Grooved Terrain on Ganymede: First Results from Galileo High-Resolution Imaging

USGS Publications Warehouse

Pappalardo, R.T.; Head, J.W.; Collins, G.C.; Kirk, R.L.; Neukum, G.; Oberst, J.; Giese, B.; Greeley, R.; Chapman, C.R.; Helfenstein, P.; Moore, Johnnie N.; McEwen, A.; Tufts, B.R.; Senske, D.A.; Herbert, Breneman H.; Klaasen, K.

1998-01-01

High-resolution Galileo imaging has provided important insight into the origin and evolution of grooved terrain on Ganymede. The Uruk Sulcus target site was the first imaged at high resolution, and considerations of resolution, viewing geometry, low image compression, and complementary stereo imaging make this region extremely informative. Contrast variations in these low-incidence angle images are extreme and give the visual impression of topographic shading. However, photometric analysis shows that the scene must owe its character to albedo variations. A close correlation of albedo variations to topography is demonstrated by limited stereo coverage, allowing extrapolation of the observed brightness and topographic relationships to the rest of the imaged area. Distinct geological units are apparent across the region, and ridges and grooves are ubiquitous within these units. The stratigraphically lowest and most heavily cratered units ("lineated grooved terrain") generally show morphologies indicative of horst-and-graben-style normal faulting. The stratigraphically highest groove lanes ("parallel ridged terrain") exhibit ridges of roughly triangular cross section, suggesting that tilt-block-style normal faulting has shaped them. These extensional-tectonic models are supported by crosscutting relationships at the margins of groove lanes. Thus, a change in tectonic style with time is suggested in the Uruk Sulcus region, varying from horst and graben faulting for the oldest grooved terrain units to tilt block normal faulting for the latest units. The morphologies and geometries of some stratigraphically high units indicate that a strike-slip component of deformation has played an important role in shaping this region of grooved terrain. The most recent tectonic episode is interpreted as right-lateral transtension, with its tectonic pattern of two contemporaneous structural orientations superimposed on older units of grooved terrain. There is little direct evidence for

Influence of musical groove on postural sway.

PubMed

Ross, Jessica M; Warlaumont, Anne S; Abney, Drew H; Rigoli, Lillian M; Balasubramaniam, Ramesh

2016-03-01

Timescales of postural fluctuation reflect underlying neuromuscular processes in balance control that are influenced by sensory information and the performance of concurrent cognitive and motor tasks. An open question is how postural fluctuations entrain to complex environmental rhythms, such as in music, which also vary on multiple timescales. Musical groove describes the property of music that encourages auditory-motor synchronization and is used to study voluntary motor entrainment to rhythmic sounds. The influence of groove on balance control mechanisms remains unexplored. We recorded fluctuations in center of pressure (CoP) of standing participants (N = 40) listening to low and high groove music and during quiet stance. We found an effect of musical groove on radial sway variability, with the least amount of variability in the high groove condition. In addition, we observed that groove influenced postural sway entrainment at various temporal scales. For example, with increasing levels of groove, we observed more entrainment to shorter, local timescale rhythmic musical occurrences. In contrast, we observed more entrainment to longer, global timescale features of the music, such as periodicity, with decreasing levels of groove. Finally, musical experience influenced the amount of postural variability and entrainment at local and global timescales. We conclude that groove in music and musical experience can influence the neural mechanisms that govern balance control, and discuss implications of our findings in terms of multiscale sensorimotor coupling. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

A Monofunctional Platinum Complex Coordinated to a Rhodium Metalloinsertor Selectively Binds Mismatched DNA in the Minor Groove

PubMed Central

Weidmann, Alyson G.; Barton, Jacqueline K.

2015-01-01

We report the synthesis and characterization of a bimetallic complex derived from a new family of potent and selective metalloinsertors containing an unusual Rh—O axial coordination. This complex incorporates a monofunctional platinum center containing only one labile site for coordination to DNA, rather than two, and coordinates DNA non-classically through adduct formation in the minor groove. This conjugate displays bifunctional, interdependent binding of mismatched DNA via metalloinsertion at a mismatch as well as covalent platinum binding. DNA sequencing experiments revealed that the preferred site of platinum coordination is not the traditional N7-guanine site in the major groove, but rather N3-adenine in the minor groove. The complex also displays enhanced cytotoxicity in mismatch repair-deficient and mismatch repair-proficient human colorectal carcinoma cell lines compared to the chemotherapeutic cisplatin, and triggers cell death via an apoptotic pathway, rather than the necrotic pathway induced by rhodium metalloinsertors. PMID:26397309

First branchial groove anomaly.

PubMed

Kumar, M; Hickey, S; Joseph, G

2000-06-01

First branchial groove anomalies are very rare. We report a case of a first branchial groove anomaly presented as an infected cyst in an 11-month-old child. Management of such lesions is complicated because of their close association with the facial nerve. Surgical management must include identification and protection of the facial nerve. Embryology and facial nerve disposition in relation to the anomaly are reviewed.

Topography and geologic characteristics of aeolian grooves in the south polar layered deposits of Mars

USGS Publications Warehouse

Bridges, N.T.; Herkenhoff, K. E.

2002-01-01

The topographic and geologic characteristics of grooves and groove-like features in the south polar layered deposits near the Mars Polar Lander/Deep Space 2 landing sites are evaluated using Mariner 9 images and their derived photoclinometry, normalized using Mars Orbiter Laser Altimeter data. Although both Mariner 9 and Viking images of the south polar layered deposits were available at the time of this study, Mariner 9 images of the grooves were selected because they were generally of higher resolution than Viking images. The dimensions and slopes of the grooves, together with orientations that nearly match the strongest winds predicted in the Martian Global Circulation Model and directions inferred from other wind indicators, suggest that they formed by aeolian scour of an easily erodible surface. Most grooves are symmetric and V-shaped in transverse profile, inconsistent with an origin involving extensional brittle deformation. Although the grooves strike along slopes and terraces of the south polar layered deposits, the variable depths and lack of terracing within the grooves themselves indicate that any stratigraphy in the uppermost 100 m of the polar layered deposits is composed of layers of similar, and relatively low, resistance. The grooves do not represent landing hazards at the scale of the Mariner 9 images (72-86 m/pixel) and therefore probably would not have affected Mars Polar Lander and Deep Space 2, had they successfully reached the surface. ?? 2002 Elsevier Science (USA).

Numerical analysis of flow in a centrifugal compressor with circumferential grooves: influence of groove location and number on flow instability

NASA Astrophysics Data System (ADS)

Chen, X.; Qin, G.; Ai, Z.; Ji, Y.

2017-08-01

As an effective and economic method for flow range enhancement, circumferential groove casing treatment (CGCT) is widely used to increase the stall margin of compressors. Different from traditional grooved casing treatments, in which the grooves are always located over the rotor in both axial and radial compressors, one or several circumferential grooves are located along the shroud side of the diffuser passage in this paper. Numerical investigations were conducted to predict the performance of a low flow rate centrifugal compressor with CGCT in diffuser. Computational fluid dynamics (CFD) analysis is performed under stage environment in order to find the optimum location of the circumferential casing groove in consideration of stall margin enhancement and efficiency gain at design point, and the impact of groove number to the effect of this grooved casing treatment configuration in enhancing the stall margin of the compressor stage is studied. The results indicate that the centrifugal compressor with circumferential groove in vaned diffuser can obtain obvious improvement in the stall margin with sacrificing design efficiency a little. Efforts were made to study blade level flow mechanisms to determine how the CGCT impacts the compressor’s stall margin (SM) and performance. The flow structures in the passage, the tip gap, and the grooves as well as their mutual interactions were plotted and analysed.

Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation.

PubMed

Schneider, T D

2001-12-01

The sequence logo for DNA binding sites of the bacteriophage P1 replication protein RepA shows unusually high sequence conservation ( approximately 2 bits) at a minor groove that faces RepA. However, B-form DNA can support only 1 bit of sequence conservation via contacts into the minor groove. The high conservation in RepA sites therefore implies a distorted DNA helix with direct or indirect contacts to the protein. Here I show that a high minor groove conservation signature also appears in sequence logos of sites for other replication origin binding proteins (Rts1, DnaA, P4 alpha, EBNA1, ORC) and promoter binding proteins (sigma(70), sigma(D) factors). This finding implies that DNA binding proteins generally use non-B-form DNA distortion such as base flipping to initiate replication and transcription.

Discovery of Grooves on Gaspra

USGS Publications Warehouse

Veverka, J.; Thomas, P.; Simonelli, D.; Belton, M.J.S.; Carr, M.; Chapman, C.; Davies, M.E.; Greeley, R.; Greenberg, R.; Head, J.; Klaasen, K.; Johnson, T.V.; Morrison, D.; Neukum, G.

1994-01-01

We report the discovery of grooves in Galileo high-resolution images of Gaspra. These features, previously seen only on Mars' satellite Phobos, are most likely related to severe impacts. Grooves on Gaspra occur as linear and pitted depressions, typically 100-200 m wide, 0.8 to 2.5 km long, and 10-20 m deep. Most occur in two major groups, one of which trends approximately parallel to the asteroid's long axis, but is offset by some 15??; the other is approximately perpendicular to this trend. The first of these directions falls along a family of planes which parallel three extensive flat facets identified by Thomas et al., Icarus 107. The occurrence of grooves on Gaspra is consistent with other indications (irregular shape, cratering record) that this asteroid has evolved through a violent collisional history. The bodywide congruence of major groove directions and other structural elements suggests that present-day Gaspra is a globally coherent body. ?? 1994 Academic Press. All rights reserved.

Skinfold thickness at 8 common cryotherapy sites in various athletic populations.

PubMed

Jutte, Lisa S; Hawkins, Jeremy; Miller, Kevin C; Long, Blaine C; Knight, Kenneth L

2012-01-01

Researchers have observed slower cooling rates in thigh muscle with greater overlying adipose tissue, suggesting that cryotherapy duration should be based on the adipose thickness of the treatment site. Skinfold data do not exist for other common cryotherapy sites, and no one has reported how those skinfolds might vary because of physical activity level or sex. To determine the variability in skinfold thickness among common cryotherapy sites relative to sex and activity level (National Collegiate Athletic Association Division I athletes, recreationally active college athletes). Descriptive laboratory study. Field. Three hundred eighty-nine college students participated; 196 Division I athletes (157 men, 39 women) were recruited during preseason physicals, and 193 recreationally active college athletes (108 men, 85 women) were recruited from physical education classes. Three skinfold measurements to within 1 mm were taken at 8 sites (inferior angle of the scapula, middle deltoid, ulnar groove, midforearm, midthigh, medial collateral ligament, midcalf, and anterior talofibular ligament [ATF]) using Lange skinfold calipers. Skinfold thickness in millimeters. We noted interactions among sex, activity level, and skinfold site. Male athletes had smaller skinfold measurements than female athletes at all sites except the ATF, scapula, and ulnar groove (F₇,₂₇₀₂ = 69.85, P < .001). Skinfold measurements were greater for recreationally active athletes than their Division I counterparts at all sites except the ATF, deltoid, and ulnar groove (F₇,₂₇₀₂ = 30.79, P < .001). Thigh skinfold measurements of recreationally active female athletes were the largest, and their ATF skinfolds were the smallest. Skinfold thickness at common cryotherapy treatment sites varied based on level of physical activity and sex. Therefore, clinicians should measure skinfold thickness to determine an appropriate cryotherapy duration.

Skinfold Thickness at 8 Common Cryotherapy Sites in Various Athletic Populations

PubMed Central

Jutte, Lisa S.; Hawkins, Jeremy; Miller, Kevin C.; Long, Blaine C.; Knight, Kenneth L.

2012-01-01

Context: Researchers have observed slower cooling rates in thigh muscle with greater overlying adipose tissue, suggesting that cryotherapy duration should be based on the adipose thickness of the treatment site. Skinfold data do not exist for other common cryotherapy sites, and no one has reported how those skinfolds might vary because of physical activity level or sex. Objective: To determine the variability in skinfold thickness among common cryotherapy sites relative to sex and activity level (National Collegiate Athletic Association Division I athletes, recreationally active college athletes). Design: Descriptive laboratory study. Setting: Field. Patients or Other Participants: Three hundred eighty-nine college students participated; 196 Division I athletes (157 men, 39 women) were recruited during preseason physicals, and 193 recreationally active college athletes (108 men, 85 women) were recruited from physical education classes. Intervention(s): Three skinfold measurements to within 1 mm were taken at 8 sites (inferior angle of the scapula, middle deltoid, ulnar groove, midforearm, midthigh, medial collateral ligament, midcalf, and anterior talofibular ligament [ATF]) using Lange skinfold calipers. Main Outcome Measure(s): Skinfold thickness in millimeters. Results: We noted interactions among sex, activity level, and skinfold site. Male athletes had smaller skinfold measurements than female athletes at all sites except the ATF, scapula, and ulnar groove (F7,2702 = 69.85, P < .001). Skinfold measurements were greater for recreationally active athletes than their Division I counterparts at all sites except the ATF, deltoid, and ulnar groove (F7,2702 = 30.79, P < .001). Thigh skinfold measurements of recreationally active female athletes were the largest, and their ATF skinfolds were the smallest. Conclusions: Skinfold thickness at common cryotherapy treatment sites varied based on level of physical activity and sex. Therefore, clinicians should measure

Synthesis and characterization of DNA minor groove binding alkylating agents.

PubMed

Iyer, Prema; Srinivasan, Ajay; Singh, Sreelekha K; Mascara, Gerard P; Zayitova, Sevara; Sidone, Brian; Fouquerel, Elise; Svilar, David; Sobol, Robert W; Bobola, Michael S; Silber, John R; Gold, Barry

2013-01-18

Derivatives of methyl 3-(1-methyl-5-(1-methyl-5-(propylcarbamoyl)-1H-pyrrol-3-ylcarbamoyl)-1H-pyrrol-3-ylamino)-3-oxopropane-1-sulfonate (1), a peptide-based DNA minor groove binding methylating agent, were synthesized and characterized. In all cases, the N-terminus was appended with an O-methyl sulfonate ester, while the C-terminus group was varied with nonpolar and polar side chains. In addition, the number of pyrrole rings was varied from 2 (dipeptide) to 3 (tripeptide). The ability of the different analogues to efficiently generate N3-methyladenine was demonstrated as was their selectivity for minor groove (N3-methyladenine) versus major groove (N7-methylguanine) methylation. Induced circular dichroism studies were used to measure the DNA equilibrium binding properties of the stable sulfone analogues; the tripeptide binds with affinity that is >10-fold higher than that of the dipeptide. The toxicities of the compounds were evaluated in alkA/tag glycosylase mutant E. coli and in human WT glioma cells and in cells overexpressing and under-expressing N-methylpurine-DNA glycosylase, which excises N3-methyladenine from DNA. The results show that equilibrium binding correlates with the levels of N3-methyladenine produced and cellular toxicity. The toxicity of 1 was inversely related to the expression of MPG in both the bacterial and mammalian cell lines. The enhanced toxicity parallels the reduced activation of PARP and the diminished rate of formation of aldehyde reactive sites observed in the MPG knockdown cells. It is proposed that unrepaired N3-methyladenine is toxic due to its ability to directly block DNA polymerization.

Structural analysis of the binding modes of minor groove ligands comprised of disubstituted benzenes

PubMed Central

Hawkins, Cheryl A.; Watson, Charles; Yan, Yinfa; Gong, Bing; Wemmer, David E.

2001-01-01

Two-dimensional homonuclear NMR was used to characterize synthetic DNA minor groove-binding ligands in complexes with oligonucleotides containing three different A-T binding sites. The three ligands studied have a C2 axis of symmetry and have the same general structural motif of a central para-substituted benzene ring flanked by two meta-substituted rings, giving the molecules a crescent shape. As with other ligands of this shape, specificity seems to arise from a tight fit in the narrow minor groove of the preferred A-T-rich sequences. We found that these ligands slide between binding subsites, behavior attributed to the fact that all of the amide protons in the ligand backbone cannot hydrogen bond to the minor groove simultaneously. PMID:11160926

High Precision 2-D Grating Groove Density Measurement

NASA Astrophysics Data System (ADS)

Zhang, Ningxiao; McEntaffer, Randall; Tedesco, Ross

2017-08-01

Our research group at Penn State University is working on producing X-ray reflection gratings with high spectral resolving power and high diffraction efficiency. To estimate our fabrication accuracy, we apply a precise 2-D grating groove density measurement to plot groove density distributions of gratings on 6-inch wafers. In addition to plotting a fixed groove density distribution, this method is also sensitive to measuring the variation of the groove density simultaneously. This system can reach a measuring accuracy (ΔN/N) of 10-3. Here we present this groove density measurement and some applications.

Formation Mechanisms for Spur and Groove Features on Fringing Reefs

NASA Astrophysics Data System (ADS)

Bramante, J. F.; Ashton, A. D.; Perron, J. T.

2016-12-01

Spur and groove systems (SAGs) are ubiquitous morphological features found on fore-reef slopes globally. SAGs consist of parallel, roughly shore-normal ridges of actively growing coral and coralline algae (spurs) separated by offshore-sloping depressions typically carpeted by a veneer of sediment (grooves). Although anecdotal observations and recent statistical analyses have reported correlations between wave exposure and the distribution of SAGs on fore-reef slopes, the physical mechanisms driving SAG formation remain poorly understood. For example, there remains significant debate regarding the importance of coral growth versus bed erosion for SAG formation. Here we investigate a hypothesis that SAG formation is controlled by feedbacks between sediment production and diffusion and coral growth. Using linear stability analysis, we find that sediment production, coral growth, and the feedbacks between them are unable to produce stable periodic structures without a sediment sink. However, if incipient grooves act as conduits for sediment transport offshore, a positive feedback can develop as the groove bed erodes through wave-driven abrasion during offshore transport. Eventually a negative feedback slows groove deepening when the groove bed is armored by sediment, and the groove bed relaxes to a sediment-veneered equilibrium profile analogous to sediment-rich shorefaces. To test this hypothesis, we apply a numerical model that incorporates coral growth and sediment production, sediment diffusion, non-linear wave-driven abrasion, and sediment advection offshore. This model produces the periodic, linear features characteristic of SAG morphology. The relative magnitude of growth, production, diffusion, abrasion, and advection rates affect periodic spacing or wavelength of the modeled SAGs. Finally, we evaluate the ability of the model to replicate geographical variability in SAG characteristics using previously published datasets and reanalysis wave data.

Droplet impact on regular micro-grooved surfaces

NASA Astrophysics Data System (ADS)

Hu, Hai-Bao; Huang, Su-He; Chen, Li-Bin

2013-08-01

We have investigated experimentally the process of a droplet impact on a regular micro-grooved surface. The target surfaces are patterned such that micro-scale spokes radiate from the center, concentric circles, and parallel lines on the polishing copper plate, using Quasi-LIGA molding technology. The dynamic behavior of water droplets impacting on these structured surfaces is examined using a high-speed camera, including the drop impact processes, the maximum spreading diameters, and the lengths and numbers of fingers at different values of Weber number. Experimental results validate that the spreading processes are arrested on all target surfaces at low velocity. Also, the experimental results at higher impact velocity demonstrate that the spreading process is conducted on the surface parallel to the micro-grooves, but is arrested in the direction perpendicular to the micro-grooves. Besides, the lengths of fingers increase observably, even when they are ejected out as tiny droplets along the groove direction, at the same time the drop recoil velocity is reduced by micro-grooves which are parallel to the spreading direction, but not by micro-grooves which are vertical to the spreading direction.

Tharsis Grooved Channel

NASA Image and Video Library

2002-12-04

The Tharsis Montes region on Mars is a major center of volcanic and tectonic activity. The channel in this image from NASA Mars Odyssey is west of the relatively small volcano called Biblis Patera although it shows no obvious relationship to that volcano. Instead, it may be related to the more distant, but more massive volcano Olympus Mons to the north. The channel may have hosted flowing lava at one time but now contains a material that has eroded into an impressive ridge-and-groove pattern. These features may be yardangs, landforms produced from the erosion by wind of sedimentary material. http://photojournal.jpl.nasa.gov/catalog/PIA04020

Effect of sonic and ultrasonic activation on organic tissue dissolution from simulated grooves in root canals using sodium hypochlorite and EDTA.

PubMed

Conde, A J; Estevez, R; Loroño, G; Valencia de Pablo, Ó; Rossi-Fedele, G; Cisneros, R

2017-10-01

To compare soft-tissue dissolution by sodium hypochlorite, with an EDTA intermediate rinse, with or without activation with passive ultrasonic activation (PUI) or sonic activation using the Endoactivator (EA) or Eddy tips (ED). The root canals of eighty-three human maxillary central incisors were chemo-mechanically prepared and the teeth split. A standardized longitudinal intracanal groove was created in one of the root halves. Eighty-three porcine palatal mucosa samples were collected, adapted to fit into the grooves and weighed. The re-assembled specimens were randomly divided into four experimental groups (n = 20), based on the final rinse: no activation; EA; PUI; ED, using 2.5% sodium hypochlorite, with an EDTA intermediate rinse. A control group (n = 3) was irrigated with distilled water without activation. The solutions were delivered using a syringe and needle 2 mm from working length. Total irrigation time was 150 s, including 60 s of activation in the specific groups. The study was carried out at 36 ± 2 °C. The porcine palatal mucosa samples were weighed after completion of the assays. Student paired t-test and anova were used to assess the intra- and intergroup weight changes. The multiple comparisons were evaluated using Bonferroni correction (α = 0.05). Weight loss occurred in all experimental groups. Irrigant activation resulted in greater weight loss when compared to the nonactivated group [vs. EA (P = 0.001); vs. PUI (P < 0.001); vs. ED (P < 0.001)]. No significant differences were found amongst the different activation systems. Activation increased the tissue-dissolving activity of irrigants from artificial grooves in root canals of maxillary central incisors. © 2016 International Endodontic Journal. Published by John Wiley & Sons Ltd.

Double-grooved nanofibre surfaces with enhanced anisotropic hydrophobicity.

PubMed

Liang, Meimei; Chen, Xin; Xu, Yang; Zhu, Lei; Jin, Xiangyu; Huang, Chen

2017-11-02

This study reports a facile method for fabricating double-grooved fibrous surfaces. The primary grooves of the surface are formed by aligned fibres, while the secondary grooves are achieved by oriented nanogrooves on the fibre surface. Investigation into the formation mechanism reveals that the nanogrooves can be readily tailored through adjusting the solvent ratio and relative humidity. With this understanding, a variety of polymers have been successfully electrospun into fibres having the same nanogrooved feature. These fibres show high resemblance to natural hierarchical structures, and thereby endowing the corresponding double-grooved surface with enhanced anisotropic hydrophobicity. A water droplet at a parallel direction to the grooves exhibits a much higher contact angle and a lower roll-off angle than the droplet at a perpendicular direction. The application potential of such anisotropic hydrophobicity has been demonstrated via a fog collection experiment, in which the double-grooved surface can harvest the largest amount of water. Moreover, the fabrication method requires neither post-treatment nor sophisticated equipment, making us anticipate that the double-grooved surface would be competitive in areas where a highly ordered surface, a large surface area and an anisotropic hydrophobicity are preferred.

Solar cell with doped groove regions separated by ridges

DOEpatents

Molesa, Steven Edward; Pass, Thomas; Kraft, Steve

2017-01-31

Solar cells with doped groove regions separated by ridges and methods of fabricating solar cells are described. In an example, a solar cell includes a substrate having a surface with a plurality of grooves and ridges. A first doped region of a first conductivity type is disposed in a first of the grooves. A second doped region of a second conductivity type, opposite the first conductivity type, is disposed in a second of the grooves. The first and second grooves are separated by one of the ridges.

DRhoGEF2 and Diaphanous Regulate Contractile Force during Segmental Groove Morphogenesis in the Drosophila Embryo

PubMed Central

Mulinari, Shai; Barmchi, Mojgan Padash

2008-01-01

Morphogenesis of the Drosophila embryo is associated with dynamic rearrangement of the actin cytoskeleton mediated by small GTPases of the Rho family. These GTPases act as molecular switches that are activated by guanine nucleotide exchange factors. One of these factors, DRhoGEF2, plays an important role in the constriction of actin filaments during pole cell formation, blastoderm cellularization, and invagination of the germ layers. Here, we show that DRhoGEF2 is equally important during morphogenesis of segmental grooves, which become apparent as tissue infoldings during mid-embryogenesis. Examination of DRhoGEF2-mutant embryos indicates a role for DRhoGEF2 in the control of cell shape changes during segmental groove morphogenesis. Overexpression of DRhoGEF2 in the ectoderm recruits myosin II to the cell cortex and induces cell contraction. At groove regression, DRhoGEF2 is enriched in cells posterior to the groove that undergo apical constriction, indicating that groove regression is an active process. We further show that the Formin Diaphanous is required for groove formation and strengthens cell junctions in the epidermis. Morphological analysis suggests that Dia regulates cell shape in a way distinct from DRhoGEF2. We propose that DRhoGEF2 acts through Rho1 to regulate acto-myosin constriction but not Diaphanous-mediated F-actin nucleation during segmental groove morphogenesis. PMID:18287521

Transmission characteristics of a subwavelength metallic slit with perpendicular groove

NASA Astrophysics Data System (ADS)

Jin, Li; Zhou, Jun; Zou, Weibo; Zhang, Haopeng; Zhang, Lingfen

2011-12-01

The transmission property of a subwavelength metallic slit with perpendicular groove is investigated by using finite element method. The lengths for the slits at both sides of the groove are set as the length of a metallic slit without groove at the surface plasmon fundamental mode resonance. In the grooved subwavelength metallic slit, enhanced transmission is found to be attributed to two kinds of resonance including surface plasmon waveguide resonance along the propagating direction and the transversely constructive interferential resonance. For the former resonance, integer antinodes of surface plasmon are formed in the groove. For the later resonance, there is a tradeoff between the maximum amplitude and the full width at half maximum of the transmitted peaks with the change of the groove width. And, the transmission enhancement of the grooved subwavelength metallic slit is related to the number of groove and the incident wavelength. Furthermore, the above resonances also exist in the structure whose lengths of metallic slits are set as the length of a slit without groove at the surface plasmon high-order mode resonance. By optimizing the geometric parameters, the transmission enhancement of the grooved subwavelength metallic slit as high as about 15367% is achieved.

Axially grooved heat pipe study

NASA Technical Reports Server (NTRS)

1977-01-01

A technology evaluation study on axially grooved heat pipes is presented. The state-of-the-art is reviewed and present and future requirements are identified. Analytical models, the Groove Analysis Program (GAP) and a closed form solution, were developed to facilitate parametric performance evaluations. GAP provides a numerical solution of the differential equations which govern the hydrodynamic flow. The model accounts for liquid recession, liquid/vapor shear interaction, puddle flow as well as laminar and turbulent vapor flow conditions. The closed form solution was developed to reduce computation time and complexity in parametric evaluations. It is applicable to laminar and ideal charge conditions, liquid/vapor shear interaction, and an empirical liquid flow factor which accounts for groove geometry and liquid recession effects. The validity of the closed form solution is verified by comparison with GAP predictions and measured data.

Micrometer for Measuring Trepanned Grooves

NASA Technical Reports Server (NTRS)

Bird, S. K.

1983-01-01

Special micrometer measures diameter of circular groove on face of large part, while part is mounted in lathe chuck. Tool has curved frame so it can reach around obstruction on centerline of part. At one end of frame is blade/ micrometer spindle for reaching into groove to be measured; this type of spindle does not rotate when micrometer thimble is turned in taking measurement. Other end of frame has sliding foot with blade.

Large Grooves in the South Polar Layered Deposits: Insights from Spacecraft Data and Terrestrial Analogs

NASA Technical Reports Server (NTRS)

Bridges, N. T.; Herkenhoff, K. E.

2000-01-01

The Martian polar layered deposits (PLD) are probably the best source of information about the recent climate history of Mars, but their origin and the mechanisms of accumulation are still a mystery. The polar layers are sedimentary deposits that most planetary scientists believe are composed of water ice and varying amounts of wind-blown dust, although their composition is poorly constrained. Interpretation of the observed polar stratigraphy in terms of global climate changes is complicated by the significant difference in surface ages between the north and south PLD inferred from crater statistics. The study reported here was undertaken as part of the landing site selection effort for the Mars Polar Lander (MPL) and Deep Space 2 (DS2) missions that made use of all available data. We used Mariner 9, Viking, and Mars Global Surveyor images of the south PLD in the area accessible to MPL and DS2 to evaluate the topography and morphology of grooves, terraced layers, and other features. Here we report on results from grooves that appear to have been carved by strong winds. Because these features are found throughout the interior of the PLD, where MPL and DS2 were targeted to land, their topographic characteristics were judged as important input for landing site safety assessment. The characteristics of the grooves also provide constraints and insights into aeolian processes in the polar regions and the effects these have on PLD ablation. Our results indicate that these grooves do not represent landing hazards at the scale of the images (approx. 80 m/pixel). Their topography and shape do not seem correlated with south PLD layering. No Earth analog of suitable scale exists, although the grooves bear some resemblance to smaller terrestrial deflation hollows found in soft sediment and ice. Additional information is contained in original extended abstract.

Spectral analysis of groove spacing on Ganymede

NASA Technical Reports Server (NTRS)

Grimm, R. E.

1984-01-01

The technique used to analyze groove spacing on Ganymede is presented. Data from Voyager images are used determine the surface topography and position of the grooves. Power spectal estimates are statistically analyzed and sample data is included.

Miranda - 'Chevron' Grooves

NASA Technical Reports Server (NTRS)

1986-01-01

This image of Miranda, obtained by Voyager 2 on approach, shows an unusual 'chevron' figure and regions of distinctly differing terrain on the Uranian moon. Voyager was 42,000 kilometers (26,000 miles) away when its narrow-angle camera acquired this clear-filter view. Grooved areas baring light and dark bands, distinct from other areas of mottled terrain, are visible at this resolution of about 600 meters (2,000 feet). The bright V-shaped feature in the grooved areas is the 'chevron' observed in earlier, lower-resolution images. Cutting across the bands are sinuous scarps, probably faults. Superimposed on both types of terrain are many bowl-shaped impact craters less than 5 km (3 mi) wide. The entire picture spans an area about 220 km (140 mi) across. The Voyager project is managed for NASA by the Jet Propulsion Laboratory.

Resistance of full veneer metal crowns with different forms of axial grooves

NASA Astrophysics Data System (ADS)

Hidayat, A. S.; Masulili, C.; Indrasari, M.

2017-08-01

Dental crowns or bridges can occasionally come loose or separate from the tooth during chewing, particularly when they are situated on small, short, and conical teeth. The main cause of this separation is a lack of retention and resistance to the tooth. There are several methods available to increase the retention and resistance of the crown during both inlay and onlay preparation, including parallelism, groove preparation, crown build-up, and surface roughness. The aim of this study was to determine the differences in resistance of full veneer metal crowns with various forms of groove preparation. The study involved the compressive strength testing of a total of 24 specimens, namely six specimens without groove preparation, six specimens with box-shaped grooves, six specimens with V-shaped grooves, and six specimens with half round grooves. The mean values of the metal crowns that separated from the teeth during testing were 27.97 ± 1.08 kgF for the crowns with box-shaped grooves, 6.15 ± 0.22 kgF for those with V-shaped grooves, 1.77 ± 0.12 kgF for those with half round grooves, and 0.95 ± 0.13 kgF for those without grooves. This study found that the resistance is best in crowns with box-shaped grooves, followed by those with V-shaped grooves, half round grooves, and those without groove. When clinicians are working on short and conical molar teeth, it is therefore recommended that box-shaped grooves are used to increase the resistance of the crown.

Functional specificity of a Hox protein mediated by the recognition of minor groove structure.

PubMed

Joshi, Rohit; Passner, Jonathan M; Rohs, Remo; Jain, Rinku; Sosinsky, Alona; Crickmore, Michael A; Jacob, Vinitha; Aggarwal, Aneel K; Honig, Barry; Mann, Richard S

2007-11-02

The recognition of specific DNA-binding sites by transcription factors is a critical yet poorly understood step in the control of gene expression. Members of the Hox family of transcription factors bind DNA by making nearly identical major groove contacts via the recognition helices of their homeodomains. In vivo specificity, however, often depends on extended and unstructured regions that link Hox homeodomains to a DNA-bound cofactor, Extradenticle (Exd). Using a combination of structure determination, computational analysis, and in vitro and in vivo assays, we show that Hox proteins recognize specific Hox-Exd binding sites via residues located in these extended regions that insert into the minor groove but only when presented with the correct DNA sequence. Our results suggest that these residues, which are conserved in a paralog-specific manner, confer specificity by recognizing a sequence-dependent DNA structure instead of directly reading a specific DNA sequence.

Realizing structural color generation with aluminum plasmonic V-groove metasurfaces

DOE PAGES

Wang, Wei; Rosenmann, Daniel; Czaplewski, David A.; ...

2017-08-14

The structural color printing based on all-aluminum plasmonic V-groove metasurfaces is demonstrated under both bright field and dark field illumination conditions. A broad visible color range is realized with the plasmonic V-groove arrays etched on aluminum surface by simply varying the groove depth while keeping the groove period as a constant. Polarization dependent structural color printing is further achieved with interlaced V-groove arrays along both the horizontal and vertical directions. Furthermore, these results pave the way towards the use of all-aluminum structural color printing platform for many practical applications such as security marking and information storage.

Realizing structural color generation with aluminum plasmonic V-groove metasurfaces

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

Wang, Wei; Rosenmann, Daniel; Czaplewski, David A.

The structural color printing based on all-aluminum plasmonic V-groove metasurfaces is demonstrated under both bright field and dark field illumination conditions. A broad visible color range is realized with the plasmonic V-groove arrays etched on aluminum surface by simply varying the groove depth while keeping the groove period as a constant. Polarization dependent structural color printing is further achieved with interlaced V-groove arrays along both the horizontal and vertical directions. Furthermore, these results pave the way towards the use of all-aluminum structural color printing platform for many practical applications such as security marking and information storage.

Spiral groove seal. [for rotating shaft

NASA Technical Reports Server (NTRS)

Ludwig, L. P.; Strom, T. N. (Inventor)

1974-01-01

Mating flat surfaces inhibit leakage of a fluid around a stationary shaft. A spiral groove produces a pumping action toward the fluid when the shaft rotates. This prevents leakage while a generated hydraulic lifting force separates the mating surfaces to minimize wear. Provision is made for placing these spiral grooves in communication with the fluid to accelerate the generation of the hydraulic lifting force.

Plasma interaction with emmissive surface with Debye-scale grooves

NASA Astrophysics Data System (ADS)

Schweigert, Irina; Burton, Thomas S.; Thompson, Gregory B.; Langendorf, Samuel; Walker, Mitchell L. R.; Keidar, Michael

2018-04-01

The sheath development over emissive grooved surface in dc discharge plasma controlled by an electron beam is studied in the experiment and in 2D kinetic simulations. Grooved hexagonal boron nitride surfaces with different aspect ratios, designed to mimic the erosion channels, were exposed to an argon plasma. The characteristic size of the grooves (1 mm and 5 mm) is about of the Debye length. The secondary electrons emission from the grooved surfaces is provided by the bombardment with energetic electrons originated from the heated powered cathode. The transition between a developed and a collapsed sheaths near emissive surface takes place with an increase of the beam electron energy. For grooved emissive surfaces, the sheath transition happens at essentially higher voltage compared to the planar one. This phenomenon is analyzed in the terms of the electron energy distribution function.

Femtosecond laser-induced blazed periodic grooves on metals.

PubMed

Hwang, Taek Yong; Guo, Chunlei

2011-07-01

In this Letter, we generate laser-induced periodic surface structures (LIPSSs) on platinum following femtosecond laser pulse irradiation. For the first time to our knowledge, we study the morphological profile of LIPSSs over a broad incident angular range, and find that the morphological profile of LIPSSs depends significantly on the incident angle of the laser beam. We show that LIPSS grooves become more asymmetric at a larger incident angle, and the morphological profile of LIPSSs formed at an incident angle over 55° eventually resembles that of a blazed grating. Our study suggests that the formation of the blazed groove structures is attributed to the selective ablation of grooves through the asymmetric periodic surface heating following femtosecond pulse irradiation. The blazed grooves are useful for controlling the diffraction efficiency of LIPSSs.

The Formation of Ganymede's Grooved Terrain: Importance of Strain Weakening

NASA Astrophysics Data System (ADS)

Bland, M. T.; McKinnon, W. B.; Showman, A. P.

2008-12-01

Nearly two-thirds of Ganymede's surface consists of relatively bright, young, tectonically deformed terrain dubbed grooved terrain. The grooved terrain consists of sets of parallel, undulatory ridges and troughs with peak to trough amplitudes of several hundred meters and periodic spacings that range from 3 to 10~km. The low slopes and periodic spacing of the grooves suggest that they formed via unstable extension of the ice lithosphere [e.g. Fink and Fletcher 1981, LPS XII; Pappalardo et al. 1998, Icarus 135]. Application of analytical models of unstable extension to Ganymede suggest that large amplitude grooves with appropriate wavelengths can form if the lithosphere is in pervasive brittle failure and if the lithospheric thermal gradient was relatively high (~45K km-1) [Dombard and McKinnon 2001, Icarus 154]; however, numerical models of unstable extension struggle to produce topographic amplitudes consistent with Ganymede's grooves (maximum amplitudes are a factor of five less than typical large amplitude grooves) [Bland and Showman 2007, Icarus 189]. The difficulties in producing large amplitude deformation may be overcome by the inclusion of strain weakening in models of groove formation. Strain weakening effects account for a material's tendency to strain more easily as viscous and/or plastic deformation accumulates, and as strain localizes in shear zones or along faults. When included in models of terrestrial extension, such effects can increase deformation amplitudes by up to several orders of magnitude [e.g. Fredericksen and Braun 2001, EPSL 188; Behn et al. 2002, EPSL 202]. Here we present the results of simulations of Ganymede's groove formation that include various strain weakening processes. Incorporation of a simple damage rheology, in which the yield strength of the ice lithosphere decreases as plastic strain accumulates, permits a factor of three increase in the amplitude of the simulated grooves, generating topography of 200~m or more. Such groove

Experimental investigation of turbulent flow in smooth and longitudinal grooved tubes

NASA Technical Reports Server (NTRS)

Nitschke, P.

1984-01-01

Turbulent flow in tubes with and without longitudinal grooves is examined. The discovery of fine grooves forming a sort of streamline pattern on the body of sharks led to the expectation that the grooves on a surface reduce the momentum change, and thus the drag. To test this thesis, drag law, velocity profile and the profile of the velocity fluctuation were determined. Results show that for moderate Reynolds numbers the drag coefficient for grooved tubes is about 3 percent smaller than that of the smooth tubes. At higher Reynolds numbers, however, the drag coefficient for grooved tubes becomes larger than that for smooth tubes. No significant differences in the velocity profiles between grooved tubes and smooth tubes are found.

Flow visualization study of grooved surface/surfactant/air sheet interaction

NASA Technical Reports Server (NTRS)

Reed, Jason C.; Weinstein, Leonard M.

1989-01-01

The effects of groove geometry, surfactants, and airflow rate have been ascertained by a flow-visualization study of grooved-surface models which addresses the possible conditions for skin friction-reduction in marine vehicles. It is found that the grooved surface geometry holds the injected bubble stream near the wall and, in some cases, results in a 'tube' of air which remains attached to the wall. It is noted that groove dimension and the use of surfactants can substantially affect the stability of this air tube; deeper grooves, surfactants with high contact angles, and angled air injection, are all found to increase the stability of the attached air tube, while convected disturbances and high shear increase interfacial instability.

Reducing Water/Hull Drag By Injecting Air Into Grooves

NASA Technical Reports Server (NTRS)

Reed, Jason C.; Bushnell, Dennis M.; Weinstein, Leonard M.

1991-01-01

Proposed technique for reduction of friction drag on hydrodynamic body involves use of grooves and combinations of surfactants to control motion of layer on surface of such body. Surface contains many rows of side-by-side, evenly spaced, longitudinal grooves. Dimensions of grooves and sharpnesses of tips in specific case depends on conditions of flow about vessel. Requires much less air than does microbubble-injection method.

Static and dynamic characteristics of parallel-grooved seals

NASA Technical Reports Server (NTRS)

Iwatsubo, Takuzo; Yang, Bo-Suk; Ibaraki, Ryuji

1987-01-01

Presented is an analytical method to determine static and dynamic characteristics of annular parallel-grooved seals. The governing equations were derived by using the turbulent lubrication theory based on the law of fluid friction. Linear zero- and first-order perturbation equations of the governing equations were developed, and these equations were analytically investigated to obtain the reaction force of the seals. An analysis is presented that calculates the leakage flow rate, the torque loss, and the rotordynamic coefficients for parallel-grooved seals. To demonstrate this analysis, we show the effect of changing number of stages, land and groove width, and inlet swirl on stability of the boiler feed water pump seals. Generally, as the number of stages increased or the grooves became wider, the leakage flow rate and rotor-dynamic coefficients decreased and the torque loss increased.

Grooved Fuel Rings for Nuclear Thermal Rocket Engines

NASA Technical Reports Server (NTRS)

Emrich, William

2009-01-01

An alternative design concept for nuclear thermal rocket engines for interplanetary spacecraft calls for the use of grooved-ring fuel elements. Beyond spacecraft rocket engines, this concept also has potential for the design of terrestrial and spacecraft nuclear electric-power plants. The grooved ring fuel design attempts to retain the best features of the particle bed fuel element while eliminating most of its design deficiencies. In the grooved ring design, the hydrogen propellant enters the fuel element in a manner similar to that of the Particle Bed Reactor (PBR) fuel element.

Grooved Terrain on Ganymede: A Galileo-based Synthesis

NASA Technical Reports Server (NTRS)

Pappalardo, Robert T.; Collins, Geoffrey C.; Head, James W.; Moore, Jeffrey M.; Schenk, Paul M.

2003-01-01

Swaths of bright "grooved terrain" (sulci) on Ganymede are 10s to 100s of kilometers wide and cross-cut the older dark terrain, forming an intricate patchwork across 2/3 of Ganymede's surface. The view of grooved terrain developed from Voyager images is that bright cells are broad graben infilled by extrusion of relatively clean (silicate-poor) liquid water, warm ice, or icy slush, and then extended and faulted. Galileo imaging has greatly improved understanding of the emplacement history and geological implications of grooved terrain, supporting a rift-like model for its formation.

The influence of mixture composition, adhesion promotor and compaction degree on the groove stability of grooved Marshall asphalt

NASA Astrophysics Data System (ADS)

Vuye, Cedric; Couscheir, Karolien; Lauriks, Leen; Van den bergh, Wim; Van Bouwel, Philippe

2017-09-01

After the first rehabilitation of runway 07R/25L in 2015, runway 01/19 was reconstructed in the summer of 2016, as part of a cycle where all runway pavements at Brussels airport are completely renovated each thirty years. The top layer is a Marshall asphalt with a polymer modified bitumen. To optimize the water drainage the central part of the runway (47 m wide) is grooved instead of applying an anti-skid layer. In this paper the focus is on the durability of the grooved top layer. Two different Marshall asphalt mixtures with a different maximum granulate size (10 mm or 14 mm) are compared, both in the laboratory and in a full-scale trial. In the laboratory the resistance against rutting and raveling are investigated for both mixtures with and without adhesion promotor, which did not show a positive effect. In the full-scale trial the compactability and impact of both a longer curing period and a variation in the degree of compaction on the groove stability is investigated for both mixtures using a heavy truck. No visual differences could be found except in areas which were undercompacted and showed more damage to the grooves.

Rear-side picosecond laser ablation of indium tin oxide micro-grooves

NASA Astrophysics Data System (ADS)

Liu, Peng; Wang, Wenjun; Mei, Xuesong; Liu, Bin; Zhao, Wanqin

2015-06-01

A comparative study of the fabrication of micro-grooves in indium tin oxide films by picosecond laser ablation for application in thin film solar cells is presented, evaluating the variation of different process parameters. Compared with traditional front-side ablation, rear-side ablation results in thinner grooves with varying laser power at a certain scan speed. In particular, and in contrast to front-side ablation, the width of the micro-grooves remains unchanged when the scan speed was changed. Thus, the micro-groove quality can be optimized by adjusting the scan speed while the groove width would not be affected. Furthermore, high-quality micro-grooves with ripple free surfaces and steep sidewalls could only be achieved when applying rear-side ablation. Finally, the formation mechanism of micro-cracks on the groove rims during rear-side ablation is analyzed and the cracks can be almost entirely eliminated by an optimization of the scan speed.

Polymer Scaffolds with Preferential Parallel Grooves Enhance Nerve Regeneration

PubMed Central

Mobasseri, Atefeh; Faroni, Alessandro; Minogue, Ben M.; Downes, Sandra; Reid, Adam J.

2015-01-01

We have modified the surface topography of poly ɛ-caprolactone (PCL) and polylactic acid (PLA) blended films to improve cell proliferation and to guide the regeneration of peripheral nerves. Films with differing shaped grooves were made using patterned silicon templates, sloped walls (SL), V-shaped (V), and square-shaped (SQ), and compared with nongrooved surfaces with micropits. The solvent cast films were tested in vitro using adult adipose-derived stem cells differentiated to Schwann cell-like cells. Cell attachment, proliferation, and cell orientation were all improved on the grooved surfaces, with SL grooves giving the best results. We present in vivo data on Sprague-Dawley rat sciatic nerve injury with a 10-mm gap, evaluating nerve regeneration at 3 weeks across a polymer nerve conduit modified with intraluminal grooves (SL, V, and SQ) and differing wall thicknesses (70, 100, 120, and 210 μm). The SL-grooved nerve conduit showed a significant improvement over the other topographical-shaped grooves, while increasing the conduit wall thickness saw no positive effect on the biological response of the regenerating nerve. Furthermore, the preferred SL-grooved conduit (C) with 70 μm wall thickness was compared with the current clinical gold standard of autologous nerve graft (Ag) in the rat 10-mm sciatic nerve gap model. At 3 weeks postsurgery, all nerve gaps across both groups were bridged with regenerated nerve fibers. At 16 weeks, features of regenerated axons were comparable between the autograft (Ag) and conduit (C) groups. End organ assessments of muscle weight, electromyography, and skin reinnervation were also similar between the groups. The comparable experimental outcome between conduit and autograft, suggests that the PCL/PLA conduit with inner lumen microstructured grooves could be used as a potential alternative treatment for peripheral nerve repair. PMID:25435096

Fibroblast adhesion and activation onto micro-machined titanium surfaces.

PubMed

Guillem-Marti, J; Delgado, L; Godoy-Gallardo, M; Pegueroles, M; Herrero, M; Gil, F J

2013-07-01

Surface modifications performed at the neck of dental implants, in the manner of micro-grooved surfaces, can reduce fibrous tissue encapsulation and prevent bacterial colonization, thereby improving fibrointegration and the formation of a biological seal. However, the applied procedures are technically complex and/or time consuming methods. The aim of this study was to analyse the fibroblast behaviour on modified titanium surfaces obtained, applying a simple and low-cost method. An array of titanium surfaces was obtained using a commercial computerized numerical control lathe, modifying the feed rate and the cutting depth. To elucidate the potential ability of the generated surfaces to activate connective tissue cells, a thorough gene (by real time - qPCR) and protein (by western blot or zymography) expression and cellular response characterization (cell morphology, cell adhesion and cell activation by secreting extracellular matrix (ECM) components and their enzyme regulators) was performed. Micro-grooved surfaces have statistically significant differences in the groove's width (approximately 10, 50 and 100 μm) depending on the applied advancing fixed speed. Field emission scanning electron microscopy images showed that fibroblasts oriented along the generated grooves, but they were only entirely accommodated on the wider grooves (≥50 μm). Micro-grooved surfaces exhibited an earlier cell attachment and activation, as seen by collagen Iα1 and fibronectin deposition and activation of ECM remodelling enzymes, compared with the other surfaces. However, fibroblasts could remain in an activated state on narrower surfaces (<50 μm) at later stages. The use of micro-grooved surfaces could improve implant integration at the gingival site with respect to polished surfaces. Micro-grooved surfaces enhance early fibroblast adhesion and activation, which could be critical for the formation of a biological seal and finally promote tissue integration. Surfaces with wider

Effectiveness of transverse grooves in rigid pavement

NASA Astrophysics Data System (ADS)

Gurney, G. F.; Bryden, J. E.

1982-10-01

Transverse grooves were installed at 11 intersection approaches on worn rigid pavement to reduce a high rate of wet road accidents. In most cases, accident reductions were experienced only at intersections with multiple negative operational characteristics, including higher approach speeds, limited sight distances, and frequent vehicle stopping for turns or stop signs. Intersections with no more than one negative characteristic generally did not benefit from grooving.

Evaporator film coefficients of grooved heat pipes

NASA Technical Reports Server (NTRS)

Kamotani, Y.

1978-01-01

The heat transfer rate in the meniscus attachment region of a grooved heat pipe evaporator is studied theoretically. The analysis shows that the evaporation takes place mainly in the region where the liquid changes its shape sharply. However, comparisons with available heat transfer data indicate that the heat transfer rate in the meniscus varying region is substantially reduced probably due to groove wall surface roughness.

Simulation of multipactor on the rectangular grooved dielectric surface

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

Cai, Libing; Wang, Jianguo, E-mail: wanguiuc@mail.xjtu.edu.cn; Northwest Institute of Nuclear Technology, Xi'an, Shaanxi 710024

2015-11-15

Multipactor discharge on the rectangular grooved dielectric surface is simulated self-consistently by using a two-and-a-half dimensional (2.5 D) electrostatic particle-in-cell (PIC) code. Compared with the electromagnetic PIC code, the former can give much more accurate solution for the space charge field caused by the multipactor electrons and the deposited surface charge. According to the rectangular groove width and height, the multipactor can be divided into four models, the spatial distributions of the multipactor electrons and the space charge fields are presented for these models. It shows that the rectangular groove in different models gives very different suppression effect on themore » multipactor, effective and efficient suppression on the multipactor can only be reached with a proper groove size.« less

Laser window with annular grooves for thermal isolation

DOEpatents

Warner, B.E.; Horton, J.A.; Alger, T.W.

1983-07-13

A laser window or other optical element which is thermally loaded, heats up and causes optical distortions because of temperature gradients between the center and the edge. A number of annular grooves, one to three or more, are formed in the element between a central portion and edge portion, producing a web portion which concentrates the thermal gradient and thermally isolates the central portion from the edge portion, producing a uniform temperature profile across the central portion and therefore reduce the optical distortions. The grooves are narrow and closely spaced with respect to the thickness of the element, and successive grooves are formed from alternate sides of the element.

Grooved Armor Plate

DTIC Science & Technology

1935-05-16

that many of the olateo tested do sux^ ass the reouired limita by a considerable margin. Therefore, the efficiency of these grooved plate...Plpte Thicknesn B>lll<tle .Llji^f - ./.. s... a’ ^ea:: of All RtSUltS !’ Teen of Rlgbeot lOf of All Reoultr. s/i«- 1830 an« 7/16" ?180

Topography and Albedo Image of Grooved Terrain on Vesta

NASA Image and Video Library

2011-11-29

These images from NASA Dawn spacecraft show part of the grooved terrain in asteroid Vesta Pinaria quadrangle, which is in the southern hemisphere. Large-scale grooves and depressions can be seen running diagonally across the image.

Presence of a groove in the lateral wall of the human orbit.

PubMed Central

Santo Neto, H; Penteado, C V; de Carvalho, V C

1984-01-01

The presence of a groove in the lateral wall of the human orbit (Royle, 1973) was found in 45 of 100 orbits examined (45%). In 15 skulls the groove was present bilaterally. The groove probably lodges an anastomosis between the middle meningeal and infraorbital blood vessels. No reference to this groove was found in general anatomical texts. Images Fig. 1 PMID:6746401

Effect of Passive Ultrasonic Activation on Organic Tissue Dissolution from Simulated Grooves in Root Canals Using Sodium Hypochlorite with or without Surfactants and EDTA.

PubMed

Estevez, Roberto; Conde, Antonio J; Valencia de Pablo, Oliver; de la Torre, Francisco; Rossi-Fedele, Giampiero; Cisneros, Rafael

2017-07-01

The aim of this study was to evaluate the porcine palatal mucosa dissolution from artificial grooves using a final rinse with sodium hypochlorite (NaOCl) with or without a surfactant or ultrasonic activation (PUI). The root canals of 130 human maxillary central incisors were chemomechanically prepared and the teeth split. A standardized longitudinal intracanal groove was created in 1 of the root halves. One hundred thirty porcine palatal mucosa samples were collected, adapted in order to fit into the grooves, and weighed. The reassembled specimens were randomly divided in 3 experimental groups (n = 40) based on their irrigation protocol (ie, positive pressure [PP] and PUI during 15 [PUI-15] or 30 seconds [PUI-30]) and divided in subgroups according to the NaOCl preparation used: Vista 6% plain (Vista Dental Products, Racine, WI) or Chlor-XTRA (Vista Dental Products) (containing surfactant). An EDTA intermediate rinse was included. Palatal mucosa weights were measured after the assays. The intergroup weight changes were statistically analyzed. Complete dissolution did not occur in any sample. Chlor-XTRA subgroups were associated with increased weight reduction compared with Vista 6% plain subgroups; however, the differences were significant (P < .05) only for PP and PUI-15. PUI-30 increased weight reduction compared with PP for both hypochlorites and PUI-15 using Vista 6% plain (P < .05). PUI-30 with Vista 6% plain performed significantly better than PP with Chlor-XTRA (P < .05). The addition of a surfactant to NaOCl and/or PUI activation increased palatal mucosa dissolution within artificial grooves in the root canal of incisor teeth. PUI agitation was often able to compensate for the absence of surfactants. Copyright © 2017 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

The SSME seal test program: Leakage tests for helically-grooved seals

NASA Technical Reports Server (NTRS)

Childs, D. W.

1983-01-01

Helically grooved annular seal configurations were tested in highly turbulent flow to determine if reduced leakage and enhanced stability would result from the pumping action of the seal. It was found that: (1) leakage of a helically grooved seals decreases with running speed; (2) leakage reduction due to increased running speed is greater at lower values of R sub a; (3) an asymptote for leakage reduction is indicated with increasing running speed; (4) leakage is reduced by reducing the ridge (minimum) and average clearances; (5) leakage increases with increasing pitch angles and with increasing groove depth. Plain seals with smooth rotors and stators will leak more than a helically grooved seal. It was also found that plain seals with a rough rotor and a rough stator leak less than a properly designed helically grooved seal. A properly designed helically grooved seal consumes at least twice as much power as a conventional annular seal.

Gas Seal Pad With Herringbone-Grooved Rotor-Stiffness and Load Capacity

NASA Technical Reports Server (NTRS)

Flemming, David P.

2006-01-01

The principle of herringbone-grooved journal bearings has been applied to the case of a seal disc running under a finger seal pad. The inward pumping action of herringbone grooves on the disc generates load capacity and stiffness to maintain a fluid film and prevent contact of the pad and disc. This mechanism does not depend on a converging film under the pad, such as analyzed in previous works. Analysis shows that significant stiffness and load capacity can be supplied by herringbone grooves. In order for the grooves to be effective, the seal pressure drop must be taken outside of the grooved portion of the rotor, but this may be acceptable in order to gain freedom from maintaining a precise film convergence.

Appraisal of transverse nasal groove: a study.

PubMed

Sathyanarayana, Belagola D; Basavaraj, Halevoor B; Nischal, Kuchangi C; Swaroop, Mukunda R; Umashankar, Puttagangu N; Agrawal, Dhruv P; Swamy, Suchetha S; Okram, Sarda

2012-01-01

Transverse nasal groove is a condition of cosmetic concern which awaits due recognition and has been widely described as a shallow groove that extends transversely over the dorsum of nose. However, we observed variations in the clinical presentations of this entity, hitherto undescribed in literature. We conducted a clinicoepidemiological study of transverse nasal lesions in patients attending our outpatient department. We conducted a prospective observational study. We screened all patients attending our out-patient department for presence of transverse nasal lesions, signs of any dermatosis and associated other skin conditions. One hundred patients were recruited in the study. Females (80%) predominated over males. Most patients were of 15-45 years age group (70%). Majority of the transverse nasal lesions were classical transverse nasal groove (39%) and others included transverse nasal line (28%), strip (28%), ridge (4%) and loop (1%). Seborrhoeic diathesis was the most common condition associated with transverse nasal lesion. Occurrence of transverse nasal line, strip, ridge and loop, in addition to classical transverse nasal groove implies that latter is actually a subset of transverse nasal lesions. Common association of this entity with seborrheic dermatitis, seborrhea and dandruff raises a possibility of whether transverse nasal lesion is a manifestation of seborrheic diathesis.

Design of well and groove microchannel bioreactors for cell culture.

PubMed

Korin, Natanel; Bransky, Avishay; Khoury, Maria; Dinnar, Uri; Levenberg, Shulamit

2009-03-01

Microfluidic bioreactors have been shown valuable for various cellular applications. The use of micro-wells/grooves bioreactors, in which micro-topographical features are used to protect sensitive cells from the detrimental effects of fluidic shear stress, is a promising approach to culture sensitive cells in these perfusion microsystems. However, such devices exhibit substantially different fluid dynamics and mass transport characteristics compared to conventional planar microchannel reactors. In order to properly design and optimize these systems, fluid and mass transport issues playing a key role in microscale bioreactors should be adequately addressed. The present work is a parametric study of micro-groove/micro-well microchannel bioreactors. Operation conditions and design parameters were theoretically examined via a numerical model. The complex flow pattern obtained at grooves of various depths was studied and the shear protection factor compared to planar microchannels was evaluated. 3D flow simulations were preformed in order to examine the shear protection factor in micro-wells, which were found to have similar attributes as the grooves. The oxygen mass transport problem, which is coupled to the fluid mechanics problem, was solved for various groove geometries and for several cell types, assuming a defined shear stress limitation. It is shown that by optimizing the groove depth, the groove bioreactor may be used to effectively maximize the number of cells cultured within it or to minimize the oxygen gradient existing in such devices. Moreover, for sensitive cells having a high oxygen demand (e.g., hepatocytes) or low endurance to shear (e.g., human embryonic stem cells), results show that the use of grooves is an enabling technology, since under the same physical conditions the cells cannot be cultured for long periods of time in a planar microchannel. In addition to the theoretical model findings, the culture of human foreskin fibroblasts in groove (30

Effect of type and location of oil groove on the performance of journal bearings

NASA Technical Reports Server (NTRS)

Vijayaraghavan, D.; Keith, T. G., Jr.

1992-01-01

A numerical study is performed of oil groove type (circumferential and axial), groove number (single and double) and groove location on journal bearing performance. The analysis involves the use of a cavitation algorithm. The interaction between cavitation phenomena and grooving is determined. Quantitative information is provided which will aid designers to better locate oil feed grooves.

Molecular Probing of the HPV-16 E6 Protein Alpha Helix Binding Groove with Small Molecule Inhibitors

PubMed Central

Rietz, Anne; Petrov, Dino P.; Bartolowits, Matthew; DeSmet, Marsha; Davisson, V. Jo; Androphy, Elliot J.

2016-01-01

The human papillomavirus (HPV) HPV E6 protein has emerged as a central oncoprotein in HPV-associated cancers in which sustained expression is required for tumor progression. A majority of the E6 protein interactions within the human proteome use an alpha-helix groove interface for binding. The UBE3A/E6AP HECT domain ubiquitin ligase binds E6 at this helix-groove interface. This enables formation of a trimeric complex with p53, resulting in destruction of this tumor suppressor. While recent x-ray crystal structures are useful, examples of small molecule probes that can modulate protein interactions at this interface are limited. To develop insights useful for potential structure-based design of ligands for HPV E6, a series of 2,6-disubstituted benzopyranones were prepared and tested as competitive antagonists of E6-E6AP helix-groove interactions. These small molecule probes were used in both binding and functional assays to evaluate recognition features of the E6 protein. Evidence for an ionic functional group interaction within the helix groove was implicated by the structure-activity among the highest affinity ligands. The molecular topographies of these protein-ligand interactions were evaluated by comparing the binding and activities of single amino acid E6 mutants with the results of molecular dynamic simulations. A group of arginine residues that form a rim-cap over the E6 helix groove offer compensatory roles in binding and recognition of the small molecule probes. The flexibility and impact on the overall helix-groove shape dictated by these residues offer new insights for structure-based targeting of HPV E6. PMID:26915086

Mutations in the substrate binding site of human heat-shock protein 70 indicate specific interaction with HLA-DR outside the peptide binding groove

PubMed Central

Rohrer, Karin M; Haug, Markus; Schwörer, Daniela; Kalbacher, Hubert; Holzer, Ursula

2014-01-01

Heat-shock protein 70 (Hsp70)–peptide complexes are involved in MHC class I-and II-restricted antigen presentation, enabling enhanced activation of T cells. As shown previously, mammalian cytosolic Hsp70 (Hsc70) molecules interact specifically with HLA-DR molecules. This interaction might be of significance as Hsp70 molecules could transfer bound antigenic peptides in a ternary complex into the binding groove of HLA-DR molecules. The present study provides new insights into the distinct interaction of Hsp70 with HLA-DR molecules. Using a quantitative binding assay, it could be demonstrated that a point mutation of amino acids alanine 406 and valine 438 in the substrate binding pocket led to reduced peptide binding compared with the wild-type Hsp70 whereas HLA-DR binding remains unaffected. The removal of the C-terminal lid neither altered the substrate binding capacity nor the Hsp70 binding characteristics to HLA-DR. A truncated variant lacking the nucleotide binding domain showed no binding interactions with HLA-DR. Furthermore, the truncated ATPase subunit of constitutively expressed Hsc70 revealed similar binding affinities to HLA-DR compared with the complete Hsc70. Hence, it can be assumed that the Hsp70–HLA-DR interaction takes place outside the peptide binding groove and is attributed to the ATPase domain of HSP70 molecules. The Hsp70-chaperoned peptides might thereby be directly transferred into the binding groove of HLA-DR, so enabling enhanced presentation of the peptide on antigen-presenting cells and leading to an improved proliferation of responding T cells as shown previously. PMID:24428437

Boundary conditions at the gas sectors of superhydrophobic grooves

NASA Astrophysics Data System (ADS)

Dubov, Alexander L.; Nizkaya, Tatiana V.; Asmolov, Evgeny S.; Vinogradova, Olga I.

2018-01-01

The hydrodynamics of liquid flowing past gas sectors of unidirectional superhydrophobic surfaces is revisited. Attention is focused on the local slip boundary condition at the liquid-gas interface, which is equivalent to the effect of a gas cavity on liquid flow. The system is characterized by a large viscosity contrast between liquid and gas μ /μg≫1 . We interpret earlier results, namely, the dependence of the local slip length on the flow direction, in terms of a tensorial local slip boundary condition and relate the eigenvalues of the local local slip tensor to the texture parameters, such as the width of the groove δ and the local depth of the groove e (y ,α ) . The latter varies in the direction y , orthogonal to the orientation of stripes, and depends on the bevel angle of the groove's edges, π /2 -α , at the point where three phases meet. Our theory demonstrates that when grooves are sufficiently deep their eigenvalues of the local slip length tensor depend only on μ /μg ,δ , and α , but not on the depth. The eigenvalues of the local slip length of shallow grooves depend on μ /μg and e (y ,α ) , although the contribution of the bevel angle is moderate. In order to assess the validity of our theory we propose an approach to solve the two-phase hydrodynamic problem, which significantly facilitates and accelerates calculations compared to conventional numerical schemes. The numerical results show that our simple analytical description obtained for limiting cases of deep and shallow grooves remains valid for various unidirectional textures.

[A case of groove pancreatitis associated with duodenal ulcer].

PubMed

Iemoto, Takao; Shiomi, Hideyuki; Masuda, Atsuhiro; Sanuki, Tsuyoshi; Kutsumi, Hiromu; Hayakumo, Takanobu; Shinzeki, Makoto; Matsumoto, Ippei; Ku, Yonson; Kanzawa, Maki; Hara, Shigeo; Azuma, Takeshi

2013-01-01

We describe a 69-year-old man with a history of multiple gastroduodenal ulcers, presenting with the onset of obstructive jaundice. Abdominal CT, MRI and EUS demonstrated a sheet-like mass in the pancreaticoduodenal groove. EUS-FNA did not reveal malignancy. Conservative treatment did not improve his clinical condition and repeated acute pancreatitis occurred during his treatment. Thus, pancreaticoduodenectomy was performed. Histopathological findings showed a duodenal ulcer penetrating the pancreas and infiltration of inflammatory cells and fibrosis in the pancreaticoduodenal groove. The spread of inflammation associated with the duodenal ulcer may have been one of the causes of groove pancreatitis.

Design of pellet surface grooves for fission gas plenum

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

Carter, T.J.; Jones, L.R.; Macici, N.

1986-01-01

In the Canada deuterium uranium pressurized heavy water reactor, short (50-cm) Zircaloy-4 clad bundles are fueled on-power. Although internal void volume within the fuel rods is adequate for the present once-through natural uranium cycle, the authors have investigated methods for increasing the internal gas storage volume needed in high-power, high-burnup, experimental ceramic fuels. This present work sought to prove the methodology for design of gas storage volume within the fuel pellets - specifically the use of grooves pressed or machined into the relatively cool pellet/cladding interface. Preanalysis and design of pellet groove shape and volume was accomplished using the TRUMPmore » heat transfer code. Postirradiation examination (PIE) was used to check the initial design and heat transfer assumptions. Fission gas release was found to be higher for the grooved pellet rods than for the comparison rods with hollow or unmodified pellets. This had been expected from the initial TRUMP thermal analyses. The ELESIM fuel modeling code was used to check in-reactor performance, but some modifications were necessary to accommodate the loss of heat transfer surface to the grooves. It was concluded that for plenum design purposes, circumferential pellet grooves could be adequately modeled by the codes TRUMP and ELESIM.« less

Mark-forming simulations of phase-change land/groove disks

NASA Astrophysics Data System (ADS)

Nishi, Yoshiko; Shimano, Takeshi; Kando, Hidehiko

2000-09-01

The track pitches of optical discs have become so narrow that it is comparable to the wavelength of laser beam. Finite-difference time-domain (FDTD) simulation, based on vector diffraction analysis, can predict the propagation of light more accurately than scalar analysis, when the size of media texture becomes sub-micron order. The authors applied FDTD simulation to land-and-groove optical disc models, and found out that the effects of 3D geometry is not negligible in analyzing the energy absorption of light inside the land- and-groove multi-layered media. The electromagnetic field in the media does not have the same intensity distribution as the incident beam. Furthermore, the heat conduction inside the media depends on the disc geometry, so the beam spots centered on land and groove makes different effects in heating the recording layers. That is, the spatial and historical profile of temperature requires 3D analysis for both incident light absorption and heat conduction. The difference in temperature profiles is applied to the phase change simulator to see the writing process of the marks in land and groove. We have integrated three simulators: FDTD analysis, heat conduction and phase change simulation. These simulators enabled to evaluate the differences in mark forming process between land and groove.

Grooved impactor and inertial trap for sampling inhalable particulate matter

DOEpatents

Loo, Billy W.

1984-01-01

An inertial trap and grooved impactor for providing a sharp cutoff for particles over 15 microns from entering an inhalable particulate sampler. The impactor head has a tapered surface and is provided with V-shaped grooves. The tapered surface functions for reducing particle blow-off or reentrainment while the grooves prevent particle bounce. Water droplets and any resuspended material over the 15 micron size are collected by the inertial trap and deposited in a reservoir associated with the impactor.

Wet Weather Crater Repair Technologies for Grooved and Smooth Pavements

DTIC Science & Technology

2018-04-30

test area needed for this project, the PCC slab was grooved by using a walk-behind saw equipped with one diamond saw- cutting blade rather than a...tent. Figure 49 shows the rainwater running off the edge of the tent. Figure 49. Tent water runoff from simulated rain. Figure 50 shows the catch...covered with the tarp. These barriers still left the pavement grooving exposed, so water was able to run freely into the basin from the grooves. The

Modified Kelvin Equations for Capillary Condensation in Narrow and Wide Grooves

NASA Astrophysics Data System (ADS)

Malijevský, Alexandr; Parry, Andrew O.

2018-03-01

We consider the location and order of capillary condensation transitions occurring in deep grooves of width L and depth D . For walls that are completely wet by liquid (contact angle θ =0 ) the transition is continuous and its location is not sensitive to the depth of the groove. However, for walls that are partially wet by liquid, where the transition is first order, we show that the pressure at which it occurs is determined by a modified Kelvin equation characterized by an edge contact angle θE describing the shape of the meniscus formed at the top of the groove. The dependence of θE on the groove depth D relies, in turn, on whether corner menisci are formed at the bottom of the groove in the low density gaslike phase. While for macroscopically wide grooves these are always present when θ <45 ° we argue that their formation is inhibited in narrow grooves. This has a number of implications including that the local pinning of the meniscus and location of the condensation transition is different depending on whether the contact angle is greater or less than a universal value θ*≈31 °. Our arguments are supported by detailed microscopic density functional theory calculations that show that the modified Kelvin equation remains highly accurate even when L and D are of the order of tens of molecular diameters.

Osteochondritis Dissecans Involving the Trochlear Groove Treated With Retrograde Drilling

PubMed Central

Kaji, Yoshio; Nakamura, Osamu; Yamaguchi, Konosuke; Yamamoto, Tetsuji

2015-01-01

Abstract Osteochondritis dissecans (OCD) occurs frequently in the humeral capitellum of the upper extremity, whereas OCD involving the trochlear groove (trochlear groove OCD) is rarely reported. A standard treatment for trochlear groove OCD has therefore not been determined, although several methods have been tried. The case of a 14-year-old male gymnast with bilateral trochlear groove OCD is presented. Retrograde drilling from the lateral condyle of the humerus was applied for the OCD lesion of the left elbow, since it was larger in size than that in the right elbow and was symptomatic. Conversely, since the right lesion was small and asymptomatic, it was managed conservatively. After treatment, consolidation of the OCD lesions was observed in both elbows. However, the time to healing was shorter in the left elbow treated surgically than in the right elbow managed conservatively. In conclusion, retrograde drilling is a very simple and minimally invasive treatment. This case suggests that retrograde drilling for trochlear groove OCD may be a useful procedure that may accelerate the healing process for OCD lesions. PMID:26356703

Infiltration of Slag Film into the Grooves on a Continuous Casting Mold

NASA Astrophysics Data System (ADS)

Cho, Jung-Wook; Jeong, Hee-Tae

2013-02-01

An analytical model is developed to clarify the slag film infiltration into grooves on a copper mold during the continuous casting of steel slabs. A grooved-type casting mold was applied to investigate the infiltration of slag film into the grooves of a pitch of 0.8 mm, width of 0.7 mm, and depth of 0.6 mm at the vicinity of a meniscus. The plant trial tests were carried out at a casting speed of 5.5 m min-1. The slag film captured at a commercial thin slab casting plant showed that both the overall and the liquid film thickness were decreased exponentially as the distance from the meniscus increases. In contrast, the infiltration of slag film into the grooves had been increased with increasing distance from the meniscus. A theoretic model has been derived based on the measured profile of slag film thickness to calculate the infiltration of slag film into the grooves. It successfully reproduces the empirical observation that infiltration ratio increased sharply along casting direction, about 80 pct at 50 mm and 95 pct at 150 mm below the meniscus. In the model calculation, the infiltration of slag film increases with increasing groove width and/or surface tension of the slag. The effect of groove depth is negligible when the width to depth ratio of the groove is larger than unity. It is expected that the developed model for slag film infiltration in this study will be widely utilized to optimize the design of groove dimensions in continuous casting molds.

Syncopation, body-movement and pleasure in groove music.

PubMed

Witek, Maria A G; Clarke, Eric F; Wallentin, Mikkel; Kringelbach, Morten L; Vuust, Peter

2014-01-01

Moving to music is an essential human pleasure particularly related to musical groove. Structurally, music associated with groove is often characterised by rhythmic complexity in the form of syncopation, frequently observed in musical styles such as funk, hip-hop and electronic dance music. Structural complexity has been related to positive affect in music more broadly, but the function of syncopation in eliciting pleasure and body-movement in groove is unknown. Here we report results from a web-based survey which investigated the relationship between syncopation and ratings of wanting to move and experienced pleasure. Participants heard funk drum-breaks with varying degrees of syncopation and audio entropy, and rated the extent to which the drum-breaks made them want to move and how much pleasure they experienced. While entropy was found to be a poor predictor of wanting to move and pleasure, the results showed that medium degrees of syncopation elicited the most desire to move and the most pleasure, particularly for participants who enjoy dancing to music. Hence, there is an inverted U-shaped relationship between syncopation, body-movement and pleasure, and syncopation seems to be an important structural factor in embodied and affective responses to groove.

Binding to the minor groove of the double-strand, tau protein prevents DNA from damage by peroxidation.

PubMed

Wei, Yan; Qu, Mei-Hua; Wang, Xing-Sheng; Chen, Lan; Wang, Dong-Liang; Liu, Ying; Hua, Qian; He, Rong-Qiao

2008-07-02

Tau, an important microtubule associated protein, has been found to bind to DNA, and to be localized in the nuclei of both neurons and some non-neuronal cells. Here, using electrophoretic mobility shifting assay (EMSA) in the presence of DNA with different chain-lengths, we observed that tau protein favored binding to a 13 bp or a longer polynucleotide. The results from atomic force microscopy also showed that tau protein preferred a 13 bp polynucleotide to a 12 bp or shorter polynucleotide. In a competitive assay, a minor groove binder distamycin A was able to replace the bound tau from the DNA double helix, indicating that tau protein binds to the minor groove. Tau protein was able to protect the double-strand from digestion in the presence of DNase I that was bound to the minor groove. On the other hand, a major groove binder methyl green as a negative competitor exhibited little effect on the retardation of tau-DNA complex in EMSA. This further indicates the DNA minor groove as the binding site for tau protein. EMSA with truncated tau proteins showed that both the proline-rich domain (PRD) and the microtubule-binding domain (MTBD) contributed to the interaction with DNA; that is to say, both PRD and MTBD bound to the minor groove of DNA and bent the double-strand, as observed by electron microscopy. To investigate whether tau protein is able to prevent DNA from the impairment by hydroxyl free radical, the chemiluminescence emitted by the phen-Cu/H(2)O(2)/ascorbate was measured. The emission intensity of the luminescence was markedly decreased when tau protein was present, suggesting a significant protection of DNA from the damage in the presence of hydroxyl free radical.

Resistance to minor groove binders.

PubMed

Colmegna, Benedetta; Uboldi, Sarah; Erba, Eugenio; D'Incalci, Maurizio

2014-03-01

In this paper multiple resistance mechanisms to minor groove binders (MGBs) are overviewed. MGBs with antitumor properties are natural products or their derivatives and, as expected, they are all substrates of P-glycoprotein (P-gp). However, a moderate expression of P-gp does not appear to reduce the sensitivity to trabectedin, the only MGB so far approved for clinical use. Resistance to this drug is often related to transcriptional mechanisms and to DNA repair pathways, particularly defects in transcription-coupled nucleotide excision repair (TC-NER). Therefore tumors resistant to trabectedin may become hypersensitive to UV rays and other DNA damaging agents acting in the major groove, such as Platinum (Pt) complexes. If this is confirmed in clinic, that will provide the rationale to combine trabectedin sequentially with Pt derivates.

Champagne Groove Lipectomy: A Safe Technique to Contour the Upper Abdomen in Abdominoplasty.

PubMed

Brooks, Ron; Nguyen, Jonathan; Chowdhry, Saeed; Tutela, John Paul; Kelishadi, Sean; Yonick, David; Choo, Joshua; Wilhelmi, Bradon J

2017-01-01

Objective: Combined liposuction and abdominoplasty, or lipoabdominoplasty, is particularly helpful in sculpting a more aesthetically pleasing abdominal contour, particularly in the supraumbilical midline groove. This groove, coined the "champagne groove" by one of our patients, is a frequently sought-after attribute by patients. However, liposuction adds time and cost to an already costly abdominoplasty. We sought to create this groove without the addition of liposuction, utilizing what we call a champagne groove lipectomy. This study reports on our champagne groove lipectomy technique and compares our complication rates with those reported in the literature for standard abdominoplasty techniques. Methods: This is a retrospective review of a single surgeon's experience at our institution over a 6-year period (2007-2012). A total of 74 patients undergoing consecutive abdominoplasty were studied, all female nonsmokers. Two groups were recognized: 64 of 74 patients underwent abdominoplasty, partial belt lipectomy, and champagne groove lipectomy, while 10 of 74 patients underwent fleur-de-lis abdominoplasty without champagne groove lipectomy. Results: Overall, 10 of 74 patients (13.5%) suffered some type of complication, which compares favorably with reported rates in the literature. The majority of complications were related to delayed wound healing or superficial wound dehiscence. Among those patients who underwent champagne groove lipectomy, complications occurred in 6 of 64 patients (9.3%), versus 4 of 10 (40%) patients undergoing fleur-de-lis abdominoplasty. Conclusions: Champagne groove lipectomy is a cost-effective alternative to lipoabdominoplasty for achieving an aesthetically pleasing upper midline abdominal contour, with complication rates comparing favorably with those reported in the literature.

Current trends in the management of pediatric patients with perineal groove.

PubMed

Esposito, Ciro; Giurin, Ida; Savanelli, Antonio; Alicchio, Francesca; Settimi, Alessandro

2011-10-01

Perineal groove is an uncommon congenital anomaly of the perineum, affecting young girls. We report our experience in the treatment of this pathology. Retrospective review of patients operated in our institution for a perineal groove between 1999 and 2007. Multidisciplinary clinic for young girls with perineal groove at the Department of Pediatrics, "Federico II" University, Naples, Italy. Six young girls (aged between 2 and 7 years) with perineal groove. In the first three patients, who were operated on before 2004, the procedure consisted in resecting the groove and closing the perineal defect using interrupted sutures; in the last three, the skin was closed with similar approach and then covered with a chemical glue to impermeabilize and protect the suture. At a long-term follow-up, two of the three patients operated before 2004 experienced dehiscence of the perineal skin due to urine and feces contamination; in the last three patients in whom the sutures were covered with glue there was no skin dehiscence, and the postoperative course was uneventful. A perineal groove is a rare anomaly in young girls. Treatment consists in the surgical excision of the groove, generally after two years of age. On the basis of our experience it is preferable to cover the suture with a chemical glue to impermeabilize the suture line and protect the skin from infections. Copyright © 2011 North American Society for Pediatric and Adolescent Gynecology. Published by Elsevier Inc. All rights reserved.

Documentation of roller-bearing effect on butterfly inspired grooves

NASA Astrophysics Data System (ADS)

Gautam, Sashank; Lang, Amy

2017-11-01

Butterfly wings are covered with scales in a roof shingle pattern which align together to form grooves. The increase or decrease of laminar friction drag depends on the flow orientation to the scales. Flow in the longitudinal direction to the grooves encounters increased surface area which increases the friction drag. However, in the transverse direction, for low Re laminar flow, a single vortex is formed inside each groove and is predicted to remain stable due to the very low Re of the flow in each cavity. These embedded vortices act as roller bearings to the flow above, such that the fluid from the outer boundary layer does not mix with fluid inside the cavities. This leads to a reduction of skin friction drag when compared to a smooth surface. When the cavity flow Re is increased beyond a critical point, the vortex becomes unstable and the low-momentum fluid in the grooves mixes with the outer boundary layer flow, increasing the drag. The objective of this experiment is to determine the critical Re where the embedded vortex transitions from a stable to an unstable state using DPIV. Subsequently, for steady vortex conditions, a comparison of skin friction drag between the grooved and flat plate can show that the butterfly scaled surface can result in sub-laminar friction drag. The National Science Foundation (Grant No. 1335848).

Combined endodontic-periodontic treatment of a palatal groove: a case report.

PubMed

Schwartz, Scott A; Koch, Michael A; Deas, David E; Powell, Charles A

2006-06-01

The palatal groove is a developmental anomaly that predisposes the tooth involved to a severe periodontal defect. When further complicated by pulp necrosis, these grooves often present a diagnostic and treatment planning challenge that requires an interdisciplinary treatment approach. This case report describes the successful collaborative management of a maxillary lateral incisor with an extensive palatal groove using a combination of nonsurgical endodontic therapy, odontoplasty, and periodontal regenerative techniques.

Syncopation, Body-Movement and Pleasure in Groove Music

PubMed Central

Witek, Maria A. G.; Clarke, Eric F.; Wallentin, Mikkel; Kringelbach, Morten L.; Vuust, Peter

2014-01-01

Moving to music is an essential human pleasure particularly related to musical groove. Structurally, music associated with groove is often characterised by rhythmic complexity in the form of syncopation, frequently observed in musical styles such as funk, hip-hop and electronic dance music. Structural complexity has been related to positive affect in music more broadly, but the function of syncopation in eliciting pleasure and body-movement in groove is unknown. Here we report results from a web-based survey which investigated the relationship between syncopation and ratings of wanting to move and experienced pleasure. Participants heard funk drum-breaks with varying degrees of syncopation and audio entropy, and rated the extent to which the drum-breaks made them want to move and how much pleasure they experienced. While entropy was found to be a poor predictor of wanting to move and pleasure, the results showed that medium degrees of syncopation elicited the most desire to move and the most pleasure, particularly for participants who enjoy dancing to music. Hence, there is an inverted U-shaped relationship between syncopation, body-movement and pleasure, and syncopation seems to be an important structural factor in embodied and affective responses to groove. PMID:24740381

Numerical investigation of a centrifugal compressor with circumferential grooves in vane diffuser

NASA Astrophysics Data System (ADS)

Chen, X. F.; Qin, G. L.; Ai, Z. J.

2015-08-01

Enhancing stall and surge margin has a great importance for the development of turbo compressors. The application of casing treatment is an effective measure to expand the stall margin and stable operation range. Numerical investigations were conducted to predict the performance of a low flow rate centrifugal compressor with circumferential groove casing treatment in vane diffuser. Numerical cases with different radial location, radial width and axial depth of a circumferential single groove and different numbers of circumferential grooves were carried out to compare the results. The CFD analyses results show that the centrifugal compressor with circumferential grooves in diffuser can extend stable range by about 9% while the efficiency over the whole operating range decreases by 0.2 to 1.7%. The evaluation based on stall margin improvement showed the optimal position for the groove to be located was indicated to exist near the leading edge of the diffuser, and a combination of position, width, depth and numbers of circumferential grooves that will maximize both surge margin range and efficiency.

Champagne Groove Lipectomy: A Safe Technique to Contour the Upper Abdomen in Abdominoplasty

PubMed Central

Brooks, Ron; Chowdhry, Saeed; Tutela, John Paul; Kelishadi, Sean; Yonick, David; Choo, Joshua; Wilhelmi, Bradon J.

2017-01-01

Objective: Combined liposuction and abdominoplasty, or lipoabdominoplasty, is particularly helpful in sculpting a more aesthetically pleasing abdominal contour, particularly in the supraumbilical midline groove. This groove, coined the “champagne groove” by one of our patients, is a frequently sought-after attribute by patients. However, liposuction adds time and cost to an already costly abdominoplasty. We sought to create this groove without the addition of liposuction, utilizing what we call a champagne groove lipectomy. This study reports on our champagne groove lipectomy technique and compares our complication rates with those reported in the literature for standard abdominoplasty techniques. Methods: This is a retrospective review of a single surgeon's experience at our institution over a 6-year period (2007-2012). A total of 74 patients undergoing consecutive abdominoplasty were studied, all female nonsmokers. Two groups were recognized: 64 of 74 patients underwent abdominoplasty, partial belt lipectomy, and champagne groove lipectomy, while 10 of 74 patients underwent fleur-de-lis abdominoplasty without champagne groove lipectomy. Results: Overall, 10 of 74 patients (13.5%) suffered some type of complication, which compares favorably with reported rates in the literature. The majority of complications were related to delayed wound healing or superficial wound dehiscence. Among those patients who underwent champagne groove lipectomy, complications occurred in 6 of 64 patients (9.3%), versus 4 of 10 (40%) patients undergoing fleur-de-lis abdominoplasty. Conclusions: Champagne groove lipectomy is a cost-effective alternative to lipoabdominoplasty for achieving an aesthetically pleasing upper midline abdominal contour, with complication rates comparing favorably with those reported in the literature. PMID:28293334

Formation of Ganymede's Grooved Terrain by Convection-Driven Resurfacing

NASA Astrophysics Data System (ADS)

Hammond, N. P.; Barr, A. C.

2013-12-01

Over half the surface of Ganymede, Jupiter's largest icy moon, is covered in grooved terrain, which is composed of 10-100 km wide swaths of sub-parallel ridges and troughs [1]. Convection in Ganymede's ice shell was originally suggested as a driving mechanism for grooved terrain formation [2] but subsequent work has argued that convective stresses were too weak to deform the surface [3] and that Ganymede's ice shell was thin and conductive during groove terrain formation [4]. However, the heat flow [5] and strain rate [6] inferred for grooved terrain formation resemble the conditions observed at the active Enceladus South Polar Terrain (SPT), where 'sluggish lid' convection may be occurring [7]. During 'sluggish lid' convection, thermal buoyancy stresses exceed the lithospheric yield stress, allowing convection to reach the surface and drive deformation [8]. Previous work shows that the heat flows and strain rates associated with sluggish lid convection are consistent with the observed heat flow and surface age of the Enceladus SPT [7, 9]. Here we use numerical models of convection in Ganymede's ice shell to show that convection can provide the heat flow and strain rate inferred for grooved terrain formation. We use the finite element model CITCOM [10] to model convection for a wide range of ice shell conditions. We use a newtonian temperature-dependent viscosity consistent with deformation by volume diffusion [11]. We impose a limited viscosity contrast between the surface and base of the ice shell to mimic the effect of an upper surface whose yield stress is less than the critical stress for sluggish lid convection [7, 12] due to impact fracturing [13], tidal flexing, and/or shallow tidal heating. We find that ice shells 10 to 80 km thick are consistent with the heat flow and strain rate inferred for grooved terrain formation. Regions above convective upwellings are consistent with conditions inferred at groove lanes. Regions above downwellings are consistent

Study of Mastoid Canals and Grooves in North Karnataka Human Skulls

PubMed Central

Hadimani, Gavishiddappa Andanappa; Bagoji, Ishwar Basavantappa

2013-01-01

Introduction: This study was undertaken to observe the frequency of mastoid canals and grooves in north Karnataka dry human skulls. 100 dry human skulls of unknown age and sex from the department of Anatomy were selected and observed for the present study. Material and Methods: The mastoid regions of dry skulls were observed for the presence of mastoid canals and grooves, if any. A metallic wire was passed through the canal for its confirmation and then the length was measured. Results: The Mastoid canals were present in 53% of the total 100 skulls observed either bilaterally or unilaterally. Mastoid grooves were present in 18% of the total skulls (100) observed. Double mastoid canal was found in 01% of total skull studied and both Mastoid canals & Mastoid grooves together were present in 02% of the total skulls (100) observed. Conclusion: The knowledge of mastoid canals and grooves is very important for otolaryngologists and neurosurgeons. Because they contain an arterial branch of occipital artery with its accompanying vein which is liable to injury resulting into severe bleeding. PMID:24086832

Study of mastoid canals and grooves in north karnataka human skulls.

PubMed

Hadimani, Gavishiddappa Andanappa; Bagoji, Ishwar Basavantappa

2013-08-01

This study was undertaken to observe the frequency of mastoid canals and grooves in north Karnataka dry human skulls. 100 dry human skulls of unknown age and sex from the department of Anatomy were selected and observed for the present study. The mastoid regions of dry skulls were observed for the presence of mastoid canals and grooves, if any. A metallic wire was passed through the canal for its confirmation and then the length was measured. The Mastoid canals were present in 53% of the total 100 skulls observed either bilaterally or unilaterally. Mastoid grooves were present in 18% of the total skulls (100) observed. Double mastoid canal was found in 01% of total skull studied and both Mastoid canals & Mastoid grooves together were present in 02% of the total skulls (100) observed. The knowledge of mastoid canals and grooves is very important for otolaryngologists and neurosurgeons. Because they contain an arterial branch of occipital artery with its accompanying vein which is liable to injury resulting into severe bleeding.

Miranda Fractures, Grooves and Craters

NASA Image and Video Library

1996-01-29

This image of the Uranian moon, Miranda, was taken Jan 24, 1986 by NASA's Voyager 2. This image reveals a bewildering variety of fractures, grooves and craters, as well as features of different albedos reflectancea. http://photojournal.jpl.nasa.gov/catalog/PIA00140

Fluidic Grooves on Doped-Ice Surface as Size-Tunable Channels

PubMed Central

Inagawa, Arinori; Harada, Makoto; Okada, Tetsuo

2015-01-01

We propose a new principle for fabrication of size-tunable fluidic nano- and microchannels with a ubiquitous green material, water. Grooves filled with a solution are spontaneously formed on the surface of ice when an appropriate dopant is incorporated. Sucrose doping allows the development of grooves with lengths of 300 μm along the boundaries of ice crystal grains. This paper focuses on controlling the size of the liquid-filled groove and reveals its applicability to size-selective differentiation of nano- and micromaterials. The width of this groove can be varied in a range of 200 nm to 4 μm by adjusting the working temperature of the frozen platform. The channel dimension is reproducible as long as the same frozen condition is employed. We demonstrate the size-selective entrapment of particles as well as the state evaluation of DNA by controlling the physical interference of the ice wall with the electrophoretic migration of particles. PMID:26601703

Fluidic Grooves on Doped-Ice Surface as Size-Tunable Channels

NASA Astrophysics Data System (ADS)

Inagawa, Arinori; Harada, Makoto; Okada, Tetsuo

2015-11-01

We propose a new principle for fabrication of size-tunable fluidic nano- and microchannels with a ubiquitous green material, water. Grooves filled with a solution are spontaneously formed on the surface of ice when an appropriate dopant is incorporated. Sucrose doping allows the development of grooves with lengths of 300 μm along the boundaries of ice crystal grains. This paper focuses on controlling the size of the liquid-filled groove and reveals its applicability to size-selective differentiation of nano- and micromaterials. The width of this groove can be varied in a range of 200 nm to 4 μm by adjusting the working temperature of the frozen platform. The channel dimension is reproducible as long as the same frozen condition is employed. We demonstrate the size-selective entrapment of particles as well as the state evaluation of DNA by controlling the physical interference of the ice wall with the electrophoretic migration of particles.

Fabrication process for polymer PLC platforms with V-grooves for passive alignment

NASA Astrophysics Data System (ADS)

Park, Suntak; Lee, Jong-Moo; Ahn, Joon Tae; Baek, Yong-Soon

2005-12-01

A method for polymer planar lightwave circuit (PLC) devices fabricated on a substrate with V-grooves is developed for passive alignment of an optical fiber to a polymer waveguide. In order to minimize thickness nonuniformity of polymer layers caused by the V-grooves, dry film resist (DFR) is used. The V-grooves are covered with the DFR before the polymer layers are spin-coated on the substrate. The DFR prevents the polymer from being filled in the V-grooves as well as from being spin-coated nonuniformly on the substrate. This process provides a simple and cost-effective fabrication method of polymer PLCs or platforms for passive alignment.

Crystal structures of yellowtail ascites virus VP4 protease: trapping an internal cleavage site trans acyl-enzyme complex in a native Ser/Lys dyad active site.

PubMed

Chung, Ivy Yeuk Wah; Paetzel, Mark

2013-05-03

Yellowtail ascites virus (YAV) is an aquabirnavirus that causes ascites in yellowtail, a fish often used in sushi. Segment A of the YAV genome codes for a polyprotein (pVP2-VP4-VP3), where processing by its own VP4 protease yields the capsid protein precursor pVP2, the ribonucleoprotein-forming VP3, and free VP4. VP4 protease utilizes the rarely observed serine-lysine catalytic dyad mechanism. Here we have confirmed the existence of an internal cleavage site, preceding the VP4/VP3 cleavage site. The resulting C-terminally truncated enzyme (ending at Ala(716)) is active, as shown by a trans full-length VP4 cleavage assay and a fluorometric peptide cleavage assay. We present a crystal structure of a native active site YAV VP4 with the internal cleavage site trapped as trans product complexes and trans acyl-enzyme complexes. The acyl-enzyme complexes confirm directly the role of Ser(633) as the nucleophile. A crystal structure of the lysine general base mutant (K674A) reveals the acyl-enzyme and empty binding site states of VP4, which allows for the observation of structural changes upon substrate or product binding. These snapshots of three different stages in the VP4 protease reaction mechanism will aid in the design of anti-birnavirus compounds, provide insight into previous site-directed mutagenesis results, and contribute to understanding of the serine-lysine dyad protease mechanism. In addition, we have discovered that this protease contains a channel that leads from the enzyme surface (adjacent to the substrate binding groove) to the active site and the deacylating water.

Flow dynamics of a spiral-groove dry-gas seal

NASA Astrophysics Data System (ADS)

Wang, Bing; Zhang, Huiqiang; Cao, Hongjun

2013-01-01

The dry-gas seal has been widely used in different industries. With increased spin speed of the rotator shaft, turbulence occurs in the gas film between the stator and rotor seal faces. For the micro-scale flow in the gas film and grooves, turbulence can change the pressure distribution of the gas film. Hence, the seal performance is influenced. However, turbulence effects and methods for their evaluation are not considered in the existing industrial designs of dry-gas seal. The present paper numerically obtains the turbulent flow fields of a spiral-groove dry-gas seal to analyze turbulence effects on seal performance. The direct numerical simulation (DNS) and Reynolds-averaged Navier-Stokes (RANS) methods are utilized to predict the velocity field properties in the grooves and gas film. The key performance parameter, open force, is obtained by integrating the pressure distribution, and the obtained result is in good agreement with the experimental data of other researchers. Very large velocity gradients are found in the sealing gas film because of the geometrical effects of the grooves. Considering turbulence effects, the calculation results show that both the gas film pressure and open force decrease. The RANS method underestimates the performance, compared with the DNS. The solution of the conventional Reynolds lubrication equation without turbulence effects suffers from significant calculation errors and a small application scope. The present study helps elucidate the physical mechanism of the hydrodynamic effects of grooves for improving and optimizing the industrial design or seal face pattern of a dry-gas seal.

Laser etching of groove structures with micro-optical fiber-enhanced irradiation

PubMed Central

2012-01-01

A microfiber is used as a laser-focusing unit to fabricate a groove structure on TiAlSiN surfaces. After one laser pulse etching, a groove with the minimum width of 265 nm is manufactured at the area. This technique of microfabricating the groove in microscale is studied. Based on the near-field intensity enhancement at the contact area between the fiber and the surface during the laser irradiation, simulation results are also presented, which agree well with the experimental results. PMID:22713521

The origin of the grooves on Phobos

NASA Technical Reports Server (NTRS)

Thomas, P. C.; Veverka, J.; Duxbury, T.

1977-01-01

Various theories for the long, linear depressions on the surface of Phobos are reviewed. Imagery from Viking Orbiters is used to map the surface distribution of the grooves, study their morphology, and date them by means of the density of superimposed impact craters. Data is presented which tends to support the hypothesis that the deep-seated fracturing was caused by a large, nearly catastrophic cratering event. It is suggested that the grooves were produced during the creation of the Stickney crater, rather than as the result of tidal stresses induced by Mars or by drag forces during the hypothetical capture of the satellite by Mars.

Getting into the GROOVE: How Building Effective Education Partnerships and Promoting Authentic Student Research through the Girls' Remotely Operated Ocean Vehicle Exploration (GROOVE) Workshop.

NASA Astrophysics Data System (ADS)

Pelz, M.; Heesemann, M.; Hoeberechts, M.

2017-12-01

This presentation outlines the pilot year of Girls' Remotely Operated Ocean Vehicle Exploration or GROOVE, a hands-on learning program created collaboratively with education partners Ocean Networks Canada and St. Margaret's School (Victoria, BC, Canada). The program features student-led activities, authentic student experiences, clearly outlined learning outcomes, teacher and student self-assessment tools, and curriculum-aligned content. Presented through the lens of STEM, students build a modified Seaperch ROV and explore and research thematic scientific concepts such as buoyancy, electronic circuitry, and deep-sea exploration. Further, students learn engineering skills such as isotropic scaling, soldering, and assembly as they build their ROV. Ocean Networks Canada (ONC), an initiative of the University of Victoria, develops, operates, and maintains cabled ocean observatory systems. These include technologies developed on the world-leading NEPTUNE and VENUS observatories and the ever-expanding network of community observatories in the Arctic and coastal British Columbia. These observatories, large and small, enable communities, users, scientists, teachers, and students to monitor real-time and historical data from the local marine environment from anywhere on the globe. GROOVE, Girls' Remotely Operated Ocean Vehicle Exploration, is ONC's newest educational program and is related to their foundational program K-12 Ocean Sense educational program. This presentation will share our experiences developing, refining, and assessing our efforts to implement GROOVE using a train-the-trainer model aimed at formal and informal K-12 educators. We will highlight lessons learned from multiple perspectives (students, participants, developers, and mentors) with the intent of informing future education and outreach initiatives.

Individual Differences in Beat Perception Affect Gait Responses to Low- and High-Groove Music

PubMed Central

Leow, Li-Ann; Parrott, Taylor; Grahn, Jessica A.

2014-01-01

Slowed gait in patients with Parkinson’s disease (PD) can be improved when patients synchronize footsteps to isochronous metronome cues, but limited retention of such improvements suggest that permanent cueing regimes are needed for long-term improvements. If so, music might make permanent cueing regimes more pleasant, improving adherence; however, music cueing requires patients to synchronize movements to the “beat,” which might be difficult for patients with PD who tend to show weak beat perception. One solution may be to use high-groove music, which has high beat salience that may facilitate synchronization, and affective properties, which may improve motivation to move. As a first step to understanding how beat perception affects gait in complex neurological disorders, we examined how beat perception ability affected gait in neurotypical adults. Synchronization performance and gait parameters were assessed as healthy young adults with strong or weak beat perception synchronized to low-groove music, high-groove music, and metronome cues. High-groove music was predicted to elicit better synchronization than low-groove music, due to its higher beat salience. Two musical tempi, or rates, were used: (1) preferred tempo: beat rate matched to preferred step rate and (2) faster tempo: beat rate adjusted to 22.5% faster than preferred step rate. For both strong and weak beat-perceivers, synchronization performance was best with metronome cues, followed by high-groove music, and worst with low-groove music. In addition, high-groove music elicited longer and faster steps than low-groove music, both at preferred tempo and at faster tempo. Low-groove music was particularly detrimental to gait in weak beat-perceivers, who showed slower and shorter steps compared to uncued walking. The findings show that individual differences in beat perception affect gait when synchronizing footsteps to music, and have implications for using music in gait rehabilitation. PMID:25374521

Aerodynamic Inner Workings of Circumferential Grooves in a Transonic Axial Compressor

NASA Technical Reports Server (NTRS)

Hah, Chunill; Mueller, Martin; Schiffer, Heinz-Peter

2007-01-01

The current paper reports on investigations of the fundamental flow mechanisms of circumferential grooves applied to a transonic axial compressor. Experimental results show that the compressor stall margin is significantly improved with the current set of circumferential grooves. The primary focus of the current investigation is to advance understanding of basic flow mechanics behind the observed improvement of stall margin. Experimental data and numerical simulations of a circumferential groove were analyzed in detail to unlock the inner workings of the circumferential grooves in the current transonic compressor rotor. A short length scale stall inception occurs when a large flow blockage is built on the pressure side of the blade near the leading edge and incoming flow spills over to the adjacent blade passage due to this blockage. The current study reveals that a large portion of this blockage is created by the tip clearance flow originating from 20% to 50% chord of the blade from the leading edge. Tip clearance flows originating from the leading edge up to 20% chord form a tip clearance core vortex and this tip clearance core vortex travels radially inward. The tip clearance flows originating from 20% to 50% chord travels over this tip clearance core vortex and reaches to the pressure side. This part of tip clearance flow is of low momentum as it is coming from the casing boundary layer and the blade suction surface boundary layer. The circumferential grooves disturb this part of the tip clearance flow close to the casing. Consequently the buildup of the induced vortex and the blockage near the pressure side of the passage is reduced. This is the main mechanism of the circumferential grooves that delays the formation of blockage near the pressure side of the passage and delays the onset of short length scale stall inception. The primary effect of the circumferential grooves is preventing local blockage near the pressure side of the blade leading edge that

Correcting groove error in gratings ruled on a 500-mm ruling engine using interferometric control.

PubMed

Mi, Xiaotao; Yu, Haili; Yu, Hongzhu; Zhang, Shanwen; Li, Xiaotian; Yao, Xuefeng; Qi, Xiangdong; Bayinhedhig; Wan, Qiuhua

2017-07-20

Groove error is one of the most important factors affecting grating quality and spectral performance. To reduce groove error, we propose a new ruling-tool carriage system based on aerostatic guideways. We design a new blank carriage system with double piezoelectric actuators. We also propose a completely closed-loop servo-control system with a new optical measurement system that can control the position of the diamond relative to the blank. To evaluate our proposed methods, we produced several gratings, including an echelle grating with 79  grooves/mm, a grating with 768  grooves/mm, and a high-density grating with 6000  grooves/mm. The results show that our methods effectively reduce groove error in ruled gratings.

Laser melting of groove defect repair on high thermal conductivity steel (HTCS-150)

NASA Astrophysics Data System (ADS)

Norhafzan, B.; Aqida, S. N.; Fazliana, F.; Reza, M. S.; Ismail, I.; Khairil, C. M.

2018-02-01

This paper presents laser melting repair of groove defect on HTCS-150 surface using Nd:YAG laser system. Laser melting process was conducted using JK300HPS Nd:YAG twin lamp laser source with 1064 nm wavelength and pulsed mode. The parameters are pulse repetition frequency (PRF) that is set from 70 to 100 Hz, average power ( P A) of 50-70 W, and laser spot size of 0.7 mm. HTCS-150 samples were prepared with groove dimension of 0.3 mm width and depths of 0.5 mm using EDM wire cut. Groove defect repaired using laser melting process on groove surface area with various parameters' process. The melted surface within the groove was characterized for subsurface hardness profile, roughness, phase identification, chemical composition, and metallographic study. The roughness analysis indicates high PRF at large spot size caused high surface roughness and low surface hardness. Grain refinement of repaired layer was analyzed within the groove as a result of rapid heating and cooling. The hardness properties of modified HTCS inside the groove and the bulk surface increased two times from as received HTCS due to grain refinement which is in agreement with Hall-Petch equation. These findings are significant to parameter design of die repair for optimum surface integrity and potential for repairing crack depth and width of less than 0.5 and 0.3 mm, respectively.

From the Bandstand to the Classroom: Thinking and Playing Grooves

ERIC Educational Resources Information Center

Baxter, Marsha; Santantasio, Christopher

2012-01-01

In this article, narratives of a salsa concert and a lesson with a Native American flute performer provide openings for exploring grooves and their application in the music classroom. The term "groove" is examined, along with some non-Western ideas about time as represented in the music of the West African Kpelle people. A sixth-grade…

[Developmental radicular groove as a cause of endodontic failure].

PubMed

Fabra Campos, H; Millet Part, J

1989-01-01

A clinical case of apical injury on an upper lateral incisor with endodontical and surgical failures in its treatment is presented. Extraction of the incisor and its study at the stereoscopic microscope showed the existence of a developmental groove running from the cingulum to the end of the root, establishing a communication between the crevice and the apical part of the tooth. Bacterial infection through the groove could provide an explanation for treatment failure.

Grooving of concrete pavements : final report.

DOT National Transportation Integrated Search

1973-08-01

This project was initiated by the Louisiana Department of Highways in cooperation with the Federal Highway Administration to determine whether transverse diamond cut grooves of a certain style (Christensen Style 7) placed in hardened concrete in seve...

Laser beam joining of optical fibers in silicon V-grooves

NASA Astrophysics Data System (ADS)

Kaufmann, Stefan; Otto, Andreas; Luz, Gerhard

2000-06-01

The increasing use of optical data transmission systems and the development of new optical components require adjustment-insensitive and reliable joining and assembling techniques. The state of the art includes the utilization of silicon submounts with anisotropically etched V-grooves. Several glass fibers are fixed in these V-grooves with adhesive. Adhesive bonds tend towards degradation under the influence of temperature and moisture. For this reason, the alternative joining processes laser beam welding and laser beam soldering are relevant. The goal is a reliable joining of optical fibers in V-grooves without damage to the fibers or the silicon submount. Because of the anomaly of silicon during phase transformation, a positive joining can be realized by laser beam welding. A melt pool is created through the energy of a Nd:YAG-laser pulse. During solidification, the volume of silicon increases and a bump is formed in the center. Experiments have shown that this phenomenon can be used for joining optical fibers in silicon-V-grooves. With suitable parameters the silicon flows half around the fiber during solidification. For each fiber, several welding points are necessary. Another promising joining method is laser bema soldering. In this case, a second silicon sheet with a solder deposit is placed on the fibers which lie in the V-grooves of the metallized silicon submount. The laser heats the upper silicon until the solder metals by heat conduction.

Plant nuclei can contain extensive grooves and invaginations

NASA Technical Reports Server (NTRS)

Collings, D. A.; Carter, C. N.; Rink, J. C.; Scott, A. C.; Wyatt, S. E.; Allen, N. S.; Brown, C. S. (Principal Investigator)

2000-01-01

Plant cells can exhibit highly complex nuclear organization. Through dye-labeling experiments in untransformed onion epidermal and tobacco culture cells and through the expression of green fluorescent protein targeted to either the nucleus or the lumen of the endoplasmic reticulum/nuclear envelope in these cells, we have visualized deep grooves and invaginations into the large nuclei of these cells. In onion, these structures, which are similar to invaginations seen in some animal cells, form tubular or planelike infoldings of the nuclear envelope. Both grooves and invaginations are stable structures, and both have cytoplasmic cores containing actin bundles that can support cytoplasmic streaming. In dividing tobacco cells, invaginations seem to form during cell division, possibly from strands of the endoplasmic reticulum trapped in the reforming nucleus. The substantial increase in nuclear surface area resulting from these grooves and invaginations, their apparent preference for association with nucleoli, and the presence in them of actin bundles that support vesicle motility suggest that the structures might function both in mRNA export from the nucleus and in protein import from the cytoplasm to the nucleus.

Effectiveness of various irrigation protocols for the removal of calcium hydroxide from artificial standardized grooves

PubMed Central

GOKTURK, Hakan; OZKOCAK, Ismail; BUYUKGEBIZ, Feyzi; DEMIR, Osman

2017-01-01

Abstract Objective The aim of this study was to investigate the ability of laser-activated irrigation (LAI), XP-endo Finisher, CanalBrush, Vibringe, passive ultrasonic irrigation (PUI), and conventional syringe irrigation systems on the removal of calcium hydroxide (CH) from simulated root canal irregularities. Material and Methods The root canals of one hundred and five extracted single-rooted teeth were instrumented using Reciproc rotary files up to size R40. The teeth were split longitudinally. Two of the three standard grooves were created in the coronal and apical section of one segment, and another in the middle part of the second segment. The standardized grooves were filled with CH and the root halves were reassembled. After 14 days, the specimens were randomly divided into 7 experimental groups (n=15/group). CH was removed as follows: Group 1: beveled needle irrigation; Group 2: double side-vented needle irrigation; Group 3: CanalBrush; Group 4: XP-endo Finisher; Group 5: Vibringe; Group 6: PUI; Group 7: LAI. The amount of remaining CH in the grooves was scored under a stereomicroscope at 20× magnification. Statistical evaluation was performed using Kruskal–Wallis and Bonferroni-Correction Mann–Whitney U tests. Results Groups 1 and 2 were the least efficient in eliminating CH from the grooves. Groups 6 and 7 eliminated more CH than the other protocols; however, no significant differences were found between these two groups (P>.05). Conclusions Nevertheless, none of the investigated protocols were able to completely remove all CH from all three root regions. LAI and PUI showed less residual CH than the other protocols from artificial grooves. PMID:28678948

Two pad axially grooved hydrostatic bearing

NASA Technical Reports Server (NTRS)

San Andres, Luis A. (Inventor)

1995-01-01

A hydrostatic bearing having two axial grooves on opposite sides of the bearing for breaking the rotational symmetry in the dynamic force coefficients thus reducing the whirl frequency ratio and increasing the damping and stiffness of the hydrostatic bearing.

Development of optimized, graded-permeability axial groove heat pipes

NASA Technical Reports Server (NTRS)

Kapolnek, Michael R.; Holmes, H. Rolland

1988-01-01

Heat pipe performance can usually be improved by uniformly varying or grading wick permeability from end to end. A unique and cost effective method for grading the permeability of an axial groove heat pipe is described - selective chemical etching of the pipe casing. This method was developed and demonstrated on a proof-of-concept test article. The process improved the test article's performance by 50 percent. Further improvement is possible through the use of optimally etched grooves.

The role of the bicipital groove in tendopathy of the long biceps tendon.

PubMed

Pfahler, M; Branner, S; Refior, H J

1999-01-01

Long biceps tendon disease is often underrated but plays an important role in anterior shoulder pain. We studied prospectively the anatomy of the bicipital groove and its relationship to clinical symptoms. Sixty-seven consecutive patients were investigated by mutual ultrasonography and radiographs of the intertubercular groove. All images were scrutinized for biceps tendon status (ultrasonography) and groove anatomy (radiography). Thirty-seven patients (21 male, 16 female, average age 48 years) had chronic anterior shoulder pain, and 30 patients (16 male, 14 female, average age 46 years) served as a control group. In 28 shoulders we found sonographic signs of tendovaginitis, and in 14 we found degenerative changes. The mean age of patients with pathologic conditions of the long biceps tendon was 40 years, significantly lower than that of the complete study group. The x-ray films revealed a great variation in the medial and total opening angle of the groove, whereas width, depth, and humeral head diameter showed sex-related differences. Radiologic signs of groove degeneration correlated in 43.6% with biceps tendon disease on the sonogram. Our study revealed statistically significant correlations between groove anatomy and long biceps tendon disease, which should be considered more while shoulder problems are evaluated.

Tunable THz notch filter with a single groove inside parallel-plate waveguides.

PubMed

Lee, Eui Su; Jeon, Tae-In

2012-12-31

A single groove in a parallel-plate waveguide (PPWG) has been applied to a tunable terahertz (THz) notch filter with a transverse-electromagnetic (TEM) mode. When the air gap between the metal plates of the PPWG is controlled from 60 to 240 μm using a motor controlled translation stage or a piezo-actuator, the resonant frequency of the notch filter is changed from 1.75 up to 0.62 THz, respectively. Therefore, the measured tunable sensitivity of the notch filter increases to 6.28 GHz/μm. The measured resonant frequencies were found to be in good agreement with the calculation using an effective groove depth. Using a finite-difference time-domain (FDTD) simulation, we also demonstrate that the sensitivity of a THz microfluidic sensor can be increased via a small air gap, a narrow groove width, and a deep groove depth.

Spontaneous formation of multiple land-and-groove structures of silica thin films

NASA Astrophysics Data System (ADS)

Takeda, Yasuhiko; Matsuoka, Yoriko; Motohiro, Tomoyoshi

1999-05-01

We found spontaneous formation of microscopic multiple land-and-groove structures of silica thin films. Silica and nickel were simultaneously deposited onto glass substrates from two opposite oblique directions to form columnar structures of silica among which nickel nanoparticles were embedded. Then nickel was dissolved in hydrochloric acid solution. After the dissolution of the nickel particles the columns of silica became very unstable and coalesced to form the multiple land-and-groove structures. The grooves are oriented to the direction perpendicular to the two deposition directions. The distances between the neighboring grooves are fairly uniform, and can be controlled between several hundred nanometers and several microns by changing the film thickness and the ratio of the nickel deposition rate to the silica deposition rate. The process found here may propose a new class of micro fabrication techniques in contrast to the artificial photolithography.

Method of forming grooves in the [011] crystalline direction

NASA Technical Reports Server (NTRS)

Marinelli, Donald Paul (Inventor)

1977-01-01

An A-B etchant is applied to a (100) surface of a body of semiconductor material, a portion of which along the (100) surface of the body is either gallium arsenide or gallium aluminum arsenide. The etchant is applied for at least 15 seconds at a temperature of approximately 80.degree. C. The A-B etchant is a solution by weight percent of 47.5%, water, 0.2% silver nitrate, 23.8% chromium trioxide and 28.5% of a 48% aqueous solution of hydrofluoric acid. As a result of the application of the A-B etchant a pattern of elongated etch pits form having their longitudinal axes along the [011] crystalline direction. Grooves are formed in the body at a surface opposite the (100) surface on which was applied the etchant. The grooves are formed along the [011] crystalline direction by aligning the longitudinal axes of the grooves with the longitudinal axes of the etch pits.

Study on the Correlation Between Dynamical Behavior and Friction/Wear Mechanism Under the Effect of Grooves

NASA Astrophysics Data System (ADS)

Zhu, Z. Y.; Mo, J. L.; Wang, D. W.; Zhao, J.; Zhu, M. H.; Zhou, Z. R.

2018-04-01

In this work, the interfacial friction and wear and vibration characteristics are studied by sliding a chromium bearing steel ball (AISI 52100) over both multi-grooved and single-grooved forged steel disks (20CrMnMo) at low and high rotating speeds in order to reveal the effect mechanism of groove-textured surface on tribological behaviors. The results show that the grooves modify the contact state of the ball and the disk at the contact interface. This consequently causes variations in the normal displacement, normal force, and friction force signals. The changes in these three signals become more pronounced with increasing groove width at a low speed. The collision behavior between the ball and the groove increase the amplitude of vibration acceleration at a high speed. The test results suggest that grooves with appropriate widths could trap wear debris on the ball surface while avoiding a strong collision between the disk and the ball, resulting in an improvement in the wear states.

Generating topography through tectonic deformation of ice lithospheres: Simulating the formation of Ganymede's grooves

NASA Astrophysics Data System (ADS)

Bland, M. T.; McKinnon, W. B.

2010-12-01

Ganymede’s iconic topography offers clues to both the satellite’s thermal evolution, and the mechanics of tectonic deformation on icy satellites. Much of Ganymede’s surface consists of bright, young terrain, with a characteristic morphology dubbed “groove terrain”. As reviewed in Pappalardo et al. (2004), in Jupiter - The Planet, Satellites, and Magnetosphere (CUP), grooved terrain consists of sets of quasi-parallel, periodically-spaced, ridges and troughs. Peak-to-trough groove amplitudes are ~500 m, with low topographic slopes (~5°). Groove spacing is strongly periodic within a single groove set, ranging from 3-17 km; shorter wavelength deformation is also apparent in high-resolution images. Grooved terrain likely formed via unstable extension of Ganymede’s ice lithosphere, which was deformed into periodically-spaced pinches and swells, and accommodated by tilt-block normal faulting. Analytical models of unstable extension support this formation mechanism [Dombard and McKinnon 2001, Icarus 154], but initial numerical models of extending ice lithospheres struggled to produce large-amplitude, groove-like deformation [Bland and Showman 2007, Icarus 189]. Here we present simulations that reproduce many of the characteristics of Ganymede’s grooves [Bland et al. 2010, Icarus in press]. By more realistically simulating the decrease in material strength after initial fault development, our model allows strain to become readily localized into discrete zones. Such strain localization leads to the formation of periodic structures with amplitudes of 200-500 m, and wavelengths of 3-20 km. The morphology of the deformation depends on both the lithospheric thermal gradient, and the rate at which material strength decreases with increasing plastic strain. Large-amplitude, graben-like structures form when material weakening occurs rapidly with increasing strain, while lower-amplitude, periodic structures form when the ice retains its strength. Thus, extension can

Readout signals calculated for near-field optical pickups with land and groove recording.

PubMed

Saito, K; Kishima, K; Ichimura, I

2000-08-10

Optical disk readout signals with a solid immersion lens (SIL) and the land-groove recording technique are calculated by use of a simplified vector-diffraction theory. In this method the full vector-diffraction theory is applied to calculate the diffracted light from the initial state of the disk, and the light scattered from the recorded marks is regarded as a perturbation. Using this method, we confirmed that the land-groove recording technique is effective as a means of cross-talk reduction even when the numerical aperture is more than 1. However, the top surface of the disk under the SIL must be flat, or the readout signal from marks recorded on a groove decays when the optical depth of the groove is greater than lambda/8.

Modeling and Analysis of the Static Characteristics and Dynamic Responses of Herringbone-grooved Thrust Bearings

NASA Astrophysics Data System (ADS)

Yu, Yunluo; Pu, Guang; Jiang, Kyle

2017-12-01

This paper describes a theoretical investigation of static and dynamic characteristics of herringbone-grooved air thrust bearings. Firstly, Finite Difference Method (FDM) and Finite Volume Method (FVM) are used in combination to solve the non-linear Reynolds equation and to find the pressure distribution of the film and the total loading capacity of the bearing. The influence of design parameters on air film gap characteristics, including the air film thickness, depth of the groove and rotating speed, are analyzed based on the FDM model. The simulation results show that hydrostatic thrust bearings can achieve a better load capacity with less air consumption than herringbone grooved thrust bearings at low compressibility number; herringbone grooved thrust bearings can achieve a higher load capacity but with more air consumption than hydrostatic thrust bearing at high compressibility number; herringbone grooved thrust bearings would lose stability at high rotating speeds, and the stability increases with the depth of the grooves.

Channel plasmon-polariton guiding by subwavelength metal grooves.

PubMed

Bozhevolnyi, Sergey I; Volkov, Valentyn S; Devaux, Eloïse; Ebbesen, Thomas W

2005-07-22

We report on realization of channel plasmon-polariton (CPP) propagation along a subwavelength metal groove. Using imaging with a near-field microscope and end-fire coupling with a tapered fiber connected to a tunable laser at telecommunication wavelengths (1425-1620 nm), we demonstrate low-loss (propagation length approximately 100 microm) and well-confined (mode width approximately 1.1 microm) CPP guiding along a triangular 0.6 microm-wide and 1 microm-deep groove in gold. We develop a simple model based on the effective-index method that accounts for the main features of CPP guiding and provides a clear physical picture of this phenomenon.

Optimal Tempo for Groove: Its Relation to Directions of Body Movement and Japanese nori

PubMed Central

Etani, Takahide; Marui, Atsushi; Kawase, Satoshi; Keller, Peter E.

2018-01-01

The tendency for groove-based music to induce body movements has been linked to multiple acoustical factors. However, it is unclear how or whether tempo affects groove, although tempo significantly affects other aspects of music perception. To address this issue, the present study investigated effects of tempo, specific rhythmic organizations of patterns, and syncopation on groove and the induction of the sensation of wanting to move. We focused on the directions of body movement in particular by taking into account nori, which is an indigenous Japanese musical term used not only synonymously with groove, but also as a spatial metaphor indicating vertical or horizontal movement directions. Thus, the present study explored how groove was felt and defined, as well as how musical factors induced the sensation of wanting to move in cross-cultural context. A listening experiment was conducted using drum breaks as stimuli. Stimuli consisted of various rhythm patterns at six tempi from 60 to 200 BPM. The main findings are that: (1) an optimal tempo for groove existed for drum breaks at around 100–120 BPM, (2) an optimal tempo existed for the sensation of wanting to move the body in specific directions (i.e., back-and-forth and side-to-side), (3) groove and nori shared a similar concept of wanting to move but differed on several points (i.e., association with sense of pulse and fast tempo). Overall, the present study suggests that there is an optimal tempo for body movement related to groove. This finding has implications for the use of music or rhythmic stimuli to induce smooth motion in rehabilitation, therapy, or dance. PMID:29692747

Mathematical modeling of photovoltaic thermal PV/T system with v-groove collector

NASA Astrophysics Data System (ADS)

Zohri, M.; Fudholi, A.; Ruslan, M. H.; Sopian, K.

2017-07-01

The use of v-groove in solar collector has a higher thermal efficiency in references. Dropping the working heat of photovoltaic panel was able to raise the electrical efficiency performance. Electrical and thermal efficiency were produced by photovoltaic thermal (PV/T) system concurrently. Mathematical modeling based on steady-state thermal analysis of PV/T system with v-groove was conducted. With matrix inversion method, the energy balance equations are explained by means of the investigative method. The comparison results show that in the PV/T system with the V-groove collector is higher temperature, thermal and electrical efficiency than other collectors.

U-Groove aluminum weld strength improvement

NASA Technical Reports Server (NTRS)

Verderaime, V.; Vaughan, R.

1996-01-01

Though butt-welds are among the most preferred joining methods in aerostructures, their strength dependence on inelastic mechanics is generally the least understood. This study investigated experimental strain distributions across a thick aluminum U-grooved weld and identified two weld process considerations for improving the multipass weld strength. The extreme thermal expansion and contraction gradient of the fusion heat input across the groove tab thickness produces severe peaking, which induces bending under uniaxial loading. The filler strain-hardening decreased with increasing filler pass sequence, producing the weakest welds on the last pass side. Current welding schedules unknowingly compound these effects which reduce the weld strength. A depeaking index model was developed to select filler pass thicknesses, pass numbers, and sequences to improve depeaking in the welding process. The intent is to combine the strongest weld pass side with the peaking induced bending tension to provide a more uniform stress and stronger weld under axial tensile loading.

The fundamental ribosomal RNA transcription initiation factor-IB (TIF-IB, SL1, factor D) binds to the rRNA core promoter primarily by minor groove contacts.

PubMed

Geiss, G K; Radebaugh, C A; Paule, M R

1997-11-14

Acanthamoeba castellanii transcription initiation factor-IB (TIF-IB) is the TATA-binding protein-containing transcription factor that binds the rRNA promoter to form the committed complex. Minor groove-specific drugs inhibit TIF-IB binding, with higher concentrations needed to disrupt preformed complexes because of drug exclusion by bound TIF-IB. TIF-IB/DNA interactions were mapped by hydroxyl radical and uranyl nitrate footprinting. TIF-IB contacts four minor grooves in its binding site. TIF-IB and DNA wrap around each other in a right-handed superhelix of high pitch, so the upstream and downstream contacts are on opposite faces of the helix. Dimethyl sulfate protection assays revealed limited contact with a few guanines in the major groove. This detailed analysis suggests significant DNA conformation dependence of the interaction.

The Effect of Expert Performance Microtiming on Listeners' Experience of Groove in Swing or Funk Music

PubMed Central

Senn, Olivier; Kilchenmann, Lorenz; von Georgi, Richard; Bullerjahn, Claudia

2016-01-01

This study tested the influence of expert performance microtiming on listeners' experience of groove. Two professional rhythm section performances (bass/drums) in swing and funk style were recorded, and the performances' original microtemporal deviations from a regular metronomic grid were scaled to several levels of magnitude. Music expert (n = 79) and non-expert (n = 81) listeners rated the groove qualities of stimuli using a newly developed questionnaire that measures three dimensions of the groove experience (Entrainment, Enjoyment, and the absence of Irritation). Findings show that music expert listeners were more sensitive to microtiming manipulations than non-experts. Across both expertise groups and for both styles, groove ratings were high for microtiming magnitudes equal or smaller than those originally performed and decreased for exaggerated microtiming magnitudes. In particular, both the fully quantized music and the music with the originally performed microtiming pattern were rated equally high on groove. This means that neither the claims of PD theory (that microtiming deviations are necessary for groove) nor the opposing exactitude hypothesis (that microtiming deviations are detrimental to groove) were supported by the data. PMID:27761117

The Effect of Expert Performance Microtiming on Listeners' Experience of Groove in Swing or Funk Music.

PubMed

Senn, Olivier; Kilchenmann, Lorenz; von Georgi, Richard; Bullerjahn, Claudia

2016-01-01

This study tested the influence of expert performance microtiming on listeners' experience of groove. Two professional rhythm section performances (bass/drums) in swing and funk style were recorded, and the performances' original microtemporal deviations from a regular metronomic grid were scaled to several levels of magnitude. Music expert ( n = 79) and non-expert ( n = 81) listeners rated the groove qualities of stimuli using a newly developed questionnaire that measures three dimensions of the groove experience ( Entrainment, Enjoyment , and the absence of Irritation ). Findings show that music expert listeners were more sensitive to microtiming manipulations than non-experts. Across both expertise groups and for both styles, groove ratings were high for microtiming magnitudes equal or smaller than those originally performed and decreased for exaggerated microtiming magnitudes. In particular, both the fully quantized music and the music with the originally performed microtiming pattern were rated equally high on groove. This means that neither the claims of PD theory (that microtiming deviations are necessary for groove) nor the opposing exactitude hypothesis (that microtiming deviations are detrimental to groove) were supported by the data.

Applied anatomy of small branches of the portal vein in transverse groove of hepatic hilum.

PubMed

Yan, Pei-ning; Tan, Wei-feng; Yang, Xin-wei; Zhang, Chuan-sen; Jiang, Xiao-qing

2014-12-01

The objective of this study was to provide the morphological details on small branches of the portal vein in transverse groove of hepatic hilum. According to the surgery significance, the small branches of portal vein in transverse groove of hepatic hilum were named as "Short hepatic portal veins (SHPVs)". SHPVs were minutely dissected in 30 adult cadaveric livers. The number, diameter, length, origin points, and entering liver sites of SHPVs were explored and measured. There were 181 SHPVs in 30 liver specimens, including 46% (83/181) from the left portal vein, 31% (56/181) from the bifurcation, and 23% (42/181) from the right portal vein. At the entering liver sites of SHPVs, 22% (40/181) supplied for segment IV, 9% (17/181) for segment V, 4% (7/181) for segment VI, 23% (41/181) for segment VII, and 42% (76/181) for segment I (caudate lobe). There were 6.0 ± 2.4 branches per liver specimen with range 3-12. The mean diameter of SHPVs was 2.25 ± 0.89 mm. The average length of SHPVs was 4.86 ± 2.12 mm. SHPVs widely existed in each liver specimen. The detailed anatomical study of SHPVs could be useful to avoid damaging the short portal branches during hepatic operations, such as isolated or combined caudate lobectomy.

Terahertz absorber based on Fano-like resonance of inverted quadrangular frustum pyramid metal grooves and sensor application

NASA Astrophysics Data System (ADS)

Yu, Yingying; Sun, Bo

2018-07-01

We investigate the multi-resonance coupling of inverted quadrangular frustum pyramid (IQFP) groove metal arrays at terahertz frequencies. The surface plasmon resonance (SPR) and groove resonance are induced, resulting in resonance coupling. The dipole of the groove resonance drives the quadrupole of the SPR and creates a sharp Fano-like resonance. The effects of geometry parameters including the width (at the bottom) and height are analyzed in detail. The results show that with the decrease in the sidewall slope of the groove, the confinement of the groove region on the electromagnetic field decreases, thereby increasing the resonance coupling. The Fano-like resonance is enhanced. The sensitivity and quality factor are discussed. The results show that the Fano-like resonance has high sensitivity and quality factor. With the increase in the sidewall slope of the groove, the sensitivity increases, and the quality factor decreases. The results show that the Fano-like resonance of IQFP groove metal arrays has a significant potential for biological monitoring and sensing.

Modifications of Ti-6Al-4V surfaces by direct-write laser machining of linear grooves

NASA Astrophysics Data System (ADS)

Ulerich, Joseph P.; Ionescu, Lara C.; Chen, Jianbo; Soboyejo, Winston O.; Arnold, Craig B.

2007-02-01

As patients who receive orthopedic implants live longer and opt for surgery at a younger age, the need to extend the in vivo lifetimes of these implants has grown. One approach is to pattern implant surfaces with linear grooves, which elicit a cellular response known as contact guidance. Lasers provide a unique method of generating these surface patterns because they are capable of modifying physical and chemical properties over multiple length scales. In this paper we explore the relationship between surface morphology and laser parameters such as fluence, pulse overlap (translation distance), number of passes, and machining environment. We find that using simple procedures involving multiple passes it is possible to manipulate groove properties such as depth, shape, sub-micron roughness, and chemical composition of the Ti-6Al-4V oxide layer. Finally, we demonstrate this procedure by machining several sets of grooves with the same primary groove parameters but varied secondary characteristics. The significance of the secondary groove characteristics is demonstrated by preliminary cell studies indicating that the grooves exhibit basic features of contact guidance and that the cell proliferation in these grooves are significantly altered despite their similar primary characteristics. With further study it will be possible to use specific laser parameters during groove formation to create optimal physical and chemical properties for improved osseointegration.

Crystal Structure of the Dithiol Oxidase DsbA Enzyme from Proteus Mirabilis Bound Non-covalently to an Active Site Peptide Ligand

PubMed Central

Kurth, Fabian; Duprez, Wilko; Premkumar, Lakshmanane; Schembri, Mark A.; Fairlie, David P.; Martin, Jennifer L.

2014-01-01

The disulfide bond forming DsbA enzymes and their DsbB interaction partners are attractive targets for development of antivirulence drugs because both are essential for virulence factor assembly in Gram-negative pathogens. Here we characterize PmDsbA from Proteus mirabilis, a bacterial pathogen increasingly associated with multidrug resistance. PmDsbA exhibits the characteristic properties of a DsbA, including an oxidizing potential, destabilizing disulfide, acidic active site cysteine, and dithiol oxidase catalytic activity. We evaluated a peptide, PWATCDS, derived from the partner protein DsbB and showed by thermal shift and isothermal titration calorimetry that it binds to PmDsbA. The crystal structures of PmDsbA, and the active site variant PmDsbAC30S were determined to high resolution. Analysis of these structures allows categorization of PmDsbA into the DsbA class exemplified by the archetypal Escherichia coli DsbA enzyme. We also present a crystal structure of PmDsbAC30S in complex with the peptide PWATCDS. The structure shows that the peptide binds non-covalently to the active site CXXC motif, the cis-Pro loop, and the hydrophobic groove adjacent to the active site of the enzyme. This high-resolution structural data provides a critical advance for future structure-based design of non-covalent peptidomimetic inhibitors. Such inhibitors would represent an entirely new antibacterial class that work by switching off the DSB virulence assembly machinery. PMID:24831013

U-shaped micro-groove fiber based on femtosecond laser processing for humidity sensing

NASA Astrophysics Data System (ADS)

Fu, Gui; Ma, Li-li; Su, Fu-fang; Shi, Meng

2018-05-01

A novel optical fiber sensor with a U-shaped micro-groove structure ablated by femtosecond laser on single-mode fiber for measuring air relative humidity (RH) is reported in this paper. In order to improve the accuracy of sensor, a graphene oxide (GO)/polyvinyl alcohol (PVA) composite film is coated on the surface of micro-groove structure. In the U-shaped micro-groove structure, the remaining core and micro-cavity in the micro-groove make up two major optical propagation paths, forming a Mach-Zehnder interferometer (MZI). The sensor has a good linear response within the RH range of 30%—85%, and the maximum sensitivity can reach 0.638 1 nm/%RH. The effect of temperature on the overall performance of the humidity sensor is also investigated. As a new type of all-fiber device, the sensor shows excellent sensitivity and stability.

Optimally oriented grooves on dental implants improve bone quality around implants under repetitive mechanical loading.

PubMed

Kuroshima, Shinichiro; Nakano, Takayoshi; Ishimoto, Takuya; Sasaki, Muneteru; Inoue, Maaya; Yasutake, Munenori; Sawase, Takashi

2017-01-15

The aim was to investigate the effect of groove designs on bone quality under controlled-repetitive load conditions for optimizing dental implant design. Anodized Ti-6Al-4V alloy implants with -60° and +60° grooves around the neck were placed in the proximal tibial metaphysis of rabbits. The application of a repetitive mechanical load was initiated via the implants (50N, 3Hz, 1800 cycles, 2days/week) at 12weeks after surgery for 8weeks. Bone quality, defined as osteocyte density and degree of biological apatite (BAp) c-axis/collagen fibers, was then evaluated. Groove designs did not affect bone quality without mechanical loading; however, repetitive mechanical loading significantly increased bone-to-implant contact, bone mass, and bone mineral density (BMD). In +60° grooves, the BAp c-axis/collagen fibers preferentially aligned along the groove direction with mechanical loading. Moreover, osteocyte density was significantly higher both inside and in the adjacent region of the +60° grooves, but not -60° grooves. These results suggest that the +60° grooves successfully transmitted the load to the bone tissues surrounding implants through the grooves. An optimally oriented groove structure on the implant surface was shown to be a promising way for achieving bone tissue with appropriate bone quality. This is the first report to propose the optimal design of grooves on the necks of dental implants for improving bone quality parameters as well as BMD. The findings suggest that not only BMD, but also bone quality, could be a useful clinical parameter in implant dentistry. Although the paradigm of bone quality has shifted from density-based assessments to structural evaluations of bone, clarifying bone quality based on structural bone evaluations remains challenging in implant dentistry. In this study, we firstly demonstrated that the optimal design of dental implant necks improved bone quality defined as osteocytes and the preferential alignment degree of biological

The resistance of high frequency inductive welded pipe to grooving corrosion in salt water

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

Duran, C.; Triess, E.; Herbsleb, G.

1986-09-01

When exposed to neutral, salt-containing waters, electric resistant welded pipe in carbon and low alloy steels with increased sulfur contents may suffer preferential corrosion attack in the weld area. Because of its appearance, this type of corrosion is called grooving corrosion. The susceptibility to grooving corrosion may be determined and quantitatively described by means of an accelerated potentiostatic exposure test. The importance of type, concentration, and temperature of the electrolytic solution; potential; test duration; and the sulfur content of the steel in the accelerated corrosion test and the susceptibility of steels to grooving corrosion are described. Line pipe in highmore » frequency inductive (HFI) welded carbon and low alloy steels are resistant to grooving corrosion particularly because of their low sulfur content.« less

Effect on Bone Architecture of Marginal Grooves in Dental Implants Under Occlusal Loaded Conditions in Beagle Dogs.

PubMed

Kato, Hatsumi; Kuroshima, Shinichiro; Inaba, Nao; Uto, Yusuke; Sawase, Takashi

2018-02-01

The aim of this study was to clarify whether marginal grooves on dental implants affect osseointegration, bone structure, and the alignment of collagen fibers to determine bone quality under loaded conditions. Anodized Ti-6Al-4V alloy dental implants, with and without marginal grooves (test and control implants, respectively), were used (3.7 × 8.0 mm). Fourth premolars and first molars of 6 beagle mandibles were extracted. Two control and test implants were placed in randomly selected healed sites at 12 weeks after tooth extraction. Screw-retained single crowns for first molars were fabricated. Euthanasia was performed at 8 weeks after the application of occlusal forces. Implant marginal bone level, bone to implant contact (BIC), bone structure around dental implants, and the alignment of collagen fibers determining bone quality were analyzed. The marginal bone level in test implants was significantly higher than that in control implants. Occlusal forces significantly increased BIC in test implants ( P = .007), whereas BIC did not change in control implants, irrespective of occlusal forces ( P = .303). Moreover, occlusal forces significantly increased BIC in test implants compared with control implants ( P = .032). Additionally, occlusal forces preferentially aligned collagen fibers in test implants, but not control implants. Hence, marginal grooves on dental implants have positive effects on increased osseointegration and adapted bone quality based on the preferential alignment of collagen fibers around dental implants under loaded conditions.

Comparative evaluation of three heat transfer enhancement strategies in a grooved channel

NASA Astrophysics Data System (ADS)

Herman, C.; Kang, E.

Results of a comparative evaluation of three heat transfer enhancement strategies for forced convection cooling of a parallel plate channel populated with heated blocks, representing electronic components mounted on printed circuit boards, are reported. Heat transfer in the reference geometry, the asymmetrically heated parallel plate channel, is compared with that for the basic grooved channel, and the same geometry enhanced by cylinders and vanes placed above the downstream edge of each heated block. In addition to conventional heat transfer and pressure drop measurements, holographic interferometry combined with high-speed cinematography was used to visualize the unsteady temperature fields in the self-sustained oscillatory flow. The locations of increased heat transfer within one channel periodicity depend on the enhancement technique applied, and were identified by analyzing the unsteady temperature distributions visualized by holographic interferometry. This approach allowed gaining insight into the mechanisms responsible for heat transfer enhancement. Experiments were conducted at moderate flow velocities in the laminar, transitional and turbulent flow regimes. Reynolds numbers were varied in the range Re=200-6500, corresponding to flow velocities from 0.076 to 2.36m/s. Flow oscillations were first observed between Re=1050 and 1320 for the basic grooved channel, and around Re=350 and 450 for the grooved channels equipped with cylinders and vanes, respectively. At Reynolds numbers above the onset of oscillations and in the transitional flow regime, heat transfer rates in the investigated grooved channels exceeded the performance of the reference geometry, the asymmetrically heated parallel plate channel. Heat transfer in the grooved channels enhanced with cylinders and vanes showed an increase by a factor of 1.2-1.8 and 1.5-3.5, respectively, when compared to data obtained for the basic grooved channel; however, the accompanying pressure drop penalties also

User's Manual for Thermal Analysis Program of Axially Grooved Heat Pipe (HTGAP)

NASA Technical Reports Server (NTRS)

Kamotani, Y.

1978-01-01

A computer program that numerically predicts the steady state temperature distribution inside an axially grooved heat pipe wall for a given groove geometry and working fluid under various heat input and output modes is described. The program computes both evaporator and condenser film coefficients. The program is able to handle both axisymmetric and nonaxisymmetric heat transfer cases. Non-axisymmetric heat transfer results either from non-uniform input at the evaporator or non-uniform heat removal from the condenser, or from both. The presence of a liquid pool in the condenser region under one-g condition also causes non-axisymmetric heat transfer, and its effect on the pipe wall temperature distribution is included in the present program. The hydrodynamic aspect of an axially grooved heat pipe is studied in the Groove Analysis Program (GAP). The present thermal analysis program assumes that the GAP program (or other similar programs) is run first so that the heat transport limit and optimum fluid charge of the heat pipe are known a priori.

Fracture toughness determination using spiral-grooved cylindrical specimen and pure torsional loading

DOEpatents

Wang, Jy-An; Liu, Kenneth C.

2003-07-08

A method for determining fracture toughness K.sub.IC of materials ranging from metallic alloys, brittle ceramics and their composites, and weldments. A cylindrical specimen having a helical V-groove with a 45.degree. pitch is subjected to pure torsion. This loading configuration creates a uniform tensile-stress crack-opening mode, and a transverse plane-strain state along the helical groove. The full length of the spiral groove is equivalent to the thickness of a conventional compact-type specimen. K.sub.IC values are determined from the fracture torque and crack length measured from the test specimen using a 3-D finite element program (TOR3D-KIC) developed for the purpose. In addition, a mixed mode (combined tensile and shear stress mode) fracture toughness value can be determined by varying the pitch of the helical groove. Since the key information needed for determining the K.sub.IC value is condensed in the vicinity of the crack tip, the specimen can be significantly miniaturized without the loss of generality.

Gradient rotating outer volume excitation (GROOVE): A novel method for single-shot two-dimensional outer volume suppression.

PubMed

Powell, Nathaniel J; Jang, Albert; Park, Jang-Yeon; Valette, Julien; Garwood, Michael; Marjańska, Małgorzata

2015-01-01

To introduce a new outer volume suppression (OVS) technique that uses a single pulse and rotating gradients to accomplish frequency-swept excitation. This new technique, which is called gradient rotating outer volume excitation (GROOVE), produces a circular or elliptical suppression band rather than suppressing the entire outer volume. Theoretical and k-space descriptions of GROOVE are provided. The properties of GROOVE were investigated with simulations, phantom, and human experiments performed using a 4T horizontal bore magnet equipped with a TEM coil. Similar suppression performance was obtained in phantom and human brain using GROOVE with circular and elliptical shapes. Simulations indicate that GROOVE requires less SAR and time than traditional OVS schemes, but traditional schemes provide a sharper transition zone and less residual signal. GROOVE represents a new way of performing OVS in which spins are excited temporally in space on a trajectory that can be tailored to fit the shape of the suppression region. In addition, GROOVE is capable of suppressing tailored regions of space with more flexibility and in a shorter period of time than conventional methods. GROOVE provides a fast, low SAR alternative to conventional OVS methods in some applications (e.g., scalp suppression). © 2014 Wiley Periodicals, Inc.

The enzymatic processing of α-dystroglycan by MMP-2 is controlled by two anchoring sites distinct from the active site

PubMed Central

Fasciglione, Giovanni Francesco; Sbardella, Diego; Sciandra, Francesca; Casella, MariaLuisa; Camerini, Serena; Crescenzi, Marco; Gori, Alessandro; Tarantino, Umberto; Cozza, Paola; Brancaccio, Andrea; Coletta, Massimo; Bozzi, Manuela

2018-01-01

Dystroglycan (DG) is a membrane receptor, belonging to the dystrophin-glycoprotein complex (DGC) and formed by two subunits, α-dystroglycan (α-DG) and β-dystroglycan (β -DG). The C-terminal domain of α-DG and the N-terminal extracellular domain of β -DG are connected, providing a link between the extracellular matrix and the cytosol. Under pathological conditions, such as cancer and muscular dystrophies, DG may be the target of metalloproteinases MMP-2 and MMP-9, contributing to disease progression. Previously, we reported that the C-terminal domain α-DG (483–628) domain is particularly susceptible to the catalytic activity of MMP-2; here we show that the α-DG 621–628 region is required to carry out its complete digestion, suggesting that this portion may represent a MMP-2 anchoring site. Following this observation, we synthesized an α-DG based-peptide, spanning the (613–651) C-terminal region. The analysis of the kinetic and thermodynamic parameters of the whole and the isolated catalytic domain of MMP-2 (cdMMP-2) has shown its inhibitory properties, indicating the presence of (at least) two binding sites for the peptide, both located within the catalytic domain, only one of the two being topologically distinct from the catalytic active groove. However, the different behavior between whole MMP-2 and cdMMP-2 envisages the occurrence of an additional binding site for the peptide on the hemopexin-like domain of MMP-2. Interestingly, mass spectrometry analysis has shown that α-DG (613–651) peptide is cleavable even though it is a very poor substrate of MMP-2, a feature that renders this molecule a promising template for developing a selective MMP-2 inhibitor. PMID:29447293

Spiral groove seal. [for hydraulic rotating shaft

NASA Technical Reports Server (NTRS)

Ludwig, L. P. (Inventor)

1973-01-01

Mating flat surfaces inhibit leakage of a fluid around a stationary shaft. A spiral groove pattern produces a pumping action toward the fluid when the shaft rotates which prevents leakage while a generated hydraulic lifting force separates the mating surfaces to minimize wear.

Longitudinal afterbody grooves and shoulder radiusing for low-speed bluff body drag reduction

NASA Technical Reports Server (NTRS)

Howard, F. G.; Quass, B. F.; Weinstein, L. M.; Bushnell, D. M.

1981-01-01

A new low-speed drag reduction approach is proposed which employs longitudinal surface V-shaped grooves cutting through the afterbody shoulder region. The test Reynolds number range was from 20,000 to 200,000 based on undisturbed free-stream flow and a body diameter of 6.08 cm. The V-grooves are shown to be most effective in reducing drag when the afterbody shoulder radius is zero. Reductions in drag of up to 33% have been measured for this condition. For large shoulder radius, the grooves are only effective at the lower Reynolds numbers of the test.

Polarizing beam splitter of deep-etched triangular-groove fused-silica gratings.

PubMed

Zheng, Jiangjun; Zhou, Changhe; Feng, Jijun; Wang, Bo

2008-07-15

We investigated the use of a deep-etched fused-silica grating with triangular-shaped grooves as a highly efficient polarizing beam splitter (PBS). A triangular-groove PBS grating is designed at a wavelength of 1550 nm to be used in optical communication. When it is illuminated in Littrow mounting, the transmitted TE- and TM-polarized waves are mainly diffracted in the minus-first and zeroth orders, respectively. The design condition is based on the average differences of the grating mode indices, which is verified by using rigorous coupled-wave analysis. The designed PBS grating is highly efficient over the C+L band range for both TE and TM polarizations (>97.68%). It is shown that such a triangular-groove PBS grating can exhibit a higher diffraction efficiency, a larger extinction ratio, and less reflection loss than the binary-phase fused-silica PBS grating.

Some effects of grooved runway configurations on aircraft tire braking traction under flooded runway conditions

NASA Technical Reports Server (NTRS)

Byrdsong, T. A.

1973-01-01

An experimental investigation was conducted to study the effect of grooved runway configurations on aircraft tire braking traction on flooded runway surfaces. The investigation was performed, utilizing size 49 x 17, type VII, aircraft tires with an inflation pressure of 170 lb per square inch at ground speeds up to approximately 120 knots. The results of this investigation indicate that when the runway is flooded, grooved surfaces provide better braking traction than an ungrooved surface and, in general, the level of braking traction was found to improve as the tire bearing pressure was increased because of an increase in the groove area of either the surface or the tire tread. Rounding the groove edges tended to degrade the tire braking capability from that developed on the same groove configuration with sharp edges. Results also indicate that braking friction coefficients for the test tires and runway surfaces decreased as ground speed was increased because of the hydroplaning effects.

Influence of edge conditions on material ejection from periodic grooves in laser shock-loaded tin

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

Rességuier, T. de; Roland, C.; Prudhomme, G.

2016-05-14

In a material subjected to high dynamic compression, the breakout of a shock wave at a rough free surface can lead to the ejection of high velocity debris. Anticipating the ballistic properties of such debris is a key safety issue in many applications involving shock loading, including pyrotechnics and inertial confinement fusion experiments. In this paper, we use laser driven shocks to investigate particle ejection from calibrated grooves of micrometric dimensions and approximately sinusoidal profile in tin samples, with various boundary conditions at the groove edges, including single groove and periodic patterns. Fast transverse shadowgraphy provides ejection velocities after shockmore » breakout. They are found to depend not only on the groove depth and wavelength, as predicted theoretically and already observed in the past, but also, unexpectedly, on the edge conditions, with a jet tip velocity significantly lower in the case of a single groove than behind a periodic pattern.« less

What Components Comprise the Measurement of the Tibial Tuberosity-Trochlear Groove Distance in a Patellar Dislocation Population?

PubMed

Tensho, Keiji; Akaoka, Yusuke; Shimodaira, Hiroki; Takanashi, Seiji; Ikegami, Shota; Kato, Hiroyuki; Saito, Naoto

2015-09-02

The tibial tuberosity-trochlear groove distance is used as an indicator for medial tibial tubercle transfer; however, to our knowledge, no studies have verified whether this distance is strongly affected by tubercle lateralization at the proximal part of the tibia. We hypothesized that the tibial tuberosity-trochlear groove distance is mainly affected by tibial tubercle lateralization at the proximal part of the tibia. Forty-four patients with a history of patellar dislocation and forty-four age and sex-matched controls were analyzed with use of computed tomography. The tibial tuberosity-trochlear groove distance, tibial tubercle lateralization, trochlear groove medialization, and knee rotation were measured and were compared between the patellar dislocation group and the control group. The association between the tibial tuberosity-trochlear groove distance and three other parameters was calculated with use of the Pearson correlation coefficient and partial correlation analysis. There were significant differences in the tibial tuberosity-trochlear groove distance (p < 0.001) and knee rotation (p < 0.001), but there was no difference in the tibial tubercle lateralization (p = 0.13) and trochlear groove medialization (p = 0.08) between the patellar dislocation group and the control group. The tibial tuberosity-trochlear groove distance had no linear correlation with tubercle lateralization (r = 0.21) or groove medialization (r = -0.15); however, knee rotation had a good positive correlation in the patellar dislocation group (r = 0.62). After adjusting for the remaining parameters, knee rotation strongly correlated with the tibial tuberosity-trochlear groove distance (r = 0.69, p < 0.001), whereas tubercle lateralization showed moderate significant correlations in the patellar dislocation group (r = 0.42; p = 0.005). Because the tibial tuberosity-trochlear groove distance is affected more by knee rotation than by tubercle malposition, its use as an indicator for

Levitation and locomotion on an air-table of plates with herringbone grooves

NASA Astrophysics Data System (ADS)

Hinch, John; de Maleprade, Helene

2017-11-01

Recent experiments in ESPCI in Paris and numerical simulations in Nano- and Microfluidics in Darmstadt have shown that plates with herringbone grooves in their base are accelerated on an air-table in the direction that the chevron grooves point. A simple two-dimensional model is constructed of the air flow down a channel with pressure controlled influx across the lower boundary. Limiting cases are considered of low and high Reynolds numbers, and of small and large pressure drop down the channel compared with the pressure drop across the porous plate. The levitation and locomotion forces are calculated. A prediction is made for the locomotive acceleration which avoids the complications of the shorter grooves which exit the front and back edges.

Structure of a Pheromone Receptor-Associated Mhc Molecule With An Open And Empty Groove

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

Olson, R.; Huey-Tubman, K.E.; Dulac, C.

2006-10-06

Neurons in the murine vomeronasal organ (VNO) express a family of class Ib major histocompatibility complex (MHC) proteins (M10s) that interact with the V2R class of VNO receptors. This interaction may play a direct role in the detection of pheromonal cues that initiate reproductive and territorial behaviors. The crystal structure of M10.5, an M10 family member, is similar to that of classical MHC molecules. However, the M10.5 counterpart of the MHC peptide-binding groove is open and unoccupied, revealing the first structure of an empty class I MHC molecule. Similar to empty MHC molecules, but unlike peptide-filled MHC proteins and non-peptide-bindingmore » MHC homologs, M10.5 is thermally unstable, suggesting that its groove is normally occupied. However, M10.5 does not bind endogenous peptides when expressed in mammalian cells or when offered a mixture of class I-binding peptides. The F pocket side of the M10.5 groove is open, suggesting that ligands larger than 8-10-mer class I-binding peptides could fit by extending out of the groove. Moreover, variable residues point up from the groove helices, rather than toward the groove as in classical MHC structures. These data suggest that M10s are unlikely to provide specific recognition of class I MHC-binding peptides, but are consistent with binding to other ligands, including proteins such as the V2Rs.« less

Erosion of a grooved surface caused by impact of particle-laden flow

NASA Astrophysics Data System (ADS)

Jung, Sohyun; Yang, Eunjin; Kim, Ho-Young

2016-11-01

Solid erosion can be a life-limiting process for mechanical elements in erosive environments, thus it is of practical importance in many industries such as construction, mining, and coal conversion. Erosion caused by particle-laden flow occurs through diverse mechanisms, such as cutting, plastic deformation, brittle fracture, fatigue and melting, depending on particle velocity, total particle mass and impingement angle. Among a variety of attempts to lessen erosion, here we investigate the effectiveness of millimeter-sized grooves on the surface. By experimentally measuring the erosion rates of smooth and triangular-grooved surfaces under various impingement angles, we find that erosion can be significantly reduced within a finite range of impingement angles. We show that such erosion resistance is attributed to the swirls of air within grooves and the differences in erosive strength of normal and slanted impact. In particular, erosion is mitigated when we increase the effective area under normal impact causing plastic deformation and fracture while decreasing the area under slanted impact that cuts the surface to a large degree. Our quantitative model for the erosion rate of grooved surfaces considering the foregoing effects agrees with the measurement results.

Correcting Nasojugal Groove with Autologous Cultured Fibroblast Injection: A Pilot Study.

PubMed

Moon, Kyung-Chul; Lee, Hyun-Su; Han, Seung-Kyu; Chung, Ho-Yun

2018-06-01

A new commercial drug that contains autologous cultured fibroblasts has been developed and approved by the United States Food and Drug Administration for improving the appearance of nasolabial folds. However, the treatment requires three sessions every 3-6 weeks. It is known that the skin overlying the nasojugal groove is thinner, and the wrinkle is generally shallower than nasolabial folds. Therefore, we hypothesized that the nasojugal groove could be improved by just one treatment session. Therefore, the purpose of this study was to evaluate the efficacy and safety of autologous cultured fibroblast injection to correct nasojugal grooves. Forty-six subjects with nasojugal grooves were enrolled in this study. They were injected with autologous cultured fibroblasts or placebo in one session. Blinded evaluators and subjects assessed the efficacy using a validated wrinkle assessment scale at 4, 12, and 24 weeks after the injection. Information of adverse events was collected at each visit. Based on the evaluators' assessment at 24 weeks after the injection, 76% of subjects treated with autologous cultured fibroblasts showed improvement whereas 0% of subjects treated with placebo showed improvement (P < 0.0001). Based on self-assessment at 24 weeks after the injection, 72% of subjects treated with autologous cultured fibroblasts and 45% of subjects treated with placebo showed improvement (P = 0.0662). There were no serious adverse events related to autologous cultured fibroblast injection. Autologous cultured fibroblast injection might be effective and safe to correct nasojugal grooves. This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

Plant Nuclei Can Contain Extensive Grooves and InvaginationsW⃞W⃞

PubMed Central

Collings, David A.; Carter, Crystal N.; Rink, Jochen C.; Scott, Amie C.; Wyatt, Sarah E.; Allen, Nina Strömgren

2000-01-01

Plant cells can exhibit highly complex nuclear organization. Through dye-labeling experiments in untransformed onion epidermal and tobacco culture cells and through the expression of green fluorescent protein targeted to either the nucleus or the lumen of the endoplasmic reticulum/nuclear envelope in these cells, we have visualized deep grooves and invaginations into the large nuclei of these cells. In onion, these structures, which are similar to invaginations seen in some animal cells, form tubular or planelike infoldings of the nuclear envelope. Both grooves and invaginations are stable structures, and both have cytoplasmic cores containing actin bundles that can support cytoplasmic streaming. In dividing tobacco cells, invaginations seem to form during cell division, possibly from strands of the endoplasmic reticulum trapped in the reforming nucleus. The substantial increase in nuclear surface area resulting from these grooves and invaginations, their apparent preference for association with nucleoli, and the presence in them of actin bundles that support vesicle motility suggest that the structures might function both in mRNA export from the nucleus and in protein import from the cytoplasm to the nucleus. PMID:11148288

Thermal performance comparison of oscillating heat pipes with and without helical micro-grooves

NASA Astrophysics Data System (ADS)

Qu, Jian; Li, Xiaojun; Xu, Qian; Wang, Qian

2017-11-01

This paper presents an experimental investigation to compare the thermal performance of three closed loop oscillating heat pipes (OHPs) with and without internal helical microgrooves at vertical and horizontal orientations. All of these OHPs were made from copper tubes and have three turns with lengths of 70, 230 and 110 mm at the evaporator, adiabatic and condenser sections, respectively. Deionized water was used as the working fluid at a volumetric filling ratio of 50%. The internal diameters (IDs) of two smooth-tube OHPs are 4.0 and 4.8 mm, respectively, and the internal diameter of micro-grooved OHP without groove structures is about 4.5 mm. Experimental results demonstrated that the addition of groove structures make the OHP remarkably outperform smooth-tube OHPs in both effective thermal conductivity and thermal resistance. The thermal resistance of vertically-oriented micro-grooved OHP could be lowered to 0.057 °C/W associated with an effective thermal conductivity of 6.1 × 104 W/ (m·K) at the input heat flux of 3.8 × 104 W/m2. Compared to smooth-tube OHPs, preliminary mechanism analysis reveals that local heat transfer coefficients both at the heating and cooling sections of micro-grooved OHP could be significantly improved. Moreover, enhanced liquid backflow to the evaporator due to microgroove-induced capillarity is also responsible for the OHP performance enhancement.

Crystal structure of the dithiol oxidase DsbA enzyme from proteus mirabilis bound non-covalently to an active site peptide ligand.

PubMed

Kurth, Fabian; Duprez, Wilko; Premkumar, Lakshmanane; Schembri, Mark A; Fairlie, David P; Martin, Jennifer L

2014-07-11

The disulfide bond forming DsbA enzymes and their DsbB interaction partners are attractive targets for development of antivirulence drugs because both are essential for virulence factor assembly in Gram-negative pathogens. Here we characterize PmDsbA from Proteus mirabilis, a bacterial pathogen increasingly associated with multidrug resistance. PmDsbA exhibits the characteristic properties of a DsbA, including an oxidizing potential, destabilizing disulfide, acidic active site cysteine, and dithiol oxidase catalytic activity. We evaluated a peptide, PWATCDS, derived from the partner protein DsbB and showed by thermal shift and isothermal titration calorimetry that it binds to PmDsbA. The crystal structures of PmDsbA, and the active site variant PmDsbAC30S were determined to high resolution. Analysis of these structures allows categorization of PmDsbA into the DsbA class exemplified by the archetypal Escherichia coli DsbA enzyme. We also present a crystal structure of PmDsbAC30S in complex with the peptide PWATCDS. The structure shows that the peptide binds non-covalently to the active site CXXC motif, the cis-Pro loop, and the hydrophobic groove adjacent to the active site of the enzyme. This high-resolution structural data provides a critical advance for future structure-based design of non-covalent peptidomimetic inhibitors. Such inhibitors would represent an entirely new antibacterial class that work by switching off the DSB virulence assembly machinery. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

A morphometric assessment and classification of coral reef spur and groove morphology

NASA Astrophysics Data System (ADS)

Duce, S.; Vila-Concejo, A.; Hamylton, S. M.; Webster, J. M.; Bruce, E.; Beaman, R. J.

2016-07-01

Spurs and grooves (SaGs) are a common and important feature of coral reef fore slopes worldwide. However, they are difficult to access and hence their morphodynamics and formation are poorly understood. We use remote sensing, with extensive ground truthing, to measure SaG morphometrics and environmental factors at 11,430 grooves across 17 reefs in the southern Great Barrier Reef, Australia. We revealed strong positive correlations between groove length, orientation and wave exposure with longer, more closely-spaced grooves oriented easterly reflecting the dominant swell regime. Wave exposure was found to be the most important factor controlling SaG distribution and morphology. Gradient of the upper reef slope was also an important limiting factor, with SaGs less likely to develop in steeply sloping (> 5°) areas. We used a subset of the morphometric data (11 reefs) to statistically define four classes of SaG. This classification scheme was tested on the remaining six reefs. SaGs in the four classes differ in morphology, groove substrate and coral cover. These differences provide insights into SaG formation mechanisms with implications to reef platform growth and evolution. We hypothesize SaG formation is dominated by coral growth processes at two classes and erosion processes at one class. A fourth class may represent relic features formed earlier in the Holocene transgression. The classes are comparable with SaGs elsewhere, suggesting the classification could be applied globally with the addition of new classes if necessary. While further research is required, we show remotely sensed SaG morphometrics can provide useful insights into reef platform evolution.

[A case of groove pancreatitis (segmental form) presented with obstructive jaundice associated with pancreatobiliary maljunction].

PubMed

Hiramatsu, Kiyoshi; Ito, Takaaki; Kaburagi, Daisuke; Arai, Riki; Maruyama, Hideki; Naganuma, Atsushi; Kato, Kenji

2008-09-01

A 52-year-old-man was admitted to our hospital for obstructive jaundice. Percutaneous transhepatic cholangio drainage (PTCD) and endscopic retrograde cholangiopancreatography (ERCP) were performed, and pointed out stenosis of lower common bile duct (CBD) and pancreatobiliary maljunction. Brushing cytology of this lesion was negative for malignancy. CT and MRI revealed chronic inflammatory change in groove lesion with no mass formation suggesting tumor. So we diagnosed groove pancreatitis (segmental form) associated with pancreatobiliary maljunction, and operation (resection of the bile duct and biliary reconstruction by Roux-en-Y) was done. Resected specimen was revealed stenosis of the bile duct formed by fibrous tissue with no malignancy compatible to groove pancreatitis pathologically. This is first reported case of groove pancreatits associated with pancreatobiliary maljunction.

DNA Replication Arrest and DNA Damage Responses Induced by Alkylating Minor Groove Binders

DTIC Science & Technology

2003-05-01

Alkylating minor groove DNA binder adozelesin is capable of inhibiting DNA replication in treated cells through a trans-acting mechanism. The trans... replication in vitro. Using purified proteins in DNA replication initiation assays, we found that RPA purified from cells treated with adozelesin in not...adozelesin has the same single-stranded DNA binding activity and support nucleotide excision repair as normal RPA, but is not able to support SV40 DNA

An Analysis of the Effects of Chip-groove Geometry on Machining Performance Using Finite Element Methods

NASA Astrophysics Data System (ADS)

Ee, K. C.; Dillon, O. W.; Jawahir, I. S.

2004-06-01

This paper discusses the influence of major chip-groove parameters of a cutting tool on the chip formation process in orthogonal machining using finite element (FE) methods. In the FE formulation, a thermal elastic-viscoplastic material model is used together with a modified Johnson-Cook material law for the flow stress. The chip back-flow angle and the chip up-curl radius are calculated for a range of cutting conditions by varying the chip-groove parameters. The analysis provides greater understanding of the effectiveness of chip-groove configurations and points a way to correlate cutting conditions with tool-wear when machining with a grooved cutting tool.

U-Groove Aluminum Weld Strength Improvement

NASA Technical Reports Server (NTRS)

Verderaime, V.; Vaughan, R.

1997-01-01

Though butt-welds are among the most preferred joining methods in aerostructures, their strength dependence on inelastic mechanics is generally the least understood. This study investigated experimental strain distributions across a thick aluminum U-grooved weld and identified two weld process considerations for improving the multipass weld strength. One is the source of peaking in which the extreme thermal expansion and contraction gradient of the fusion heat input across the groove tab thickness produces severe angular distortion that induces bending under uniaxial loading. The other is the filler strain hardening decreasing with increasing filler pass sequences, producing the weakest welds on the last weld pass side. Both phenomena are governed by weld pass sequences. Many industrial welding schedules unknowingly compound these effects, which reduce the weld strength. A depeaking index model was developed to select filler pass thickness, pass numbers, and sequences to improve depeaking in the welding process. The result was to select the number and sequence of weld passes to reverse the peaking angle such as to combine the strongest weld pass side with the peaking induced bending tension component side to provide a more uniform stress and stronger weld under axial tensile loading.

Synthesis of structurally diverse major groove DNA interstrand crosslinks using three different aldehyde precursors

PubMed Central

Mukherjee, Shivam; Guainazzi, Angelo; Schärer, Orlando D.

2014-01-01

DNA interstrand crosslinks (ICLs) are extremely cytotoxic lesions that block essential cellular processes, such as replication and transcription. Crosslinking agents are widely used in cancer chemotherapy and form an array of structurally diverse ICLs. Despite the clinical success of these agents, resistance of tumors to crosslinking agents, for example, through repair of these lesions by the cellular machinery remains a problem. We have previously reported the synthesis of site-specific ICLs mimicking those formed by nitrogen mustards to facilitate the studies of cellular responses to ICL formation. Here we extend these efforts and report the synthesis of structurally diverse major groove ICLs that induce severe, little or no distortion in the DNA. Our approach employs the incorporation of aldehyde precursors of different lengths into complementary strands and ICL formation using a double reductive amination with a variety of amines. Our studies provide insight into the structure and reactivity parameters of ICL formation by double reductive amination and yield a set of diverse ICLs that will be invaluable for exploring structure–activity relationships in ICL repair. PMID:24782532

Recognition of AT-Rich DNA Binding Sites by the MogR Repressor

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

Shen, Aimee; Higgins, Darren E.; Panne, Daniel

2009-07-22

The MogR transcriptional repressor of the intracellular pathogen Listeria monocytogenes recognizes AT-rich binding sites in promoters of flagellar genes to downregulate flagellar gene expression during infection. We describe here the 1.8 A resolution crystal structure of MogR bound to the recognition sequence 5' ATTTTTTAAAAAAAT 3' present within the flaA promoter region. Our structure shows that MogR binds as a dimer. Each half-site is recognized in the major groove by a helix-turn-helix motif and in the minor groove by a loop from the symmetry-related molecule, resulting in a 'crossover' binding mode. This oversampling through minor groove interactions is important for specificity.more » The MogR binding site has structural features of A-tract DNA and is bent by approximately 52 degrees away from the dimer. The structure explains how MogR achieves binding specificity in the AT-rich genome of L. monocytogenes and explains the evolutionary conservation of A-tract sequence elements within promoter regions of MogR-regulated flagellar genes.« less

[The supportive outcome of periodontal non-surgical therapy to severe chronic periodontitis accompanied with malformed lingual groove in lateral incisor for 6 years: a case report].

PubMed

Li, Zheng; Kang, Jun

2011-06-01

To track the initiating and developing process of one case diagnosed as chronic periodontitis accompanied with malformed lingual groove in maxillary lateral incisor and report the long-term prognosis to the periodontal conservative and supportive therapy. The patient was diagnosed with mild chronic periodontitis 6 years ago and accepted routine periodontal scaling and root planning (SRP) plus supportive periodontal therapy (SPT) one time. Two years later the periodontal condition deteriorated by deep pockets in molars and severe bone destruction around the maxillary lateral incisor with malformed lingual groove. After SRP in sites which pocket depth more than 4mm plus root canal therapy and lingual groove plasty of maxillary right lateral incisor, the SPT regularly proceeded at 3rd, 6th and 12th month. At present the whole periodontal tissue was healthy, the bone lesion around maxillary lateral incisor recovered well, the tooth had no mobile, the cosmetic effect andtooth function was in good state, and the patient was very satisfied.

[Microsurgical removal of olfactory groove meningiomas].

PubMed

Liang, Ri-Sheng; Zhou, Liang-Fu; Mao, Ying; Zhang, Rong; Yang, Wei-Zhong

2011-01-01

To explore an effective method for further improving the surgical results of treatment of olfactory groove meningiomas. Sixty seven cases of olfactory groove meningiomas were treated by microneurosurgery, among which fifty seven were de novo cases, eight were recurrent tumors and the other two re-recurrent cases. Modified Derome approach was used in 12 cases, bilateral subfrontal approach in 28 cases, modified pterional approach in 21 cases and unilateral subfrontal approach in six cases. Tumors were resected microsurgically with radical removal of invaded dura, bone, and paranasal sinus mucosa. Reconstruction was performed in patients with skull base defect. Simpson grade I removal was accomplished in 59 cases, grade II in seven cases and grade IV in one case. Among 57 patients with de novo tumor, Simpson I resection was accomplished in 54 cases. Postoperative rhinorrhea and intracranial infection occurred in one case and was cured after temporal lumbar CSF drainage and antibiotic therapy. Two patients (2.9%) died within one month after operation, i.e.one aged patient of heart failure and the other of severe hypothalamus complication. Forty seven patients (72.3%) were followed up from one to ten years with an average of five years and four months. With the exception of two cases died, among the alive 45 patients, there were only three patients with tumor recurrence, which had undergone Simpson II or IV tumor resection. No recurrence was found in cases with Simpson I tumor removal. Previous blurred vision was not improved in three patients, hemiparalysis in two patients, and the other patients recovered well, resuming previous jobs or being able to take care themselves. Total tumor removal (Simpson I) should be the surgical goal for treatment of olfactory groove meningiomas, especially for de novo cases. An appropriate approach is fundamental in the effort to remove an OGM totally. Appropriate anterior skull base reconstruction with vascularized material is

Cycle time improvement for plastic injection moulding process by sub groove modification in conformal cooling channel

NASA Astrophysics Data System (ADS)

Kamarudin, K.; Wahab, M. S.; Batcha, M. F. M.; Shayfull, Z.; Raus, A. A.; Ahmed, Aqeel

2017-09-01

Mould designers have been struggling for the improvement of the cooling system performance, despite the fact that the cooling system complexity is physically limited by the fabrication capability of the conventional tooling methods. However, the growth of Solid Free Form Technology (SFF) allow the mould designer to develop more than just a regular conformal cooling channel. Numerous researchers demonstrate that conformal cooling channel was tremendously given significant result in the improvement of productivity and quality in the plastic injection moulding process. This paper presents the research work that applies the passive enhancement method in square shape cooling channel to enhance the efficiency of cooling performance by adding the sub groove to the cooling channel itself. Previous design that uses square shape cooling channel was improved by adding various numbers of sub groove to meet the best sub groove design that able reduced the cooling time. The effect of sub groove design on cooling time was investigated by Autodesk Modlflow Insight software. The simulation results showed that the various sub groove designs give different values to ejection time. The Design 7 showed the lowest value of ejection time with 24.3% increment. The addition of sub groove significantly increased a coolant velocity and a rate of heat transfer from molten plastic to coolant.

Imidazopyridine/Pyrrole and hydroxybenzimidazole/pyrrole pairs for DNA minor groove recognition.

PubMed

Renneberg, Dorte; Dervan, Peter B

2003-05-14

The DNA binding properties of fused heterocycles imidazo[4,5-b]pyridine (Ip) and hydroxybenzimidazole (Hz) paired with pyrrole (Py) in eight-ring hairpin polyamides are reported. The recognition profile of Ip/Py and Hz/Py pairs were compared to the five-membered ring pairs Im/Py and Hp/Py on a DNA restriction fragment at four 6-base pair recognition sites which vary at a single position 5'-TGTNTA-3', where N = G, C, T, A. The Ip/Py pair distinguishes G.C from C.G, T.A, and A.T, and the Hz/Py pair distinguishes T.A from A.T, G.C, and C.G, affording a new set of heterocycle pairs to target the four Watson-Crick base pairs in the minor groove of DNA.

Comparison of computational methods to model DNA minor groove binders.

PubMed

Srivastava, Hemant Kumar; Chourasia, Mukesh; Kumar, Devesh; Sastry, G Narahari

2011-03-28

There has been a profound interest in designing small molecules that interact in sequence-selective fashion with DNA minor grooves. However, most in silico approaches have not been parametrized for DNA ligand interaction. In this regard, a systematic computational analysis of 57 available PDB structures of noncovalent DNA minor groove binders has been undertaken. The study starts with a rigorous benchmarking of GOLD, GLIDE, CDOCKER, and AUTODOCK docking protocols followed by developing QSSR models and finally molecular dynamics simulations. In GOLD and GLIDE, the orientation of the best score pose is closer to the lowest rmsd pose, and the deviation in the conformation of various poses is also smaller compared to other docking protocols. Efficient QSSR models were developed with constitutional, topological, and quantum chemical descriptors on the basis of B3LYP/6-31G* optimized geometries, and with this ΔT(m) values of 46 ligands were predicted. Molecular dynamics simulations of the 14 DNA-ligand complexes with Amber 8.0 show that the complexes are stable in aqueous conditions and do not undergo noticeable fluctuations during the 5 ns production run, with respect to their initial placement in the minor groove region.

Binding to the DNA Minor Groove by Heterocyclic Dications: From AT Specific Monomers to GC Recognition with Dimers

PubMed Central

Nanjunda, Rupesh; Wilson, W. David

2012-01-01

Compounds that bind in the DNA minor groove have provided critical information on DNA molecular recognition, they have found extensive uses in biotechnology and they are providing clinically useful drugs against diseases as diverse as cancer and sleeping sickness. This review focuses on the development of clinically useful heterocyclic diamidine minor groove binders. These compounds have shown us that the classical model for minor groove binding in AT DNA sequences must be expanded in several ways: compounds with nonstandard shapes can bind strongly to the groove, water can be directly incorporated into the minor groove complex in an interfacial interaction, and the compounds can form cooperative stacked dimers to recognize GC and mixed AT/GC base pair sequences. PMID:23255206

Design of nano-groove photonic crystal cavities in lithium niobate.

PubMed

Li, Yihang; Wang, Cheng; Loncar, Marko

2015-06-15

We propose a novel design of photonic-crystal nanobeam cavities in lithium niobate (LN) for both TE and TM modes, addressing problems associated with tilted sidewalls, which commonly result from dry etching. Using optimized periodical nano-groove structures, the proposed devices could achieve quality factors as high as 3.9×10(6) with a modal volume of 5.0 (λ/n)3. We also show that such a design is promising for applications in nonlinear optics by theoretically predicting the efficiencies for electro-optic modulation and second-harmonic generation. The proposed nano-groove structures and design rules could also be applied for other material platforms that possess tilted sidewalls.

DNA minor groove electrostatic potential: influence of sequence-specific transitions of the torsion angle gamma and deoxyribose conformations.

PubMed

Zhitnikova, M Y; Shestopalova, A V

2017-11-01

The structural adjustments of the sugar-phosphate DNA backbone (switching of the γ angle (O5'-C5'-C4'-C3') from canonical to alternative conformations and/or C2'-endo → C3'-endo transition of deoxyribose) lead to the sequence-specific changes in accessible surface area of both polar and non-polar atoms of the grooves and the polar/hydrophobic profile of the latter ones. The distribution of the minor groove electrostatic potential is likely to be changing as a result of such conformational rearrangements in sugar-phosphate DNA backbone. Our analysis of the crystal structures of the short free DNA fragments and calculation of their electrostatic potentials allowed us to determine: (1) the number of classical and alternative γ angle conformations in the free B-DNA; (2) changes in the minor groove electrostatic potential, depending on the conformation of the sugar-phosphate DNA backbone; (3) the effect of the DNA sequence on the minor groove electrostatic potential. We have demonstrated that the structural adjustments of the DNA double helix (the conformations of the sugar-phosphate backbone and the minor groove dimensions) induce changes in the distribution of the minor groove electrostatic potential and are sequence-specific. Therefore, these features of the minor groove sizes and distribution of minor groove electrostatic potential can be used as a signal for recognition of the target DNA sequence by protein in the implementation of the indirect readout mechanism.

Scattering by a groove in an impedance plane

NASA Technical Reports Server (NTRS)

Bindiganavale, Sunil; Volakis, John L.

1993-01-01

An analysis of two-dimensional scattering from a narrow groove in an impedance plane is presented. The groove is represented by a impedance surface and the problem reduces to that of scattering from an impedance strip in an otherwise uniform impedance plane. On the basis of this model, appropriate integral equations are constructed using a form of the impedance plane Green's functions involving rapidly convergent integrals. The integral equations are solved by introducing a single basis representation of the equivalent current on the narrow impedance insert. Both transverse electric (TE) and transverse magnetic (TM) polarizations are treated. The resulting solution is validated by comparison with results from the standard boundary integral method (BIM) and a high frequency solution. It is found that the presented solution for narrow impedance inserts can be used in conjunction with the high frequency solution for the characterization of impedance inserts of any given width.

Unified design of sinusoidal-groove fused-silica grating.

PubMed

Feng, Jijun; Zhou, Changhe; Cao, Hongchao; Lu, Peng

2010-10-20

A general design rule of deep-etched subwavelength sinusoidal-groove fused-silica grating as a highly efficient polarization-independent or polarization-selective device is studied based on the simplified modal method, which shows that the device structure depends little on the incident wavelength, but mainly on the ratio of groove depth to incident wavelength and the ratio of wavelength to grating period. These two ratios could be used as the design guidelines for wavelength-independent structure from deep ultraviolet to far infrared. The optimized grating profile with a different function as a polarizing beam splitter, a polarization-independent two-port beam splitter, or a polarization-independent grating with high efficiency of -1st order is obtained at a wavelength of 1064 nm, and verified by using the rigorous coupled-wave analysis. The performance of the sinusoidal grating is better than a conventional rectangular one, which could be useful for practical applications.

Development of spiral-groove self-acting face seals

NASA Technical Reports Server (NTRS)

Obrien, M.

1977-01-01

An experimental evaluation and a 100-hour endurance test were performed on a spiral groove geometry, self-acting face seal. The seal was tested and operated successfully at maximum conditions of 243.8 m/s surface speed, 199.9 N/sq cm air pressure, and 645.4K (702 F) air temperature. The maximum speed condition of 243.8 m/s was obtained at a shaft speed of 72,500 rpm. Seal wear, gas leakage, and sealing element temperature were monitored during the test. Condition of the seal at the completion of the test was documented and found acceptable for further use. The spiral groove wear rate measured during the endurance test indicates a minimum potential seal life of over 2700 hours. Seal air leakage measured during the test program is within the range considered acceptable for consideration for use in a small gas turbine engine.

Dance, Music, Meter and Groove: A Forgotten Partnership.

PubMed

Fitch, W Tecumseh

2016-01-01

I argue that core aspects of musical rhythm, especially "groove" and syncopation, can only be fully understood in the context of their origins in the participatory social experience of dance. Musical meter is first considered in the context of bodily movement. I then offer an interpretation of the pervasive but somewhat puzzling phenomenon of syncopation in terms of acoustic emphasis on certain offbeat components of the accompanying dance style. The reasons for the historical tendency of many musical styles to divorce themselves from their dance-based roots are also briefly considered. To the extent that musical rhythms only make sense in the context of bodily movement, researchers interested in ecologically valid approaches to music cognition should make a more concerted effort to extend their analyses to dance, particularly if we hope to understand the cognitive constraints underlying rhythmic aspects of music like meter and groove.

Features and applications of the Groove Analysis Program (GAP)

NASA Technical Reports Server (NTRS)

Ku, Jentung; Nguyen, Tu M.; Brennan, Patrick J.

1995-01-01

An IBM Personal Computer (PC) version of the Groove Analysis program (GAP) was developed to predict the steady state heat transport capability of an axially grooved heat pipe for a specified groove geometry and working fluid. In the model, the capillary limit is determined by the numerical solution of the differential equation for momentum conservation with the appropriate boundary conditions. This governing equation accounts for the hydrodynamic losses due to friction in liquid and vapor flows and due to liquid/vapor shear interaction. Back-pumping in both 0-g and 1-g is accounted for in the boundary condition at the condenser end. Slug formation in 0-g and puddle flow in 1-g are also considered in the model. At the user's discretion, the code will perform the analysis for various fluid inventories (undercharge, nominal charge, overcharge, or a fixed fluid charge) and heat pipe elevations. GAP will also calculate the minimum required heat pipe wall thickness for pressure containment at design temperatures that are greater than or lower than the critical temperature of the working fluid. This paper discusses the theory behind the development of the GAP model. It also presents the many useful and powerful capabilities of the model. Furthermore, a correlation of flight test performance data and the predictions using GAP are presented and discussed.

Morphology of the Lesser Tuberosity and Intertubercular Groove in Patients With Arthroscopically Confirmed Subscapularis and Biceps Tendon Pathology.

PubMed

Shah, Shaan H; Small, Kirstin M; Sinz, Nathan J; Higgins, Laurence D

2016-06-01

To evaluate for an association between the morphology of the lesser tuberosity and intertubercular groove and subscapularis tendon tears and biceps tendon pathology. Sixty-six patients with arthroscopically confirmed subscapularis tendon tears were compared with 59 demographically matched control patients who underwent magnetic resonance imaging or computed tomography arthrography examination of the shoulder. Measurements of the lesser tuberosity and intertubercular groove included maximum depth of the intertubercular groove, intertubercular groove depth at the midpoint of the glenoid, lesser tuberosity length, length from the top of the humeral head to the point of maximum depth of the intertubercular groove, length from the top of the humeral head to the top of the lesser tuberosity, and medial wall angle and depth. Patients with subscapularis tears showed a significantly decreased depth of the intertubercular groove at the mid glenoid (P = .01), shorter length of the lesser tuberosity (P = .002), and greater distance from the top of the humeral head to the top of the lesser tuberosity (P = .02). There was a trend toward a decreased medial wall angle (P = .07) and greater distance from the top of the humeral head to the point of maximum intertubercular groove depth (P = .06). Patients with biceps tendon pathology showed a significantly decreased depth of the intertubercular groove at the mid glenoid (P = .001), shorter length of the lesser tuberosity (P = .0003), greater distance from the top of the humeral head to the top of the lesser tuberosity (P = .01), and decreased medial wall angle (P = .01) and depth (P = .03). There are several morphologic factors related to the lesser tuberosity and intertubercular groove that are associated with both subscapularis tendon tears and biceps tendon pathology. Level III, case-control study. Copyright © 2016 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

Numerical analysis of lateral illumination lightpipes using elliptical grooves

NASA Astrophysics Data System (ADS)

Sánchez-Guerrero, Guillermo E.; Viera-González, Perla M.; Martínez-Guerra, Edgar; Ceballos-Herrera, Daniel E.

2017-09-01

Lightpipes are used for illumination in applications such as back-lighting or solar cell concentrators due to the high irradiance uniformity, but its optimal design requires several parameters. This work presents a procedure to design a square lightpipe to control the light-extraction on its lateral face using commercial LEDs placed symmetrically in the lightpipe frontal face. We propose the use of grooves using total internal reflection placed successively in the same face of extraction to control the area of emission. The LED area of emission is small compared with the illuminated area, and, as expected, the lateral face total power is attenuated. These grooves reduce the optical elements in the system and can control areas of illumination. A mathematical and numerical analysis are presented to determine the dependencies on the light-extraction.

A Surface Groove Essential for Viral Bcl-2 Function During Chronic Infection In Vivo

PubMed Central

Petros, Andrew M; Nettesheim, David; van Dyk, Linda F.; Labrada, Lucia; Speck, Samuel H; Levine, Beth

2005-01-01

Antiapoptotic Bcl-2 family proteins inhibit apoptosis in cultured cells by binding BH3 domains of proapoptotic Bcl-2 family members via a hydrophobic BH3 binding groove on the protein surface. We investigated the physiological importance of the BH3 binding groove of an antiapoptotic Bcl-2 protein in mammals in vivo by analyzing a viral Bcl-2 family protein. We show that the γ-herpesvirus 68 (γHV68) Bcl-2 family protein (γHV68 v-Bcl-2), which is known to inhibit apoptosis in cultured cells, inhibits both apoptosis in primary lymphocytes and Bax toxicity in yeast. Nuclear magnetic resonance determination of the γHV68 v-Bcl-2 structure revealed a BH3 binding groove that binds BH3 domain peptides from proapoptotic Bcl-2 family members Bax and Bak via a molecular mechanism shared with host Bcl-2 family proteins, involving a conserved arginine in the BH3 peptide binding groove. Mutations of this conserved arginine and two adjacent amino acids to alanine (SGR to AAA) within the BH3 binding groove resulted in a properly folded protein that lacked the capacity of the wild-type γHV68 v-Bcl-2 to bind Bax BH3 peptide and to block Bax toxicity in yeast. We tested the physiological importance of this v-Bcl-2 domain during viral infection by engineering viral mutants encoding a v-Bcl-2 containing the SGR to AAA mutation. This mutation resulted in a virus defective for both efficient reactivation of γHV68 from latency and efficient persistent γHV68 replication. These studies demonstrate an essential functional role for amino acids in the BH3 peptide binding groove of a viral Bcl-2 family member during chronic infection. PMID:16201011

Design analysis of a self-acting spiral-groove ring seal for counter-rotating shafts

NASA Technical Reports Server (NTRS)

Dirusso, E.

1983-01-01

A self-acting spiral groove inter-shaft ring seal of nominal 16.33 cm (6.43 in.) diameter for sealing fan bleed air between counter-rotating hafts in advanced turbofan engines was analyzed. The analysis focused on the lift force characteristics of the spiral grooves. A NASA Lewis developed computer program for predicting the performance of gas lubricated face seals was used to optimize the spiral groove geometry to produce maximum lift force. Load capacity curves (lift force as function of film thickness) were generated for four advanced turbofan engine operating conditions at relative seal speeds ranging from 17,850 to 29,800 rpm, sealed air pressures from 6 to 42 N/sq cm (9 to 60 psi) absolute and temperatures from 95 deg to 327 C (203 deg to 620 F). The relative seal sliding speed range was 152 to 255 m/sec (500 to 836 ft/sec). The analysis showed that the spiral grooves are capable of producing sufficient lift force such that the ring seal will operate in a noncontacting mode over the operating range of typical advanced turbofan engines.

The origin of Phobos grooves from ejecta launched from impact craters on Mars: Tests of the hypothesis

NASA Astrophysics Data System (ADS)

Ramsley, Kenneth R.; Head, James W.

2013-01-01

The surface of the martian moon Phobos is characterized by parallel and intersecting grooves that bear resemblance to secondary crater chains observed on planetary surfaces. Murray (2011) has hypothesized that the main groove-forming process on Phobos is the intersection of Phobos with ejecta from primary impact events on Mars to produce chains of secondary craters. The hypothesis infers a pattern of parallel jets of ejecta, either fluidized or solidified, that break into equally-spaced fragments and disperse uniformly along-trajectory during the flight from Mars to Phobos. At the moment of impact with Phobos the dispersed fragments emplace secondary craters that are aligned along strike corresponding to the flight pattern of ejecta along trajectory. The aspects of the characteristics of grooves on Phobos cited by this hypothesis that might be explained by secondary ejecta include: their observed linearity, parallelism, planar alignment, pitted nature, change in character along strike, and a "zone of avoidance" where ejecta from Mars is predicted not to impact (Murray, 2011). To test the hypothesis we plot precise Keplerian orbits for ejecta from Mars (elliptical and hyperbolic with periapsis located below the surface of Mars). From these trajectories we: (1) set the fragment dispersion limits of ejecta patterns required to emplace the more typically well-organized parallel grooves observed in returned images from Phobos; (2) plot ranges of the ejecta flight durations from Mars to Phobos and map regions of exposure; (3) utilize the same exposure map to observe trajectory-defined ejecta exposure shadows; (4) observe hemispheric exposure in response to shorter and longer durations of ejecta flight; (5) assess the viability of ejecta emplacing the large family of grooves covering most of the northern hemisphere of Phobos; and (6) plot the arrival of parallel lines of ejecta emplacing chains of craters at oblique incident angles. We also assess the bulk volume of

Study on the Optimal Groove Shape and Glue Material for Fiber Bragg Grating Measuring Bolts.

PubMed

Zhao, Yiming; Zhang, Nong; Si, Guangyao; Li, Xuehua

2018-06-02

Fiber Bragg grating (FBG) measuring bolts, as a useful tool to evaluate the behaviors of steel bolts in underground engineering, can be manufactured by gluing the FBG sensors inside the grooves, which are usually symmetrical cuts along the steel bolt rod. The selection of the cut shape and the glue types could perceivably affect the final supporting strength of the bolts. Unfortunately, the impact of cut shape and glue type on bolting strength is not yet clear. In this study, based on direct tension tests, full tensile load⁻displacement curves of rock bolts with different groove shapes were obtained and analyzed. The effects of groove shape on the bolt strength were discussed, and the stress redistribution in the cross-section of a rock bolt with different grooves was simulated using ANSYS. The results indicated that the trapezoidal groove is best for manufacturing the FBG bolt due to its low reduction of supporting strength. Four types of glues commonly used for the FBG sensors were assessed by conducting tensile tests on the mechanical testing and simulation system and the static and dynamic optical interrogators system. Using linear regression analysis, the relationship between the reflected wavelength of FBG sensors and tensile load was obtained. Practical recommendations for glue selection in engineering practice are also provided.

Safety Modification of Cam-and-Groove Hose Coupling

NASA Technical Reports Server (NTRS)

Schwindt, Paul; Littlefield, Alan

2008-01-01

A modification has been made in the mating halves of a cam-and-groove hose coupling to prevent rapid separation of the halves in the event that the cam levers are released while the fluid in the hose is pressurized. The need for this modification arises because commercial off-the-shelf cam-and-groove hose-coupling halves do not incorporate safety features to prevent separation in the pressurized state. Especially when the pressurized fluid is compressible (e.g., steam or compressed air), the separated halves can be propelled with considerable energy, causing personal injury and/or property damage. Therefore, one purpose served by the modification is to provide for venting to release compressive energy in a contained and safe manner while preventing personal injury and/or property damage. Another purpose served by the modification, during the process of connecting the coupling halves, is to ensure that the coupling halves are properly aligned before the cam levers can be locked into position.

Hydrodynamic simulations of microjetting from shock-loaded grooves

NASA Astrophysics Data System (ADS)

Roland, C.; de Rességuier, T.; Sollier, A.; Lescoute, E.; Soulard, L.; Loison, D.

2017-01-01

The interaction of a shock wave with a free surface which has geometrical defects, such as cavities or grooves, may lead to the ejection of micrometric debris at velocities of km/s. This process can be involved in many applications, like pyrotechnics or industrial safety. Recent laser shock experiments reported elsewhere in this conference have provided some insight into jet formation as well as jet tip velocities for various groove angles and shock pressures. Here, we present hydrodynamic simulations of these experiments, in both 2D and 3D geometries, using both finite element method and smoothed particle hydrodynamics. Numerical results are compared to several theoretical predictions including the Richtmyer-Meshkov instabilities. The role of the elastic-plastic behavior on jet formation is illustrated. Finally, the possibility to simulate the late stage of jet expansion and fragmentation is explored, to evaluate the mass distribution of the ejecta and their ballistic properties, still essentially unknown in the experiments.

Treatment of combined endodontic: periodontic lesion by sealing of palato-radicular groove using biodentine.

PubMed

Naik, Mayuri; de Ataide, Ida de Noronha; Fernandes, Marina; Lambor, Rajan

2014-11-01

Palatoradicular groove is a developmental anomaly which is predominantly found in maxillary lateral incisors. It provides a susceptible alcove for the progression of localised periodontal inflammation which can further cause pulpal involvement. This case report describes the successful treatment of a large periodontic - endodontic lesion usingnon surgical endodontic therapy and biodentine for the sealing of the palatoradicular groove.

One-dimensional arrangement of nanoparticles utilizing the V-groove and cage shaped proteins

NASA Astrophysics Data System (ADS)

Ban, Takahiko; Uenuma, Mutsunori; Migita, Shinji; Okamoto, Naofumi; Ishikawa, Yasuaki; Uraoka, Yukiharu; Yamashita, Ichiro; Yamamoto, Shin-ichi

2017-06-01

The one-dimensional arrangement of nanoparticles (NPs) was performed using a V-groove and ferritins as spherical shell proteins. The V-groove was synthesized by lithography and anisotropic etching of a Si substrate. Ferritin has an outer diameter of 12 nm and an inner diameter of 6 nm, and various inorganic substances can be formed into the cavity. In this study, iron oxide, cobalt oxide, and indium oxide cores were used. The surface potential of ferritin can be changed by genetic modification. Particularly, by using Fer8-K98E, NPs could be arranged one-dimensionally onto the bottom of the V-groove. In addition, we succeeded in selectively forming a one-dimensional array of one layer, two layers, and three layers by changing the protein concentration. This experiment is expected to be applicable to various one-dimensional devices.

The behavior of the skin-friction coefficient of a turbulent boundary layer flow over a flat plate with differently configured transverse square grooves

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

Wahidi, R.; Chakroun, W.; Al-Fahed, S.

2005-11-01

Skin-friction coefficient of turbulent boundary layer flow over a smooth-wall with transverse square grooves was investigated. Four grooved-wall cases were investigated. The four grooved-wall configurations are single 5mm square grooved-wall, and 5mm square grooves spaced 10, 20 and 40 element widths apart in the streamwise direction. Laser-Doppler Anemometer (LDA) was used for the mean velocity and turbulence intensity measurements. The skin-friction coefficient determined from the velocity profile increases sharply just downstream of the groove. This overshoot is followed by an undershoot and then relaxation back to the smooth-wall value. This behavior is observed in most grooved-wall cases. Integrating the skin-frictionmore » coefficient in the streamwise direction indicates that there is an increase in the overall drag in all the grooved-wall cases.« less

Treatment of combined endodontic: periodontic lesion by sealing of palato-radicular groove using biodentine

PubMed Central

Naik, Mayuri; de Ataide, Ida de Noronha; Fernandes, Marina; Lambor, Rajan

2014-01-01

Introduction: Palatoradicular groove is a developmental anomaly which is predominantly found in maxillary lateral incisors. It provides a susceptible alcove for the progression of localised periodontal inflammation which can further cause pulpal involvement. This case report describes the successful treatment of a large periodontic – endodontic lesion usingnon surgical endodontic therapy and biodentine for the sealing of the palatoradicular groove. PMID:25506153

Mg2+ in the Major Groove Modulates B-DNA Structure and Dynamics

PubMed Central

Guéroult, Marc; Boittin, Olivier; Mauffret, Oliver; Etchebest, Catherine; Hartmann, Brigitte

2012-01-01

This study investigates the effect of Mg2+ bound to the DNA major groove on DNA structure and dynamics. The analysis of a comprehensive dataset of B-DNA crystallographic structures shows that divalent cations are preferentially located in the DNA major groove where they interact with successive bases of (A/G)pG and the phosphate group of 5′-CpA or TpG. Based on this knowledge, molecular dynamics simulations were carried out on a DNA oligomer without or with Mg2+ close to an ApG step. These simulations showed that the hydrated Mg2+ forms a stable intra-strand cross-link between the two purines in solution. ApG generates an electrostatic potential in the major groove that is particularly attractive for cations; its intrinsic conformation is well-adapted to the formation of water-mediated hydrogen bonds with Mg2+. The binding of Mg2+ modulates the behavior of the 5′-neighboring step by increasing the BII (ε-ζ>0°) population of its phosphate group. Additional electrostatic interactions between the 5′-phosphate group and Mg2+ strengthen both the DNA-cation binding and the BII character of the 5′-step. Cation binding in the major groove may therefore locally influence the DNA conformational landscape, suggesting a possible avenue for better understanding how strong DNA distortions can be stabilized in protein-DNA complexes. PMID:22844516

Crystal Structures of Human Choline Kinase Isoforms in Complex with Hemicholinium-3 Single Amino Acid near the Active Site Influences Inhibitor Sensitivity

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

Hong, Bum Soo; Allali-Hassani, Abdellah; Tempel, Wolfram

2010-07-06

Human choline kinase (ChoK) catalyzes the first reaction in phosphatidylcholine biosynthesis and exists as ChoK{alpha} ({alpha}1 and {alpha}2) and ChoK{beta} isoforms. Recent studies suggest that ChoK is implicated in tumorigenesis and emerging as an attractive target for anticancer chemotherapy. To extend our understanding of the molecular mechanism of ChoK inhibition, we have determined the high resolution x-ray structures of the ChoK{alpha}1 and ChoK{beta} isoforms in complex with hemicholinium-3 (HC-3), a known inhibitor of ChoK. In both structures, HC-3 bound at the conserved hydrophobic groove on the C-terminal lobe. One of the HC-3 oxazinium rings complexed with ChoK{alpha}1 occupied the choline-bindingmore » pocket, providing a structural explanation for its inhibitory action. Interestingly, the HC-3 molecule co-crystallized with ChoK{beta} was phosphorylated in the choline binding site. This phosphorylation, albeit occurring at a very slow rate, was confirmed experimentally by mass spectroscopy and radioactive assays. Detailed kinetic studies revealed that HC-3 is a much more potent inhibitor for ChoK{alpha} isoforms ({alpha}1 and {alpha}2) compared with ChoK{beta}. Mutational studies based on the structures of both inhibitor-bound ChoK complexes demonstrated that Leu-401 of ChoK{alpha}2 (equivalent to Leu-419 of ChoK{alpha}1), or the corresponding residue Phe-352 of ChoK{beta}, which is one of the hydrophobic residues neighboring the active site, influences the plasticity of the HC-3-binding groove, thereby playing a key role in HC-3 sensitivity and phosphorylation.« less

Multiphysics Modeling of a Single Channel in a Nuclear Thermal Propulsion Grooved Ring Fuel Element

NASA Technical Reports Server (NTRS)

Kim, Tony; Emrich, William J., Jr.; Barkett, Laura A.; Mathias, Adam D.; Cassibry, Jason T.

2013-01-01

In the past, fuel rods have been used in nuclear propulsion applications. A new fuel element concept that reduces weight and increases efficiency uses a stack of grooved discs. Each fuel element is a flat disc with a hole on the interior and grooves across the top. Many grooved ring fuel elements for use in nuclear thermal propulsion systems have been modeled, and a single flow channel for each design has been analyzed. For increased efficiency, a fuel element with a higher surface-area-to-volume ratio is ideal. When grooves are shallower, i.e., they have a lower surface area, the results show that the exit temperature is higher. By coupling the physics of turbulence with those of heat transfer, the effects on the cooler gas flowing through the grooves of the thermally excited solid can be predicted. Parametric studies were done to show how a pressure drop across the axial length of the channels will affect the exit temperatures of the gas. Geometric optimization was done to show the behaviors that result from the manipulation of various parameters. Temperature profiles of the solid and gas showed that more structural optimization is needed to produce the desired results. Keywords: Nuclear Thermal Propulsion, Fuel Element, Heat Transfer, Computational Fluid Dynamics, Coupled Physics Computations, Finite Element Analysis

Analysis of transmission through slit and multiple grooves structures for biosensors

NASA Astrophysics Data System (ADS)

Kim, Bong Ho; Nakarmi, Bikash; Won, Yong Hyub

2015-03-01

We analyze the transmission property of nanostructures made on silver and gold metal for the applications in optical biosensors. Various structures such as slit only, slit groove slit, and multiple slit and groove structures are taken into account to find the effect of various physical parameters such as number of grooves, number of slits and others on the transmission of different wavelength light sources through the structure. A broad wavelength of 400 nm to 900 nm is used to analyze the transmission through the structure. With these structures and broad light source, change in transmission intensity is analyzed with the change in the refractive index. The change in refractive index of the analyte varies transmission intensity and wavelength shift at the output beam which can be used for sensing the amount of analyte such as monitoring glucose amount on blood/saliva, hydrogen peroxide and others. The detection of these analytes can be used to detect the different disease. The analysis of the transmittance through the nanostructure can be used for the detection of several disease such as diabetes and others through the saliva, blood and others non-invasively.

Users' Manual for Computer Code SPIRALI Incompressible, Turbulent Spiral Grooved Cylindrical and Face Seals

NASA Technical Reports Server (NTRS)

Walowit, Jed A.; Shapiro, Wilbur

2005-01-01

The SPIRALI code predicts the performance characteristics of incompressible cylindrical and face seals with or without the inclusion of spiral grooves. Performance characteristics include load capacity (for face seals), leakage flow, power requirements and dynamic characteristics in the form of stiffness, damping and apparent mass coefficients in 4 degrees of freedom for cylindrical seals and 3 degrees of freedom for face seals. These performance characteristics are computed as functions of seal and groove geometry, load or film thickness, running and disturbance speeds, fluid viscosity, and boundary pressures. A derivation of the equations governing the performance of turbulent, incompressible, spiral groove cylindrical and face seals along with a description of their solution is given. The computer codes are described, including an input description, sample cases, and comparisons with results of other codes.

Hydrodynamically Lubricated and Grooved Biomimetic Self-Adapting Surfaces

PubMed Central

Jackson, Robert L.; Lei, Jiang

2014-01-01

In many machines and mechanical components, there is a need for new bearing technologies to reduce friction and wear, and provide precision control of motion when the load is varied. This can be provided by electronically controlled actuators and sensors on the surfaces, but then the system reliability can be an issue. In contrast, biomimetic surfaces can be created that adapt mechanically to variations in load. This work uses numerical methods to research the use of self-adapting surfaces for bearings that are based on the deformable nature of biological materials such as articular cartilage. These surfaces are designed to change their profiles to achieve a desired behavior, without any external control. The surfaces change their profile to control the film height and tilt of the bearing to a near constant value for different loads. If the surfaces are tilted, the grooved self-adapting surfaces will also react with a larger restoring moment than a conventional grooved surface. These surfaces could be beneficial to applications where electrical systems and controls are not feasible. PMID:24956441

Hydrodynamically lubricated and grooved biomimetic self-adapting surfaces.

PubMed

Jackson, Robert L; Lei, Jiang

2014-06-04

In many machines and mechanical components, there is a need for new bearing technologies to reduce friction and wear, and provide precision control of motion when the load is varied. This can be provided by electronically controlled actuators and sensors on the surfaces, but then the system reliability can be an issue. In contrast, biomimetic surfaces can be created that adapt mechanically to variations in load. This work uses numerical methods to research the use of self-adapting surfaces for bearings that are based on the deformable nature of biological materials such as articular cartilage. These surfaces are designed to change their profiles to achieve a desired behavior, without any external control. The surfaces change their profile to control the film height and tilt of the bearing to a near constant value for different loads. If the surfaces are tilted, the grooved self-adapting surfaces will also react with a larger restoring moment than a conventional grooved surface. These surfaces could be beneficial to applications where electrical systems and controls are not feasible.

An optical biosensor using MEMS-based V-grooves

NASA Astrophysics Data System (ADS)

Tian, Ye; Ma, Xiaodong; Zou, Xiaotian; Wu, Nan; Wang, Xingwei

2011-05-01

An optical fiber biosensor featuring miniaturization, electromagnetic interference (EMI)-immunity, and flexibility is presented. The sensor was fabricated by aligning two gold-deposited optical single-mode fiber facets inside V-grooves on a silicon chip to form a Fabry-Perot (FP) cavity. The mirrors on the fiber facets were made of deposited gold (Au) films, which provided a high finesse to produce a highly sensitivity. Microelectromechanical systems (MEMS) fabrication techniques were used to precisely control the profile and angle of the V-grooves on the silicon. The biotin-terminated thiol molecule was firstly immobilized on the gold surface. Subsequently, the molecules of Neutravidin were specifically bound to the biotin-terminated self-assembled monolayers (SAMs). The induced changes of cavity length and refractive index (RI) upon the gold surface lead to an optical path difference (OPD) of the FP cavity, which was detected by demodulating the transmission spectrum phase shift. By taking advantage of MEMS techniques, multiple biosensors can be integrated into one small silicon chip for detecting various biomolecule targets simultaneously.

13. GROOVED FOOTING (CONSTRUCTION KEY) EXTENDING ABOVE CEMENT FLOOR IN ...

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

13. GROOVED FOOTING (CONSTRUCTION KEY) EXTENDING ABOVE CEMENT FLOOR IN FIRST UNLINED SECTION BEYOND SOUTH PORTAL. - Salinas River Project, Cuesta Tunnel, Southeast of U.S. 101, San Luis Obispo, San Luis Obispo County, CA

Aluminum U-groove weld enhancement based on experimental stress analyses

NASA Technical Reports Server (NTRS)

Verderaime, V.; Vaughan, R.

1995-01-01

Though butt-welds are among the most preferred joining methods in aerostructures because of their sealing and assembly integrity and general elastic performance; their inelastic mechanics are generally the least understood. This study investigated experimental strain distributions across a thick aluminum U-grooved weld and identified two weld process considerations for improving the multipass weld strength. The extreme thermal expansion and contraction gradient of the fusion heat input across the tab thickness between the grooves produce severe peaking, which induces bending moment under uniaxial loading. The filler strain hardening decreased with increasing filler pass sequence. These combined effects reduce the weld strength, and a depeaking index model was developed to select filler pass thicknesses, pass numbers, and sequences to improve the welding process results over the current normal weld schedule.

Solution structure of a highly stable DNA duplex conjugated to a minor groove binder.

PubMed Central

Kumar, S; Reed, M W; Gamper, H B; Gorn, V V; Lukhtanov, E A; Foti, M; West, J; Meyer, R B; Schweitzer, B I

1998-01-01

The tripeptide 1,2-dihydro-(3 H )-pyrrolo[3,2- e ]indole-7-carboxylate (CDPI3) binds to the minor groove of DNA with high affinity. When this minor groove binder is conjugated to the 5'-end of short oligonucleotides the conjugates form unusually stable hybrids with complementary DNA and thus may have useful diagnostic and/or therapeutic applications. In order to gain an understanding of the structural interactions between the CDPI3minor groove binding moiety and the DNA, we have determined and compared the solution structure of a duplex consisting of oligodeoxyribonucleotide 5'-TGATTATCTG-3' conjugated at the 5'-end to CDPI3 and its complementary strand to an unmodified control duplex of the same sequence using nuclear magnetic resonance techniques. Thermal denaturation studies indicated that the hybrid of this conjugate with its complementary strand had a melting temperature that was 30 degrees C higher compared with the unmodified control duplex. Following restrained molecular dynamics and relaxation matrix refinement, the solution structure of the CDPI3-conjugated DNA duplex demonstrated that the overall shape of the duplex was that of a straight B-type helix and that the CDPI3moiety was bound snugly in the minor groove, where it was stabilized by extensive van der Waal's interactions. PMID:9443977

Solution structure of a highly stable DNA duplex conjugated to a minor groove binder.

PubMed

Kumar, S; Reed, M W; Gamper, H B; Gorn, V V; Lukhtanov, E A; Foti, M; West, J; Meyer, R B; Schweitzer, B I

1998-02-01

The tripeptide 1,2-dihydro-(3 H )-pyrrolo[3,2- e ]indole-7-carboxylate (CDPI3) binds to the minor groove of DNA with high affinity. When this minor groove binder is conjugated to the 5'-end of short oligonucleotides the conjugates form unusually stable hybrids with complementary DNA and thus may have useful diagnostic and/or therapeutic applications. In order to gain an understanding of the structural interactions between the CDPI3minor groove binding moiety and the DNA, we have determined and compared the solution structure of a duplex consisting of oligodeoxyribonucleotide 5'-TGATTATCTG-3' conjugated at the 5'-end to CDPI3 and its complementary strand to an unmodified control duplex of the same sequence using nuclear magnetic resonance techniques. Thermal denaturation studies indicated that the hybrid of this conjugate with its complementary strand had a melting temperature that was 30 degrees C higher compared with the unmodified control duplex. Following restrained molecular dynamics and relaxation matrix refinement, the solution structure of the CDPI3-conjugated DNA duplex demonstrated that the overall shape of the duplex was that of a straight B-type helix and that the CDPI3moiety was bound snugly in the minor groove, where it was stabilized by extensive van der Waal's interactions.

Cratering and Grooved Terrain on Ganymede

NASA Technical Reports Server (NTRS)

1979-01-01

This color picture as acquired by Voyager 1 during its approach to Ganymede on Monday afternoon (the 5th of March). At ranges between about 230 to 250 thousand km. The image shows detail on the surface with a resolution of four and a half km. This picture is just south of PIA001515 (P21161) and shows more craters. It also shows the two distinctive types of terrain found by Voyager, the darker ungrooved regions and the lighter areas which show the grooves or fractures in abundance. The most striking features are the bright ray craters which havE a distinctly 'bluer' color appearing white against the redder background. Ganymede's surface is known to contain large amounts of surface ice and it appears that these relatively young craters have spread bright fresh ice materials over the surface. Likewise, the lighter color and reflectivity of the grooved areas suggests that here too, there is cleaner ice. We see ray craters with all sizes of ray patterns, ranging from extensive systems of the crater in the northern part of this picture, which has rays at least 300-500 kilometers long, down to craters which have only faint remnants of bright ejecta patterns. This variation suggests that, as on the Moon, there are processes which act to darken ray material, probably 'gardening' by micrometeoroid impact. JPL manages and controls the Voyager project for NASA's Office of Space Science.

The Effectiveness of the "Golfer's Groove" in Improving Golfers' Scores

ERIC Educational Resources Information Center

Yost, Michael; And Others

1976-01-01

Use of the "golfer's groove," a device for controlling the angle and plane of a practicing golfer's swing, significantly influences the accuracy with which male and female college students can be taught to drive golfballs. (MB)

4. DETAIL VIEW OF TRIPLE TONGUE AND GROOVE CRIBBING USED ...

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

4. DETAIL VIEW OF TRIPLE TONGUE AND GROOVE CRIBBING USED IN DAM CONSTRUCTION, NORTH EAST OF EAST DAM, LOOKING NORTH - Three Bears Lake & Dams, East Dam, North of Marias Pass, East Glacier Park, Glacier County, MT

An analytical solution for the squeeze film between a nondeformable sphere and groove

NASA Technical Reports Server (NTRS)

Allen, C. W.; Wilson, M. P.

1972-01-01

An analysis is presented to compute the film thickness, pressure and load relations between a rigid ball and rigid groove in normal approach when lubricated by a fluid with an exponential pressure-viscosity relationship. The geometry of the ball-groove system is reduced to the equivalent system of a paraboloid approaching a flat plate. Exact and approximate solutions are presented for the load and pressure relations. There is found to be a limiting load for a given geometry and lubricant regardless of the rate of approach.

Narrow groove welding gas diffuser assembly and welding torch

DOEpatents

Rooney, Stephen J.

2001-01-01

A diffuser assembly is provided for narrow groove welding using an automatic gas tungsten arc welding torch. The diffuser assembly includes a manifold adapted for adjustable mounting on the welding torch which is received in a central opening in the manifold. Laterally extending manifold sections communicate with a shield gas inlet such that shield gas supplied to the inlet passes to gas passages of the manifold sections. First and second tapered diffusers are respectively connected to the manifold sections in fluid communication with the gas passages thereof. The diffusers extend downwardly along the torch electrode on opposite sides thereof so as to release shield gas along the length of the electrode and at the distal tip of the electrode. The diffusers are of a transverse width which is on the order of the thickness of the electrode so that the diffusers can, in use, be inserted into a narrow welding groove before and after the electrode in the direction of the weld operation.

Laser Surface Hardening of Groove Edges

NASA Astrophysics Data System (ADS)

Hussain, A.; Hamdani, A. H.; Akhter, R.; Aslam, M.

2013-06-01

Surface hardening of groove-edges made of 3Cr13 Stainless Steel has been carried out using 500 W CO2 laser with a rectangular beam of 2.5×3 mm2. The processing speed was varied from 150-500 mm/min. It was seen that the hardened depth increases with increase in laser interaction time. A maximum hardened depth of around 1mm was achieved. The microhardness of the transformed zone was 2.5 times the hardness of base metal. The XRD's and microstructural analysis were also reported.

Effects of hierarchical features on longevity of submerged superhydrophobic surfaces with parallel grooves

NASA Astrophysics Data System (ADS)

Hemeda, A. A.; Gad-el-Hak, M.; Tafreshi, H. Vahedi

2014-08-01

While the air-water interface over superhydrophobic surfaces decorated with hierarchical micro- or nanosized geometrical features have shown improved stability under elevated pressures, their underwater longevity—-the time that it takes for the surface to transition to the Wenzel state—-has not been studied. The current work is devised to study the effects of such hierarchical features on the longevity of superhydrophobic surfaces. For the sake of simplicity, our study is limited to superhydrophobic surfaces composed of parallel grooves with side fins. The effects of fins on the critical pressure—-the pressure at which the surface starts transitioning to the Wenzel state—-and longevity are predicted using a mathematical approach based on the balance of forces across the air-water interface. Our results quantitatively demonstrate that the addition of hierarchical fins significantly improves the mechanical stability of the air-water interface, due to the high advancing contact angles that can be achieved when an interface comes in contact with the fins sharp corners. For longevity on the contrary, the hierarchical fins were only effective at hydrostatic pressures below the critical pressure of the original smooth-walled groove. Our results indicate that increasing the length of the fins decreases the critical pressure of a submerged superhydrophobic groove but increases its longevity. Increasing the thickness of the fins can improve both the critical pressure and longevity of a submerged groove. The mathematical framework presented in this paper can be used to custom-design superhydrophobic surfaces for different applications.

Torque scaling in small-gap Taylor-Couette flow with smooth or grooved wall

NASA Astrophysics Data System (ADS)

Zhu, Bihai; Ji, Zengqi; Lou, Zhengkun; Qian, Pengcheng

2018-03-01

The torque in the Taylor-Couette flow for radius ratios η ≥0.97 , with smooth or grooved wall static outer cylinders, is studied experimentally, with the Reynolds number of the inner cylinder reaching up to Rei=2 ×105 , corresponding to the Taylor number up to Ta =5 ×1010 . The grooves are perpendicular to the mean flow, and similar to the structure of a submersible motor stator. It is found that the dimensionless torque G , at a given Rei and η , is significantly greater for grooved cases than smooth cases. We compare our experimental torques for the smooth cases to the fit proposed by Wendt [F. Wendt, Ing.-Arch. 4, 577 (1993), 10.1007/BF02084936] and the fit proposed by Bilgen and Boulos [E. Bilgen and R. Boulos, J Fluids Eng. 95, 122 (1973), 10.1115/1.3446944], which shows both fits are outside their range for small gaps. Furthermore, an additional dimensionless torque (angular velocity flux) N uω in the smooth cases exhibits an effective scaling of N uω˜T a0.39 in the ultimate regime, which occurs at a lower Taylor number, Ta ≈3.5 ×107 , than the well-explored η =0.714 case (at Ta ≈3 ×108 ). The same effective scaling exponent, 0.39, is also evident in the grooved cases, but for η =0.97 and 0.985, there is a peak before this exponent appears.

Development of spiral-groove self-acting seals for helicopter engines

NASA Technical Reports Server (NTRS)

Obrien, M.

1979-01-01

A spiral-groove, self-acting face seal was rig tested at advanced gas turbine operating conditions to determine wear and leakage rates. The spiral-groove, self-acting geometry was located in the rotating seal seat. Seal component wear induced by start-stop operation was measured after subjecting the test seal to 176 start-stop cycles. Wear occurring during normal operation was documented throughout a 75-hour endurance test. Seal air leakage was also measured. During endurance operation, the seal was subjected to operating conditions bounded by the values surface speed - 244 m/s (800 ft/sec), air pressure - 148 N/sq cm abs (215 psia), and air temperature - 622 K (660 F). The post-test condition of the seal components was documented. Wear data is presented in tabular form, while seal air leakage is presented graphically, as a function of pressure and speed.

Effect of groove width of modified current collector on internal short circuit of abused lithium-ion battery

NASA Astrophysics Data System (ADS)

Wang, Meng; Shi, Yang; Noelle, Daniel J.; Le, Anh V.; Qiao, Yu

2017-10-01

In a lithium-ion battery (LIB), mechanical abuse often leads to internal short circuits (ISC) that trigger thermal runaway. We investigated a thermal-runaway mitigation (TRM) technique using a modified current collector. By generating surface grooves on the current collector, the area of electrodes directly involved in ISC could be largely reduced, which decreased the ISC current. The TRM mechanism took effect immediately after the LIB was damaged. The testing data indicate that the groove width is a critical factor. With optimized groove width, this technique may enable robust and multifunctional design of LIB cells for large-scale energy-storage units.

In Vitro Retentive Effect of Groove, Sandblasting, and Cement Type on Stainless Steel Crowns in Primary Molars.

PubMed

Pathak, Sidhant; Shashibhushan, K K; Bharath, K P; Poornima, P; Reddy, V V Subba

2015-01-01

The purpose of this study was to evaluate and compare the effect of placing vertical grooves, sandblasting, and luting cements on the retention of stainless steel crowns (SSCs). Eighty extracted primary molars were mounted in acrylic blocks. Specimens were divided into Group 1 (RelyX U200) and Group 2 (Smart Cem2). Teeth in each group were further subdivided into Subgroup A (no vertical grooves and no sandblasting), Subgroup B (vertical grooves), Subgroup C (sandblasting of crowns), and Subgroup D (vertical grooves and sandblasting of crowns). After cementation, SSCs were pulled off using a universal testing machine. One-way analysis of variance was used for statistical analyses. In Groups 1 and 2, the highest retentive strengths were found in Subgroup D (1,124 and 783 kPa, respectively), followed by Subgroup C (1,066 and 748 kPa, respectively), Subgroup A (762 and 356 kPa, respectively), and Subgroup B (743 and 314 kPa, respectively). Retentive strength in Group one was significantly higher than in Group two; Subgroups A and B were significantly lower than C and D. RelyX U200 showed higher retentive strength than Smart Cem2. Sandblasting increased the retention strength, whereas a vertical groove had no significant effect on retention.

In and out of the minor groove: interaction of an AT-rich DNA with the drug CD27

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

Acosta-Reyes, Francisco J.; Dardonville, Christophe; Koning, Harry P. de

New features of an antiprotozoal DNA minor-groove binding drug, which acts as a cross-linking agent, are presented. It also fills the minor groove of DNA completely and prevents the access of proteins. These features are also expected for other minor-groove binding drugs when associated with suitable DNA targets. The DNA of several pathogens is very rich in AT base pairs. Typical examples include the malaria parasite Plasmodium falciparum and the causative agents of trichomoniasis and trypanosomiases. This fact has prompted studies of drugs which interact with the minor groove of DNA, some of which are used in medical practice. Previousmore » studies have been performed almost exclusively with the AATT sequence. New features should be uncovered through the study of different DNA sequences. In this paper, the crystal structure of the complex of the DNA duplex d(AAAATTTT){sub 2} with the dicationic drug 4, 4′-bis(imidazolinylamino)diphenylamine (CD27) is presented. The drug binds to the minor groove of DNA as expected, but it shows two new features that have not previously been described: (i) the drugs protrude from the DNA and interact with neighbouring molecules, so that they may act as cross-linking agents, and (ii) the drugs completely cover the whole minor groove of DNA and displace bound water. Thus, they may prevent the access to DNA of proteins such as AT-hook proteins. These features are also expected for other minor-groove binding drugs when associated with all-AT DNA. These findings allow a better understanding of this family of compounds and will help in the development of new, more effective drugs. New data on the biological interaction of CD27 with the causative agent of trichomoniasis, Trichomonas vaginalis, are also reported.« less

Combustor exhaust emissions with air-atomizing splash-groove fuel injectors burning Jet A and Diesel number 2 fuels

NASA Technical Reports Server (NTRS)

Ingebo, R. D.; Norgren, C. T.

1975-01-01

Air-atomizing, splash-groove injectors were shown to improve primary-zone fuel spreading and reduce combustor exhaust emissions for Jet A and diesel number 2 fuels. With Jet A fuel large-orifice, splash-groove injectors the oxides-of-nitrogen emission index was reduced, but emissions of carbon monoxide, unburned hydrocarbons, or smoke were unaffected. Small-orifice, splash-groove injectors did not reduce oxides of nitrogen, but reduced the smoke number and carbon monoxide and unburned-hydrocarbon emission indices. With diesel number 2 fuel, the small-orifice, splash-groove injectors reduced oxides of nitrogen by 19 percent, smoke number by 28 percent, carbon monoxide by 75 percent, and unburned hydrocarbons by 50 percent. Smoke number and unburned hydrocarbons were twice as high with diesel number 2 as with Jet A fuel. Combustor blowout limits were similar for diesel number 2 and Jet A fuels.

Influence of the Groove on Barrier Surface on Creeping Discharge Characteristics in N2 Gas under µs Pulse Voltage

NASA Astrophysics Data System (ADS)

Ueno, Hideki; Kawano, Taichi; Sakamoto, Naoki; Nakayama, Hiroshi

For a needle-plane electrode system with a barrier, which establishes the electric field across the axis of a groove, creeping discharge characteristics in N2 gas under µs pulse voltage applications have been investigated. The distance h between the barrier surface and the needle tip as well as the distance M between the groove center and the needle tip were changed. In the case of h=0.3mm, when the needle tip is located near the far-side groove edge from the plane electrode (M=0.6mm), the flashover voltage has the maximum value. At that time, a growth of a corona is suppressed near the groove edge. These unique characteristics should associate with a field relaxation.

HCV IRES domain IIb affects the configuration of coding RNA in the 40S subunit's decoding groove

PubMed Central

Filbin, Megan E.; Kieft, Jeffrey S.

2011-01-01

Hepatitis C virus (HCV) uses a structured internal ribosome entry site (IRES) RNA to recruit the translation machinery to the viral RNA and begin protein synthesis without the ribosomal scanning process required for canonical translation initiation. Different IRES structural domains are used in this process, which begins with direct binding of the 40S ribosomal subunit to the IRES RNA and involves specific manipulation of the translational machinery. We have found that upon initial 40S subunit binding, the stem–loop domain of the IRES that contains the start codon unwinds and adopts a stable configuration within the subunit's decoding groove. This configuration depends on the sequence and structure of a different stem–loop domain (domain IIb) located far from the start codon in sequence, but spatially proximal in the IRES•40S complex. Mutation of domain IIb results in misconfiguration of the HCV RNA in the decoding groove that includes changes in the placement of the AUG start codon, and a substantial decrease in the ability of the IRES to initiate translation. Our results show that two distal regions of the IRES are structurally communicating at the initial step of 40S subunit binding and suggest that this is an important step in driving protein synthesis. PMID:21606179

HCV IRES domain IIb affects the configuration of coding RNA in the 40S subunit's decoding groove.

PubMed

Filbin, Megan E; Kieft, Jeffrey S

2011-07-01

Hepatitis C virus (HCV) uses a structured internal ribosome entry site (IRES) RNA to recruit the translation machinery to the viral RNA and begin protein synthesis without the ribosomal scanning process required for canonical translation initiation. Different IRES structural domains are used in this process, which begins with direct binding of the 40S ribosomal subunit to the IRES RNA and involves specific manipulation of the translational machinery. We have found that upon initial 40S subunit binding, the stem-loop domain of the IRES that contains the start codon unwinds and adopts a stable configuration within the subunit's decoding groove. This configuration depends on the sequence and structure of a different stem-loop domain (domain IIb) located far from the start codon in sequence, but spatially proximal in the IRES•40S complex. Mutation of domain IIb results in misconfiguration of the HCV RNA in the decoding groove that includes changes in the placement of the AUG start codon, and a substantial decrease in the ability of the IRES to initiate translation. Our results show that two distal regions of the IRES are structurally communicating at the initial step of 40S subunit binding and suggest that this is an important step in driving protein synthesis.

Swift heavy ion irradiation of CaF2 - from grooves to hillocks in a single ion track

NASA Astrophysics Data System (ADS)

Gruber, Elisabeth; Salou, Pierre; Bergen, Lorenz; El Kharrazi, Mourad; Lattouf, Elie; Grygiel, Clara; Wang, Yuyu; Benyagoub, Abdenacer; Levavasseur, Delphine; Rangama, Jimmy; Lebius, Henning; Ban-d'Etat, Brigitte; Schleberger, Marika; Aumayr, Friedrich

2016-10-01

A novel form of ion-tracks, namely nanogrooves and hillocks, are observed on CaF2 after irradiation with xenon and lead ions of about 100 MeV kinetic energy. The irradiation is performed under grazing incidence (0.3°-3°) which forces the track to a region in close vicinity to the surface. Atomic force microscopy imaging of the impact sites with high spatial resolution reveals that the surface track consists in fact of three distinct parts: each swift heavy ion impacting on the CaF2 surface first opens a several 100 nm long groove bordered by a series of nanohillocks on both sides. The end of the groove is marked by a huge single hillock and the further penetration of the swift projectile into deeper layers of the target is accompanied by a single protrusion of several 100 nm in length slowly fading until the track vanishes. By comparing experimental data for various impact angles with results of a simulation, based on a three-dimensional version of the two-temperature-model (TTM), we are able to link the crater and hillock formation to sublimation and melting processes of CaF2 due to the local energy deposition by swift heavy ions.

Normal Modes Expose Active Sites in Enzymes.

PubMed

Glantz-Gashai, Yitav; Meirson, Tomer; Samson, Abraham O

2016-12-01

Accurate prediction of active sites is an important tool in bioinformatics. Here we present an improved structure based technique to expose active sites that is based on large changes of solvent accessibility accompanying normal mode dynamics. The technique which detects EXPOsure of active SITes through normal modEs is named EXPOSITE. The technique is trained using a small 133 enzyme dataset and tested using a large 845 enzyme dataset, both with known active site residues. EXPOSITE is also tested in a benchmark protein ligand dataset (PLD) comprising 48 proteins with and without bound ligands. EXPOSITE is shown to successfully locate the active site in most instances, and is found to be more accurate than other structure-based techniques. Interestingly, in several instances, the active site does not correspond to the largest pocket. EXPOSITE is advantageous due to its high precision and paves the way for structure based prediction of active site in enzymes.

Normal Modes Expose Active Sites in Enzymes

PubMed Central

Glantz-Gashai, Yitav; Samson, Abraham O.

2016-01-01

Accurate prediction of active sites is an important tool in bioinformatics. Here we present an improved structure based technique to expose active sites that is based on large changes of solvent accessibility accompanying normal mode dynamics. The technique which detects EXPOsure of active SITes through normal modEs is named EXPOSITE. The technique is trained using a small 133 enzyme dataset and tested using a large 845 enzyme dataset, both with known active site residues. EXPOSITE is also tested in a benchmark protein ligand dataset (PLD) comprising 48 proteins with and without bound ligands. EXPOSITE is shown to successfully locate the active site in most instances, and is found to be more accurate than other structure-based techniques. Interestingly, in several instances, the active site does not correspond to the largest pocket. EXPOSITE is advantageous due to its high precision and paves the way for structure based prediction of active site in enzymes. PMID:28002427

Development of an equine groove model to induce metacarpophalangeal osteoarthritis: a pilot study on 6 horses.

PubMed

Maninchedda, Ugo; Lepage, Olivier M; Gangl, Monika; Hilairet, Sandrine; Remandet, Bernard; Meot, Francoise; Penarier, Geraldine; Segard, Emilie; Cortez, Pierre; Jorgensen, Christian; Steinberg, Régis

2015-01-01

The aim of this work was to develop an equine metacarpophalangeal joint model that induces osteoarthritis that is not primarily mediated by instability or inflammation. The study involved six Standardbred horses. Standardized cartilage surface damage or "grooves" were created arthroscopically on the distal dorsal aspect of the lateral and medial metacarpal condyles of a randomly chosen limb. The contralateral limb was sham operated. After 2 weeks of stall rest, horses were trotted 30 minutes every other day for 8 weeks, then evaluated for lameness and radiographed. Synovial fluid was analyzed for cytology and biomarkers. At 10 weeks post-surgery, horses were euthanized for macroscopic and histologic joint evaluation. Arthroscopic grooving allowed precise and identical damage to the cartilage of all animals. Under the controlled exercise regime, this osteoarthritis groove model displayed significant radiographic, macroscopic, and microscopic degenerative and reactive changes. Histology demonstrated consistent surgically induced grooves limited to non-calcified cartilage and accompanied by secondary adjacent cartilage lesions, chondrocyte necrosis, chondrocyte clusters, cartilage matrix softening, fissuring, mild subchondral bone inflammation, edema, and osteoblastic margination. Synovial fluid biochemistry and cytology demonstrated significantly elevated total protein without an increase in prostaglandin E2, neutrophils, or chondrocytes. This equine metacarpophalangeal groove model demonstrated that standardized non-calcified cartilage damage accompanied by exercise triggered altered osteochondral morphology and cartilage degeneration with minimal or inefficient repair and little inflammatory response. This model, if validated, would allow for assessment of disease processes and the effects of therapy.

The effect of shoe soling tread groove width on the coefficient of friction with different sole materials, floors, and contaminants.

PubMed

Li, Kai Way; Chen, Chin Jung

2004-11-01

Tread groove design is very common in footwear. However, coefficient of friction (COF) measurements between the footwear material and floor using a slipmeter were commonly performed using flat footwear pads. Such measurements might underestimate the actual slip resistance of the footwear pad. This research investigates the effects of the tread groove width on the measured COF using four footwear materials, three floors, and four liquid-contamination conditions using a Brungraber Mark II slipmeter. The analysis of variance results indicated that the footwear material, floor, contamination conditions, and groove width were all significant (p < 0.0001) factors affecting the measured COF. The hypothesis that wider tread grooves result in higher COF values was true with some exceptions especially on oil contaminated floors. A regression model, with an R2 of 0.91, was established to describe and predict the relationship between the COF and the tread groove width under footwear material/floor/contamination conditions.

Roughness-Induced Magnetic Domain in Fe Thin Films on Land-and-Groove Structures Studied by Spin-Polarized Secondary Electron Microscopy

NASA Astrophysics Data System (ADS)

Ueda, Shigenori; Iwasaki, Yoh; Ushioda, Sukekatsu

2003-10-01

The magnetic domain structures of Fe thin films on two-dimensionally arranged land-and-groove structures have been studied by spin-polarized secondary electron microscopy (SP-SEM) under an applied dc field. The coercive force on the land area was found to be higher than that on the groove area under magnetization reversal. The surface roughness measured by atomic force microscopy (AFM) was greater on the land area than on the groove area. The roughness-induced high-coercivity on the land prevented the reversed magnetic domain on the groove from spreading over the land in the initial magnetization reversal. This result indicates that surface roughness is an important factor in domain size control of thin magnetic films.

Effectiveness of noise barriers installed adjacent to transverse grooved concrete pavement.

DOT National Transportation Integrated Search

2009-10-16

In recent years the Ohio Department of Transportation (ODOT) has reconstructed a number of roadways where asphalt pavements were replaced with random transverse grooved concrete pavements. Upon completion, residents living adjacent to the reconstruct...

J{sub IC} evaluation of the smooth and the side-grooved CT specimen in the reactor pressure vessel steel (SA508-3)

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

Oh, S.W.; Lim, M.B.; Kim, T.H.

1993-12-31

The elastic-plastic fracture toughness J{sub IC} of SA508-3 forging steel was investigated by using CT-type specimens. The thickness of the smooth specimen is B{sub 0} = 25.4 mm and the side groove specimen is B{sub N} = 20.4 mm and the side groove deep is S{center_dot}G = [(B{sub 0} {minus} B{sub N})/B{sub 0}] {times} 100 = 19.7% and the groove angle is 90{degree}. The J{sub IC} tests estimated according to the method proposed in the ASTM E813-81 and JSME S001-81. The side-grooved specimen have the advantage of J{sub IC} estimation, it is much easier to determine the onset of ductilemore » tearing by the R-curve method and it improved accuracy and scatter of the toughness values thus determined, provided all the size-requirements for the specimen prescribed in the JSME method were satisfied. But it is difficult to find by the ASTM method. The critical stretched zone width (SZW{sub C}) of the side-grooved specimens found to be smaller than that previously determined for the standard CT specimens without side-grooves. This was attributed to higher triaxiality produced by the side-grooves. The stretched zone width method gave slightly larger J{sub IC} values than those by the R-curve method for SA508-3, as has been observed for the standard specimen without side-groove.« less

Influence of structural parameters of deep groove ball bearings on vibration

NASA Astrophysics Data System (ADS)

Yu, Guangwei; Wu, Rui; Xia, Wei

2018-04-01

Taking 6201 bearing as the research object, a dynamic model of 4 degrees of freedom is established to solve the vibration characteristics such as the displacement, velocity and acceleration of deep groove ball bearings by MATLAB and Runge-Kutta method. By calculating the theoretical value of the frequency of the rolling element passing through the outer ring and the simulation value of the model, it can be known that the theoretical calculation value and the simulation value have good consistency. By the experiments, the measured values and simulation values are consistent. Using the mathematical model, the effect of structural parameters on vibration is obtained. The method in the paper is testified to be feasible and the results can be used as references for the design, manufacturing and testing of deep groove ball bearings.

Investigation of accident reduction by grooved concrete pavement : final report.

DOT National Transportation Integrated Search

1979-06-01

This report is a category 2 experimental project evaluation written in conjunction with EHS-I-10-3(93)158 and EHS-I-12-1(44)0 contracted to groove hardened PCC pavement. In it the wear characteristics, pavement texture, skid resistance, and the accid...

9. DETAIL VIEW OF 2' TONGUE AND GROOVE PLANKING IN ...

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

9. DETAIL VIEW OF 2' TONGUE AND GROOVE PLANKING IN WATER CONTROL BOX. THIS SAME PLANKING IS USED AS CRIBBING FOR BOTH EAST DAM AND WEST DAM - Three Bears Lake & Dams, Water Control Box, North of Marias Pass, East Glacier Park, Glacier County, MT

The location of the peroneus longus tendon in the cuboid groove: sonographic study in various positions of the ankle-foot in asymptomatic volunteers.

PubMed

Choo, Hye Jung; Lee, Sun Joo; Huang, Brady K; Resnick, Donald L

2018-04-10

To evaluate the normal location of the peroneus longus tendon (PL) in the cuboid groove in various ankle-foot positions by ultrasonography in asymptomatic volunteers. Ultrasonographic assessment of the PL in the cuboid groove was performed in 20 feet of ten healthy volunteers. Each PL was examined in five ankle-foot positions (i.e., neutral, dorsiflexion, plantar-flexion, supination, and pronation). The PL location was qualitatively categorized as "inside" when the PL was entirely within the cuboid groove, as "overlying" when some part of the PL was perched on the cuboid tuberosity, and as "outside" when the PL was entirely on the cuboid tuberosity. For quantitative evaluation of the PL location, the distance between the PL and the cuboid groove was measured. The width of the cuboid groove was measured in the neutral position. The PL location did not significantly change with changes in the ankle-foot position. Qualitatively, an "overlying" PL was the most common type, regardless of the ankle-foot position. "Inside" PLs were found in only 35, 20, 30, 25, and 35% of feet in neutral, dorsiflexion, plantar-flexion, supination, and pronation positions, respectively. The quantitative PL location was also not significantly different among all ankle-foot positions and it was significantly negatively correlated with the cuboid groove width. In healthy volunteers, 65% or more of the PLs were partially or completely located outside of the cuboid groove, regardless of the ankle-foot position. The PL location relative to the cuboid groove was related to the cuboid groove width.

Numerical study of the collar wave characteristics and the effects of grooves in acoustic logging while drilling

NASA Astrophysics Data System (ADS)

Yang, Yufeng; Guan, Wei; Hu, Hengshan; Xu, Minqiang

2017-05-01

Large-amplitude collar wave covering formation signals is still a tough problem in acoustic logging-while-drilling (LWD) measurements. In this study, we investigate the propagation and energy radiation characteristics of the monopole collar wave and the effects of grooves on reducing the interference to formation waves by finite-difference calculations. We found that the collar wave radiates significant energy into the formation by comparing the waveforms between a collar within an infinite fluid, and the acoustic LWD in different formations with either an intact or a truncated collar. The collar wave recorded on the outer surface of the collar consists of the outward-radiated energy direct from the collar (direct collar wave) and that reflected back from the borehole wall (reflected collar wave). All these indicate that the significant effects of the borehole-formation structure on collar wave were underestimated in previous studies. From the simulations of acoustic LWD with a grooved collar, we found that grooves broaden the frequency region of low collar-wave excitation and attenuate most of the energy of the interference waves by multireflections. However, grooves extend the duration of the collar wave and convert part of the collar-wave energy originally kept in the collar into long-duration Stoneley wave. Interior grooves are preferable to exterior ones because both the low-frequency and the high-frequency parts of the collar wave can be reduced and the converted inner Stoneley wave is relatively difficult to be recorded on the outer surface of the collar. Deeper grooves weaken the collar wave more greatly, but they result in larger converted Stoneley wave especially for the exterior ones. The interference waves, not only the direct collar wave but also the reflected collar wave and the converted Stoneley waves, should be overall considered for tool design.

Design analysis of a self-acting spiral-groove ring seal for counter-rotating shafts. [o ring seals

NASA Technical Reports Server (NTRS)

Dirusso, E.

1983-01-01

A self-acting spiral groove inter-shaft ring seal of nominal 16.33 cm (6.43 in.) diameter for sealing fan bleed air between counter rotating shafts in advanced turbofan engines was analyzed. The analysis focused on the lift force characteristics of the spiral grooves. A NASA Lewis developed computer program for predicting the performance of gas lubricated face seals was used to optimize the spiral groove geometry to produce maximum lift force. Load capacity curves (lift force as function of film thickness) were generated for four advanced turbofan engine operating conditions at relative seal speeds ranging from 17,850 to 29,800 rpm, sealed air pressures from 6 to 42 N/sq cm (9 to 60 psi) absolute and temperatures from 95 to 327 C (203 to 620 F). The relative seal sliding speed range was 152 to 255 m/sec (500 to 836 ft/sec). The analysis showed that the spiral grooves are capable of producing sufficient lift force such that the ring seal will operate in a noncontacting mode over the operating range of typical advanced turbofan engines.

The 1.3 A resolution structure of the RNA tridecamer r(GCGUUUGAAACGC): metal ion binding correlates with base unstacking and groove contraction.

PubMed

Timsit, Youri; Bombard, Sophie

2007-12-01

Metal ions play a key role in RNA folding and activity. Elucidating the rules that govern the binding of metal ions is therefore an essential step for better understanding the RNA functions. High-resolution data are a prerequisite for a detailed structural analysis of ion binding on RNA and, in particular, the observation of monovalent cations. Here, the high-resolution crystal structures of the tridecamer duplex r(GCGUUUGAAACGC) crystallized under different conditions provides new structural insights on ion binding on GAAA/UUU sequences that exhibit both unusual structural and functional properties in RNA. The present study extends the repertory of RNA ion binding sites in showing that the two first bases of UUU triplets constitute a specific site for sodium ions. A striking asymmetric pattern of metal ion binding in the two equivalent halves of the palindromic sequence demonstrates that sequence and its environment act together to bind metal ions. A highly ionophilic half that binds six metal ions allows, for the first time, the observation of a disodium cluster in RNA. The comparison of the equivalent halves of the duplex provides experimental evidences that ion binding correlates with structural alterations and groove contraction.

Source Listings for Computer Code SPIRALI Incompressible, Turbulent Spiral Grooved Cylindrical and Face Seals

NASA Technical Reports Server (NTRS)

Walowit, Jed A.; Shapiro, Wibur

2005-01-01

This is the source listing of the computer code SPIRALI which predicts the performance characteristics of incompressible cylindrical and face seals with or without the inclusion of spiral grooves. Performance characteristics include load capacity (for face seals), leakage flow, power requirements and dynamic characteristics in the form of stiffness, damping and apparent mass coefficients in 4 degrees of freedom for cylindrical seals and 3 degrees of freedom for face seals. These performance characteristics are computed as functions of seal and groove geometry, load or film thickness, running and disturbance speeds, fluid viscosity, and boundary pressures.

Design and performance of compliant thrust bearing with spiral-groove membranes on resilient supports

NASA Technical Reports Server (NTRS)

Licht, L.; Anderson, W. J.; Doroff, S. W.

1980-01-01

Novel thrust bearings with spiral-groove flexible membranes mounted on resilient supports were designed and their performance demonstrated. Advantages of surface compliance were combined with the superior load-capacity of the spiral-groove geometry. Loads of 127-150N were supported on an area 42 sq cm, at speeds of 43,000-45,000 rpm and mean clearances of 15-20 microns. Support-worthiness was proved when tested in conjunction with foil journal-bearings and a 19N rotor, excited in a pitching mode by a total unbalance of 43 micron-N.

Design and experimental study on Fresnel lens of the combination of equal-width and equal-height of grooves

NASA Astrophysics Data System (ADS)

Guo, Limin; Liu, Youqiang; Huang, Rui; Wang, Zhiyong

2017-06-01

High concentrating PV systems rely on large Fresnel lens that must be precisely oriented in the direction of the Sun to maintain high concentration ratio. We propose a new Fresnel lens design method combining equal-width and equal-height of grooves in this paper based on the principle of focused spot maximum energy. In the ring band near the center of Fresnel lens, the design with equal-width grooves is applied, and when the given condition is reached, the design with equal-height grooves is introduced near the edges of the Fresnel lens, which ensures all the lens grooves are planar. In this paper, we establish a Fresnel lens design example model by Solidworks, and simulate it with the software ZEMAX. An experimental test platform is built to test, and the simulation correctness is proved by experiments. Experimental result shows the concentrating efficiency of this example is 69.3%, slightly lower than the simulation result 75.1%.

A New Method of Administering the Grooved Pegboard Test: Performance as a Function of Handedness and Sex

ERIC Educational Resources Information Center

Bryden, P.J.; Roy, E.A.

2005-01-01

The purpose of the present study was twofold: first to examine the influences of sex and handedness on manual performance on the Grooved Pegboard Test; and secondly to provide normative data for two versions (Place and Remove tasks) of the Grooved Pegboard Test, as previous work (Bryden & Roy, 1999) had suggested that the Remove task of the…

Capillary Contact Angle in a Completely Wet Groove

NASA Astrophysics Data System (ADS)

Parry, A. O.; Malijevský, A.; Rascón, C.

2014-10-01

We consider the phase equilibria of a fluid confined in a deep capillary groove of width L with identical side walls and a bottom made of a different material. All walls are completely wet by the liquid. Using density functional theory and interfacial models, we show that the meniscus separating liquid and gas phases at two phase capillary coexistence meets the bottom capped end of the groove at a capillary contact angle θcap(L) which depends on the difference between the Hamaker constants. If the bottom wall has a weaker wall-fluid attraction than the side walls, then θcap>0 even though all the isolated walls are themselves completely wet. This alters the capillary condensation transition which is now first order; this would be continuous in a capped capillary made wholly of either type of material. We show that the capillary contact angle θcap(L) vanishes in two limits, corresponding to different capillary wetting transitions. These occur as the width (i) becomes macroscopically large, and (ii) is reduced to a microscopic value determined by the difference in Hamaker constants. This second wetting transition is characterized by large scale fluctuations and essential critical singularities arising from marginal interfacial interactions.

Disk in a groove with friction: An analysis of static equilibrium and indeterminacy

NASA Astrophysics Data System (ADS)

Donolato, Cesare

2018-05-01

This note studies the statics of a rigid disk placed in a V-shaped groove with frictional walls and subjected to gravity and a torque. The two-dimensional equilibrium problem is formulated in terms of the angles that contact forces form with the normal to the walls. This approach leads to a single trigonometric equation in two variables whose domain is determined by Coulomb's law of friction. The properties of solutions (existence, uniqueness, or indeterminacy) as functions of groove angle, friction coefficient and applied torque are derived by a simple geometric representation. The results modify some of the conclusions by other authors on the same problem.

Aptamer sensor for cocaine using minor groove binder based energy transfer.

PubMed

Zhou, Jinwen; Ellis, Amanda V; Kobus, Hilton; Voelcker, Nicolas H

2012-03-16

We report on an optical aptamer sensor for cocaine detection. The cocaine sensitive fluorescein isothiocyanate (FITC)-labeled aptamer underwent a conformational change from a partial single-stranded DNA with a short hairpin to a double-stranded T-junction in the presence of the target. The DNA minor groove binder Hoechst 33342 selectively bound to the double-stranded T-junction, bringing the dye within the Förster radius of FITC, and therefore initiating minor groove binder based energy transfer (MBET), and reporting on the presence of cocaine. The sensor showed a detection limit of 0.2 μM. The sensor was also implemented on a carboxy-functionalized polydimethylsiloxane (PDMS) surface by covalently immobilizing DNA aptamers. The ability of surface-bound cocaine detection is crucial for the development of microfluidic sensors. Copyright © 2012 Elsevier B.V. All rights reserved.

UTILITY ROOM WITH CANEC PANEL CEILING AND TONGUE AND GROOVE ...

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

UTILITY ROOM WITH CANEC PANEL CEILING AND TONGUE AND GROOVE WALL BOARDS. VIEW FACING NORTHWEST - Camp H.M. Smith and Navy Public Works Center Manana Title VII (Capehart) Housing, Four-Bedroom, Single-Family Type 10, Birch Circle, Elm Drive, Elm Circle, and Date Drive, Pearl City, Honolulu County, HI

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

Study of heat transfer due to turbulent flow of nanofluids through rib-groove channel

NASA Astrophysics Data System (ADS)

Al-Shamani, A. N.; Sopian, K.; Abed, A. M.; Alghoul, M. A.; Ruslan, M. H.; Mat, S.

2015-09-01

Nanofluids for improve characteristics flow in a rib-groove channel are investigate. The continuity, momentum and energy equations were solved by FLUENT program. The bottom wall of channel is heated while the upper wall is symmetry, the left side velocity inlet, and the right side is outlet (pressure out). Four different rib-groove shapes are used. Four different types of nanoparticles, Al2O3, CuO, SiO2, and ZnO with different volumes fractions in the range of 1% to 4% and different nanoparticle diameter in the range of 25 nm to 70 nm, are dispersed in the base fluid water are used. In this paper, several parameters such as different Reynolds numbers in the range of 10000 < Re < 40000 are investigated. The numerical results indicate that the trapezoidal with increasing height in the flow direction rib- trapezoidal groove has the best heat transfer and high Nusselt number; the nanofluids with SiO2 have the best behavior. The Nusselt number increases as the volume fraction increases and it decreases as the nanoparticle diameter increases.

Analysis of focusing error signals by differential astigmatic method under off-center tracking in the land-groove-type optical disk

NASA Astrophysics Data System (ADS)

Shinoda, Masahisa; Nakatani, Hidehiko

2015-04-01

We theoretically calculate the behavior of the focusing error signal in the land-groove-type optical disk when the objective lens traverses on out of the radius of the optical disk. The differential astigmatic method is employed instead of the conventional astigmatic method for generating the focusing error signals. The signal behaviors are compared and analyzed in terms of the gain difference of the slope sensitivity of the focusing error signals from the land and the groove. In our calculation, the format of digital versatile disc-random access memory (DVD-RAM) is adopted as the land-groove-type optical disk model, and advantageous conditions for suppressing the gain difference are investigated. The calculation method and results described in this paper will be reflected in the next generation land-groove-type optical disks.

Probing binding hot spots at protein-RNA recognition sites.

PubMed

Barik, Amita; Nithin, Chandran; Karampudi, Naga Bhushana Rao; Mukherjee, Sunandan; Bahadur, Ranjit Prasad

2016-01-29

We use evolutionary conservation derived from structure alignment of polypeptide sequences along with structural and physicochemical attributes of protein-RNA interfaces to probe the binding hot spots at protein-RNA recognition sites. We find that the degree of conservation varies across the RNA binding proteins; some evolve rapidly compared to others. Additionally, irrespective of the structural class of the complexes, residues at the RNA binding sites are evolutionary better conserved than those at the solvent exposed surfaces. For recognitions involving duplex RNA, residues interacting with the major groove are better conserved than those interacting with the minor groove. We identify multi-interface residues participating simultaneously in protein-protein and protein-RNA interfaces in complexes where more than one polypeptide is involved in RNA recognition, and show that they are better conserved compared to any other RNA binding residues. We find that the residues at water preservation site are better conserved than those at hydrated or at dehydrated sites. Finally, we develop a Random Forests model using structural and physicochemical attributes for predicting binding hot spots. The model accurately predicts 80% of the instances of experimental ΔΔG values in a particular class, and provides a stepping-stone towards the engineering of protein-RNA recognition sites with desired affinity. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

EUV efficiency of a 6000-grooves per mm diffraction grating

NASA Technical Reports Server (NTRS)

Hurwitz, Mark; Bowyer, Stuart; Edelstein, Jerry; Harada, Tatsuo; Kita, Toshiaki

1990-01-01

In order to explore whether grooves ruled mechanically at a density of 6000 per mm can perform well at EUV wavelengths, a sample grating is measured with this density in an EUV calibration facility. Measurements are presented of the planar uniform line-space diffraction grating's efficiency and large-angle scattering.

Regenerated collagen fibers with grooved surface texture: Physicochemical characterization and cytocompatibility.

PubMed

Wang, Xiang; Wu, Tong; Wang, Wei; Huang, Chen; Jin, Xiangyu

2016-01-01

A novel type of protein fibers, regenerated collagen fibers (RC) from cattle skin, was prepared through wet-spinning. Due to the combined effect of solvent exchange and subsequent drawing process, the fibers were found to have a grooved surface texture. The grooves provided not only ordered topographical cues, but also increased surface area. Protein content of the RC fibers was confirmed by Fourier Transform infrared spectroscopy (FTIR) and ninhydrin color reaction. The fibers could be readily fabricated into nonwovens or other textiles, owning to their comparable physical properties to other commercialized fibers. Cell growth behavior on RC nonwovens suggested both early adhesion and prompt proliferation. The high moisture regain, good processability, along with the excellent cytocompatibility indicated that the RC fibers and nonwovens developed in this study might offer a good candidate for biomedical and healthcare applications. Copyright © 2015 Elsevier B.V. All rights reserved.

Biological Glue Application in Repair of Atrioventricular Groove Rupture: A Case Report

PubMed Central

Durukan, Ahmet Baris; Serter, Fatih Tanzer; Gurbuz, Hasan Alper; Tavlasoglu, Murat; Ucar, Halil Ibrahim; Yorgancioglu, Cem

2014-01-01

Abstract Atrioventricular groove rupture is a rare, albeit mortal, complication following mitral valve surgery. Avoidance is the best strategy but it cannot fully prevent the occurrence of this complication. Several repair techniques have been described with varying success rates; however, the rarity of the complication precludes consensus about the safest technique. Here we report two cases of posterior atrioventricular groove rupture. Both cases were diagnosed immediately after the cessation of cardiopulmonary bypass. Repair was performed successfully with a technique involving the use of biological glue. The postoperative course was uneventful for both of them. Both cases are well with normally functioning mitral prostheses; one with a follow-up time of 5.5 years and the other 10 months. We believe that the glue provides additional hemostasis and support to the repaired area. PMID:25870633

Electrified Flow in Slender V-Groove Microchannels: Generalized Stability of Steady State Configurations

NASA Astrophysics Data System (ADS)

Markeviciute, Vilda; White, Nicholas; Troian, Sandra

2017-11-01

Although spontaneous capillary flow can be an especially rapid process in slender open microchannels resembling V-grooves, enhanced flow control is possible through implementation of electric field distributions which generate opposing electrohydrodynamic pressures along the air/liquid interface to modulate the capillary pressures. Important fundamental work by Romero and Yost (1996) and Weislogel(1996) has elucidated the behavior of Newtonian films in slender V-grooves driven to flow solely by the streamwise change in capillary pressure due to the change in radius of curvature of the circular arc describing the interface of wetting or non-wetting fluids. Here we augment the Romero and Yost model with inclusion of Maxwell stresses for perfectly conducting wetting films and examine which electric field distributions allow formation of steady state film shapes for various inlet and outlet boundary conditions. We investigate the stability of these steady solutions to small perturbations in film thickness using a generalized stability analysis. These results reveal how the ratio of Maxwell to capillary stresses influences the degree of linearized transient growth or decay for thin films confined to flow within an open V-groove. Funding from the 2017 Caltech Summer Undergraduate Research Fellowship Program (Markeviciute) as well as a 2017 NASA Space Technology Research Fellowship (White) is gratefully acknowledged.

The suppression effect of a periodic surface with semicircular grooves on the high power microwave long pill-box window multipactor phenomenon

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

Zhang, Xue, E-mail: zhangxue.iecas@yahoo.com; Wang, Yong; Fan, Junjie

2014-09-15

To improve the transmitting power in an S-band klystron, a long pill-box window that has a disk with grooves with a semicircular cross section is theoretically investigated and simulated. A Monte-Carlo algorithm is used to track the secondary electron trajectories and analyze the multipactor scenario in the long pill-box window and on the grooved surface. Extending the height of the long-box window can decrease the normal electric field on the surface of the window disk, but the single surface multipactor still exists. It is confirmed that the window disk with periodic semicircular grooves can explicitly suppress the multipactor and predominantlymore » depresses the local field enhancement and the bottom continuous multipactor. The difference between semicircular and sharp boundary grooves is clarified numerically and analytically.« less

The suppression effect of a periodic surface with semicircular grooves on the high power microwave long pill-box window multipactor phenomenon

NASA Astrophysics Data System (ADS)

Zhang, Xue; Wang, Yong; Fan, Junjie; Zhong, Yong; Zhang, Rui

2014-09-01

To improve the transmitting power in an S-band klystron, a long pill-box window that has a disk with grooves with a semicircular cross section is theoretically investigated and simulated. A Monte-Carlo algorithm is used to track the secondary electron trajectories and analyze the multipactor scenario in the long pill-box window and on the grooved surface. Extending the height of the long-box window can decrease the normal electric field on the surface of the window disk, but the single surface multipactor still exists. It is confirmed that the window disk with periodic semicircular grooves can explicitly suppress the multipactor and predominantly depresses the local field enhancement and the bottom continuous multipactor. The difference between semicircular and sharp boundary grooves is clarified numerically and analytically.

Comparative Investigation and Operational Performance Characteristics of a Wick Assisted and Axially Square Grooved Heat Pipe

NASA Astrophysics Data System (ADS)

Naik, Rudra, Dr.; Rama Narasihma, K., Dr.; Anikivi, Atmanand

2018-04-01

The present work reported here involves the experimental investigation and performance evaluation of wick assisted and axially square grooved heat pipes of outer diameter 8mm, inner diameter 4mm with a length of 150mm.The objective of this work is to design, fabricate and test the heat pipes with and without an axial square groove for horizontal and gravity assisted conditions. The performance of the heat pipes was measured in terms of thermal resistance and heat transfer coefficients. In the present investigation four different working fluids were chosen namely acetone, ethanol, methanol and distilled water. Experiments were conducted by varying the heat load from 2 W to 10 W for different fill charge ratios in the range of 25% to 75% of evaporator volume for wick assisted heat pipe and 8 W to 18 W for axially square grooved heat pipe. From the experiments, it was found that there is a steady increase in temperature with the increase in heat input. The overall heat transfer coefficient was found to increase with the increase heat load for wick assisted heat pipe. In case of axially square grooved heat pipe, an attempt was made to experiment the heat pipe in different orientations. The maximum heat transfer coefficient of 7000 W/m2 °C is found for Acetone at 180° orientation.

Active aerodynamic drag reduction on morphable cylinders

NASA Astrophysics Data System (ADS)

Guttag, M.; Reis, P. M.

2017-12-01

We study a mechanism for active aerodynamic drag reduction on morphable grooved cylinders, whose topography can be modified pneumatically. Our design is inspired by the morphology of the Saguaro cactus (Carnegiea gigantea), which possesses an array of axial grooves, thought to help reduce aerodynamic drag, thereby enhancing the structural robustness of the plant under wind loading. Our analog experimental samples comprise a spoked rigid skeleton with axial cavities, covered by a stretched elastomeric film. Decreasing the inner pressure of the sample produces axial grooves, whose depth can be accurately varied, on demand. First, we characterize the relation between groove depth and pneumatic loading through a combination of precision mechanical experiments and finite element simulations. Second, wind tunnel tests are used to measure the aerodynamic drag coefficient (as a function of Reynolds number) of the grooved samples, with different levels of periodicity and groove depths. We focus specifically on the drag crisis and systematically measure the associated minimum drag coefficient and the critical Reynolds number at which it occurs. The results are in agreement with the classic literature of rough cylinders, albeit with an unprecedented level of precision and resolution in varying topography using a single sample. Finally, we leverage the morphable nature of our system to dynamically reduce drag for varying aerodynamic loading conditions. We demonstrate that actively controlling the groove depth yields a drag coefficient that decreases monotonically with Reynolds number and is significantly lower than the fixed sample counterparts. These findings open the possibility for the drag reduction of grooved cylinders to be operated over a wide range of flow conditions.

In-Roll Stress Analysis Considering Air-Entrainment at the Roll-Inlet with the Effect of Grooves on Nip Roll Surface

NASA Astrophysics Data System (ADS)

Sasaki, Masashi; Tanimoto, Koshi; Kohno, Kazukiyo; Takahashi, Sadamu; Kometani, Hideo; Hashimoto, Hiromu

High-speed winding of paper web sometimes leads the winding system into unstable states, interlayer slippage of wound roll, paper breakage and so on, due to the excessive air-entrainment at the roll-inlet of nip contact region. These phenomena are more frequently observed on coated paper or plastic film comparing with newspaper, because the former allows little permeation of air and their surface roughness is small. Therefore, it is of vital importance to clarify the in-roll stress of wound roll considering the effect of air-entrainment. Generally, it is known that the amount of air-entrainment is affected by grooving shape of nip roll surface. In this paper, we focused on the grooving shape and investigated the relationship with the air-entrainment into two rolls being pressed each other and the grooving shape in order to achieve stable winding at high speed. We conducted experiments using small sized test machine. Entrained air-film thickness was evaluated applying the solution of the elasto-hydrodynamic lubrication for foil bearing with the consideration of nip profile at the grooved area. Air film thickness was measured to ensure the applicability of the above theory. Consequently, we found that the air film thickness can be estimated considering the effect of grooves on the nip roll surface, and that the validity of the above estimations was ensured from experimental investigations. Furthermore, it became to be able to propose the optimal shape of grooves on nip roll surface to maintain the stable winding at high speed and at large-diameter in reel.

Intercalation and de-intercalation pathway of proflavine through the minor and major grooves of DNA: roles of water and entropy.

PubMed

Sasikala, Wilbee D; Mukherjee, Arnab

2013-05-07

DNA intercalation is a clinically relevant biophysical process due to its potential to inhibit the growth and survival of tumor cells and microbes through the arrest of the transcription and replication processes. Extensive kinetic and thermodynamic studies have followed since the discovery of the intercalative binding mode. However, the molecular mechanism and the origin of the thermodynamic and kinetic profile of the process are still not clear. Here we have constructed the free energy landscape of intercalation, de-intercalation and dissociation from both the major and minor grooves of DNA using extensive all-atom metadynamics simulations, capturing both the free energy barriers and stability in close agreement with fluorescence kinetic experiments. In the intercalated state, an alternate orientation of proflavine is found with an almost equal stability compared to the crystal orientation, however, separated by a 5.0 kcal mol(-1) barrier that decreases as the drug approaches the groove edges. This study provides a comprehensive picture in comparison with experiments, which indicates that the intercalation and de-intercalation of proflavine happen through the major groove side, although the effective intercalation barrier increases because the path of intercalation goes through the stable (abortive) minor groove bound state, making the process a millisecond long one in excellent agreement with the experiments. The molecular origin of the higher barrier for the intercalation from the minor groove side is attributed to the desolvation energy of DNA and the loss of entropy, while the barrier from the major groove, in the absence of desolvation energy, is primarily entropic.

[Lymphogranuloma venereum: new serovariant L2b and old "groove sign"].

PubMed

de Lavaissière, M; Nougué, J

2013-08-01

An ongoing lymphogranuloma venereum (LGV) outbreak has been reported in several European countries since 2003, related to a new variant L2b. This serovar appears to affect men who have sex with men (MSM), most of them being co-infected with the Human Immunodeficiency Virus (HIV). The secondary stage of LGV may involve lymph nodes and the inguinal form has sometimes been described on each side of the inguinal ligament thus named the "groove sign". We report the case of LGV serovariant L2b acquired by an heterosexual intercourse in an HIV seronegative patient who presented with an inguinal lymph node and a "groove sign". This is an uncommon but suggestive sign of LGV and we suggest that the clinical presentation of L2b LGV might not be so different than other variants and than the 20th century authors' description. Such a new Chlamydia trachomatis variant may circulate in other populations than MSM in Europe and clinical awareness must prevail.

Theoretical approach to obtaining dynamic characteristics of noncontacting spiral-grooved seals

NASA Technical Reports Server (NTRS)

Iwatsubo, Takuzo; Yang, Bo-Suk; Ibaraki, Ryuji

1987-01-01

The dynamic characteristics of spiral-grooved seals are theoretically obtained by using the Navier-Stokes equation. First, with the inertia term of the fluid considered, the flow and pressure in the steady state are obtained for the directions parallel to and perpendicular to the groove. Next, the dynamic character is obtained by analyzing the steady state and by analyzing the labyrinth seal. As a result, the following conclusions were drawn: (1) As the land width becomes shorter or the helix angle decreases, the cross-coupling stiffness, direct and cross-coupling damping, and add mass coefficients decrease; (2) As the axial Reynolds number increases, the stiffness and damping coefficients increase. But the add mass coefficient is not influenced by the axial Reynolds number; (3) The rotational Reynolds number influences greatly the direct and cross-coupling stiffness and direct damping coefficients; and (4) As the journal rotating frequency increases, the leakage flow decreases. Therefore zero net leakage flow is possible at a particular rotating frequency.

Site-specific cleavage of the transactivation response site of human immunodeficiency virus RNA with a tat-based chemical nuclease.

PubMed Central

Jayasena, S D; Johnston, B H

1992-01-01

tat, an essential transactivator of gene transcription in the human immunodeficiency virus (HIV), is believed to activate viral gene expression by binding to the transactivation response (TAR) site located at the 5' end of all viral mRNAs. The TAR element forms a stem-loop structure containing a 3-nucleotide bulge that is the site for tat binding and is required for transactivation. Here we report the synthesis of a site-specific chemical ribonuclease based on the TAR binding domain of the HIV type 1 (HIV-1) tat. A peptide consisting of this 24-amino acid domain plus an additional C-terminal cysteine residue was chemically synthesized and covalently linked to 1,10-phenanthroline at the cysteine residue. The modified peptide binds to TAR sequences of both HIV-1 and HIV-2 and, in the presence of cupric ions and a reducing agent, cleaves these RNAs at specific sites. Cleavage sites on TAR sequences are consistent with peptide binding to the 3-nucleotide bulge, and the relative displacement of cleavage sites on the two strands suggests peptide binding to the major groove of the RNA. These results and existing evidence of the rapid cellular uptake of tat-derived peptides suggest that chemical nucleases based on tat may be useful for inactivating HIV mRNA in vivo. Images PMID:1565648

Influence of groove size and reinforcements addition on mechanical properties and microstructure of friction stir welded joints

NASA Astrophysics Data System (ADS)

Reddy Baridula, Ravinder; Ibrahim, Abdullah Bin; Yahya, Che Ku Mohammad Faizal Bin Che Ku; Kulkarni, Ratnakar; Varma Ramaraju, Ramgopal

2018-03-01

The butt joints fabricated by friction stir welding were found to have more strength than the joints obtained by conventional joining process. The important outcome of this process is the successful fabrication of surface composites with improved properties. Thus in order to further enhance the strength of the dissimilar alloy joints the reinforcements can be deposited in to the aluminium matrix during the process of friction stir welding. In the present study the multi-walled carbon nanotubes were embedded in to the groove by varying the width during joining of dissimilar alloys AA2024 and AA7075. Four widths were selected with constant depth and optimum process parameters were selected to fabricate the sound welded joints. The results show that the mechanical properties of the fabricated butt joints were influenced by the size of the groove, due to variation in the deposition of reinforcement in the stir zone. The microstructural study and identification of the elements of the welded joints show that the reinforcements deposition is influenced by the size of the groove. It has also been observed that the groove with minimum width is more effective than higher width. The mechanical properties are found to be improved due to the pinning of grain boundaries.

Dissecting the active site of a photoreceptor protein

NASA Astrophysics Data System (ADS)

Hoff, Wouter; Hara, Miwa; Ren, Jie; Moghadam, Farzaneh; Xie, Aihua; Kumauchi, Masato

While enzymes are quite large molecules, functionally important chemical events are often limited to a small region of the protein: the active site. The physical and chemical properties of residues at such active sites are often strongly altered compared to the same groups dissolved in water. Understanding such effects is important for unraveling the mechanisms underlying protein function and for protein engineering, but has proven challenging. Here we report on our ongoing efforts on using photoactive yellow protein (PYP), a bacterial photoreceptor, as a model system for such effects. We will report on the following questions: How many residues affect active site properties? Are these residues in direct physical contact with the active site? Can functionally important residues be recognized in the crystal structure of a protein? What structural resolution is needed to understand active sites? What spectroscopic techniques are most informative? Which weak interactions dominate active site properties?

Active site dynamics of ribonuclease.

PubMed Central

Brünger, A T; Brooks, C L; Karplus, M

1985-01-01

The stochastic boundary molecular dynamics method is used to study the structure, dynamics, and energetics of the solvated active site of bovine pancreatic ribonuclease A. Simulations of the native enzyme and of the enzyme complexed with the dinucleotide substrate CpA and the transition-state analog uridine vanadate are compared. Structural features and dynamical couplings for ribonuclease residues found in the simulation are consistent with experimental data. Water molecules, most of which are not observed in crystallographic studies, are shown to play an important role in the active site. Hydrogen bonding of residues with water molecules in the free enzyme is found to mimic the substrate-enzyme interactions of residues involved in binding. Networks of water stabilize the cluster of positively charged active site residues. Correlated fluctuations between the uridine vanadate complex and the distant lysine residues are mediated through water and may indicate a possible role for these residues in stabilizing the transition state. Images PMID:3866234

Grain boundary grooving induced by the anisotropic surface drift diffusion driven by the capillary and electromigration forces: Simulations

NASA Astrophysics Data System (ADS)

Akyildiz, Oncu; Omer Ogurtani, Tarik

2011-08-01

The morphological evolution kinetics of a bicrystal thin film induced by anisotropic surface drift diffusion and driven by the applied electrostatic field is investigated via self consistent dynamical computer simulations. The physico-mathematical model, which is based upon the irreversible thermodynamic treatment of surfaces and interfaces with singularities [T. O. Ogurtani, J. Chem. Phys. 124, 144706 (2006)], provided us with auto-control on the otherwise free-motion of the triple junction at the intersection of the grooving surface and the grain boundary, without having any a priori assumption on the equilibrium dihedral angles. The destruction of the symmetry of the freshly formed grain boundary grooves under the anisotropic surface diffusion driven by the concurrent action of the capillarity and electromigration is observed. After prolonged exposure times the applied electric field above the well defined threshold level modifies Mullins' familiar stationary state time law as, t¯1/4, and causes the premature termination of the groove penetration because of the current crowding at the tips of counteracting grain boundary-grooves initiated on both sides of the test modulus. That finding indicates that the electromigration plays the same role as a healing agent [T. O. Ogurtani, J. Appl. Phys. 106, 053503 (2009)] in arresting the thermal grooving, thereby avoiding the premature interconnect failure as in the case of surface roughening and crack initiation caused by compressive stress gradients. The role of the electromigration and wetting parameter on the ridge/slit formations are thoroughly investigated in this study and the prerequisite conditions are also identified.

Low dielectric response in enzyme active site

PubMed Central

Mertz, Edward L.; Krishtalik, Lev I.

2000-01-01

The kinetics of charge transfer depend crucially on the dielectric reorganization of the medium. In enzymatic reactions that involve charge transfer, atomic dielectric response of the active site and of its surroundings determines the efficiency of the protein as a catalyst. We report direct spectroscopic measurements of the reorganization energy associated with the dielectric response in the active site of α-chymotrypsin. A chromophoric inhibitor of the enzyme is used as a spectroscopic probe. We find that water strongly affects the dielectric reorganization in the active site of the enzyme in solution. The reorganization energy of the protein matrix in the vicinity of the active site is similar to that of low-polarity solvents. Surprisingly, water exhibits an anomalously high dielectric response that cannot be described in terms of the dielectric continuum theory. As a result, sequestering the active site from the aqueous environment inside low-dielectric enzyme body dramatically reduces the dielectric reorganization. This reduction is particularly important for controlling the rate of enzymatic reactions. PMID:10681440

Using mutagenesis to explore conserved residues in the RNA-binding groove of influenza A virus nucleoprotein for antiviral drug development

NASA Astrophysics Data System (ADS)

Liu, Chia-Lin; Hung, Hui-Chen; Lo, Shou-Chen; Chiang, Ching-Hui; Chen, I.-Jung; Hsu, John T.-A.; Hou, Ming-Hon

2016-02-01

Nucleoprotein (NP) is the most abundant type of RNA-binding viral protein in influenza A virus-infected cells and is necessary for viral RNA transcription and replication. Recent studies demonstrated that influenza NP is a valid target for antiviral drug development. The surface of the groove, covered with numerous conserved residues between the head and body domains of influenza A NP, plays a crucial role in RNA binding. To explore the mechanism by which NP binds RNA, we performed a series of site-directed mutagenesis in the RNA-binding groove, followed by surface plasmon resonance (SPR), to characterize the interactions between RNA and NP. Furthermore, a role of Y148 in NP stability and NP-RNA binding was evaluated. The aromatic residue of Y148 was found to stack with a nucleotide base. By interrupting the stacking interaction between Y148 and an RNA base, we identified an influenza virus NP inhibitor, (E, E)-1,7-bis(4-hydroxy-3-methoxyphenyl) -1,6-heptadiene-3,5-dione; this inhibitor reduced the NP’s RNA-binding affinity and hindered viral replication. Our findings will be useful for the development of new drugs that disrupt the interaction between RNA and viral NP in the influenza virus.

Olfactory groove meningiomas: approaches and complications.

PubMed

Aguiar, Paulo Henrique Pires de; Tahara, Adriana; Almeida, Antonio Nogueira; Simm, Renata; Silva, Arnaldo Neves da; Maldaun, Marcos Vinicius Calfatt; Panagopoulos, Alexandros Theodoros; Zicarelli, Carlos Alexandre; Silva, Pedro Gabriel

2009-09-01

Olfactory groove meningiomas (OGM) account for 4.5% of all intracranial meningiomas. We report 21 patients with OGMs. Tumors were operated on using three surgical approaches: bifrontal (7 patients), fronto-pterional (11 patients) and fronto-orbital (3 patients). Total tumor removal (Simpson Grade 1) was achieved in 13 patients and Simpson II in 8 patients. Perioperative mortality was 4.76%. The average size of the OGM was 4.3+/-1.1cm. The overall recurrence rate was 19%. We preferred to use the pterional approach, which provides quick access to the tumor with less brain exposure. It also allows complete drainage of cisternal cerebrospinal fluid, providing a good level of brain relaxation during surgery. However, for long, thin tumors, hemostasis can be difficult using this approach.

DETAILED VIEW OF THE CARPORT WITH TWO TONGUE AND GROOVE ...

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

DETAILED VIEW OF THE CARPORT WITH TWO TONGUE AND GROOVE DOORS TO THE STORAGE CLOSET. REPLACEMENT VINYL VENTED SOFFIT MATERIAL IS VISIBLE IN THIS SHOT - Camp H.M. Smith and Navy Public Works Center Manana Title VII (Capehart) Housing, U-Shaped Two-Bedroom Single-Family Type 6, Birch Circle, Elm Drive, Elm Circle, and Date Drive, Pearl City, Honolulu County, HI

Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site

PubMed Central

Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

2016-01-01

Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide. PMID:26908655

Development of an Equine Groove Model to Induce Metacarpophalangeal Osteoarthritis: A Pilot Study on 6 Horses

PubMed Central

Maninchedda, Ugo; Lepage, Olivier M.; Gangl, Monika; Hilairet, Sandrine; Remandet, Bernard; Meot, Francoise; Penarier, Geraldine; Segard, Emilie; Cortez, Pierre; Jorgensen, Christian; Steinberg, Régis

2015-01-01

The aim of this work was to develop an equine metacarpophalangeal joint model that induces osteoarthritis that is not primarily mediated by instability or inflammation. The study involved six Standardbred horses. Standardized cartilage surface damage or “grooves” were created arthroscopically on the distal dorsal aspect of the lateral and medial metacarpal condyles of a randomly chosen limb. The contralateral limb was sham operated. After 2 weeks of stall rest, horses were trotted 30 minutes every other day for 8 weeks, then evaluated for lameness and radiographed. Synovial fluid was analyzed for cytology and biomarkers. At 10 weeks post-surgery, horses were euthanized for macroscopic and histologic joint evaluation. Arthroscopic grooving allowed precise and identical damage to the cartilage of all animals. Under the controlled exercise regime, this osteoarthritis groove model displayed significant radiographic, macroscopic, and microscopic degenerative and reactive changes. Histology demonstrated consistent surgically induced grooves limited to non-calcified cartilage and accompanied by secondary adjacent cartilage lesions, chondrocyte necrosis, chondrocyte clusters, cartilage matrix softening, fissuring, mild subchondral bone inflammation, edema, and osteoblastic margination. Synovial fluid biochemistry and cytology demonstrated significantly elevated total protein without an increase in prostaglandin E2, neutrophils, or chondrocytes. This equine metacarpophalangeal groove model demonstrated that standardized non-calcified cartilage damage accompanied by exercise triggered altered osteochondral morphology and cartilage degeneration with minimal or inefficient repair and little inflammatory response. This model, if validated, would allow for assessment of disease processes and the effects of therapy. PMID:25680102

Determinig the Shape Coefficient A of Groove on the Pen for the Shaft

NASA Astrophysics Data System (ADS)

Křístek, Ivo; Havlík, Jiří; Mosler, Václav; Daniš, Igor

2017-12-01

This article focuses on creating a diagram for determining the shape coefficient α for a tongue groove on the shaft. Experimental determination of curve diagrams by comparing diagrams and monograms used using FEM calculations.

Presentation of computer code SPIRALI for incompressible, turbulent, plane and spiral grooved cylindrical and face seals

NASA Technical Reports Server (NTRS)

Walowit, Jed A.

1994-01-01

A viewgraph presentation is made showing the capabilities of the computer code SPIRALI. Overall capabilities of SPIRALI include: computes rotor dynamic coefficients, flow, and power loss for cylindrical and face seals; treats turbulent, laminar, Couette, and Poiseuille dominated flows; fluid inertia effects are included; rotor dynamic coefficients in three (face) or four (cylindrical) degrees of freedom; includes effects of spiral grooves; user definable transverse film geometry including circular steps and grooves; independent user definable friction factor models for rotor and stator; and user definable loss coefficients for sudden expansions and contractions.

Self-consistent simulation of radio frequency multipactor on micro-grooved dielectric surface

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

Cai, Libing; Wang, Jianguo, E-mail: wanguiuc@mail.xjtu.edu.cn; Northwest Institute of Nuclear Technology, Xi'an, Shaanxi 710024

2015-02-07

The multipactor plays a key role in the surface breakdown on the feed dielectric window irradiated by high power microwave. To study the suppression of multipactor, a 2D electrostatic PIC-MCC simulation code was developed. The space charge field, including surface deposited charge and multipactor electron charge field, is obtained by solving 2D Poisson's equation in time. Therefore, the simulation is self-consistent and does not require presetting a fixed space charge field. By using this code, the self-consistent simulation of the RF multipactor on the periodic micro-grooved dielectric surface is realized. The 2D space distributions of the multipactor electrons and spacemore » charge field are presented. From the simulation results, it can be found that only half slopes have multipactor discharge when the slope angle exceeds a certain value, and the groove presents a pronounced suppression effect on the multipactor.« less

Grooved nanowires from self-assembling hairpin molecules for solar cells.

PubMed

Tevis, Ian D; Tsai, Wei-Wen; Palmer, Liam C; Aytun, Taner; Stupp, Samuel I

2012-03-27

One of the challenges facing bulk heterojunction organic solar cells is obtaining organized films during the phase separation of intimately mixed donor and acceptor components. We report here on the use of hairpin-shaped sexithiophene molecules to generate by self-assembly grooved nanowires as the donor component in bulk heterojunction solar cells. Photovoltaic devices were fabricated via spin-casting to produce by solvent evaporation a percolating network of self-assembled nanowires and fullerene acceptors. Thermal annealing was found to increase power conversion efficiencies by promoting domain growth while still maintaining this percolating network of nanostructures. The benefits of self-assembly and grooved nanowires were examined by building devices from a soluble sexithiophene derivative that does not form one-dimensional structures. In these systems, excessive phase separation caused by thermal annealing leads to the formation of defects and lower device efficiencies. We propose that the unique hairpin shape of the self-assembling molecules allows the nanowires as they form to interact well with the fullerenes in receptor-ligand type configurations at the heterojunction of the two domains, thus enhancing device efficiencies by 23%. © 2012 American Chemical Society

Nail findings in patients with psoriatic arthritis: A cross-sectional study with special reference to transverse grooves.

PubMed

Zenke, Yukari; Ohara, Yuri; Kobayashi, Daiki; Arai, Satoru; Kishimoto, Mitsumasa; Okada, Masato; Eto, Hikaru

2017-11-01

Patients with psoriatic arthritis (PsA) commonly present with nail manifestations; however, little is known about these manifestations. This study investigated whether nail findings can be used to discriminate between PsA and psoriasis without arthritis. We performed a retrospective analysis of 118 patients with PsA and 974 patients with psoriasis without arthritis who visited St. Luke's International Hospital (Tokyo, Japan) between July 2003 and February 2015. Patients with PsA were classified according to the Classification of Psoriatic Arthritis criteria. Skin lesion severity was assessed by using the Psoriasis Area and Severity Index, and 9 types of nail findings were investigated. The incidence of nail involvement in patients with PsA was 67.6%. Female sex, presence of transverse grooves, onycholysis, and splinter hemorrhages were significantly related to PsA, with transverse grooves demonstrating the strongest association (odds ratio, 5.01; 95% confidence interval, 2.31-10.8; P < .01). Furthermore, the presence of transverse grooves was strongly related to both distal interphalangeal arthritis and enthesitis. The PsA population was relatively small. Nail findings enabled us to distinguish patients with PsA from those without arthritis. The presence of transverse grooves is significantly associated with PsA and may be associated with distal interphalangeal arthritis and enthesitis. Copyright © 2017 American Academy of Dermatology, Inc. Published by Elsevier Inc. All rights reserved.

Simultaneous minimization of leaf travel distance and tongue-and-groove effect for segmental intensity-modulated radiation therapy.

PubMed

Dai, Jianrong; Que, William

2004-12-07

This paper introduces a method to simultaneously minimize the leaf travel distance and the tongue-and-groove effect for IMRT leaf sequences to be delivered in segmental mode. The basic idea is to add a large enough number of openings through cutting or splitting existing openings for those leaf pairs with openings fewer than the number of segments so that all leaf pairs have the same number of openings. The cutting positions are optimally determined with a simulated annealing technique called adaptive simulated annealing. The optimization goal is set to minimize the weighted summation of the leaf travel distance and tongue-and-groove effect. Its performance was evaluated with 19 beams from three clinical cases; one brain, one head-and-neck and one prostate case. The results show that it can reduce the leaf travel distance and (or) tongue-and-groove effect; the reduction of the leaf travel distance reaches its maximum of about 50% when minimized alone; the reduction of the tongue-and-groove reaches its maximum of about 70% when minimized alone. The maximum reduction in the leaf travel distance translates to a 1 to 2 min reduction in treatment delivery time per fraction, depending on leaf speed. If the method is implemented clinically, it could result in significant savings in treatment delivery time, and also result in significant reduction in the wear-and-tear of MLC mechanics.

Study of a Tricarbide Grooved Ring Fuel Element for Nuclear Thermal Propulsion

NASA Technical Reports Server (NTRS)

Taylor, Brian; Emrich, Bill; Tucker, Dennis; Barnes, Marvin; Donders, Nicolas; Benensky, Kelsa

2018-01-01

Deep space exploration, especially that of Mars, is on the horizon as the next big challenge for space exploration. Nuclear propulsion, through which high thrust and efficiency can be achieved, is a promising option for decreasing the cost and logistics of such a mission. Work on nu- clear thermal engines goes back to the days of the NERVA program. Currently, nuclear thermal propulsion is under development again in various forms to provide a superior propulsion system for deep space exploration. The authors have been working to develop a concept nuclear thermal engine that uses a grooved ring fuel element as an alternative to the traditional hexagonal rod design. The authors are also studying the use of carbide fuels. The concept was developed in order to increase surface area and heat transfer to the propellant. The use of carbides would also raise the operating temperature of the reactor. It is hoped that this could lead to a higher thrust to weight nuclear thermal engine. This paper describes the modeling of neutronics, heat transfer, and fluid dynamics of this alternative nuclear fuel element geometry. Fabrication experiments of grooved rings from carbide refractory metals are also presented along with material characterization and interactions with a hot hydrogen environment. Results of experiments and associated analysis are desired densities with some success in material distribution and reaching a solid solution. Future work is needed to improve distribution of material, minimize oxidation during the milling process, and de ne a fabrication process that will serve for constructing grooved ring fuel rods for large system tests.

Ventifacts at the Pathfinder landing site

USGS Publications Warehouse

Bridges, N.T.; Greeley, R.; Haldemann, A.F.C.; Herkenhoff, K. E.; Kraft, M.; Parker, T.J.; Ward, A.W.

1999-01-01

About half of the rocks at the Mars Pathfinder Ares Vallis landing site appear to be ventifacts, rocks abraded by windborne particles. Comparable resolution images taken by the Imager for Mars Pathfinder (IMP) camera and the Viking landers show that ventifacts are more abundant at the Pathfinder site. The ventifacts occur in several forms, including rocks with faceted edges, finger-like projections, elongated pits, flutes, grooves, and possible rills. The trends of elongated pits, flutes, grooves, and rills cluster at ???280-330?? clockwise from north and generally dip 10-30?? away from their trend direction. These orientations are indicative of southeast to northwest winds and differ from the trend of wind tails at the landing site, the direction of local wind streaks, and predictions of the Global Circulation Model, all of which indicate northeast to southwest winds. The disparity between these data sets strongly suggests that local circulation patterns have changed since the abrasion of the ventifacted rocks. The greater number of ventifacts at the Pathfinder site compared to either of the Viking sites is most easily explained as being due to a larger supply of abrading particles, composed of either sand-sized grains or indurated dust aggregates, and higher surface roughness, which should increase the momentum of saltating grains. The Pathfinder ventifacts may have formed shortly after the deposition of outflow channel sediments nearly 2 Gry ago, when a large local supply of abrading particles should have been abundant and atmospheric conditions may have been more conducive to rock abrasion from saltating grains. Based on how ventifacts form on Earth, the several ventifact forms seen at the Pathfinder site and their presence on some rocks but not on others are probably due to local airflow conditions, original rock shape, exposure duration, rock movement, and to a lesser extent, rock lithology. The abundance of ventifacts at the Pathfinder site, together with

Surface diffusivity measurements on 8mol.% yttrium oxide-zirconia bicrystals via grain boundary grooving experiments

NASA Astrophysics Data System (ADS)

Nassirou, Maissarath

Thermal grooving at grain boundaries (GBs) is a capillary-driven evolution of surface topography in the region where the grain boundary emerges at a free surface. The study of these topographic changes can provide insight into surface energetics, and in our particular case, the measurement of surface diffusivity. We have measured the surface diffusion coefficient of 8mol% Y 2O3-ZrO2 by studying the formation of thermal grooves. We studied a total of five bicrystals, with well defined orientation relationships; random [110] -60°, random [001] -30°, Sigma13 [001]/{510}, Sigma13 [001]/{320}, Sigma5 [001]/{210}. Our calculations employed the Herring relation (1951), in which the variation in the chemical potential is related to changes in topography. The samples were annealed at 1300°C and 1400°C for various period of time. Atomic Force Microscopy was used to determine the exact geometry of the thermal grooves. A first approach consisted of estimating the diffusion coefficient by using Mullins' equation. yx=0= dsDs1/ 4gb2g s12G 5/4( WkTgs) 1/4t 1/4 Where y(x =0) is the groove depth at the GB triple junction, O is the atomic volume, gs is the surface tension, gb is the grain boundary surface energy, ds is the thickness of the diffusion layer, t is the annealing time, and Ds is the surface diffusion coefficient. In Mullins' derivation, the atomic structure of the surface was ignored and it was assumed that the surface energy is independent of crystallographic orientation. In the case of zirconia, the surface energy is anisotropic. We will describe in this work a new approach to measuring surface diffusivity which accounts for the surface energy anisotropy. The study of these bicrystals will emphasize the effect of grain boundary structure on the surface diffusion coefficient, and it is for that purpose that we selected bicrystals with different tilt axes and angles. The results obtained using the equation set we have developed will be compared to those obtained by

Olfactory groove meningiomas.

PubMed

Hentschel, Stephen J; DeMonte, Franco

2003-06-15

Olfactory groove meningiomas (OGMs) arise over the cribriform plate and may reach very large sizes prior to presentation. They can be differentiated from tuberculum sellae meningiomas because OGMs arise more anterior in the skull base and displace the optic nerve and chiasm inferiorly rather than superiorly. The authors searched the neurosurgery database at the M. D. Anderson Cancer Center for cases of OGM treated between 1993 and 2003. The records of these patients were then reviewed retrospectively for details regarding clinical presentation, imaging findings, surgical results and complications, and follow-up status. Thirteen patients, (12 women and one man, mean age 56 years) harbored OGMs (mean size 5.7 cm). All patients underwent bifrontal craniotomies and biorbital osteotomies. There were 11 complete resections (including the hyperostotic bone and dura of the cribriform plate and any extension into the ethmoid sinuses) and two subtotal resections with minimal residual tumor left in patients with recurrent lesions. No complication directly due to the surgery occurred in any patient. There were no recurrences in a mean follow-up period of 2 years (range 0-5 years). With current microsurgical techniques, the results of OGM resection are excellent, with a high rate of total resection and a low incidence of complications. All hyperostotic bone should be removed with the dura of the anterior skull base to minimize the risk of recurrence.

Unusually Strong Binding to the DNA Minor Groove by a Highly Twisted Benzimidazole-Diphenylether: Induced Fit and Bound Water†

PubMed Central

Tanious, Farial A.; Laine, William; Peixoto, Paul; Bailly, Christian; Goodwin, Kristie D.; Lewis, Mark A.; Long, Eric C.; Georgiadis, Millie M.; Tidwell, Richard R.; Wilson, W. David

2008-01-01

RT29 is a dicationic diamidine derivative that does not obey the classical “rules” for shape and functional group placement that are expected to result in strong binding and specific recognition of the DNA minor groove. The compound contains a benzimidazole-diphenyl ether core that is flanked by the amidine cations. The diphenyl ether is highly twisted and gives the entire compound too much curvature to fit well to the shape of the minor groove. DNaseI footprinting, fluorescence intercalator displacement studies and circular dichroism spectra, however, indicate that the compound is an AT specific minor groove binding agent. Even more surprisingly, quantitative biosensor-surface plasmon resonance and isothermal titration calorimetric results indicate that the compound binds with exceptional strength to certain AT sequences in DNA with a large negative enthalpy of binding. Crystallographic results for the DNA complex of RT29 compared to calculated results for the free compound show that the compound undergoes significant conformational changes to enhance its minor groove interactions. In addition, a water molecule is incorporated directly into the complex to complete the compound-DNA interface and it forms an essential link between the compound and base pair edges at the floor of the minor groove. The calculated ΔCp value for complex formation is substantially less than the experimentally observed value in support of water being an intrinsic part of the complex with a major contribution to the ΔCp value. Both the induced fit conformational changes of the compound and the bound water are essential for strong binding to DNA by RT29. PMID:17506529

Microjetting from grooved surfaces in metallic samples subjected to laser driven shocks

NASA Astrophysics Data System (ADS)

de Rességuier, T.; Lescoute, E.; Sollier, A.; Prudhomme, G.; Mercier, P.

2014-01-01

When a shock wave propagating in a solid sample reflects from a free surface, geometrical effects predominantly governed by the roughness and defects of that surface may lead to the ejection of tiny jets that may breakup into high velocity, approximately micrometer-size fragments. This process referred to as microjetting is a major safety issue for engineering applications such as pyrotechnics or armour design. Thus, it has been widely studied both experimentally, under explosive and impact loading, and theoretically. In this paper, microjetting is investigated in the specific loading conditions associated to laser shocks: very short duration of pressure application, very high strain rates, small spatial scales. Material ejection from triangular grooves in the free surface of various metallic samples is studied by combining transverse optical shadowgraphy and time-resolved velocity measurements. The influences of the main parameters (groove angle, shock pressure, nature of the metal) on jet formation and ejection velocity are quantified, and the results are compared to theoretical estimates.

Microjetting from grooved surfaces in metallic samples subjected to laser driven shocks

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

Rességuier, T. de, E-mail: resseguier@ensma.fr; Lescoute, E.; Sollier, A.

2014-01-28

When a shock wave propagating in a solid sample reflects from a free surface, geometrical effects predominantly governed by the roughness and defects of that surface may lead to the ejection of tiny jets that may breakup into high velocity, approximately micrometer-size fragments. This process referred to as microjetting is a major safety issue for engineering applications such as pyrotechnics or armour design. Thus, it has been widely studied both experimentally, under explosive and impact loading, and theoretically. In this paper, microjetting is investigated in the specific loading conditions associated to laser shocks: very short duration of pressure application, verymore » high strain rates, small spatial scales. Material ejection from triangular grooves in the free surface of various metallic samples is studied by combining transverse optical shadowgraphy and time-resolved velocity measurements. The influences of the main parameters (groove angle, shock pressure, nature of the metal) on jet formation and ejection velocity are quantified, and the results are compared to theoretical estimates.« less

TEM00 mode Nd:YAG solar laser by side-pumping a grooved rod

NASA Astrophysics Data System (ADS)

Vistas, Cláudia R.; Liang, Dawei; Almeida, Joana; Guillot, Emmanuel

2016-05-01

A simple TEM00 mode solar laser system with a grooved Nd:YAG rod pumped through a heliostat-parabolic mirror system is reported here. The radiation coupling capacity of a fused silica tube lens was combined with the multipass pumping ability of a 2 V-shaped cavity to provide efficient side-pumping along a 4.0 mm diameter grooved Nd:YAG single-crystal rod. TEM00 mode solar laser power of 3.4 W was measured by adopting an asymmetric large-mode laser resonant cavity. Record TEM00 mode solar laser collection efficiency of 3.4 W/m2and slope efficiency of 1.9% was achieved, which corresponds to 1.8 and 2.4 times more than the previous TEM00 mode Nd:YAG solar laser using the PROMES-CNRS heliostat-parabolic mirror system, respectively.

Holes and grooves: the contribution of microscopy and taphonomy to the problem of art origins.

PubMed

D'Errico, F; Villa, P

1997-07-01

Optical and scanning electron microscopy, comparative anatomy, data from modern and Pleistocene carnivore accumulations, and analysis of archeological materials show that some of the pieces interpreted by various scholars as engraved or perforated bones from European Lower and Middle Paleolithic sites (such as Pech de l'Azé II, Stránska Skála, Kulna, Bois Roche and Cueva Morin) are not early manifestations of non-utilitarian behavior. Putative engravings are in fact vascular grooves, while perforated pieces are partially-digested bones regurgitated by hyenas. The current debate on art origins has often been centered on the symbolic value and cognitive implications of these and similar pieces without a first-hand analysis of the objects to provide convincing demonstration of the human origins of the marks. Such demonstration is a necessary prerequisite to any discussion of their significance for the evolution of symbolic behavior.

XIAP inhibits caspase-3 and -7 using two binding sites: evolutionarily conserved mechanism of IAPs

PubMed Central

Scott, Fiona L; Denault, Jean-Bernard; Riedl, Stefan J; Shin, Hwain; Renatus, Martin; Salvesen, Guy S

2005-01-01

The X-linked inhibitor of apoptosis protein (XIAP) uses its second baculovirus IAP repeat domain (BIR2) to inhibit the apoptotic executioner caspase-3 and -7. Structural studies have demonstrated that it is not the BIR2 domain itself but a segment N-terminal to it that directly targets the activity of these caspases. These studies failed to demonstrate a role of the BIR2 domain in inhibition. We used site-directed mutagenesis of BIR2 and its linker to determine the mechanism of executioner caspase inhibition by XIAP. We show that the BIR2 domain contributes substantially to inhibition of executioner caspases. A surface groove on BIR2, which also binds to Smac/DIABLO, interacts with a neoepitope generated at the N-terminus of the caspase small subunit following activation. Therefore, BIR2 uses a two-site interaction mechanism to achieve high specificity and potency for inhibition. Moreover, for caspase-7, the precise location of the activating cleavage is critical for subsequent inhibition. Since apical caspases utilize this cleavage site differently, we predict that the origin of the death stimulus should dictate the efficiency of inhibition by XIAP. PMID:15650747

The structures of the SNM1A and SNM1B/Apollo nuclease domains reveal a potential basis for their distinct DNA processing activities

PubMed Central

Allerston, Charles K.; Lee, Sook Y.; Newman, Joseph A.; Schofield, Christopher J.; McHugh, Peter J.; Gileadi, Opher

2015-01-01

The human SNM1A and SNM1B/Apollo proteins are members of an extended family of eukaryotic nuclease containing a motif related to the prokaryotic metallo-β-lactamase (MBL) fold. SNM1A is a key exonuclease during replication-dependent and transcription-coupled interstrand crosslink repair, while SNM1B/Apollo is required for maintaining telomeric overhangs. Here, we report the crystal structures of SNM1A and SNM1B at 2.16 Å. While both proteins contain a typical MBL-β-CASP domain, a region of positive charge surrounds the active site of SNM1A, which is absent in SNM1B and explains the greater apparent processivity of SNM1A. The structures of both proteins also reveal a putative, wide DNA-binding groove. Extensive mutagenesis of this groove, coupled with detailed biochemical analysis, identified residues that did not impact on SNM1A catalytic activity, but drastically reduced its processivity. Moreover, we identified a key role for this groove for efficient digestion past DNA interstrand crosslinks, facilitating the key DNA repair reaction catalysed by SNM1A. Together, the architecture and dimensions of this groove, coupled to the surrounding region of high positive charge, explain the remarkable ability of SNM1A to accommodate and efficiently digest highly distorted DNA substrates, such as those containing DNA lesions. PMID:26582912

Activation of phenylalanine hydroxylase by phenylalanine does not require binding in the active site.

PubMed

Roberts, Kenneth M; Khan, Crystal A; Hinck, Cynthia S; Fitzpatrick, Paul F

2014-12-16

Phenylalanine hydroxylase (PheH), a liver enzyme that catalyzes the hydroxylation of excess phenylalanine in the diet to tyrosine, is activated by phenylalanine. The lack of activity at low levels of phenylalanine has been attributed to the N-terminus of the protein's regulatory domain acting as an inhibitory peptide by blocking substrate access to the active site. The location of the site at which phenylalanine binds to activate the enzyme is unknown, and both the active site in the catalytic domain and a separate site in the N-terminal regulatory domain have been proposed. Binding of catecholamines to the active-site iron was used to probe the accessibility of the active site. Removal of the regulatory domain increases the rate constants for association of several catecholamines with the wild-type enzyme by ∼2-fold. Binding of phenylalanine in the active site is effectively abolished by mutating the active-site residue Arg270 to lysine. The k(cat)/K(phe) value is down 10⁴ for the mutant enzyme, and the K(m) value for phenylalanine for the mutant enzyme is >0.5 M. Incubation of the R270K enzyme with phenylalanine also results in a 2-fold increase in the rate constants for catecholamine binding. The change in the tryptophan fluorescence emission spectrum seen in the wild-type enzyme upon activation by phenylalanine is also seen with the R270K mutant enzyme in the presence of phenylalanine. Both results establish that activation of PheH by phenylalanine does not require binding of the amino acid in the active site. This is consistent with a separate allosteric site, likely in the regulatory domain.

Activation of Phenylalanine Hydroxylase by Phenylalanine Does Not Require Binding in the Active Site

PubMed Central

2015-01-01

Phenylalanine hydroxylase (PheH), a liver enzyme that catalyzes the hydroxylation of excess phenylalanine in the diet to tyrosine, is activated by phenylalanine. The lack of activity at low levels of phenylalanine has been attributed to the N-terminus of the protein’s regulatory domain acting as an inhibitory peptide by blocking substrate access to the active site. The location of the site at which phenylalanine binds to activate the enzyme is unknown, and both the active site in the catalytic domain and a separate site in the N-terminal regulatory domain have been proposed. Binding of catecholamines to the active-site iron was used to probe the accessibility of the active site. Removal of the regulatory domain increases the rate constants for association of several catecholamines with the wild-type enzyme by ∼2-fold. Binding of phenylalanine in the active site is effectively abolished by mutating the active-site residue Arg270 to lysine. The kcat/Kphe value is down 104 for the mutant enzyme, and the Km value for phenylalanine for the mutant enzyme is >0.5 M. Incubation of the R270K enzyme with phenylalanine also results in a 2-fold increase in the rate constants for catecholamine binding. The change in the tryptophan fluorescence emission spectrum seen in the wild-type enzyme upon activation by phenylalanine is also seen with the R270K mutant enzyme in the presence of phenylalanine. Both results establish that activation of PheH by phenylalanine does not require binding of the amino acid in the active site. This is consistent with a separate allosteric site, likely in the regulatory domain. PMID:25453233

CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex.

PubMed

Bae, Brian; Chen, James; Davis, Elizabeth; Leon, Katherine; Darst, Seth A; Campbell, Elizabeth A

2015-09-08

A key point to regulate gene expression is at transcription initiation, and activators play a major role. CarD, an essential activator in Mycobacterium tuberculosis, is found in many bacteria, including Thermus species, but absent in Escherichia coli. To delineate the molecular mechanism of CarD, we determined crystal structures of Thermus transcription initiation complexes containing CarD. The structures show CarD interacts with the unique DNA topology presented by the upstream double-stranded/single-stranded DNA junction of the transcription bubble. We confirm that our structures correspond to functional activation complexes, and extend our understanding of the role of a conserved CarD Trp residue that serves as a minor groove wedge, preventing collapse of the transcription bubble to stabilize the transcription initiation complex. Unlike E. coli RNAP, many bacterial RNAPs form unstable promoter complexes, explaining the need for CarD.

Quantum spill-out in few-nanometer metal gaps: Effect on gap plasmons and reflectance from ultrasharp groove arrays

NASA Astrophysics Data System (ADS)

Skjølstrup, Enok J. H.; Søndergaard, Thomas; Pedersen, Thomas G.

2018-03-01

Plasmons in ultranarrow metal gaps are highly sensitive to the electron density profile at the metal surfaces. Using a quantum mechanical approach and assuming local response, we study the effects of electron spill-out on gap plasmons and reflectance from ultrasharp metal grooves. We demonstrate that the mode index of ultranarrow gap plasmons converges to the bulk refractive index in the limit of vanishing gap and, thereby, rectify the unphysical divergence found in classical models. Surprisingly, spill-out also significantly increases the plasmonic absorption for few-nanometer gaps and lowers the reflectance from arrays of ultrasharp metal grooves. These findings are explained in terms of enhanced gap plasmon absorption taking place inside the gap 1-2 Å from the walls and delocalization near the groove bottom. Reflectance calculations taking spill-out into account are shown to be in much better agreement with measurements compared with classical models.

Non-competitive inhibition by active site binders.

PubMed

Blat, Yuval

2010-06-01

Classical enzymology has been used for generations to understand the interactions of inhibitors with their enzyme targets. Enzymology tools enabled prediction of the biological impact of inhibitors as well as the development of novel, more potent, ones. Experiments designed to examine the competition between the tested inhibitor and the enzyme substrate(s) are the tool of choice to identify inhibitors that bind in the active site. Competition between an inhibitor and a substrate is considered a strong evidence for binding of the inhibitor in the active site, while the lack of competition suggests binding to an alternative site. Nevertheless, exceptions to this notion do exist. Active site-binding inhibitors can display non-competitive inhibition patterns. This unusual behavior has been observed with enzymes utilizing an exosite for substrate binding, isomechanism enzymes, enzymes with multiple substrates and/or products and two-step binding inhibitors. In many of these cases, the mechanisms underlying the lack of competition between the substrate and the inhibitor are well understood. Tools like alternative substrates, testing the enzyme reaction in the reverse direction and monitoring inhibition time dependence can be applied to enable distinction between 'badly behaving' active site binders and true exosite inhibitors.

Study of a Tricarbide Grooved Ring Fuel Element for Nuclear Thermal Propulsion

NASA Technical Reports Server (NTRS)

Taylor, Brian; Emrich, Bill; Tucker, Dennis; Barnes, Marvin; Donders, Nicolas; Benensky, Kelsa

2018-01-01

Deep space exploration, especially that of Mars, is on the horizon as the next big challenge for space exploration. Nuclear propulsion, through which high thrust and efficiency can be achieved, is a promising option for decreasing the cost and logistics of such a mission. Work on nuclear thermal engines goes back to the days of the NERVA program. Currently, nuclear thermal propulsion is under development again in various forms to provide a superior propulsion system for deep space exploration. The authors have been working to develop a concept nuclear thermal engine that uses a grooved ring fuel element as an alternative to the traditional hexagonal rod design. The authors are also studying the use of carbide fuels. The concept was developed in order to increase surface area and heat transfer to the propellant. The use of carbides would also raise the operating temperature of the reactor. It is hoped that this could lead to a higher thrust to weight nuclear thermal engine. This paper describes the modeling of neutronics, heat transfer, and fluid dynamics of this alternative nuclear fuel element geometry. Fabrication experiments of grooved rings from carbide refractory metals are also presented along with material characterization and interactions with a hot hydrogen environment. Results of experiments and associated analysis are discussed. The authors demonstrated success in reaching desired densities with some success in material distribution and reaching a solid solution. Future work is needed to improve distribution of material, minimize oxidation during the milling process, and define a fabrication process that will serve for constructing grooved ring fuel rods for large system tests.

Safety Oversight of Decommissioning Activities at DOE Nuclear Sites

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

Zull, Lawrence M.; Yeniscavich, William

2008-01-15

The Defense Nuclear Facilities Safety Board (Board) is an independent federal agency established by Congress in 1988 to provide nuclear safety oversight of activities at U.S. Department of Energy (DOE) defense nuclear facilities. The activities under the Board's jurisdiction include the design, construction, startup, operation, and decommissioning of defense nuclear facilities at DOE sites. This paper reviews the Board's safety oversight of decommissioning activities at DOE sites, identifies the safety problems observed, and discusses Board initiatives to improve the safety of decommissioning activities at DOE sites. The decommissioning of former defense nuclear facilities has reduced the risk of radioactive materialmore » contamination and exposure to the public and site workers. In general, efforts to perform decommissioning work at DOE defense nuclear sites have been successful, and contractors performing decommissioning work have a good safety record. Decommissioning activities have recently been completed at sites identified for closure, including the Rocky Flats Environmental Technology Site, the Fernald Closure Project, and the Miamisburg Closure Project (the Mound site). The Rocky Flats and Fernald sites, which produced plutonium parts and uranium materials for defense needs (respectively), have been turned into wildlife refuges. The Mound site, which performed R and D activities on nuclear materials, has been converted into an industrial and technology park called the Mound Advanced Technology Center. The DOE Office of Legacy Management is responsible for the long term stewardship of these former EM sites. The Board has reviewed many decommissioning activities, and noted that there are valuable lessons learned that can benefit both DOE and the contractor. As part of its ongoing safety oversight responsibilities, the Board and its staff will continue to review the safety of DOE and contractor decommissioning activities at DOE defense nuclear sites.« less

Standardized performance tests of collectors of solar thermal energy: Prototype moderately concentrating grooved collectors

NASA Technical Reports Server (NTRS)

1976-01-01

Prototypes of moderately concentrating grooved collectors were tested with a solar simulator for varying inlet temperature, flux level, and incident angle. Collector performance is correlated in terms of inlet temperature and flux level.

Effects of reset stators and a rotating, grooved stator hub on performance of a 1.92-pressure-ratio compressor stage

NASA Technical Reports Server (NTRS)

Lewis, G. W., Jr.; Urasek, D. C.; Reid, L.

1977-01-01

The overall performance and blade-element performance of a transonic fan stage are presented for two modified test configurations and are compared with the unmodified stage. Tests were conducted with reset stators 2 deg open and reset stators with a rotating grooved stator hub. Detailed radial and circumferential (behind stator) surveys of the flow conditions were made over the stable operating range at rotative speeds of 70, 90, and 100 percent of design speed. Reset stator blade tests indicated a small increase in stage efficiency, pressure ratio, and maximum weight flow at each speed. Performance with reset stators and a rotating, grooved stator hub resulted in an additional increase in stage efficiency and pressure ratio at all speeds. The rotating grooved stator hub reduced hub losses considerably.

Narrow groove plasmonic nano-gratings for surface plasmon resonance sensing

PubMed Central

Dhawan, Anuj; Canva, Michael; Vo-Dinh, Tuan

2011-01-01

We present a novel surface plasmon resonance (SPR) configuration based on narrow groove (sub-15 nm) plasmonic nano-gratings such that normally incident radiation can be coupled into surface plasmons without the use of prism-coupling based total internal reflection, as in the classical Kretschmann configuration. This eliminates the angular dependence requirements of SPR-based sensing and allows development of robust miniaturized SPR sensors. Simulations based on Rigorous Coupled Wave Analysis (RCWA) were carried out to numerically calculate the reflectance - from different gold and silver nano-grating structures - as a function of the localized refractive index of the media around the SPR nano-gratings as well as the incident radiation wavelength and angle of incidence. Our calculations indicate substantially higher differential reflectance signals, on localized change of refractive index in the narrow groove plasmonic gratings, as compared to those obtained from conventional SPR-based sensing systems. Furthermore, these calculations allow determination of the optimal nano-grating geometric parameters - i. e. nanoline periodicity, spacing between the nanolines, as well as the height of the nanolines in the nano-grating - for highest sensitivity to localized change of refractive index, as would occur due to binding of a biomolecule target to a functionalized nano-grating surface. PMID:21263620

Commissioning of the tongue-and-groove modelling in treatment planning systems: from static fields to VMAT treatments

NASA Astrophysics Data System (ADS)

Hernandez, Victor; Vera-Sánchez, Juan Antonio; Vieillevigne, Laure; Saez, Jordi

2017-08-01

Adequate modelling of the multi-leaf collimator (MLC) by treatment planning systems (TPS) is essential for accurate dose calculations in intensity-modulated radiation-therapy. For this reason modern TPSs incorporate MLC characteristics such as the leaf end curvature, MLC transmission and the tongue-and-groove. However, the modelling of the tongue-and-groove is often neglected during TPS commissioning and it is not known how accurate it is. This study evaluates the dosimetric consequences of the tongue-and-groove effect for two different MLC models using both film dosimetry and ionisation chambers. A set of comprehensive tests are presented that evaluate the ability of TPSs to accurately model this effect in (a) static fields, (b) sliding window beams and (c) VMAT arcs. The tests proposed are useful for the commissioning of TPSs and for the validation of major upgrades. With the ECLIPSE TPS, relevant differences were found between calculations and measurements for beams with dynamic MLCs in the presence of the TG effect, especially for the High Definition MLC, small gap sizes and the 1 mm calculation grid. For this combination, dose differences as high as 10% and 7% were obtained for dynamic MLC gaps of 5 mm and 10 mm, respectively. These differences indicate inadequate modelling of the tongue-and-groove effect, which might not be identified without the proposed tests. In particular, the TPS tended to underestimate the calculated dose, which may require tuning of other configuration parameters in the TPS (such as the dosimetric leaf gap) in order to maximise the agreement between calculations and measurements in clinical plans. In conclusion, a need for better modelling of the MLC by TPSs is demonstrated, one of the relevant aspects being the tongue-and-groove effect. This would improve the accuracy of TPS calculations, especially for plans using small MLC gaps, such as plans with small target volumes or high complexities. Improved modelling of the MLC would

Biomimetic "Cactus Spine" with Hierarchical Groove Structure for Efficient Fog Collection.

PubMed

Bai, Fan; Wu, Juntao; Gong, Guangming; Guo, Lin

2015-07-01

A biomimetic "cactus spine" with hierarchical groove structure is designed and fabricated using simple electrospinning. This novel artificial cactus spine possesses excellent fog collection and water transportation ability. A model cactus equipped with artificial spines also shows a great water storage capacity. The results can be helpful in the development of water collectors and may make a contribution to the world water crisis.

Unilateral endonasal transcribriform approach with septal transposition for olfactory groove meningioma: can olfaction be preserved?

PubMed

Youssef, A Samy; Sampath, Raghuram; Freeman, Jacob L; Mattingly, Jameson K; Ramakrishnan, Vijay R

2016-10-01

Loss of olfaction has been considered inevitable in endoscopic endonasal resection of olfactory groove meningiomas. Olfaction preservation may be feasible through an endonasal unilateral transcribriform approach, with the option for expansion using septal transposition and contralateral preservation of the olfactory apparatus. An expanded unilateral endonasal transcribriform approach with septal transposition was performed in five cadaver heads. The approach was applied in a surgical case of a 24 × 26-mm olfactory groove meningioma originating from the right cribriform plate with partially intact olfaction. The surgical approach offered adequate exposure to the anterior skull base bilaterally. The nasal/septal mucosa was preserved on the contralateral side. Gross total resection of the meningioma was achieved with the successful preservation of the contralateral olfactory apparatus and preoperative olfaction. Six months later, the left nasal cavity showed no disruption of the mucosal lining and the right side was at the appropriate stage of healing for a harvested nasoseptal flap. One year later, the preoperative olfactory function was intact and favorably viewed by the patient. Objective testing of olfaction showed microsomia. Olfaction preservation may be feasible in the endoscopic endonasal resection of a unilateral olfactory groove meningioma through a unilateral transcribriform approach with septal transposition and preservation of the contralateral olfactory apparatus.

Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot

NASA Technical Reports Server (NTRS)

Su, L.; Chen, L.; Egli, M.; Berger, J. M.; Rich, A.

1999-01-01

Many viruses regulate translation of polycistronic mRNA using a -1 ribosomal frameshift induced by an RNA pseudoknot. A pseudoknot has two stems that form a quasi-continuous helix and two connecting loops. A 1.6 A crystal structure of the beet western yellow virus (BWYV) pseudoknot reveals rotation and a bend at the junction of the two stems. A loop base is inserted in the major groove of one stem with quadruple-base interactions. The second loop forms a new minor-groove triplex motif with the other stem, involving 2'-OH and triple-base interactions, as well as sodium ion coordination. Overall, the number of hydrogen bonds stabilizing the tertiary interactions exceeds the number involved in Watson-Crick base pairs. This structure will aid mechanistic analyses of ribosomal frameshifting.

Effectiveness of noise barriers installed adjacent to transverse grooved concrete pavement : executive summary report.

DOT National Transportation Integrated Search

2009-10-16

In recent years the Ohio Department of Transportation (ODOT) has reconstructed a number of roadways where asphalt pavements were replaced with concrete pavements which were finished with a random transverse grooved surface texture (ODOT specification...

Ionizable Side Chains at Catalytic Active Sites of Enzymes

PubMed Central

Jimenez-Morales, David; Liang, Jie

2012-01-01

Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1072 Å3. The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes. PMID:22484856

Microbial mutagenic effects of the DNA minor groove binder pibenzimol (Hoechst 33258) and a series of mustard analogues.

PubMed

Ferguson, L R; Denny, W A

1995-06-01

A series of aniline mustards and half-mustards targeted to DNA by linkage (through a polymethylene chain) to the bisbenzimidazole chromophore of pibenzimol (Hoechst 33258) have been evaluated for their mutagenic properties, as estimated in three strains of Salmonella typhimurium, and for their mitotic crossing-over and petite mutagenesis activities in Saccharomyces cerevisiae strain D5. Agarose gel electrophoresis studies showed that only the derivative with the longest linker chain cross-linked DNA, with the remaining compounds being monoalkylators. The parent (non-alkylator) minor groove binding ligand (Hoechst 33258) was inactive in the bacterial strains TA98 or TA100 but weakly mutagenic in TA102, and caused neither mitotic crossing-over nor 'petite' mutagenesis in yeast. Aniline half-mustard itself (monoalkylator) was an effective base-pair substitution mutagen (events in S. typhimurium strain TA100) with some frameshift mutagenesis activity in TA98, but showed only weak effects in the yeast assays, whereas aniline mustard (cross-linker) was inactive in these bacterial systems but caused substantial amounts of mitotic crossing-over in yeast. The composite molecules studied here showed effects more characteristic of the minor groove binding chromophore than of alkylating moieties. All showed weak mutagenic activity in TA102 and none in TA98. The only compound to show significant mitotic crossing-over ability was the long-chain derivative which cross-linked DNA. For most of the compounds, the mutagenicity data provided no supportive evidence for DNA alkylation. Since other evidence suggests this does occur readily, it is likely to have a different target to that seen with untargeted aniline mustards. The significant antitumor activity and low mutagenic potential shown by these compounds make them worthy of further study.

NMR solution structure of an N2-guanine DNA adduct derived from the potent tumorigen dibenzo[a,l]pyrene: Intercalation from the minor groove with ruptured Watson-Crick base pairing

PubMed Central

Tang, Yijin; Liu, Zhi; Ding, Shuang; Lin, Chin H.; Cai, Yuqin; Rodriguez, Fabian A.; Sayer, Jane M.; Jerina, Donald M.; Amin, Shantu; Broyde, Suse; Geacintov, Nicholas E.

2012-01-01

The most potent tumorigen identified among the polycyclic aromatic hydrocarbons (PAH) is the non-planar fjord region dibenzo[a,l]pyrene (DB[a,l]P). It is metabolically activated in vivo through the widely-studied diol epoxide (DE) pathway to form covalent adducts with DNA bases, predominantly guanine and adenine. The (+)-11S,12R,13R,14S DE enantiomer forms adducts via its C14-position with the exocyclic amino group of guanine. Here, we present the first NMR solution structure of a DB[a,l]P-derived adduct, the 14R (+)-trans-anti-DB[a,l]P–N2-dG (DB[a,l]P-dG) lesion in double-stranded DNA. In contrast to the stereochemically identical benzo[a]pyrene-derived N2-dG adduct (B[a]P-dG) in which the B[a]P rings reside in the B-DNA minor groove on the 3’-side of the modifed deoxyguanosine, in the DB[a,l]P-derived adduct the DB[a,l]P rings intercalate into the duplex on the 3’-side of the modified base from the sterically crowded minor groove. Watson-Crick base pairing of the modified guanine with the partner cytosine is broken, but these bases retain some stacking with the bulky DB[a,l]P ring system. This new theme in PAH DE - DNA adduct conformation differs from: (1) the classical intercalation motif where Watson-Crick base-pairing is intact at the lesion site, and (2) the base-displaced intercalation motif in which the damaged base and its partner are extruded from the helix . The structural considerations that lead to the intercalated conformation of the DB[a,l]P-dG lesion in contrast to the minor groove alignment of the B[a]P-dG adduct, and the implications of the DB[a,l]P-dG conformational motif for the recognition of such DNA lesions by the human nucleotide excision repair apparatus, are discussed. PMID:23121427

Definition of a simple statistical parameter for the quantification of orientation in two dimensions: application to cells on grooves of nanometric depths.

PubMed

Davidson, P; Bigerelle, M; Bounichane, B; Giazzon, M; Anselme, K

2010-07-01

Contact guidance is generally evaluated by measuring the orientation angle of cells. However, statistical analyses are rarely performed on these parameters. Here we propose a statistical analysis based on a new parameter sigma, the orientation parameter, defined as the dispersion of the distribution of orientation angles. This parameter can be used to obtain a truncated Gaussian distribution that models the distribution of the data between -90 degrees and +90 degrees. We established a threshold value of the orientation parameter below which the data can be considered to be aligned within a 95% confidence interval. Applying our orientation parameter to cells on grooves and using a modelling approach, we established the relationship sigma=alpha(meas)+(52 degrees -alpha(meas))/(1+C(GDE)R) where the parameter C(GDE) represents the sensitivity of cells to groove depth, and R the groove depth. The values of C(GDE) obtained allowed us to compare the contact guidance of human osteoprogenitor (HOP) cells across experiments involving different groove depths, times in culture and inoculation densities. We demonstrate that HOP cells are able to identify and respond to the presence of grooves 30, 100, 200 and 500 nm deep and that the deeper the grooves, the higher the cell orientation. The evolution of the sensitivity (C(GDE)) with culture time is roughly sigmoidal with an asymptote, which is a function of inoculation density. The sigma parameter defined here is a universal parameter that can be applied to all orientation measurements and does not require a mathematical background or knowledge of directional statistics. Copyright 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Flight trajectory of a rotating golf ball with grooves

NASA Astrophysics Data System (ADS)

Baek, Moonheum; Kim, Jooha; Choi, Haecheon

2014-11-01

Dimples are known to reduce drag on a sphere by the amount of 50% as compared to a smooth surface. Despite the advantage of reducing drag, dimples deteriorate the putting accuracy owing to their sharp edges. To minimize this putting error but maintain the same flight distance, we have devised a grooved golf ball (called G ball hereafter) for several years. In this study, we modify the shape and pattern of grooves, and investigate the flow characteristics of the G ball by performing wind-tunnel experiments at the Reynolds numbers of 0 . 5 ×105 - 2 . 5 ×105 and the spin ratios (ratio of surface velocity to the free-stream velocity) of 0 - 0.6 that include the real golf-ball velocity and rotational speed. We measure the drag and lift forces on the rotating G ball and compare them with those of a smooth ball and two well-known dimpled balls. The lift-to-drag ratio of the G ball is much higher than that of a smooth ball and is in between those of the two dimpled balls. The trajectories of flying golf balls are computed. The flight distance of G ball is almost the same as that of one dimpled ball but slightly shorter than that of the other dimpled ball. The fluid-dynamic aspects of these differences will be discussed at the talk. Supported by 2011-0028032, 2014M3C1B1033980.

Discriminative structural approaches for enzyme active-site prediction.

PubMed

Kato, Tsuyoshi; Nagano, Nozomi

2011-02-15

Predicting enzyme active-sites in proteins is an important issue not only for protein sciences but also for a variety of practical applications such as drug design. Because enzyme reaction mechanisms are based on the local structures of enzyme active-sites, various template-based methods that compare local structures in proteins have been developed to date. In comparing such local sites, a simple measurement, RMSD, has been used so far. This paper introduces new machine learning algorithms that refine the similarity/deviation for comparison of local structures. The similarity/deviation is applied to two types of applications, single template analysis and multiple template analysis. In the single template analysis, a single template is used as a query to search proteins for active sites, whereas a protein structure is examined as a query to discover the possible active-sites using a set of templates in the multiple template analysis. This paper experimentally illustrates that the machine learning algorithms effectively improve the similarity/deviation measurements for both the analyses.

Analysis of behavior of focusing error signals generated by astigmatic method when a focused spot moves beyond the radius of a land-groove-type optical disk

NASA Astrophysics Data System (ADS)

Shinoda, Masahisa; Nakatani, Hidehiko; Nakai, Kenya; Ohmaki, Masayuki

2015-09-01

We theoretically calculate behaviors of focusing error signals generated by an astigmatic method in a land-groove-type optical disk. The focusing error signal from the land does not coincide with that from the groove. This behavior is enhanced when a focused spot of an optical pickup moves beyond the radius of the optical disk. A gain difference between the slope sensitivities of focusing error signals from the land and the groove is an important factor with respect to stable focusing servo control. In our calculation, the format of digital versatile disc-random access memory (DVD-RAM) is adopted as the land-groove-type optical disk model, and the dependences of the gain difference on various factors are investigated. The gain difference strongly depends on the optical intensity distribution of the laser beam in the optical pickup. The calculation method and results in this paper will be reflected in newly developed land-groove-type optical disks.

Ionizable side chains at catalytic active sites of enzymes.

PubMed

Jimenez-Morales, David; Liang, Jie; Eisenberg, Bob

2012-05-01

Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1,072 Å(3). The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes.

Nanoscale Plasmonic V-Groove Waveguides for the Interrogation of Single Fluorescent Bacterial Cells.

PubMed

Lotan, Oren; Bar-David, Jonathan; Smith, Cameron L C; Yagur-Kroll, Sharon; Belkin, Shimshon; Kristensen, Anders; Levy, Uriel

2017-09-13

We experimentally demonstrate the interrogation of an individual Escherichia coli cell using a nanoscale plasmonic V-groove waveguide. Several different configurations were studied. The first involved the excitation of the cell in a liquid environment because it flows on top of the waveguide nanocoupler, while the obtained fluorescence is coupled into the waveguide and collected at the other nanocoupler. The other two configurations involved the positioning of the bacterium within the nanoscale waveguide and its excitation in a dry environment either directly from the top or through waveguide modes. This is achieved by taking advantage of the waveguide properties not only for light guiding but also as a mechanical tool for trapping the bacteria within the V-grooves. The obtained results are supported by a set of numerical simulations, shedding more light on the mechanism of excitation. This demonstration paves the way for the construction of an efficient bioplasmonic chip for diverse cell-based sensing applications.

Enhancement of fluorescence quenching and exciplex formation in DNA major groove by double incorporation of modified fluorescent deoxyuridines.

PubMed

Tanaka, Makiko; Oguma, Kazuhiro; Saito, Yoshio; Saito, Isao

2012-06-15

5-(1-Naphthalenylethynyl)-2'-deoxyuridine ((N)U) and 5-[(4-cyano-1-naphthalenyl)ethynyl]-2'-deoxyuridine ((CN)U) were synthesized and incorporated into oligodeoxynucleotides. Fluorescence emissions of modified duplexes containing double (N)U were efficiently quenched depending upon the sequence pattern of the naphthalenes in DNA major groove, as compared to the duplex possessing single (N)U. When one of the naphthalene moieties has a cyano substituent, the exciplex emission from the chromophores in DNA major groove was observed at longer wavelength. Copyright © 2012 Elsevier Ltd. All rights reserved.

Generalized Stability Analysis of Capillary Flow in Slender V-Grooves

NASA Astrophysics Data System (ADS)

White, Nicholas; Troian, Sandra

2017-11-01

Spontaneous capillary flow, an especially rapid process in slender open microchannels resembling V-grooves, is of significant importance to many applications requiring passive robust flow control. Many types of biomedical devices for point-of-care use in developing countries are being designed around this principle. Important fundamental work by Romero and Yost (1996) and Weislogel (1996) elucidated the behavior of Newtonian films in slender V-grooves driven to flow by the streamwise change in capillary pressure due to the change in radius of curvature of the circular arc describing the interface of wetting or non-wetting fluids. Self-similar solutions describing Washburn type dynamics were found but other solutions are possible. Here we extend the Romero and Yost model to include a variety of inlet and outlet boundary conditions and examine the transient growth and generalized stability of perturbations to steady state and self-similar flows. Although most cases examined for wetting fluids exhibit robust stability against small perturbations, some exceptions reveal unstable flow. In total, these results support decades of experimental work which has found this method of flow control to be especially reliable, robust and self-healing. The authors gratefully acknowledge financial support from the 2016 NASA/Jet Propulsion Laboratory President's and Director's Fund as well as a 2017 NASA Space Technology Research Fellowship.

Design, fabrication and test of a hydrogen heat pipe. [extruding and grooving 6063-T6 aluminum tubes for cryogenic heat pipes

NASA Technical Reports Server (NTRS)

Alario, J.

1979-01-01

Re-entrant groove technology was extended to hydrogen heat pipes. Parametric analyses are presented which optimize the theoretical design while considering the limitations of state-of-the-art extrusion technology. The 6063-T6 aluminum extrusion is 14.6 mm OD with a wall thickness of 1.66 mm and contains 20 axial grooves which surround a central 9.3 mm diameter vapor core. Each axial groove is 0.775 mm diameter with a 0.33 mm opening. An excess vapor reservoir is provided at the evaporator to minimize the pressure containment hazard during ambient storage. Modifications to the basic re-entrant groove profile resulted in improved overall performance. While the maximum heat transport capacity decreased slightly to 103 w-m the static wicking height increased markedly to 4.5 cm. The heat pipe became operational between 20 and 30 K after a cooldown from 77 K without any difficulty. Steady state performance data taken over a 19 to 23 K temperature range indicated: (1) maximum heat transport capacity of 5.4 w-m; (2) static wicking height of 1.42 cm; and (3) overall heat pipe conductance of 1.7 watts/deg C.

Enhanced Broadband Electromagnetic Absorption in Silicon Film with Photonic Crystal Surface and Random Gold Grooves Reflector

PubMed Central

Chen, Zhi-Hui; Qiao, Na; Yang, Yibiao; Ye, Han; Liu, Shaoding; Wang, Wenjie; Wang, Yuncai

2015-01-01

We show a hybrid structure consisting of Si film with photonic crystal surface and random triangular gold grooves reflector at the bottom, which is capable of realizing efficient, broad-band, wide-angle optical absorption. It is numerically demonstrated that the enhanced absorption in a broad wavelength range (0.3–9.9 μm) due to the scattering effect of both sides of the structure and the created resonance modes. Larger thickness and period are favored to enhance the absorption in broader wavelength range. Substantial electric field concentrates in the grooves of surface photonic crystal and in the Si film. Our structure is versatile for solar cells, broadband photodetection and stealth coating. PMID:26238270

Time-resolved measurement of single pulse femtosecond laser-induced periodic surface structure formation induced by a pre-fabricated surface groove.

PubMed

Kafka, K R P; Austin, D R; Li, H; Yi, A Y; Cheng, J; Chowdhury, E A

2015-07-27

Time-resolved diffraction microscopy technique has been used to observe the formation of laser-induced periodic surface structures (LIPSS) from the interaction of a single femtosecond laser pulse (pump) with a nano-scale groove mechanically formed on a single-crystal Cu substrate. The interaction dynamics (0-1200 ps) was captured by diffracting a time-delayed, frequency-doubled pulse (probe) from nascent LIPSS formation induced by the pump with an infinity-conjugate microscopy setup. The LIPSS ripples are observed to form asynchronously, with the first one forming after 50 ps and others forming sequentially outward from the groove edge at larger time delays. A 1-D analytical model of electron heating including both the laser pulse and surface plasmon polariton excitation at the groove edge predicts ripple period, melt spot diameter, and qualitatively explains the asynchronous time-evolution of LIPSS formation.

Metal active site elasticity linked to activation of homocysteine in methionine synthases

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

Koutmos, Markos; Pejchal, Robert; Bomer, Theresa M.

2008-04-02

Enzymes possessing catalytic zinc centers perform a variety of fundamental processes in nature, including methyl transfer to thiols. Cobalamin-independent (MetE) and cobalamin-dependent (MetH) methionine synthases are two such enzyme families. Although they perform the same net reaction, transfer of a methyl group from methyltetrahydrofolate to homocysteine (Hcy) to form methionine, they display markedly different catalytic strategies, modular organization, and active site zinc centers. Here we report crystal structures of zinc-replete MetE and MetH, both in the presence and absence of Hcy. Structural investigation of the catalytic zinc sites of these two methyltransferases reveals an unexpected inversion of zinc geometry uponmore » binding of Hcy and displacement of an endogenous ligand in both enzymes. In both cases a significant movement of the zinc relative to the protein scaffold accompanies inversion. These structures provide new information on the activation of thiols by zinc-containing enzymes and have led us to propose a paradigm for the mechanism of action of the catalytic zinc sites in these and related methyltransferases. Specifically, zinc is mobile in the active sites of MetE and MetH, and its dynamic nature helps facilitate the active site conformational changes necessary for thiol activation and methyl transfer.« less

The structures of the SNM1A and SNM1B/Apollo nuclease domains reveal a potential basis for their distinct DNA processing activities.

PubMed

Allerston, Charles K; Lee, Sook Y; Newman, Joseph A; Schofield, Christopher J; McHugh, Peter J; Gileadi, Opher

2015-12-15

The human SNM1A and SNM1B/Apollo proteins are members of an extended family of eukaryotic nuclease containing a motif related to the prokaryotic metallo-β-lactamase (MBL) fold. SNM1A is a key exonuclease during replication-dependent and transcription-coupled interstrand crosslink repair, while SNM1B/Apollo is required for maintaining telomeric overhangs. Here, we report the crystal structures of SNM1A and SNM1B at 2.16 Å. While both proteins contain a typical MBL-β-CASP domain, a region of positive charge surrounds the active site of SNM1A, which is absent in SNM1B and explains the greater apparent processivity of SNM1A. The structures of both proteins also reveal a putative, wide DNA-binding groove. Extensive mutagenesis of this groove, coupled with detailed biochemical analysis, identified residues that did not impact on SNM1A catalytic activity, but drastically reduced its processivity. Moreover, we identified a key role for this groove for efficient digestion past DNA interstrand crosslinks, facilitating the key DNA repair reaction catalysed by SNM1A. Together, the architecture and dimensions of this groove, coupled to the surrounding region of high positive charge, explain the remarkable ability of SNM1A to accommodate and efficiently digest highly distorted DNA substrates, such as those containing DNA lesions. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Electrophoresis in ice surface grooves for probing protein affinity to a specific plane of ice crystal.

PubMed

Inagawa, Arinori; Okada, Yusuke; Okada, Tetsuo

2018-06-01

Channel-like grooves are formed on the surface of frozen aqueous sucrose. They are filled with a freeze concentrated solution (FCS) and act as an efficient size-tunable separation field for micro and nanoparticles. The width of the channel can be easily varied by changing the temperature. Because the channel width decreases with decreasing temperature, particles become immobilized due to physical interference from the ice wall when the temperature reaches a threshold point specific to the particle size. Surface modification of particles can add a factor of chemical interaction between the particles and ice walls. In this study, anti-freeze proteins (AFPs) are anchored on 1µm-polystyrene (PS) particles, and their behavior in the surface grooves on the ice is studied. The threshold temperature is an effective criterion for evaluating chemical interactions between particles and ice walls. The AFP binding on 1µm PS particles lowers the threshold temperature by 2.5°C, indicating interactions between AFPs on the PS particles and the ice wall. Because the AFPs studied here show selectivity towards the prism plane, it is critical that the prism plane of the ice crystal is in contact with the FCS in the surface grooves. Copyright © 2017 Elsevier B.V. All rights reserved.

NDE and DE of PWSCC Found in the J-Groove Weld of a Removed-From-Service Control Rod Drive Mechanism

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

Cumblidge, Stephen E.; Doctor, Steven R.; Schuster, George J.

2008-01-01

Studies conducted at the Pacific Northwest National Laboratory (PNNL) in Richland, Washington focused on assessing the effectiveness of nondestructive examination (NDE) techniques for inspecting control rod drive mechanism (CRDM) nozzles and J-groove weldments. The primary objective of this work is to provide information to the United States Nuclear Regulatory Commission (US NRC) on the effectiveness of NDE methods as related to the in-service inspection of CRDM nozzles and J-groove weldments, and to enhance the knowledge base of primary water stress corrosion cracking (PWSCC) through destructive characterization of the CRDM assemblies. Two CRDM assemblies were removed from service, decontaminated, and thenmore » used in a series of laboratory NDE and DE measurements; this report addresses the following questions: 1) What did each NDE technique detect?, 2) What did each NDE technique miss?, 3) How accurately did each NDE technique characterize the detected flaws?, and finally 4) What were the basis for the NDE techniques performance? Two CRDM assemblies including the CRDM nozzle, the J-groove weld, buttering, and a portion of the ferritic head material were selected for this study. This paper focuses on a CRDM assembly that contained suspected PWSCC, based on in-service inspection data and through-wall leakage. The laboratory NDE measurements used to examine the CRDM assembly followed standard industry techniques for conducting in-service inspections of CRDM nozzles and the crown of the J-groove welds and buttering. These techniques included eddy current testing, time of flight diffraction ultrasound, and penetrant testing. In addition, other laboratory-based NDE methods were employed to conduct inspections of the CRDM assembly with particular emphasis on inspecting the J-groove weld and buttering. These techniques included volumetric ultrasonic inspection of the J-groove weld metal, visual testing via replicant material of the J-groove weld and high resolution

Nicotinamide Cofactors Suppress Active-Site Labeling of Aldehyde Dehydrogenases.

PubMed

Stiti, Naim; Chandrasekar, Balakumaran; Strubl, Laura; Mohammed, Shabaz; Bartels, Dorothea; van der Hoorn, Renier A L

2016-06-17

Active site labeling by (re)activity-based probes is a powerful chemical proteomic tool to globally map active sites in native proteomes without using substrates. Active site labeling is usually taken as a readout for the active state of the enzyme because labeling reflects the availability and reactivity of active sites, which are hallmarks for enzyme activities. Here, we show that this relationship holds tightly, but we also reveal an important exception to this rule. Labeling of Arabidopsis ALDH3H1 with a chloroacetamide probe occurs at the catalytic Cys, and labeling is suppressed upon nitrosylation and oxidation, and upon treatment with other Cys modifiers. These experiments display a consistent and strong correlation between active site labeling and enzymatic activity. Surprisingly, however, labeling is suppressed by the cofactor NAD(+), and this property is shared with other members of the ALDH superfamily and also detected for unrelated GAPDH enzymes with an unrelated hydantoin-based probe in crude extracts of plant cell cultures. Suppression requires cofactor binding to its binding pocket. Labeling is also suppressed by ALDH modulators that bind at the substrate entrance tunnel, confirming that labeling occurs through the substrate-binding cavity. Our data indicate that cofactor binding adjusts the catalytic Cys into a conformation that reduces the reactivity toward chloroacetamide probes.

Interaction of Nevirapine with the Peptide Binding Groove of HLA-DRB1*01:01 and Its Effect on the Conformation of HLA-Peptide Complex.

PubMed

Hirasawa, Makoto; Hagihara, Katsunobu; Abe, Koji; Ando, Osamu; Hirayama, Noriaki

2018-06-04

Human leukocyte antigen (HLA)-DRB1*01:01 has been shown to be involved in nevirapine-induced hepatic hypersensitivity reactions. In the present study, in silico docking simulations and molecular dynamics simulations were performed to predict the interaction mode of nevirapine with the peptide binding groove of HLA-DRB1*01:01 and its possible effect on the position and orientation of the ligand peptide derived from hemagglutinin (HA). In silico analyses suggested that nevirapine interacts with HLA-DRB1*01:01 around the P4 pocket within the peptide binding groove and the HA peptide stably binds on top of nevirapine at the groove. The analyses also showed that binding of nevirapine at the groove will significantly change the inter-helical distances of the groove. An in vitro competitive assay showed that nevirapine (1000 μM) increases the binding of the HA peptide to HLA-DRB1*01:01 in an allele-specific manner. These results indicate that nevirapine might interact directly with the P4 pocket and modifies its structure, which could change the orientation of loaded peptides and the conformation of HLA-DRB1*01:01; these changes could be distinctively recognized by T-cell receptors. Through this molecular mechanism, nevirapine might stimulate the immune system, resulting in hepatic hypersensitivity reactions.

Nuclear magnetic resonance solution structure of an N(2)-guanine DNA adduct derived from the potent tumorigen dibenzo[a,l]pyrene: intercalation from the minor groove with ruptured Watson-Crick base pairing.

PubMed

Tang, Yijin; Liu, Zhi; Ding, Shuang; Lin, Chin H; Cai, Yuqin; Rodriguez, Fabian A; Sayer, Jane M; Jerina, Donald M; Amin, Shantu; Broyde, Suse; Geacintov, Nicholas E

2012-12-04

The most potent tumorigen identified among the polycyclic aromatic hydrocarbons (PAH) is the nonplanar fjord region dibenzo[a,l]pyrene (DB[a,l]P). It is metabolically activated in vivo through the widely studied diol epoxide (DE) pathway to form covalent adducts with DNA bases, predominantly guanine and adenine. The (+)-11S,12R,13R,14S DE enantiomer forms adducts via its C14 position with the exocyclic amino group of guanine. Here, we present the first nuclear magnetic resonance solution structure of a DB[a,l]P-derived adduct, the 14R-(+)-trans-anti-DB[a,l]P-N(2)-dG (DB[a,l]P-dG) lesion in double-stranded DNA. In contrast to the stereochemically identical benzo[a]pyrene-derived N(2)-dG adduct (B[a]P-dG) in which the B[a]P rings reside in the B-DNA minor groove on the 3'-side of the modifed deoxyguanosine, in the DB[a,l]P-derived adduct the DB[a,l]P rings intercalate into the duplex on the 3'-side of the modified base from the sterically crowded minor groove. Watson-Crick base pairing of the modified guanine with the partner cytosine is broken, but these bases retain some stacking with the bulky DB[a,l]P ring system. This new theme in PAH DE-DNA adduct conformation differs from (1) the classical intercalation motif in which Watson-Crick base pairing is intact at the lesion site and (2) the base-displaced intercalation motif in which the damaged base and its partner are extruded from the helix. The structural considerations that lead to the intercalated conformation of the DB[a,l]P-dG lesion in contrast to the minor groove alignment of the B[a]P-dG adduct, and the implications of the DB[a,l]P-dG conformational motif for the recognition of such DNA lesions by the human nucleotide excision repair apparatus, are discussed.

Quantum mechanical design of enzyme active sites.

PubMed

Zhang, Xiyun; DeChancie, Jason; Gunaydin, Hakan; Chowdry, Arnab B; Clemente, Fernando R; Smith, Adam J T; Handel, T M; Houk, K N

2008-02-01

The design of active sites has been carried out using quantum mechanical calculations to predict the rate-determining transition state of a desired reaction in presence of the optimal arrangement of catalytic functional groups (theozyme). Eleven versatile reaction targets were chosen, including hydrolysis, dehydration, isomerization, aldol, and Diels-Alder reactions. For each of the targets, the predicted mechanism and the rate-determining transition state (TS) of the uncatalyzed reaction in water is presented. For the rate-determining TS, a catalytic site was designed using naturalistic catalytic units followed by an estimation of the rate acceleration provided by a reoptimization of the catalytic site. Finally, the geometries of the sites were compared to the X-ray structures of related natural enzymes. Recent advances in computational algorithms and power, coupled with successes in computational protein design, have provided a powerful context for undertaking such an endeavor. We propose that theozymes are excellent candidates to serve as the active site models for design processes.

Evaluation of a Spiral Groove Geometry for Improvement of Hemolysis Level in a Hydrodynamically Levitated Centrifugal Blood Pump.

PubMed

Murashige, Tomotaka; Kosaka, Ryo; Sakota, Daisuke; Nishida, Masahiro; Kawaguchi, Yasuo; Yamane, Takashi; Maruyama, Osamu

2015-08-01

The purpose of this study is to evaluate a spiral groove geometry for a thrust bearing to improve the hemolysis level in a hydrodynamically levitated centrifugal blood pump. We compared three geometric models: (i) the groove width is the same as the ridge width at any given polar coordinate (conventional model); (ii) the groove width contracts inward from 9.7 to 0.5 mm (contraction model); and (iii) the groove width expands inward from 0.5 to 4.2 mm (expansion model). To evaluate the hemolysis level, an impeller levitation performance test and in vitro hemolysis test were conducted using a mock circulation loop. In these tests, the driving conditions were set at a pressure head of 200 mm Hg and a flow rate of 4.0 L/min. As a result of the impeller levitation performance test, the bottom bearing gaps of the contraction and conventional models were 88 and 25 μm, respectively. The impeller of the expansion model touched the bottom housing. In the hemolysis test, the relative normalized index of hemolysis (NIH) ratios of the contraction model in comparison with BPX-80 and HPM-15 were 0.6 and 0.9, respectively. In contrast, the relative NIH ratios of the conventional model in comparison with BPX-80 and HPM-15 were 9.6 and 13.7, respectively. We confirmed that the contraction model achieved a large bearing gap and improved the hemolysis level in a hydrodynamically levitated centrifugal blood pump. Copyright © 2015 International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

Computer-Aided Drug Discovery: Molecular Docking of Diminazene Ligands to DNA Minor Groove

ERIC Educational Resources Information Center

Kholod, Yana; Hoag, Erin; Muratore, Katlynn; Kosenkov, Dmytro

2018-01-01

The reported project-based laboratory unit introduces upper-division undergraduate students to the basics of computer-aided drug discovery as a part of a computational chemistry laboratory course. The students learn to perform model binding of organic molecules (ligands) to the DNA minor groove with computer-aided drug discovery (CADD) tools. The…

Processing of high-precision ceramic balls with a spiral V-groove plate

NASA Astrophysics Data System (ADS)

Feng, Ming; Wu, Yongbo; Yuan, Julong; Ping, Zhao

2017-03-01

As the demand for high-performance bearings gradually increases, ceramic balls with excellent properties, such as high accuracy, high reliability, and high chemical durability used, are extensively used for highperformance bearings. In this study, a spiral V-groove plate method is employed in processing high-precision ceramic balls. After the kinematic analysis of the ball-spin angle and enveloped lapping trajectories, an experimental rig is constructed and experiments are conducted to confirm the feasibility of this method. Kinematic analysis results indicate that the method not only allows for the control of the ball-spin angle but also uniformly distributes the enveloped lapping trajectories over the entire ball surface. Experimental results demonstrate that the novel spiral Vgroove plate method performs better than the conventional concentric V-groove plate method in terms of roundness, surface roughness, diameter difference, and diameter decrease rate. Ceramic balls with a G3-level accuracy are achieved, and their typical roundness, minimum surface roughness, and diameter difference are 0.05, 0.0045, and 0.105 μm, respectively. These findings confirm that the proposed method can be applied to high-accuracy and high-consistency ceramic ball processing.

Dynamic Behavior of Spiral-Groove and Rayleigh-Step Self-Acting Face Seals

NASA Technical Reports Server (NTRS)

Dirusso, Eliseo

1984-01-01

Tests were performed to determine the dynamic behavior and establish baseline dynamic data for five self-acting face seals employing Rayleigh-step lift-pads and inward pumping as well as outward-pumping spiral grooves for the lift-generating mechanism. The primary parameters measured in the tests were film thickness, seal seat axial motion, and seal frictional torque. The data show the dynamic response of the film thickness to the motion of the seal seat. The inward-pumping spiral-groove seals exhibited a high-amplitude film thickness vibratory mode with a frequency of four times the shaft speed. This mode was not observed in the other seals tested. The tests also revealed that high film thickness vibration amplitude produces considerably higher average film thickness than do low amplitude film thickness vibrations. The seals were tested at a constant face load of 73 N (16.4 lb) with ambient air at room temperature and atmospheric pressure as the fluid medium. The test speed range was from 7000 to 17000 rpm. Seal tangential speed range was 34.5 to 83.7 m/sec (113 to 274 ft/sec).

Analysis of mandibular second molars with fused roots and shallow radicular grooves by using micro-computed tomography.

PubMed

Amoroso-Silva, Pablo; De Moraes, Ivaldo Gomes; Marceliano-Alves, Marilia; Bramante, Clovis Monteiro; Zapata, Ronald Ordinola; Hungaro Duarte, Marco Antonio

2018-01-01

This study aimed to describe the morphological and morphometric aspects of fused mandibular second molars with radicular shallow grooves using micro-computed tomography (CT). Eighty-eight mandibular second molars with fused roots were scanned in a micro-CT scanner at a voxel size of 19.6 μm. After reconstruction, only molars without C-shaped roots and presenting shallow radicular grooves were selected. 30 molars were chosen for further analysis. Canal cross-sections were classified according to Fan's modified classification (C1, C2, C3, and C4) and morphometric parameters at the apical region, examination of accessory foramina and tridimensional configuration were evaluated. Three-dimensional reconstructions indicated a higher prevalence of merging type ( n = 22). According to Fan's modified classification, the C4 configuration was predominant in the 3 apical mm. Roundness median values revealed a more round-shaped canals at 3 mm (0.72) than at 2 (0.63) and 1 (0.61) mm from the apex. High values of major and minor diameters were observed in the canals of these evaluated sections. In addition, few accessory apical foramina were observed at 1 and 2 mm from the apex. The average distance between last accessory foramina and the anatomic apex was 1.17 mm. A less complex internal anatomy is found when a mandibular second molar presents fused roots with shallow radicular grooves. The merging type canal was frequently observed. Moreover, the C4 configuration was predominant at a point 3 mm from the apex and presented rounded canals, large apical diameters, and few accessory foramina. The cervical and middle thirds presented C3 and C1 canal configurations most frequently. A minor morphological complexity is found when fused mandibular second molars present shallow radicular grooves.

Characterisation of a grooved heat pipe with an anodised surface

NASA Astrophysics Data System (ADS)

Solomon, A. Brusly; Ram Kumar, A. M.; Ramachandran, K.; Pillai, B. C.; Senthil Kumar, C.; Sharifpur, Mohsen; Meyer, Josua P.

2017-03-01

A grooved heat pipe (GHP) is an important device for managing heat in space applications such as satellites and space stations, as it works efficiently in the absence of gravity. Apart from the above application, axial GHPs are used in many applications, such as electronic cooling units for temperature control and permafrost cooling. Improving the performance of GHPs is essential for better cooling and thermal management. In the present study, the effect of anodization on the heat transfer characteristics of a GHP is studied with R600a as a working fluid. In addition, the effects of fill ratio, inclination angle and heat inputs on the heat transfer performance of a GHP are studied. Furthermore, the effect of heat flux on dimensional numbers, such as the Webber, Bond, Kutateladze and condensation numbers, are studied. The inclination angle, heat input and fill ratio of GHPs are varied in the range of 0°-90°, 25-250 W and 10-70 % respectively. It is found that the above parameters have a significant effect on the performance of a GHP. Due to the anodisation, the maximum enhancement in heat transfer coefficient at the evaporator is 39 % for a 90° inclination at a heat flux of 11 kW/m2. The reported performance enhancement of a GHP may be due to the large numbers of nucleation sites created by the anodisation process and enhancement in the capillary force due to the coating.

Mechanical grooving effect on the gettering efficiency of crystalline silicon based solar cells

NASA Astrophysics Data System (ADS)

Zarroug, Ahmed; Hamed, Zied Ben; Derbali, Lotfi; Ezzaouia, Hatem

2017-04-01

This paper examines a gettering process of Czochralski silicon (CZ) via mechanical texture, followed by two step heat treatment in the presence of porous silicon layer (PSL) under oxygen flow gas. It is shown that a process with PS has a positive trend of improvement in the electronic quality, and found to be more efficient when used in combination with mechanical grooving. We obtained a significant increase of the effective minority carrier lifetime and majority charge carriers mobility. Thus, there is an apparent decrease in the resistivity. These parameters were estimated through a The Quasi-Steady-State Photo-Conductance technique (QSSPC), the van Der Pauw method and Hall Effect. Particularly, we have made obvious that the large enhancement of the electronic quality of the wafers can be related to the presence of grooves, the influence during which the gettering process is of importance to overcome the unexpected saturation phenomena. The current voltage I-V characteristics of all samples had been measured under illumination. They were shown to enhance the photovoltaic properties of solar cells.

Multipacting in a grooved choke joint at SRF gun for BNL ERL prototype

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

Xu, W.; Ben-Zvi, I.; Belomestnykh, S.

2011-03-28

The 703 MHz superconducting gun for BNL ERL prototype was tested at JLab with and without choke-joint and cathode stalk. Without choke-joint and cathode stalk, the gradient reached was 25 MV/m with Q{sup 0} {approx} 6E9. The gun cathode insertion port is equipped with a grooved choke joint for multipacting suppression. We carried out tests with choke-joint and cathode stalk. The test results show that there are at least two barriers at about 3.5 MV/m and 5 MV/m. We considered several possibilities and finally found that fine details of the grooved shape are important for multipacting suppression. A triangular groovemore » with round crest may cause strong multipacting in the choke-joint at 3.5 MV/m, 5 MV/m and 10 MV/m. This paper presents the primary test results of the gun and discusses the multipacting analysis in the choke-joint. It also suggests possible solutions for the gun and multipacting suppressing for a similar structure.« less

Replacement of seam welded hot reheat pipe using narrow groove GTA machine welding

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

Richardson, R.R.; Yanes, J.; Bryant, R.

1995-12-31

Southern California Edison, recognizing a potential safety concern, scrutinized its existing seam welded hot reheat pipe manufactured by the same supplier as that which failed. Alternatives were narrowed to two in dealing with the installed seam welded pipe. The overriding consideration, however, was one of safety. With this in mind, the utility company evaluated replacement of the seam welded hot reheat pipe with seamless pipe or increasing the frequency of its inspection program. Although increased inspection was much costly, pipe replacement was chosen due to potential safety concerns with seam welded pipe even with more frequent inspection. The utility companymore » then proceeded to determine the most effective method to complete this work. Analysis showed machine-made (automatic) gas tungsten arc welds (GTAW) as the method of choice due to cleanliness and superior mechanical properties. In conjunction with this method, the narrow groove (3{degree} bevel) weld joint as opposed to the traditional groove (37 1/2{degree} bevel) was shown to provide significant technical advantages.« less

Active and regulatory sites of cytosolic 5'-nucleotidase.

PubMed

Pesi, Rossana; Allegrini, Simone; Careddu, Maria Giovanna; Filoni, Daniela Nicole; Camici, Marcella; Tozzi, Maria Grazia

2010-12-01

Cytosolic 5'-nucleotidase (cN-II), which acts preferentially on 6-hydroxypurine nucleotides, is essential for the survival of several cell types. cN-II catalyses both the hydrolysis of nucleotides and transfer of their phosphate moiety to a nucleoside acceptor through formation of a covalent phospho-intermediate. Both activities are regulated by a number of phosphorylated compounds, such as diadenosine tetraphosphate (Ap₄A), ADP, ATP, 2,3-bisphosphoglycerate (BPG) and phosphate. On the basis of a partial crystal structure of cN-II, we mutated two residues located in the active site, Y55 and T56. We ascertained that the ability to catalyse the transfer of phosphate depends on the presence of a bulky residue in the active site very close to the aspartate residue that forms the covalent phospho-intermediate. The molecular model indicates two possible sites at which adenylic compounds may interact. We mutated three residues that mediate interaction in the first activation site (R144, N154, I152) and three in the second (F127, M436 and H428), and found that Ap₄A and ADP interact with the same site, but the sites for ATP and BPG remain uncertain. The structural model indicates that cN-II is a homotetrameric protein that results from interaction through a specific interface B of two identical dimers that have arisen from interaction of two identical subunits through interface A. Point mutations in the two interfaces and gel-filtration experiments indicated that the dimer is the smallest active oligomerization state. Finally, gel-filtration and light-scattering experiments demonstrated that the native enzyme exists as a tetramer, and no further oligomerization is required for enzyme activation. © 2010 The Authors Journal compilation © 2010 FEBS.

Water in the Active Site of Ketosteroid Isomerase

PubMed Central

Hanoian, Philip; Hammes-Schiffer, Sharon

2011-01-01

Classical molecular dynamics simulations were utilized to investigate the structural and dynamical properties of water in the active site of ketosteroid isomerase (KSI) to provide insight into the role of these water molecules in the enzyme-catalyzed reaction. This reaction is thought to proceed via a dienolate intermediate that is stabilized by hydrogen bonding with residues Tyr16 and Asp103. A comparative study was performed for the wild-type (WT) KSI and the Y16F, Y16S, and Y16F/Y32F/Y57F (FFF) mutants. These systems were studied with three different bound ligands: equilenin, which is an intermediate analog, and the intermediate states of two steroid substrates. Several distinct water occupation sites were identified in the active site of KSI for the WT and mutant systems. Three additional sites were identified in the Y16S mutant that were not occupied in WT KSI or the other mutants studied. The number of water molecules directly hydrogen bonded to the ligand oxygen was approximately two waters in the Y16S mutant, one water in the Y16F and FFF mutants, and intermittent hydrogen bonding of one water molecule in WT KSI. The molecular dynamics trajectories of the Y16F and FFF mutants reproduced the small conformational changes of residue 16 observed in the crystal structures of these two mutants. Quantum mechanical/molecular mechanical calculations of 1H NMR chemical shifts of the protons in the active site hydrogen-bonding network suggest that the presence of water in the active site does not prevent the formation of short hydrogen bonds with far-downfield chemical shifts. The molecular dynamics simulations indicate that the active site water molecules exchange much more frequently for WT KSI and the FFF mutant than for the Y16F and Y16S mutants. This difference is most likely due to the hydrogen-bonding interaction between Tyr57 and an active site water molecule that is persistent in the Y16F and Y16S mutants but absent in the FFF mutant and significantly less

Water in the active site of ketosteroid isomerase.

PubMed

Hanoian, Philip; Hammes-Schiffer, Sharon

2011-08-09

Classical molecular dynamics simulations were utilized to investigate the structural and dynamical properties of water in the active site of ketosteroid isomerase (KSI) to provide insight into the role of these water molecules in the enzyme-catalyzed reaction. This reaction is thought to proceed via a dienolate intermediate that is stabilized by hydrogen bonding with residues Tyr16 and Asp103. A comparative study was performed for the wild-type (WT) KSI and the Y16F, Y16S, and Y16F/Y32F/Y57F (FFF) mutants. These systems were studied with three different bound ligands: equilenin, which is an intermediate analog, and the intermediate states of two steroid substrates. Several distinct water occupation sites were identified in the active site of KSI for the WT and mutant systems. Three additional sites were identified in the Y16S mutant that were not occupied in WT KSI or the other mutants studied. The number of water molecules directly hydrogen bonded to the ligand oxygen was approximately two in the Y16S mutant and one in the Y16F and FFF mutants, with intermittent hydrogen bonding of one water molecule in WT KSI. The molecular dynamics trajectories of the Y16F and FFF mutants reproduced the small conformational changes of residue 16 observed in the crystal structures of these two mutants. Quantum mechanical/molecular mechanical calculations of (1)H NMR chemical shifts of the protons in the active site hydrogen-bonding network suggest that the presence of water in the active site does not prevent the formation of short hydrogen bonds with far-downfield chemical shifts. The molecular dynamics simulations indicate that the active site water molecules exchange much more frequently for WT KSI and the FFF mutant than for the Y16F and Y16S mutants. This difference is most likely due to the hydrogen-bonding interaction between Tyr57 and an active site water molecule that is persistent in the Y16F and Y16S mutants but absent in the FFF mutant and significantly less probable

Minor groove binding of a bis-quaternary ammonium compound: the crystal structure of SN 7167 bound to d(CGCGAATTCGCG)2.

PubMed Central

Squire, C J; Clark, G R; Denny, W A

1997-01-01

The X-ray crystal structure of the complex between the synthetic antitumour and antiviral DNA binding ligand SN 7167 and the DNA oligonucleotide d(CGCGAATTCGCG)2 has been determined to an R factor of 18.3% at 2.6 A resolution. The ligand is located within the minor groove and covers almost 6 bp with the 1-methylpyridinium ring extending as far as the C9-G16 base pair and the 1-methylquinolinium ring lying between the G4-C21 and A5-T20 base pairs. The ligand interacts only weakly with the DNA, as evidenced by long range contacts and shallow penetration into the groove. This structure is compared with that of the complex between the parent compound SN 6999 and the alkylated DNA sequence d(CGC[e6G]AATTCGCG)2. There are significant differences between the two structures in the extent of DNA bending, ligand conformation and groove binding. PMID:9321660

Active Site Characterization of Proteases Sequences from Different Species of Aspergillus.

PubMed

Morya, V K; Yadav, Virendra K; Yadav, Sangeeta; Yadav, Dinesh

2016-09-01

A total of 129 proteases sequences comprising 43 serine proteases, 36 aspartic proteases, 24 cysteine protease, 21 metalloproteases, and 05 neutral proteases from different Aspergillus species were analyzed for the catalytically active site residues using MEROPS database and various bioinformatics tools. Different proteases have predominance of variable active site residues. In case of 24 cysteine proteases of Aspergilli, the predominant active site residues observed were Gln193, Cys199, His364, Asn384 while for 43 serine proteases, the active site residues namely Asp164, His193, Asn284, Ser349 and Asp325, His357, Asn454, Ser519 were frequently observed. The analysis of 21 metalloproteases of Aspergilli revealed Glu298 and Glu388, Tyr476 as predominant active site residues. In general, Aspergilli species-specific active site residues were observed for different types of protease sequences analyzed. The phylogenetic analysis of these 129 proteases sequences revealed 14 different clans representing different types of proteases with diverse active site residues.

Half-of-the-sites reactivity of outer-membrane phospholipase A against an active-site-directed inhibitor.

PubMed

Ubarretxena-Belandia, I; Cox, R C; Dijkman, R; Egmond, M R; Verheij, H M; Dekker, N

1999-03-01

The reaction of a novel active-site-directed phospholipase A1 inhibitor with the outer-membrane phospholipase A (OMPLA) was investigated. The inhibitor 1-p-nitrophenyl-octylphosphonate-2-tridecylcarbamoyl-3-et hanesulfonyl -amino-3-deoxy-sn-glycerol irreversibly inactivated OMPLA. The inhibition reaction did not require the cofactor calcium or an unprotonated active-site His142. The inhibition of the enzyme solubilized in hexadecylphosphocholine micelles was characterized by a rapid (t1/2 = 20 min) and complete loss of enzymatic activity, concurrent with the covalent modification of 50% of the active-site serines, as judged from the amount of p-nitrophenolate (PNP) released. Modification of the remaining 50% occurred at a much lower rate, indicative of half-of-the-sites reactivity against the inhibitor of this dimeric enzyme. Inhibition of monomeric OMPLA solubilized in hexadecyl-N,N-dimethyl-1-ammonio-3-propanesulfonate resulted in an equimolar monophasic release of PNP, concurrent with the loss of enzymatic activity (t1/2 = 14 min). The half-of-the-sites reactivity is discussed in view of the dimeric nature of this enzyme.

Physical activity and cancer risk: dose-response and cancer, all sites and site-specific.

PubMed

Thune, I; Furberg, A S

2001-06-01

The association between physical activity and overall and site-specific cancer risk is elaborated in relation to whether any observed dose-response association between physical activity and cancer can be interpreted in terms of how much physical activity (type, intensity, duration, frequency) is needed to influence site- and gender-specific cancer risk. Observational studies were reviewed that have examined the independent effect of the volume of occupational physical activity (OPA) and/or leisure time physical activity (LPA) on overall and site-specific cancer risk. The evidence of cohort and case-control studies suggests that both leisure time and occupational physical activity protect against overall cancer risk, with a graded dose-response association suggested in both sexes. Confounding effects such as diet, body weight, and parity are often included as a covariate in the analyses, with little influence on the observed associations. A crude graded inverse dose-response association was observed between physical activity and colon cancer in 48 studies including 40,674 colon/colorectal cancer cases for both sexes. A dose-response effect of physical activity on colon cancer risk was especially observed, when participation in activities of at least moderate activity (>4.5 MET) and demonstrated by activities expressed as MET-hours per week. An observed inverse association with a dose-response relationship between physical activity and breast cancer was also identified in the majority of the 41 studies including 108,031 breast cancer cases. The dose-response relationship was in particular observed in case-control studies and supported by observations in cohort studies when participation in activities of at least moderate activity (>4.5 MET) and demonstrated by activities expressed by MET-hours per week. This association between physical activity and breast cancer risk is possibly dependent on age at exposure, age at diagnosis, menopausal status and other effect

Active Site Metal Occupancy and Cyclic Di-GMP Phosphodiesterase Activity of Thermotoga maritima HD-GYP.

PubMed

Miner, Kyle D; Kurtz, Donald M

2016-02-16

HD-GYPs make up a subclass of the metal-dependent HD phosphohydrolase superfamily and catalyze conversion of cyclic di(3',5')-guanosine monophosphate (c-di-GMP) to 5'-phosphoguanylyl-(3'→5')-guanosine (pGpG) and GMP. Until now, the only reported crystal structure of an HD-GYP that also exhibits c-di-GMP phosphodiesterase activity contains a His/carboxylate ligated triiron active site. However, other structural and phylogenetic correlations indicate that some HD-GYPs contain dimetal active sites. Here we provide evidence that an HD-GYP c-di-GMP phosphodiesterase, TM0186, from Thermotoga maritima can accommodate both di- and trimetal active sites. We show that an as-isolated iron-containing TM0186 has an oxo/carboxylato-bridged diferric site, and that the reduced (diferrous) form is necessary and sufficient to catalyze conversion of c-di-GMP to pGpG, but that conversion of pGpG to GMP requires more than two metals per active site. Similar c-di-GMP phosphodiesterase activities were obtained with divalent iron or manganese. On the basis of activity correlations with several putative metal ligand residue variants and molecular dynamics simulations, we propose that TM0186 can accommodate both di- and trimetal active sites. Our results also suggest that a Glu residue conserved in a subset of HD-GYPs is required for formation of the trimetal site and can also serve as a labile ligand to the dimetal site. Given the anaerobic growth requirement of T. maritima, we suggest that this HD-GYP can function in vivo with either divalent iron or manganese occupying di- and trimetal sites.

The method for measuring the groove density of variable-line-space gratings with elimination of the eccentricity effect

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

Wang, Qingbo; Liu, Zhengkun, E-mail: zhkliu@ustc.edu.cn; Chen, Huoyao

2015-02-15

To eliminate the eccentricity effect, a new method for measuring the groove density of a variable-line-space grating was adapted. Based on grating equation, groove density is calculated by measuring the internal angles between zeroth-order and first-order diffracted light for two different wavelengths with the same angle of incidence. The measurement system mainly includes two laser sources, a phase plate, plane mirror, and charge coupled device. The measurement results of a variable-line-space grating demonstrate that the experiment data agree well with theoretical values, and the value of measurement error (ΔN/N) is less than 2.72 × 10{sup −4}.

Diffusional correlations among multiple active sites in a single enzyme.

PubMed

Echeverria, Carlos; Kapral, Raymond

2014-04-07

Simulations of the enzymatic dynamics of a model enzyme containing multiple substrate binding sites indicate the existence of diffusional correlations in the chemical reactivity of the active sites. A coarse-grain, particle-based, mesoscopic description of the system, comprising the enzyme, the substrate, the product and solvent, is constructed to study these effects. The reactive and non-reactive dynamics is followed using a hybrid scheme that combines molecular dynamics for the enzyme, substrate and product molecules with multiparticle collision dynamics for the solvent. It is found that the reactivity of an individual active site in the multiple-active-site enzyme is reduced substantially, and this effect is analyzed and attributed to diffusive competition for the substrate among the different active sites in the enzyme.

Effect of Groove Design and Post-Weld Heat Treatment on Microstructure and Mechanical Properties of P91 Steel Weld

NASA Astrophysics Data System (ADS)

Pandey, C.; Mahapatra, M. M.

2016-07-01

The martensitic creep-resistant steel designated as ASTM A335 for plate and as P91 for pipe is primarily used for high-temperature and high-pressure applications in steam power plants due to its excellent high-temperature properties such as high creep strength, high thermal conductivity, low thermal expansion, and so on. However, in the case of welded joints of such steels, the presence of an inter-critical heat-affected zone (IC-HAZ) can cause the joint to have lower creep strength than the base metal. In the present study, the effect of post-welding heat treatment (PWHT) and weld groove designs on the overall microstructure and mechanical properties of P91 steel pipe welds produced by the gas tungsten arc welding process was studied. Various regions of welded joints were characterized in detail for hardness and metallographic and tensile properties. Sub-size tensile samples were also tested to evaluate the mechanical properties of the weld metal and heat-affected zone (HAZ) with respect to PWHT. After PWHT, a homogenous microstructure was observed in the HAZ and tensile test fracture samples revealed shifting of the fracture location from the IC-HAZ to the fine-grained heat-affected zone. Before PWHT, the conventional V-grooved welded joints exhibited higher tensile strength compared to the narrow-grooved joints. However, after PWHT, both narrow- and V-grooved joints exhibited similar strength. Fractography of the samples indicates the presence of carbide precipitates such as Cr23C6, VC, and NbC on the fracture surface.

Impact of pyrrolidine-bispyrrole DNA minor groove binding agents and chirality on global proteomic profile in Escherichia Coli.

PubMed

Yang, Ya-Ting; Lin, Chun-Yu; Jeng, Jingyueh; Ong, Chi-Wi

2013-05-23

There is great interest in the design of small molecules that selectively target minor grooves of duplex DNA for controlling specific gene expression implicated in a disease. The design of chiral small molecules for rational drug design has attracted increasing attention due to the chirality of DNA. Yet, there is limited research on the chirality effect of minor groove binders on DNA interaction, especially at the protein expression level. This paper is an attempt to illustrate that DNA binding affinity might not provide a full picture on the biological activities. Drug interacting at the genomic level can be translated to the proteomic level. Here we have illustrated that although the chiral bispyrrole-pyrrolidine-oligoamides, PySSPy and PyRSPy, showed low binding affinity to DNA, their influence at the proteomic level is significant. More importantly, the chirality also plays a role. Two-dimensional proteomic profile to identify the differentially expressed protein in Escherichia coli DH5α (E coli DH5α) were investigated. E coli DH5α incubated with the chiral PySSPy and PyRSPy, diastereomeric at the pyrrolidine ring, showed differential expression of eighteen proteins as observed through two dimensional proteomic profiling. These eighteen proteins identified by MALDI_TOF/TOF MS include antioxidant defense, DNA protection, protein synthesis, chaperone, and stress response proteins. No statistically significant toxicity was observed at the tested drug concentrations as measured via MTT assay. The current results showed that the chiral PySSPy and PyRSPy impact on the proteomic profiling of E coli DH5α, implicating the importance of drug chirality on biological activities at the molecular level.

Finding the Groove: A Grounded Theory Study on Leading Others to a Productive Path

ERIC Educational Resources Information Center

Williams, Roshann Reed

2011-01-01

Finding the groove was systematically discovered directly from data following the classical grounded theory methodology developed by Glaser and Strauss (1967) and further developed by Glaser (1965, 1978, 1992, 1998, 2001). This basic social process emerged from data as the pattern of behavior that leaders proceed through to increase performer…

Olfactory Groove Meningiomas: Comparison of Extent of Frontal Lobe Changes After Lateral and Bifrontal Approaches.

PubMed

Nanda, Anil; Maiti, Tanmoy K; Bir, Shyamal C; Konar, Subhas K; Guthikonda, Bharat

2016-10-01

Olfactory groove meningiomas often are behaviorally silent. Numerous surgical approaches have been described in the literature for the successful removal of these meningiomas. Lateral (pterional/frontolateral) and anterior (bifrontal/fronto-orbito-basal) approaches with their various modifications remain the 2 major corridors in resecting them. In this study, we discuss our experience in microsurgical treatment of these tumors at our institution and assess the extent of frontal lobe damage after the resection of tumor. We reviewed the medical records of patients who underwent surgical excision of olfactory groove meningiomas from 1990 to 2014. To measure the extent of frontal lobe damage via lateral and anterior approaches, we measured the volume of porencephalic cave in the postoperative magnetic resonance imaging by using Brainlab software. The ratio of volume of porencephalic cave to tumor was measured between 2 sides and 2 approaches. Fifty-seven patients with olfactory groove meningiomas, who underwent 62 microsurgical resection procedures in 1990-2014 were included in the study (74% were more than 5 cm at presentation). Pterional and bifrontal craniotomies were the most commonly used approaches. At follow-up, the volume of porencephalic cave after lateral approach was significantly less in the side contralateral to craniotomy irrespective of tumor size. The difference between ratio of volume of porencephalic cave and initial tumor was significantly less after lateral approaches, when compared to anterior approaches. Lateral approaches (pterional/frontolateral) resulted in less frontal lobe change and better olfactory preservation in comparison to anterior approaches in present series. Published by Elsevier Inc.

INJURIES OF THE SAGITTAL GROOVE OF THE PROXIMAL PHALANX IN WARMBLOOD HORSES DETECTED WITH LOW-FIELD MAGNETIC RESONANCE IMAGING: 19 CASES (2007-2016).

PubMed

Gold, Sarah J; Werpy, Natasha M; Gutierrez-Nibeyro, Santiago D

2017-05-01

Sagittal groove injuries of the proximal phalanx are an important cause of lameness in performance horses. The purpose of this retrospective case series study was to describe standing low-field magnetic resonance imaging (MRI) characteristics of these injuries in a group of Warmblood horses. Horses with an MRI diagnosis of sagittal groove injuries involving the proximal phalanx and that had follow-up MRI and clinical outcome information were included. Findings from clinical examinations, diagnostic tests, and other imaging modalities were recorded. All MRI studies were retrieved for re-evaluation by an experienced, board-certified veterinary radiologist. A total of 19 horses met inclusion criteria. All horses had MRI lesions consistent with unilateral or bilateral sagittal groove injuries of the proximal phalanx and abnormal mineralization of the sagittal ridge of the third metacarpal/metatarsal bone. Fifteen horses (79%) had concurrent osteoarthritis of the affected metacarpophalangeal/metatarsophalangeal joint. Eighteen horses received conservative therapy and all horses still had osseous abnormalities detected at the time of follow-up MRI. Thirteen horses (68.5%) were still lame at the time of follow-up, whereas the other six horses (31.5%) had become sound and returned to the previous level of exercise. Findings indicated that, for mature Warmblood horses, acute or chronic injuries of the sagittal groove of the proximal phalanx may have variable standing low-field MRI characteristics. Based on this sample of 19 horses, findings also indicated that the prognosis for performance soundness in horses diagnosed with sagittal groove injury of the proximal phalanx and concurrent osteoarthritis is poor. © 2017 American College of Veterinary Radiology.

Groove micro-structure optical fiber refractive index sensor with nanoscale gold film based on surface plasmon resonance

NASA Astrophysics Data System (ADS)

Zhang, Zhen; Li, Shuguang; Liu, Qiang; Feng, Xinxing; Zhang, Shuhuan; Wang, Yujun; Wu, Junjun

2018-07-01

A groove micro-structure optical fiber refractive index sensor with nanoscale gold film based on surface plasmon resonance (SPR) is proposed and analyzed by the finite element method (FEM). Numerical results show that the average sensitivity is 15,933 nm/refractive index unit (RIU) with the refractive index of analyte ranging from 1.40 to 1.43 and the maximum sensitivity is 28,600 nm/RIU and the resolution of the sensor is 3.50 × 10-8 RIU. The groove micro-structure optical fiber refractive index sensor do some changes on the D-shaped fiber sensor, compared with conventional D-shaped fiber sensor, it has a higher sensitivity and it is easier to produce than the traditional SPR sensor.

Direct instrumental identification of catalytically active surface sites

NASA Astrophysics Data System (ADS)

Pfisterer, Jonas H. K.; Liang, Yunchang; Schneider, Oliver; Bandarenka, Aliaksandr S.

2017-09-01

The activity of heterogeneous catalysts—which are involved in some 80 per cent of processes in the chemical and energy industries—is determined by the electronic structure of specific surface sites that offer optimal binding of reaction intermediates. Directly identifying and monitoring these sites during a reaction should therefore provide insight that might aid the targeted development of heterogeneous catalysts and electrocatalysts (those that participate in electrochemical reactions) for practical applications. The invention of the scanning tunnelling microscope (STM) and the electrochemical STM promised to deliver such imaging capabilities, and both have indeed contributed greatly to our atomistic understanding of heterogeneous catalysis. But although the STM has been used to probe and initiate surface reactions, and has even enabled local measurements of reactivity in some systems, it is not generally thought to be suited to the direct identification of catalytically active surface sites under reaction conditions. Here we demonstrate, however, that common STMs can readily map the catalytic activity of surfaces with high spatial resolution: we show that by monitoring relative changes in the tunnelling current noise, active sites can be distinguished in an almost quantitative fashion according to their ability to catalyse the hydrogen-evolution reaction or the oxygen-reduction reaction. These data allow us to evaluate directly the importance and relative contribution to overall catalyst activity of different defects and sites at the boundaries between two materials. With its ability to deliver such information and its ready applicability to different systems, we anticipate that our method will aid the rational design of heterogeneous catalysts.

The identity of the active site of oxalate decarboxylase and the importance of the stability of active-site lid conformations1

PubMed Central

Just, Victoria J.; Burrell, Matthew R.; Bowater, Laura; McRobbie, Iain; Stevenson, Clare E. M.; Lawson, David M.; Bornemann, Stephen

2007-01-01

Oxalate decarboxylase (EC 4.1.1.2) catalyses the conversion of oxalate into carbon dioxide and formate. It requires manganese and, uniquely, dioxygen for catalysis. It forms a homohexamer and each subunit contains two similar, but distinct, manganese sites termed sites 1 and 2. There is kinetic evidence that only site 1 is catalytically active and that site 2 is purely structural. However, the kinetics of enzymes with mutations in site 2 are often ambiguous and all mutant kinetics have been interpreted without structural information. Nine new site-directed mutants have been generated and four mutant crystal structures have now been solved. Most mutants targeted (i) the flexibility (T165P), (ii) favoured conformation (S161A, S164A, D297A or H299A) or (iii) presence (Δ162–163 or Δ162–164) of a lid associated with site 1. The kinetics of these mutants were consistent with only site 1 being catalytically active. This was particularly striking with D297A and H299A because they disrupted hydrogen bonds between the lid and a neighbouring subunit only when in the open conformation and were distant from site 2. These observations also provided the first evidence that the flexibility and stability of lid conformations are important in catalysis. The deletion of the lid to mimic the plant oxalate oxidase led to a loss of decarboxylase activity, but only a slight elevation in the oxalate oxidase side reaction, implying other changes are required to afford a reaction specificity switch. The four mutant crystal structures (R92A, E162A, Δ162–163 and S161A) strongly support the hypothesis that site 2 is purely structural. PMID:17680775

Role of active site rigidity in activity: MD simulation and fluorescence study on a lipase mutant.

PubMed

Kamal, Md Zahid; Mohammad, Tabrez Anwar Shamim; Krishnamoorthy, G; Rao, Nalam Madhusudhana

2012-01-01

Relationship between stability and activity of enzymes is maintained by underlying conformational flexibility. In thermophilic enzymes, a decrease in flexibility causes low enzyme activity while in less stable proteins such as mesophiles and psychrophiles, an increase in flexibility is associated with enhanced enzyme activity. Recently, we identified a mutant of a lipase whose stability and activity were enhanced simultaneously. In this work, we probed the conformational dynamics of the mutant and the wild type lipase, particularly flexibility of their active site using molecular dynamic simulations and time-resolved fluorescence techniques. In contrast to the earlier observations, our data show that active site of the mutant is more rigid than wild type enzyme. Further investigation suggests that this lipase needs minimal reorganization/flexibility of active site residues during its catalytic cycle. Molecular dynamic simulations suggest that catalytically competent active site geometry of the mutant is relatively more preserved than wild type lipase, which might have led to its higher enzyme activity. Our study implies that widely accepted positive correlation between conformation flexibility and enzyme activity need not be stringent and draws attention to the possibility that high enzyme activity can still be accomplished in a rigid active site and stable protein structures. This finding has a significant implication towards better understanding of involvement of dynamic motions in enzyme catalysis and enzyme engineering through mutations in active site.

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 8 2011-07-01 2011-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing waste...

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 9 2013-07-01 2013-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing waste...

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 9 2012-07-01 2012-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing waste...

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 8 2010-07-01 2010-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing waste...

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 9 2014-07-01 2014-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing waste...

Indicine N-oxide binds to tubulin at a distinct site and inhibits the assembly of microtubules: a mechanism for its cytotoxic activity.

PubMed

Appadurai, Prakash; Rathinasamy, Krishnan

2014-02-10

Indicine N-oxide, a pyrrolizidine alkaloid present in the plant Heliotropium indicum had shown promising cytotoxic activity in various tumor models. The compound exhibited severe toxicity to hepatocytes and bone marrow cells. The present work was aimed to evaluate the molecular mechanism of the toxicity of indicine N-oxide. We found that indicine N-oxide inhibited the proliferation of various cancer cell lines in a concentration dependent manner with IC50 ranging from 46 to 100 μM. At the half maximal inhibitory concentration it blocked the cell cycle progression at mitosis without significantly altering the organization of the spindle and interphase microtubules. The toxicities of the compound at higher concentrations are attributed to its severe depolymerizing effect on both the interphase and spindle microtubules. Binding studies using purified goat brain tubulin indicated that indicine N-oxide binds to tubulin at a distinct site not shared by colchicine or taxol. It decreased the polymer mass of both purified tubulin and MAP-rich tubulin. It was found to induce cleavage of DNA using pUC18 plasmid. The interactions of indicine N-oxide on DNA were also confirmed by computational analysis; which predicted its binding site at the minor groove of DNA. These studies bring to light that the toxicities of indicine N-oxide were due to its DNA damaging effects and depolymerization of microtubules. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Incremental Drag due to Grooves and Threads for KE (Kinetic Energy) Projectiles

DTIC Science & Technology

1989-03-01

RFI • CTsB TF * - MF (3a) q L where TF1 is the Thread Factor defined as: TF 0.84 + 0.117 P - o (3b) where p is the groove pitch in inches, MF1 is...g2) MF RF CD (4) where TF11 and TF1 2 are the thread factors for the threads of pitch p, and P2, respectively. 5 One can notice the large

Analysis and Design of a Double-Divert Spiral Groove Seal

NASA Technical Reports Server (NTRS)

Zheng, Xiaoqing; Berard, Gerald

2007-01-01

This viewgraph presentation describes the design and analysis of a double spiral groove seal. The contents include: 1) Double Spiral Design Features; 2) Double Spiral Operational Features; 3) Mating Ring/Rotor Assembly; 4) Seal Ring Assembly; 5) Insert Segment Joints; 6) Rotor Assembly Completed Prototype Parts; 7) Seal Assembly Completed Prototype Parts; 8) Finite Element Analysis; 9) Computational Fluid Dynamics (CFD) Analysis; 10) Restrictive Orifice Design; 11) Orifice CFD Model; 12) Orifice Results; 13) Restrictive Orifice; 14) Seal Face Coning; 15) Permanent Magnet Analysis; 16) Magnetic Repulsive Force; 17) Magnetic Repulsive Test Results; 18) Spin Testing; and 19) Testing and Validation.

A Bridging Water Anchors the Tethered 5-(3-Aminopropyl)-2′-deoxyuridine Amine in the DNA Major Groove Proximate to the N+2 C·G Base Pair: Implications for Formation of Interstrand 5′-GNC-3′ Cross-Links by Nitrogen Mustards‡

PubMed Central

Wang, Feng; Li, Feng; Ganguly, Manjori; Marky, Luis A.; Gold, Barry; Egli, Martin; Stone, Michael P.

2009-01-01

Site-specific insertion of 5-(3-aminopropyl)-2′-deoxyuridine (Z3dU) and 7-deaza-dG into the Dickerson-Drew dodecamers 5′-d(C1G2C3G4A5A6T7T8C9Z10C11G12)-3′ · 5′-d(C13G14C15G16A17A18T19T20-C21Z22C23G24)-3′ (named DDDZ10) and 5′-d(C1G2C3G4A5A6T7X8C9Z10C11G12)-3′ · 5′-d(C13G14C15G16A17A18-T19X20C21Z22C23G24)-3′ (named DDD2+Z10)(X = Z3dU; Z = 7-deaza-dG) suggests a mechanism underlying the formation of interstrand N+2 DNA cross-links by nitrogen mustards, e.g., melphalan and mechlorethamine. Analysis of the DDD2+Z10 duplex reveals that the tethered cations at base pairs A5 · X20 and X8 · A17 extend within the major groove in the 3′-direction, toward conserved Mg2+ binding sites located adjacent to N+2 base pairs C3 · Z22 and Z10 · C15. Bridging waters located between the tethered amines and either Z10 or Z22 O6 stabilize the tethered cations and allow interactions with the N + 2 base pairs without DNA bending. Incorporation of 7-deaza-dG into the DDD2+Z10 duplex weakens but does not eliminate electrostatic interactions between tethered amines and Z10 O6 and Z22 O6. The results suggest a mechanism by which tethered N7-dG aziridinium ions, the active species involved in formation of interstrand 5′-GNC-3′ cross-links by nitrogen mustards, modify the electrostatics of the major groove and position the aziridinium ions proximate to the major groove edge of the N+2 C · G base pair, facilitating interstrand cross-linking. PMID:18549246

Inosine Can Increase DNA's Susceptibility to Photo-oxidation by a RuII Complex due to Structural Change in the Minor Groove.

PubMed

Keane, Páraic M; Hall, James P; Poynton, Fergus E; Poulsen, Bjørn C; Gurung, Sarah P; Clark, Ian P; Sazanovich, Igor V; Towrie, Michael; Gunnlaugsson, Thorfinnur; Quinn, Susan J; Cardin, Christine J; Kelly, John M

2017-08-01

Key to the development of DNA-targeting phototherapeutic drugs is determining the interplay between the photoactivity of the drug and its binding preference for a target sequence. For the photo-oxidising lambda-[Ru(TAP) 2 (dppz)] 2+ (Λ-1) (dppz=dipyridophenazine) complex bound to either d{T 1 C 2 G 3 G 4 C 5 G 6 C 7 C 8 G 9 A 10 } 2 (G9) or d{TCGGCGCCIA} 2 (I9), the X-ray crystal structures show the dppz intercalated at the terminal T 1 C 2 ;G 9 A 10 step or T 1 C 2 ;I 9 A 10 step. Thus substitution of the G 9 nucleobase by inosine does not affect intercalation in the solid state although with I9 the dppz is more deeply inserted. In solution it is found that the extent of guanine photo-oxidation, and the rate of back electron-transfer, as determined by pico- and nanosecond time-resolved infrared and transient visible absorption spectroscopy, is enhanced in I9, despite it containing the less oxidisable inosine. This is attributed to the nature of the binding in the minor groove due to the absence of an NH 2 group. Similar behaviour and the same binding site in the crystal are found for d{TTGGCGCCAA} 2 (A9). In solution, we propose that intercalation occurs at the C 2 G 3 ;C 8 I 9 or T 2 G 3 ;C 8 A 9 steps, respectively, with G 3 the likely target for photo-oxidation. This demonstrates how changes in the minor groove (in this case removal of an NH 2 group) can facilitate binding of Ru II dppz complexes and hence influence any sensitised reactions occurring at these sites. No similar enhancement of photooxidation on binding to I9 is found for the delta enantiomer. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Strike-Slip Faulting Processes on Ganymede: Global Morphological Mapping and Structural Interpretation of Grooved and Transitional Terrains

NASA Astrophysics Data System (ADS)

Burkhard, L. M.; Cameron, M. E.; Smith-Konter, B. R.; Seifert, F.; Pappalardo, R. T.; Collins, G. C.

2015-12-01

Ganymede's fractured surface reveals many large-scale, morphologically distinct regions of inferred distributed shear and strike-slip faulting that may be important to the structural development of its surface and in the transition from dark to light (grooved) materials. To better understand the role of strike-slip tectonism in shaping Ganymede's complex icy surface, we perform a detailed mapping of key examples of strike-slip morphologies (i.e., en echelon structures, strike-slip duplexes, laterally offset pre-existing features, and possible strained craters) from Galileo and Voyager images. We focus on complex structures associated with grooved terrain (e.g. Nun Sulcus, Dardanus Sulcus, Tiamat Sulcus, and Arbela Sulcus) and terrains transitional from dark to light terrain (e.g. the boundary between Nippur Sulcus and Marius Regio, including Byblus Sulcus and Philus Sulcus). Detailed structural interpretations suggest strong evidence of strike-slip faulting in some regions (i.e., Nun and Dardanus Sulcus); however, further investigation of additional strike-slip structures is required of less convincing regions (i.e., Byblus Sulcus). Where applicable, these results are synthesized into a global database representing an inferred sense of shear for many of Ganymede's fractures. Moreover, when combined with existing observations of extensional features, these results help to narrow down the range of possible principal stress directions that could have acted at the regional or global scale to produce grooved terrain on Ganymede.

Direct inhibition of the DNA-binding activity of POU transcription factors Pit-1 and Brn-3 by selective binding of a phenyl-furan-benzimidazole dication.

PubMed

Peixoto, Paul; Liu, Yang; Depauw, Sabine; Hildebrand, Marie-Paule; Boykin, David W; Bailly, Christian; Wilson, W David; David-Cordonnier, Marie-Hélène

2008-06-01

The development of small molecules to control gene expression could be the spearhead of future-targeted therapeutic approaches in multiple pathologies. Among heterocyclic dications developed with this aim, a phenyl-furan-benzimidazole dication DB293 binds AT-rich sites as a monomer and 5'-ATGA sequence as a stacked dimer, both in the minor groove. Here, we used a protein/DNA array approach to evaluate the ability of DB293 to specifically inhibit transcription factors DNA-binding in a single-step, competitive mode. DB293 inhibits two POU-domain transcription factors Pit-1 and Brn-3 but not IRF-1, despite the presence of an ATGA and AT-rich sites within all three consensus sequences. EMSA, DNase I footprinting and surface-plasmon-resonance experiments determined the precise binding site, affinity and stoichiometry of DB293 interaction to the consensus targets. Binding of DB293 occurred as a cooperative dimer on the ATGA part of Brn-3 site but as two monomers on AT-rich sites of IRF-1 sequence. For Pit-1 site, ATGA or AT-rich mutated sequences identified the contribution of both sites for DB293 recognition. In conclusion, DB293 is a strong inhibitor of two POU-domain transcription factors through a cooperative binding to ATGA. These findings are the first to show that heterocyclic dications can inhibit major groove transcription factors and they open the door to the control of transcription factors activity by those compounds.

Dispersal in the communally breeding groove-billed ani (Crotophaga sulcirostris)

USGS Publications Warehouse

Bowen, B.S.; Koford, Rolf R.; Vehrencamp, S.L.

1989-01-01

We studied dispersal in a color-banded population of the Groove-billed Ani (Crotophaga sulcirostris) in Costa Rica. Eight percent of the young alive at the end of the breeding season bred on their natal territories the next year and 4% remained but did not breed. Thirteen percent dispersed successfully within the study area and bred in communal groups or simple pairs. The remaining 75% of the young birds disappeared from the study area. Young males remained in the study area as breeders more frequently than did young females. Breeding dispersal occurred, with at least 9% of the adult population moving to a new territory each year.We used a demographic model to estimate the following dispersal fates for young birds. For both males and females, 62% of the young alive at the end of the breeding season in which they hatched obtained a breeding position the next year. Of those that dispersed from their natal territories, 59 to 70% of the males and 64 to 74% of the females obtained breeding positions. Of those that bred the year after they hatched, 22% of the males and 2% of the females bred in their natal units, 34% of the males and 6% of the females bred within the study area but outside their natal units, and 44% of the males and 92% of the females bred outside the study area. We estimated that all of the males and 28% of the females that bred the year after they hatched were within three territories of their natal sites.

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2012 CFR

2012-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2011 CFR

2011-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2013 CFR

2013-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2010 CFR

2010-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2014 CFR

2014-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

Use of KW-2189, a DNA minor groove-binding agent, in patients with hepatocellular carcinoma: a north central cancer treatment group (NCCTG) phase II clinical trial.

PubMed

Alberts, Steven R; Suman, Vera J; Pitot, Henry C; Camoriano, John K; Rubin, Joseph

2007-01-01

Hepatocellular carcinoma (HCC) is a common cancer in certain portions of the world. Currently no effective therapies exist for patients with advanced or metastatic HCC. KW-2189, a DNA minor groove-binding agent, has shown promising activity against HCC in preclinical evaluations. A phase II study was conducted to evaluate the activity of KW-2189 in patients with histologic or cytologic confirmed advanced or metastatic HCC who had no prior systemic therapy. Patients received KW-2189 at a dose of 0.5 mg/m2 administered on day 1 of a 6-week cycle. The primary endpoint of the trial was objective regression. Other endpoints included toxicity, disease-free survival, and overall survival. Due to hematologic toxicity the dose of KW-2189 was reduced to 0.375 mg/m2 after 11 patients had been enrolled into the trial. Due to continued significant hematologic toxicity in the next five patients enrolled at the lower dose the trial was closed to accrual. Two responses were seen in patients enrolled at the higher dose, including one sustained CR. KW-2189 showed evidence of anti-tumor activity in HCC. However, because of significant and prolonged hematologic toxicity, when given as a single dose every 6 weeks, further development of this drug in HCC is not possible. Further exploration of DNA minor groove-binding agents in the treatment of HCC appears warranted.

Into the groove: instructive silk-polypyrrole films with topographical guidance cues direct DRG neurite outgrowth.

PubMed

Hardy, John G; Khaing, Zin Z; Xin, Shangjing; Tien, Lee W; Ghezzi, Chiara E; Mouser, David J; Sukhavasi, Rushi C; Preda, Rucsanda C; Gil, Eun S; Kaplan, David L; Schmidt, Christine E

2015-01-01

Instructive biomaterials capable of controlling the behaviour of the cells are particularly interesting scaffolds for tissue engineering and regenerative medicine. Novel biomaterials are particularly important in societies with rapidly aging populations, where demand for organ/tissue donations is greater than their supply. Herein we describe the preparation of electrically conductive silk film-based nerve tissue scaffolds that are manufactured using all aqueous processing. Aqueous solutions of Bombyx mori silk were cast on flexible polydimethylsiloxane substrates with micrometer-scale grooves on their surfaces, allowed to dry, and annealed to impart β-sheets to the silk which assures that the materials are stable for further processing in water. The silk films were rendered conductive by generating an interpenetrating network of polypyrrole and polystyrenesulfonate in the silk matrix. Films were incubated in an aqueous solution of pyrrole (monomer), polystyrenesulfonate (dopant) and iron chloride (initiator), after which they were thoroughly washed to remove low molecular weight components (monomers, initiators, and oligomers) and dried, yielding conductive films with sheet resistances of 124 ± 23 kΩ square(-1). The micrometer-scale grooves that are present on the surface of the films are analogous to the natural topography in the extracellular matrix of various tissues (bone, muscle, nerve, skin) to which cells respond. Dorsal root ganglions (DRG) adhere to the films and the grooves in the surface of the films instruct the aligned growth of processes extending from the DRG. Such materials potentially enable the electrical stimulation (ES) of cells cultured on them, and future in vitro studies will focus on understanding the interplay between electrical and topographical cues on the behaviour of cells cultured on them.

Do size, shape, and alignment parameters of the femoral condyle affect the trochlear groove tracking? A morphometric study based on 3D- computed tomography models in Chinese people.

PubMed

Du, Zhe; Chen, Shichang; Yan, Mengning; Yue, Bing; Zeng, Yiming; Wang, You

2017-01-06

Our study aimed to investigate whether geometrical features (size, shape, or alignment parameters) of the femoral condyle affect the morphology of the trochlear groove. Computed tomography models of 195 femurs (97 and 98 knees from male and female subjects, respectively) were reconstructed into three-dimensional models and categorised into four types of trochlear groove morphology based on the position of the turning point in relation to the mechanical axis (types 45°, 60°, 75°, and 90°). Only subjects with healthy knees were included, whereas individuals with previous knee trauma or knee pain, soft tissue injury, osteoarthritis, or other chronic diseases of the musculoskeletal system were excluded. The size parameters were: radius of the best-fit cylinder, anteroposterior dimension of the lateral condyles (AP), and distal mediolateral dimension (ML). The shape parameters were: aspect ratio (AP/ML), arc angle, and proximal- and distal- end angles. The alignment parameters were: knee valgus physiologic angle (KVPA), mechanical medial distal femoral angle (mMDFA), and hip-knee-ankle angle (HKA). All variables were measured in the femoral condyle models, and the means for each groove type were compared using one-way analysis of variance. No significant difference among groove types was observed regarding size parameters. There were significant differences when comparing type 45° with types 60°, 75°, and 90° regarding aspect ratio and distal-end angle (p < 0.05), but not regarding proximal-end angle. There were significant differences when comparing type 90° with types 45°, 60°, and 75° regarding KVPA, mMDFA, and HKA (p < 0.05). Among size, shape, and alignment parameters, the latter two exhibited partial influence on the morphology of the trochlear groove. Shape parameters affected the trochlear groove for trochlear type 45°, for which the femoral condyle was relatively flat, whereas alignment parameters affected the trochlear groove for trochlear

Friction characteristics of three 30 by 11.5-14.5, type 8, aircraft tires with various tread groove patterns and rubber compounds

NASA Technical Reports Server (NTRS)

Yager, T. J.; Mccarty, J. L.

1977-01-01

A test program was conducted to evaluate friction performance and wear characteristics on wet runways of three 30 x 11.5-14.5, type, aircraft tires having two different tread patterns and natural rubber contents. All test tires had the standard three circumferential groove tread, but two had molded transverse grooves which extended from shoulder to shoulder. The tread rubber content of the two tires with transverse grooves differed in that one had a 100 percent natural rubber tread and the other had a rubber tread composition that was 30 percent synthetic and 70 percent natural. The third test tire had the conventional 100 percent natural rubber tread. Results indicate that the differences in tire tread design and rubber composition do not significantly affect braking and cornering friction capability on wet or dry surfaces. Braking performance of the tires decreases with increased speed, with increased yaw angle and, at higher speeds, with increased wetness of the surface.

High density, optically corrected, micro-channel cooled, v-groove monolithic laser diode array

DOEpatents

Freitas, Barry L.

1998-01-01

An optically corrected, micro-channel cooled, high density laser diode array achieves stacking pitches to 33 bars/cm by mounting laser diodes into V-shaped grooves. This design will deliver>4kW/cm2 of directional pulsed laser power. This optically corrected, micro-channel cooled, high density laser is usable in all solid state laser systems which require efficient, directional, narrow bandwidth, high optical power density pump sources.

The carboxy-terminal αN helix of the archaeal XerA tyrosine recombinase is a molecular switch to control site-specific recombination.

PubMed

Serre, Marie-Claude; El Arnaout, Toufic; Brooks, Mark A; Durand, Dominique; Lisboa, Johnny; Lazar, Noureddine; Raynal, Bertrand; van Tilbeurgh, Herman; Quevillon-Cheruel, Sophie

2013-01-01

Tyrosine recombinases are conserved in the three kingdoms of life. Here we present the first crystal structure of a full-length archaeal tyrosine recombinase, XerA from Pyrococcus abyssi, at 3.0 Å resolution. In the absence of DNA substrate XerA crystallizes as a dimer where each monomer displays a tertiary structure similar to that of DNA-bound Tyr-recombinases. Active sites are assembled in the absence of dif except for the catalytic Tyr, which is extruded and located equidistant from each active site within the dimer. Using XerA active site mutants we demonstrate that XerA follows the classical cis-cleavage reaction, suggesting rearrangements of the C-terminal domain upon DNA binding. Surprisingly, XerA C-terminal αN helices dock in cis in a groove that, in bacterial tyrosine recombinases, accommodates in trans αN helices of neighbour monomers in the Holliday junction intermediates. Deletion of the XerA C-terminal αN helix does not impair cleavage of suicide substrates but prevents recombination catalysis. We propose that the enzymatic cycle of XerA involves the switch of the αN helix from cis to trans packing, leading to (i) repositioning of the catalytic Tyr in the active site in cis and (ii) dimer stabilisation via αN contacts in trans between monomers.

The Principal Genetic Determinants for Nasopharyngeal Carcinoma in China Involve the HLA Class I Antigen Recognition Groove

PubMed Central

Tang, Minzhong; Lautenberger, James A.; Gao, Xiaojiang; Sezgin, Efe; Hendrickson, Sher L.; Troyer, Jennifer L.; David, Victor A.; Guan, Li; Mcintosh, Carl E.; Guo, Xiuchan; Zheng, Yuming; Liao, Jian; Deng, Hong; Malasky, Michael; Kessing, Bailey; Winkler, Cheryl A.; Carrington, Mary; dé The, Guy; Zeng, Yi; O'Brien, Stephen J.

2012-01-01

Nasopharyngeal carcinoma (NPC) is an epithelial malignancy facilitated by Epstein-Barr Virus infection. Here we resolve the major genetic influences for NPC incidence using a genome-wide association study (GWAS), independent cohort replication, and high-resolution molecular HLA class I gene typing including 4,055 study participants from the Guangxi Zhuang Autonomous Region and Guangdong province of southern China. We detect and replicate strong association signals involving SNPs, HLA alleles, and amino acid (aa) variants across the major histocompatibility complex-HLA-A, HLA –B, and HLA -C class I genes (PHLA-A-aa-site-62 = 7.4×10−29; P HLA-B-aa-site-116 = 6.5×10−19; P HLA-C-aa-site-156 = 6.8×10−8 respectively). Over 250 NPC-HLA associated variants within HLA were analyzed in concert to resolve separate and largely independent HLA-A, -B, and -C gene influences. Multivariate logistical regression analysis collapsed significant associations in adjacent genes spanning 500 kb (OR2H1, GABBR1, HLA-F, and HCG9) as proxies for peptide binding motifs carried by HLA- A*11:01. A similar analysis resolved an independent association signal driven by HLA-B*13:01, B*38:02, and B*55:02 alleles together. NPC resistance alleles carrying the strongly associated amino acid variants implicate specific class I peptide recognition motifs in HLA-A and -B peptide binding groove as conferring strong genetic influence on the development of NPC in China. PMID:23209447

Computer simulation of the active site of human serum cholinesterase

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

Kefang Jiao; Song Li; Zhengzheng Lu

1996-12-31

The first 3D-structure of acetylchelinesterase from Torpedo California electric organ (T.AChE) was published by JL. Sussman in 1991. We have simulated 3D-structure of human serum cholinesterase (H.BuChE) and the active site of H.BuChE. It is discovered by experiment that the residue of H.BuChE is still active site after a part of H.BuChE is cut. For example, the part of 21KD + 20KD is active site of H.BuChE. The 20KD as it is. Studies on these peptides by Hemelogy indicate that two active peptides have same negative electrostatic potential maps diagram. These negative electrostatic areas attached by acetyl choline with positivemore » electrostatic potency. We predict that 147...236 peptide of AChE could be active site because it was as 20KD as with negative electrostatic potential maps. We look forward to proving from other ones.« less

The Tongue-in-Groove Technique in Primary and Revision Rhinoplasty.

PubMed

Datema, Frank R; Lohuis, Peter J F M

2016-08-01

The tongue-in-groove (TIG) is a conservative but powerful surgical suture technique to control tip rotation and projection, to set an appropriate alar-columellar relationship, to straighten a caudal septal deviation, and to stabilize the nasal base. TIG is suitable in primary and most revision cases and is easily combined with other surgical techniques. Seventeen years after its popularization, the TIG technique is embedded in modern-day rhinoplasty literature and teaching material. This article describes indications and considerations during external primary and revision rhinoplasty, based on clinical experience and the available literature. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

De novo active sites for resurrected Precambrian enzymes

NASA Astrophysics Data System (ADS)

Risso, Valeria A.; Martinez-Rodriguez, Sergio; Candel, Adela M.; Krüger, Dennis M.; Pantoja-Uceda, David; Ortega-Muñoz, Mariano; Santoyo-Gonzalez, Francisco; Gaucher, Eric A.; Kamerlin, Shina C. L.; Bruix, Marta; Gavira, Jose A.; Sanchez-Ruiz, Jose M.

2017-07-01

Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefore either plausibly exist or at least have existed at the primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds for protein engineering and demonstrate that a new active site can be generated through a single hydrophobic-to-ionizable amino acid replacement that generates a partially buried group with perturbed physico-chemical properties. We provide experimental and computational evidence that conformational flexibility can assist the emergence and subsequent evolution of new active sites by improving substrate and transition-state binding, through the sampling of many potentially productive conformations. Our results suggest a mechanism for the emergence of primordial enzymes and highlight the potential of ancestral reconstruction as a tool for protein engineering.

Artificial neural network modeling of a deflector in a grooved channel as well as optimization of its effective parameters

NASA Astrophysics Data System (ADS)

Abdollahi, Azita; Shams, Mehrzad; Abdollahi, Anita

2018-01-01

One of methods available to increase the rate of heat transfer in channels with parallel plates is making grooves in them. But, the fundamental problem of this method is the formation of stagnation zone in the grooves and as a result formation a zone with low energy transfer. In this paper, the effect of placing curved deflectors (geometries with elliptical forms) in channel on thermal and hydraulic characteristic of the fluid flow- with the aim of directing of the flow into the grooves and as a result increasing the rate of heat transfer in this zone- are investigated and heat transfer coefficient and pressure drop are calculated for different values of Reynolds number and geometrical parameters of the deflector (its small and large radiuses). The results show that the presence of the deflector in the channel significantly increases the heat transfer rate compare to the channel without deflector. Of course, it should be noted that this work also increases the pressure drop. So, finally in order to determine configurations of the deflector causing minimum pressure drop, maximum Nusselt number or a balance between them, optimization algorithm consisting of artificial neural network and multi-objective genetic algorithm was utilized to calculate the optimal values of these parameters.

Undercut Rocks at the MER Gusev Landing Site

NASA Technical Reports Server (NTRS)

Landis, Geoffrey A.

2004-01-01

On January 3 2004, the NASA Spirit rover landed on the plains inside the Gusev Crater in the southern hemisphere of Mars, and has made observations of the landing site and nearby region in visual and infrared wavelengths, as well as making in-situ measurements of rocks and soil. A number of rocks at the Gusev site are perched, with a significant undercut above the surface; additional rocks show a feature of being eroded or etched at a height of one to three centimeters immediately above the soil line. Some rocks also show terracing, and others show a two-tone pattern of albedo, with a distinct dividing line between a lighter area near the surface and a darker color above the surface. In a small number of cases, the dividing line is correlated with a visible horizontal groove in the rock, most likely indicating an earlier location of burial of the rock. A number of explanations for this undercutting are possible. Perched rocks can be placed on the surface by deflation of the soil from underneath the rock. The surface etching may be abrasion due to reptation. Reptation, or surface creep, occurs as sand moves without leaving the surface, as small (100-200 micron particles) moved by saltation set larger particles in motion. These large particles are effective at abrading the rocks at the surface level. The structure of "ripple" features at the site is evidence to support reptation at the Gusev site. An alternate explanation is etching at the surface by chemically active grit.

Investigation of a Tricarbide Grooved Ring Fuel Element for a Nuclear Thermal Rocket

NASA Technical Reports Server (NTRS)

Taylor, Brian D.; Emrich, Bill; Tucker, Dennis; Barnes, Marvin; Donders, Nicolas; Benensky, Kelsa

2017-01-01

Deep space exploration, especially that of Mars, is on the horizon as the next big challenge for space exploration. Nuclear propulsion, through which high thrust and efficiency can be achieved, is a promising option for decreasing the cost and logistics of such a mission. Work on nuclear thermal engines goes back to the days of the NERVA program. Currently, nuclear thermal propulsion is under development again in various forms to provide a superior propulsion system for deep space exploration. The authors have been working to develop a concept nuclear thermal engine that uses a grooved ring fuel element as an alternative to the traditional hexagonal rod design. The authors are also studying the use of carbide fuels. The concept was developed in order to increase surface area and heat transfer to the propellant. The use of carbides would also raise the temperature limitations of the reactor. It is hoped that this could lead to a higher thrust to weight nuclear thermal engine. This paper describes the modeling of neutronics, heat transfer, and fluid dynamics of this alternative nuclear fuel element geometry. Fabrication experiments of grooved rings from carbide refractory metals are also presented along with material characterization and interactions with a hot hydrogen environment.

Molecular dynamics explorations of active site structure in designed and evolved enzymes.

PubMed

Osuna, Sílvia; Jiménez-Osés, Gonzalo; Noey, Elizabeth L; Houk, K N

2015-04-21

This Account describes the use of molecular dynamics (MD) simulations to reveal how mutations alter the structure and organization of enzyme active sites. As proposed by Pauling about 70 years ago and elaborated by many others since then, biocatalysis is efficient when functional groups in the active site of an enzyme are in optimal positions for transition state stabilization. Changes in mechanism and covalent interactions are often critical parts of enzyme catalysis. We describe our explorations of the dynamical preorganization of active sites using MD, studying the fluctuations between active and inactive conformations normally concealed to static crystallography. MD shows how the various arrangements of active site residues influence the free energy of the transition state and relates the populations of the catalytic conformational ensemble to the enzyme activity. This Account is organized around three case studies from our laboratory. We first describe the importance of dynamics in evaluating a series of computationally designed and experimentally evolved enzymes for the Kemp elimination, a popular subject in the enzyme design field. We find that the dynamics of the active site is influenced not only by the original sequence design and subsequent mutations but also by the nature of the ligand present in the active site. In the second example, we show how microsecond MD has been used to uncover the role of remote mutations in the active site dynamics and catalysis of a transesterase, LovD. This enzyme was evolved by Tang at UCLA and Codexis, Inc., and is a useful commercial catalyst for the production of the drug simvastatin. X-ray analysis of inactive and active mutants did not reveal differences in the active sites, but relatively long time scale MD in solution showed that the active site of the wild-type enzyme preorganizes only upon binding of the acyl carrier protein (ACP) that delivers the natural acyl group to the active site. In the absence of bound ACP

Cooperative autoinhibition and multi-level activation mechanisms of calcineurin

PubMed Central

Li, Sheng-Jie; Wang, Jue; Ma, Lei; Lu, Chang; Wang, Jie; Wu, Jia-Wei; Wang, Zhi-Xin

2016-01-01

The Ca2+/calmodulin-dependent protein phosphatase calcineurin (CN), a heterodimer composed of a catalytic subunit A and an essential regulatory subunit B, plays critical functions in various cellular processes such as cardiac hypertrophy and T cell activation. It is the target of the most widely used immunosuppressants for transplantation, tacrolimus (FK506) and cyclosporin A. However, the structure of a large part of the CNA regulatory region remains to be determined, and there has been considerable debate concerning the regulation of CN activity. Here, we report the crystal structure of full-length CN (β isoform), which revealed a novel autoinhibitory segment (AIS) in addition to the well-known autoinhibitory domain (AID). The AIS nestles in a hydrophobic intersubunit groove, which overlaps the recognition site for substrates and immunosuppressant-immunophilin complexes. Indeed, disruption of this AIS interaction results in partial stimulation of CN activity. More importantly, our biochemical studies demonstrate that calmodulin does not remove AID from the active site, but only regulates the orientation of AID with respect to the catalytic core, causing incomplete activation of CN. Our findings challenge the current model for CN activation, and provide a better understanding of molecular mechanisms of CN activity regulation. PMID:26794871

Relocating the Active-Site Lysine in Rhodopsin: 2. Evolutionary Intermediates.

PubMed

Devine, Erin L; Theobald, Douglas L; Oprian, Daniel D

2016-08-30

The visual pigment rhodopsin is a G protein-coupled receptor that covalently binds its retinal chromophore via a Schiff base linkage to an active-site Lys residue in the seventh transmembrane helix. Although this residue is strictly conserved among all type II retinylidene proteins, we found previously that the active-site Lys in bovine rhodopsin (Lys296) can be moved to three other locations (G90K, T94K, S186K) while retaining the ability to form a pigment with retinal and to activate transducin in a light-dependent manner [ Devine et al. ( 2013 ) Proc. Natl. Acad. Sci. USA 110 , 13351 - 13355 ]. Because the active-site Lys is not functionally constrained to be in helix seven, it is possible that it could relocate within the protein, most likely via an evolutionary intermediate with two active-site Lys. Therefore, in this study we characterized potential evolutionary intermediates with two Lys in the active site. Four mutant rhodopsins were prepared in which the original Lys296 was left untouched and a second Lys residue was substituted for G90K, T94K, S186K, or F293K. All four constructs covalently bind 11-cis-retinal, form a pigment, and activate transducin in a light-dependent manner. These results demonstrate that rhodopsin can tolerate a second Lys in the retinal binding pocket and suggest that an evolutionary intermediate with two Lys could allow migration of the Schiff base Lys to a position other than the observed, highly conserved location in the seventh TM helix. From sequence-based searches, we identified two groups of natural opsins, insect UV cones and neuropsins, that contain Lys residues at two positions in their active sites and also have intriguing spectral similarities to the mutant rhodopsins studied here.

Polarization-independent triangular-groove fused-silica gratings with high efficiency at a wavelength of 1550 nm

NASA Astrophysics Data System (ADS)

Cao, Hongchao; Zhou, Changhe; Feng, Jijun; Lv, Peng; Ma, Jianyong

2010-11-01

We describe polarization-independent triangular-groove fused-silica gratings illuminated by incident lights in the C + L bands as (de)multiplexers for dense wavelength division multiplexing (DWDM) application. The physical mechanisms of the grating can be shown clearly by using the simplified modal method with consideration of the corresponding accumulated average phase difference of two excited propagating grating modes, which illustrates that the grating structure depends mainly on the ratio of the average effective indices difference to the incident wavelength. Exact grating profile is optimized by using the rigorous coupled-wave analysis (RCWA). With the optimized grating parameters, the grating exhibits diffraction efficiencies of greater than 90% under TE- and TM-polarized incident lights for 101 nm spectral bandwidths (1500-1601 nm) and it can reach an efficiency of more than 99% for both polarizations at a wavelength of 1550 nm. Without loss of metal absorption, coating of dielectric film layers, the designed triangular-groove fused-silica grating should be of great interest for DWDM application.

Modern Microsurgical Resection of Olfactory Groove Meningiomas by Classical Bicoronal Subfrontal Approach without Orbital Osteotomies

PubMed Central

Farooq, Ghulam; Rehman, Lal; Bokhari, Irum; Rizvi, Syed Raza Hussain

2018-01-01

Background: The olfactory groove meningioma has always been surgically challenging. The common microscopic surgical procedures exercised involve modification of pterional or sub-frontal approaches with or without orbital osteotomies. However, we believe that orbital osteotomies are not mandatory to achieve gross total resection. Hence, this study was performed to evaluate the surgical outcomes of olfactory groove meningioma with bicoronal sub frontal approach but without orbital osteotomies. Materials and Methods: The study was performed by reviewing the medical charts, neuroimaging data, and follow-up data of 19 patients who were treated micro surgically for olfactory groove meningioma without orbital osteotomies in our department. Mean overall follow up period of our study was 5 years. Statistical analysis was done by means of IBM SPSS Software version 19. Results: Nineteen patients (1 male and 18 female patients, with an age range of 35-67 years; average age of patients' 51±7.5 years) of OGM were managed in our department. All patients were evaluated by MRI Brain with and without Gadolinium, CTA, CT Scan both axial and Coronal sequences. Most common symptom reported was head ache (80%), others include; urinary incontinence (26%), seizures (78%), decreased visual acuity (79%), papilledema (74%), personality changes (68%) and olfactory loss was reported in 57% of the patients. Post-operative complications include; CSF accumulation (5%), hematoma at tumor bed (10%), skin infection (5%) and mild post-operative brain edema (26%). Mortality rate was 5%. During 5 years of follow-up, we recorded one recurrence which was after 26 months and successfully removed in reoperation. Conclusion: Bi-coronal sub frontal approach appears to be an excellent technique for Olfactory Meningioma removal as practiced by most neurosurgeons. Nevertheless, it is not mandatory to carry out orbital osteotomy to acquire optimal surgical outcome as is advocated by some Authors. PMID:29682018

Modern Microsurgical Resection of Olfactory Groove Meningiomas by Classical Bicoronal Subfrontal Approach without Orbital Osteotomies.

PubMed

Farooq, Ghulam; Rehman, Lal; Bokhari, Irum; Rizvi, Syed Raza Hussain

2018-01-01

The olfactory groove meningioma has always been surgically challenging. The common microscopic surgical procedures exercised involve modification of pterional or sub-frontal approaches with or without orbital osteotomies. However, we believe that orbital osteotomies are not mandatory to achieve gross total resection. Hence, this study was performed to evaluate the surgical outcomes of olfactory groove meningioma with bicoronal sub frontal approach but without orbital osteotomies. The study was performed by reviewing the medical charts, neuroimaging data, and follow-up data of 19 patients who were treated micro surgically for olfactory groove meningioma without orbital osteotomies in our department. Mean overall follow up period of our study was 5 years. Statistical analysis was done by means of IBM SPSS Software version 19. Nineteen patients (1 male and 18 female patients, with an age range of 35-67 years; average age of patients' 51±7.5 years) of OGM were managed in our department. All patients were evaluated by MRI Brain with and without Gadolinium, CTA, CT Scan both axial and Coronal sequences. Most common symptom reported was head ache (80%), others include; urinary incontinence (26%), seizures (78%), decreased visual acuity (79%), papilledema (74%), personality changes (68%) and olfactory loss was reported in 57% of the patients. Post-operative complications include; CSF accumulation (5%), hematoma at tumor bed (10%), skin infection (5%) and mild post-operative brain edema (26%). Mortality rate was 5%. During 5 years of follow-up, we recorded one recurrence which was after 26 months and successfully removed in reoperation. Bi-coronal sub frontal approach appears to be an excellent technique for Olfactory Meningioma removal as practiced by most neurosurgeons. Nevertheless, it is not mandatory to carry out orbital osteotomy to acquire optimal surgical outcome as is advocated by some Authors.

SSME seal test program: Test results for smooth, hole-pattern and helically-grooved stators

NASA Technical Reports Server (NTRS)

Childs, Dara W.

1987-01-01

All of the listed seals were tested in a liquid Halon test facility at high Reynolds numbers. In addition, a helically-grooved-stator seal was tested in an air seal facility. An analysis of the test results with comparisons to theoretical predictions supports the following conclusions: (1) For small seals, the Hirs' friction-factor model is more restricted than had been thought; (2) For smooth seals, predictions of stiffness and damping improve markedly as the radical clearance is reduced; (3) Friction-factor data for hole-pattern-seal stators frequently deviates from the Hirs model; (4) Predictions of stiffness and damping coefficients for hole-pattern-stator seals is generally reasonable; (5) Tests for the hole-pattern stators at reduced clearances show no clear optimum for hole-pattern seals with respect to either hole-area ratio or hole depth to minimum clearance ratios; (6) Tests of these hole-pattern stators show no significant advantage in net damping over smooth seals; (7) Tests of helically-grooved seal stators in Halon show reasonable agreement between theory and prediction for leakage and direct stiffness but poor agreement for the net damping coefficient.

Grooves to tubes: evolution of the venom delivery system in a Late Triassic "reptile"

NASA Astrophysics Data System (ADS)

Mitchell, Jonathan S.; Heckert, Andrew B.; Sues, Hans-Dieter

2010-12-01

Venom delivery systems occur in a wide range of extant and fossil vertebrates and are primarily based on oral adaptations. Teeth range from unmodified (Komodo dragons) to highly specialized fangs similar to hypodermic needles (protero- and solenoglyphous snakes). Developmental biologists have documented evidence for an infolding pathway of fang evolution, where the groove folds over to create the more derived condition. However, the oldest known members of venomous clades retain the same condition as their extant relatives, resulting in no fossil evidence for the transition. Based on a comparison of previously known specimens with newly discovered teeth from North Carolina, we describe a new species of the Late Triassic archosauriform Uatchitodon and provide detailed analyses that provide evidence for both venom conduction and document a complete structural series from shallow grooves to fully enclosed tubular canals. While known only from teeth, Uatchitodon is highly diagnostic in possessing compound serrations and for having two venom canals on each tooth in the dentition. Further, although not a snake, Uatchitodon sheds light on the evolutionary trajectory of venom delivery systems in amniotes and provide solid evidence for venom conduction in archosaur-line diapsids.

High density, optically corrected, micro-channel cooled, v-groove monolithic laser diode array

DOEpatents

Freitas, B.L.

1998-10-27

An optically corrected, micro-channel cooled, high density laser diode array achieves stacking pitches to 33 bars/cm by mounting laser diodes into V-shaped grooves. This design will deliver > 4kW/cm{sup 2} of directional pulsed laser power. This optically corrected, micro-channel cooled, high density laser is usable in all solid state laser systems which require efficient, directional, narrow bandwidth, high optical power density pump sources. 13 figs.

Planar spoof plasmonic ultra-wideband filter based on low-loss and compact terahertz waveguide corrugated with dumbbell grooves.

PubMed

Zhou, Yong Jin; Yang, Bao Jia

2015-05-10

Although subwavelength planar terahertz (THz) plasmonic devices can be implemented based on planar spoof surface plasmons (SPs), they still suffer from a little high propagation loss. Here the dispersion and propagation characteristics of the spoof plasmonic waveguide composed of double metal strips corrugated with dumbbell shaped grooves have been investigated. It has been found that much lower propagation loss and longer propagation length can be achieved based on the waveguide compared with the conventional spoof plasmonic waveguide with rectangular grooves. Moreover, the waveguide can implement a decrease in size of about 22%. An ultra-wideband THz plasmonic filter for planar circuits has been demonstrated based on the proposed waveguide. The experimental verification at the microwave frequency has been conducted by scaling up the geometry size of the filter.

Allosteric site-mediated active site inhibition of PBP2a using Quercetin 3-O-rutinoside and its combination.

PubMed

Rani, Nidhi; Vijayakumar, Saravanan; P T V, Lakshmi; Arunachalam, Annamalai

2016-08-01

Recent crystallographic study revealed the involvement of allosteric site in active site inhibition of penicillin binding protein (PBP2a), where one molecule of Ceftaroline (Cef) binds to the allosteric site of PBP2a and paved way for the other molecule (Cef) to bind at the active site. Though Cef has the potency to inhibit the PBP2a, its adverse side effects are of major concern. Previous studies have reported the antibacterial property of Quercetin derivatives, a group of natural compounds. Hence, the present study aims to evaluate the effect of Quercetin 3-o-rutinoside (Rut) in allosteric site-mediated active site inhibition of PBP2a. The molecular docking studies between allosteric site and ligands (Rut, Que, and Cef) revealed a better binding efficiency (G-score) of Rut (-7.790318) and Cef (-6.194946) with respect to Que (-5.079284). Molecular dynamic (MD) simulation studies showed significant changes at the active site in the presence of ligands (Rut and Cef) at allosteric site. Four different combinations of Rut and Cef were docked and their G-scores ranged between -6.320 and -8.623. MD studies revealed the stability of the key residue (Ser403) with Rut being at both sites, compared to other complexes. Morphological analysis through electron microscopy confirmed that combination of Rut and Cefixime was able to disturb the bacterial cell membrane in a similar fashion to that of Rut and Cefixime alone. The results of this study indicate that the affinity of Rut at both sites were equally good, with further validations Rut could be considered as an alternative for inhibiting MRSA growth.

Influence of active site location on catalytic activity in de novo-designed zinc metalloenzymes.

PubMed

Zastrow, Melissa L; Pecoraro, Vincent L

2013-04-17

While metalloprotein design has now yielded a number of successful metal-bound and even catalytically active constructs, the question of where to put a metal site along a linear, repetitive sequence has not been thoroughly addressed. Often several possibilities in a given sequence may exist that would appear equivalent but may in fact differ for metal affinity, substrate access, or protein dynamics. We present a systematic variation of active site location for a hydrolytically active ZnHis3O site contained within a de novo-designed three-stranded coiled coil. We find that the maximal rate, substrate access, and metal-binding affinity are dependent on the selected position, while catalytic efficiency for p-nitrophenyl acetate hydrolysis can be retained regardless of the location of the active site. This achievement demonstrates how efficient, tailor-made enzymes which control rate, pKa, substrate and solvent access (and selectivity), and metal-binding affinity may be realized. These findings may be applied to the more advanced de novo design of constructs containing secondary interactions, such as hydrogen-bonding channels. We are now confident that changes to location for accommodating such channels can be achieved without location-dependent loss of catalytic efficiency. These findings bring us closer to our ultimate goal of incorporating the secondary interactions we believe will be necessary in order to improve both active site properties and the catalytic efficiency to be competitive with the native enzyme, carbonic anhydrase.

The rem Mutations in the ATP-Binding Groove of the Rad3/XPD Helicase Lead to Xeroderma pigmentosum-Cockayne Syndrome-Like Phenotypes

PubMed Central

Montelone, Beth A.; Aguilera, Andrés

2014-01-01

The eukaryotic TFIIH complex is involved in Nucleotide Excision Repair and transcription initiation. We analyzed three yeast mutations of the Rad3/XPD helicase of TFIIH known as rem (recombination and mutation phenotypes). We found that, in these mutants, incomplete NER reactions lead to replication fork breaking and the subsequent engagement of the homologous recombination machinery to restore them. Nevertheless, the penetrance varies among mutants, giving rise to a phenotype gradient. Interestingly, the mutations analyzed reside at the ATP-binding groove of Rad3 and in vivo experiments reveal a gain of DNA affinity upon damage of the mutant Rad3 proteins. Since mutations at the ATP-binding groove of XPD in humans are present in the Xeroderma pigmentosum-Cockayne Syndrome (XP-CS), we recreated rem mutations in human cells, and found that these are XP-CS-like. We propose that the balance between the loss of helicase activity and the gain of DNA affinity controls the capacity of TFIIH to open DNA during NER, and its persistence at both DNA lesions and promoters. This conditions NER efficiency and transcription resumption after damage, which in human cells would explain the XP-CS phenotype, opening new perspectives to understand the molecular basis of the role of XPD in human disease. PMID:25500814

The rem mutations in the ATP-binding groove of the Rad3/XPD helicase lead to Xeroderma pigmentosum-Cockayne syndrome-like phenotypes.

PubMed

Herrera-Moyano, Emilia; Moriel-Carretero, María; Montelone, Beth A; Aguilera, Andrés

2014-12-01

The eukaryotic TFIIH complex is involved in Nucleotide Excision Repair and transcription initiation. We analyzed three yeast mutations of the Rad3/XPD helicase of TFIIH known as rem (recombination and mutation phenotypes). We found that, in these mutants, incomplete NER reactions lead to replication fork breaking and the subsequent engagement of the homologous recombination machinery to restore them. Nevertheless, the penetrance varies among mutants, giving rise to a phenotype gradient. Interestingly, the mutations analyzed reside at the ATP-binding groove of Rad3 and in vivo experiments reveal a gain of DNA affinity upon damage of the mutant Rad3 proteins. Since mutations at the ATP-binding groove of XPD in humans are present in the Xeroderma pigmentosum-Cockayne Syndrome (XP-CS), we recreated rem mutations in human cells, and found that these are XP-CS-like. We propose that the balance between the loss of helicase activity and the gain of DNA affinity controls the capacity of TFIIH to open DNA during NER, and its persistence at both DNA lesions and promoters. This conditions NER efficiency and transcription resumption after damage, which in human cells would explain the XP-CS phenotype, opening new perspectives to understand the molecular basis of the role of XPD in human disease.

An analysis of tire tread wear groove patterns and the effect of heteroscedasticity on tire tread wear statistics

DOT National Transportation Integrated Search

1985-09-01

This report examines the groove wear variability among tires subjected to the : Uniform Tire Quality Grading (UTQC) test procedure for determining tire tread wear. : The effects of heteroscedasticity (variable variance) on a previously reported : sta...

Dance, Music, Meter and Groove: A Forgotten Partnership

PubMed Central

Fitch, W. Tecumseh

2016-01-01

I argue that core aspects of musical rhythm, especially “groove” and syncopation, can only be fully understood in the context of their origins in the participatory social experience of dance. Musical meter is first considered in the context of bodily movement. I then offer an interpretation of the pervasive but somewhat puzzling phenomenon of syncopation in terms of acoustic emphasis on certain offbeat components of the accompanying dance style. The reasons for the historical tendency of many musical styles to divorce themselves from their dance-based roots are also briefly considered. To the extent that musical rhythms only make sense in the context of bodily movement, researchers interested in ecologically valid approaches to music cognition should make a more concerted effort to extend their analyses to dance, particularly if we hope to understand the cognitive constraints underlying rhythmic aspects of music like meter and groove. PMID:26973489

Active Sites Environmental Monitoring Program: Mid-FY 1991 report

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

Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

1991-10-01

This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) from October 1990 through March 1991. The ASEMP was established in 1989 by Solid Waste Operations and the Environmental Sciences Division to provide early detection and performance monitoring at active low-level radioactive waste (LLW) disposal sites in Solid Waste Storage Area (SWSA) 6 and transuranic (TRU) waste storage sites in SWSA 5 as required by chapters II and III of US Department of Energy Order 5820.2A. Monitoring results continue to demonstrate the no LLW is being leached from the storage vaults on the tumulus pads. Loading ofmore » vaults on Tumulus II began during this reporting period and 115 vaults had been loaded by the end of March 1991.« less

Virtual Screening of Peptide and Peptidomimetic Fragments Targeted to Inhibit Bacterial Dithiol Oxidase DsbA.

PubMed

Duprez, Wilko; Bachu, Prabhakar; Stoermer, Martin J; Tay, Stephanie; McMahon, Róisín M; Fairlie, David P; Martin, Jennifer L

2015-01-01

Antibacterial drugs with novel scaffolds and new mechanisms of action are desperately needed to address the growing problem of antibiotic resistance. The periplasmic oxidative folding system in Gram-negative bacteria represents a possible target for anti-virulence antibacterials. By targeting virulence rather than viability, development of resistance and side effects (through killing host native microbiota) might be minimized. Here, we undertook the design of peptidomimetic inhibitors targeting the interaction between the two key enzymes of oxidative folding, DsbA and DsbB, with the ultimate goal of preventing virulence factor assembly. Structures of DsbB--or peptides--complexed with DsbA revealed key interactions with the DsbA active site cysteine, and with a hydrophobic groove adjacent to the active site. The present work aimed to discover peptidomimetics that target the hydrophobic groove to generate non-covalent DsbA inhibitors. The previously reported structure of a Proteus mirabilis DsbA active site cysteine mutant, in a non-covalent complex with the heptapeptide PWATCDS, was used as an in silico template for virtual screening of a peptidomimetic fragment library. The highest scoring fragment compound and nine derivatives were synthesized and evaluated for DsbA binding and inhibition. These experiments discovered peptidomimetic fragments with inhibitory activity at millimolar concentrations. Although only weakly potent relative to larger covalent peptide inhibitors that interact through the active site cysteine, these fragments offer new opportunities as templates to build non-covalent inhibitors. The results suggest that non-covalent peptidomimetics may need to interact with sites beyond the hydrophobic groove in order to produce potent DsbA inhibitors.

Self-aliquoting micro-grooves in combination with laser ablation-ICP-mass spectrometry for the analysis of challenging liquids: quantification of lead in whole blood.

PubMed

Nischkauer, Winfried; Vanhaecke, Frank; Limbeck, Andreas

2016-08-01

We present a technique for the fast screening of the lead concentration in whole blood samples using laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS). The whole blood sample is deposited on a polymeric surface and wiped across a set of micro-grooves previously engraved into the surface. The engraving of the micro-grooves was accomplished with the same laser system used for LA-ICP-MS analysis. In each groove, a part of the liquid blood is trapped, and thus, the sample is divided into sub-aliquots. These aliquots dry quasi instantly and are then investigated by means of LA-ICP-MS. For quantification, external calibration against aqueous standard solutions was relied on, with iron as an internal standard to account for varying volumes of the sample aliquots. The (208)Pb/(57)Fe nuclide ratio used for quantification was obtained via a data treatment protocol so far only used in the context of isotope ratio determination involving transient signals. The method presented here was shown to provide reliable results for Recipe ClinChek® Whole Blood Control levels I-III (nos. 8840-8842), with a repeatability of typically 3 % relative standard deviation (n = 6, for Pb at 442 μg L(-1)). Spiked and non-spiked real whole blood was analysed as well, and the results were compared with those obtained via dilution and sectorfield ICP-MS. A good agreement between both methods was observed. The detection limit (3 s) for lead in whole blood was established to be 10 μg L(-1) for the laser ablation method presented here. Graphical Abstract Micro-grooves are filled with whole blood, dried, and analyzed by laser ablation ICP-mass spectrometry. Notice that the laser moves in perpendicular direction with regard to the micro-grooves.

From old alkylating agents to new minor groove binders.

PubMed

Puyo, Stéphane; Montaudon, Danièle; Pourquier, Philippe

2014-01-01

Alkylating agents represent the oldest class of anticancer agents with the approval of mechloretamine by the FDA in 1949. Even though their clinical use is far beyond the use of new targeted therapies, they still occupy a major place in the treatment of specific malignancies, sometimes representing the unique option for the treatment of refractory tumors. Here, we are reviewing the major classes of alkylating agents, with a particular focus on the latest generations of compounds that specifically target the minor groove of the DNA. These naturally occurring derivatives have a unique mechanism of action that explains the recent regain of interest in developing new classes of alkylating agents that could be used in combination with other anticancer drugs to enhance tumor response in the clinic. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Sutureless Technique to Fix the Great Saphenous Vein along the Atrioventricular Groove Using Fibrin Glue in Off-Pump Coronary Artery Bypass Grafting.

PubMed

Ohira, Suguru; Doi, Kiyoshi; Yaku, Hitoshi

2016-04-05

We describe a simple method to fix the great saphenous vein graft (SVG) to the right coronary artery along the atrioventricular groove using fibrin glue in off-pump coronary artery bypass grafting (OPCAB). After completion of the proximal anastomosis, the SVG was placed along the atrioventricular groove to the acute margin. Fibrin glue was sprayed using pressurized carbon dioxide gas. A distal anastomosis was subsequently performed after rotating the heart to expose the posterior descending artery. It is a straightforward and reproducible technique to determine the optimal length of the SVG and prevent kinking or stretching of the graft, especially in OPCAB.

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.

Flow Regime Transition in Inner Grooved Minichannel Cold Plates for Cooling Hybrid Electric Power Electronics

DTIC Science & Technology

2013-01-01

reentrant cavities) Corrugated or fluted tubes Screens Inner grooved tubes ( microfin tubes ) Fins Electrohydrodynamic field effect 3.1 Convective... microfin geometries, including 3-D geometries, but most commercial vendors continue to manufacture seamless tubes (46). Figure 6a shows the...enhancement technologies are compiled in table 4. Table 4. Comparison of leading refrigeration tube performance (42). Metric Microfin Tube Twisted

All the catalytic active sites of MoS 2 for hydrogen evolution

DOE PAGES

Li, Guoqing; Zhang, Du; Qiao, Qiao; ...

2016-11-29

MoS 2 presents a promising low-cost catalyst for the hydrogen evolution reaction (HER), but the understanding about its active sites has remained limited. Here we present an unambiguous study of the catalytic activities of all possible reaction sites of MoS 2, including edge sites, sulfur vacancies, and grain boundaries. We demonstrate that, in addition to the well-known catalytically active edge sites, sulfur vacancies provide another major active site for the HER, while the catalytic activity of grain boundaries is much weaker. Here, the intrinsic turnover frequencies (Tafel slopes) of the edge sites, sulfur vacancies, and grain boundaries are estimated tomore » be 7.5 s –1 (65–75 mV/dec), 3.2 s –1 (65–85 mV/dec), and 0.1 s –1 (120–160 mV/dec), respectively. We also demonstrate that the catalytic activity of sulfur vacancies strongly depends on the density of the vacancies and the local crystalline structure in proximity to the vacancies. Unlike edge sites, whose catalytic activity linearly depends on the length, sulfur vacancies show optimal catalytic activities when the vacancy density is in the range of 7–10%, and the number of sulfur vacancies in high crystalline quality MoS 2 is higher than that in low crystalline quality MoS 2, which may be related with the proximity of different local crystalline structures to the vacancies.« less

Machine-Learning Methods Enable Exhaustive Searches for Active Bimetallic Facets and Reveal Active Site Motifs for CO 2 Reduction

DOE PAGES

Ulissi, Zachary W.; Tang, Michael T.; Xiao, Jianping; ...

2017-07-27

Bimetallic catalysts are promising for the most difficult thermal and electrochemical reactions, but modeling the many diverse active sites on polycrystalline samples is an open challenge. Here, we present a general framework for addressing this complexity in a systematic and predictive fashion. Active sites for every stable low-index facet of a bimetallic crystal are enumerated and cataloged, yielding hundreds of possible active sites. The activity of these sites is explored in parallel using a neural-network-based surrogate model to share information between the many density functional theory (DFT) relaxations, resulting in activity estimates with an order of magnitude fewer explicit DFTmore » calculations. Sites with interesting activity were found and provide targets for follow-up calculations. This process was applied to the electrochemical reduction of CO 2 on nickel gallium bimetallics and indicated that most facets had similar activity to Ni surfaces, but a few exposed Ni sites with a very favorable on-top CO configuration. This motif emerged naturally from the predictive modeling and represents a class of intermetallic CO 2 reduction catalysts. These sites rationalize recent experimental reports of nickel gallium activity and why previous materials screens missed this exciting material. Most importantly these methods suggest that bimetallic catalysts will be discovered by studying facet reactivity and diversity of active sites more systematically.« less

Machine-Learning Methods Enable Exhaustive Searches for Active Bimetallic Facets and Reveal Active Site Motifs for CO 2 Reduction

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

Ulissi, Zachary W.; Tang, Michael T.; Xiao, Jianping

Bimetallic catalysts are promising for the most difficult thermal and electrochemical reactions, but modeling the many diverse active sites on polycrystalline samples is an open challenge. Here, we present a general framework for addressing this complexity in a systematic and predictive fashion. Active sites for every stable low-index facet of a bimetallic crystal are enumerated and cataloged, yielding hundreds of possible active sites. The activity of these sites is explored in parallel using a neural-network-based surrogate model to share information between the many density functional theory (DFT) relaxations, resulting in activity estimates with an order of magnitude fewer explicit DFTmore » calculations. Sites with interesting activity were found and provide targets for follow-up calculations. This process was applied to the electrochemical reduction of CO 2 on nickel gallium bimetallics and indicated that most facets had similar activity to Ni surfaces, but a few exposed Ni sites with a very favorable on-top CO configuration. This motif emerged naturally from the predictive modeling and represents a class of intermetallic CO 2 reduction catalysts. These sites rationalize recent experimental reports of nickel gallium activity and why previous materials screens missed this exciting material. Most importantly these methods suggest that bimetallic catalysts will be discovered by studying facet reactivity and diversity of active sites more systematically.« less

Mutation at a strictly conserved, active site tyrosine in the copper amine oxidase leads to uncontrolled oxygenase activity.

PubMed

Chen, Zhi-Wei; Datta, Saumen; Dubois, Jennifer L; Klinman, Judith P; Mathews, F Scott

2010-08-31

The copper amine oxidases carry out two copper-dependent processes: production of their own redox-active cofactor (2,4,5-trihydroxyphenylalanine quinone, TPQ) and the subsequent oxidative deamination of substrate amines. Because the same active site pocket must facilitate both reactions, individual active site residues may serve multiple roles. We have examined the roles of a strictly conserved active site tyrosine Y305 in the copper amine oxidase from Hansenula polymorpha kinetically, spetroscopically (Dubois and Klinman (2006) Biochemistry 45, 3178), and, in the present work, structurally. While the Y305A enzyme is almost identical to the wild type, a novel, highly oxygenated species replaces TPQ in the Y305F active sites. This new structure not only provides the first direct detection of peroxy intermediates in cofactor biogenesis but also indicates the critical control of oxidation chemistry that can be conferred by a single active site residue.

Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme.

PubMed Central

Hermann, T; Auffinger, P; Scott, W G; Westhof, E

1997-01-01

In the presence of magnesium ions, cleavage by the hammerhead ribozyme RNA at a specific residue leads to 2'3'-cyclic phosphate and 5'-OH extremities. In the cleavage reaction an activated ribose 2'-hydroxyl group attacks its attached 3'-phosphate. Molecular dynamics simulations of the crystal structure of the hammerhead ribozyme, obtained after flash-freezing of crystals under conditions where the ribozyme is active, provide evidence that a mu-bridging OH-ion is located between two Mg2+ions close to the cleavable phosphate. Constrained simulations show further that a flip from the C3'- endo to the C2'- endo conformation of the ribose at the cleavable phosphate brings the 2'-hydroxyl in proximity to both the attacked phosphorous atom and the mu-bridging OH-ion. Thus, the simulations lead to a detailed new insight into the mechanism of hammerhead ribozyme cleavage where a mu-hydroxo bridged magnesium cluster, located on the deep groove side, provides an OH-ion that is able to activate the 2'-hydroxyl nucleophile after a minor and localized conformational change in the RNA. PMID:9254698

Structural Insights into the Assembly of the Adeno-associated Virus Type 2 Rep68 Protein on the Integration Site AAVS1*

PubMed Central

Musayev, Faik N.; Zarate-Perez, Francisco; Bishop, Clayton; Burgner, John W.; Escalante, Carlos R.

2015-01-01

Adeno-associated virus (AAV) is the only eukaryotic virus with the property of establishing latency by integrating site-specifically into the human genome. The integration site known as AAVS1 is located in chromosome 19 and contains multiple GCTC repeats that are recognized by the AAV non-structural Rep proteins. These proteins are multifunctional, with an N-terminal origin-binding domain (OBD) and a helicase domain joined together by a short linker. As a first step to understand the process of site-specific integration, we proceeded to characterize the recognition and assembly of Rep68 onto the AAVS1 site. We first determined the x-ray structure of AAV-2 Rep68 OBD in complex with the AAVS1 DNA site. Specificity is achieved through the interaction of a glycine-rich loop that binds the major groove and an α-helix that interacts with a downstream minor groove on the same face of the DNA. Although the structure shows a complex with three OBD molecules bound to the AAVS1 site, we show by using analytical centrifugation and electron microscopy that the full-length Rep68 forms a heptameric complex. Moreover, we determined that a minimum of two direct repeats is required to form a stable complex and to melt DNA. Finally, we show that although the individual domains bind DNA poorly, complex assembly requires oligomerization and cooperation between its OBD, helicase, and the linker domains. PMID:26370092

A Bridging Water Anchors the Tethered 5-(3-Aminopropyl)-2′-deoxyuridine Amine in the DNA Major Groove Proximate to the N+2 C·G Base Pair: Implications for Formation of Interstrand 5′-GNC-3′ Cross-Links by Nitrogen Mustards

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

Wang, Feng; Li, Feng; Ganguly, Manjori

2008-11-14

Site-specific insertion of t-(3-aminopropyl)-2'-deoxyuridine (Z3dU) and 7-deaza-dG into the Dickerson-Drew dodecamers 5'-d(C{sup 1}G{sup 2}C{sup 3}G{sup 4}A{sup 5}A{sup 6}T{sup 7}T{sup 8}C{sup 9}{und Z}{sup 10}C{sup 11}G{sup 12})-3'{center_dot}5'-d (C{sup 13}G{sup 14}C{sup 15}G{sup 16}A{sup 17}A{sup 18}T{sup 19}T{sup 20}C{sup 21}{und Z}{sup 22}C{sup 23}G{sup 24})-3' (named DDD{sup Z10}) and 5'-d(C{sup 1}G{sup 2}C{sup 3}G{sup 4}A{sup 5}A{sup 6}T{sup 7}{und X}{sup 20}C{sup 21}{und Z}{sup 22}C{sup 23}G{sup 24})-3' (named DDD{sup 2+Z10}) (X = 73dU; Z = 7-deaza-dG) suggests a mechanism underlying the formation of interstrand N+2 DNA cross-links by nitrogen mustards, e.g., melphalan and mechlorethamine. Analysis of the DDD{sup 2+Z10} duplex reveals that the tethered cations at base pairs A{supmore » 5}{center_dot}X{sup 20} and X{sup 8}{center_dot}A{sup 17} extend within the major groove in the 3'-direction, toward conserved Mg{sup 2+} binding sites located adjacent to N+2 base pairs C{sup 3}{center_dot}Z{sup 22} and Z{sup 10}{center_dot}C{sup 15}. Bridging waters located between the tethered amines and either Z{sup 10} or Z{sup 22} O{sup 6} stabilize the tethered cations and allow interactions with the N + 2 base pairs without DNA bending. Incorporation of 7-deaza-dG into the DDD{sup 2+Z10} duplex weakens but does not eliminate electrostatic interactions between tethered amines and Z{sup 10} O{sup 6} and Z{sup 22} O{sup 6}. The results suggest a mechanism by which tethered N7-dG aziridinium ions, the active species involved in formation of interstrand 5'-GNC-3' cross-links by nitrogen mustards, modify the electrostatics of the major groove and position the aziridinium ions proximate to the major groove edge of the N+2 C{center_dot}G base pair, facilitating interstrand cross-linking.« less

Mechanistic aspects of thioflavin-T self-aggregation and DNA binding: evidence for dimer attack on DNA grooves.

PubMed

Biancardi, A; Biver, T; Burgalassi, A; Mattonai, M; Secco, F; Venturini, M

2014-10-07

Thioflavin-T (TFT) is a fluorescent marker widely employed in biomedical research but the mechanism of its binding to polynucleotides has been poorly understood. This paper presents a study of the mechanisms of TFT self-aggregation and binding to DNA. Relaxation kinetics of TFT solutions show that the cyanine undergoes dimerization followed by dimer isomerisation. The interaction of TFT with DNA has been investigated using static methods, such as spectrophotometric and spectrofluorometric titrations under different conditions (salt content, temperature), fluorescence quenching, viscometric experiments and the T-jump relaxation method. The combined use of these techniques enabled us to show that the TFT monomer undergoes intercalation between the DNA base pairs and external binding according to a branched mechanism. Moreover, it has also been observed that, under dye excess conditions, the TFT dimer binds to the DNA grooves. The molecular structures of intercalated TFT and the groove-bound TFT dimer are obtained by performing QM/MM MD simulations.

Functional Evolution of PLP-dependent Enzymes based on Active-Site Structural Similarities

PubMed Central

Catazaro, Jonathan; Caprez, Adam; Guru, Ashu; Swanson, David; Powers, Robert

2014-01-01

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5’-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the Comparison of Protein Active Site Structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. PMID:24920327

Chapter 12: Daily Patterns of Marbled Murrelet Activity at Inland Sites

Treesearch

Nancy L. Naslund; Brian P. O’Donnell

1995-01-01

Patterns in the daily activity of Marbled Murrelets (Brachyramphus marmoratus) at inland sites has been studied throughout their range from California to Alaska. Murrelets are most active at inland sites around dawn, and to a lesser degree, at dusk. Throughout their range, peak levels of activity (detections) occur in the hour around dawn, but...

Olfactory groove meningioma: discussion of clinical presentation and surgical outcomes following excision via the subcranial approach.

PubMed

Pepper, Jon-Paul; Hecht, Sarah L; Gebarski, Stephen S; Lin, Erin M; Sullivan, Stephen E; Marentette, Lawrence J

2011-11-01

To describe surgical outcomes and radiographic features of olfactory groove meningiomas treated by excision through the subcranial approach. Special emphasis is placed on paranasal sinus and orbit involvement. Retrospective review of a series of patients. Nineteen patients underwent excision of olfactory groove meningioma (OGM) via the transglabellar/subcranial approach between December 1995 and November 2009. Nine patients had previously undergone prior resection at outside institutions, and four had prior radiotherapy in addition to a prior excision. Transglabellar/subcranial surgical approach to the anterior skull base was performed. Tumor histology included three World Health Organization (WHO) grade III lesions, one WHO grade II lesion, and 15 WHO grade I lesions. Fourteen patients had evidence of extension into the paranasal sinuses, with the ethmoid sinus being most commonly involved. Kaplan-Meier estimates of mean overall and disease-free survival were 121.45 months and 93.03 months, respectively. The mean follow-up interval was 41.0 months, and at the time of data analysis three patients had recurrent tumors. Seven (36.8%) patients experienced a major complication in the perioperative period; there were no perioperative mortalities. Orbit invasion was observed in four patients, with optic nerve impingement in 11 patients. Of these, three patients had long-term diplopia. No patients experienced worsening of preoperative visual acuity. Olfactory groove meningiomas demonstrate a propensity to spread into the paranasal sinuses, particularly in recurrent cases. Given a tendency for infiltrative recurrence along the skull base, this disease represents an important area of collaboration between neurosurgery and otolaryngology. The subcranial approach offers excellent surgical access for excision, particularly for recurrences that involve the paranasal sinuses and optic apparatus. Copyright © 2011 The American Laryngological, Rhinological, and Otological Society

An Active Site Water Network in the Plasminogen Activator Pla from Yersinia pestis

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

Eren, Elif; Murphy, Megan; Goguen, Jon

2010-08-13

The plasminogen activator Pla from Yersinia pestis is an outer membrane protease (omptin) that is important for the virulence of plague. Here, we present the high-resolution crystal structure of wild-type, enzymatically active Pla at 1.9 {angstrom}. The structure shows a water molecule located between active site residues D84 and H208, which likely corresponds to the nucleophilic water. A number of other water molecules are present in the active site, linking residues important for enzymatic activity. The R211 sidechain in loop L4 is close to the nucleophilic water and possibly involved in the stabilization of the oxyanion intermediate. Subtle conformational changesmore » of H208 result from the binding of lipopolysaccharide to the outside of the barrel, explaining the unusual dependence of omptins on lipopolysaccharide for activity. The Pla structure suggests a model for the interaction with plasminogen substrate and provides a more detailed understanding of the catalytic mechanism of omptin proteases.« less

Binding site size limit of the 2:1 pyrrole-imidazole polyamide-DNA motif.

PubMed Central

Kelly, J J; Baird, E E; Dervan, P B

1996-01-01

Polyamides containing N-methylimidazole (Im) and N-methylpyrrole (Py) amino acids can be combined in antiparallel side-by-side dimeric complexes for sequence-specific recognition in the minor groove of DNA. Six polyamides containing three to eight rings bind DNA sites 5-10 bp in length, respectively. Quantitative DNase I footprint titration experiments demonstrate that affinity maximizes and is similar at ring sizes of five, six, and seven. Sequence specificity decreases as the length of the polyamides increases beyond five rings. These results provide useful guidelines for the design of new polyamides that bind longer DNA sites with enhanced affinity and specificity. Images Fig. 4 PMID:8692930

Anisotropic Covalency Contributions to Superexchange Pathways in Type One Copper Active Sites

PubMed Central

2015-01-01

Type one (T1) Cu sites deliver electrons to catalytic Cu active sites: the mononuclear type two (T2) Cu site in nitrite reductases (NiRs) and the trinuclear Cu cluster in the multicopper oxidases (MCOs). The T1 Cu and the remote catalytic sites are connected via a Cys-His intramolecular electron-transfer (ET) bridge, which contains two potential ET pathways: P1 through the protein backbone and P2 through the H-bond between the Cys and the His. The high covalency of the T1 Cu–S(Cys) bond is shown here to activate the T1 Cu site for hole superexchange via occupied valence orbitals of the bridge. This covalency-activated electronic coupling (HDA) facilitates long-range ET through both pathways. These pathways can be selectively activated depending on the geometric and electronic structure of the T1 Cu site and thus the anisotropic covalency of the T1 Cu–S(Cys) bond. In NiRs, blue (π-type) T1 sites utilize P1 and green (σ-type) T1 sites utilize P2, with P2 being more efficient. Comparing the MCOs to NiRs, the second-sphere environment changes the conformation of the Cys-His pathway, which selectively activates HDA for superexchange by blue π sites for efficient turnover in catalysis. These studies show that a given protein bridge, here Cys-His, provides different superexchange pathways and electronic couplings depending on the anisotropic covalencies of the donor and acceptor metal sites. PMID:25310460

Functional evolution of PLP-dependent enzymes based on active-site structural similarities.

PubMed

Catazaro, Jonathan; Caprez, Adam; Guru, Ashu; Swanson, David; Powers, Robert

2014-10-01

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5'-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the comparison of protein active site structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional-fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. © 2014 Wiley Periodicals, Inc.

Active-site solvent replenishment observed during human carbonic anhydrase II catalysis.

PubMed

Kim, Jin Kyun; Lomelino, Carrie L; Avvaru, Balendu Sankara; Mahon, Brian P; McKenna, Robert; Park, SangYoun; Kim, Chae Un

2018-01-01

Human carbonic anhydrase II (hCA II) is a zinc metalloenzyme that catalyzes the reversible hydration/dehydration of CO 2 /HCO 3 - . Although hCA II has been extensively studied to investigate the proton-transfer process that occurs in the active site, its underlying mechanism is still not fully understood. Here, ultrahigh-resolution crystallographic structures of hCA II cryocooled under CO 2 pressures of 7.0 and 2.5 atm are presented. The structures reveal new intermediate solvent states of hCA II that provide crystallographic snapshots during the restoration of the proton-transfer water network in the active site. Specifically, a new intermediate water (W I ') is observed next to the previously observed intermediate water W I , and they are both stabilized by the five water molecules at the entrance to the active site (the entrance conduit). Based on these structures, a water network-restructuring mechanism is proposed, which takes place at the active site after the nucleophilic attack of OH - on CO 2 . This mechanism explains how the zinc-bound water (W Zn ) and W1 are replenished, which are directly responsible for the reconnection of the His64-mediated proton-transfer water network. This study provides the first 'physical' glimpse of how a water reservoir flows into the hCA II active site during its catalytic activity.

Human topoisomerase I poisoning: docking protoberberines into a structure-based binding site model

NASA Astrophysics Data System (ADS)

Kettmann, Viktor; Košt'álová, Daniela; Höltje, Hans-Dieter

2004-12-01

Using the X-ray crystal structure of the human topoisomerase I (top1) - DNA cleavable complex and the Sybyl software package, we have developed a general model for the ternary cleavable complex formed with four protoberberine alkaloids differing in the substitution on the terminal phenyl rings and covering a broad range of the top1-poisoning activities. This model has the drug intercalated with its planar chromophore between the -1 and +1 base pairs flanking the cleavage site, with the nonplanar portion pointing into the minor groove. The ternary complexes were geometry-optimized and relative interaction energies, computed by using the Tripos force field, were found to rank in correct order the biological potency of the compounds; in addition, the model is also consistent with the top1-poisoning inactivity of berberine, a major prototype of the protoberberine alkaloids. The model might serve as a rational basis for elaboration of the most active compound as a lead structure, in order to develop more potent top1 poisons as next generation anti-cancer drugs.

Efficient unidirectional launching of surface plasmons by a cascade asymmetric-groove structure.

PubMed

Song, Xue-Yang; Zhang, Zhengxing; Liao, Huimin; Li, Zhi; Sun, Chengwei; Chen, Jianjun; Gong, Qihuang

2016-03-28

Increasing the unidirectional launching efficiency of surface plasmon polaritons (SPPs) is crucial in plasmonics. Here, we demonstrate that this efficiency may be improved by cascading subwavelength unidirectional SPP launching units. A unidirectional SPP launching efficiency of at least 46% and an extinction ratio of 40 are experimentally demonstrated using a cascade asymmetric-groove structure. Meanwhile, the device is ultracompact, and has a lateral dimension of only 1.1 μm. The proposed structure also presents a broadband response and is easy to fabricate. This high-performance wavelength-scale unidirectional SPP launcher represents an important development in practical SPP sources.

Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites.

PubMed

Ribeiro, António J M; Holliday, Gemma L; Furnham, Nicholas; Tyzack, Jonathan D; Ferris, Katherine; Thornton, Janet M

2018-01-04

M-CSA (Mechanism and Catalytic Site Atlas) is a database of enzyme active sites and reaction mechanisms that can be accessed at www.ebi.ac.uk/thornton-srv/m-csa. Our objectives with M-CSA are to provide an open data resource for the community to browse known enzyme reaction mechanisms and catalytic sites, and to use the dataset to understand enzyme function and evolution. M-CSA results from the merging of two existing databases, MACiE (Mechanism, Annotation and Classification in Enzymes), a database of enzyme mechanisms, and CSA (Catalytic Site Atlas), a database of catalytic sites of enzymes. We are releasing M-CSA as a new website and underlying database architecture. At the moment, M-CSA contains 961 entries, 423 of these with detailed mechanism information, and 538 with information on the catalytic site residues only. In total, these cover 81% (195/241) of third level EC numbers with a PDB structure, and 30% (840/2793) of fourth level EC numbers with a PDB structure, out of 6028 in total. By searching for close homologues, we are able to extend M-CSA coverage of PDB and UniProtKB to 51 993 structures and to over five million sequences, respectively, of which about 40% and 30% have a conserved active site. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Active Site Gate Dynamics Modulate the Catalytic Activity of the Ubiquitination Enzyme E2-25K.

PubMed

Rout, Manoj K; Lee, Brian L; Lin, Aiyang; Xiao, Wei; Spyracopoulos, Leo

2018-05-03

The ubiquitin proteasome system (UPS) signals for degradation of proteins through attachment of K48-linked polyubiquitin chains, or alterations in protein-protein recognition through attachment of K63-linked chains. Target proteins are ubiquitinated in three sequential chemical steps by a three-component enzyme system. Ubiquitination, or E2 enzymes, catalyze the central step by facilitating reaction of a target protein lysine with the C-terminus of Ub that is attached to the active site cysteine of the E2 through a thioester bond. E2 reactivity is modulated by dynamics of an active site gate, whose central residue packs against the active site cysteine in a closed conformation. Interestingly, for the E2 Ubc13, which specifically catalyzes K63-linked ubiquitination, the central gate residue adopts an open conformation. We set out to determine if active site gate dynamics play a role in catalysis for E2-25K, which adopts the canonical, closed gate conformation, and which selectively synthesizes K48-linked ubiquitin chains. Gate dynamics were characterized using mutagenesis of key residues, combined with enzyme kinetics measurements, and main chain NMR relaxation. The experimental data were interpreted with all atom MD simulations. The data indicate that active site gate opening and closing rates for E2-25K are precisely balanced.

Outcomes After Conservative, Endoscopic, and Surgical Treatment of Groove Pancreatitis: A Systematic Review.

PubMed

Kager, Liesbeth M; Lekkerkerker, Selma J; Arvanitakis, Marianna; Delhaye, Myriam; Fockens, Paul; Boermeester, Marja A; van Hooft, Jeanin E; Besselink, Marc G

2017-09-01

Groove pancreatitis (GP) is a focal form of chronic pancreatitis affecting the paraduodenal groove area, for which consensus on diagnosis and management is lacking. We performed a systematic review of the literature to determine patient characteristics and imaging features of GP and to evaluate clinical outcomes after treatment. Eight studies were included reporting on 335 GP patients with a median age of 47 years (range, 34 to 64 y), with 90% male, 87% smokers, and 87% alcohol consumption, and 47 months (range, 15 to 122 mo) of follow-up. Most patients presented with abdominal pain (91%) and/or weight loss (78%). Imaging frequently showed cystic lesions (91%) and duodenal stenosis (60%).Final treatment was conservative (eg, pain medication) in 29% of patients. Endoscopic treatment (eg, pseudocyst drainage) was applied in 19% of patients-34% of these patients were subsequently referred for surgery. Overall, 59% of patients were treated surgically (eg, pancreatoduodenectomy). Complete symptom relief was observed in 50% of patients who were treated conservatively, 57% who underwent endoscopic treatment, and 79% who underwent surgery. GP is associated with male gender, smoking, and alcohol consumption. The vast majority of patients presents with abdominal pain and with cystic lesions on imaging. Although surgical treatment seems to be the most effective, both conservative and endoscopic treatment are successful in about half of patients. A stepwise treatment algorithm starting with the least invasive treatment options seems advisable.

Disturbance of DNA conformation by the binding of testosterone-based platinum drugs via groove-face and intercalative interactions: a molecular dynamics simulation study

PubMed Central

2013-01-01

Background To explore novel platinum-based anticancer agents that are distinct from the structure and interaction mode of the traditional cisplatin by forming the bifunctional intrastrand 1,2 GpG adduct, the monofunctional platinum + DNA adducts with extensive non-covalent interactions had been studied. It was reported that the monofunctional testosterone-based platinum(II) agents present the high anticancer activity. Moreover, it was also found that the testosterone-based platinum agents could cause the DNA helix to undergo significant unwinding and bending over the non-testosterone-based platinum agents. However, the interaction mechanisms of these platinum agents with DNA at the atomic level are not yet clear so far. Results In the present work, we used molecular dynamics (MD) simulations and DNA conformational dynamics calculations to study the DNA distortion properties of the testosterone-based platinum + DNA, the improved testosterone-based platinum + DNA and the non-testosterone-based platinum + DNA adducts. The results show that the intercalative interaction of the improved flexible testosterone-based platinum agent with DNA molecule could cause larger DNA conformational distortion than the groove-face interaction of the rigid testosterone-based platinum agent with DNA molecule. Further investigations for the non-testosterone-based platinum agent reveal the occurrence of insignificant change of DNA conformation due to the absence of testosterone ligand in such agent. Based on the DNA dynamics analysis, the DNA base motions relating to DNA groove parameter changes and hydrogen bond destruction of DNA base pairs were also discussed in this work. Conclusions The flexible linker in the improved testosterone-based platinum agent causes an intercalative interaction with DNA in the improved testosterone-based platinum + DNA adduct, which is different from the groove-face interaction caused by a rigid linker in the testosterone-based platinum

SABER: A computational method for identifying active sites for new reactions

PubMed Central

Nosrati, Geoffrey R; Houk, K N

2012-01-01

A software suite, SABER (Selection of Active/Binding sites for Enzyme Redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (Barker and Thornton, Bioinformatics 2003;19:1644–1649). SABER is used to explore the Protein Data Bank (PDB) to locate proteins with a specific 3D arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. As a proof-of-principle test, SABER was used to identify enzymes that have the same catalytic group arrangement present in o-succinyl benzoate synthase (OSBS). Among the highest-scoring scaffolds identified by the SABER search for enzymes with the same catalytic group arrangement as OSBS were l-Ala d/l-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE), both of which have been redesigned to become effective OSBS catalysts, demonstrated by experiments. Next, we used SABER to search for naturally existing active sites in the PDB with catalytic groups similar to those present in the designed Kemp elimination enzyme KE07. From over 2000 geometric matches to the KE07 active site, SABER identified 23 matches that corresponded to residues from known active sites. The best of these matches, with a 0.28 Å catalytic atom RMSD to KE07, was then redesigned to be compatible with the Kemp elimination using RosettaDesign. We also used SABER to search for potential Kemp eliminases using a theozyme predicted to provide a greater rate acceleration than the active site of KE07, and used Rosetta to create a design based on the proteins identified. PMID:22492397

SABER: a computational method for identifying active sites for new reactions.

PubMed

Nosrati, Geoffrey R; Houk, K N

2012-05-01

A software suite, SABER (Selection of Active/Binding sites for Enzyme Redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (Barker and Thornton, Bioinformatics 2003;19:1644-1649). SABER is used to explore the Protein Data Bank (PDB) to locate proteins with a specific 3D arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. As a proof-of-principle test, SABER was used to identify enzymes that have the same catalytic group arrangement present in o-succinyl benzoate synthase (OSBS). Among the highest-scoring scaffolds identified by the SABER search for enzymes with the same catalytic group arrangement as OSBS were L-Ala D/L-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE), both of which have been redesigned to become effective OSBS catalysts, demonstrated by experiments. Next, we used SABER to search for naturally existing active sites in the PDB with catalytic groups similar to those present in the designed Kemp elimination enzyme KE07. From over 2000 geometric matches to the KE07 active site, SABER identified 23 matches that corresponded to residues from known active sites. The best of these matches, with a 0.28 Å catalytic atom RMSD to KE07, was then redesigned to be compatible with the Kemp elimination using RosettaDesign. We also used SABER to search for potential Kemp eliminases using a theozyme predicted to provide a greater rate acceleration than the active site of KE07, and used Rosetta to create a design based on the proteins identified. Copyright © 2012 The Protein Society.

'Unconventional' coordination chemistry by metal chelating fragments in a metalloprotein active site.

PubMed

Martin, David P; Blachly, Patrick G; Marts, Amy R; Woodruff, Tessa M; de Oliveira, César A F; McCammon, J Andrew; Tierney, David L; Cohen, Seth M

2014-04-09

The binding of three closely related chelators: 5-hydroxy-2-methyl-4H-pyran-4-thione (allothiomaltol, ATM), 3-hydroxy-2-methyl-4H-pyran-4-thione (thiomaltol, TM), and 3-hydroxy-4H-pyran-4-thione (thiopyromeconic acid, TPMA) to the active site of human carbonic anhydrase II (hCAII) has been investigated. Two of these ligands display a monodentate mode of coordination to the active site Zn(2+) ion in hCAII that is not recapitulated in model complexes of the enzyme active site. This unprecedented binding mode in the hCAII-thiomaltol complex has been characterized by both X-ray crystallography and X-ray spectroscopy. In addition, the steric restrictions of the active site force the ligands into a 'flattened' mode of coordination compared with inorganic model complexes. This change in geometry has been shown by density functional computations to significantly decrease the strength of the metal-ligand binding. Collectively, these data demonstrate that the mode of binding by small metal-binding groups can be significantly influenced by the protein active site. Diminishing the strength of the metal-ligand bond results in unconventional modes of metal coordination not found in typical coordination compounds or even carefully engineered active site models, and understanding these effects is critical to the rational design of inhibitors that target clinically relevant metalloproteins.

Enhanced enzyme kinetic stability by increasing rigidity within the active site.

PubMed

Xie, Yuan; An, Jiao; Yang, Guangyu; Wu, Geng; Zhang, Yong; Cui, Li; Feng, Yan

2014-03-14

Enzyme stability is an important issue for protein engineers. Understanding how rigidity in the active site affects protein kinetic stability will provide new insight into enzyme stabilization. In this study, we demonstrated enhanced kinetic stability of Candida antarctica lipase B (CalB) by mutating the structurally flexible residues within the active site. Six residues within 10 Å of the catalytic Ser(105) residue with a high B factor were selected for iterative saturation mutagenesis. After screening 2200 colonies, we obtained the D223G/L278M mutant, which exhibited a 13-fold increase in half-life at 48 °C and a 12 °C higher T50(15), the temperature at which enzyme activity is reduced to 50% after a 15-min heat treatment. Further characterization showed that global unfolding resistance against both thermal and chemical denaturation also improved. Analysis of the crystal structures of wild-type CalB and the D223G/L278M mutant revealed that the latter formed an extra main chain hydrogen bond network with seven structurally coupled residues within the flexible α10 helix that are primarily involved in forming the active site. Further investigation of the relative B factor profile and molecular dynamics simulation confirmed that the enhanced rigidity decreased fluctuation of the active site residues at high temperature. These results indicate that enhancing the rigidity of the flexible segment within the active site may provide an efficient method for improving enzyme kinetic stability.

GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms.

PubMed

Moraes, João P A; Pappa, Gisele L; Pires, Douglas E V; Izidoro, Sandro C

2017-07-03

Enzyme active sites are important and conserved functional regions of proteins whose identification can be an invaluable step toward protein function prediction. Most of the existing methods for this task are based on active site similarity and present limitations including performing only exact matches on template residues, template size restraints, despite not being capable of finding inter-domain active sites. To fill this gap, we proposed GASS-WEB, a user-friendly web server that uses GASS (Genetic Active Site Search), a method based on an evolutionary algorithm to search for similar active sites in proteins. GASS-WEB can be used under two different scenarios: (i) given a protein of interest, to match a set of specific active site templates; or (ii) given an active site template, looking for it in a database of protein structures. The method has shown to be very effective on a range of experiments and was able to correctly identify >90% of the catalogued active sites from the Catalytic Site Atlas. It also managed to achieve a Matthew correlation coefficient of 0.63 using the Critical Assessment of protein Structure Prediction (CASP 10) dataset. In our analysis, GASS was ranking fourth among 18 methods. GASS-WEB is freely available at http://gass.unifei.edu.br/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Applying the Brakes to Multi-Site SR Protein Phosphorylation: Substrate-Induced Effects on the Splicing Kinase SRPK1†

PubMed Central

Aubol, Brandon E.; Adams, Joseph A.

2011-01-01

To investigate how a protein kinase interacts with its protein substrate during extended, multi-site phosphorylation, the kinetic mechanism of a protein kinase involved in mRNA splicing control was investigated using rapid quench flow techniques. The protein kinase SRPK1 phosphorylates approximately 10 serines in the arginine-serine-rich domain (RS domain) of the SR protein SRSF1 in a C-to-N-terminal direction, a modification that directs this essential splicing factor from the cytoplasm to the nucleus. Transient-state kinetic experiments illustrate that the first phosphate is added rapidly onto the RS domain of SRSF1 (t1/2 = 0.1 sec) followed by slower, multi-site phosphorylation at the remaining serines (t1/2 = 15 sec). Mutagenesis experiments suggest that efficient phosphorylation rates are maintained by an extensive hydrogen bonding and electrostatic network between the RS domain of the SR protein and the active site and docking groove of the kinase. Catalytic trapping and viscosometric experiments demonstrate that while the phosphoryl transfer step is fast, ADP release limits multi-site phosphorylation. By studying phosphate incorporation into selectively pre-phosphorylated forms of the enzyme-substrate complex, the kinetic mechanism for site-specific phosphorylation along the reaction coordinate was assessed. The binding affinity of the SR protein, the phosphoryl transfer rate and ADP exchange rate were found to decline significantly as a function of progressive phosphorylation in the RS domain. These findings indicate that the protein substrate actively modulates initiation, extension and termination events associated with prolonged, multi-site phosphorylation. PMID:21728354

Duplex and triplex formation of mixed pyrimidine oligonucleotides with stacking of phenyl-triazole moieties in the major groove.

PubMed

Andersen, Nicolai Krog; Døssing, Holger; Jensen, Frank; Vester, Birte; Nielsen, Poul

2011-08-05

5-(1-Phenyl-1,2,3-triazol-4-yl)-2'-deoxycytidine was synthesized from a modified CuAAC protocol and incorporated into mixed pyrimidine oligonucleotide sequences together with the corresponding 5-(1-phenyl-1,2,3-triazol-4-yl)-2'-deoxyuridine. With consecutive incorporations of the two modified nucleosides, improved duplex formation with a complementary RNA and improved triplex formation with a complementary DNA duplex were observed. The improvement is due to π-π stacking of the phenyl-triazole moieties in the major groove. The strongest stacking and most pronounced positive influence on thermal stability was found in between the uridine analogues or with the cytidine analogue placed in the 3' direction to the uridine analogue. Modeling indicated a different orientation of the phenyl-triazole moieties in the major groove to account for the difference between the two nucleotides. The modified oligonucleotides were all found to be significantly stabilized toward nucleolytic degration.

Testing of a single graded groove variable conductance heat pipe

NASA Astrophysics Data System (ADS)

Kapolnek, Michael R.; Holmes, H. R.; Hager, Brian

1992-07-01

Variable conductance heat pipes (VCHPs) with transport capacities in the 50,000 to 100,000 Watt-inch range will be required to transport the large heat loads anticipated for advanced spacecraft. A high-reliability, nonarterial constant conductance heat pipe with this capacity, the Single Graded Groove (SGG) heat pipe, was developed for NASA's Space Station Freedom. The design and testing of a variable conductance SGG heat pipe are described. Response of the pipe to startup and heat load changes was excellent. After correcting for condenser temperature changes, the evaporator temperature varied by only +/- 4 F for large evaporator heat load changes. The surface tension difference between ends of the gas blocked region was found to measurably affect the performance of the pipe. Performance was negligibly affected by Marangoni flow in the gas blocked region.

Forming Ganymede's grooves at smaller strain: Toward a self-consistent local and global strain history for Ganymede

NASA Astrophysics Data System (ADS)

Bland, Michael T.; McKinnon, William B.

2015-01-01

The ubiquity of tectonic features formed in extension, and the apparent absence of ones formed in contraction, has led to the hypothesis that Ganymede has undergone global expansion in its past. Determining the magnitude of such expansion is challenging however, and extrapolation of locally or regionally inferred strains to global scales often results in strain estimates that exceed those based on global constraints. Here we use numerical simulations of groove terrain formation to develop a strain history for Ganymede that is generally consistent at local, regional, and global scales. These simulations reproduce groove-like amplitudes, wavelengths, and average slopes at modest regional extensions (10-15%). The modest strains are more consistent with global constraints on Ganymede's expansion. Yet locally, we also find that surface strains can be much larger (30-60%) in the same simulations, consistent with observations of highly-extended impact craters. Thus our simulations satisfy both the smallest-scale and largest-scale inferences of strain on Ganymede. The growth rate of the topography is consistent with (or exceeds) predictions of analytical models, and results from the use of a non-associated plastic rheology that naturally permits localization of brittle failure (plastic strain) into linear fault-like shear zones. These fault-like zones are organized into periodically-spaced graben-like structures with stepped, steeply-dipping faults. As in previous work, groove amplitudes and wavelengths depend on both the imposed heat flux and surface temperature, but because our brittle strength increases with depth, we find (for the parameters explored) that the growth rate of topography is initially faster for lower heat flows. We observe a transition to narrow rifting for higher heat flows and larger strains, which is a potential pathway for breakaway margin or band formation.

Facebook, Twitter Activities Sites, Location and Students' Interest in Learning

ERIC Educational Resources Information Center

Igbo, J. N.; Ezenwaji, Ifeyinwa; Ajuziogu, Christiana U.

2018-01-01

This study was carried out to ascertain the influence of social networking sites activities (twitter and Facebook) on secondary school students' interest in learning It also considered the impact of these social networking sites activities on location of the students. Two research questions and two null hypotheses guided the study. Mean and…

Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 1

PubMed Central

2016-01-01

Serum paraoxonase 1 (PON1) is a native lactonase capable of promiscuously hydrolyzing a broad range of substrates, including organophosphates, esters, and carbonates. Structurally, PON1 is a six-bladed β-propeller with a flexible loop (residues 70–81) covering the active site. This loop contains a functionally critical Tyr at position 71. We have performed detailed experimental and computational analyses of the role of selected Y71 variants in the active site stability and catalytic activity in order to probe the role of Y71 in PON1’s lactonase and organophosphatase activities. We demonstrate that the impact of Y71 substitutions on PON1’s lactonase activity is minimal, whereas the kcat for the paraoxonase activity is negatively perturbed by up to 100-fold, suggesting greater mutational robustness of the native activity. Additionally, while these substitutions modulate PON1’s active site shape, volume, and loop flexibility, their largest effect is in altering the solvent accessibility of the active site by expanding the active site volume, allowing additional water molecules to enter. This effect is markedly more pronounced in the organophosphatase activity than the lactonase activity. Finally, a detailed comparison of PON1 to other organophosphatases demonstrates that either a similar “gating loop” or a highly buried solvent-excluding active site is a common feature of these enzymes. We therefore posit that modulating the active site hydrophobicity is a key element in facilitating the evolution of organophosphatase activity. This provides a concrete feature that can be utilized in the rational design of next-generation organophosphate hydrolases that are capable of selecting a specific reaction from a pool of viable substrates. PMID:28026940

Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 1.

PubMed

Blaha-Nelson, David; Krüger, Dennis M; Szeler, Klaudia; Ben-David, Moshe; Kamerlin, Shina Caroline Lynn

2017-01-25

Serum paraoxonase 1 (PON1) is a native lactonase capable of promiscuously hydrolyzing a broad range of substrates, including organophosphates, esters, and carbonates. Structurally, PON1 is a six-bladed β-propeller with a flexible loop (residues 70-81) covering the active site. This loop contains a functionally critical Tyr at position 71. We have performed detailed experimental and computational analyses of the role of selected Y71 variants in the active site stability and catalytic activity in order to probe the role of Y71 in PON1's lactonase and organophosphatase activities. We demonstrate that the impact of Y71 substitutions on PON1's lactonase activity is minimal, whereas the k cat for the paraoxonase activity is negatively perturbed by up to 100-fold, suggesting greater mutational robustness of the native activity. Additionally, while these substitutions modulate PON1's active site shape, volume, and loop flexibility, their largest effect is in altering the solvent accessibility of the active site by expanding the active site volume, allowing additional water molecules to enter. This effect is markedly more pronounced in the organophosphatase activity than the lactonase activity. Finally, a detailed comparison of PON1 to other organophosphatases demonstrates that either a similar "gating loop" or a highly buried solvent-excluding active site is a common feature of these enzymes. We therefore posit that modulating the active site hydrophobicity is a key element in facilitating the evolution of organophosphatase activity. This provides a concrete feature that can be utilized in the rational design of next-generation organophosphate hydrolases that are capable of selecting a specific reaction from a pool of viable substrates.

Characterization of the active site properties of CYP4F12.

PubMed

Eksterowicz, John; Rock, Dan A; Rock, Brooke M; Wienkers, Larry C; Foti, Robert S

2014-10-01

Cytochrome P450 4F12 is a drug-metabolizing enzyme that is primarily expressed in the liver, kidney, colon, small intestine, and heart. The properties of CYP4F12 that may impart an increased catalytic selectivity (decreased promiscuity) were explored through in vitro metabolite elucidation, kinetic isotope effect experiments, and computational modeling of the CYP4F12 active site. By using astemizole as a probe substrate for CYP4F12 and CYP3A4, it was observed that although CYP4F12 favored astemizole O-demethylation as the primary route of metabolism, CYP3A4 was capable of metabolizing astemizole at multiple sites on the molecule. Deuteration of astemizole at the site of O-demethylation resulted in an isotope effect of 7.1 as well as an 8.3-fold decrease in the rate of clearance for astemizole by CYP4F12. Conversely, although an isotope effect of 3.8 was observed for the formation of the O-desmethyl metabolite when deuterated astemizole was metabolized by CYP3A4, there was no decrease in the clearance of astemizole. Development of a homology model of CYP4F12 based on the crystal structure of cytochrome P450 BM3 predicted an active site volume for CYP4F12 that was approximately 76% of the active site volume of CYP3A4. As predicted, multiple favorable binding orientations were available for astemizole docked into the active site of CYP3A4, but only a single binding orientation with the site of O-demethylation oriented toward the heme was identified for CYP4F12. Overall, it appears that although CYP4F12 may be capable of binding similar ligands to other cytochrome P450 enzymes such as CYP3A4, the ability to achieve catalytically favorable orientations may be inherently more difficult because of the increased steric constraints of the CYP4F12 active site. Copyright © 2014 by The American Society for Pharmacology and Experimental Therapeutics.

Deletion of loop fragment adjacent to active site diminishes the stability and activity of exo-inulinase.

PubMed

Arjomand, Maryam Rezaei; Habibi-Rezaei, Mehran; Ahmadian, Gholamreza; Hassanzadeh, Malihe; Karkhane, Ali Asghar; Asadifar, Mandana; Amanlou, Massoud

2016-11-01

Inulinases are classified as hydrolases and widely used in the food and medical industries. Here, we report the deletion of a six-membered adjacent active site loop fragment ( 74 YGSDVT 79 sequence) from third Ω-loop of the exo-inulinase containing aspartate residue from Aspergillus niger to study its structural and functional importance. Site-directed mutagenesis was used to create the mutant of the exo-inulinase (Δ6SL). To investigate the stability of the region spanning this loop, MD simulations were performed 80ns for 20-85 residues. Molecular docking was performed to compare the interactions in the active sites of enzymes with fructose as a ligand. Accordingly, the functional thermostability of the exo-inulinase was significantly decreased upon loop fragment deletion. Evaluation of the kinetics parameters (V max , K m , k cat and, k cat /K m ) and activation energy (E a ) of the catalysis of enzymes indicated the importance of the deleted sequence on the catalytic performance of the enzyme. In conclusion, six-membered adjacent active site loop fragment not only plays a crucial role in the stability of the enzyme, but also it involves in the enzyme catalysis through lowering the activation energy of the catalysis and effective improving the catalytic performance. Copyright © 2016. Published by Elsevier B.V.

The C-terminal helix of ribosomal P stalk recognizes a hydrophobic groove of elongation factor 2 in a novel fashion.

PubMed

Tanzawa, Takehito; Kato, Koji; Girodat, Dylan; Ose, Toyoyuki; Kumakura, Yuki; Wieden, Hans-Joachim; Uchiumi, Toshio; Tanaka, Isao; Yao, Min

2018-04-06

Archaea and eukaryotes have ribosomal P stalks composed of anchor protein P0 and aP1 homodimers (archaea) or P1•P2 heterodimers (eukaryotes). These P stalks recruit translational GTPases to the GTPase-associated center in ribosomes to provide energy during translation. The C-terminus of the P stalk is known to selectively recognize GTPases. Here we investigated the interaction between the P stalk and elongation factor 2 by determining the structures of Pyrococcus horikoshii EF-2 (PhoEF-2) in the Apo-form, GDP-form, GMPPCP-form (GTP-form), and GMPPCP-form bound with 11 C-terminal residues of P1 (P1C11). Helical structured P1C11 binds to a hydrophobic groove between domain G and subdomain G' of PhoEF-2, where is completely different from that of aEF-1α in terms of both position and sequence, implying that such interaction characteristic may be requested by how GTPases perform their functions on the ribosome. Combining PhoEF-2 P1-binding assays with a structural comparison of current PhoEF-2 structures and molecular dynamics model of a P1C11-bound GDP form, the conformational changes of the P1C11-binding groove in each form suggest that in response to the translation process, the groove has three states: closed, open, and release for recruiting and releasing GTPases.

The Crystal Structure of a Quercetin 2,3-Dioxygenase from Bacillus subtilis Suggests Modulation of Enzyme Activity by a Change in the Metal Ion at the Active Site(s)

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

Gopal, B.; Madan, Lalima L.; Betz, Stephen F.

2010-11-10

Common structural motifs, such as the cupin domains, are found in enzymes performing different biochemical functions while retaining a similar active site configuration and structural scaffold. The soil bacterium Bacillus subtilis has 20 cupin genes (0.5% of the total genome) with up to 14% of its genes in the form of doublets, thus making it an attractive system for studying the effects of gene duplication. There are four bicupins in B. subtilis encoded by the genes yvrK, yoaN, yxaG, and ywfC. The gene products of yvrK and yoaN function as oxalate decarboxylases with a manganese ion at the active site(s),more » whereas YwfC is a bacitracin synthetase. Here we present the crystal structure of YxaG, a novel iron-containing quercetin 2,3-dioxygenase with one active site in each cupin domain. Yxag is a dimer, both in solution and in the crystal. The crystal structure shows that the coordination geometry of the Fe ion is different in the two active sites of YxaG. Replacement of the iron at the active site with other metal ions suggests modulation of enzymatic activity in accordance with the Irving-Williams observation on the stability of metal ion complexes. This observation, along with a comparison with the crystal structure of YvrK determined recently, has allowed for a detailed structure-function analysis of the active site, providing clues to the diversification of function in the bicupin family of proteins.« less

Grooved Glaucoma Drainage Devices That Continuously Deliver Cyclosporine A Decrease Postsurgical Scar Formation in Rabbit Eyes.

PubMed

Dai, Zhaoxing; Yu, Xiaobo; Sun, Jianguo; Sun, Xinghuai

2017-03-01

To study the functional outcomes of filtration surgery by implanting improved glaucoma drainage devices (GDDs) comprising surface grooves and a composite coating of cyclosporine A (CsA) and PLGA in experimental rabbit eyes. Improved GDDs were designed and prepared by modifying normal GDD with surface grooves and a CsA-PLGA composite coating. Normal GDDs, grooved GDDs (G-GDDs), and G-GDDs with a CsA-PLGA composite coating (CsA@G-GDD) were implanted into 18 rabbit eyes (six eyes per group). The intraocular pressure (IOP), bleb survival time, bleb morphology, and anterior chamber reactions were assessed for up to 12 weeks after GDD implantation. The IOPs were compared statistically among the three groups. Bleb morphology was quantified using the Indiana Bleb Appearance Grading Scale. Anterior chamber radiography was performed to check whether the filtrating pathway was blocked, and determine the drainage time and diffusion area of the contrast agent. Hematoxylin and eosin staining and immunohistochemistry were conducted to assess how the GDDs slowed or prevented scar formation. The improved GDDs were successfully prepared and implanted in 18 rabbit eyes without severe surgical complications. Bleb survival time was significantly longer and IOP was significantly lower in the G-GDD and CsA@G-GDD groups compared with the GDD group (all, P < 0.001). Blebs were significantly higher in the CsA@G-GDD group than in the GDD and G-GDD groups (P = 0.003). Anterior chamber radiography revealed more unobstructed filtration channels in the CsA@G-GDD group than in the GDD group (P = 0.032). Postsurgical scar formation was less extensive in the G-GDD and CsA@G-GDD groups than in the GDD group. Compared with the normal GDDs, G-GDDs with a CsA-PLGA coating inhibited postsurgical scar formation and improved the surgical success rate, and might represent an alternative to existing glaucoma filtration devices.

Traction suture modification to tongue-in-groove caudal septoplasty.

PubMed

Indeyeva, Y A; Lee, T S; Gordin, E; Chan, D; Ducic, Y

2018-02-01

Caudal septal deviation leads to unfavorable esthetic as well as functional effects on the nasal airway. A modification to the tongue-in-groove (TIG) technique to correct these caudal septal deformities is described. With placement of a temporary suspension suture to the caudal septum, manual traction is applied, assuring that the caudal septum remains in the midline position while it is being secured with multiple through-and-through, trans-columellar and trans-septal sutures. From 2003 to 2016, 148 patients underwent endonasal septoplasty using this modified technique, with excellent functional and cosmetic outcomes and a revision rate of 1.4%. This modified TIG technique replaces the periosteal suture that secures the caudal septum to the midline nasal crest in the original TIG technique. This simplifies the procedure and minimizes the risk of securing the caudal septum off-midline when used in endonasal septoplasty. Copyright © 2017 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Identification of Residues in the Lipopolysaccharide ABC Transporter That Coordinate ATPase Activity with Extractor Function

PubMed Central

Simpson, Brent W.; Owens, Tristan W.; Orabella, Matthew J.; Davis, Rebecca M.; May, Janine M.; Trauger, Sunia A.

2016-01-01

ABSTRACT The surface of most Gram-negative bacteria is covered with lipopolysaccharide (LPS), creating a permeability barrier against toxic molecules, including many antimicrobials. To assemble LPS on their surface, Gram-negative bacteria must extract newly synthesized LPS from the inner membrane, transport it across the aqueous periplasm, and translocate it across the outer membrane. The LptA to -G proteins assemble into a transenvelope complex that transports LPS from the inner membrane to the cell surface. The Lpt system powers LPS transport from the inner membrane by using a poorly characterized ATP-binding cassette system composed of the ATPase LptB and the transmembrane domains LptFG. Here, we characterize a cluster of residues in the groove region of LptB that is important for controlling LPS transport. We also provide the first functional characterization of LptFG and identify their coupling helices that interact with the LptB groove. Substitutions at conserved residues in these coupling helices compromise both the assembly and function of the LptB2FG complex. Defects in LPS transport conferred by alterations in the LptFG coupling helices can be rescued by changing a residue in LptB that is adjacent to functionally important residues in the groove region. This suppression is achieved by increasing the ATPase activity of the LptB2FG complex. Taken together, these data identify a specific binding site in LptB for the coupling helices of LptFG that is responsible for coupling of ATP hydrolysis by LptB with LptFG function to achieve LPS extraction. PMID:27795402

A hybrid QM/MM simulation study of intramolecular proton transfer in the pyridoxal 5'-phosphate in the active site of transaminase: influence of active site interaction on proton transfer.

PubMed

Dutta Banik, Sindrila; Chandra, Amalendu

2014-09-25

Pyridoxal 5'-phosphate (PLP) Schiff base, a versatile cofactor, exhibits a tautomeric equilibrium that involves an intramolecular proton transfer between the N-protonated zwitterionic ketoenamine tautomer and the O-protonated covalent enolimine tautomer. It has been postulated that for the catalytic activity, the PLP has to be in the zwitterionic ketoenamine tautomeric form. However, the exact position of the tautomeric equilibrium of Schiff base in the active site of PLP-dependent enzyme is not known yet. In the present work, we investigated the tautomeric equilibrium for the external aldimine state of PLP aspartate (PLP-Asp) Schiff base in the active site of aspartate aminotransferase (AspAT) using combined quantum mechanical and molecular mechanical simulations. The main focus of the present study is to analyze the factors that control the tautomeric equilibrium in the active sites of various PLP-dependent enzymes. The results show that the ketoenamine tautomer is more preferred than the enolimine tautomer both in the gas and aqueous phases as well as in the active site of AspAT. Current simulations show that the active site of AspAT is more suitable for the ketoenamine tautomer compared to the enolimine tautomer. Interestingly, the Tyr225 acts as a proton donor to the phenolic oxygen in the ketoenamine tautomer, while in the covalent enolimine tautomer, it acts as a proton acceptor to the phenolic oxygen. Finally, the metadynamics study confirms this result. The calculated free energy barrier is about 7.5 kcal/mol. A comparative analysis of the microenvironment created by the active site residues of three different PLP-dependent enzymes (aspartate aminotransferase, Dopa decarboxylase, and Ala-racemase) has been carried out to understand the controlling factor(s) of the tautomeric equilibrium. The analysis shows that the intermolecular hydrogen bonding between active site residues and the phenolic oxygen of PLP shifts the tautomeric equilibrium toward the N