both electronic and ionic transport owing to the continuous pathways for electrons and hierarchical pores for ion diffusion. CPGs also provide high surface area and solvent compatibility, similar to natural gels. With these improved properties, CPGs have been explored to enable novel conceptual devices in diverse applications from smart electronics and ultrasensitive biosensors, to energy storage and conversion devices. CPGs have also been adopted for developing hybrid materials with multifunctionalities, such as stimuli responsiveness, self-healing properties, and super-repellency to liquid. With synthetically tunable physical/chemical properties, CPGs emerge as a unique material platform to develop novel multifunctional materials that have the potential to impact electronics, energy, and environmental technologies. We hope that this Account promotes further efforts toward synthetic control, fundamental investigation, and application exploration of CPGs.

Structure and dynamics of star-forming galaxies across the history of the Universe using GRBs

NASA Astrophysics Data System (ADS)

Thöne, Christina; Fynbo, Johan; de Ugarte Postigo, Antonio

2015-08-01

Gamma-ray bursts are exploding massive stars and some of the most luminous explosions in the Universe. They can serve as powerful light houses that probe the structure and abundances of the dense ISM in their hosts at almost any redshift and not accessible by other types of observations, e.g. using quasars. Since 2009 our collaboration has collected UV to nIR medium-resolution spectra of over 70 GRB afterglows using the ESO/VLT X-shooter spectrograph. Our sample covers a redshift range from 0.06 to 6.3 allowing us to study the dynamics of the ISM in star-forming galaxies from the nearby Universe out to the epoch of reionization and for the first time in a statistically sound way. Absorption lines usually show a rich structure of different components due to galaxy dynamics, turbulences or in-/outflows and different ionization levels seem to arise from different regions in the host. Fine-structure lines some of which are uniquely observed in GRB hosts are excited in the dense regions close to the GRB site itself. For some host with z < 3 we can also simultaenously observe emission lines from the hot ISM, comparing the origin of hot and cold gas within the same galaxy. The large wavelength coverage of the sample gives us the unique opportunity to study the evolution of gas dynamics across most of the time galaxies have existed, how the gas structure changed over time and what is the importance and consistency of in- and ouflows. Here we will present the X-shooter GRB afterglow sample, our results on the study of absorption and emission line features and compare the observed structures with theoretical models of galaxies to get a unique insight on the distrubution and dynamics of the ISM in starforming galaxies at any redshift.

Using non-invasive molecular spectroscopic techniques to detect unique aspects of protein Amide functional groups and chemical properties of modeled forage from different sourced-origins.

PubMed

Ji, Cuiying; Zhang, Xuewei; Yu, Peiqiang

2016-03-05

The non-invasive molecular spectroscopic technique-FT/IR is capable to detect the molecular structure spectral features that are associated with biological, nutritional and biodegradation functions. However, to date, few researches have been conducted to use these non-invasive molecular spectroscopic techniques to study forage internal protein structures associated with biodegradation and biological functions. The objectives of this study were to detect unique aspects and association of protein Amide functional groups in terms of protein Amide I and II spectral profiles and chemical properties in the alfalfa forage (Medicago sativa L.) from different sourced-origins. In this study, alfalfa hay with two different origins was used as modeled forage for molecular structure and chemical property study. In each forage origin, five to seven sources were analyzed. The molecular spectral profiles were determined using FT/IR non-invasive molecular spectroscopy. The parameters of protein spectral profiles included functional groups of Amide I, Amide II and Amide I to II ratio. The results show that the modeled forage Amide I and Amide II were centered at 1653 cm(-1) and 1545 cm(-1), respectively. The Amide I spectral height and area intensities were from 0.02 to 0.03 and 2.67 to 3.36 AI, respectively. The Amide II spectral height and area intensities were from 0.01 to 0.02 and 0.71 to 0.93 AI, respectively. The Amide I to II spectral peak height and area ratios were from 1.86 to 1.88 and 3.68 to 3.79, respectively. Our results show that the non-invasive molecular spectroscopic techniques are capable to detect forage internal protein structure features which are associated with forage chemical properties. Copyright © 2015 Elsevier B.V. All rights reserved.

ION PRODUCING MECHANISM (ARC EXTERNAL TO BLOCK)

DOEpatents

Brobeck, W.H.

1958-09-01

This patent pentains to an ion producing mechanism employed in a calutron which has the decided advantage of an increased amount of ionization effectuated by the arc, and a substantially uniform arc in poiat of time, i arc location and along the arc length. The unique features of the disclosed ion source lie in the specific structural arrangement of the source block, gas ionizing passage, filament shield and filament whereby the arc is established both within the ionizing passage and immediately outside the exit of the ionizing passage at the block face.

Terminal-oriented computer-communication networks.

NASA Technical Reports Server (NTRS)

Schwartz, M.; Boorstyn, R. R.; Pickholtz, R. L.

1972-01-01

Four examples of currently operating computer-communication networks are described in this tutorial paper. They include the TYMNET network, the GE Information Services network, the NASDAQ over-the-counter stock-quotation system, and the Computer Sciences Infonet. These networks all use programmable concentrators for combining a multiplicity of terminals. Included in the discussion for each network is a description of the overall network structure, the handling and transmission of messages, communication requirements, routing and reliability consideration where applicable, operating data and design specifications where available, and unique design features in the area of computer communications.

Nanofluidic mixing via hybrid surface

NASA Astrophysics Data System (ADS)

Ye, Ziran; Li, Shunbo; Zhou, Bingpu; Hui, Yu Sanna; Shen, Rong; Wen, Weijia

2014-10-01

We report the design and fabrication of the nanofluidic mixer comprising hybrid hydrophobic/hydrophilic micro-patterns on the top and bottom walls of the nanochannel. The unique feature of such mixer is that, without any geometric structure inside the nanochannel, the mixing can be realized solely by the hybrid surfaces. Besides, the mixing length in nanomixer has been significantly shortened comparing to micromixer. We attribute the mixing achievement to be caused by the convection and chaotic flows of two fluids along the hybrid surface due to the large surface-to-volume ratio of the nanochannel.

Nanofluidic mixing via hybrid surface

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

Ye, Ziran; Li, Shunbo; Zhou, Bingpu

2014-10-20

We report the design and fabrication of the nanofluidic mixer comprising hybrid hydrophobic/hydrophilic micro-patterns on the top and bottom walls of the nanochannel. The unique feature of such mixer is that, without any geometric structure inside the nanochannel, the mixing can be realized solely by the hybrid surfaces. Besides, the mixing length in nanomixer has been significantly shortened comparing to micromixer. We attribute the mixing achievement to be caused by the convection and chaotic flows of two fluids along the hybrid surface due to the large surface-to-volume ratio of the nanochannel.

Changing culture in the home health setting: strategies for success.

PubMed

Boan, David

2006-01-01

Organizational culture is generally defined as the internal attributes of the staff, such as their values, beliefs, and attitudes. Although technically accurate as a definition, personal attributes defy direct intervention, leading some to question whether it is possible to change culture. It is proposed that it is possible to change the personal internal attributes that define organizational culture by changing the characteristic structures and behaviors of the organization that shape those attributes. This model, called the Quality Capability Model, creates an approach to culture change that accommodates the unique features of home health.

The effect of nanoparticle size on in vivo pharmacokinetics and cellular interaction

PubMed Central

Hoshyar, Nazanin; Gray, Samantha; Han, Hongbin; Bao, Gang

2016-01-01

Nanoparticle-based technologies offer exciting new approaches to disease diagnostics and therapeutics. To take advantage of unique properties of nanoscale materials and structures, the size, shape and/or surface chemistry of nanoparticles need to be optimized, allowing their functionalities to be tailored for different biomedical applications. Here we review the effects of nanoparticle size on cellular interaction and in vivo pharmacokinetics, including cellular uptake, biodistribution and circulation half-life of nanoparticles. Important features of nanoparticle probes for molecular imaging and modeling of nanoparticle size effects are also discussed. PMID:27003448

Cajanusflavanols A-C, Three Pairs of Flavonostilbene Enantiomers from Cajanus cajan.

PubMed

He, Qi-Fang; Wu, Zhen-Long; Huang, Xiao-Jun; Zhong, Yuan-Lin; Li, Man-Mei; Jiang, Ren-Wang; Li, Yao-Lan; Ye, Wen-Cai; Wang, Ying

2018-02-02

Three pairs of new flavonostilbene enantiomers, cajanusflavanols A-C (1-3), along with their putative biogenetic precursors 4-6, were isolated from Cajanus cajan. Compound 1 possesses an unprecedented carbon skeleton featuring a unique highly functionalized cyclopenta[1,2,3-de]isobenzopyran-1-one tricyclic core. Compounds 2 and 3 are the first examples of methylene-unit-linked flavonostilbenes. Their structures with absolute configurations were elucidated by spectroscopic analyses, X-ray diffraction, and computational calculations. Compounds 1 and 2 exhibited significant in vitro anti-inflammatory activities.

Brainhack: a collaborative workshop for the open neuroscience community.

PubMed

Cameron Craddock, R; S Margulies, Daniel; Bellec, Pierre; Nolan Nichols, B; Alcauter, Sarael; A Barrios, Fernando; Burnod, Yves; J Cannistraci, Christopher; Cohen-Adad, Julien; De Leener, Benjamin; Dery, Sebastien; Downar, Jonathan; Dunlop, Katharine; R Franco, Alexandre; Seligman Froehlich, Caroline; J Gerber, Andrew; S Ghosh, Satrajit; J Grabowski, Thomas; Hill, Sean; Sólon Heinsfeld, Anibal; Matthew Hutchison, R; Kundu, Prantik; R Laird, Angela; Liew, Sook-Lei; J Lurie, Daniel; G McLaren, Donald; Meneguzzi, Felipe; Mennes, Maarten; Mesmoudi, Salma; O'Connor, David; H Pasaye, Erick; Peltier, Scott; Poline, Jean-Baptiste; Prasad, Gautam; Fraga Pereira, Ramon; Quirion, Pierre-Olivier; Rokem, Ariel; S Saad, Ziad; Shi, Yonggang; C Strother, Stephen; Toro, Roberto; Q Uddin, Lucina; D Van Horn, John; W Van Meter, John; C Welsh, Robert; Xu, Ting

2016-01-01

Brainhack events offer a novel workshop format with participant-generated content that caters to the rapidly growing open neuroscience community. Including components from hackathons and unconferences, as well as parallel educational sessions, Brainhack fosters novel collaborations around the interests of its attendees. Here we provide an overview of its structure, past events, and example projects. Additionally, we outline current innovations such as regional events and post-conference publications. Through introducing Brainhack to the wider neuroscience community, we hope to provide a unique conference format that promotes the features of collaborative, open science.

GAMMA AND X-RAY DOSIMETER AND DOSIMETRIC METHOD

DOEpatents

Taplin, G.V.; Douglas, C.H.; Sigoloff, S.C.

1958-08-19

An improvement in colorimetric gamma and x-ray dosimeter systems and a self-contained. hand carried dostmeter of the afore-mentioned type ts described. A novel point of the invention ltes in the addition of specific quantities of certain normalizing agents to the two phase chlorinated hydro-carbon-aqueous dyc colortmetric dosimeter to eliminate the after reaction and thereby extend the utility of such systein. The structure of the two phase colorimetric dosimeter tubes and the carrying case for the tubes of the portable dosimeter are unique features.

Professionalism, bureaucracy and patriotism: the VA as a health care megasystem.

PubMed

Rosenheck, R

The Veterans Administration supports the largest integrated psychiatry service in the country. As our oldest and largest "megasystem," this service offers a unique opportunity for examining distinctive features of such large health care delivery systems. Characteristic experiences of mental health professionals in this system are described and the system is analyzed in terms of its organizational tasks, structure and cultures. Psychiatry will be practiced, in the future, in similarly large scale organizations. Understanding the nature and workings of such organizations is likely to become essential to effective and satisfying professional work.

NASA-ARC 91.5-cm airborne infrared telescope. [tracking mechanism

NASA Technical Reports Server (NTRS)

Mobley, R. E.; Brown, T. M.

1979-01-01

A 91.5 cm aperture telescope installed aboard NASA-Lockheed C-141A aircraft for the performance of infrared astronomy is described. A unique feature of the telescope is that its entire structure is supported by a 41 cm spherical air bearing which effectively uncouples it from aircraft angular motion, and with inertial stabilization and star tracking, limits tracking errors to less than 1 arc second in most applications. A general description of the system, a summary of its performance, and a detailed description of an offset tracking mechanism is presented.

Ferric chloride-graphite intercalation compounds as anode materials for Li-ion batteries.

PubMed

Wang, Lili; Zhu, Yongchun; Guo, Cong; Zhu, Xiaobo; Liang, Jianwen; Qian, Yitai

2014-01-01

Ferric chloride-graphite intercalation compounds (FeCl3 -GICs) with stage 1 and stage 2 structures were synthesized by reacting FeCl3 and expanded graphite (EG) in air in a stainless-steel autoclave. As rechargeable Li-ion batteries, these FeCl3 -GICs exhibit high capacity, excellent cycling stability, and superior rate capability, which could be attributed to their unique intercalation features. This work may enable new possibilities for the fabrication of Li-ion batteries. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Wagner, Drew T.; Zeng, Jia; Bailey, Constance B.

In an effort to uncover the structural motifs and biosynthetic logic of the relatively uncharacterized trans-acyltransferase polyketide synthases, we have begun the dissection of the enigmatic dehydrating bimodules common in these enzymatic assembly lines. We report the 1.98 Å resolution structure of a ketoreductase (KR) from the first half of a type A dehydrating bimodule and the 2.22 Å resolution structure of a dehydratase (DH) from the second half of a type B dehydrating bimodule. The KR, from the third module of the bacillaene synthase, and the DH, from the tenth module of the difficidin synthase, possess features not observedmore » in structurally characterized homologs. The DH architecture provides clues for how it catalyzes a unique double dehydration. Correlations between the chemistries proposed for dehydrating bimodules and bioinformatic analysis indicate that type A dehydrating bimodules generally produce an α/β-cis alkene moiety, while type B dehydrating bimodules generally produce an α/β-trans, γ/δ-cis diene moiety.« less

3D flower-like hierarchical Ag@nickel-cobalt hydroxide microsphere with enhanced electrochemical properties

NASA Astrophysics Data System (ADS)

Lv, Zijian; Zhong, Qin; Bu, Yunfei; Wu, Junpeng

2016-10-01

The morphology and electrical conductivity are essential to electrochemical performance of electrode materials in renewable energy conversion and storage technologies such as fuel cells and supercapacitors. Here, we explored a facile method to grow Ag@nickel-cobalt layered double hydroxide (Ag@Ni/Co-LDHs) with 3D flower-like microsphere structure. The results show the morphology of Ni/Co-LDHs varies with the introduction of Ag species. The prepared Ag@Ni/Co-LDHs not only exhibits an open hierarchical structure with high specific capacitance but also shows good electrical conductivity to support fast electron transport. Benefiting from the unique structural features, these flower-like Ag@Ni/Co-LDHs microspheres have impressive specific capacitance as high as 1768 F g-1 at 1 A g-1. It can be concluded that engineering the structure of the electrode can increase the efficiency of the specific capacitance as a battery-type electrode for hybrid supercapacitors.

The Fpg/Nei family of DNA glycosylases: substrates, structures, and search for damage.

PubMed

Prakash, Aishwarya; Doublié, Sylvie; Wallace, Susan S

2012-01-01

During the initial stages of the base excision DNA repair pathway, DNA glycosylases are responsible for locating and removing the majority of endogenous oxidative base lesions. The bifunctional formamidopyrimidine DNA glycosylase (Fpg) and endonuclease VIII (Nei) are members of the Fpg/Nei family, one of the two families of glycosylases that recognize oxidized DNA bases, the other being the HhH/GPD (or Nth) superfamily. Structural and biochemical developments over the past decades have led to novel insights into the mechanism of damage recognition by the Fpg/Nei family of enzymes. Despite the overall structural similarity among members of this family, these enzymes exhibit distinct features that make them unique. This review summarizes the current structural knowledge of the Fpg/Nei family members, emphasizes their substrate specificities, and describes how these enzymes search for lesions. Copyright © 2012 Elsevier Inc. All rights reserved.

Single-shot mega-electronvolt ultrafast electron diffraction for structure dynamic studies of warm dense matter

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

Mo, M. Z., E-mail: mmo09@slac.stanford.edu; Shen, X.; Chen, Z.

We have developed a single-shot mega-electronvolt ultrafast-electron-diffraction system to measure the structural dynamics of warm dense matter. The electron probe in this system is featured by a kinetic energy of 3.2 MeV and a total charge of 20 fC, with the FWHM pulse duration and spot size at sample of 350 fs and 120 μm respectively. We demonstrate its unique capability by visualizing the atomic structural changes of warm dense gold formed from a laser-excited 35-nm freestanding single-crystal gold foil. The temporal evolution of the Bragg peak intensity and of the liquid signal during solid-liquid phase transition are quantitatively determined.more » This experimental capability opens up an exciting opportunity to unravel the atomic dynamics of structural phase transitions in warm dense matter regime.« less

Single-shot mega-electronvolt ultrafast electron diffraction for structure dynamic studies of warm dense matter

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

Mo, M. Z.; Shen, X.; Chen, Z.

We have developed a single-shot mega-electronvolt ultrafast-electron-diffraction system to measure the structural dynamics of warm dense matter. The electron probe in this system is featured by a kinetic energy of 3.2 MeV and a total charge of 20 fC, with the FWHM pulse duration and spot size at sample of 350 fs and 120 µm respectively. We demonstrate its unique capability by visualizing the atomic structural changes of warm dense gold formed from a laser-excited 35-nm freestanding single-crystal gold foil. The temporal evolution of the Bragg peak intensity and of the liquid signal during solid-liquid phase transition are quantitatively determined.more » This experimental capability opens up an exciting opportunity to unravel the atomic dynamics of structural phase transitions in warm dense matter regime« less

Highly Transparent Water-Repelling Surfaces based on Biomimetic Hierarchical Structure

NASA Astrophysics Data System (ADS)

Wooh, Sanghyuk; Koh, Jai; Yoon, Hyunsik; Char, Kookheon

2013-03-01

Nature is a great source of inspiration for creating unique structures with special functions. The representative examples of water-repelling surfaces in nature, such as lotus leaves, rose petals, and insect wings, consist of an array of bumps (or long hairs) and nanoscale surface features with different dimension scales. Herein, we introduced a method of realizing multi-dimensional hierarchical structures and water-repellancy of the surfaces with different drop impact scenarios. The multi-dimensional hierarchical structures were fabricated by soft imprinting method with TiO2 nanoparticle pastes. In order to achieve the enhanced hydrophobicity, fluorinated moieties were attached to the etched surfaces to lower the surface energy. As a result, super-hydrophobic surfaces with high transparency were realized (over 176° water contact angle), and for further investigation, these hierarchical surfaces with different drop impact scenarios were characterized by varying the impact speed, drop size, and the geometry of the surfaces.

A multi-structural and multi-functional integrated fog collection system in cactus.

PubMed

Ju, Jie; Bai, Hao; Zheng, Yongmei; Zhao, Tianyi; Fang, Ruochen; Jiang, Lei

2012-01-01

Multiple biological structures have demonstrated fog collection abilities, such as beetle backs with bumps and spider silks with periodic spindle-knots and joints. Many Cactaceae species live in arid environments and are extremely drought-tolerant. Here we report that one of the survival systems of the cactus Opuntia microdasys lies in its efficient fog collection system. This unique system is composed of well-distributed clusters of conical spines and trichomes on the cactus stem; each spine contains three integrated parts that have different roles in the fog collection process according to their surface structural features. The gradient of the Laplace pressure, the gradient of the surface-free energy and multi-function integration endow the cactus with an efficient fog collection system. Investigations of the structure-function relationship in this system may help us to design novel materials and devices to collect water from fog with high efficiencies.

Powering the programmed nanostructure and function of gold nanoparticles with catenated DNA machines

NASA Astrophysics Data System (ADS)

Elbaz, Johann; Cecconello, Alessandro; Fan, Zhiyuan; Govorov, Alexander O.; Willner, Itamar

2013-06-01

DNA nanotechnology is a rapidly developing research area in nanoscience. It includes the development of DNA machines, tailoring of DNA nanostructures, application of DNA nanostructures for computing, and more. Different DNA machines were reported in the past and DNA-guided assembly of nanoparticles represents an active research effort in DNA nanotechnology. Several DNA-dictated nanoparticle structures were reported, including a tetrahedron, a triangle or linear nanoengineered nanoparticle structures; however, the programmed, dynamic reversible switching of nanoparticle structures and, particularly, the dictated switchable functions emerging from the nanostructures, are missing elements in DNA nanotechnology. Here we introduce DNA catenane systems (interlocked DNA rings) as molecular DNA machines for the programmed, reversible and switchable arrangement of different-sized gold nanoparticles. We further demonstrate that the machine-powered gold nanoparticle structures reveal unique emerging switchable spectroscopic features, such as plasmonic coupling or surface-enhanced fluorescence.

Single-shot mega-electronvolt ultrafast electron diffraction for structure dynamic studies of warm dense matter

DOE PAGES

Mo, M. Z.; Shen, X.; Chen, Z.; ...

2016-08-04

We have developed a single-shot mega-electronvolt ultrafast-electron-diffraction system to measure the structural dynamics of warm dense matter. The electron probe in this system is featured by a kinetic energy of 3.2 MeV and a total charge of 20 fC, with the FWHM pulse duration and spot size at sample of 350 fs and 120 µm respectively. We demonstrate its unique capability by visualizing the atomic structural changes of warm dense gold formed from a laser-excited 35-nm freestanding single-crystal gold foil. The temporal evolution of the Bragg peak intensity and of the liquid signal during solid-liquid phase transition are quantitatively determined.more » This experimental capability opens up an exciting opportunity to unravel the atomic dynamics of structural phase transitions in warm dense matter regime« less

Application of outlier analysis for baseline-free damage diagnosis

NASA Astrophysics Data System (ADS)

Kim, Seung Dae; In, Chi Won; Cronin, Kelly E.; Sohn, Hoon; Harries, Kent

2006-03-01

As carbon fiber-reinforced polymer (CFRP) laminates have been widely accepted as valuable materials for retrofitting civil infrastructure systems, an appropriate assessment of bonding conditions between host structures and CFRP laminates becomes a critical issue to guarantee the performance of CFRP strengthened structures. This study attempts to develop a continuous performance monitoring system for CFRP strengthened structures by autonomously inspecting the bonding conditions between the CFRP layers and the host structure. The uniqueness of this study is to develop a new concept and theoretical framework of nondestructive testing (NDT), in which debonding is detected "without using past baseline data." The proposed baseline-free damage diagnosis is achieved in two stages. In the first step, features sensitive to debonding of the CFPR layers but insensitive to loading conditions are extracted based on a concept referred to as a time reversal process. This time reversal process allows extracting damage-sensitive features without direct comparison with past baseline data. Then, a statistical damage classifier will be developed in the second step to make a decision regarding the bonding condition of the CFRP layers. The threshold necessary for decision making will be adaptively determined without predetermined threshold values. Monotonic and fatigue load tests of full-scale CFRP strengthened RC beams are conducted to demonstrate the potential of the proposed reference-free debonding monitoring system.

Chemically Active, Porous 3D-Printed Thermoplastic Composites.

PubMed

Evans, Kent A; Kennedy, Zachary C; Arey, Bruce W; Christ, Josef F; Schaef, Herbert T; Nune, Satish K; Erikson, Rebecca L

2018-05-02

Metal-organic frameworks (MOFs) exhibit exceptional properties and are widely investigated because of their structural and functional versatility relevant to catalysis, separations, and sensing applications. However, their commercial or large-scale application is often limited by their powder forms which make integration into devices challenging. Here, we report the production of MOF-thermoplastic polymer composites in well-defined and customizable forms and with complex internal structural features accessed via a standard three-dimensional (3D) printer. MOFs (zeolitic imidazolate framework; ZIF-8) were incorporated homogeneously into both poly(lactic acid) (PLA) and thermoplastic polyurethane (TPU) matrices at high loadings (up to 50% by mass), extruded into filaments, and utilized for on-demand access to 3D structures by fused deposition modeling. Printed, rigid PLA/MOF composites display a large surface area (SA avg = 531 m 2 g -1 ) and hierarchical pore features, whereas flexible TPU/MOF composites achieve a high surface area (SA avg = 706 m 2 g -1 ) by employing a simple method developed to expose obstructed micropores postprinting. Critically, embedded particles in the plastic matrices retain their ability to participate in chemical interactions characteristic of the parent framework. The fabrication strategies were extended to other MOFs and illustrate the potential of 3D printing to create unique porous and high surface area chemically active structures.

Structural and functional insights into the role of the N-terminal Mps1 TPR domain in the SAC (spindle assembly checkpoint).

PubMed

Thebault, Philippe; Chirgadze, Dimitri Y; Dou, Zhen; Blundell, Tom L; Elowe, Sabine; Bolanos-Garcia, Victor M

2012-12-15

The SAC (spindle assembly checkpoint) is a surveillance system that ensures the timely and accurate transmission of the genetic material to offspring. The process implies kinetochore targeting of the mitotic kinases Bub1 (budding uninhibited by benzamidine 1), BubR1 (Bub1 related) and Mps1 (monopolar spindle 1), which is mediated by the N-terminus of each kinase. In the present study we report the 1.8 Å (1 Å=0.1 nm) crystal structure of the TPR (tetratricopeptide repeat) domain in the N-terminal region of human Mps1. The structure reveals an overall high similarity to the TPR motif of the mitotic checkpoint kinases Bub1 and BubR1, and a number of unique features that include the absence of the binding site for the kinetochore structural component KNL1 (kinetochore-null 1; blinkin), and determinants of dimerization. Moreover, we show that a stretch of amino acids at the very N-terminus of Mps1 is required for dimer formation, and that interfering with dimerization results in mislocalization and misregulation of kinase activity. The results of the present study provide an important insight into the molecular details of the mitotic functions of Mps1 including features that dictate substrate selectivity and kinetochore docking.

3-D Digitization of Stereoscopic Jet-in-Crossflow Vortex Structure Images via Augmented Reality

NASA Astrophysics Data System (ADS)

Sigurdson, Lorenz; Strand, Christopher; Watson, Graeme; Nault, Joshua; Tucker, Ryan

2006-11-01

Stereoscopic images of smoke-laden vortex flows have proven useful for understanding the topology of the embedded 3-D vortex structures. Images from two cameras allow a perception of the 3-D structure via the use of red/blue eye glasses. The human brain has an astonishing capacity to calculate and present to the observer the complex turbulent smoke volume. We have developed a technique whereby a virtual cursor is introduced to the perception, which creates an ``augmented reality.'' The perceived position of this cursor in the 3-D field can be precisely controlled by the observer. It can be brought near a characteristic vortex structure in order to digitally estimate the spatial coordinates of that feature. A calibration procedure accounts for camera positioning. Vortex tubes can be traced and recorded for later or real time supersposition of tube skeleton models. These models can be readily digitally obtained for display in graphics systems to allow complete exploration from any location or perspective. A unique feature of this technology is the use of the human brain to naturally perform the difficult computation of the shape of the translucent smoke volume. Examples are given of application to low velocity ratio and Reynolds number elevated jets-in-crossflow.

Tectonic Evolution of Bell Regio, Venus: Regional Stress, Lithospheric Flexure, and Edifice Stresses

NASA Astrophysics Data System (ADS)

Rogers, P. G.; Zuber, M. T.

1996-03-01

Analyses of the tectonic features associated with large volcanoes provide important insight into the relationship between volcanic and tectonic processes and the stress state of a planet's crust over time, and provide constraints on the local and regional geologic evolution. This investigation focuses on the tectonism and volcanism of Bell Regio, a major highland uplift n Venus. The stress environments and resulting tectonic features associated with the major volcanic edifices in this region are examined using Magellan ynthetic aperture radar (SAR) images and altimeter measurements of topography. The major volcanoes of Bell Regio, Tepev Mons and the "Eastern Volcanic Center" (EVC), exhibit tectonic characteristics that are unique relative to other volcanic edifices on Venus. The most prominent distinctions are the lack of large rift zones within the overall highland uplift and the presence of radial tectonic and concentric fractures associated with the major edifices. This study examines the regional stress field in Bell Regio through analysis of structural features believed to be a consequence of lithospheric flexure due to volcanic loading and tectonic features that likely resulted from edifice stresses associated with magma chamber inflation.

A pediatric intramedullary spinal cord tumor with unusual solid-cystic and papillary features: a case report.

PubMed

Iwasaki, Takeshi; Kato, Masako; Horie, Yasushi; Kato, Shinsuke; Akatsuka, Keiichi; Watanabe, Takashi; Kuwamoto, Satoshi; Murakami, Ichiro; Hayashi, Kazuhiko

2011-12-01

Spinal cord tumors are rare in children. We report a novel case of pediatric intramedullary spinal cord tumor with unusual solid-cystic and papillary features. Clinically, the patient presented at the age of 3 years with motor deficit and urinary incontinence, and MRI demonstrated multilocular cystic lesions in the thoracic spine. Histologically the tumor consisted of solid, sheet-like components and branching papillary structures, and immunohistochemistry demonstrated positive reactivity for epithelial membrane antigen, cytokeratins (7, AE1/3, CAM5.2), E-cadherin and transthyretin, and negativity for GFAP, S-100 protein, synaptophysin and neurofilament. These histological and immunohistochemical findings appeared to be unique, and were not compatible with the features of classical ependymoma or choroid plexus papilloma. The clinical behavior, characterized by relatively rapid tumor regrowth after surgical resection and a relatively high MIB-1 labeling index, suggest that this tumor might have had moderate malignant potential. This pediatric case appears to be particularly informative with regard to the tumor biology or tumorigenesis of intramedullary spinal cord tumor with unusual solid-cystic and papillary features. © 2011 Japanese Society of Neuropathology.

Bioinformatic pipelines in Python with Leaf

PubMed Central

2013-01-01

Background An incremental, loosely planned development approach is often used in bioinformatic studies when dealing with custom data analysis in a rapidly changing environment. Unfortunately, the lack of a rigorous software structuring can undermine the maintainability, communicability and replicability of the process. To ameliorate this problem we propose the Leaf system, the aim of which is to seamlessly introduce the pipeline formality on top of a dynamical development process with minimum overhead for the programmer, thus providing a simple layer of software structuring. Results Leaf includes a formal language for the definition of pipelines with code that can be transparently inserted into the user’s Python code. Its syntax is designed to visually highlight dependencies in the pipeline structure it defines. While encouraging the developer to think in terms of bioinformatic pipelines, Leaf supports a number of automated features including data and session persistence, consistency checks between steps of the analysis, processing optimization and publication of the analytic protocol in the form of a hypertext. Conclusions Leaf offers a powerful balance between plan-driven and change-driven development environments in the design, management and communication of bioinformatic pipelines. Its unique features make it a valuable alternative to other related tools. PMID:23786315

Reaction-diffusion processes at the nano- and microscales

NASA Astrophysics Data System (ADS)

Epstein, Irving R.; Xu, Bing

2016-04-01

The bottom-up fabrication of nano- and microscale structures from primary building blocks (molecules, colloidal particles) has made remarkable progress over the past two decades, but most research has focused on structural aspects, leaving our understanding of the dynamic and spatiotemporal aspects at a relatively primitive stage. In this Review, we draw inspiration from living cells to argue that it is now time to move beyond the generation of structures and explore dynamic processes at the nanoscale. We first introduce nanoscale self-assembly, self-organization and reaction-diffusion processes as essential features of cells. Then, we highlight recent progress towards designing and controlling these fundamental features of life in abiological systems. Specifically, we discuss examples of reaction-diffusion processes that lead to such outcomes as self-assembly, self-organization, unique nanostructures, chemical waves and dynamic order to illustrate their ubiquity within a unifying context of dynamic oscillations and energy dissipation. Finally, we suggest future directions for research on reaction-diffusion processes at the nano- and microscales that we find hold particular promise for a new understanding of science at the nanoscale and the development of new kinds of nanotechnologies for chemical transport, chemical communication and integration with living systems.

Ethnic and Gender Considerations in the Use of Facial Injectables: African-American Patients.

PubMed

Burgess, Cheryl; Awosika, Olabola

2015-11-01

The United States is becoming increasingly more diverse as the nonwhite population continues to rise faster than ever. By 2044, the US Census Bureau projects that greater than 50% of the US population will be of nonwhite descent. Ethnic patients are the quickest growing portion of the cosmetic procedures market, with African-Americans comprising 7.1% of the 22% of ethnic minorities who received cosmetic procedures in the United States in 2014. The cosmetic concerns and natural features of this ethnic population are unique and guided by differing structural and aging processes than their white counterparts. As people of color increasingly seek nonsurgical cosmetic procedures, dermatologists and cosmetic surgeons must become aware that the Westernized look does not necessarily constitute beauty in these diverse people. The use of specialized aesthetic approaches and understanding of cultural and ethnic-specific features are warranted in the treatment of these patients. This article will review the key principles to consider when treating African-American patients, including the average facial structure of African-Americans, the impact of their ethnicity on aging and structure of face, and soft-tissue augmentation strategies specific to African-American skin.

Comprehensive Structural Characterization of the Bacterial Homospermidine Synthase–an Essential Enzyme of the Polyamine Metabolism

PubMed Central

Krossa, Sebastian; Faust, Annette; Ober, Dietrich; Scheidig, Axel J.

2016-01-01

The highly conserved bacterial homospermidine synthase (HSS) is a key enzyme of the polyamine metabolism of many proteobacteria including pathogenic strains such as Legionella pneumophila and Pseudomonas aeruginosa; The unique usage of NAD(H) as a prosthetic group is a common feature of bacterial HSS, eukaryotic HSS and deoxyhypusine synthase (DHS). The structure of the bacterial enzyme does not possess a lysine residue in the active center and thus does not form an enzyme-substrate Schiff base intermediate as observed for the DHS. In contrast to the DHS the active site is not formed by the interface of two subunits but resides within one subunit of the bacterial HSS. Crystal structures of Blastochloris viridis HSS (BvHSS) reveal two distinct substrate binding sites, one of which is highly specific for putrescine. BvHSS features a side pocket in the direct vicinity of the active site formed by conserved amino acids and a potential substrate discrimination, guiding, and sensing mechanism. The proposed reaction steps for the catalysis of BvHSS emphasize cation-π interaction through a conserved Trp residue as a key stabilizer of high energetic transition states. PMID:26776105

Synthesis, crystal structures and properties of lead phosphite compounds

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

Song, Jun-Ling, E-mail: s070054@e.ntu.edu.sg; Hu, Chun-Li; Xu, Xiang

2015-11-15

Here, we report the preparation and characterization of two lead(II) phosphites, namely, Pb{sub 2}(HPO{sub 3}){sub 2} and Pb{sub 2}(HPO{sub 3})(NO{sub 3}){sub 2} through hydrothermal reaction or simple solution synthesis, respectively. A new lead phosphite, namely, Pb{sub 2}(HPO{sub 3}){sub 2}, crystallizes in the noncentrosymmetric space group Cmc2{sub 1} (no. 36), which features 3D framework formed by the interconnection of 2D layer of lead(II) phosphites and 1D chain of [Pb(HPO{sub 3}){sub 5}]{sub ∞}. The nonlinear optical properties of Pb{sub 2}(HPO{sub 3})(NO{sub 3}){sub 2} have been studied for the first time. The synergistic effect of the stereo-active lone-pairs on Pb{sup 2+} cations andmore » π-conjugated NO{sub 3} units in Pb{sub 2}(HPO{sub 3})(NO{sub 3}){sub 2} produces a moderate second harmonic generation (SHG) response of ∼1.8×KDP (KH{sub 2}PO{sub 4}), which is phase matchable (type I). IR, UV–vis spectra and thermogravimetric analysis (TGA) for the two compounds were also measured. - Graphical abstract: Two lead phosphites Pb{sub 2}(HPO{sub 3}){sub 2} and Pb{sub 2}(HPO{sub 3})(NO{sub 3}){sub 2} are studied. A new lead phosphite Pb{sub 2}(HPO{sub 3}){sub 2} features a unique 3D framework structure and Pb{sub 2}(HPO{sub 3})(NO{sub 3}){sub 2} shows a moderate SHG response of ∼1.8×KDP (KH{sub 2}PO{sub 4}). - Highlights: • A new lead phosphite, Pb{sub 2}(HPO{sub 3}){sub 2} is reported. • Pb{sub 2}(HPO{sub 3}){sub 2} features a unique 3D framework structure. • NLO property of Pb{sub 2}(HPO{sub 3})(NO{sub 3}){sub 2} is investigated. • Pb{sub 2}(HPO{sub 3})(NO{sub 3}){sub 2} produces a moderate SHG response of ∼1.8×KDP (KH{sub 2}PO{sub 4}).« less

Crystal structure of the toxin Msmeg_6760, the structural homolog of Mycobacterium tuberculosis Rv2035, a novel type II toxin involved in the hypoxic response

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

Bajaj, R. Alexandra; Arbing, Mark A.; Shin, Annie

The structure of Msmeg_6760, a protein of unknown function, has been determined. Biochemical and bioinformatics analyses determined that Msmeg_6760 interacts with a protein encoded in the same operon, Msmeg_6762, and predicted that the operon is a toxin–antitoxin (TA) system. Structural comparison of Msmeg_6760 with proteins of known function suggests that Msmeg_6760 binds a hydrophobic ligand in a buried cavity lined by large hydrophobic residues. Access to this cavity could be controlled by a gate–latch mechanism. The function of the Msmeg_6760 toxin is unknown, but structure-based predictions revealed that Msmeg_6760 and Msmeg_6762 are homologous to Rv2034 and Rv2035, a predicted novelmore » TA system involved inMycobacterium tuberculosislatency during macrophage infection. The Msmeg_6760 toxin fold has not been previously described for bacterial toxins and its unique structural features suggest that toxin activation is likely to be mediated by a novel mechanism.« less

Remarkably similar antigen receptors among a subset of patients with chronic lymphocytic leukemia

PubMed Central

Ghiotto, Fabio; Fais, Franco; Valetto, Angelo; Albesiano, Emilia; Hashimoto, Shiori; Dono, Mariella; Ikematsu, Hideyuki; Allen, Steven L.; Kolitz, Jonathan; Rai, Kanti R.; Nardini, Marco; Tramontano, Anna; Ferrarini, Manlio; Chiorazzi, Nicholas

2004-01-01

Studies of B cell antigen receptors (BCRs) expressed by leukemic lymphocytes from patients with B cell chronic lymphocytic leukemia (B-CLL) suggest that B lymphocytes with some level of BCR structural restriction become transformed. While analyzing rearranged VHDJH and VLJL genes of 25 non–IgM-producing B-CLL cases, we found five IgG+ cases that display strikingly similar BCRs (use of the same H- and L-chain V gene segments with unique, shared heavy chain third complementarity-determining region [HCDR3] and light chain third complementarity-determining region [LCDR3] motifs). These H- and L-chain characteristics were not identified in other B-CLL cases or in normal B lymphocytes whose sequences are available in the public databases. Three-dimensional modeling studies suggest that these BCRs could bind the same antigenic epitope. The structural features of the B-CLL BCRs resemble those of mAb’s reactive with carbohydrate determinants of bacterial capsules or viral coats and with certain autoantigens. These findings suggest that the B lymphocytes that gave rise to these IgG+ B-CLL cells were selected for this unique BCR structure. This selection could have occurred because the precursors of the B-CLL cells were chosen for their antigen-binding capabilities by antigen(s) of restricted nature and structure, or because the precursors derived from a B cell subpopulation with limited BCR heterogeneity, or both. PMID:15057307

Identification of a Unique Fe-S Cluster Binding Site in a Glycyl-Radical Type Microcompartment Shell Protein

PubMed Central

Thompson, Michael C.; Wheatley, Nicole M.; Jorda, Julien; Sawaya, Michael R.; Gidaniyan, Soheil D.; Ahmed, Hoda; Yang, Zhongyu; McCarty, Krystal N.; Whitelegge, Julian P.; Yeates, Todd O.

2014-01-01

Recently, progress has been made toward understanding the functional diversity of bacterial microcompartment (MCP) systems, which serve as protein-based metabolic organelles in diverse microbes. New types of MCPs have been identified, including the glycyl-radical propanediol (Grp) MCP. Within these elaborate protein complexes, BMC-domain shell proteins assemble to form a polyhedral barrier that encapsulates the enzymatic contents of the MCP. Interestingly, the Grp MCP contains a number of shell proteins with unusual sequence features. GrpU is one such shell protein, whose amino acid sequence is particularly divergent from other members of the BMC-domain superfamily of proteins that effectively defines all MCPs. Expression, purification, and subsequent characterization of the protein showed, unexpectedly, that it binds an iron-sulfur cluster. We determined X-ray crystal structures of two GrpU orthologs, providing the first structural insight into the homohexameric BMC-domain shell proteins of the Grp system. The X-ray structures of GrpU, both obtained in the apo form, combined with spectroscopic analyses and computational modeling, show that the metal cluster resides in the central pore of the BMC shell protein at a position of broken 6-fold symmetry. The result is a structurally polymorphic iron-sulfur cluster binding site that appears to be unique among metalloproteins studied to date. PMID:25102080

Crystal Structure and Oligomeric State of the RetS Signaling Kinase Sensory Domain

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

Jing, X.; Jaw, J; Robinson, H

2010-01-01

The opportunistic pathogen Pseudomonas aeruginosa may cause both acute and chronic-persistent infections in predisposed individuals. Acute infections require the presence of a functional type III secretion system (T3SS), whereas chronic P. aeruginosa infections are characterized by the formation of drug-resistant biofilms. The T3SS and biofilm formation are reciprocally regulated by the signaling kinases LadS, RetS, and GacS. RetS downregulates biofilm formation and upregulates expression of the T3SS through a unique mechanism. RetS forms a heterodimeric complex with GacS and thus prevents GacS autophosphorylation and downstream signaling. The signals that regulate RetS are not known but RetS possesses a distinctive periplasmicmore » sensor domain that is believed to serve as receptor for the regulatory ligand. We have determined the crystal structure of the RetS sensory domain at 2.0 {angstrom} resolution. The structure closely resembles those of carbohydrate binding modules of other proteins, suggesting that the elusive ligands are likely carbohydrate moieties. In addition to the conserved beta-sandwich structure, the sensory domain features two alpha helices which create a unique surface topology. Protein-protein crosslinking and fluorescence energy transfer experiments also revealed that the sensory domain dimerizes with a dissociation constant of K{sub d} = 580 {+-} 50 nM, a result with interesting implications for our understanding of the underlying signaling mechanism.« less

Dental Evidence in Forensic Identification - An Overview, Methodology and Present Status.

PubMed

Krishan, Kewal; Kanchan, Tanuj; Garg, Arun K

2015-01-01

Forensic odontology is primarily concerned with the use of teeth and oral structures for identification in a legal context. Various forensic odontology techniques help in the identification of the human remains in incidents such as terrorists' attacks, airplane, train and road accidents, fires, mass murders, and natural disasters such as tsunamis, earth quakes and floods, etc. (Disaster Victim Identification-DVI). Dental structures are the hardest and well protected structures in the body. These structures resist decomposition and high temperatures and are among the last ones to disintegrate after death. The principal basis of the dental identification lies in the fact that no two oral cavities are alike and the teeth are unique to an individual. The dental evidence of the deceased recovered from the scene of crime/occurrence is compared with the ante-mortem records for identification. Dental features such as tooth morphology, variations in shape and size, restorations, pathologies, missing tooth, wear patterns, crowding of the teeth, colour and position of the tooth, rotations and other peculiar dental anomalies give every individual a unique identity. In absence of ante-mortem dental records for comparison, the teeth can help in the determination of age, sex, race/ethnicity, habits, occupations, etc. which can give further clues regarding the identity of the individuals. This piece of writing gives an overview of dental evidence, its use in forensic identification and its limitations.

Dental Evidence in Forensic Identification – An Overview, Methodology and Present Status

PubMed Central

Krishan, Kewal; Kanchan, Tanuj; Garg, Arun K

2015-01-01

Forensic odontology is primarily concerned with the use of teeth and oral structures for identification in a legal context. Various forensic odontology techniques help in the identification of the human remains in incidents such as terrorists’ attacks, airplane, train and road accidents, fires, mass murders, and natural disasters such as tsunamis, earth quakes and floods, etc. (Disaster Victim Identification-DVI). Dental structures are the hardest and well protected structures in the body. These structures resist decomposition and high temperatures and are among the last ones to disintegrate after death. The principal basis of the dental identification lies in the fact that no two oral cavities are alike and the teeth are unique to an individual. The dental evidence of the deceased recovered from the scene of crime/occurrence is compared with the ante-mortem records for identification. Dental features such as tooth morphology, variations in shape and size, restorations, pathologies, missing tooth, wear patterns, crowding of the teeth, colour and position of the tooth, rotations and other peculiar dental anomalies give every individual a unique identity. In absence of ante-mortem dental records for comparison, the teeth can help in the determination of age, sex, race/ethnicity, habits, occupations, etc. which can give further clues regarding the identity of the individuals. This piece of writing gives an overview of dental evidence, its use in forensic identification and its limitations. PMID:26312096

Avian Egg and Egg Coat.

PubMed

Okumura, Hiroki

2017-01-01

An ovulated egg of vertebrates is surrounded by unique extracellular matrix, the egg coat or zona pellucida, playing important roles in fertilization and early development. The vertebrate egg coat is composed of two to six zona pellucida (ZP) glycoproteins that are characterized by the evolutionarily conserved ZP-domain module and classified into six subfamilies based on phylogenetic analyses. Interestingly, investigations of biochemical and functional features of the ZP glycoproteins show that the roles of each ZP-glycoprotein family member in the egg-coat formation and the egg-sperm interactions seemingly vary across vertebrates. This might be one reason why comprehensive understandings of the molecular basis of either architecture or physiological functions of egg coat still remain elusive despite more than 3 decades of intensive investigations. In this chapter, an overview of avian egg focusing on the oogenesis are provided in the first section, and unique features of avian egg coat, i.e., perivitelline layer, including the morphology, biogenesis pathway, and physiological functions are discussed mainly on chicken and quail in terms of the characteristics of ZP glycoproteins in the following sections. In addition, these features of avian egg coat are compared to mammalian zona pellucida, from the viewpoint that the structural and functional varieties of ZP glycoproteins might be associated with the evolutionary adaptation to their reproductive strategies. By comparing the egg coat of birds and mammals whose reproductive strategies are largely different, new insights into the molecular mechanisms of vertebrate egg-sperm interactions might be provided.

Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications

PubMed Central

Mo, Liuting; Lu, Chun-Hua; Fu, Ting

2016-01-01

Hydrogels are crosslinked hydrophilic polymers that can absorb a large amount of water. By their hydrophilic, biocompatible and highly tunable nature, hydrogels can be tailored for applications in bioanalysis and biomedicine. Of particular interest are DNA-based hydrogels owing to the unique features of nucleic acids. Since the discovery of DNA double helical structure, interest in DNA has expanded beyond its genetic role to applications in nanotechnology and materials science. In particular, DNA-based hydrogels present such remarkable features as stability, flexibility, precise programmability, stimuli-responsive DNA conformations, facile synthesis and modification. Moreover, functional nucleic acids (FNAs) have allowed the construction of hydrogels based on aptamers, DNAzymes, i-motif nanostructures, siRNAs and CpG oligodeoxynucleotides to provide additional molecular recognition, catalytic activities and therapeutic potential, making them key players in biological analysis and biomedical applications. To date, a variety of applications have been demonstrated with FNA-based hydrogels, including biosensing, environmental analysis, controlled drug release, cell adhesion and targeted cancer therapy. In this review, we focus on advances in the development of FNA-based hydrogels, which have fully incorporated both the unique features of FNAs and DNA-based hydrogels. We first introduce different strategies for constructing DNA-based hydrogels. Subsequently, various types of FNAs and the most recent developments of FNA-based hydrogels for bioanalytical and biomedical applications are described with some selected examples. Finally, the review provides an insight into the remaining challenges and future perspectives of FNA-based hydrogels. PMID:26758955

Secondary structural entropy in RNA switch (Riboswitch) identification.

PubMed

Manzourolajdad, Amirhossein; Arnold, Jonathan

2015-04-28

RNA regulatory elements play a significant role in gene regulation. Riboswitches, a widespread group of regulatory RNAs, are vital components of many bacterial genomes. These regulatory elements generally function by forming a ligand-induced alternative fold that controls access to ribosome binding sites or other regulatory sites in RNA. Riboswitch-mediated mechanisms are ubiquitous across bacterial genomes. A typical class of riboswitch has its own unique structural and biological complexity, making de novo riboswitch identification a formidable task. Traditionally, riboswitches have been identified through comparative genomics based on sequence and structural homology. The limitations of structural-homology-based approaches, coupled with the assumption that there is a great diversity of undiscovered riboswitches, suggests the need for alternative methods for riboswitch identification, possibly based on features intrinsic to their structure. As of yet, no such reliable method has been proposed. We used structural entropy of riboswitch sequences as a measure of their secondary structural dynamics. Entropy values of a diverse set of riboswitches were compared to that of their mutants, their dinucleotide shuffles, and their reverse complement sequences under different stochastic context-free grammar folding models. Significance of our results was evaluated by comparison to other approaches, such as the base-pairing entropy and energy landscapes dynamics. Classifiers based on structural entropy optimized via sequence and structural features were devised as riboswitch identifiers and tested on Bacillus subtilis, Escherichia coli, and Synechococcus elongatus as an exploration of structural entropy based approaches. The unusually long untranslated region of the cotH in Bacillus subtilis, as well as upstream regions of certain genes, such as the sucC genes were associated with significant structural entropy values in genome-wide examinations. Various tests show that there is in fact a relationship between higher structural entropy and the potential for the RNA sequence to have alternative structures, within the limitations of our methodology. This relationship, though modest, is consistent across various tests. Understanding the behavior of structural entropy as a fairly new feature for RNA conformational dynamics, however, may require extensive exploratory investigation both across RNA sequences and folding models.

The grinding tip of the sea urchin tooth exhibits exquisite control over calcite crystal orientation and Mg distribution

PubMed Central

Ma, Yurong; Aichmayer, Barbara; Paris, Oskar; Fratzl, Peter; Meibom, Anders; Metzler, Rebecca A.; Politi, Yael; Addadi, Lia; Gilbert, P. U. P. A.; Weiner, Steve

2009-01-01

The sea urchin tooth is a remarkable grinding tool. Even though the tooth is composed almost entirely of calcite, it is used to grind holes into a rocky substrate itself often composed of calcite. Here, we use 3 complementary high-resolution tools to probe aspects of the structure of the grinding tip: X-ray photoelectron emission spectromicroscopy (X-PEEM), X-ray microdiffraction, and NanoSIMS. We confirm that the needles and plates are aligned and show here that even the high Mg polycrystalline matrix constituents are aligned with the other 2 structural elements when imaged at 20-nm resolution. Furthermore, we show that the entire tooth is composed of 2 cooriented polycrystalline blocks that differ in their orientations by only a few degrees. A unique feature of the grinding tip is that the structural elements from each coaligned block interdigitate. This interdigitation may influence the fracture process by creating a corrugated grinding surface. We also show that the overall Mg content of the tooth structural elements increases toward the grinding tip. This probably contributes to the increasing hardness of the tooth from the periphery to the tip. Clearly the formation of the tooth, and the tooth tip in particular, is amazingly well controlled. The improved understanding of these structural features could lead to the design of better mechanical grinding and cutting tools. PMID:19332795

A novel approach to internal crown characterization for coniferous tree species classification

NASA Astrophysics Data System (ADS)

Harikumar, A.; Bovolo, F.; Bruzzone, L.

2016-10-01

The knowledge about individual trees in forest is highly beneficial in forest management. High density small foot- print multi-return airborne Light Detection and Ranging (LiDAR) data can provide a very accurate information about the structural properties of individual trees in forests. Every tree species has a unique set of crown structural characteristics that can be used for tree species classification. In this paper, we use both the internal and external crown structural information of a conifer tree crown, derived from a high density small foot-print multi-return LiDAR data acquisition for species classification. Considering the fact that branches are the major building blocks of a conifer tree crown, we obtain the internal crown structural information using a branch level analysis. The structure of each conifer branch is represented using clusters in the LiDAR point cloud. We propose the joint use of the k-means clustering and geometric shape fitting, on the LiDAR data projected onto a novel 3-dimensional space, to identify branch clusters. After mapping the identified clusters back to the original space, six internal geometric features are estimated using a branch-level analysis. The external crown characteristics are modeled by using six least correlated features based on cone fitting and convex hull. Species classification is performed using a sparse Support Vector Machines (sparse SVM) classifier.

The grinding tip of the sea urchin tooth exhibits exquisite control over calcite crystal orientation and Mg distribution.

PubMed

Ma, Yurong; Aichmayer, Barbara; Paris, Oskar; Fratzl, Peter; Meibom, Anders; Metzler, Rebecca A; Politi, Yael; Addadi, Lia; Gilbert, P U P A; Weiner, Steve

2009-04-14

The sea urchin tooth is a remarkable grinding tool. Even though the tooth is composed almost entirely of calcite, it is used to grind holes into a rocky substrate itself often composed of calcite. Here, we use 3 complementary high-resolution tools to probe aspects of the structure of the grinding tip: X-ray photoelectron emission spectromicroscopy (X-PEEM), X-ray microdiffraction, and NanoSIMS. We confirm that the needles and plates are aligned and show here that even the high Mg polycrystalline matrix constituents are aligned with the other 2 structural elements when imaged at 20-nm resolution. Furthermore, we show that the entire tooth is composed of 2 cooriented polycrystalline blocks that differ in their orientations by only a few degrees. A unique feature of the grinding tip is that the structural elements from each coaligned block interdigitate. This interdigitation may influence the fracture process by creating a corrugated grinding surface. We also show that the overall Mg content of the tooth structural elements increases toward the grinding tip. This probably contributes to the increasing hardness of the tooth from the periphery to the tip. Clearly the formation of the tooth, and the tooth tip in particular, is amazingly well controlled. The improved understanding of these structural features could lead to the design of better mechanical grinding and cutting tools.

Containerless protein crystal growth method

NASA Technical Reports Server (NTRS)

Rhim, Won-Kyu; Chung, Sang K.

1991-01-01

A method of growing protein crystals from levitated drops is introduced and unique features of containerless approach in 1-g and micro-G laboratories are discussed. Electrostatic multidrop levitation system which is capable of simultaneous four drop levitation is described. A method of controlling protein saturation level in a programmed way is introduced and discussed. Finally, some of the unique features of containerless approach of protein crystal growth in space are discussed and summarized.

Evolution of the arginase fold and functional diversity

PubMed Central

Dowling, Daniel P.; Costanzo, Luigi Di; Gennadios, Heather A.; Christianson, David W.

2009-01-01

The large number of protein structures deposited in the Protein Data Bank allows for the identification of novel structural superfamilies based on conservation of fold in addition to conservation of amino acid sequence. Since sequence diverges more rapidly than fold in protein evolution, proteins with little or no significant sequence identity are occasionally observed to adopt similar folds, thereby reflecting unanticipated evolutionary relationships. Here, we review the unique α/β fold first observed in the manganese metalloenzyme rat liver arginase, consisting of a parallel 8 stranded β-sheet surrounded by several helices, and its evolutionary relationship with the zinc-requiring and/or iron-requiring histone deacetylases and acetylpolyamine amidohydrolases. Structural comparisons reveal key features of the core α/β fold that contribute to the divergent metal ion specificity and stoichiometry required for the chemical and biological functions of these enzymes. PMID:18360740

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

Mouterde, Timothée; Lehoucq, Gaëlle; Xavier, Stéphane

Nanometre-scale features with special shapes impart a broad spectrum of unique properties to the surface of insects. These properties are essential for the animal’s survival, and include the low light reflectance of moth eyes, the oil repellency of springtail carapaces and the ultra-adhesive nature of palmtree bugs. Antireflective mosquito eyes and cicada wings are also known to exhibit some antifogging and self-cleaning properties. In all cases, the combination of small feature size and optimal shape provides exceptional surface properties. In this work, we investigate the underlying antifogging mechanism in model materials designed to mimic natural systems, and explain the importancemore » of the texture’s feature size and shape. While exposure to fog strongly compromises the water-repellency of hydrophobic structures, this failure can be minimized by scaling the texture down to nanosize. Furthermore, this undesired effect even becomes non-measurable if the hydrophobic surface consists of nanocones, which generate antifogging efficiency close to unity and water departure of droplets smaller than 2 μm.« less

Antifogging abilities of model nanotextures

DOE PAGES

Mouterde, Timothée; Lehoucq, Gaëlle; Xavier, Stéphane; ...

2017-02-27

Nanometre-scale features with special shapes impart a broad spectrum of unique properties to the surface of insects. These properties are essential for the animal’s survival, and include the low light reflectance of moth eyes, the oil repellency of springtail carapaces and the ultra-adhesive nature of palmtree bugs. Antireflective mosquito eyes and cicada wings are also known to exhibit some antifogging and self-cleaning properties. In all cases, the combination of small feature size and optimal shape provides exceptional surface properties. In this work, we investigate the underlying antifogging mechanism in model materials designed to mimic natural systems, and explain the importancemore » of the texture’s feature size and shape. While exposure to fog strongly compromises the water-repellency of hydrophobic structures, this failure can be minimized by scaling the texture down to nanosize. Furthermore, this undesired effect even becomes non-measurable if the hydrophobic surface consists of nanocones, which generate antifogging efficiency close to unity and water departure of droplets smaller than 2 μm.« less

Antifogging abilities of model nanotextures

NASA Astrophysics Data System (ADS)

Mouterde, Timothée; Lehoucq, Gaëlle; Xavier, Stéphane; Checco, Antonio; Black, Charles T.; Rahman, Atikur; Midavaine, Thierry; Clanet, Christophe; Quéré, David

2017-06-01

Nanometre-scale features with special shapes impart a broad spectrum of unique properties to the surface of insects. These properties are essential for the animal’s survival, and include the low light reflectance of moth eyes, the oil repellency of springtail carapaces and the ultra-adhesive nature of palmtree bugs. Antireflective mosquito eyes and cicada wings are also known to exhibit some antifogging and self-cleaning properties. In all cases, the combination of small feature size and optimal shape provides exceptional surface properties. In this work, we investigate the underlying antifogging mechanism in model materials designed to mimic natural systems, and explain the importance of the texture’s feature size and shape. While exposure to fog strongly compromises the water-repellency of hydrophobic structures, this failure can be minimized by scaling the texture down to nanosize. This undesired effect even becomes non-measurable if the hydrophobic surface consists of nanocones, which generate antifogging efficiency close to unity and water departure of droplets smaller than 2 μm.

Transient and Big Are Key Features of an Invertebrate T-type Channel (LCav3) from the Central Nervous System of Lymnaea stagnalis*

PubMed Central

Senatore, Adriano; Spafford, J. David

2010-01-01

Here we describe features of the first non-mammalian T-type calcium channel (LCav3) expressed in vitro. This molluscan channel possesses combined biophysical properties that are reminiscent of all mammalian T-type channels. It exhibits T-type features such as “transient” kinetics, but the “tiny” label, usually associated with Ba2+ conductance, is hard to reconcile with the “bigness” of this channel in many respects. LCav3 is 25% larger than any voltage-gated ion channel expressed to date. It codes for a massive, 322-kDa protein that conducts large macroscopic currents in vitro. LCav3 is also the most abundant Ca2+ channel transcript in the snail nervous system. A window current at typical resting potentials appears to be at least as large as that reported for mammalian channels. This distant gene provides a unique perspective to analyze the structural, functional, drug binding, and evolutionary aspects of T-type channels. PMID:20056611

How do seal whiskers suppress vortex shedding

NASA Astrophysics Data System (ADS)

Rinehart, Aidan; Flaherty, Justin; Bunjavick, Joseph; Shyam, Vikram; Zhang, Wei

2016-11-01

Certain seal whiskers possess a unique geometry that significantly reduces the vortex-induced vibration; which has attracted great attention to understand how the unique shape re-organizes the wake structure and its potential for passive flow control. The shape of the whiskers can be described as an elliptical cross-section that is lofted along the length of the whisker. Along the entire length of the whisker the ellipse varies in major and minor axis as well as angle of incidence with respect to the axis of the whisker. Of particular interest in this study is to identify what effect the angle of incidence has on the flow structure around the whisker, which has been overlooked in the past. The study will analyze the wake structure behind various scaled-up whisker models using particle image velocimitry (PIV). These whisker models share common geometry dimensions except for the angle of incidence. Flow conditions are created in a water channel and a wind tunnel, covering a wide range of Reynolds number (a few hundreds to thousands), similar to the ambient flow environment of seals and to the targeted aero-propulsion applications. This study will help address knowledge gaps in understanding of how certain geometry features of seal whiskers influence the wake and establish best practices for its application as effective passive flow control strategy.

Local numerical modelling of ultrasonic guided waves in linear and nonlinear media

NASA Astrophysics Data System (ADS)

Packo, Pawel; Radecki, Rafal; Kijanka, Piotr; Staszewski, Wieslaw J.; Uhl, Tadeusz; Leamy, Michael J.

2017-04-01

Nonlinear ultrasonic techniques provide improved damage sensitivity compared to linear approaches. The combination of attractive properties of guided waves, such as Lamb waves, with unique features of higher harmonic generation provides great potential for characterization of incipient damage, particularly in plate-like structures. Nonlinear ultrasonic structural health monitoring techniques use interrogation signals at frequencies other than the excitation frequency to detect changes in structural integrity. Signal processing techniques used in non-destructive evaluation are frequently supported by modeling and numerical simulations in order to facilitate problem solution. This paper discusses known and newly-developed local computational strategies for simulating elastic waves, and attempts characterization of their numerical properties in the context of linear and nonlinear media. A hybrid numerical approach combining advantages of the Local Interaction Simulation Approach (LISA) and Cellular Automata for Elastodynamics (CAFE) is proposed for unique treatment of arbitrary strain-stress relations. The iteration equations of the method are derived directly from physical principles employing stress and displacement continuity, leading to an accurate description of the propagation in arbitrarily complex media. Numerical analysis of guided wave propagation, based on the newly developed hybrid approach, is presented and discussed in the paper for linear and nonlinear media. Comparisons to Finite Elements (FE) are also discussed.

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

PubMed

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

2013-01-01

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

The cell's nucleolus: an emerging target for chemotherapeutic intervention.

PubMed

Pickard, Amanda J; Bierbach, Ulrich

2013-09-01

The transient nucleolus plays a central role in the up-regulated synthesis of ribosomal RNA (rRNA) to sustain ribosome biogenesis, a hallmark of aberrant cell growth. This function, in conjunction with its unique pathohistological features in malignant cells and its ability to mediate apoptosis, renders this sub-nuclear structure a potential target for chemotherapeutic agents. In this Minireview, structurally and functionally diverse small molecules are discussed that have been reported to either interact with the nucleolus directly or perturb its function indirectly by acting on its dynamic components. These molecules include all major classes of nucleic-acid-targeted agents, antimetabolites, kinase inhibitors, anti-inflammatory drugs, natural product antibiotics, oligopeptides, as well as nanoparticles. Together, these molecules are invaluable probes of structure and function of the nucleolus. They also provide a unique opportunity to develop novel strategies for more selective and therefore better-tolerated chemotherapeutic intervention. In this regard, inhibition of RNA polymerase-I-mediated rRNA synthesis appears to be a promising mechanism for killing cancer cells. The recent development of molecules targeted at G-quadruplex-forming rRNA gene sequences, which are currently undergoing clinical trials, seems to attest to the success of this approach. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Physics of protein folding

NASA Astrophysics Data System (ADS)

Finkelstein, A. V.; Galzitskaya, O. V.

2004-04-01

Protein physics is grounded on three fundamental experimental facts: protein, this long heteropolymer, has a well defined compact three-dimensional structure; this structure can spontaneously arise from the unfolded protein chain in appropriate environment; and this structure is separated from the unfolded state of the chain by the “all-or-none” phase transition, which ensures robustness of protein structure and therefore of its action. The aim of this review is to consider modern understanding of physical principles of self-organization of protein structures and to overview such important features of this process, as finding out the unique protein structure among zillions alternatives, nucleation of the folding process and metastable folding intermediates. Towards this end we will consider the main experimental facts and simple, mostly phenomenological theoretical models. We will concentrate on relatively small (single-domain) water-soluble globular proteins (whose structure and especially folding are much better studied and understood than those of large or membrane and fibrous proteins) and consider kinetic and structural aspects of transition of initially unfolded protein chains into their final solid (“native”) 3D structures.

Distinguishing early and late brain aging from the Alzheimer's disease spectrum: consistent morphological patterns across independent samples.

PubMed

Doan, Nhat Trung; Engvig, Andreas; Zaske, Krystal; Persson, Karin; Lund, Martina Jonette; Kaufmann, Tobias; Cordova-Palomera, Aldo; Alnæs, Dag; Moberget, Torgeir; Brækhus, Anne; Barca, Maria Lage; Nordvik, Jan Egil; Engedal, Knut; Agartz, Ingrid; Selbæk, Geir; Andreassen, Ole A; Westlye, Lars T

2017-09-01

Alzheimer's disease (AD) is a debilitating age-related neurodegenerative disorder. Accurate identification of individuals at risk is complicated as AD shares cognitive and brain features with aging. We applied linked independent component analysis (LICA) on three complementary measures of gray matter structure: cortical thickness, area and gray matter density of 137 AD, 78 mild (MCI) and 38 subjective cognitive impairment patients, and 355 healthy adults aged 18-78 years to identify dissociable multivariate morphological patterns sensitive to age and diagnosis. Using the lasso classifier, we performed group classification and prediction of cognition and age at different age ranges to assess the sensitivity and diagnostic accuracy of the LICA patterns in relation to AD, as well as early and late healthy aging. Three components showed high sensitivity to the diagnosis and cognitive status of AD, with different relationships with age: one reflected an anterior-posterior gradient in thickness and gray matter density and was uniquely related to diagnosis, whereas the other two, reflecting widespread cortical thickness and medial temporal lobe volume, respectively, also correlated significantly with age. Repeating the LICA decomposition and between-subject analysis on ADNI data, including 186 AD, 395 MCI and 220 age-matched healthy controls, revealed largely consistent brain patterns and clinical associations across samples. Classification results showed that multivariate LICA-derived brain characteristics could be used to predict AD and age with high accuracy (area under ROC curve up to 0.93 for classification of AD from controls). Comparison between classifiers based on feature ranking and feature selection suggests both common and unique feature sets implicated in AD and aging, and provides evidence of distinct age-related differences in early compared to late aging. Copyright © 2017 Elsevier Inc. All rights reserved.

Structural and functional studies on Ribonuclease S, retro S and retro-inverso S peptides

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

Pal-Bhowmick, Ipsita; Pati Pandey, Ramendra; Jarori, Gotam K.

2007-12-21

Ribonuclease S peptide and S protein offer a unique complementation system to understand the finer features of molecular recognition. In the present study the S peptide (1-16), and its retro and retro-inverso analogs have been analyzed for their structural and biological attributes. RPHPLC, CD, and NMR analyses have revealed that the physicochemical and conformational properties of the S peptide are distinct from those of its retro and retro-inverso analogs. On the functional side, while the S peptide complemented the S protein to give RNase activity, was recognized by anti-S peptide antibodies and induced T cell proliferation, neither the retro normore » the retro-inverso S peptides could do so.« less

Thin SOI lateral IGBT with band-to-band tunneling mechanism

NASA Astrophysics Data System (ADS)

Fu, Qiang; Tang, Zhaohuan; Tan, Kaizhou; Wang, Zhikuan; Mei, Yong

2017-06-01

In this paper, a novel 200V lateral IGBT on thin SOI layer with a band-to-band tunneling junction near the anode is proposed. The structure and the operating mechanism of the proposed IGBT are described and discussed. Its main feature is that the novel IGBT structure has a unique abrupt doped p++/n++ tunneling junction in the side of the anode. By utilizing the reverse bias characteristics of the tunneling junction, the proposed IGBT can achieve excellent reverse conducting performance. Numerical simulations suggest that a low reverse conduction voltage drop VR=-1.6V at a current density of 100A/cm2 and a soft factor S=0.63 of the build-in diode are achieved.

Photovoltaic module mounting system

DOEpatents

Miros, Robert H. J.; Mittan, Margaret Birmingham; Seery, Martin N; Holland, Rodney H

2012-09-18

A solar array mounting system having unique installation, load distribution, and grounding features, and which is adaptable for mounting solar panels having no external frame. The solar array mounting system includes flexible, pedestal-style feet and structural links connected in a grid formation on the mounting surface. The photovoltaic modules are secured in place via the use of attachment clamps that grip the edge of the typically glass substrate. The panel mounting clamps are then held in place by tilt brackets and/or mid-link brackets that provide fixation for the clamps and align the solar panels at a tilt to the horizontal mounting surface. The tilt brackets are held in place atop the flexible feet and connected link members thus creating a complete mounting structure.

Photovoltaic module mounting system

DOEpatents

Miros, Robert H. J. [Fairfax, CA; Mittan, Margaret Birmingham [Oakland, CA; Seery, Martin N [San Rafael, CA; Holland, Rodney H [Novato, CA

2012-04-17

A solar array mounting system having unique installation, load distribution, and grounding features, and which is adaptable for mounting solar panels having no external frame. The solar array mounting system includes flexible, pedestal-style feet and structural links connected in a grid formation on the mounting surface. The photovoltaic modules are secured in place via the use of attachment clamps that grip the edge of the typically glass substrate. The panel mounting clamps are then held in place by tilt brackets and/or mid-link brackets that provide fixation for the clamps and align the solar panels at a tilt to the horizontal mounting surface. The tilt brackets are held in place atop the flexible feet and connected link members thus creating a complete mounting structure.

Peeling the onion: the outer layers of Cryptococcus neoformans.

PubMed

Agustinho, Daniel P; Miller, Liza C; Li, Lucy X; Doering, Tamara L

2018-01-01

Cryptococcus neoformans is an opportunistic fungal pathogen that is ubiquitous in the environment. It causes a deadly meningitis that is responsible for over 180,000 deaths worldwide each year, including 15% of all AIDS-related deaths. The high mortality rates for this infection, even with treatment, suggest a need for improved therapy. Unique characteristics of C. neoformans may suggest directions for drug discovery. These include features of three structures that surround the cell: the plasma membrane, the cell wall around it, and the outermost polysaccharide capsule. We review current knowledge of the fundamental biology of these fascinating structures and highlight open questions in the field, with the goal of stimulating further investigation that will advance basic knowledge and human health.

Novel Multidisciplinary Models Assess the Capabilities of Smart Structures to Manage Vibration, Sound, and Thermal Distortion in Aeropropulsion Components

NASA Technical Reports Server (NTRS)

Saravanos, Dimitris A.

1997-01-01

The development of aeropropulsion components that incorporate "smart" composite laminates with embedded piezoelectric actuators and sensors is expected to ameliorate critical problems in advanced aircraft engines related to vibration, noise emission, and thermal stability. To facilitate the analytical needs of this effort, the NASA Lewis Research Center has developed mechanics and multidisciplinary computational models to analyze the complicated electromechanical behavior of realistic smart-structure configurations operating in combined mechanical, thermal, and acoustic environments. The models have been developed to accommodate the particular geometries, environments, and technical challenges encountered in advanced aircraft engines, yet their unique analytical features are expected to facilitate application of this new technology in a variety of commercial applications.

Peeling the onion: the outer layers of Cryptococcus neoformans

PubMed Central

Agustinho, Daniel P; Miller, Liza C; Li, Lucy X; Doering, Tamara L

2018-01-01

Cryptococcus neoformans is an opportunistic fungal pathogen that is ubiquitous in the environment. It causes a deadly meningitis that is responsible for over 180,000 deaths worldwide each year, including 15% of all AIDS-related deaths. The high mortality rates for this infection, even with treatment, suggest a need for improved therapy. Unique characteristics of C. neoformans may suggest directions for drug discovery. These include features of three structures that surround the cell: the plasma membrane, the cell wall around it, and the outermost polysaccharide capsule. We review current knowledge of the fundamental biology of these fascinating structures and highlight open questions in the field, with the goal of stimulating further investigation that will advance basic knowledge and human health. PMID:29742198

Crystal structure of a papain-fold protein without the catalytic residue: a novel member in the cysteine proteinase family.

PubMed

Zhang, Min; Wei, Zhiyi; Chang, Shaojie; Teng, Maikun; Gong, Weimin

2006-04-21

A 31kDa cysteine protease, SPE31, was isolated from the seeds of a legume plant, Pachyrizhus erosus. The protein was purified, crystallized and the 3D structure solved using molecular replacement. The cDNA was obtained by RT PCR followed by amplification using mRNA isolated from the seeds of the legume plant as a template. Analysis of the cDNA sequence and the 3D structure indicated the protein to belong to the papain family. Detailed analysis of the structure revealed an unusual replacement of the conserved catalytic Cys with Gly. Replacement of another conserved residue Ala/Gly by a Phe sterically blocks the access of the substrate to the active site. A polyethyleneglycol molecule and a natural peptide fragment were bound to the surface of the active site. Asn159 was found to be glycosylated. The SPE31 cDNA sequence shares several features with P34, a protein found in soybeans, that is implicated in plant defense mechanisms as an elicitor receptor binding to syringolide. P34 has also been shown to interact with vegetative storage proteins and NADH-dependent hydroxypyruvate reductase. These roles suggest that SPE31 and P34 form a unique subfamily within the papain family. The crystal structure of SPE31 complexed with a natural peptide ligand reveals a unique active site architecture. In addition, the clear evidence of glycosylated Asn159 provides useful information towards understanding the functional mechanism of SPE31/P34.

Structure-dependent performance of TiO 2/C as anode material for Na-ion batteries

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

He, Hanna; Gan, Qingmeng; Wang, Haiyan

The performance of energy storage materials is highly dependent on their nanostructures. Herein, hierarchical rod-in-tube TiO 2 with a uniform carbon coating is synthesized as the anode material for sodium-ion batteries by a facile solvothermal method. This unique structure consists of a tunable nanorod core, interstitial hollow spaces, and a functional nanotube shell assembled from two-dimensional nanosheets. By adjusting the types of solvents used and reaction time, the morphologies of TiO 2/C composites can be tuned to nanoparticles, microrods, rod-in-tube structures, or microtubes. Among these materials, rod-in-tube TiO 2 with a uniform carbon coating shows the highest electronic conductivity, specificmore » surface area (336.4 m(2) g(-1)), and porosity, and these factors lead to the best sodium storage capability. Benefiting from the unique structural features and improved electronic/ionic conductivity, the as-obtained rod-in-tube TiO2/C in coin cell tests exhibits a high discharge capacity of 277.5 and 153.9 mAh g(-1) at 50 and 5000 mA g(-1), respectively, and almost 100% capacity retention over 14,000 cycles at 5000 mA g(-1). In operando high-energy X-ray diffraction further confirms the stable crystal structure of the rod-in-tube TiO 2/C during Na+ insertion/extraction. This work highlights that nanostructure design is an effective strategy to achieve advanced energy storage materials.« less

The Osborne 1.

ERIC Educational Resources Information Center

McWilliams, Peter

1982-01-01

Describes the unique features, available software, performance capabilities, system options, costs, advantages, disadvantages, and eccentricities of the Osborne 1 microcomputer. A table summarizes specifications, features, and costs. (JL)

3D Seismic Interpretation of a Plio-Pleistocene Mass Transport Deposit in the Deepwater Taranaki Basin of New Zealand

NASA Astrophysics Data System (ADS)

Rusconi, Francisco Jose

A series of Plio-Pleistocene mass transport deposits (MTD) have been identified in the deepwater Taranaki Basin, in New Zealand, using the Romney 3D seismic survey, which covers an area of approximately 2000 km2. One of these MTDs has been chosen for description and interpretation based on high confidence mapping of its boundary surfaces. The deposit exhibits an array of interesting features similar to those documented by researchers elsewhere plus a unique basal feature unlike those previously observed. The basal shear surface exhibits erosional features such as grooves, "monkey fingers", and glide tracks. Internally, the MTD is typically characterized by low impedance, chaotic, semi-transparent reflectors surrounding isolated coherent packages of seismic facies interpreted as intact blocks rafted within the mass transport complex. Distally, the deposit presents outrunner blocks and pressure ridges. The new element described in this work consists of a composite feature that includes a protruding obstacle ("shield block") on the paleo-seafloor that acted as a barrier to subsequent flows as they advanced downslope. These blocks disrupt the incoming flow and result in elongate, downflow negative features ("erosional shadow scours"), which are then infilled by the mass transport deposit, and are preserved as elongate isochore thicks. Kinematic evidence provided by various structures suggests that the MTD flow direction was SE-NW toward bathyal depths. The features presented and the absence of extensional headwall structures, such as local arcuate glide planes and rotated slide blocks, suggest that this part of the deposit belongs to the translational to distal domain of the MTD, and its source area is expected to be somewhere toward the SE in a paleo continental slope.

Carbon-based layer-by-layer nanostructures: from films to hollow capsules

NASA Astrophysics Data System (ADS)

Hong, Jinkee; Han, Jung Yeon; Yoon, Hyunsik; Joo, Piljae; Lee, Taemin; Seo, Eunyong; Char, Kookheon; Kim, Byeong-Su

2011-11-01

Over the past years, the layer-by-layer (LbL) assembly has been widely developed as one of the most powerful techniques to prepare multifunctional films with desired functions, structures and morphologies because of its versatility in the process steps in both material and substrate choices. Among various functional nanoscale objects, carbon-based nanomaterials, such as carbon nanotubes and graphene sheets, are promising candidates for emerging science and technology with their unique physical, chemical, and mechanical properties. In particular, carbon-based functional multilayer coatings based on the LbL assembly are currently being actively pursued as conducting electrodes, batteries, solar cells, supercapacitors, fuel cells and sensor applications. In this article, we give an overview on the use of carbon materials in nanostructured films and capsules prepared by the LbL assembly with the aim of unraveling the unique features and their applications of carbon multilayers prepared by the LbL assembly.

BTKbase, mutation database for X-linked agammaglobulinemia (XLA).

PubMed Central

Vihinen, M; Brandau, O; Brandén, L J; Kwan, S P; Lappalainen, I; Lester, T; Noordzij, J G; Ochs, H D; Ollila, J; Pienaar, S M; Riikonen, P; Saha, B K; Smith, C I

1998-01-01

X-linked agammaglobulinemia (XLA) is an immunodeficiency caused by mutations in the gene coding for Bruton's agammaglobulinemia tyrosine kinase (BTK). A database (BTKbase) of BTK mutations has been compiled and the recent update lists 463 mutation entries from 406 unrelated families showing 303 unique molecular events. In addition to mutations, the database also lists variants or polymorphisms. Each patient is given a unique patient identity number (PIN). Information is included regarding the phenotype including symptoms. Mutations in all the five domains of BTK have been noticed to cause the disease, the most common event being missense mutations. The mutations appear almost uniformly throughout the molecule and frequently affect CpG sites that code for arginine residues. The putative structural implications of all the missense mutations are given in the database. The improved version of the registry having a number of new features is available at http://www. helsinki.fi/science/signal/btkbase.html PMID:9399844

Electric papers of graphene-coated Co₃O₄ fibers for high-performance lithium-ion batteries.

PubMed

Yang, Xiaoling; Fan, Kaicai; Zhu, Yihua; Shen, Jianhua; Jiang, Xin; Zhao, Peng; Luan, Shaorong; Li, Chunzhong

2013-02-01

A facile strategy to synthesize the novel composite paper of graphene nanosheets (GNS) coated Co(3)O(4) fibers is reported as an advanced anode material for high-performance lithium-ion batteries (LIBs). The GNS were able to deposit onto Co(3)O(4) fibers and form the coating via electrostatic interactions. The unique hybrid paper is evaluated as an anode electrode for LIBs, and it exhibits a very large reversible capacity (∼840 mA h g(-1) after 40 cycles), excellent cyclic stability and good rate capacity. The substantially excellent electrochemical performance of the graphene/Co(3)O(4) composite paper is the result from its unique features. Notably, the flexible structure of graphenic scaffold and the strong interaction between graphene and Co(3)O(4) fibers are beneficial for providing excellent electronic conductivity, short transportation length for lithium ions, and elastomeric space to accommodate volume varies upon Li(+) insertion/extraction.

Advancements in zebrafish applications for 21st century toxicology.

PubMed

Garcia, Gloria R; Noyes, Pamela D; Tanguay, Robert L

2016-05-01

The zebrafish model is the only available high-throughput vertebrate assessment system, and it is uniquely suited for studies of in vivo cell biology. A sequenced and annotated genome has revealed a large degree of evolutionary conservation in comparison to the human genome. Due to our shared evolutionary history, the anatomical and physiological features of fish are highly homologous to humans, which facilitates studies relevant to human health. In addition, zebrafish provide a very unique vertebrate data stream that allows researchers to anchor hypotheses at the biochemical, genetic, and cellular levels to observations at the structural, functional, and behavioral level in a high-throughput format. In this review, we will draw heavily from toxicological studies to highlight advances in zebrafish high-throughput systems. Breakthroughs in transgenic/reporter lines and methods for genetic manipulation, such as the CRISPR-Cas9 system, will be comprised of reports across diverse disciplines. Copyright © 2016 Elsevier Inc. All rights reserved.

Advancements in zebrafish applications for 21st century toxicology

PubMed Central

Garcia, Gloria R.; Noyes, Pamela D.; Tanguay, Robert L.

2016-01-01

The zebrafish model is the only available high-throughput vertebrate assessment system, and it is uniquely suited for studies of in vivo cell biology. A sequenced and annotated genome has revealed a large degree of evolutionary conservation in comparison to the human genome. Due to our shared evolutionary history, the anatomical and physiological features of fish are highly homologous to humans, which facilitates studies relevant to human health. In addition, zebrafish provide a very unique vertebrate data stream that allows researchers to anchor hypotheses at the biochemical, genetic, and cellular levels to observations at the structural, functional, and behavioral level in a high-throughput format. In this review, we will draw heavily from toxicological studies to highlight advances in zebrafish high-throughput systems. Breakthroughs in transgenic/reporter lines and methods for genetic manipulation, such as the CRISPR-Cas9 system, will be comprised of reports across diverse disciplines. PMID:27016469

Strong Broadband Terahertz Optical Activity through Control of the Blaschke Phase with Chiral Metasurfaces

NASA Astrophysics Data System (ADS)

Cole, Michael A.; Chen, Wen-chen; Liu, Mingkai; Kruk, Sergey S.; Padilla, Willie J.; Shadrivov, Ilya V.; Powell, David A.

2017-07-01

We demonstrate terahertz chiral metamaterials that achieve resonant transmission and strong optical activity. This response is realized in a metasurface coupled to its Babinet complement, with additional twist. Uniquely, the optical activity achieved in this type of metamaterial is weakly dispersive around the resonant transmission maxima, but it can be highly dispersive around the transmission minima. It has recently been shown that this unique optical activity response is closely related to zeros in the transmission spectra of circular polarizations through the Kramers-Kronig relations and strong resonant features in the optical activity spectrum corresponding to the Blaschke phase terms. Here we demonstrate how modifying the meta-atom geometry greatly affects the location and magnitude of these Blaschke phase terms. We study three different meta-atoms, which are variations on the simple cross structure. Their responses are measured using terahertz time-domain spectroscopy and analyzed via numerical simulations.

Unique crater morphologies on Vesta, and the context of a deep regolith and intermediate gravity

NASA Astrophysics Data System (ADS)

Hoffmann, M.; Nathues, A.; Vincent, J. B.; Sierks, H.

2012-04-01

The Dawn spacecraft orbiting the minor planet Vesta has revealed details of the surface properties on a key object for the understanding of the evolution processes in an early epoch of our planetary system. In order to understand these phenomena the three dimensional structure of the surface must be deduced from identifiable processes known to be present elsewhere in the planetary system. Therefore the morphology of impact craters and their geological context (Keil 2002, Clark et al. 2002) plays an important role. They expose material at significant depth in the surface layers, they show a chronologic sequence of rearrangement of the original uppermost layer of Vesta, and their apparent mechanical properties fill the gap between topographic roughness and micro-structural photometric roughness and porosity. Many impact craters on Vesta show significant differences to impact craters on the Moon and Mercury, where their morphology is basically dominated by a rigid surface, and to those on volatile-rich surfaces like on Mars or the icy satellites of the outer planets. The closest match with Vestan crater morphologies is that with those on Lutetia (Vincent et al. 2012). This similarity can be seen by signs of granular fluidity in land-slide phenomena. A prominent and unique property of craters on Vesta is the occurrence of features showing singular concentric central pits, which so far have been associated with liquid materials: either molten rock on Mercury or the Moon, or the liquefaction of ice on Mars, Ganymede, and Callisto (Schultz, 1988). Selected from a collection of 200 sample features in the diameter range 1 to 30 km, some prototypes of this type are presented as indicators of such a porous regolith. The prototypes include simple hopper-shaped to pan-shaped features (the basic structure), but also a subclass with approximately circular symmetric multiple-depression structure (features typically larger than 10 km), and a subclass with unusual halo shapes not observed in regular impact craters. Main criteria of establishment of a causal link between the outer halo and the inner depression are the unique coincidence of their morphologies, the consistency from an 'evolutionary' point of view, and a statistically significant excess with respect to the expected number of chance configurations. These criteria have been tested and confirmed. The variety of features with the basic structure is consistent with more than a single kind of process. Several active and passive modes of their generation could be identified by the observational evidence, e.g. the collapse of a porous area shaken by the seismic wave from an impact into a regolith layer with high porosity. The required geophysical context is the presence of a sufficiently deep layer of regolith, a suitable distribution of size and shapes of its constituents, a deposit under low velocity and low pressure conditions, and a specific seismic history. These conditions are met by the giant impacts on Vesta, the 'intermediate' gravity (escape velocity sufficient for retention of ejecta but small for complete structural destruction by re-impactors), and the environment of craters of intermediate diameter (in the range of 10 km). Then significantly deep layers with similar properties can be created with the intact porosity of a fractal aggregate (Kaye, 1989). Diagnostic data are the histograms of the local distribution, the determination of surface roughness on all scales. Test areas on opposite sides of Vesta with areas of 400 km2 show differences in the abundance of pit craters to normal ones by a factor of two. Locally the fraction of pit craters exceeds 50% of all, whereas elsewhere they are obviously rare. Since under-abundance is found in the low albedo hemisphere of Vesta, a correlation with composition is indicated. The existence of the necessary conditions for the formation of a porous regolith has been tested by calculation of the trajectories of crater ejecta on the rapidly rotating object Vesta. Results show that on the trailing side of the original impact the opportunity for very slow re-impacts (less than a few meters per second) is significantly enhanced. Also the traveling times for the seismic wave and the arrival of ejecta have been compared, resulting in consistent details of the distance distribution of the related compactions. Further evidence comes from the analysis of brightness profiles of the surface which demonstrates local smoothing. The distribution of diameter ratio of halo to central depression matches that found for the Iovian satellite Callisto, thus hinting to the granular fluidity of the regolith on Vesta. Another unique type of interacting craters on Vesta is shown, which is related to different stages of compaction of the regolith. Concluding, it is shown that for individual features strong indications are found for a common origin of a crater and a surrounding halo by identifiable processes. A completely equivalent environment of impacts has been created by Lohse et al (2004) in laboratory, resulting in strikingly similar features. Therefore the paradigms of crater erosion and saturation have to be expanded to porous collapses. Age determinations by crater counts are affected. Although it is obvious that also some of these features were created by chance, even then the outcome in the sense of a compaction process can be studied.

Change of the image of the city in process of using traffic infrastructure

NASA Astrophysics Data System (ADS)

Alihodžić, Rifat; Vasiljević Tomić, Dragana; Iablonskii, Leonid

2017-10-01

Unique urban image cannot be experienced without moving within its structure. This paper deals with phenomenology considering changes of images of the city and influential factors closely related to it. Infrastructure gives basic structural scheme of every city, so its planning requires a high level proficiency. Some changes in these images can be observed during longer period of time. Sometimes it includes rapid changes of temporal layers, generated by building new urban elements on the exact same place where the old ones existed; while lighter change during the time passing is a regular occurrence. Creating completely new urban frames, caused by expanding the city, represents its dynamical variant. Topography is a significant factor, giving distinctive feature to the urbanity. This paper considers factors identified as generators of the change of the urban image, based on research so far. The structural elements are considered with the utmost attention. The importance of the city landmark, monumental complexes not possessing these features but having the importance in image of the city stability (as well as the inhabitants’ memory) are crucial elements of identifying its picture. Another significant factor is related to individual personal experience. However, there are also certain factors of significance features, but not considered within this paper. One such factor is change in coloring, being the special topic itself. The purpose of this work is to indicate that urban planning requires special attention in order to keep continuous nature of the urban image for the city to preserve its visual identity.

Novel unimorph deformable mirror for space applications

NASA Astrophysics Data System (ADS)

Verpoort, Sven; Rausch, Peter; Wittrock, Ulrich

2017-11-01

We have developed a new type of unimorph deformable mirror, designed to correct for low-order Zernike modes. The mirror has a clear optical aperture of 50 mm combined with large peak-to-valley Zernike amplitudes of up to 35 μm. Newly developed fabrication processes allow the use of prefabricated super-polished and coated glass substrates. The mirror's unique features suggest the use in several astronomical applications like the precompensation of atmospheric aberrations seen by laser beacons and the use in woofer-tweeter systems. Additionally, the design enables an efficient correction of the inevitable wavefront error imposed by the floppy structure of primary mirrors in future large space-based telescopes. We have modeled the mirror by using analytical as well as finite element models. We will present design, key features and manufacturing steps of the deformable mirror.

An unconventional family 1 uracil DNA glycosylase in Nitratifractor salsuginis.

PubMed

Li, Jing; Chen, Ran; Yang, Ye; Zhang, Zhemin; Fang, Guang-Chen; Xie, Wei; Cao, Weiguo

2017-12-01

The uracil DNA glycosylase superfamily consists of at least six families with a diverse specificity toward DNA base damage. Family 1 uracil N-glycosylase (UNG) exhibits exclusive specificity on uracil-containing DNA. Here, we report a family 1 UNG homolog from Nitratifractor salsuginis with distinct biochemical features that differentiate it from conventional family 1 UNGs. Globally, the crystal structure of N. salsuginisUNG shows a few additional secondary structural elements. Biochemical and enzyme kinetic analysis, coupled with structural determination, molecular modeling, and molecular dynamics simulations, shows that N. salsuginisUNG contains a salt bridge network that plays an important role in DNA backbone interactions. Disruption of the amino acid residues involved in the salt bridges greatly impedes the enzymatic activity. A tyrosine residue in motif 1 (GQDPY) is one of the distinct sequence features setting family 1 UNG apart from other families. The crystal structure of Y81G mutant indicates that several subtle changes may account for its inactivity. Unlike the conventional family 1 UNG enzymes, N. salsuginisUNG is not inhibited by Ugi, a potent inhibitor specific for family 1 UNG. This study underscores the diversity of paths that a uracil DNA glycosylase may take to acquire its unique structural and biochemical properties during evolution. Structure data are available in the PDB under accession numbers 5X3G and 5X3H. © 2017 Federation of European Biochemical Societies.

The Crystal Structure Analysis of Group B Streptococcus Sortase C1: A Model for the ;Lid; Movement upon Substrate Binding

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

Khare, Baldeep; Fu, Zheng-Qing; Huang, I-Hsiu

2012-02-07

A unique feature of the class-C-type sortases, enzymes essential for Gram-positive pilus biogenesis, is the presence of a flexible 'lid' anchored in the active site. However, the mechanistic details of the 'lid' displacement, suggested to be a critical prelude for enzyme catalysis, are not yet known. This is partly due to the absence of enzyme-substrate and enzyme-inhibitor complex crystal structures. We have recently described the crystal structures of the Streptococcus agalactiae SAG2603 V/R sortase SrtC1 in two space groups (type II and type III) and that of its 'lid' mutant and proposed a role of the 'lid' as a protectormore » of the active-site hydrophobic environment. Here, we report the crystal structures of SAG2603 V/R sortase C1 in a different space group (type I) and that of its complex with a small-molecule cysteine protease inhibitor. We observe that the catalytic Cys residue is covalently linked to the small-molecule inhibitor without lid displacement. However, the type I structure provides a view of the sortase SrtC1 lid displacement while having structural elements similar to a substrate sorting motif suitably positioned in the active site. We propose that these major conformational changes seen in the presence of a substrate mimic in the active site may represent universal features of class C sortase substrate recognition and enzyme activation.« less

High-resolution crystal structure of a polyextreme GH43 glycosidase from Halothermothrix orenii with α-l-arabinofuranosidase activity

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

Hassan, Noor; Karolinska Institutet, Stockholm; Kori, Lokesh D.

2015-02-19

The crystal structure of the H. orenii glycosidase was determined by molecular replacement and refined at 1.10 Å resolution. A gene from the heterotrophic, halothermophilic marine bacterium Halothermothrix orenii has been cloned and overexpressed in Escherichia coli. This gene encodes the only glycoside hydrolase of family 43 (GH43) produced by H. orenii. The crystal structure of the H. orenii glycosidase was determined by molecular replacement and refined at 1.10 Å resolution. As for other GH43 members, the enzyme folds as a five-bladed β-propeller. The structure features a metal-binding site on the propeller axis, near the active site. Based on thermalmore » denaturation data, the H. orenii glycosidase depends on divalent cations in combination with high salt for optimal thermal stability against unfolding. A maximum melting temperature of 76°C was observed in the presence of 4 M NaCl and Mn{sup 2+} at pH 6.5. The gene encoding the H. orenii GH43 enzyme has previously been annotated as a putative α-l-arabinofuranosidase. Activity was detected with p-nitrophenyl-α-l-arabinofuranoside as a substrate, and therefore the name HoAraf43 was suggested for the enzyme. In agreement with the conditions for optimal thermal stability against unfolding, the highest arabinofuranosidase activity was obtained in the presence of 4 M NaCl and Mn{sup 2+} at pH 6.5, giving a specific activity of 20–36 µmol min{sup −1} mg{sup −1}. The active site is structurally distinct from those of other GH43 members, including arabinanases, arabinofuranosidases and xylanases. This probably reflects the special requirements for degrading the unique biomass available in highly saline aqueous ecosystems, such as halophilic algae and halophytes. The amino-acid distribution of HoAraf43 has similarities to those of mesophiles, thermophiles and halophiles, but also has unique features, for example more hydrophobic amino acids on the surface and fewer buried charged residues.« less

Structural insights into xenobiotic and inhibitor binding to human aldehyde oxidase.

PubMed

Coelho, Catarina; Foti, Alessandro; Hartmann, Tobias; Santos-Silva, Teresa; Leimkühler, Silke; Romão, Maria João

2015-10-01

Aldehyde oxidase (AOX) is a xanthine oxidase (XO)-related enzyme with emerging importance due to its role in the metabolism of drugs and xenobiotics. We report the first crystal structures of human AOX1, substrate free (2.6-Å resolution) and in complex with the substrate phthalazine and the inhibitor thioridazine (2.7-Å resolution). Analysis of the protein active site combined with steady-state kinetic studies highlight the unique features, including binding and substrate orientation at the active site, that characterize human AOX1 as an important drug-metabolizing enzyme. Structural analysis of the complex with the noncompetitive inhibitor thioridazine revealed a new, unexpected and fully occupied inhibitor-binding site that is structurally conserved among mammalian AOXs and XO. The new structural insights into the catalytic and inhibition mechanisms of human AOX that we now report will be of great value for the rational analysis of clinical drug interactions involving inhibition of AOX1 and for the prediction and design of AOX-stable putative drugs.

A parallel implementation of the Wuchty algorithm with additional experimental filters to more thoroughly explore RNA conformational space.

PubMed

Stone, Jonathan W; Bleckley, Samuel; Lavelle, Sean; Schroeder, Susan J

2015-01-01

We present new modifications to the Wuchty algorithm in order to better define and explore possible conformations for an RNA sequence. The new features, including parallelization, energy-independent lonely pair constraints, context-dependent chemical probing constraints, helix filters, and optional multibranch loops, provide useful tools for exploring the landscape of RNA folding. Chemical probing alone may not necessarily define a single unique structure. The helix filters and optional multibranch loops are global constraints on RNA structure that are an especially useful tool for generating models of encapsidated viral RNA for which cryoelectron microscopy or crystallography data may be available. The computations generate a combinatorially complete set of structures near a free energy minimum and thus provide data on the density and diversity of structures near the bottom of a folding funnel for an RNA sequence. The conformational landscapes for some RNA sequences may resemble a low, wide basin rather than a steep funnel that converges to a single structure.

Smart Metamaterial Based on the Simplex Tensegrity Pattern.

PubMed

Al Sabouni-Zawadzka, Anna; Gilewski, Wojciech

2018-04-26

In the present paper, a novel cellular metamaterial that was based on a tensegrity pattern is presented. The material is constructed from supercells, each of which consists of eight 4-strut simplex modules. The proposed metamaterial exhibits some unusual properties, which are typical for smart structures. It is possible to control its mechanical characteristics by adjusting the level of self-stress or by changing the properties of structural members. A continuum model is used to identify the qualitative properties of the considered metamaterial, and to estimate how the applied self-stress and the characteristics of cables and struts affect the whole structure. The performed analyses proved that the proposed structure can be regarded as a smart metamaterial with orthotropic properties. One of its most important features are unique values of Poisson’s ratio, which can be either positive or negative, depending on the applied control parameters. Moreover, all of the mechanical characteristics of the proposed metamaterial are prone to structural control.

Structural Basis of Wee Kinases Functionality and Inactivation by Diverse Small Molecule Inhibitors.

PubMed

Zhu, Jin-Yi; Cuellar, Rebecca A; Berndt, Norbert; Lee, Hee Eun; Olesen, Sanne H; Martin, Mathew P; Jensen, Jeffrey T; Georg, Gunda I; Schönbrunn, Ernst

2017-09-28

Members of the Wee family of kinases negatively regulate the cell cycle via phosphorylation of CDK1 and are considered potential drug targets. Herein, we investigated the structure-function relationship of human Wee1, Wee2, and Myt1 (PKMYT1). Purified recombinant full-length proteins and kinase domain constructs differed substantially in phosphorylation states and catalytic competency, suggesting complex mechanisms of activation. A series of crystal structures reveal unique features that distinguish Wee1 and Wee2 from Myt1 and establish the structural basis of differential inhibition by the widely used Wee1 inhibitor MK-1775. Kinome profiling and cellular studies demonstrate that, in addition to Wee1 and Wee2, MK-1775 is an equally potent inhibitor of the polo-like kinase PLK1. Several previously unrecognized inhibitors of Wee kinases were discovered and characterized. Combined, the data provide a comprehensive view on the catalytic and structural properties of Wee kinases and a framework for the rational design of novel inhibitors thereof.

Structural insight into arginine methylation by the mouse protein arginine methyltransferase 7: a zinc finger freezes the mimic of the dimeric state into a single active site.

PubMed

Cura, Vincent; Troffer-Charlier, Nathalie; Wurtz, Jean Marie; Bonnefond, Luc; Cavarelli, Jean

2014-09-01

Protein arginine methyltransferase 7 (PRMT7) is a type III arginine methyltransferase which has been implicated in several biological processes such as transcriptional regulation, DNA damage repair, RNA splicing, cell differentiation and metastasis. PRMT7 is a unique but less characterized member of the family of PRMTs. The crystal structure of full-length PRMT7 from Mus musculus refined at 1.7 Å resolution is described. The PRMT7 structure is composed of two catalytic modules in tandem forming a pseudo-dimer and contains only one AdoHcy molecule bound to the N-terminal module. The high-resolution crystal structure presented here revealed several structural features showing that the second active site is frozen in an inactive state by a conserved zinc finger located at the junction between the two PRMT modules and by the collapse of two degenerated AdoMet-binding loops.

MACF1 gene structure: a hybrid of plectin and dystrophin.

PubMed

Gong, T W; Besirli, C G; Lomax, M I

2001-11-01

Mammalian MACF1 (Macrophin1; previously named ACF7) is a giant cytoskeletal linker protein with three known isoforms that arise by alternative splicing. We isolated a 19.1-kb cDNA encoding a fourth isoform (MACF1-4) with a unique N-terminus. Instead of an N-terminal actin-binding domain found in the other three isoforms, MACF1-4 has eight plectin repeats. The MACF1 gene is located on human Chr 1p32, contains at least 102 exons, spans over 270 kb, and gives rise to four major isoforms with different N-termini. The genomic organization of the actin-binding domain is highly conserved in mammalian genes for both plectin and BPAG1. All eight plectin repeats are encoded by one large exon; this feature is similar to the genomic structure of plectin. The intron positions within spectrin repeats in MACF1 are very similar to those in the dystrophin gene. This demonstrates that MACF1 has characteristic features of genes for two classes of cytoskeletal proteins, i.e., plectin and dystrophin.

The adaptation of polar fishes to climatic changes: Structure, function and phylogeny of haemoglobin.

PubMed

Verde, Cinzia; Giordano, Daniela; di Prisco, Guido

2008-01-01

In the Antarctic, fishes of dominant suborder Notothenioidei have evolved in a unique thermal scenario. Phylogenetically related taxa of the suborder live in a wide range of latitudes, in Antarctic, sub-Antarctic and temperate oceans. Consequently, they offer a remarkable opportunity to study the physiological and biochemical characters gained and, conversely, lost during their evolutionary history. The evolutionary perspective has also been pursued by comparative studies of some features of the heme protein devoted to O(2) transport in fish living in the other polar region, the Arctic. The two polar regions differ by age and isolation. Fish living in each habitat have undergone regional constraints and fit into different evolutionary histories. The aim of this contribution is to survey the current knowledge of molecular structure, functional features, phylogeny and adaptations of the haemoglobins of fish thriving in the Antarctic, sub-Antarctic and Arctic regions (with some excursions in the temperate latitudes), in search of insights into the convergent processes evolved in response to cooling. Current climate change may disturb adaptation, calling for strategies aimed at neutralising threats to biodiversity.

Using cellular automata to generate image representation for biological sequences.

PubMed

Xiao, X; Shao, S; Ding, Y; Huang, Z; Chen, X; Chou, K-C

2005-02-01

A novel approach to visualize biological sequences is developed based on cellular automata (Wolfram, S. Nature 1984, 311, 419-424), a set of discrete dynamical systems in which space and time are discrete. By transforming the symbolic sequence codes into the digital codes, and using some optimal space-time evolvement rules of cellular automata, a biological sequence can be represented by a unique image, the so-called cellular automata image. Many important features, which are originally hidden in a long and complicated biological sequence, can be clearly revealed thru its cellular automata image. With biological sequences entering into databanks rapidly increasing in the post-genomic era, it is anticipated that the cellular automata image will become a very useful vehicle for investigation into their key features, identification of their function, as well as revelation of their "fingerprint". It is anticipated that by using the concept of the pseudo amino acid composition (Chou, K.C. Proteins: Structure, Function, and Genetics, 2001, 43, 246-255), the cellular automata image approach can also be used to improve the quality of predicting protein attributes, such as structural class and subcellular location.

Pattern recognition applied to seismic signals of Llaima volcano (Chile): An evaluation of station-dependent classifiers

NASA Astrophysics Data System (ADS)

Curilem, Millaray; Huenupan, Fernando; Beltrán, Daniel; San Martin, Cesar; Fuentealba, Gustavo; Franco, Luis; Cardona, Carlos; Acuña, Gonzalo; Chacón, Max; Khan, M. Salman; Becerra Yoma, Nestor

2016-04-01

Automatic pattern recognition applied to seismic signals from volcanoes may assist seismic monitoring by reducing the workload of analysts, allowing them to focus on more challenging activities, such as producing reports, implementing models, and understanding volcanic behaviour. In a previous work, we proposed a structure for automatic classification of seismic events in Llaima volcano, one of the most active volcanoes in the Southern Andes, located in the Araucanía Region of Chile. A database of events taken from three monitoring stations on the volcano was used to create a classification structure, independent of which station provided the signal. The database included three types of volcanic events: tremor, long period, and volcano-tectonic and a contrast group which contains other types of seismic signals. In the present work, we maintain the same classification scheme, but we consider separately the stations information in order to assess whether the complementary information provided by different stations improves the performance of the classifier in recognising seismic patterns. This paper proposes two strategies for combining the information from the stations: i) combining the features extracted from the signals from each station and ii) combining the classifiers of each station. In the first case, the features extracted from the signals from each station are combined forming the input for a single classification structure. In the second, a decision stage combines the results of the classifiers for each station to give a unique output. The results confirm that the station-dependent strategies that combine the features and the classifiers from several stations improves the classification performance, and that the combination of the features provides the best performance. The results show an average improvement of 9% in the classification accuracy when compared with the station-independent method.

LINKING LUNG AIRWAY STRUCTURE TO PULMONARY FUNCTION VIA COMPOSITE BRIDGE REGRESSION

PubMed Central

Chen, Kun; Hoffman, Eric A.; Seetharaman, Indu; Jiao, Feiran; Lin, Ching-Long; Chan, Kung-Sik

2017-01-01

The human lung airway is a complex inverted tree-like structure. Detailed airway measurements can be extracted from MDCT-scanned lung images, such as segmental wall thickness, airway diameter, parent-child branch angles, etc. The wealth of lung airway data provides a unique opportunity for advancing our understanding of the fundamental structure-function relationships within the lung. An important problem is to construct and identify important lung airway features in normal subjects and connect these to standardized pulmonary function test results such as FEV1%. Among other things, the problem is complicated by the fact that a particular airway feature may be an important (relevant) predictor only when it pertains to segments of certain generations. Thus, the key is an efficient, consistent method for simultaneously conducting group selection (lung airway feature types) and within-group variable selection (airway generations), i.e., bi-level selection. Here we streamline a comprehensive procedure to process the lung airway data via imputation, normalization, transformation and groupwise principal component analysis, and then adopt a new composite penalized regression approach for conducting bi-level feature selection. As a prototype of composite penalization, the proposed composite bridge regression method is shown to admit an efficient algorithm, enjoy bi-level oracle properties, and outperform several existing methods. We analyze the MDCT lung image data from a cohort of 132 subjects with normal lung function. Our results show that, lung function in terms of FEV1% is promoted by having a less dense and more homogeneous lung comprising an airway whose segments enjoy more heterogeneity in wall thicknesses, larger mean diameters, lumen areas and branch angles. These data hold the potential of defining more accurately the “normal” subject population with borderline atypical lung functions that are clearly influenced by many genetic and environmental factors. PMID:28280520

The unique functional role of the C-HS hydrogen bond in the substrate specificity and enzyme catalysis of type 1 methionine aminopeptidase.

PubMed

Reddi, Ravikumar; Singarapu, Kiran Kumar; Pal, Debnath; Addlagatta, Anthony

2016-07-19

It is intriguing how nature attains recognition specificity between molecular interfaces where there is no apparent scope for classical hydrogen bonding or polar interactions. Methionine aminopeptidase (MetAP) is one such enzyme where this fascinating conundrum is at play. In this study, we demonstrate that a unique C-HS hydrogen bond exists between the enzyme methionine aminopeptidase (MetAP) and its N-terminal-methionine polypeptide substrate, which allows specific interaction between apparent apolar interfaces, imposing a strict substrate recognition specificity and efficient catalysis, a feature replicated in Type I MetAPs across all kingdoms of life. We evidence this evolutionarily conserved C-HS hydrogen bond through enzyme assays on wild-type and mutant MetAP proteins from Mycobacterium tuberculosis that show a drastic difference in catalytic efficiency. The X-ray crystallographic structure of the methionine bound protein revealed a conserved water bridge and short contacts involving the Met side-chain, a feature also observed in MetAPs from other organisms. Thermal shift assays showed a remarkable 3.3 °C increase in melting temperature for methionine bound protein compared to its norleucine homolog, where C-HS interaction is absent. The presence of C-HS hydrogen bonding was also corroborated by nuclear magnetic resonance spectroscopy through a change in chemical shift. Computational chemistry studies revealed the unique role of the electrostatic environment in facilitating the C-HS interaction. The significance of this atypical hydrogen bond is underscored by the fact that the function of MetAP is essential for any living cell.

HIV is Now a Manageable Long-Term Condition, But What Makes it Unique? A Qualitative Study Exploring Views About Distinguishing Features from Multi-Professional HIV Specialists in North West England.

PubMed

Jelliman, Pauline; Porcellato, Lorna

HIV is evolving from a life-threatening infection to a long-term, manageable condition because of medical advances, radical changes in health and social care policy, and the impact of an aging population. However, HIV remains complex, presenting unique characteristics distinguishing it from other long-term conditions (LTCs). Our aim in this qualitative descriptive study was to identify and explore these features in the context of LTCs. A focus group (FG) method was used to gather the views and experiences of multi-professional HIV specialists who worked in North West England. Twenty-four staff participated in FGs (n = 3), which were audio recorded, manually transcribed, and thematically analyzed. We found four main themes: (a) stigma, (b) challenges faced by HIV specialists, (c) lack HIV-related knowledge, and (d) unique features, termed "stand alone." We concluded that these distinguishing features hindered full recognition and acceptance of HIV as an LTC. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

Evaluation of the automatic optical authentication technologies for control systems of objects

NASA Astrophysics Data System (ADS)

Averkin, Vladimir V.; Volegov, Peter L.; Podgornov, Vladimir A.

2000-03-01

The report considers the evaluation of the automatic optical authentication technologies for the automated integrated system of physical protection, control and accounting of nuclear materials at RFNC-VNIITF, and for providing of the nuclear materials nonproliferation regime. The report presents the nuclear object authentication objectives and strategies, the methodology of the automatic optical authentication and results of the development of pattern recognition techniques carried out under the ISTC project #772 with the purpose of identification of unique features of surface structure of a controlled object and effects of its random treatment. The current decision of following functional control tasks is described in the report: confirmation of the item authenticity (proof of the absence of its substitution by an item of similar shape), control over unforeseen change of item state, control over unauthorized access to the item. The most important distinctive feature of all techniques is not comprehensive description of some properties of controlled item, but unique identification of item using minimum necessary set of parameters, properly comprising identification attribute of the item. The main emphasis in the technical approach is made on the development of rather simple technological methods for the first time intended for use in the systems of physical protection, control and accounting of nuclear materials. The developed authentication devices and system are described.

Computer-based classification of bacteria species by analysis of their colonies Fresnel diffraction patterns

NASA Astrophysics Data System (ADS)

Suchwalko, Agnieszka; Buzalewicz, Igor; Podbielska, Halina

2012-01-01

In the presented paper the optical system with converging spherical wave illumination for classification of bacteria species, is proposed. It allows for compression of the observation space, observation of Fresnel patterns, diffraction pattern scaling and low level of optical aberrations, which are not possessed by other optical configurations. Obtained experimental results have shown that colonies of specific bacteria species generate unique diffraction signatures. Analysis of Fresnel diffraction patterns of bacteria colonies can be fast and reliable method for classification and recognition of bacteria species. To determine the unique features of bacteria colonies diffraction patterns the image processing analysis was proposed. Classification can be performed by analyzing the spatial structure of diffraction patterns, which can be characterized by set of concentric rings. The characteristics of such rings depends on the bacteria species. In the paper, the influence of basic features and ring partitioning number on the bacteria classification, is analyzed. It is demonstrated that Fresnel patterns can be used for classification of following species: Salmonella enteritidis, Staplyococcus aureus, Proteus mirabilis and Citrobacter freundii. Image processing is performed by free ImageJ software, for which a special macro with human interaction, was written. LDA classification, CV method, ANOVA and PCA visualizations preceded by image data extraction were conducted using the free software R.

Imaging Modalities Relevant to Intracranial Pressure Assessment in Astronauts: A Case-Based Discussion

NASA Technical Reports Server (NTRS)

Sargsyan, Ashot E.; Kramer, Larry A.; Hamilton, Douglas R.; Hamilton, Douglas R.; Fogarty, Jennifer; Polk, J. D.

2010-01-01

Introduction: Intracranial pressure (ICP) elevation has been inferred or documented in a number of space crewmembers. Recent advances in noninvasive imaging technology offer new possibilities for ICP assessment. Most International Space Station (ISS) partner agencies have adopted a battery of occupational health monitoring tests including magnetic resonance imaging (MRI) pre- and postflight, and high-resolution sonography of the orbital structures in all mission phases including during flight. We hypothesize that joint consideration of data from the two techniques has the potential to improve quality and continuity of crewmember monitoring and care. Methods: Specially designed MRI and sonographic protocols were used to image eyes and optic nerves (ON) including the meningeal sheaths. Specific crewmembers multi-modality imaging data were analyzed to identify points of mutual validation as well as unique features of complementary nature. Results and Conclusion: Magnetic resonance imaging (MRI) and high-resolution sonography are both tomographic methods, however images obtained by the two modalities are based on different physical phenomena and use different acquisition principles. Consideration of the images acquired by these two modalities allows cross-validating findings related to the volume and fluid content of the ON subarachnoid space, shape of the globe, and other anatomical features of the orbit. Each of the imaging modalities also has unique advantages, making them complementary techniques.

[Analysis of Conformational Features of Watson-Crick Duplex Fragments by Molecular Mechanics and Quantum Mechanics Methods].

PubMed

Poltev, V I; Anisimov, V M; Sanchez, C; Deriabina, A; Gonzalez, E; Garcia, D; Rivas, F; Polteva, N A

2016-01-01

It is generally accepted that the important characteristic features of the Watson-Crick duplex originate from the molecular structure of its subunits. However, it still remains to elucidate what properties of each subunit are responsible for the significant characteristic features of the DNA structure. The computations of desoxydinucleoside monophosphates complexes with Na-ions using density functional theory revealed a pivotal role of DNA conformational properties of single-chain minimal fragments in the development of unique features of the Watson-Crick duplex. We found that directionality of the sugar-phosphate backbone and the preferable ranges of its torsion angles, combined with the difference between purines and pyrimidines. in ring bases, define the dependence of three-dimensional structure of the Watson-Crick duplex on nucleotide base sequence. In this work, we extended these density functional theory computations to the minimal' fragments of DNA duplex, complementary desoxydinucleoside monophosphates complexes with Na-ions. Using several computational methods and various functionals, we performed a search for energy minima of BI-conformation for complementary desoxydinucleoside monophosphates complexes with different nucleoside sequences. Two sequences are optimized using ab initio method at the MP2/6-31++G** level of theory. The analysis of torsion angles, sugar ring puckering and mutual base positions of optimized structures demonstrates that the conformational characteristic features of complementary desoxydinucleoside monophosphates complexes with Na-ions remain within BI ranges and become closer to the corresponding characteristic features of the Watson-Crick duplex crystals. Qualitatively, the main characteristic features of each studied complementary desoxydinucleoside monophosphates complex remain invariant when different computational methods are used, although the quantitative values of some conformational parameters could vary lying within the limits typical for the corresponding family. We observe that popular functionals in density functional theory calculations lead to the overestimated distances between base pairs, while MP2 computations and the newer complex functionals produce the structures that have too close atom-atom contacts. A detailed study of some complementary desoxydinucleoside monophosphate complexes with Na-ions highlights the existence of several energy minima corresponding to BI-conformations, in other words, the complexity of the relief pattern of the potential energy surface of complementary desoxydinucleoside monophosphate complexes. This accounts for variability of conformational parameters of duplex fragments with the same base sequence. Popular molecular mechanics force fields AMBER and CHARMM reproduce most of the conformational characteristics of desoxydinucleoside monophosphates and their complementary complexes with Na-ions but fail to reproduce some details of the dependence of the Watson-Crick duplex conformation on the nucleotide sequence.

Ambient response of a unique performance-based design building with dynamic response modification features

USGS Publications Warehouse

Çelebi, Mehmet; Huang, Moh; Shakal, Antony; Hooper, John; Klemencic, Ron

2012-01-01

A 64-story, performance-based design building with reinforced concrete core shear-walls and unique dynamic response modification features (tuned liquid sloshing dampers and buckling-restrained braces) has been instrumented with a monitoring array of 72 channels of accelerometers. Ambient vibration data recorded are analyzed to identify modes and associated frequencies and damping. The low-amplitude dynamic characteristics are considerably different than those computed from design analyses, but serve as a baseline against which to compare with future strong shaking responses. Such studies help to improve our understanding of the effectiveness of the added features to the building and help improve designs in the future.

The interplay of hydrogen bonding and dispersion in phenol dimer and trimer: structures from broadband rotational spectroscopy.

PubMed

Seifert, Nathan A; Steber, Amanda L; Neill, Justin L; Pérez, Cristóbal; Zaleski, Daniel P; Pate, Brooks H; Lesarri, Alberto

2013-07-21

The structures of the phenol dimer and phenol trimer complexes in the gas phase have been determined using chirped-pulse Fourier transform microwave spectroscopy in the 2-8 GHz band. All fourteen (13)C and (18)O phenol dimer isotopologues were assigned in natural abundance. A full heavy atom experimental substitution structure was determined, and a least-squares fit ground state r0 structure was determined by proper constraint of the M06-2X/6-311++g(d,p) ab initio structure. The structure of phenol dimer features a water dimer-like hydrogen bond, as well as a cooperative contribution from inter-ring dispersion. Comparisons between the experimental structure and previously determined experimental structures, as well as ab initio structures from various levels of theory, are discussed. For phenol trimer, a C3 symmetric barrel-like structure is found, and an experimental substitution structure was determined via measurement of the six unique (13)C isotopologues. The least-squares fit rm((1)) structure reveals a similar interplay between hydrogen bonding and dispersion in the trimer, with water trimer-like hydrogen bonding and C-H···π interactions.

Support and Development of Workflow Protocols for High Throughput Single-Lap-Joint Testing-Experimental

DTIC Science & Technology

2013-04-01

preparation, and presence of an overflow fillet for a high strength epoxy and ductile methacylate adhesive. A unique feature of this study was the...of expanding adhesive joint test configurations as part of the GEMS program. 15. SUBJECT TERMS single lap joint, adhesion, aluminum, epoxy ... epoxy and ductile methacylate adhesive. A unique feature of this study was the use of untrained GEMS (Gains in the Education of Mathematics and Sci

Nonlinear mechanics of non-rigid origami: an efficient computational approach

NASA Astrophysics Data System (ADS)

Liu, K.; Paulino, G. H.

2017-10-01

Origami-inspired designs possess attractive applications to science and engineering (e.g. deployable, self-assembling, adaptable systems). The special geometric arrangement of panels and creases gives rise to unique mechanical properties of origami, such as reconfigurability, making origami designs well suited for tunable structures. Although often being ignored, origami structures exhibit additional soft modes beyond rigid folding due to the flexibility of thin sheets that further influence their behaviour. Actual behaviour of origami structures usually involves significant geometric nonlinearity, which amplifies the influence of additional soft modes. To investigate the nonlinear mechanics of origami structures with deformable panels, we present a structural engineering approach for simulating the nonlinear response of non-rigid origami structures. In this paper, we propose a fully nonlinear, displacement-based implicit formulation for performing static/quasi-static analyses of non-rigid origami structures based on `bar-and-hinge' models. The formulation itself leads to an efficient and robust numerical implementation. Agreement between real models and numerical simulations demonstrates the ability of the proposed approach to capture key features of origami behaviour.

Nonlinear mechanics of non-rigid origami: an efficient computational approach.

PubMed

Liu, K; Paulino, G H

2017-10-01

Origami-inspired designs possess attractive applications to science and engineering (e.g. deployable, self-assembling, adaptable systems). The special geometric arrangement of panels and creases gives rise to unique mechanical properties of origami, such as reconfigurability, making origami designs well suited for tunable structures. Although often being ignored, origami structures exhibit additional soft modes beyond rigid folding due to the flexibility of thin sheets that further influence their behaviour. Actual behaviour of origami structures usually involves significant geometric nonlinearity, which amplifies the influence of additional soft modes. To investigate the nonlinear mechanics of origami structures with deformable panels, we present a structural engineering approach for simulating the nonlinear response of non-rigid origami structures. In this paper, we propose a fully nonlinear, displacement-based implicit formulation for performing static/quasi-static analyses of non-rigid origami structures based on 'bar-and-hinge' models. The formulation itself leads to an efficient and robust numerical implementation. Agreement between real models and numerical simulations demonstrates the ability of the proposed approach to capture key features of origami behaviour.

R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

PubMed

Rahrig, Ryan R; Petrov, Anton I; Leontis, Neocles B; Zirbel, Craig L

2013-07-01

The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/.

Development of automated optical verification technologies for control systems

NASA Astrophysics Data System (ADS)

Volegov, Peter L.; Podgornov, Vladimir A.

1999-08-01

The report considers optical techniques for automated verification of object's identity designed for control system of nuclear objects. There are presented results of experimental researches and results of development of pattern recognition techniques carried out under the ISTC project number 772 with the purpose of identification of unique feature of surface structure of a controlled object and effects of its random treatment. Possibilities of industrial introduction of the developed technologies in frames of USA and Russia laboratories' lab-to-lab cooperation, including development of up-to-date systems for nuclear material control and accounting are examined.

The cetaceopteryx: A global range military transport aircraft

NASA Technical Reports Server (NTRS)

Brivkalns, Chad; English, Nicole; Kazemi, Tahmineh; Kopel, Kim; Kroger, Seth; Ortega, ED

1993-01-01

This paper presents a design of a military transport aircraft capable of carrying 800,000 lbs of payload from any point in the United States to any other point in the world. Such massive airlift requires aggressive use of advanced technology and a unique configuration. The Cetaceopteyx features a joined wing, canard and six turbofan engines. The aircraft has a cost 1.07 billion (1993) dollars each. This paper presents in detail the mission description, preliminary sizing, aircraft configuration, wing design, fuselage design, empennage design, propulsion system, landing gear design, structures, drag, stability and control, systems layout, and cost analysis of the aircraft.

Imaging 2D optical diffuse reflectance in skeletal muscle

NASA Astrophysics Data System (ADS)

Ranasinghesagara, Janaka; Yao, Gang

2007-04-01

We discovered a unique pattern of optical reflectance from fresh prerigor skeletal muscles, which can not be described using existing theories. A numerical fitting function was developed to quantify the equiintensity contours of acquired reflectance images. Using this model, we studied the changes of reflectance profile during stretching and rigor process. We found that the prominent anisotropic features diminished after rigor completion. These results suggested that muscle sarcomere structures played important roles in modulating light propagation in whole muscle. When incorporating the sarcomere diffraction in a Monte Carlo model, we showed that the resulting reflectance profiles quantitatively resembled the experimental observation.

Bile Salt-like Dienones Having a Novel Skeleton or a Rare Substitution Pattern Function as Chemical Cues in Adult Sea Lamprey.

PubMed

Li, Ke; Scott, Anne M; Brant, Cory O; Fissette, Skye D; Riedy, Joseph J; Hoye, Thomas R; Li, Weiming

2017-09-01

Two novel sulfated bile salt-like dienones, featuring either a unique, rearranged side chain or a rare cis-11,12-diol on the steroidal C-ring, herein named petromyzene A (1) and B (2), respectively, were isolated from water conditioned with spawning male sea lamprey (Petromyzon marinus; a jawless vertebrate animal). The structures of these natural products were elucidated by mass spectrometry and NMR spectroscopy. Petromyzenes A and B exhibited high olfactory potency for adult sea lamprey and strong behavioral attraction for spawning females.

Atypical Intracranial Epidermoid Cysts: Rare Anomalies with Unique Radiological Features

PubMed Central

Law, Eric K. C.; Lee, Ryan K. L.; Ng, Alex W. H.; Siu, Deyond Y. W.; Ng, Ho-Keung

2015-01-01

Epidermoid cysts are benign slow growing extra-axial tumours that insinuate between brain structures, while their occurrences in intra-axial or intradiploic locations are exceptionally rare. We present the clinical, imaging, and pathological findings in two patients with atypical epidermoid cysts. CT and MRI findings for the first case revealed an intraparenchymal epidermoid cyst that demonstrated no restricted diffusion. The second case demonstrated an aggressive epidermoid cyst that invaded into the intradiploic spaces, transverse sinus, and the calvarium. The timing of ectodermal tissue sequestration during fetal development may account for the occurrence of atypical epidermoid cysts. PMID:25667778