Molecular dynamics simulations of high energy cascade in ordered alloys: Defect production and subcascade division

Energy Technology Data Exchange (ETDEWEB)

Crocombette, Jean-Paul, E-mail: jpcrocombette@cea.fr [CEA, DEN, Service de Recherches de Métallurgie Physique, UPSay, F-91191 Gif-sur-Yvette (France); Van Brutzel, Laurent [CEA, DEN, Service de Corrosion et du Comportement des Matériaux dans leur Environnement, UPSay, F-91191 Gif-sur-Yvette (France); Simeone, David [CEA, DEN, Service de Recherches de Métallurgie Appliqué, Matériaux Fonctionnels pour l' Energie, CNRS-CEA-ECP, UPSay, F-91191 Gif-sur-Yvette (France); Luneville, Laurence [CEA, DEN, Service d' Etudes des Réacteurs et de Mathématiques Appliquées, Matériaux Fonctionnels pour l' Energie, CNRS-CEA-ECP, UPSay, F-91191 Gif-sur-Yvette (France)

2016-06-15

Displacement cascades have been calculated in two ordered alloys (Ni{sub 3}Al and UO{sub 2}) in the molecular dynamics framework using the CMDC (Cell Molecular Dynamics for Cascade) code (J.-P. Crocombette and T. Jourdan, Nucl. Instrum. Meth. B 352, 9 (2015)) for energies ranking between 0.1 and 580 keV. The defect production has been compared to the prediction of the NRT (Norgett, Robinson and Torrens) standard. One observes a decrease with energy of the number of defects compared to the NRT prediction at intermediate energies but, unlike what is commonly observed in elemental solids, the number of produced defects does not always turn to a linear variation with ballistic energy at high energies. The fragmentation of the cascade into subcascades has been studied through the analysis of surviving defect pockets. It appears that the common knowledge equivalence of linearity of defect production and subcascades division does not hold in general for alloys. We calculate the average number of subcascades and average number of defects per subcascades as a function of ballistic energy. We find an unexpected variety of behaviors for these two average quantities above the threshold for subcascade formation.

Molecular dynamics simulations of high energy cascade in ordered alloys: Defect production and subcascade division

International Nuclear Information System (INIS)

Crocombette, Jean-Paul; Van Brutzel, Laurent; Simeone, David; Luneville, Laurence

2016-01-01

Displacement cascades have been calculated in two ordered alloys (Ni_3Al and UO_2) in the molecular dynamics framework using the CMDC (Cell Molecular Dynamics for Cascade) code (J.-P. Crocombette and T. Jourdan, Nucl. Instrum. Meth. B 352, 9 (2015)) for energies ranking between 0.1 and 580 keV. The defect production has been compared to the prediction of the NRT (Norgett, Robinson and Torrens) standard. One observes a decrease with energy of the number of defects compared to the NRT prediction at intermediate energies but, unlike what is commonly observed in elemental solids, the number of produced defects does not always turn to a linear variation with ballistic energy at high energies. The fragmentation of the cascade into subcascades has been studied through the analysis of surviving defect pockets. It appears that the common knowledge equivalence of linearity of defect production and subcascades division does not hold in general for alloys. We calculate the average number of subcascades and average number of defects per subcascades as a function of ballistic energy. We find an unexpected variety of behaviors for these two average quantities above the threshold for subcascade formation.

Molecular defects of the growth hormone receptor gene, including a new mutation, in Laron syndrome patients in Israel: relationship between defects and ethnic groups.

Science.gov (United States)

Shevah, Orit; Rubinstein, Menachem; Laron, Zvi

2004-10-01

Laron Syndrome, first described in Israel, is a form of dwarfism similar to isolated growth hormone deficiency caused by molecular defects in the GH receptor gene. To characterize the molecular defects of the GH-R in Laron syndrome patients followed in our clinic. Of the 63 patients in the cohort, we investigated 31 patients and 32 relatives belonging to several ethnic origins. Molecular analysis of the GH-R gene was performed using the single strand conformation polymorphism and DNA sequencing techniques. Eleven molecular defects including a novel mutation were found. Twenty-two patients carried mutations in the extracellular domain, one in the transmembrane domain, and 3 siblings with typical Laron syndrome presented a normal GH-R. Of interest are, on one hand, different mutations within the same ethnic groups: W-15X and 5, 6 exon deletion in Jewish-Iraqis, and E180 splice and 5, 6 exon deletion in Jewish-Moroccans; and on the other hand, identical findings in patients from distinct regions: the 785-1 G to T mutation in an Israeli-Druze and a Peruvian patient. A polymorphism in exon 6, Gly168Gly, was found in 15 probands. One typical Laron patient from Greece was heterozygous for R43X in exon 4 and heterozygous for Gly168Gly. In addition, a novel mutation in exon 5: substitution of T to G replacing tyrosine 86 for aspartic acid (Y86D) is described. This study demonstrates: a) an increased focal incidence of Laron syndrome in different ethnic groups from our area with a high incidence of consanguinity; and b) a relationship between molecular defects of the GH-R, ethnic group and geographic area.

Molecular marker studies in riverine buffaloes, for characterization and diagnosis of genetic defects

International Nuclear Information System (INIS)

Yadav, B.R.

2005-01-01

The buffalo is probably the last livestock species to have been domesticated, with many genetic, physiological and behavioural traits not yet well understood. Molecular markers have been used for characterizing animals and breeds, diagnosing diseases and identifying anatomical and physiological anomalies. RFLP studies showed low heterozygosity, but genomic and oligonucleotide probes showed species-specific bands useful for identification of carcass or other unknown samples. Use of RAPD revealed band frequencies, band sharing frequencies, genetic distances, and genetic and identity indexes in different breeds. Bovine microsatellite primers indicate that 70.9% of bovine loci were conserved in buffalo. Allele numbers, sizes, frequencies, heterozygosity and polymorphism information content showed breed-specific patterns. Different marker types - genomic and oligonucleotide probes, RAPD and microsatellites - are useful in parent identification. Individual specific DNA fingerprinting techniques were applied with twin-born animal (XX/XY) chimerism, sex identification, anatomically defective and XO individuals. Molecular markers are a potential tool for geneticists and breeders to evaluate existing germplasm and to manipulate it to develop character-specific strains and to provide the basis for effective genetic conservation. (author)

Displacement cascades and defects annealing in tungsten, Part I: Defect database from molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Setyawan, Wahyu [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Nandipati, Giridhar [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Roche, Kenneth J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Univ. of Washington, Seattle, WA (United States); Heinisch, Howard L. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Wirth, Brian D. [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab., Oak Ridge, TN (United States); Kurtz, Richard J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

2015-07-01

Molecular dynamics simulations have been used to generate a comprehensive database of surviving defects due to displacement cascades in bulk tungsten. Twenty-one data points of primary knock-on atom (PKA) energies ranging from 100 eV (sub-threshold energy) to 100 keV (~780^×_Ed, where _Ed = 128 eV is the average displacement threshold energy) have been completed at 300 K, 1025 K and 2050 K. Within this range of PKA energies, two regimes of power-law energy-dependence of the defect production are observed. A distinct power-law exponent characterizes the number of Frenkel pairs produced within each regime. The two regimes intersect at a transition energy which occurs at approximately 250^×_Ed. The transition energy also marks the onset of the formation of large self-interstitial atom (SIA) clusters (size 14 or more). The observed defect clustering behavior is asymmetric, with SIA clustering increasing with temperature, while the vacancy clustering decreases. This asymmetry increases with temperature such that at 2050 K (~0.5_Tm) practically no large vacancy clusters are formed, meanwhile large SIA clusters appear in all simulations. The implication of such asymmetry on the long-term defect survival and damage accumulation is discussed. In addition, <100> {110} SIA loops are observed to form directly in the highest energy cascades, while vacancy <100> loops are observed to form at the lowest temperature and highest PKA energies, although the appearance of both the vacancy and SIA loops with Burgers vector of <100> type is relatively rare.

Adsorption modes of molecular iodine on defected boron nitrides: A DFT study

Science.gov (United States)

Arabieh, Masoud; Azar, Yavar Taghipour

2018-03-01

The interaction of molecular iodine with pristine and monovacant boron-nitride quantum dots (QDs) have been investigated using density functional theory. It was found that removing one B or N single atom significantly decreased the calculated Eg values at various exchange functional. In B-defected BN system, the localized spin densities canceled each other and overall polarization of system was found to be equal to unity. For N-defected system there was smaller spin densities localized on each closest B atoms. Both B- and N-vacancies caused appearance of new states in gap region. Our calculation revealed that spin density and polarization of defected system are localized on vacancy region and other atoms did not take part in this polarization. The results of electron localization function for N-DBN showed there was high density region at the position of removed nitrogen atom. The calculated adsorption energies implied that there was no significant chemical interaction between iodine molecule and pristine BN sheet. We suggested that when a deficiency was imposed to the BN sheet, the reactivity of the modified system toward iodine molecule significantly could increase. We found strong interaction between iodine and nitrogen atoms of B-DBN system. In the case of I2/N-DBN system the neighbor atoms had no contribution in spin polarization of the system and it seemed that all spin density of system transferred to the iodine molecule after adsorption. Strong correlation between molecular iodine orientation and BN-QDs via their interactions type has been clarified in this work. These findings may provide a deeper insight into halogen molecules interactions with low dimensional defected boron nitrides.

Thermodynamical analyses of molecular simulations of dislocation-defect interactions: simulations at 0 K

International Nuclear Information System (INIS)

Monnet, G.

2008-01-01

Full text of publication follows. Static molecular (SM) simulations of dislocation-defect interaction are analysed through a framework of different interaction regimes, in which the applied work has different roles. In most regimes, the applied work is transformed into elastic energy, a dissipative energy resulting from the lattice friction and a large quantity of energy needed to enable the dislocation to bow out when it is pinned by the defect. While the dissipative work is entirely evacuated in SM simulations, the elastic and curvature energies contribute to a large increase of the internal energy of the system. A method is presented in this work to evaluate the curvature energy and the result is compared to prediction of the line tension model. These analyses allow the determination of the dislocation-defect interaction energy. (author)

A large-scale molecular dynamics study of the divacancy defect in graphene

International Nuclear Information System (INIS)

Leyssale, Jean-Marc; Vignoles, Gerard L.

2014-01-01

We report on the dynamical behavior of single divacancy defects in large graphene sheets as studied by extensive classical molecular dynamics (MD) simulations at high temperatures and static calculations. In the first part of the paper, the ability of the used interatomic potential to properly render the stability and dynamics (energy barriers) of such defects is validated against electronic structure calculations from the literature. Then, results from MD simulations are presented. In agreement with recent TEM studies, some mobility is observed through a series of Stone-Wales-like bond rotations involving the 5-8-5, 555-777, and 5555-6-7777 reconstructions. Although these three structures are by far the most probable structures of the DV defect, not less than 18 other full reconstructions, including the experimentally observed 55-66-77 defect, were occasionally observed in the ∼1.5 μs of MD trajectories analyzed in this work. Most of these additional reconstructions have moderate formation energies and can be formed by a bond rotation mechanism from one of the aforementioned structures, with a lower activation energy than the one required to form a Stone-Wales defect in graphene. Therefore their future experimental observation is highly probable. The results presented here also suggest that the barrier to a conventional Stone-Wales transformation (the formation of two pentagon/heptagon pairs from four hexagons) can be significantly reduced in the vicinity of an existing defect, strengthening a recently proposed melting mechanism for graphene based on the aggregation of Stone-Wales defects. From a structural point of view, in addition to pentagons, heptagons, and octagons, these new DV reconstructions can also contain four- and nine-member rings and show a particularly large spatial extent of up to 13 rings (42 atoms) against three (14 atoms) for the original 5-8-5 defect. (authors)

A targeted sequencing panel identifies rare damaging variants in multiple genes in the cranial neural tube defect, anencephaly.

Science.gov (United States)

Ishida, M; Cullup, T; Boustred, C; James, C; Docker, J; English, C; Lench, N; Copp, A J; Moore, G E; Greene, N D E; Stanier, P

2018-04-01

Neural tube defects (NTDs) affecting the brain (anencephaly) are lethal before or at birth, whereas lower spinal defects (spina bifida) may lead to lifelong neurological handicap. Collectively, NTDs rank among the most common birth defects worldwide. This study focuses on anencephaly, which despite having a similar frequency to spina bifida and being the most common type of NTD observed in mouse models, has had more limited inclusion in genetic studies. A genetic influence is strongly implicated in determining risk of NTDs and a molecular diagnosis is of fundamental importance to families both in terms of understanding the origin of the condition and for managing future pregnancies. Here we used a custom panel of 191 NTD candidate genes to screen 90 patients with cranial NTDs (n = 85 anencephaly and n = 5 craniorachischisis) with a targeted exome sequencing platform. After filtering and comparing to our in-house control exome database (N = 509), we identified 397 rare variants (minor allele frequency, MAF < 1%), 21 of which were previously unreported and predicted damaging. This included 1 frameshift (PDGFRA), 2 stop-gained (MAT1A; NOS2) and 18 missense variations. Together with evidence for oligogenic inheritance, this study provides new information on the possible genetic causation of anencephaly. © 2017 The Authors. Clinical Genetics published by John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Role of the bond defect for structural transformations between crystalline and amorphous silicon: A molecular-dynamics study

International Nuclear Information System (INIS)

Stock, D. M.; Weber, B.; Gaertner, K.

2000-01-01

The relation between the bond defect, which is a topological defect, and structural transformations between crystalline and amorphous silicon, is studied by molecular-dynamics simulations. The investigation of 1-keV boron implantation into crystalline silicon proves that the bond defect can also be generated directly by collisional-induced bond switching in addition to its formation by incomplete recombination of primary defects. This supports the assumption that the bond defect may play an important role in the amorphization process of silicon by light ions. The analysis of the interface between (001) silicon and amorphous silicon shows that there are two typical defect configurations at the interface which result from two different orientations of the bond defect with respect to the interface. Thus the bond defect appears to be a characteristic structural feature of the interface. Moreover, annealing results indicate that the bond defect acts as a growth site for interface-mediated crystallization

Defective Glycinergic Synaptic Transmission in Zebrafish Motility Mutants

OpenAIRE

Hirata, Hiromi; Carta, Eloisa; Yamanaka, Iori; Harvey, Robert J.; Kuwada, John Y.

2010-01-01

Glycine is a major inhibitory neurotransmitter in the spinal cord and brainstem. Recently, in vivo analysis of glycinergic synaptic transmission has been pursued in zebrafish using molecular genetics. An ENU mutagenesis screen identified two behavioral mutants that are defective in glycinergic synaptic transmission. Zebrafish bandoneon (beo) mutants have a defect in glrbb, one of the duplicated glycine receptor (GlyR) β subunit genes. These mutants exhibit a loss of glycinergic synaptic ...

A molecular dynamics simulation study of irradiation induced defects in gold nanowire

Science.gov (United States)

Liu, Wenqiang; Chen, Piheng; Qiu, Ruizhi; Khan, Maaz; Liu, Jie; Hou, Mingdong; Duan, Jinglai

2017-08-01

Displacement cascade in gold nanowires was studied using molecular dynamics computer simulations. Primary knock-on atoms (PKAs) with different kinetic energies were initiated either at the surface or at the center of the nanowires. We found three kinds of defects that were induced by the cascade, including point defects, stacking faults and crater at the surface. The starting points of PKAs influence the number of residual point defects, and this consequently affect the boundary of anti-radiation window which was proposed by calculation of diffusion of point defects to the free surface of nanowires. Formation of stacking faults that expanded the whole cross-section of gold nanowires was observed when the PKA's kinetic energy was higher than 5 keV. Increasing the PKA's kinetic energy up to more than 10 keV may lead to the formation of crater at the surface of nanowires due to microexplosion of hot atoms. At this energy, PKAs started from the center of nanowires can also result in the creation of crater because length of cascade region is comparable to diameter of nanowires. Both the two factors, namely initial positions of PKAs as well as the craters induced by higher energy irradiation, would influence the ability of radiation resistance of metal nanowires.

Identifying the influence of the intrinsic defects in Gd-doped ZnO thin-films

KAUST Repository

Flemban, Tahani H.; Sequeira, M. C.; Zhang, Z.; Venkatesh, S.; Alves, E.; Lorenz, K.; Roqan, Iman S.

2016-01-01

Gd-doped ZnO thin films were prepared using pulsed laser deposition at different oxygen pressures and varied Gd concentrations. The effects of oxygen deficiency-related defects on the Gd incorporation, optical and structural properties, were explored by studying the impact of oxygen pressure during deposition and post-growth thermal annealing in vacuum. Rutherford Backscattering Spectrometry revealed that the Gd concentration increases with increasing oxygen pressure for samples grown with the same Gd-doped ZnO target. Unexpectedly, the c-lattice parameter of the samples tends to decrease with increasing Gd concentration, suggesting that Gd-defect complexes play an important role in the structural properties. Using low-temperature photoluminescence(PL), Raman measurements and density functional theory calculations, we identified oxygen vacancies as the dominant intrinsic point defects. PL spectra show a defect band related to oxygen vacancies for samples grown at oxygen deficiency.

Identifying the influence of the intrinsic defects in Gd-doped ZnO thin-films

KAUST Repository

Flemban, Tahani H.

2016-02-08

Gd-doped ZnO thin films were prepared using pulsed laser deposition at different oxygen pressures and varied Gd concentrations. The effects of oxygen deficiency-related defects on the Gd incorporation, optical and structural properties, were explored by studying the impact of oxygen pressure during deposition and post-growth thermal annealing in vacuum. Rutherford Backscattering Spectrometry revealed that the Gd concentration increases with increasing oxygen pressure for samples grown with the same Gd-doped ZnO target. Unexpectedly, the c-lattice parameter of the samples tends to decrease with increasing Gd concentration, suggesting that Gd-defect complexes play an important role in the structural properties. Using low-temperature photoluminescence(PL), Raman measurements and density functional theory calculations, we identified oxygen vacancies as the dominant intrinsic point defects. PL spectra show a defect band related to oxygen vacancies for samples grown at oxygen deficiency.

A comparison of neural tube defects identified by two independent routine recording systems for congenital malformations in Northern Ireland.

Science.gov (United States)

Nevin, N C; McDonald, J R; Walby, A L

1978-12-01

The efficiency of two systems for recording congenital malformations has been compared; one system, the Registrar General's Congenital Malformation Notification, is based on registering all malformed infants, and the other, the Child Health System, records all births. In Northern Ireland for three years [1974--1976], using multiple sources of ascertainment, a total of 686 infants with neural tube defects was identified among 79 783 live and stillbirths. The incidence for all neural tube defects in 8 60 per 1 000 births. The Registrar General's Congenital Malformation Notification System identified 83.6% whereas the Child Health System identified only 63.3% of all neural tube defects. Both systems together identified 86.2% of all neural tube defects. The two systems are suitable for monitoring of malformations and the addition of information from the Genetic Counselling Clinics would enhance the data for epidemiological studies.

Threshold defect production in silicon determined by density functional theory molecular dynamics simulations

International Nuclear Information System (INIS)

Holmstroem, E.; Kuronen, A.; Nordlund, K.

2008-01-01

We studied threshold displacement energies for creating stable Frenkel pairs in silicon using density functional theory molecular dynamics simulations. The average threshold energy over all lattice directions was found to be 36±2 STAT ±2 SYST eV, and thresholds in the directions and were found to be 20±2 SYST eV and 12.5±1.5 SYST eV, respectively. Moreover, we found that in most studied lattice directions, a bond defect complex is formed with a lower threshold than a Frenkel pair. The average threshold energy for producing either a bond defect or a Frenkel pair was found to be 24±1 STAT ±2 SYST eV

Array-based molecular karyotyping in 115 VATER/VACTERL and VATER/VACTERL-like patients identifies disease-causing copy number variations.

Science.gov (United States)

Zhang, Rong; Marsch, Florian; Kause, Franziska; Degenhardt, Franziska; Schmiedeke, Eeberhard; Märzheuser, Stefanie; Hoppe, Bernd; Bachour, Haitham; Boemers, Thomas M; Schäfer, Matthias; Spychalski, Nicole; Neser, Jörg; Leonhardt, Johannes; Kosch, Ferdinand; Ure, Benno; Gómez, Barbara; Lacher, Martin; Deffaa, Oliver J; Palta, Markus; Wittekindt, Boris; Kleine, Katharina; Schmedding, Andrea; Grasshoff-Derr, Sabine; Ven, Amelie van der; Heilmann-Heimbach, Stefanie; Zwink, Nadine; Jenetzky, Ekkehart; Ludwig, Michael; Reutter, Heiko

2017-07-17

The acronym VATER/VACTERL refers to the rare nonrandom association of the following component features (CF): vertebral defects (V), anorectal malformations (A), cardiac defects (C), tracheoesophageal fistula with or without esophageal atresia, renal malformations (R), and limb defects (L). Patients presenting with at least three CFs are diagnosed as having VATER/VACTERL association while patients presenting with only two CFs are diagnosed as having VATER/VACTERL-like phenotypes. Recently, rare causative copy number variations (CNVs) have been identified in patients with VATER/VACTERL association and VATER/VACTERL-like phenotypes. To detect further causative CNVs we performed array based molecular karyotyping in 75 VATER/VACTERL and 40 VATER/VACTERL-like patients. Following the application of stringent filter criteria, we identified 13 microdeletions and seven microduplications in 20 unrelated patients all of which were absent in 1,307 healthy inhouse controls (n microdeletion at 17q12 was confirmed to be de novo. Three microdeletions at 5q23.1, 16q23.3, 22q11.21, and one microduplication at 10q11.21 were all absent in the available parent. Microdeletion of chromosomal region 22q11.21 was previously found in VATER/VACTERL patients rendering it to be causative in our patient. The remaining 15 CNVs were inherited from a healthy parent. In two of 115 patients' causative CNVs were found (2%). The remaining identified rare CNVs represent candidates for further evaluation. Rare inherited CNVs may constitute modifiers of, or contributors to, multifactorial VATER/VACTERL or VATER/VACTERL-like phenotypes. Birth Defects Research 109:1063-1069, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Identifying Structural Flow Defects in Disordered Solids Using Machine-Learning Methods

Science.gov (United States)

Cubuk, E. D.; Schoenholz, S. S.; Rieser, J. M.; Malone, B. D.; Rottler, J.; Durian, D. J.; Kaxiras, E.; Liu, A. J.

2015-03-01

We use machine-learning methods on local structure to identify flow defects—or particles susceptible to rearrangement—in jammed and glassy systems. We apply this method successfully to two very different systems: a two-dimensional experimental realization of a granular pillar under compression and a Lennard-Jones glass in both two and three dimensions above and below its glass transition temperature. We also identify characteristics of flow defects that differentiate them from the rest of the sample. Our results show it is possible to discern subtle structural features responsible for heterogeneous dynamics observed across a broad range of disordered materials.

Molecular dynamics study of vacancy-like defects in a model glass : static behaviour

Science.gov (United States)

Delaye, J. M.; Limoge, Y.

1993-10-01

The possibility of defining vacancy-like defects in a Lennard-Jones glass is searched for in a systematic manner. Considering different relaxation levels of the same system, as well as different external pressures, we use a Molecular Dynamics simulation method, to study at constant volume or external pressure, the relaxation of a “piece” of glass, after the sudden removal of an atom. Three typical kinds of behaviour can be observed: the persistence of the empty volume left by the missing atom, its migration by clearly identifiable atomic jumps and the dissipation “on the spot”. A careful analysis of the probabilities of these three kinds of behaviour shows that a meaningful definition of vacancy-like defects can be given in a Lennard-Jones glass. Dans cet article, nous nous penchons de façon systématique sur la possibilité de définir des défauts de type lacunaire dans un verre de Lennard-Jones, à différents niveaux de relaxation et de pression, par une méthode de simulation numérique en dynamique moléculaire à volume ou à pression constants. Le défaut est créé en supprimant un atome et en suivant la réponse du système. Nous observons trois comportements typiques : la persistance sur place du “trou” laissé par l'atome supprimé, sa migration par des sauts atomiques clairement identifiés et enfin sa dissipation sur place. Une analyse détaillée de ces trois comportements montre qu'il est possible dans un verre de Lennard-Jones de définir des défauts de type lacunaire.

A further case of a Prader-Willi syndrome phenotype in a patient with Angelman syndrome molecular defect

Directory of Open Access Journals (Sweden)

De Molfetta Greice Andreotti

2002-01-01

Full Text Available Angelman syndrome (AS and Prader-Willi syndrome (PWS are distinct human neurogenetic disorders; however, a clinical overlap between AS and PWS has been identified. We report on a further case of a patient showing the PWS phenotype with the AS molecular defect. Despite the PWS phenotype, the DNA methylation analysis of SNRPN revealed an AS pattern. Cytogenetic and FISH analysis showed normal chromosomes 15 and microsatellite analysis showed heterozygous loci inside and outside the 15q11-13 region. The presence of these atypical cases could be more frequent than previously expected and we reinforce that the DNA methylation analysis is important for the correct diagnosis of severe mental deficiency, congenital hypotonia and obesity.

Positron annihilation studies of defects in molecular beam epitaxy grown III-V layers

International Nuclear Information System (INIS)

Umlor, M.T.; Keeble, D.J.; Cooke, P.W.

1994-01-01

A summary of recent positron annihilation experiments on molecular beam epitaxy (MBE) grown III-V layers is Presented. Variable energy positron beam measurements on Al 0.32 Ga 0.68 As undoped and Si doped have been completed. Positron trapping at a open volume defect in Al 0.32 Ga 0.68 :Si for temperatures from 300 to 25 K in the dark was observed. The positron trap was lost after 1.3 eV illumination at 25K. These results indicate an open volume defect is associated with the local structure of the deep donor state of the DX center. Stability of MBE GaAs to thermal annealing war, investigated over the temperature range of 230 to 700 degrees C, Proximity wafer furnace anneals in flowing argon were used, Samples grown above 450 degrees C were shown to be stable but for sample below this temperature an anneal induced vacancy related defect was produced for anneals between 400 and 500 degrees C. The nature of the defect was shown to be different for material grown at 350 and 230 degrees C. Activation energies of 2.5 eV to 2.3 eV were obtained from isochronal anneal experiments for samples grown at 350 and 230 degrees C, respectively

Convergent molecular defects underpin diverse neurodegenerative diseases.

Science.gov (United States)

Tofaris, George K; Buckley, Noel J

2018-02-19

In our ageing population, neurodegenerative disorders carry an enormous personal, societal and economic burden. Although neurodegenerative diseases are often thought of as clinicopathological entities, increasing evidence suggests a considerable overlap in the molecular underpinnings of their pathogenesis. Such overlapping biological processes include the handling of misfolded proteins, defective organelle trafficking, RNA processing, synaptic health and neuroinflammation. Collectively but in different proportions, these biological processes in neurons or non-neuronal cells lead to regionally distinct patterns of neuronal vulnerability and progression of pathology that could explain the disease symptomology. With the advent of patient-derived cellular models and novel genetic manipulation tools, we are now able to interrogate this commonality despite the cellular complexity of the brain in order to develop novel therapeutic strategies to prevent or arrest neurodegeneration. Here, we describe broadly these concepts and their relevance across neurodegenerative diseases. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Effect of point defects on the thermal conductivity of UO2: molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Liu, Xiang-Yang [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Stanek, Christopher Richard [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Andersson, Anders David Ragnar [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2015-07-21

The thermal conductivity of uranium dioxide (UO₂) fuel is an important materials property that affects fuel performance since it is a key parameter determining the temperature distribution in the fuel, thus governing, e.g., dimensional changes due to thermal expansion, fission gas release rates, etc. [1] The thermal conductivity of UO₂ nuclear fuel is also affected by fission gas, fission products, defects, and microstructural features such as grain boundaries. Here, molecular dynamics (MD) simulations are carried out to determine quantitatively, the effect of irradiation induced point defects on the thermal conductivity of UO₂, as a function of defect concentrations, for a range of temperatures, 300 – 1500 K. The results will be used to develop enhanced continuum thermal conductivity models for MARMOT and BISON by INL. These models express the thermal conductivity as a function of microstructure state-variables, thus enabling thermal conductivity models with closer connection to the physical state of the fuel [2].

Process and device for identifying nuclear reactor neutron absorber rod etancheity defect

International Nuclear Information System (INIS)

Pelletier, J.; Parrat, D.

1990-01-01

For identifying defects in the sealing of neutron absorbing rods. The rod is placed in a pressure tight enclosure filled with a chemically agressive solution. After a time the pressure is released to allow the solution come out of the rod. An analysis of the solution allows the detection of radioactive isotopes of metals which are in the rod [fr

Extracting and identifying concrete structural defects in GPR images

Science.gov (United States)

Ye, Qiling; Jiao, Liangbao; Liu, Chuanxin; Cao, Xuehong; Huston, Dryver; Xia, Tian

2018-03-01

Traditionally most GPR data interpretations are performed manually. With the advancement of computing technologies, how to automate GPR data interpretation to achieve high efficiency and accuracy has become an active research subject. In this paper, analytical characterizations of major defects in concrete structures, including delamination, air void and moisture in GPR images, are performed. In the study, the image features of different defects are compared. Algorithms are developed for defect feature extraction and identification. For validations, both simulation results and field test data are utilized.

Defect distribution in low-temperature molecular beam epitaxy grown Si/Si(100), improved depth profiling with monoenergetic positrons

International Nuclear Information System (INIS)

Szeles, C.; Asoka-Kumar, P.; Lynn, K.G.; Gossmann, H.; Unterwald, F.C.; Boone, T.

1995-01-01

The depth distribution of open-volume defects has been studied in Si(100) crystals grown by molecular beam epitaxy at 300 degree C by the variable-energy monoenergetic positron beam technique combined with well-controlled chemical etching. This procedure gave a 10 nm depth resolution which is a significant improvement over the inherent depth resolving power of the positron beam technique. The epitaxial layer was found to grow defect-free up to 80 nm, from the interface, where small vacancy clusters, larger than divacancies, appear. The defect density then sharply increases toward the film surface. The result clearly shows that the nucleation of small open-volume defects is a precursor state to the breakdown of epitaxy and to the evolution of an amorphous film

The intellectual capacity of patients with Laron syndrome (LS) differs with various molecular defects of the growth hormone receptor gene. Correlation with CNS abnormalities.

Science.gov (United States)

Shevah, O; Kornreich, L; Galatzer, A; Laron, Z

2005-12-01

The correlation between the molecular defects of the GH receptor (R), psychosocial development and brain abnormalities were evaluated in 10 patients with Laron syndrome (LS), in whom all data were available. The findings revealed that the intelligence quotient (IQ) and abnormalities in the brain of the patients with LS differ with various molecular defects of the GH-receptor. The most severe mental deficits and brain pathology occurred in patients with 3, 5, 6 exon deletion. Patients with point mutations in exons 2, 4 and 7 presented various degrees of medium to mild CNS abnormalities that correlated with the IQ. Notably, the patient with the E180 splice mutation in exon 6 had a normal IQ, which fits the report on normal IQ in a large Ecuadorian cohort with the same mutation. This is the first report to support a correlation between IQ, brain abnormalities and localization of the molecular defects in the GH-R gene. As all patients with LS are IGF-I-deficient, it must be assumed that other as yet unknown factors related to the molecular defects in the GH-R are the major cause of the differences in intellect and brain abnormalities.

Effects of in-cascade defect clustering on near-term defect evolution

Energy Technology Data Exchange (ETDEWEB)

Heinisch, H.L. [Pacific Northwest National Lab., Richland, WA (United States)

1997-08-01

The effects of in-cascade defect clustering on the nature of the subsequent defect population are being studied using stochastic annealing simulations applied to cascades generated in molecular dynamics (MD) simulations. The results of the simulations illustrates the strong influence of the defect configuration existing in the primary damage state on subsequent defect evolution. The large differences in mobility and stability of vacancy and interstitial defects and the rapid one-dimensional diffusion of small, glissile interstitial loops produced directly in cascades have been shown to be significant factors affecting the evolution of the defect distribution. In recent work, the effects of initial cluster sizes appear to be extremely important.

Point defects in solids

International Nuclear Information System (INIS)

Anon.

1978-01-01

The principal properties of point defects are studied: thermodynamics, electronic structure, interactions with etended defects, production by irradiation. Some measuring methods are presented: atomic diffusion, spectroscopic methods, diffuse scattering of neutron and X rays, positron annihilation, molecular dynamics. Then points defects in various materials are investigated: ionic crystals, oxides, semiconductor materials, metals, intermetallic compounds, carbides, nitrides [fr

Clinicopathologic factors identify sporadic mismatch repair-defective colon cancers

DEFF Research Database (Denmark)

Halvarsson, Britta; Anderson, Harald; Domanska, Katarina

2008-01-01

Identification of sporadic mismatch repair (MMR)-defective colon cancers is increasingly demanded for decisions on adjuvant therapies. We evaluated clinicopathologic factors for the identification of these prognostically favorable tumors. Histopathologic features in 238 consecutive colon cancers...... and excluded 61.5% of the tumors from MMR testing. This clinicopathologic index thus successfully selects MMR-defective colon cancers. Udgivelsesdato: 2008-Feb...

Growth of defect-free GaAsSbN axial nanowires via self-catalyzed molecular beam epitaxy

Science.gov (United States)

Sharma, Manish; Deshmukh, Prithviraj; Kasanaboina, Pavan; Reynolds, C. Lewis, Jr.; Liu, Yang; Iyer, Shanthi

2017-12-01

Bandgap reduction of 10% by incorporation of a dilute amount of N is reported for the first time, in axial GaAsSb nanowires (NWs) grown on Si (111) via Ga-assisted molecular beam epitaxy. Impact of N incorporation on the surface morphology, NW growth kinetics, and their structural and optical properties were examined. Dilute nitride NWs with Sb composition of 7 at% did not exhibit any noticeable planar defects, as revealed by the absence of satellite twin peaks in the selected-area diffraction pattern and high-resolution transmission electron microscopy imaging. Point defects were also minimal in as-grown dilute nitride NWs, as ascertained from the comparison of low-temperature photoluminescence spectra as well as the shape and shift of Raman modes, with in situ annealed NWs in different ambients. Evidence of enhanced incorporation of N was found in the NWs in situ annealed in N ambient, but with deteriorated optical quality due to simultaneous creation of N-induced defects. The lack of any noticeable defects in the as-grown GaAsSbN NWs demonstrates the advantage of the vapor-liquid-solid mechanism responsible for growth of axial configuration over the vapor-solid growth mechanism for core-shell NWs as well as their thin film counterpart, which commonly exhibit N-induced point defects.

Molecular analysis of expansion, differentiation, and growth factor treatment of human chondrocytes identifies differentiation markers and growth-related genes.

Science.gov (United States)

Benz, Karin; Breit, Stephen; Lukoschek, Martin; Mau, Hans; Richter, Wiltrud

2002-04-26

This study is intended to optimise expansion and differentiation of cultured human chondrocytes by growth factor application and to identify molecular markers to monitor their differentiation state. We dissected the molecular consequences of matrix release, monolayer, and 3D-alginate culture, growth factor optimised expansion, and re-differentiation protocols by gene expression analysis. Among 19 common cartilage molecules assessed by cDNA array, six proved best to monitor differentiation. Instant down-regulation at release of cells from the matrix was strongest for COL 2A1, fibromodulin, and PRELP while LUM, CHI3L1, and CHI3L2 were expansion-related. Both gene sets reflected the physiologic effects of the most potent growth-inducing (PDGF-BB) and proteoglycan-inducing (BMP-4) factors. Only CRTAC1 expression correlated with 2D/3D switches while the molecular phenotype of native chondrocytes was not restored. The markers and optimised protocols we suggest can help to improve cell therapy of cartilage defects and chondrocyte differentiation from stem cell sources.

Combining the 3D model generated from point clouds and thermography to identify the defects presented on the facades of a building

Science.gov (United States)

Huang, Yishuo; Chiang, Chih-Hung; Hsu, Keng-Tsang

2018-03-01

Defects presented on the facades of a building do have profound impacts on extending the life cycle of the building. How to identify the defects is a crucial issue; destructive and non-destructive methods are usually employed to identify the defects presented on a building. Destructive methods always cause the permanent damages for the examined objects; on the other hand, non-destructive testing (NDT) methods have been widely applied to detect those defects presented on exterior layers of a building. However, NDT methods cannot provide efficient and reliable information for identifying the defects because of the huge examination areas. Infrared thermography is often applied to quantitative energy performance measurements for building envelopes. Defects on the exterior layer of buildings may be caused by several factors: ventilation losses, conduction losses, thermal bridging, defective services, moisture condensation, moisture ingress, and structure defects. Analyzing the collected thermal images can be quite difficult when the spatial variations of surface temperature are small. In this paper the authors employ image segmentation to cluster those pixels with similar surface temperatures such that the processed thermal images can be composed of limited groups. The surface temperature distribution in each segmented group is homogenous. In doing so, the regional boundaries of the segmented regions can be identified and extracted. A terrestrial laser scanner (TLS) is widely used to collect the point clouds of a building, and those point clouds are applied to reconstruct the 3D model of the building. A mapping model is constructed such that the segmented thermal images can be projected onto the 2D image of the specified 3D building. In this paper, the administrative building in Chaoyang University campus is used as an example. The experimental results not only provide the defect information but also offer their corresponding spatial locations in the 3D model.

Identifying open-volume defects in doped and undoped perovskite-type LaCoO3, PbTiO3, and BaTiO3

International Nuclear Information System (INIS)

Ghosh, Vinita J.; Nielsen, Bent; Friessnegg, Thomas

2000-01-01

Dopants, vacancies, and impurity-vacancy clusters have a substantial impact on the properties of perovskite-type metal oxides (general formula ABO 3 ). In order to determine synthesis and processing conditions that optimize the desirable properties of these materials a careful study of these defects is required. It is essential to identify the defects and to map the defect densities. Positron annihilation spectroscopy has often been used to identify vacancy-type defects. Calculations of the positron lifetime and Doppler-broadened profiles of the positron-electron annihilation radiation in undoped and doped LaCoO 3 , PbTiO 3 , and BaTiO 3 are reported, and compared with available experimental data. The results show that these positron techniques are excellent for studying open-volume defects, vacancy-impurity complexes, and for identifying the sublattice occupied by the dopants. (c) 2000 The American Physical Society

USING THE PARETO DIAGRAM AND FMEA (FAILURE MODE AND EFFECTS ANALYSIS TO IDENTIFY KEY DEFECTS IN A PRODUCT

Directory of Open Access Journals (Sweden)

Michał ZASADZIEŃ

2014-10-01

Full Text Available The article presents the results of studies conducted in a company manufacturing aluminium forgings for the automotive industry. The aim of the research was to identify the defects which form during the production process as well as the locations and causes of their occurrence. Selected quality management tools were used in the process. Based on the FMEA and the costs generated by the identified defects, a hierarchy of them was created for the company along with a proposal of improvements in case of the most significant ones in order to reduce their number and increase the detection efficiency.

Molecular dynamics simulation of defect formation during energetic Cu deposition

International Nuclear Information System (INIS)

Gilmore, Charles M.; Sprague, James A.

2002-01-01

The deposition of energetic Cu atoms from 5 to 80 eV onto (0 0 1) Cu was simulated with molecular dynamics. The Cu-Cu interaction potential was a spline of the embedded atom potential developed from equilibrium data, and the universal scattering potential. Incident Cu atoms substituted for first layer substrate atoms by an exchange process at energies as low as 5 eV. Incident Cu atoms of 20 eV penetrated to the second substrate layer, and 20 eV was sufficient energy to produce interstitial defects. Incident atoms of 80 eV penetrated to the third atomic layer, produced interstitials 12 atomic layers into the substrate by focused replacement collision sequences, and produced sputtered atoms with a 16% yield. Interstitial clusters of up to 7 atoms were observed. The observed mechanisms of film growth included: the direct deposition of atoms into film equilibrium atom positions, the exchange of substrate atoms to equilibrium film atoms positions, and the migration of interstitials to equilibrium film atom positions. The relative frequency of each process was a function of incident energy. Since all observed growth mechanisms resulted in film atoms in equilibrium atomic positions, these simulations suggest that stresses in homoepitaxial Cu thin films are due to point defects. Vacancies would produce tensile strain and interstitial atoms would produce compressive strain in the films. It is proposed that immobile interstitial clusters could be responsible for retaining interstitial atoms and clusters in growing metal thin films

What can we learn from Raman Spectroscopy on irradiation-induced defects in UO2?

International Nuclear Information System (INIS)

Desgranges, L.; Martin, Ph.; Simon, P.; Guimbretiere, G.; Baldinozzi, G.

2014-01-01

Recent results on irradiated UO 2 by Raman spectroscopy evidenced Raman lines that are characteristic of irradiation-induced defects. Three main mechanisms are identified to explain their origin: resonant Raman, formation of new molecular entities, or breakdown in symmetry. Arguments are given to consider breakdown in symmetry as the predominant mechanism. A tentative description of the defects at the origin of this symmetry breakdown is proposed in terms of coordination polyhedrons of uranium. This discussion led us to consider that the Raman defect modes could be related to area with different stoichiometry. (authors)

Ectopic expression of Ptf1a induces spinal defects, urogenital defects, and anorectal malformations in Danforth's short tail mice.

Directory of Open Access Journals (Sweden)

Kei Semba

Full Text Available Danforth's short tail (Sd is a semidominant mutation on mouse chromosome 2, characterized by spinal defects, urogenital defects, and anorectal malformations. However, the gene responsible for the Sd phenotype was unknown. In this study, we identified the molecular basis of the Sd mutation. By positional cloning, we identified the insertion of an early transposon in the Sd candidate locus approximately 12-kb upstream of Ptf1a. We found that insertion of the transposon caused overexpression of three neighboring genes, Gm13344, Gm13336, and Ptf1a, in Sd mutant embryos and that the Sd phenotype was not caused by disruption of an as-yet-unknown gene in the candidate locus. Using multiple knockout and knock-in mouse models, we demonstrated that misexpression of Ptf1a, but not of Gm13344 or Gm13336, in the notochord, hindgut, cloaca, and mesonephros was sufficient to replicate the Sd phenotype. The ectopic expression of Ptf1a in the caudal embryo resulted in attenuated expression of Cdx2 and its downstream target genes T, Wnt3a, and Cyp26a1; we conclude that this is the molecular basis of the Sd phenotype. Analysis of Sd mutant mice will provide insight into the development of the spinal column, anus, and kidney.

Identifying subsurface detachment defects by acoustic tracing

Czech Academy of Sciences Publication Activity Database

Sklodowski, R.; Drdácký, Miloš; Sklodowski, M.

2013-01-01

Roč. 56, June (2013), s. 56-64 ISSN 0963-8695 R&D Projects: GA ČR(CZ) GBP105/12/G059 Institutional support: RVO:68378297 Keywords : acoustic excitation * plaster detachment defects * frequency response * inspection systems * signal processing Subject RIV: JN - Civil Engineering Impact factor: 1.717, year: 2013 http://www.sciencedirect.com/science/article/pii/S0963869513000303

Molecular dynamics study on the interaction of a dislocation and radiation induced defect clusters in Fcc crystals

International Nuclear Information System (INIS)

Hideo, Kaburaki; Tomoko, Kadoyoshi; Futoshi, Shimizu; Hajime; Kimizuka; Shiro, Jitsukawa

2003-01-01

Irradiation of high-energy neutrons and charged particles into solids is known to cause a significant change in mechanical properties, in particular, hardening of metals. Hardening of solids arises as a result of interactions of dislocations with irradiation induced defect clusters. Molecular dynamics method combined with the visualization method has been used to elucidate these complex pinning structures in details. In particular, we have successfully observed the transient process for the formation of a super-jog from an edge dislocation and interstitial and vacancy clusters under irradiation cascade conditions. Parallel molecular dynamics programs, called as Parallel Molecular Dynamics Stencil (PMDS), have been developed in order to perform these large scale simulations for materials simulations. The contents of the program and its parallel performance are also reported. (authors)

P-N defect in GaNP studied by optically detected magnetic resonance

International Nuclear Information System (INIS)

Chen, W.M.; Thinh, N.Q.; Vorona, I.P.; Buyanova, I.A.; Xin, H.P.; Tu, C.W.

2003-01-01

We provide experimental evidence for an intrinsic defect in GaNP from optically detected magnetic resonance (ODMR). This defect is identified as a P-N complex, exhibiting hyperfine structure due to interactions with a nuclear spin I=((1)/(2)) of one P atom and also a nuclear spin I=1 due to one N atom. The introduction of the defect is assisted by the incorporation of N within the studied N composition range of up to 3.1%, under non-equilibrium growth conditions during gas-source molecular beam epitaxy. The corresponding ODMR spectrum was found to be isotropic, suggesting an A 1 symmetry of the defect state. The localization of the electron wave function at the P-N defect in GaNP is found to be even stronger than that for the isolated P Ga antisite in its parent binary compound GaP

Effect of growth temperature on defects in epitaxial GaN film grown by plasma assisted molecular beam epitaxy

Directory of Open Access Journals (Sweden)

S. S. Kushvaha

2014-02-01

Full Text Available We report the effect of growth temperature on defect states of GaN epitaxial layers grown on 3.5 μm thick GaN epi-layer on sapphire (0001 substrates using plasma assisted molecular beam epitaxy. The GaN samples grown at three different substrate temperatures at 730, 740 and 750 °C were characterized using atomic force microscopy and photoluminescence spectroscopy. The atomic force microscopy images of these samples show the presence of small surface and large hexagonal pits on the GaN film surfaces. The surface defect density of high temperature grown sample is smaller (4.0 × 108 cm−2 at 750 °C than that of the low temperature grown sample (1.1 × 109 cm−2 at 730 °C. A correlation between growth temperature and concentration of deep centre defect states from photoluminescence spectra is also presented. The GaN film grown at 750 °C exhibits the lowest defect concentration which confirms that the growth temperature strongly influences the surface morphology and affects the optical properties of the GaN epitaxial films.

Partial correction of a severe molecular defect in hemophilia A, because of errors during expression of the factor VIII gene

Energy Technology Data Exchange (ETDEWEB)

Young, M.; Antonarakis, S.E. [Univ. of Geneva (Switzerland); Inaba, Hiroshi [Tokyo Medical College (Japan)] [and others

1997-03-01

Although the molecular defect in patients in a Japanese family with mild to moderately severe hemophilia A was a deletion of a single nucleotide T within an A{sub 8}TA{sub 2} sequence of exon 14 of the factor VIII gene, the severity of the clinical phenotype did not correspond to that expected of a frameshift mutation. A small amount of functional factor VIII protein was detected in the patient`s plasma. Analysis of DNA and RNA molecules from normal and affected individuals and in vitro transcription/translation suggested a partial correction of the molecular defect, because of the following: (i) DNA replication/RNA transcription errors resulting in restoration of the reading frame and/or (ii) {open_quotes}ribosomal frameshifting{close_quotes} resulting in the production of normal factor VIII polypeptide and, thus, in a milder than expected hemophilia A. All of these mechanisms probably were promoted by the longer run of adenines, A{sub 10} instead of A{sub 8}TA{sub 2}, after the delT. Errors in the complex steps of gene expression therefore may partially correct a severe frameshift defect and ameliorate an expected severe phenotype. 36 refs., 6 figs.

Photographic guide of selected external defect indicators and associated internal defects in sugar maple

Science.gov (United States)

Everette D. Rast; John A. Beaton; David L. Sonderman

1991-01-01

To properly classify or grade logs or trees, one must be able to correctly identify defect indicators and assess the effect of the underlying defect on possible end products. This guide assists the individual in identifying the surface defect indicator and shows the progressive stages of the defect throughout its development for sugar maple. Eleven types of external...

Photographic guide of selected external defect indicators and associated internal defects in yellow-poplar

Science.gov (United States)

Everette D. Rast; John A. Beaton; David L. Sonderman

1991-01-01

To properly classify or grade logs or trees, one must be able to correctly identify defect indicators and assess the effect of the underlying defect on possible end products. This guide assists the individual in identifying the surface defect indicator and shows the progressive stages of the defect throughout its development for yellow-poplar. Twelve types of external...

Photographic guide of selected external defect indicators and associated internal defects in yellow birch

Science.gov (United States)

Everette D. Rast; John A. Beaton; David L. Sonderman

1991-01-01

To properly classify or grade logs or trees, one must be able to correctly identify defect indicators and assess the effect of the underlying defect on possible end products. This guide assists the individual in identifying the surface defect indicator and shows the progressive stages of the defect throughout its development for yellow birch. Eleven types of external...

Various Stone-Wales defects in phagraphene

Science.gov (United States)

Openov, L. A.; Podlivaev, A. I.

2016-08-01

Various Stone-Wales defects in phagraphene, which is a graphene allotrope, predicted recently are studied in terms of the nonorthogonal tight-binding model. The energies of the defect formation and the heights of energy barriers preventing the formation and annealing of the defects are found. Corresponding frequency factors in the Arrhenius formula are calculated. The evolution of the defect structure is studied in the real-time mode using the molecular dynamics method.

Formation of grown-in defects in molecular beam epitaxial Ga(In)NP: Effects of growth conditions and postgrowth treatments

International Nuclear Information System (INIS)

Dagnelund, D.; Buyanova, I. A.; Wang, X. J.; Chen, W. M.; Utsumi, A.; Furukawa, Y.; Wakahara, A.; Yonezu, H.

2008-01-01

Effects of growth conditions and post-growth treatments, such as presence of N ions, N 2 flow, growth temperature, In alloying, and postgrowth rapid thermal annealing (RTA), on formation of grown-in defects in Ga(In)NP prepared by molecular beam epitaxy are studied in detail by the optically detected magnetic resonance (ODMR) technique. Several common residual defects, such as two Ga-interstitial defects (i.e., Ga i -A and Ga i -B) and two unidentified defects with a g factor around 2 (denoted by S1 and S2), are closely monitored. Bombardment of impinging N ions on grown sample surface is found to facilitate formation of these defects. Higher N 2 flow is shown to have an even more profound effect than a higher number of ions in introducing these defects. Incorporation of a small amount of In (e.g., 5.1%) in GaNP seems to play a minor role in the formation of the defects. In GaInNP with 45% of In; however, the defects were found to be abundant. Effect of RTA on the defects is found to depend on initial configurations of Ga i -related defects formed during the growth. In the alloys where the Ga i -A and Ga i -B defects are absent in the as-grown samples (i.e., GaNP grown at a low temperature of 460 deg. C), the concentrations of the two Ga i defects are found to increase after postgrowth RTA. This indicates that the defects originally introduced in the as-grown alloys have been transformed into the more thermally stable Ga i -A and Ga i -B during RTA. On the other hand, when the Ga i -A and Ga i -B are readily abundant (e.g., at higher growth temperatures (≥500 deg. C), RTA leads to a slight reduction of the Ga i -A and Ga i -B ODMR signals. The S2 defect is also shown to be thermally stable upon the RTA treatment

Expanding the clinical spectrum associated with defects in CNTNAP2 and NRXN1

Directory of Open Access Journals (Sweden)

Ullmann Reinhard

2011-08-01

Full Text Available Abstract Background Heterozygous copy-number and missense variants in CNTNAP2 and NRXN1 have repeatedly been associated with a wide spectrum of neuropsychiatric disorders such as developmental language and autism spectrum disorders, epilepsy and schizophrenia. Recently, homozygous or compound heterozygous defects in either gene were reported as causative for severe intellectual disability. Methods 99 patients with severe intellectual disability and resemblance to Pitt-Hopkins syndrome and/or suspected recessive inheritance were screened for mutations in CNTNAP2 and NRXN1. Molecular karyotyping was performed in 45 patients. In 8 further patients with variable intellectual disability and heterozygous deletions in either CNTNAP2 or NRXN1, the remaining allele was sequenced. Results By molecular karyotyping and mutational screening of CNTNAP2 and NRXN1 in a group of severely intellectually disabled patients we identified a heterozygous deletion in NRXN1 in one patient and heterozygous splice-site, frameshift and stop mutations in CNTNAP2 in four patients, respectively. Neither in these patients nor in eight further patients with heterozygous deletions within NRXN1 or CNTNAP2 we could identify a defect on the second allele. One deletion in NRXN1 and one deletion in CNTNAP2 occurred de novo, in another family the deletion was also identified in the mother who had learning difficulties, and in all other tested families one parent was shown to be healthy carrier of the respective deletion or mutation. Conclusions We report on patients with heterozygous defects in CNTNAP2 or NRXN1 associated with severe intellectual disability, which has only been reported for recessive defects before. These results expand the spectrum of phenotypic severity in patients with heterozygous defects in either gene. The large variability between severely affected patients and mildly affected or asymptomatic carrier parents might suggest the presence of a second hit, not

Graphene defects induced by ion beam

Science.gov (United States)

Gawlik, Grzegorz; Ciepielewski, Paweł; Baranowski, Jacek; Jagielski, Jacek

2017-10-01

The CVD graphene deposited on the glass substrate was bombarded by molecular carbon ions C3+ C6+ hydrocarbon ions C3H4+ and atomic ions He+, C+, N+, Ar+, Kr+ Yb+. Size and density of ion induced defects were estimated from evolution of relative intensities of Raman lines D (∼1350 1/cm), G (∼1600 1/cm), and D‧ (∼1620 1/cm) with ion fluence. The efficiency of defect generation by atomic ions depend on ion mass and energy similarly as vacancy generation directly by ion predicted by SRIM simulations. However, efficiency of defect generation in graphene by molecular carbon ions is essentially higher than summarized efficiency of similar group of separate atomic carbon ions of the same energy that each carbon ion in a cluster. The evolution of the D/D‧ ratio of Raman lines intensities with ion fluence was observed. This effect may indicate evolution of defect nature from sp3-like at low fluence to a vacancy-like at high fluence. Observed ion graphene interactions suggest that the molecular ion interacts with graphene as single integrated object and should not be considered as a group of atomic ions with partial energy.

Rapid screening for nuclear genes mutations in isolated respiratory chain complex I defects.

Science.gov (United States)

Pagniez-Mammeri, Hélène; Lombes, Anne; Brivet, Michèle; Ogier-de Baulny, Hélène; Landrieu, Pierre; Legrand, Alain; Slama, Abdelhamid

2009-04-01

Complex I or reduced nicotinamide adenine dinucleotide (NADH): ubiquinone oxydoreductase deficiency is the most common cause of respiratory chain defects. Molecular bases of complex I deficiencies are rarely identified because of the dual genetic origin of this multi-enzymatic complex (nuclear DNA and mitochondrial DNA) and the lack of phenotype-genotype correlation. We used a rapid method to screen patients with isolated complex I deficiencies for nuclear genes mutations by Surveyor nuclease digestion of cDNAs. Eight complex I nuclear genes, among the most frequently mutated (NDUFS1, NDUFS2, NDUFS3, NDUFS4, NDUFS7, NDUFS8, NDUFV1 and NDUFV2), were studied in 22 cDNA fragments spanning their coding sequences in 8 patients with a biochemically proved complex I deficiency. Single nucleotide polymorphisms and missense mutations were detected in 18.7% of the cDNA fragments by Surveyor nuclease treatment. Molecular defects were detected in 3 patients. Surveyor nuclease screening is a reliable method for genotyping nuclear complex I deficiencies, easy to interpret, and limits the number of sequence reactions. Its use will enhance the possibility of prenatal diagnosis and help us for a better understanding of complex I molecular defects.

Defective myoblasts identified in Duchenne muscular dystrophy.

OpenAIRE

Blau, H M; Webster, C; Pavlath, G K

1983-01-01

A defect in the proliferative capacity of satellite cells, mononucleated precursors of mature muscle fibers, was found in clonal analyses of cells cultured from Duchenne muscular dystrophy (DMD) patients. The total yield of myoblasts per gram of muscle biopsy was decreased to 5% of normal. Of the DMD myoblast clones obtained, a large proportion contained a morphological class of flat distended cells that had an increased generation time and ceased to proliferate beyond 100-1,000 cells but cou...

Who named the quantum defect?

International Nuclear Information System (INIS)

Rau, A.R.P.; Inokuti, M.

1997-01-01

The notion of the quantum defect is important in atomic and molecular spectroscopy and also in unifying spectroscopy with collision theory. In the latter context, the quantum defect may be viewed as an ancestor of the phase shift. However, the origin of the term quantum defect does not seem to be explained in standard textbooks. It occurred in a 1921 paper by Schroedinger, preceding quantum mechanics, yet giving the correct meaning as an index of the short-range interactions with the core of an atom. The authors present the early history of the quantum-defect idea, and sketch its recent developments

Point defect balance in epitaxial GaSb

International Nuclear Information System (INIS)

Segercrantz, N.; Slotte, J.; Makkonen, I.; Kujala, J.; Tuomisto, F.; Song, Y.; Wang, S.

2014-01-01

Positron annihilation spectroscopy in both conventional and coincidence Doppler broadening mode is used for studying the effect of growth conditions on the point defect balance in GaSb:Bi epitaxial layers grown by molecular beam epitaxy. Positron annihilation characteristics in GaSb are also calculated using density functional theory and compared to experimental results. We conclude that while the main positron trapping defect in bulk samples is the Ga antisite, the Ga vacancy is the most prominent trap in the samples grown by molecular beam epitaxy. The results suggest that the p–type conductivity is caused by different defects in GaSb grown with different methods.

Kinetics of interstitial defects in α-Fe: The effect from uniaxial stress

Energy Technology Data Exchange (ETDEWEB)

Kang, Changwoo [Department of Nuclear Engineering, Texas A& M University, College Station, TX 77843 (United States); Wang, Qingyu [College of Nuclear Science and Technology, Harbin Engineering University, Harbin 150001 (China); Shao, Lin, E-mail: lshao@tamu.edu [Department of Nuclear Engineering, Texas A& M University, College Station, TX 77843 (United States)

2017-03-15

Understanding defect kinetics in a stress field is important for multiscale modeling of materials degradation of nuclear materials. By means of molecular dynamics and molecular statics simulations, we calculate formation and migration energies of self-interstitial atoms (SIA) and SIA clusters (up to size of 5 interstitials) in alpha Fe and identify their stable configurations under uniaxial tensile strains. By applying uniaxial stress along [111], <111> oriented single SIA defects become more stable than <110> oriented SIA, which is opposite to stress-free condition. Diffusion of single SIA defects under [111] tensile stress is facilitated along [111] direction and the diffusion becomes one dimensional (1D). For SIA clusters, their diffusion under zero stress has gradual transition from three dimensional (3D) for small clusters to one dimensional (1D) for large clusters. Under the tensile stress along [111], the 3D to 1D transition is accelerated. For large SIA clusters, the stress effect is quickly saturated with less diffusivity enhancement in comparison with small SIA clusters.

The familial hyperchylomicronemia syndrome: New insights into underlying genetic defects

Energy Technology Data Exchange (ETDEWEB)

Santamarina-Fojo, S.; Brewer, H.B. (National Inst. of Health, Bethesda, MD (United States))

1991-02-20

This case history reports the diagnosis of familial hyperchylomicronemia, a rare genetic syndrome inherited as an autosomal recessive trait. It is characterized by severe fasting hypertriglyceridemia and massive accumulations of chylomicrons in plasma. The two major molecular defects in the disease are a deficiency of lipoprotein lipase or of apo C-II. The location of the mutations in the human apolipoprotein (apo) C-II gene are identified.

Novel Mutation of LRP6 Identified in Chinese Han Population Links Canonical WNT Signaling to Neural Tube Defects.

Science.gov (United States)

Shi, Zhiwen; Yang, Xueyan; Li, Bin-Bin; Chen, Shuxia; Yang, Luming; Cheng, Liangping; Zhang, Ting; Wang, Hongyan; Zheng, Yufang

2018-01-15

Neural tube defects (NTDs), the second most frequent cause of human congenital abnormalities, are debilitating birth defects due to failure of neural tube closure. It has been shown that noncanonical WNT/planar cell polarity (PCP) signaling is required for convergent extension (CE), the initiation step of neural tube closure (NTC). But the effect of canonical WNT//β-catenin signaling during NTC is still elusive. LRP6 (low density lipoprotein receptor related proteins 6) was identified as a co-receptor for WNT/β-catenin signaling, but recent studies showed that it also can mediate WNT/PCP signaling. In this study, we screened mutations in the LRP6 gene in 343 NTDs and 215 ethnically matched normal controls of Chinese Han population. Three rare missense mutations (c.1514A>G, p.Y505C); c.2984A>G, p.D995G; and c.4280C>A, p.P1427Q) of the LRP6 gene were identified in Chinese NTD patients. The Y505C mutation is a loss-of-function mutation on both WNT/β-catenin and PCP signaling. The D995G mutation only partially lost inhibition on PCP signaling without affecting WNT/β-catenin signaling. The P1427Q mutation dramatically increased WNT/β-catenin signaling but only mildly loss of inhibition on PCP signaling. All three mutations failed to rescue CE defects caused by lrp6 morpholino oligos knockdown in zebrafish. Of interest, when overexpressed, D995G did not induce any defects, but Y505C and P1427Q caused more severe CE defects in zebrafish. Our results suggested that over-active canonical WNT signaling induced by gain-of-function mutation in LRP6 could also contribute to human NTDs, and a balanced WNT/β-catenin and PCP signaling is probably required for proper neural tube development. Birth Defects Research 110:63-71, 2018. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Clinicopathologic factors identify sporadic mismatch repair-defective colon cancers

DEFF Research Database (Denmark)

Halvarsson, Britta; Anderson, Harald; Domanska, Katarina

2008-01-01

Identification of sporadic mismatch repair (MMR)-defective colon cancers is increasingly demanded for decisions on adjuvant therapies. We evaluated clinicopathologic factors for the identification of these prognostically favorable tumors. Histopathologic features in 238 consecutive colon cancers...

A Systems Biology Framework Identifies Molecular Underpinnings of Coronary Heart Disease

Science.gov (United States)

Huan, Tianxiao; Zhang, Bin; Wang, Zhi; Joehanes, Roby; Zhu, Jun; Johnson, Andrew D.; Ying, Saixia; Munson, Peter J.; Raghavachari, Nalini; Wang, Richard; Liu, Poching; Courchesne, Paul; Hwang, Shih-Jen; Assimes, Themistocles L.; McPherson, Ruth; Samani, Nilesh J.; Schunkert, Heribert; Meng, Qingying; Suver, Christine; O'Donnell, Christopher J.; Derry, Jonathan; Yang, Xia; Levy, Daniel

2013-01-01

Objective Genetic approaches have identified numerous loci associated with coronary heart disease (CHD). The molecular mechanisms underlying CHD gene-disease associations, however, remain unclear. We hypothesized that genetic variants with both strong and subtle effects drive gene subnetworks that in turn affect CHD. Approach and Results We surveyed CHD-associated molecular interactions by constructing coexpression networks using whole blood gene expression profiles from 188 CHD cases and 188 age- and sex-matched controls. 24 coexpression modules were identified including one case-specific and one control-specific differential module (DM). The DMs were enriched for genes involved in B-cell activation, immune response, and ion transport. By integrating the DMs with altered gene expression associated SNPs (eSNPs) and with results of GWAS of CHD and its risk factors, the control-specific DM was implicated as CHD-causal based on its significant enrichment for both CHD and lipid eSNPs. This causal DM was further integrated with tissue-specific Bayesian networks and protein-protein interaction networks to identify regulatory key driver (KD) genes. Multi-tissue KDs (SPIB and TNFRSF13C) and tissue-specific KDs (e.g. EBF1) were identified. Conclusions Our network-driven integrative analysis not only identified CHD-related genes, but also defined network structure that sheds light on the molecular interactions of genes associated with CHD risk. PMID:23539213

Low defect densities in molecular beam epitaxial GaAs achieved by isoelectronic In doping

Science.gov (United States)

Bhattacharya, P. K.; Dhar, S.; Berger, P.; Juang, F.-Y.

1986-01-01

A study has been made of the effects of adding small amounts of In (0.2-1.2 pct) to GaAs grown by molecular beam epitaxy. The density of four electron traps decreases in concentration by an order of magnitude, and the peak intensities of prominent emissions in the excitonic spectra are reduced with increase in In content. Based on the higher surface migration rate of In, compared to Ga, at the growth temperatures it is apparent that the traps and the excitonic transitions are related to point defects. This agrees with earlier observations by Briones and Collins (1982) and Skromme et al. (1985).

Genes Important for Schizosaccharomyces pombe Meiosis Identified Through a Functional Genomics Screen

Science.gov (United States)

Blyth, Julie; Makrantoni, Vasso; Barton, Rachael E.; Spanos, Christos; Rappsilber, Juri; Marston, Adele L.

2018-01-01

Meiosis is a specialized cell division that generates gametes, such as eggs and sperm. Errors in meiosis result in miscarriages and are the leading cause of birth defects; however, the molecular origins of these defects remain unknown. Studies in model organisms are beginning to identify the genes and pathways important for meiosis, but the parts list is still poorly defined. Here we present a comprehensive catalog of genes important for meiosis in the fission yeast, Schizosaccharomyces pombe. Our genome-wide functional screen surveyed all nonessential genes for roles in chromosome segregation and spore formation. Novel genes important at distinct stages of the meiotic chromosome segregation and differentiation program were identified. Preliminary characterization implicated three of these genes in centrosome/spindle pole body, centromere, and cohesion function. Our findings represent a near-complete parts list of genes important for meiosis in fission yeast, providing a valuable resource to advance our molecular understanding of meiosis. PMID:29259000

Molecular dynamics simulation on the formation and annihilation behaviors of radiation defects in Li2O

International Nuclear Information System (INIS)

Takuji Oda; Satoru Tanaka; Yasuhisa Oya

2006-01-01

The influence of radiation defects is one of the main factors that determine tritium release behavior from blanket breeding materials in fusion reactors. Classical molecular dynamics simulation (MD) is a powerful technique to investigate the radiation damage processes, because it can provide atomic-scale information on the defects. In this study, we conducted radiation simulation for Li 2 O using MD and analyzed formation and annihilation behaviors of radiation defects, as a fundamental research for radiation response of Li-containing oxides. Buckingham type two-body potential model was used. In order to remove the unphysical impulsive force at short inter-ionic distances in Buckingham model, each potential function was connected to that of the ZBL potential models at around 0.8 A. NEV ensemble was employed with the initial simulation temperature of 0 K. 10 x 10 x 10 supercell consisting of 4000 Li 2 O was used as a unit cell under 3D periodic boundary conditions. Radiation simulation was initiated by introducing an energy of a certain direction to an ion, as a displacement energy. The lowest displacement energy by which a defect was created and survived beyond 5 ps was regarded as the threshold energy. 42 and 21 displacement directions were surveyed for Li and O, respectively, based on the symmetry of the Li 2 O crystal. In both Li and O defect formations, [100] displacement shows significantly lower threshold energy than [111] displacement. Li defects were easily created than O defects almost in all directions. In fact, the average threshold energy except [111] displacement, which possesses extremely high threshold energy, was 21 eV for Li and 49 eV for O. In some cases, no defect could survive beyond 5 ps even by higher displacement energies than the threshold energy, due to the self-annealing effect. The self-annealing completed basically within 1 ps after introduction of displacement energy. At around this time, velocity distribution of all ions in the system

Three-dimensional interactive Molecular Dynamics program for the study of defect dynamics in crystals

Science.gov (United States)

Patriarca, M.; Kuronen, A.; Robles, M.; Kaski, K.

2007-01-01

The study of crystal defects and the complex processes underlying their formation and time evolution has motivated the development of the program ALINE for interactive molecular dynamics experiments. This program couples a molecular dynamics code to a Graphical User Interface and runs on a UNIX-X11 Window System platform with the MOTIF library, which is contained in many standard Linux releases. ALINE is written in C, thus giving the user the possibility to modify the source code, and, at the same time, provides an effective and user-friendly framework for numerical experiments, in which the main parameters can be interactively varied and the system visualized in various ways. We illustrate the main features of the program through some examples of detection and dynamical tracking of point-defects, linear defects, and planar defects, such as stacking faults in lattice-mismatched heterostructures. Program summaryTitle of program:ALINE Catalogue identifier:ADYJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYJ_v1_0 Program obtainable from: CPC Program Library, Queen University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: Computers:DEC ALPHA 300, Intel i386 compatible computers, G4 Apple Computers Installations:Laboratory of Computational Engineering, Helsinki University of Technology, Helsinki, Finland Operating systems under which the program has been tested:True64 UNIX, Linux-i386, Mac OS X 10.3 and 10.4 Programming language used:Standard C and MOTIF libraries Memory required to execute with typical data:6 Mbytes but may be larger depending on the system size No. of lines in distributed program, including test data, etc.:16 901 No. of bytes in distributed program, including test data, etc.:449 559 Distribution format:tar.gz Nature of physical problem:Some phenomena involving defects take place inside three-dimensional crystals at times which can be hardly predicted. For this reason they are

Computer simulation of defect cluster

Energy Technology Data Exchange (ETDEWEB)

Kuramoto, Eiichi [Kyushu Univ., Kasuga, Fukuoka (Japan). Research Inst. for Applied Mechanics

1996-04-01

In order to elucidate individual element process of various defects and defect clusters of used materials under irradiation environments, interatomic potential with reliability was investigated. And for comparison with experimental results, it is often required to adopt the temperature effect and to investigate in details mechanism of one dimensional motion of micro conversion loop and so forth using the molecular dynamic (MD) method. Furthermore, temperature effect is also supposed for stable structure of defects and defect clusters, and many problems relating to alloy element are also remained. And, simulation on photon life at the defects and defect clusters thought to be important under comparison with equipment can also be supposed an improvement of effectiveness due to relation to theses products. In this paper, some topics in such flow was extracted to explain them. In particular, future important problems will be potential preparation of alloy, structure, dynamic behavior and limited temperature of intralattice atomic cluster. (G.K.)

Improved tensile and buckling behavior of defected carbon nanotubes utilizing boron nitride coating – A molecular dynamic study

Energy Technology Data Exchange (ETDEWEB)

Badjian, H.; Setoodeh, A.R., E-mail: setoodeh@sutech.ac.ir

2017-02-15

Synthesizing inorganic nanostructures such as boron nitride nanotubes (BNNTs) have led to immense studies due to their many interesting functional features such as piezoelectricity, high temperature resistance to oxygen, electrical insulation, high thermal conductivity and very long lengths as physical features. In order to utilize the superior properties of pristine and defected carbon nanotubes (CNTs), a hybrid nanotube is proposed in this study by forming BNNTs surface coating on the CNTs. The benefits of such coating on the tensile and buckling behavior of single-walled CNTs (SWCNTs) are illustrated through molecular dynamics (MD) simulations of the resulted nanostructures during the deformation. The AIREBO and Tersoff-Brenner potentials are employed to model the interatomic forces between the carbon and boron nitride atoms, respectively. The effects of chiral indices, aspect ratio, presence of mono-vacancy defects and coating dimension on coated/non-coated CNTs are examined. It is demonstrated that the coated defective CNTs exhibit remarkably enhanced ultimate strength, buckling load capacity and Young's modulus. The proposed coating not only enhances the mechanical properties of the resulted nanostructure, but also conceals it from few external factors impacting the behavior of the CNT such as humidity and high temperature.

Molecular dynamics study on welding a defected graphene by a moving fullerene

International Nuclear Information System (INIS)

Cai, Kun; Wan, Jing; Yu, Jingzhou; Cai, Haifang; Qin, Qinghua

2016-01-01

Highlights: • Fullerene (FN) is adopted to weld the gap on a graphene (GN) sheet using molecular dynamics simulation. • The mechanism is that the dangling sp"1 carbon atoms on both sides of gap are excited by FN to form new sp"2-sp"2 carbon bonds. • The velocity of FN influences the welding result due to the fact that the deformation of GN depends on the velocity of FN. • A complex nanostructure, e.g., cone, can be formed by the present method, which will be applicable in nano fabrication/manufacturing. - Abstract: When a composite nanostructure is fabricated through van der Waals interaction only, the interaction among components may be sensitive to environmental conditions. To endow such a structure with relative stability, new covalent bonds should be applied. In this paper, a welding method for welding a circular graphene with a defect gap through a moving fullerene (C240 or C540 buckyball) is presented. When the buckyball moves above the gap, the two faces of the gap are attracted to each other and the distance between the two faces is shortened. When the dangling carbon atoms on both faces of the gap are excited to form new normal sp"2-sp"2 carbon bonds, the gap can be sewn up quickly. Molecular dynamics simulations are presented to demonstrate the welding process. When the gap is a sector, an ideal cone can be fabricated using the present method.

Molecular dynamics study on welding a defected graphene by a moving fullerene

Energy Technology Data Exchange (ETDEWEB)

Cai, Kun, E-mail: kuncai99@163.com [College of Water Resources and Architectural Engineering, Northwest A& F University, Yangling 712100 (China); Research School of Engineering, The Australian National University, ACT 2601 (Australia); Wan, Jing; Yu, Jingzhou; Cai, Haifang [College of Water Resources and Architectural Engineering, Northwest A& F University, Yangling 712100 (China); Qin, Qinghua [Research School of Engineering, The Australian National University, ACT 2601 (Australia)

2016-07-30

Highlights: • Fullerene (FN) is adopted to weld the gap on a graphene (GN) sheet using molecular dynamics simulation. • The mechanism is that the dangling sp{sup 1} carbon atoms on both sides of gap are excited by FN to form new sp{sup 2}-sp{sup 2} carbon bonds. • The velocity of FN influences the welding result due to the fact that the deformation of GN depends on the velocity of FN. • A complex nanostructure, e.g., cone, can be formed by the present method, which will be applicable in nano fabrication/manufacturing. - Abstract: When a composite nanostructure is fabricated through van der Waals interaction only, the interaction among components may be sensitive to environmental conditions. To endow such a structure with relative stability, new covalent bonds should be applied. In this paper, a welding method for welding a circular graphene with a defect gap through a moving fullerene (C240 or C540 buckyball) is presented. When the buckyball moves above the gap, the two faces of the gap are attracted to each other and the distance between the two faces is shortened. When the dangling carbon atoms on both faces of the gap are excited to form new normal sp{sup 2}-sp{sup 2} carbon bonds, the gap can be sewn up quickly. Molecular dynamics simulations are presented to demonstrate the welding process. When the gap is a sector, an ideal cone can be fabricated using the present method.

Secondary defects in non-metallic solids

International Nuclear Information System (INIS)

Ashbee, K.H.G.; Hobbs, L.W.

1977-01-01

This paper points out features of secondary defect formation which are peculiar to non-metallic solids (excluding elemental semiconductors). Most of the materials of interest are compounds of two or more (usually more or less ionic) atomic species, and immediate consequence of which is a need to maintain both stoichiometry (or accommodate non-stoichiometry) and order. Primary defects in these solids, whether produced thermally, chemically or by irradiation, seldom are present or aggregate in exactly stoichiometric proportions, and the resulting extending defect structures can be quite distinct from those found in metallic solids. Where stoichiometry is maintained, it is often convenient to describe extended defects in terms of alterations in the arrangement of 'molecular' units. The adoption of this procedure enables several novel features of extended defect structures in non-metals to be explained. There are several ways in which a range of non-stoichiometry can be accommodated, which include structural elimination of point defects, nucleation of new coherent phases of altered stoichiometry, and decomposition. (author)

Theory of Defects in Semiconductors

CERN Document Server

Drabold, David A

2007-01-01

Semiconductor science and technology is the art of defect engineering. The theoretical modeling of defects has improved dramatically over the past decade. These tools are now applied to a wide range of materials issues: quantum dots, buckyballs, spintronics, interfaces, amorphous systems, and many others. This volume presents a coherent and detailed description of the field, and brings together leaders in theoretical research. Today's state-of-the-art, as well as tomorrow’s tools, are discussed: the supercell-pseudopotential method, the GW formalism,Quantum Monte Carlo, learn-on-the-fly molecular dynamics, finite-temperature treatments, etc. A wealth of applications are included, from point defects to wafer bonding or the propagation of dislocation.

Cellular and Molecular Defects Underlying Invasive Fungal Infections—Revelations from Endemic Mycoses

Directory of Open Access Journals (Sweden)

Pamela P. Lee

2017-06-01

Full Text Available The global burden of fungal diseases has been increasing, as a result of the expanding number of susceptible individuals including people living with human immunodeficiency virus (HIV, hematopoietic stem cell or organ transplant recipients, patients with malignancies or immunological conditions receiving immunosuppressive treatment, premature neonates, and the elderly. Opportunistic fungal pathogens such as Aspergillus, Candida, Cryptococcus, Rhizopus, and Pneumocystis jiroveci are distributed worldwide and constitute the majority of invasive fungal infections (IFIs. Dimorphic fungi such as Histoplasma capsulatum, Coccidioides spp., Paracoccidioides spp., Blastomyces dermatiditis, Sporothrix schenckii, Talaromyces (Penicillium marneffei, and Emmonsia spp. are geographically restricted to their respective habitats and cause endemic mycoses. Disseminated histoplasmosis, coccidioidomycosis, and T. marneffei infection are recognized as acquired immunodeficiency syndrome (AIDS-defining conditions, while the rest also cause high rate of morbidities and mortalities in patients with HIV infection and other immunocompromised conditions. In the past decade, a growing number of monogenic immunodeficiency disorders causing increased susceptibility to fungal infections have been discovered. In particular, defects of the IL-12/IFN-γ pathway and T-helper 17-mediated response are associated with increased susceptibility to endemic mycoses. In this review, we put together the various forms of endemic mycoses on the map and take a journey around the world to examine how cellular and molecular defects of the immune system predispose to invasive endemic fungal infections, including primary immunodeficiencies, individuals with autoantibodies against interferon-γ, and those receiving biologic response modifiers. Though rare, these conditions provide importance insights to host defense mechanisms against endemic fungi, which can only be appreciated in unique

Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles

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Farshad Farshidfar

2017-03-01

Full Text Available Cholangiocarcinoma (CCA is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDH mutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDH mutant subtype. More broadly, we found that IDH mutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance.

Mechanisms of defect production and atomic mixing in high energy displacement cascades: A molecular dynamics study

International Nuclear Information System (INIS)

Diaz de la Rubia, T.; Guinan, M.W.

1991-01-01

We have performed molecular dynamics computer simulation studies of displacement cascades in Cu at low temperature. For 25 keV recoils we observe the splitting of a cascade into subcascades and show that cascades in Cu may lead to the formation of vacancy and interstitial dislocation loops. We discuss a new mechanism of defect production based on the observation of interstitial prismatic dislocation loop punching from cascades at 10 K. We also show that below the subcascade threshold, atomic mixing in the cascade is recoil-energy dependent and obtain a mixing efficiency that scales as the square root of the primary recoil energy. 44 refs., 12 figs

Defects in dilute nitrides

International Nuclear Information System (INIS)

Chen, W.M.; Buyanova, I.A.; Tu, C.W.; Yonezu, H.

2005-01-01

We provide a brief review our recent results from optically detected magnetic resonance studies of grown-in non-radiative defects in dilute nitrides, i.e. Ga(In)NAs and Ga(Al,In)NP. Defect complexes involving intrinsic defects such as As Ga antisites and Ga i self interstitials were positively identified.Effects of growth conditions, chemical compositions and post-growth treatments on formation of the defects are closely examined. These grown-in defects are shown to play an important role in non-radiative carrier recombination and thus in degrading optical quality of the alloys, harmful to performance of potential optoelectronic and photonic devices based on these dilute nitrides. (author)

The effects of defects on copper melting under hydrostatic and shock loading

Energy Technology Data Exchange (ETDEWEB)

Luo, Shengnian [Los Alamos National Laboratory; An, Qi [Los Alamos National Laboratory; Germann, Timothy C [Los Alamos National Laboratory; Han, Li - Bo [USTC

2009-07-24

With molecular dynamics (MD) simulations, we investigate the effects of defects on Cu melting under hydrostatic and shock wave loading. We explore preexistent defects including vacancies, stacking faults and grain boundaries, as well as shock-induced defects. Depending on defect characteristics (energy and concentration), defects may have negligible or considerable effects on melting at MD scales However, it is expected that defects have more pronounced effects at heating rates lower than the MD rates.

Defect production in Ar irradiated graphene membranes under different initial applied strains

Energy Technology Data Exchange (ETDEWEB)

Martinez-Asencio, J., E-mail: jesusmartinez@ua.es [Dept. Física Aplicada, Facultad de Ciencias, Fase II, Universidad de Alicante, Alicante E-036090 (Spain); Ruestes, C.J.; Bringa, E. [CONICET and Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Mendoza 5500 (Argentina); Caturla, M.J. [Dept. Física Aplicada, Facultad de Ciencias, Fase II, Universidad de Alicante, Alicante E-036090 (Spain)

2017-02-15

Highlights: • Defects in graphene membranes are formed due to 140 eV Ar ions irradiation using MD. • Different initial strains are applied, which influence the type and number of defects. • Mono-vacancies, di-vacancies and tri-vacancies production behaves linearly with dose. • The total number of defects under compression is slightly higher than under tension. - Abstract: Irradiation with low energy Ar ions of graphene membranes gives rise to changes in the mechanical properties of this material. These changes have been associated to the production of defects, mostly isolated vacancies. However, the initial state of the graphene membrane can also affect its mechanical response. Using molecular dynamics simulations we have studied defect production in graphene membranes irradiated with 140 eV Ar ions up to a dose of 0.075 × 10{sup 14} ions/cm{sup 2} and different initial strains, from −0.25% (compressive strain) to 0.25% (tensile strain). For all strains, the number of defects increases linearly with dose with a defect production of about 80% (80 defects every 100 ions). Defects are mostly single vacancies and di-vacancies, although some higher order clusters are also observed. Two different types of di-vacancies have been identified, the most common one being two vacancies at first nearest neighbours distance. Differences in the total number of defects with the applied strain are observed which is related to the production of a higher number of di-vacancies under compressive strain compared to tensile strain. We attribute this effect to the larger out-of-plane deformations of compressed samples that could favor the production of defects in closer proximity to others.

Nanocarbon: Defect Architectures and Properties

Science.gov (United States)

Vuong, Amanda

The allotropes of carbon make its solid phases amongst the most diverse of any element. It can occur naturally as graphite and diamond, which have very different properties that make them suitable for a wide range of technological and commercial purposes. Recent developments in synthetic carbon include Highly Oriented Pyrolytic Graphite (HOPG) and nano-carbons, such as fullerenes, nanotubes and graphene. The main industrial application of bulk graphite is as an electrode material in steel production, but in purified nuclear graphite form, it is also used as a moderator in Advanced Gas-cooled Reactors across the United Kingdom. Both graphene and graphite are damaged over time when subjected to bombardment by electrons, neutrons or ions, and these have a wide range of effects on their physical and electrical properties, depending on the radiation flux and temperature. This research focuses on intrinsic defects in graphene and dimensional change in nuclear graphite. The method used here is computational chemistry, which complements physical experiments. Techniques used comprise of density functional theory (DFT) and molecular dynamics (MD), which are discussed in chapter 2 and chapter 3, respectively. The succeeding chapters describe the results of simulations performed to model defects in graphene and graphite. Chapter 4 presents the results of ab initio DFT calculations performed to investigate vacancy complexes that are formed in AA stacked bilayer graphene. In AB stacking, carbon atoms surrounding the lattice vacancies can form interlayer structures with sp2 bonding that are lower in energy compared to in-plane reconstructions. From the investigation of AA stacking, sp2 interlayer bonding of adjacent multivacancy defects in registry creates a type of stable sp2 bonded wormhole between the layers. Also, a new class of mezzanine structure characterised by sp3 interlayer bonding, resembling a prismatic vacancy loop has also been identified. The mezzanine, which is a

Simulating the production of free defects in irradiated metals

International Nuclear Information System (INIS)

Heinisch, H.L.

1995-01-01

Under cascade-producing irradiation by high energy neutrons or charged particles, only a small fraction of the initially displaced atoms contribute to the population of free defects that are available to migrate throughout the metal and cause microstructural changes. Although, in principle, computer simulations of free defect production could best be done using molecular dynamics, in practice, the wide ranges of time and distance scales involved can be done only by a combination of atomistic models that employ various levels of approximation. An atomic-scale, multi-model approach has been developed that combines molecular dynamics, binary collision models and stochastic annealing simulation. The annealing simulation is utilized in calibrating binary collision simulations to the results of molecular dynamics calculations, as well as to model the subsequent migration of the defects on more macroscopic time and size scales. The annealing simulation and the method of calibrating the multi-model approach are discussed, and the results of simulations of cascades in copper are presented. The temperature dependence of free defect production following simulated annealing of isolated cascades in copper shows a differential in the fractions of free vacancies and interstitial defects escaping from the cascade above stage V. This differential, a consequence of the direct formation of interstitial clusters in cascades and the relative thermal stability of vacancy and interstitial clusters during subsequent annealing, is the basis for the production bias mechanism of void swelling. (orig.)

Positron lifetime calculation for defects and defect clusters in graphite

International Nuclear Information System (INIS)

Onitsuka, T.; Ohkubo, H.; Takenaka, M.; Tsukuda, N.; Kuramoto, E.

2000-01-01

Calculations of positron lifetime have been made for vacancy type defects in graphite and compared with experimental results. Defect structures were obtained in a model graphite lattice after including relaxation of whole lattice as determined by the molecular dynamics method, where the interatomic potential given by Pablo Andribet, Dominguez-Vazguez, Mari Carmen Perez-Martin, Alonso, Jimenez-Rodriguez [Nucl. Instrum. and Meth. 115 (1996) 501] was used. For the defect structures obtained via lattice relaxation positron lifetime was calculated under the so-called atomic superposition method. Positron lifetimes 204 and 222 ps were obtained for the graphite matrix and a single vacancy, respectively, which can be compared with the experimental results 208 and 233 ps. For planar vacancy clusters, e.g., vacancy loops, lifetime calculation was also made and indicated that lifetime increases with the number of vacancies in a cluster. This is consistent with the experimental result in the region of higher annealing temperature (above 1200 deg. C), where the increase of positron lifetime is seen, probably corresponding to the clustering of mobile vacancies

Multiscale crystal defect dynamics: A coarse-grained lattice defect model based on crystal microstructure

Science.gov (United States)

Lyu, Dandan; Li, Shaofan

2017-10-01

Crystal defects have microstructure, and this microstructure should be related to the microstructure of the original crystal. Hence each type of crystals may have similar defects due to the same failure mechanism originated from the same microstructure, if they are under the same loading conditions. In this work, we propose a multiscale crystal defect dynamics (MCDD) model that models defects by considering its intrinsic microstructure derived from the microstructure or material genome of the original perfect crystal. The main novelties of present work are: (1) the discrete exterior calculus and algebraic topology theory are used to construct a scale-up (coarse-grained) dual lattice model for crystal defects, which may represent all possible defect modes inside a crystal; (2) a higher order Cauchy-Born rule (up to the fourth order) is adopted to construct atomistic-informed constitutive relations for various defect process zones, and (3) an hierarchical strain gradient theory based finite element formulation is developed to support an hierarchical multiscale cohesive (process) zone model for various defects in a unified formulation. The efficiency of MCDD computational algorithm allows us to simulate dynamic defect evolution at large scale while taking into account atomistic interaction. The MCDD model has been validated by comparing of the results of MCDD simulations with that of molecular dynamics (MD) in the cases of nanoindentation and uniaxial tension. Numerical simulations have shown that MCDD model can predict dislocation nucleation induced instability and inelastic deformation, and thus it may provide an alternative solution to study crystal plasticity.

A study of defects in diamond

International Nuclear Information System (INIS)

Hunt, D.C.

1999-01-01

Defects, intrinsic and extrinsic, in natural and synthetic diamond, have been studied using Electron Paramagnetic Resonance (EPR) and optical absorption techniques. EPR measurements have been used in conjunction with infrared absorption to identify the defect-induced one-phonon infrared spectra produced by ionised single substitutional nitrogen, N s + . This N s + spectrum is characterised by a sharp peak at the Raman energy, 1332 cm -1 , accompanied by several broader resonances at 950(5), 1050(5), and 1095(5) cm -1 . Detailed concentration measurements show that a concentration of 5.5(5) ppm gives rise to an absorption of 1 cm -1 at 1332 cm -1 . The optical absorption band ND1, identified as the negative vacancy (V - ), is frequently used by diamond spectroscopists to measure the concentration of V - . Isoya has identified V - in the EPR spectra of irradiated diamond. The accuracy of EPR in determining concentrations, has been used to correlate the integrated absorption of the ND1 zero-phonon line to the concentration of V - centres. The parameter derived from this correlation is ∼16 times smaller than the previously accepted value obtained by indirect methods. A systematic study has been made - using EPR and optical absorption techniques - of synthetic type IIa diamonds, which have been irradiated with 2 MeV electrons in a specially developed dewar, allowing irradiation down to a measured sample temperature of 100K. Measurement of defect creation rates of the neutral vacancy and EPR defects, show a radical difference in the production rate of the EPR defect R2 between irradiation with the sample held at 100K and 350K. At 100K its production rate is 1.1(1) cm -1 , ∼10 times greater that at 350K. Observation of the di- -split interstitial (Ri) after irradiation at 100K proves the self-interstitial in diamond must be mobile at 100K, under the conditions of irradiation. Further study of the properties of the R2 defect (the most dominant EPR after electron

Quantum computing with defects.

Science.gov (United States)

Weber, J R; Koehl, W F; Varley, J B; Janotti, A; Buckley, B B; Van de Walle, C G; Awschalom, D D

2010-05-11

Identifying and designing physical systems for use as qubits, the basic units of quantum information, are critical steps in the development of a quantum computer. Among the possibilities in the solid state, a defect in diamond known as the nitrogen-vacancy (NV(-1)) center stands out for its robustness--its quantum state can be initialized, manipulated, and measured with high fidelity at room temperature. Here we describe how to systematically identify other deep center defects with similar quantum-mechanical properties. We present a list of physical criteria that these centers and their hosts should meet and explain how these requirements can be used in conjunction with electronic structure theory to intelligently sort through candidate defect systems. To illustrate these points in detail, we compare electronic structure calculations of the NV(-1) center in diamond with those of several deep centers in 4H silicon carbide (SiC). We then discuss the proposed criteria for similar defects in other tetrahedrally coordinated semiconductors.

The electronic transport properties of defected bilayer sliding armchair graphene nanoribbons

Science.gov (United States)

Mohammadi, Amin; Haji-Nasiri, Saeed

2018-04-01

By applying non-equilibrium Green's functions (NEGF) in combination with tight-binding (TB) model, we investigate and compare the electronic transport properties of perfect and defected bilayer armchair graphene nanoribbons (BAGNRs) under finite bias. Two typical defects which are placed in the middle of top layer (i.e. single vacancy (SV) and stone wale (SW) defects) are examined. The results reveal that in both perfect and defected bilayers, the maximum current refers to β-AB, AA and α-AB stacking orders, respectively, since the intermolecular interactions are stronger in them. Moreover it is observed that a SV decreases the current in all stacking orders, but the effects of a SW defect is nearly unpredictable. Besides, we introduced a sequential switching behavior and the effects of defects on the switching performance is studied as well. We found that a SW defect can significantly improve the switching behavior of a bilayer system. Transmission spectrum, band structure, molecular energy spectrum and molecular projected self-consistent Hamiltonian (MPSH) are analyzed subsequently to understand the electronic transport properties of these bilayer devices which can be used in developing nano-scale bilayer systems.

Patterning and gastrulation defects caused by the tw18 lethal are due to loss of Ppp2r1a

Directory of Open Access Journals (Sweden)

Lisette Lange

2017-06-01

Full Text Available The mouse t haplotype, a variant 20 cM genomic region on Chromosome 17, harbors 16 embryonic control genes identified by recessive lethal mutations isolated from wild mouse populations. Due to technical constraints so far only one of these, the tw5 lethal, has been cloned and molecularly characterized. Here we report the molecular isolation of the tw18 lethal. Embryos carrying the tw18 lethal die from major gastrulation defects commencing with primitive streak formation at E6.5. We have used transcriptome and marker gene analyses to describe the molecular etiology of the tw18 phenotype. We show that both WNT and Nodal signal transduction are impaired in the mutant epiblast, causing embryonic patterning defects and failure of primitive streak and mesoderm formation. By using a candidate gene approach, gene knockout by homologous recombination and genetic rescue, we have identified the gene causing the tw18 phenotype as Ppp2r1a, encoding the PP2A scaffolding subunit PR65alpha. Our work highlights the importance of phosphatase 2A in embryonic patterning, primitive streak formation, gastrulation, and mesoderm formation downstream of WNT and Nodal signaling.

Serine biosynthesis and transport defects.

Science.gov (United States)

El-Hattab, Ayman W

2016-07-01

l-serine is a non-essential amino acid that is biosynthesized via the enzymes phosphoglycerate dehydrogenase (PGDH), phosphoserine aminotransferase (PSAT), and phosphoserine phosphatase (PSP). Besides its role in protein synthesis, l-serine is a potent neurotrophic factor and a precursor of a number of essential compounds including phosphatidylserine, sphingomyelin, glycine, and d-serine. Serine biosynthesis defects result from impairments of PGDH, PSAT, or PSP leading to systemic serine deficiency. Serine biosynthesis defects present in a broad phenotypic spectrum that includes, at the severe end, Neu-Laxova syndrome, a lethal multiple congenital anomaly disease, intermediately, infantile serine biosynthesis defects with severe neurological manifestations and growth deficiency, and at the mild end, the childhood disease with intellectual disability. A serine transport defect resulting from deficiency of the ASCT1, the main transporter for serine in the central nervous system, has been recently described in children with neurological manifestations that overlap with those observed in serine biosynthesis defects. l-serine therapy may be beneficial in preventing or ameliorating symptoms in serine biosynthesis and transport defects, if started before neurological damage occurs. Herein, we review serine metabolism and transport, the clinical, biochemical, and molecular aspects of serine biosynthesis and transport defects, the mechanisms of these diseases, and the potential role of serine therapy. Copyright © 2016 Elsevier Inc. All rights reserved.

Characterization of point defects in monolayer arsenene

Science.gov (United States)

Liang, Xiongyi; Ng, Siu-Pang; Ding, Ning; Wu, Chi-Man Lawrence

2018-06-01

Topological defects that are inevitably found in 2D materials can dramatically affect their properties. Using density functional theory (DFT) calculations and ab initio molecular dynamics (AIMD) method, the structural, thermodynamic, electronic and magnetic properties of six types of typical point defects in arsenene, i.e. the Stone-Wales defect, single and double vacancies and adatoms, were systemically studied. It was found that these defects were all more easily generated in arsenene with lower formation energies than those with graphene and silicene. Stone-Wales defects can be transformed from pristine arsenene by overcoming a barrier of 2.19 eV and single vacancy defects tend to coalesce into double vacancy defects by diffusion. However, a type of adatom defect does not exhibit kinetic stability at room temperature. In addition, SV defects and another type of adatom defect can remarkably affect the electronic and magnetic properties of arsenene, e.g. they can introduce localized states near the Fermi level, as well as a strongly local magnetic moment due to dangling bond and unpaired electron. Furthermore, the simulated scanning tunneling microscopy (STM) and Raman spectroscopy were computed and the types of point defects can be fully characterized by correlating the STM images and Raman spectra to the defective atomistic structures. The results provide significant insights to the effect of defects in arsenene for potential applications, as well as identifications of two helpful tools (STM and Raman spectroscopy) to distinguish the type of defects in arsenene for future experiments.

Electronic Rydberg wavepacket effects on molecular vibration

International Nuclear Information System (INIS)

Hughes, I.G.; Meacher, D.R.

1994-01-01

Electronic wavepacket states of molecular hydrogen are considered which represent the situation of a spectator electron orbiting a molecular core. A quantum defect theory approach is used to determine the energy level structure, wavefunctions and molecular potentials, which is valid in regions where the quantum defects approach zero. In such a region the orbital motion of the wavepacket leads to a periodic variation in the molecular vibration frequency of the order of 100 cm -1 . Possible detection schemes are discussed. (author)

Defects in new protective aprons

International Nuclear Information System (INIS)

Glaze, S.; LeBlanc, A.D.; Bushong, S.C.

1984-01-01

Upon careful examination, several defects have been detected in new protective aprons. The nature of the defects is identified and described. Although the occurrence of such defects has not exceeded 5%, they are significant enough to warrant return of the lead apron to the supplier. It is recommended that the integrity of all new protective aprons be verified upon receipt as well as at yearly intervals

Comparing hair-morphology and molecular methods to identify fecal samples from Neotropical felids.

Directory of Open Access Journals (Sweden)

Carlos C Alberts

Full Text Available To avoid certain problems encountered with more-traditional and invasive methods in behavioral-ecology studies of mammalian predators, such as felids, molecular approaches have been employed to identify feces found in the field. However, this method requires a complete molecular biology laboratory, and usually also requires very fresh fecal samples to avoid DNA degradation. Both conditions are normally absent in the field. To address these difficulties, identification based on morphological characters (length, color, banding, scales and medullar patterns of hairs found in feces could be employed as an alternative. In this study we constructed a morphological identification key for guard hairs of eight Neotropical felids (jaguar, oncilla, Geoffroy's cat, margay, ocelot, Pampas cat, puma and jaguarundi and compared its efficiency to that of a molecular identification method, using the ATP6 region as a marker. For this molecular approach, we simulated some field conditions by postponing sample-conservation procedures. A blind test of the identification key obtained a nearly 70% overall success rate, which we considered equivalent to or better than the results of some molecular methods (probably due to DNA degradation found in other studies. The jaguar, puma and jaguarundi could be unequivocally discriminated from any other Neotropical felid. On a scale ranging from inadequate to excellent, the key proved poor only for the margay, with only 30% of its hairs successfully identified using this key; and have intermediate success rates for the remaining species, the oncilla, Geoffroy's cat, ocelot and Pampas cat, were intermediate. Complementary information about the known distributions of felid populations may be necessary to substantially improve the results obtained with the key. Our own molecular results were even better, since all blind-tested samples were correctly identified. Part of these identifications were made from samples kept in suboptimal

What’s new in genetics of congenital heart defects

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Maria Cristina Digilio

2016-12-01

Full Text Available Epidemiological studies, clinical observations and advances in molecular genetics are contributing to the understanding of the etiology of congenital heart defects (CHDs. Several phenotype-genotype correlation studies have suggested that specific morphogenetic mechanisms put in motion by genes can result in a specific cardiac phenotype. The use of new technologies has increased the possibility of identification of new genes and chromosomal loci in syndromic and non-syndromic CHDs. There are a number of methods available for genetic research studies of CHDs, including cytogenetic analysis, linkage and association studies, copy number variation (CNV and DNA micro-array analysis, and whole exome sequencing. The altered dosage of contigous genes included inside CNVs can produce new syndromic CHDs, so that several different new genomic conditions have been identified. These include duplication 22q11.2 syndrome, distal 22q11.2 deletion syndrome, deletion and duplication 1q21.1, deletion 1p36 syndrome. Molecular techniques as whole exome sequancing has lead to the identification of new genes for monogenic syndromes with CHD, as for example in Adams-Oliver, Noonan and Kabuki syndrome. The variable expressivity and reduced penetrance of CHDs in genetic syndromes is likely influenced by genetic factors, and several studies have been performed showing the involvement of modifier genes. It is not easy to define precisely the genetic defects underlying non-syndromic CHDs, due to the genetic and clinical heterogeneity of these malformations. Recent experimental studies have identified multiple CNVs contributing to non-syndromic CHD. The number of identified genes for non-syndromic CHDs is at this time limited and each of the identified gene has been shown to be implicated only in a small proportion of CHD. The application of new technologies to specific cases of CHD and pedigrees with familial recurrence and filtering genes mapping in CNV regions can probably

Gauge theory and defects in solids

CERN Document Server

Edelen, DGB

2012-01-01

This new series Mechanics and Physics of Discrete Systems aims to provide a coherent picture of the modern development of discrete physical systems. Each volume will offer an orderly perspective of disciplines such as molecular dynamics, crystal mechanics and/or physics, dislocation, etc. Emphasized in particular are the fundamentals of mechanics and physics that play an essential role in engineering applications.Volume 1, Gauge Theory and Defects in Solids, presents a detailed development of a rational theory of the dynamics of defects and damage in solids. Solutions to field e

Investigation of Shrinkage Defect in Castings by Quantitative Ishikawa Diagram

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Chokkalingam B.

2017-03-01

Full Text Available Metal casting process involves processes such as pattern making, moulding and melting etc. Casting defects occur due to combination of various processes even though efforts are taken to control them. The first step in the defect analysis is to identify the major casting defect among the many casting defects. Then the analysis is to be made to find the root cause of the particular defect. Moreover, it is especially difficult to identify the root causes of the defect. Therefore, a systematic method is required to identify the root cause of the defect among possible causes, consequently specific remedial measures have to be implemented to control them. This paper presents a systematic procedure to identify the root cause of shrinkage defect in an automobile body casting (SG 500/7 and control it by the application of Pareto chart and Ishikawa diagram. with quantitative Weightage. It was found that the root causes were larger volume section in the cope, insufficient feeding of riser and insufficient poured metal in the riser. The necessary remedial measures were taken and castings were reproduced. The shrinkage defect in the castings was completely eliminated.

Proceedings of the European Meeting on Positron Studies of Defects

International Nuclear Information System (INIS)

1987-01-01

The meeting dealt with both theoretical and experimental aspects of positron studies of defects using conventional and novel positron techniques. The subjects are indicated in the following headings: (1) theory of positrons in imperfect solids, (2) vacancies in metals and alloys, (3) dislocation and deformation effects, (4) amorphous alloys and fine-grained materials, (5) phase transitions, (6) precipitation phenomena, (7) gas impurity-defect interaction and irradiation effects, (8) defects in elemental semiconductors, (9) defects in compound semiconductors, (10) slow positron studies of defects, (11) defects in oxides and halides, (12) defects in molecular solids, and (13) advances in experimental techniques and data treatment. Althogether 141 contributions (invited plenary lectures, short lectures, and posters) are presented as titles with abstracts. Most of them are in INIS scope and are processed individually for the database

Fanconi anemia: a disorder defective in the DNA damage response.

Science.gov (United States)

Kitao, Hiroyuki; Takata, Minoru

2011-04-01

Fanconi anemia (FA) is a cancer predisposition disorder characterized by progressive bone marrow failure, congenital developmental defects, chromosomal abnormalities, and cellular hypersensitivity to DNA interstrand crosslink (ICL) agents. So far mutations in 14 FANC genes were identified in FA or FA-like patients. These gene products constitute a common ubiquitin-phosphorylation network called the "FA pathway" and cooperate with other proteins involved in DNA repair and cell cycle control to repair ICL lesions and to maintain genome stability. In this review, we summarize recent exciting discoveries that have expanded our view of the molecular mechanisms operating in DNA repair and DNA damage signaling.

Usher syndrome (sensorineural deafness and retinitis pigmentosa): pathogenesis, molecular diagnosis and therapeutic approaches.

Science.gov (United States)

Bonnet, Crystel; El-Amraoui, Aziz

2012-02-01

Usher syndrome (USH) is the most prevalent cause of hereditary deafness-blindness in humans. In this review, we pinpoint new insights regarding the molecular mechanisms defective in this syndrome, its molecular diagnosis and prospective therapies. Animal models wherein USH proteins were targeted at different maturation stages of the auditory hair cells have been engineered, shedding new light on the development and functioning of the hair bundle, the sound receptive structure. Improved protocols and guidelines for early molecular diagnosis of USH (USH genotyping microarrays, otochips and complete Sanger sequencing of the 366 coding exons of identified USH genes) have been developed. Approaches to alleviate or cure hearing and visual impairments have been initiated, leading to various degrees of functional rescuing. Whereas the mechanisms underlying hearing impairment in USH patients are being unraveled, showing in particular that USH1 proteins are involved in the shaping of the hair bundle and the functioning of the mechanoelectrical transduction machinery, the mechanisms underlying the retinal defects are still unclear. Efforts to improve clinical diagnosis have been successful. Yet, despite some encouraging results, further development of therapeutic approaches is necessary to ultimately treat this dual sensory defect.

Nuclear Pasta: Topology and Defects

Science.gov (United States)

da Silva Schneider, Andre; Horowitz, Charles; Berry, Don; Caplan, Matt; Briggs, Christian

2015-04-01

A layer of complex non-uniform phases of matter known as nuclear pasta is expected to exist at the base of the crust of neutron stars. Using large scale molecular dynamics we study the topology of some pasta shapes, the formation of defects and how these may affect properties of neutron star crusts.

Defect formation in fluoropolymer films at their condensation from a gas phase

Science.gov (United States)

Luchnikov, P. A.

2018-01-01

The questions of radiation defects, factors of influence of electronic high-frequency discharge plasma components on the molecular structure and properties of the fluoropolymer vacuum films synthesized on a substrate from a gas phase are considered. It is established that at sedimentation of fluoropolymer coverings from a gas phase in high-frequency discharge plasma in films there are radiation defects in molecular and supramolecular structure because of the influence of active plasma components which significantly influence their main properties.

Radial collapse and physical mechanism of carbon nanotube with divacancy and 5-8-5 defects

International Nuclear Information System (INIS)

Zhang Ya-Ping; Ling Cui-Cui; Li Gui-Xia; Zhu Hai-Feng; Zhang Meng-Yu

2015-01-01

By employing molecular mechanics and molecular dynamics simulations, we investigate the radial collapses and elasticities of different chiral single-walled carbon nanotubes (SWCNTs) with divacancy, and 5-8-5 defects. It is found that divacancy and 5-8-5 defect can reduce the collapse pressure (P c ) of SWCNT (10, 10) while 5-8-5 defect can greatly increase P c of SWCNT (17, 0). For example, 5-8-5 defect can make P c of SWCNT (17, 0) increase by 500%. A model is established to understand the effects of chirality, divacancy, and 5-8-5 defect on radial collapse of SWCNTs. The results are particularly of value for understanding the mechanical behavior of SWCNT with divacancy, and the 5-8-5 defect that may be considered as a filler of high loading composites. (paper)

A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury.

Science.gov (United States)

Yu, Chenggang; Boutté, Angela; Yu, Xueping; Dutta, Bhaskar; Feala, Jacob D; Schmid, Kara; Dave, Jitendra; Tawa, Gregory J; Wallqvist, Anders; Reifman, Jaques

2015-02-01

The multifactorial nature of traumatic brain injury (TBI), especially the complex secondary tissue injury involving intertwined networks of molecular pathways that mediate cellular behavior, has confounded attempts to elucidate the pathology underlying the progression of TBI. Here, systems biology strategies are exploited to identify novel molecular mechanisms and protein indicators of brain injury. To this end, we performed a meta-analysis of four distinct high-throughput gene expression studies involving different animal models of TBI. By using canonical pathways and a large human protein-interaction network as a scaffold, we separately overlaid the gene expression data from each study to identify molecular signatures that were conserved across the different studies. At 24 hr after injury, the significantly activated molecular signatures were nonspecific to TBI, whereas the significantly suppressed molecular signatures were specific to the nervous system. In particular, we identified a suppressed subnetwork consisting of 58 highly interacting, coregulated proteins associated with synaptic function. We selected three proteins from this subnetwork, postsynaptic density protein 95, nitric oxide synthase 1, and disrupted in schizophrenia 1, and hypothesized that their abundance would be significantly reduced after TBI. In a penetrating ballistic-like brain injury rat model of severe TBI, Western blot analysis confirmed our hypothesis. In addition, our analysis recovered 12 previously identified protein biomarkers of TBI. The results suggest that systems biology may provide an efficient, high-yield approach to generate testable hypotheses that can be experimentally validated to identify novel mechanisms of action and molecular indicators of TBI. © 2014 The Authors. Journal of Neuroscience Research Published by Wiley Periodicals, Inc.

Genomic analyses identify molecular subtypes of pancreatic cancer.

Science.gov (United States)

Bailey, Peter; Chang, David K; Nones, Katia; Johns, Amber L; Patch, Ann-Marie; Gingras, Marie-Claude; Miller, David K; Christ, Angelika N; Bruxner, Tim J C; Quinn, Michael C; Nourse, Craig; Murtaugh, L Charles; Harliwong, Ivon; Idrisoglu, Senel; Manning, Suzanne; Nourbakhsh, Ehsan; Wani, Shivangi; Fink, Lynn; Holmes, Oliver; Chin, Venessa; Anderson, Matthew J; Kazakoff, Stephen; Leonard, Conrad; Newell, Felicity; Waddell, Nick; Wood, Scott; Xu, Qinying; Wilson, Peter J; Cloonan, Nicole; Kassahn, Karin S; Taylor, Darrin; Quek, Kelly; Robertson, Alan; Pantano, Lorena; Mincarelli, Laura; Sanchez, Luis N; Evers, Lisa; Wu, Jianmin; Pinese, Mark; Cowley, Mark J; Jones, Marc D; Colvin, Emily K; Nagrial, Adnan M; Humphrey, Emily S; Chantrill, Lorraine A; Mawson, Amanda; Humphris, Jeremy; Chou, Angela; Pajic, Marina; Scarlett, Christopher J; Pinho, Andreia V; Giry-Laterriere, Marc; Rooman, Ilse; Samra, Jaswinder S; Kench, James G; Lovell, Jessica A; Merrett, Neil D; Toon, Christopher W; Epari, Krishna; Nguyen, Nam Q; Barbour, Andrew; Zeps, Nikolajs; Moran-Jones, Kim; Jamieson, Nigel B; Graham, Janet S; Duthie, Fraser; Oien, Karin; Hair, Jane; Grützmann, Robert; Maitra, Anirban; Iacobuzio-Donahue, Christine A; Wolfgang, Christopher L; Morgan, Richard A; Lawlor, Rita T; Corbo, Vincenzo; Bassi, Claudio; Rusev, Borislav; Capelli, Paola; Salvia, Roberto; Tortora, Giampaolo; Mukhopadhyay, Debabrata; Petersen, Gloria M; Munzy, Donna M; Fisher, William E; Karim, Saadia A; Eshleman, James R; Hruban, Ralph H; Pilarsky, Christian; Morton, Jennifer P; Sansom, Owen J; Scarpa, Aldo; Musgrove, Elizabeth A; Bailey, Ulla-Maja Hagbo; Hofmann, Oliver; Sutherland, Robert L; Wheeler, David A; Gill, Anthony J; Gibbs, Richard A; Pearson, John V; Waddell, Nicola; Biankin, Andrew V; Grimmond, Sean M

2016-03-03

Integrated genomic analysis of 456 pancreatic ductal adenocarcinomas identified 32 recurrently mutated genes that aggregate into 10 pathways: KRAS, TGF-β, WNT, NOTCH, ROBO/SLIT signalling, G1/S transition, SWI-SNF, chromatin modification, DNA repair and RNA processing. Expression analysis defined 4 subtypes: (1) squamous; (2) pancreatic progenitor; (3) immunogenic; and (4) aberrantly differentiated endocrine exocrine (ADEX) that correlate with histopathological characteristics. Squamous tumours are enriched for TP53 and KDM6A mutations, upregulation of the TP63∆N transcriptional network, hypermethylation of pancreatic endodermal cell-fate determining genes and have a poor prognosis. Pancreatic progenitor tumours preferentially express genes involved in early pancreatic development (FOXA2/3, PDX1 and MNX1). ADEX tumours displayed upregulation of genes that regulate networks involved in KRAS activation, exocrine (NR5A2 and RBPJL), and endocrine differentiation (NEUROD1 and NKX2-2). Immunogenic tumours contained upregulated immune networks including pathways involved in acquired immune suppression. These data infer differences in the molecular evolution of pancreatic cancer subtypes and identify opportunities for therapeutic development.

Using Genetic Buffering Relationships Identified in Fission Yeast To Elucidate the Molecular Pathology of Tuberous Sclerosis

Science.gov (United States)

2016-07-01

tsc1 and tsc2 loss of function mutations in Schizosaccharomyces pombe. Northeast Regional Yeast Meeting, June 16-17, University at Buffalo, The State...AWARD NUMBER: W81XWH-14-1-0169 TITLE: Using Genetic Buffering Relationships Identified in Fission Yeast To Elucidate the Molecular Pathology of...SUBTITLE Using Genetic Buffering Relationships Identified in Fission 5a. CONTRACT NUMBER W81XWH-14-1-0169 Yeast to Elucidate the Molecular Pathology

Key Questions in Building Defect Prediction Models in Practice

Science.gov (United States)

Ramler, Rudolf; Wolfmaier, Klaus; Stauder, Erwin; Kossak, Felix; Natschläger, Thomas

The information about which modules of a future version of a software system are defect-prone is a valuable planning aid for quality managers and testers. Defect prediction promises to indicate these defect-prone modules. However, constructing effective defect prediction models in an industrial setting involves a number of key questions. In this paper we discuss ten key questions identified in context of establishing defect prediction in a large software development project. Seven consecutive versions of the software system have been used to construct and validate defect prediction models for system test planning. Furthermore, the paper presents initial empirical results from the studied project and, by this means, contributes answers to the identified questions.

Mobility of a 5|7 defect in carbon nanotubes

Energy Technology Data Exchange (ETDEWEB)

Lee, Youngmin; Han, Jihoon; Im, Seyoung [Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology (KAIST), Science Town, Daejeon, 305-701 (Korea, Republic of); Lee, In-Ho, E-mail: sim@kaist.ac.kr [Korea Research Institute of Standards and Science (KRISS), Daejeon, 305-600 (Korea, Republic of)

2011-03-11

The movement of a 5|7 defect in the plastic deformations of a carbon nanotube (CNT) plays the role of dislocation glide in the plastic deformations of metals. This work is concerned with the atomic shift mechanism of the 5|7 defect and the energy barrier when the CNT is subjected to tensile loading. Action-derived molecular dynamics (ADMD) is applied to find the minimum energy path and the energy barrier. It is found that the tensile loads make it easy for the 5|7 defect to glide, and lower the energy barrier. The minimum load level that makes a 5|7 defect glide freely with no energy barrier in the presence of an adatom is obtained.

Mobility of a 5|7 defect in carbon nanotubes

International Nuclear Information System (INIS)

Lee, Youngmin; Han, Jihoon; Im, Seyoung; Lee, In-Ho

2011-01-01

The movement of a 5|7 defect in the plastic deformations of a carbon nanotube (CNT) plays the role of dislocation glide in the plastic deformations of metals. This work is concerned with the atomic shift mechanism of the 5|7 defect and the energy barrier when the CNT is subjected to tensile loading. Action-derived molecular dynamics (ADMD) is applied to find the minimum energy path and the energy barrier. It is found that the tensile loads make it easy for the 5|7 defect to glide, and lower the energy barrier. The minimum load level that makes a 5|7 defect glide freely with no energy barrier in the presence of an adatom is obtained.

Coarse-grained molecular dynamics modeling of the kinetics of lamellar BCP defect annealing

Science.gov (United States)

Peters, Andrew J.; Lawson, Richard A.; Nation, Benjamin D.; Ludovice, Peter J.; Henderson, Clifford L.

2015-03-01

Directed self-assembly of block copolymers (BCPs) is a process that has received great interest in the field of nanomanufacturing in the past decade, and great strides towards forming high quality aligned patterns have been made. But state of the art methods still yield defectivities orders of magnitude higher than is necessary in semi-conductor fabrication even though free energy calculations suggest that equilibrium defectivities are much lower than is necessary for economic semi-conductor fabrication. This disparity suggests that the main problem may lie in the kinetics of defect removal. This work uses a coarse-grained model to study the rates, pathways, and dependencies of healing a common defect to give insight into the fundamental processes that control defect healing and give guidance on optimal process conditions for BCP-DSA. It is found that infinitely thick films yield an exponential drop in defect heal rate above χN ~ 30. Below χN ~ 30, the rate of transport was similar to the rate at which the transition state was reached so that the overall rate changed only slightly. The energy barrier in periodic simulations increased with 0.31 χN on average. Thin film simulations show no change in rate associated with the energy barrier below χN ~ 50, and then show an increase in energy barrier scaling with 0.16χN. Thin film simulations always begin to heal at either the free interface or the BCP-underlayer interface where the increased A-B contact area associated with the transition state will be minimized, while the infinitely thick films must start healing in the bulk where the A-B contact area is increased. It is also found that cooperative chain movement is required for the defect to start healing.

The quantum defect: Early history and recent developments

International Nuclear Information System (INIS)

Rau, A.R.; Inokuti, M.

1997-01-01

The notion of the quantum defect is important in atomic and molecular spectroscopy and also in unifying spectroscopy with collision theory. In the latter context, the quantum defect may be viewed as an ancestor of the phase shift. However, the origin of the term open-quotes quantum defectclose quotes does not seem to be explained in standard textbooks. It occurred in a 1921 paper by Schroedinger, preceding quantum mechanics, yet giving the correct meaning as an index of the short-range interactions with the core of an atom. We present the early history of the quantum-defect idea, and sketch its recent developments. copyright 1997 American Association of Physics Teachers

Defining the molecular pathologies in cloaca malformation: similarities between mouse and human

Directory of Open Access Journals (Sweden)

Laura A. Runck

2014-04-01

Full Text Available Anorectal malformations are congenital anomalies that form a spectrum of disorders, from the most benign type with excellent functional prognosis, to very complex, such as cloaca malformation in females in which the rectum, vagina and urethra fail to develop separately and instead drain via a single common channel into the perineum. The severity of this phenotype suggests that the defect occurs in the early stages of embryonic development of the organs derived from the cloaca. Owing to the inability to directly investigate human embryonic cloaca development, current research has relied on the use of mouse models of anorectal malformations. However, even studies of mouse embryos lack analysis of the earliest stages of cloaca patterning and morphogenesis. Here we compared human and mouse cloaca development and retrospectively identified that early mis-patterning of the embryonic cloaca might underlie the most severe forms of anorectal malformation in humans. In mouse, we identified that defective sonic hedgehog (Shh signaling results in early dorsal-ventral epithelial abnormalities prior to the reported defects in septation. This is manifested by the absence of Sox2 and aberrant expression of keratins in the embryonic cloaca of Shh knockout mice. Shh knockout embryos additionally develop a hypervascular stroma, which is defective in BMP signaling. These epithelial and stromal defects persist later, creating an indeterminate epithelium with molecular alterations in the common channel. We then used these animals to perform a broad comparison with patients with mild-to-severe forms of anorectal malformations including cloaca malformation. We found striking parallels with the Shh mouse model, including nearly identical defective molecular identity of the epithelium and surrounding stroma. Our work strongly suggests that early embryonic cloacal epithelial differentiation defects might be the underlying cause of severe forms of anorectal malformations

Nucleic acid-based approaches to investigate microbial-related cheese quality defects

Directory of Open Access Journals (Sweden)

Daniel eO Sullivan

2013-01-01

Full Text Available AbstractThe microbial profile of cheese is a primary determinant of cheese quality. Microorganisms can contribute to aroma and taste defects, form biogenic amines, cause gas and secondary fermentation defects, and can contribute to cheese pinking and mineral deposition issues. These defects may be as a result of seasonality and the variability in the composition of the milk supplied, variations in cheese processing parameters, as well as the nature and number of the non-starter microorganisms which come from the milk or other environmental sources. Such defects can be responsible for production and product recall costs and thus represent a significant economic burden for the dairy industry worldwide. Traditional non-molecular approaches are often considered biased and have inherently slow turnaround times. Molecular techniques can provide early and rapid detection of defects that result from the presence of specific spoilage microbes and, ultimately, assist in enhancing cheese quality and reducing costs. Here we review the DNA-based methods that are available to detect/quantify spoilage bacteria, and relevant metabolic pathways, in cheeses and, in the process, highlight how these strategies can be employed to improve cheese quality and reduce the associated economic burden on cheese processors.

Cortical GABA markers identify a molecular subtype of psychotic and bipolar disorders.

Science.gov (United States)

Volk, D W; Sampson, A R; Zhang, Y; Edelson, J R; Lewis, D A

2016-09-01

Deficits in gamma aminobutyric acid (GABA) neuron-related markers, including the GABA-synthesizing enzyme GAD67, the calcium-binding protein parvalbumin, the neuropeptide somatostatin, and the transcription factor Lhx6, are most pronounced in a subset of schizophrenia subjects identified as having a 'low GABA marker' (LGM) molecular phenotype. Furthermore, schizophrenia shares degrees of genetic liability, clinical features and cortical circuitry abnormalities with schizoaffective disorder and bipolar disorder. Therefore, we determined the extent to which a similar LGM molecular phenotype may also exist in subjects with these disorders. Transcript levels for GAD67, parvalbumin, somatostatin, and Lhx6 were quantified using quantitative PCR in prefrontal cortex area 9 of 184 subjects with a diagnosis of schizophrenia (n = 39), schizoaffective disorder (n = 23) or bipolar disorder (n = 35), or with a confirmed absence of any psychiatric diagnoses (n = 87). A blinded clustering approach was employed to determine the presence of a LGM molecular phenotype across all subjects. Approximately 49% of the subjects with schizophrenia, 48% of the subjects with schizoaffective disorder, and 29% of the subjects with bipolar disorder, but only 5% of unaffected subjects, clustered in the cortical LGM molecular phenotype. These findings support the characterization of psychotic and bipolar disorders by cortical molecular phenotype which may help elucidate more pathophysiologically informed and personalized medications.

Atomistic simulation of damage production by atomic and molecular ion irradiation in GaN

International Nuclear Information System (INIS)

Ullah, M. W.; Kuronen, A.; Nordlund, K.; Djurabekova, F.; Karaseov, P. A.; Titov, A. I.

2012-01-01

We have studied defect production during single atomic and molecular ion irradiation having an energy of 50 eV/amu in GaN by molecular dynamics simulations. Enhanced defect recombination is found in GaN, in accordance with experimental data. Instantaneous damage shows non-linearity with different molecular projectile and increasing molecular mass. Number of instantaneous defects produced by the PF 4 molecule close to target surface is four times higher than that for PF 2 molecule and three times higher than that calculated as a sum of the damage produced by one P and four F ion irradiation (P+4×F). We explain this non-linearity by energy spike due to molecular effects. On the contrary, final damage created by PF 4 and PF 2 shows a linear pattern when the sample cools down. Total numbers of defects produced by Ag and PF 4 having similar atomic masses are comparable. However, defect-depth distributions produced by these species are quite different, also indicating molecular effect.

Defective glycinergic synaptic transmission in zebrafish motility mutants

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Hiromi Hirata

2010-01-01

Full Text Available Glycine is a major inhibitory neurotransmitter in the spinal cord and brainstem. Recently, in vivo analysis of glycinergic synaptic transmission has been pursued in zebrafish using molecular genetics. An ENU mutagenesis screen identified two behavioral mutants that are defective in glycinergic synaptic transmission. Zebrafish bandoneon (beo mutants have a defect in glrbb, one of the duplicated glycine receptor (GlyR β subunit genes. These mutants exhibit a loss of glycinergic synaptic transmission due to a lack of synaptic aggregation of GlyRs. Due to the consequent loss of reciprocal inhibition of motor circuits between the two sides of the spinal cord, motor neurons activate simultaneously on both sides resulting in bilateral contraction of axial muscles of beo mutants, eliciting the so-called ‘accordion’ phenotype. Similar defects in GlyR subunit genes have been observed in several mammals and are the basis for human hyperekplexia/startle disease. By contrast, zebrafish shocked (sho mutants have a defect in slc6a9, encoding GlyT1, a glycine transporter that is expressed by astroglial cells surrounding the glycinergic synapse in the hindbrain and spinal cord. GlyT1 mediates rapid uptake of glycine from the synaptic cleft, terminating synaptic transmission. In zebrafish sho mutants, there appears to be elevated extracellular glycine resulting in persistent inhibition of postsynaptic neurons and subsequent reduced motility, causing the ‘twitch once’ phenotype. We review current knowledge regarding zebrafish ‘accordion’ and ‘twitch once’ mutants, including beo and sho, and report the identification of a new α2 subunit that revises the phylogeny of zebrafish GlyRs.

Defective Glycinergic Synaptic Transmission in Zebrafish Motility Mutants

Science.gov (United States)

Hirata, Hiromi; Carta, Eloisa; Yamanaka, Iori; Harvey, Robert J.; Kuwada, John Y.

2009-01-01

Glycine is a major inhibitory neurotransmitter in the spinal cord and brainstem. Recently, in vivo analysis of glycinergic synaptic transmission has been pursued in zebrafish using molecular genetics. An ENU mutagenesis screen identified two behavioral mutants that are defective in glycinergic synaptic transmission. Zebrafish bandoneon (beo) mutants have a defect in glrbb, one of the duplicated glycine receptor (GlyR) β subunit genes. These mutants exhibit a loss of glycinergic synaptic transmission due to a lack of synaptic aggregation of GlyRs. Due to the consequent loss of reciprocal inhibition of motor circuits between the two sides of the spinal cord, motor neurons activate simultaneously on both sides resulting in bilateral contraction of axial muscles of beo mutants, eliciting the so-called ‘accordion’ phenotype. Similar defects in GlyR subunit genes have been observed in several mammals and are the basis for human hyperekplexia/startle disease. By contrast, zebrafish shocked (sho) mutants have a defect in slc6a9, encoding GlyT1, a glycine transporter that is expressed by astroglial cells surrounding the glycinergic synapse in the hindbrain and spinal cord. GlyT1 mediates rapid uptake of glycine from the synaptic cleft, terminating synaptic transmission. In zebrafish sho mutants, there appears to be elevated extracellular glycine resulting in persistent inhibition of postsynaptic neurons and subsequent reduced motility, causing the ‘twitch-once’ phenotype. We review current knowledge regarding zebrafish ‘accordion’ and ‘twitch-once’ mutants, including beo and sho, and report the identification of a new α2 subunit that revises the phylogeny of zebrafish GlyRs. PMID:20161699

Modeling defect production in high energy collision cascades

International Nuclear Information System (INIS)

Heinisch, H.L.; Singh, B.N.

1993-01-01

A multi-model approach roach (MMA) to simulating defect production processes at the atomic scale is described that incorporates molecular dynamics (MD), binary collision approximation (BCA) calculations and stochastic annealing simulations. The central hypothesis of the MMA is that the simple, fast computer codes capable of simulating large numbers of high energy cascades (e.g., BCA codes) can be made to yield the correct defect configurations when their parameters are calibrated using the results of the more physically realistic MD simulations. The calibration procedure is investigated using results of MD simulations of 25 keV cascades in copper. The configurations of point defects are extracted from the MD cascade simulations at the end of the collisional phase, similar to the information obtained with a binary collision model. The MD collisional phase defect configurations are used as input to the ALSOME annealing simulation code, and values of the ALSOME quenching parameters are determined that yield the best fit to the post-quenching defect configurations of the MD simulations

Combined computational and experimental study of Ar beam induced defect formation in graphite

International Nuclear Information System (INIS)

Pregler, Sharon K.; Hayakawa, Tetsuichiro; Yasumatsu, Hisato; Kondow, Tamotsu; Sinnott, Susan B.

2007-01-01

Irradiation of graphite, commonly used in nuclear power plants, is known to produce structural damage. Here, experimental and computational methods are used to study defect formation in graphite during Ar irradiation at incident energies of 50 eV. The experimental samples are analyzed with scanning tunneling microscopy to quantify the size distribution of the defects that form. The computational approach is classical molecular dynamic simulations that illustrate the mechanisms by which the defects are produced. The results indicate that defects in graphite grow in concentrated areas and are nucleated by the presence of existing defects

Effects of various defects on the mechanical properties of black phosphorene

Science.gov (United States)

Nguyen, Danh-Truong; Le, Minh-Quy; Nguyen, Van-Trang; Bui, Thanh-Lam

2017-12-01

The present work investigates the effects of seven types of defects on the mechanical properties of black phosphorene. Molecular dynamics finite element method with Stillinger-Weber potential is used to simulate the uniaxial tensile tests of the pristine and defective black phosphorene sheets. Young's modulus, fracture stress, and fracture strain of the pristine and defective black phosphorene sheets are estimated. Comparison of the influence of different types of defects on the mechanical response of black phosphorene is considered. Fracture mechanism of various defective black phosphorene sheets is also analyzed. It is found that effect of the defects on Young's modulus of black phosphorene is insignificant. In contrast, due to defects fracture stress and fracture strain can reduce up to 53% and 69%, respectively. Results provide a landscape on the mechanical properties of defective black phosphorene and are useful for the design of nanodevices with black phosphorene in future applications.

In Situ Observation of Antisite Defect Formation during Crystal Growth

International Nuclear Information System (INIS)

Kramer, M. J.; Napolitano, R. E.; Mendelev, M. I.

2010-01-01

In situ x-ray diffraction (XRD) coupled with molecular dynamics (MD) simulations have been used to quantify antisite defect trapping during crystallization. Rietveld refinement of the XRD data revealed a marked lattice distortion which involves an a axis expansion and a c axis contraction of the stable C11b phase. The observed lattice response is proportional in magnitude to the growth rate, suggesting that the behavior is associated with the kinetic trapping of lattice defects. MD simulations demonstrate that this lattice response is due to incorporation of 1% to 2% antisite defects during growth.

Molecular biology of human muscle disease

Energy Technology Data Exchange (ETDEWEB)

Dunne, P.W.; Epstein, H.F. (Baylor Coll. of Medicine, Houston, TX (United States))

1991-01-01

The molecular revolution that is transforming the entire biomedical field has had far-reaching impact in its application to inherited human muscle disease. The gene for Duchenne muscular dystrophy was one of the first cloned without knowledge of the defective protein product. This success was based upon the availability of key chromosomal aberrations that provided molecular landmarks for the disease locus. Subsequent discoveries regarding the mode of expression for this gene, the structure and localization of its protein product dystrophin, and molecular diagnosis of affected and carrier individuals constitute a paradigm for investigation of human genetics. Finding the gene for myotonic muscular dystrophy is requiring the brute force approach of cloning several million bases of DNA, identifying expressed sequences, and characterizing candidate genes. The gene that causes hypertrophic cardiomyopathy has been found serendipitously to be one of the genetic markers on chromosome 14, the {beta} myosin heavy chain.

Photochemical Creation of Fluorescent Quantum Defects in Semiconducting Carbon Nanotube Hosts.

Science.gov (United States)

Wu, Xiaojian; Kim, Mijin; Kwon, Hyejin; Wang, YuHuang

2018-01-15

Quantum defects are an emerging class of synthetic single-photon emitters that hold vast potential for near-infrared imaging, chemical sensing, materials engineering, and quantum information processing. Herein, we show that it is possible to optically direct the synthetic creation of molecularly tunable fluorescent quantum defects in semiconducting single-walled carbon nanotube hosts through photochemical reactions. By exciting the host semiconductor with light that resonates with its electronic transition, we find that halide-containing aryl groups can covalently bond to the sp 2 carbon lattice. The introduced quantum defects generate bright photoluminescence that allows tracking of the reaction progress in situ. We show that the reaction is independent of temperature but correlates strongly with the photon energy used to drive the reaction, suggesting a photochemical mechanism rather than photothermal effects. This type of photochemical reactions opens the possibility to control the synthesis of fluorescent quantum defects using light and may enable lithographic patterning of quantum emitters with electronic and molecular precision. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Observation of point defects in impurity-doped zinc selenide films using a monoenergetic positron beam

International Nuclear Information System (INIS)

Miyajima, T.; Okuyama, H.; Akimoto, K.; Mori, Y.; Wei, L.; Tanigawa, S.

1992-01-01

We studied point defects in ZnSe films grown by molecular beam epitaxy using the positron annihilation method. We found that doping with Ga atoms induces vacancy-type defects such as Zn vacancies, and that heavy doping with oxygen atoms induces interstitial type defects. We think that these defects are one of the causes of active carrier saturation in doped ZnSe films. (author)

Interaction between dangling bonds in vacancy-defects in silicon

International Nuclear Information System (INIS)

Caldas, M.J.; Fazzio, A.

1983-01-01

The 'defect-molecule' model in the simplest scheme (without configuration interaction) is reviewed and the concept of 'delocalized dangling-bonds' is explorated in the study of the interaction between the unsaturated hybrids of the mono and divacancy in silicon. The 'defect-molecule' hamiltonian is written in parametric form, and the parameters are extracted from full self-consistent calculations for both systems carried out through the MS-Xα molecular cluster model. (Author) [pt

Quantum computing with defects

Science.gov (United States)

Varley, Joel

2011-03-01

The development of a quantum computer is contingent upon the identification and design of systems for use as qubits, the basic units of quantum information. One of the most promising candidates consists of a defect in diamond known as the nitrogen-vacancy (NV-1) center, since it is an individually-addressable quantum system that can be initialized, manipulated, and measured with high fidelity at room temperature. While the success of the NV-1 stems from its nature as a localized ``deep-center'' point defect, no systematic effort has been made to identify other defects that might behave in a similar way. We provide guidelines for identifying other defect centers with similar properties. We present a list of physical criteria that these centers and their hosts should meet and explain how these requirements can be used in conjunction with electronic structure theory to intelligently sort through candidate systems. To elucidate these points, we compare electronic structure calculations of the NV-1 center in diamond with those of several deep centers in 4H silicon carbide (SiC). Using hybrid functionals, we report formation energies, configuration-coordinate diagrams, and defect-level diagrams to compare and contrast the properties of these defects. We find that the NC VSi - 1 center in SiC, a structural analog of the NV-1 center in diamond, may be a suitable center with very different optical transition energies. We also discuss how the proposed criteria can be translated into guidelines to discover NV analogs in other tetrahedrally coordinated materials. This work was performed in collaboration with J. R. Weber, W. F. Koehl, B. B. Buckley, A. Janotti, C. G. Van de Walle, and D. D. Awschalom. This work was supported by ARO, AFOSR, and NSF.

Coarse-grained molecular dynamics modeling of the kinetics of lamellar block copolymer defect annealing

Science.gov (United States)

Peters, Andrew J.; Lawson, Richard A.; Nation, Benjamin D.; Ludovice, Peter J.; Henderson, Clifford L.

2016-01-01

State-of-the-art block copolymer (BCP)-directed self-assembly (DSA) methods still yield defect densities orders of magnitude higher than is necessary in semiconductor fabrication despite free-energy calculations that suggest equilibrium defect densities are much lower than is necessary for economic fabrication. This disparity suggests that the main problem may lie in the kinetics of defect removal. This work uses a coarse-grained model to study the rates, pathways, and dependencies of healing a common defect to give insight into the fundamental processes that control defect healing and give guidance on optimal process conditions for BCP-DSA. It is found that bulk simulations yield an exponential drop in defect heal rate above χN˜30. Thin films show no change in rate associated with the energy barrier below χN˜50, significantly higher than the χN values found previously for self-consistent field theory studies that neglect fluctuations. Above χN˜50, the simulations show an increase in energy barrier scaling with 1/2 to 1/3 of the bulk systems. This is because thin films always begin healing at the free interface or the BCP-underlayer interface, where the increased A-B contact area associated with the transition state is minimized, while the infinitely thick films cannot begin healing at an interface.

Molecular beam epitaxy of GaN(0001) utilizing NH3 and/or NH+x ions: Growth kinetics and defect structure

International Nuclear Information System (INIS)

Lee, N.; Powell, R.C.; Kim, Y.; Greene, J.E.

1995-01-01

Gas-source molecular beam epitaxy (GS-MBE), utilizing Ga and NH 3 , and reactive-ion MBE (RIMBE), incorporating both thermal NH 3 and low-energy NH + x ions, were used to grow single crystal GaN(0001) layers on Al 2 O 3 (0001) at temperatures T s between 700 and 850 degree C with deposition rates of 0.2--0.5 μm h -1 . The RIMBE experiments were carried out with incident NH + x /Ga flux ratios J NH + x /J Ga =1.9--3.2 and NH + x acceleration energies E NH + x =45--90 eV. Plan-view and cross-sectional transmission electron microscopy analyses showed that the primary defects in the GS-MBE films were threading dislocations having either pure edge or mixed edge/screw characteristics with Burgers vectors bar b=1/3 left-angle 2 bar 1 bar 10 right-angle, basal-plane stacking faults with displacement vectors bar R=1/6 left-angle 02 bar 23 right-angle, and prismatic stacking faults with bar R=1/2 left-angle bar 1101 right-angle. In the case of RIMBE films, no stacking faults or residual ion-induced defects were observed with E NH + x =45 eV and T s ≥800 degree C. However, increasing E NH + x to ≥60 eV at T s =800 degree C gave rise to the formation of residual ion-induced point-defect clusters observable by transmission electron microscopy (TEM). Increasing T s to 850 degree C with E NH + x ≥60 eV resulted in the ion-induced defects aggregating to form interstitial basal and prismatic dislocation loops, whose number densities depended upon the ion flux, with Burgers vectors 1/2 left-angle 0001 right-angle and 1/3 left-angle 2 bar 1 bar 10 right-angle, respectively. (Abstract Truncated)

Time and temperature dependence of cascade induced defect production in in situ experiments and computer simulation

International Nuclear Information System (INIS)

Ishino, Shiori

1993-01-01

Understanding of the defect production and annihilation processes in a cascade is important in modelling of radiation damage for establishing irradiation correlation. In situ observation of heavy ion radiation damage has a great prospect in this respect. Time and temperature dependence of formation and annihilation of vacancy clusters in a cascade with a time resolution of 30 ms has been studied with a facility which comprises a heavy ion accelerator and an electron microscope. Formation and annihilation rates of defect clusters have been separately measured by this technique. The observed processes have been analysed by simple kinetic equations, taking into account the sink effect of surface and the defect clusters themselves together with the annihilation process due to thermal emission of vacancies from the defect clusters. Another tool to study time and temperature dependence of defect production in a cascade is computer simulation. Recent results of molecular dynamics calculations on the temperature dependence of cascade evolution are presented, including directional and temperature dependence of the lengths of replacement collision sequences, temperature dependence of the process to reach thermal equilibrium and so on. These results are discussed under general time frame of radiation damage evolution covering from 10 -15 to 10 9 s, and several important issues for the general understanding have been identified. (orig.)

Identifying apple surface defects using principal components analysis and artifical neural networks

Science.gov (United States)

Artificial neural networks and principal components were used to detect surface defects on apples in near-infrared images. Neural networks were trained and tested on sets of principal components derived from columns of pixels from images of apples acquired at two wavelengths (740 nm and 950 nm). I...

Molecular dynamics studies of defect formation during heteroepitaxial growth of InGaN alloys on (0001) GaN surfaces.

Science.gov (United States)

Gruber, J; Zhou, X W; Jones, R E; Lee, S R; Tucker, G J

2017-05-21

We investigate the formation of extended defects during molecular-dynamics (MD) simulations of GaN and InGaN growth on (0001) and ([Formula: see text]) wurtzite-GaN surfaces. The simulated growths are conducted on an atypically large scale by sequentially injecting nearly a million individual vapor-phase atoms towards a fixed GaN surface; we apply time-and-position-dependent boundary constraints that vary the ensemble treatments of the vapor-phase, the near-surface solid-phase, and the bulk-like regions of the growing layer. The simulations employ newly optimized Stillinger-Weber In-Ga-N-system potentials, wherein multiple binary and ternary structures are included in the underlying density-functional-theory training sets, allowing improved treatment of In-Ga-related atomic interactions. To examine the effect of growth conditions, we study a matrix of >30 different MD-growth simulations for a range of In x Ga 1-x N-alloy compositions (0 ≤  x  ≤ 0.4) and homologous growth temperatures [0.50 ≤  T/T * m ( x ) ≤ 0.90], where T * m ( x ) is the simulated melting point. Growths conducted on polar (0001) GaN substrates exhibit the formation of various extended defects including stacking faults/polymorphism, associated domain boundaries, surface roughness, dislocations, and voids. In contrast, selected growths conducted on semi-polar ([Formula: see text]) GaN, where the wurtzite-phase stacking sequence is revealed at the surface, exhibit the formation of far fewer stacking faults. We discuss variations in the defect formation with the MD growth conditions, and we compare the resulting simulated films to existing experimental observations in InGaN/GaN. While the palette of defects observed by MD closely resembles those observed in the past experiments, further work is needed to achieve truly predictive large-scale simulations of InGaN/GaN crystal growth using MD methodologies.

Size Effect of Defects on the Mechanical Properties of Graphene

Science.gov (United States)

Park, Youngho; Hyun, Sangil

2018-03-01

Graphene, a two-dimensional material, has been studied and utilized for its excellent material properties. In reality, achieving a pure single-crystalline structure in graphene is difficult, so usually graphene may have various types of defects in it. Vacancies, Stone-Wales defects, and grain boundaries can drastically change the material properties of graphene. Graphene with vacancy defects has been of interest because it is a two-dimensional analogy of three-dimensional porous materials. It has efficient material properties, and can function as a part of modern devices. The mechanical properties have been studied by using molecular dynamics for either a single vacancy defect with various sizes or multiple vacancy defects with same defect ratios. However, it is not clear which one has more influence on the mechanical properties between the size of the defects and the defect ratio. Therefore, we investigated the hole-size effect on the mechanical properties of single-crystalline graphene at various defect ratios. A void defect with large size can have a rather high tensile modulus with a low fracture strain compared to a void defect with small size. We numerically found that the tensile properties of scattered single vacancies is similar to that of amorphous graphene. We suspect that this is due to the local orbital change of the carbon atoms near the boundary of the void defects, so-called the interfacial phase.

Identification and molecular characterization of a naturally occurring RNA virus mutant defective in the initiation of host recovery

International Nuclear Information System (INIS)

Xin Hongwu; Ding Shouwei

2003-01-01

The host recovery response is characterized by the disappearance of disease symptoms and activation of the RNA silencing virus resistance in the new growth following an initial symptomatic infection. However, it is not clear what triggers the initiation of recovery, which occurs naturally only in some virus-host interactions. Here we report the identification and characterization of a spontaneous mutant of Tobacco streak virus (TSV) that became defective in triggering recovery in tobacco plants. Infectious full-length cDNA clones corresponding to the tripartite RNA genome were constructed from both the wild-type and the nonrecovery mutant of TSV (TSVnr), the first sets of infectious cDNA clones from an Ilarvirus. Genetic and molecular analyses identified an A → G mutation in the TSVnr genome that was sufficient to confer nonrecovery when introduced into TSV. The mutation was located in the intergenic region of RNA 3 upstream of the mapped transcriptional start site of the coat protein mRNA. Intriguingly, induction of recovery by TSV was not accompanied by virus clearance and TSV consistently accumulated to significantly higher levels than TSVnr did even though TSVnr-infected plants displayed severe symptoms throughout the course of infection. Thus, our findings indicate that recovery of host can be initiated by minimal genetic changes in a viral genome and may occur in the absence of virus clearance. Mechanisms possibly involved in the initiation of host recovery are discussed

Indicators for Building Process without Final Defects -

DEFF Research Database (Denmark)

Jørgensen, Kirsten; Rasmussen, Grane Mikael Gregaard; Thuesen, Christian Langhoff

2011-01-01

This article introduces the preliminary data analysis, as well as the underlying theories and methods for identifying the indicators for building process without final defects. Since 2004, the Benchmark Centre for the Danish Construction Sector (BEC) has collected information about legal defects...

Defect properties of InGaAsN layers grown as sub-monolayer digital alloys by molecular beam epitaxy

Science.gov (United States)

Baranov, Artem I.; Gudovskikh, Alexander S.; Kudryashov, Dmitry A.; Lazarenko, Alexandra A.; Morozov, Ivan A.; Mozharov, Alexey M.; Nikitina, Ekaterina V.; Pirogov, Evgeny V.; Sobolev, Maxim S.; Zelentsov, Kirill S.; Egorov, Anton Yu.; Darga, Arouna; Le Gall, Sylvain; Kleider, Jean-Paul

2018-04-01

The defect properties of InGaAsN dilute nitrides grown as sub-monolayer digital alloys (SDAs) by molecular beam epitaxy for photovoltaic application were studied by space charge capacitance spectroscopy. Alloys of i-InGaAsN (Eg = 1.03 eV) were lattice-matched grown on GaAs wafers as a superlattice of InAs/GaAsN with one monolayer of InAs (solar cells. Low p-type background doping was demonstrated at room temperature in samples with InGaAsN layers 900 nm and 1200 nm thick (less 1 × 1015 cm-3). According to admittance spectroscopy and deep-level transient spectroscopy measurements, the SDA approach leads to defect-free growth up to a thickness of 900 nm. An increase in thickness to 1200 nm leads to the formation of non-radiative recombination centers with an activation energy of 0.5 eV (NT = 8.4 × 1014 cm-3) and a shallow defect level at 0.20 eV. The last one leads to the appearance of additional doping, but its concentration is low (NT = 5 × 1014 cm-3) so it does not affect the photoelectric properties. However, further increase in thickness to 1600 nm, leads to significant growth of its concentration to (3-5) × 1015 cm-3, while the concentration of deep levels becomes 1.3 × 1015 cm-3. Therefore, additional free charge carriers appearing due to ionization of the shallow level change the band diagram from p-i-n to p-n junction at room temperature. It leads to a drop of the external quantum efficiency due to the effect of pulling electric field decrease in the p-n junction and an increased number of non-radiative recombination centers that negatively impact lifetimes in InGaAsN.

Chemical characterisation of non-defective and defective green arabica and robusta coffees by electrospray ionization-mass spectrometry (ESI-MS).

Science.gov (United States)

Mendonça, Juliana C F; Franca, Adriana S; Oliveira, Leandro S; Nunes, Marcella

2008-11-15

The coffee roasted in Brazil is considered to be of low quality, due to the presence of defective coffee beans that depreciate the beverage quality. These beans, although being separated from the non-defective ones prior to roasting, are still commercialized in the coffee trading market. Thus, it was the aim of this work to verify the feasibility of employing ESI-MS to identify chemical characteristics that will allow the discrimination of Arabica and Robusta species and also of defective and non-defective coffees. Aqueous extracts of green (raw) defective and non-defective coffee beans were analyzed by direct infusion electrospray ionization mass spectrometry (ESI-MS) and this technique provided characteristic fingerprinting mass spectra that not only allowed for discrimination of species but also between defective and non-defective coffee beans. ESI-MS profiles in the positive mode (ESI(+)-MS) provided separation between defective and non-defective coffees within a given species, whereas ESI-MS profiles in the negative mode (ESI(-)-MS) provided separation between Arabica and Robusta coffees. Copyright © 2008 Elsevier Ltd. All rights reserved.

Identifying the molecular functions of electron transport proteins using radial basis function networks and biochemical properties.

Science.gov (United States)

Le, Nguyen-Quoc-Khanh; Nguyen, Trinh-Trung-Duong; Ou, Yu-Yen

2017-05-01

The electron transport proteins have an important role in storing and transferring electrons in cellular respiration, which is the most proficient process through which cells gather energy from consumed food. According to the molecular functions, the electron transport chain components could be formed with five complexes with several different electron carriers and functions. Therefore, identifying the molecular functions in the electron transport chain is vital for helping biologists understand the electron transport chain process and energy production in cells. This work includes two phases for discriminating electron transport proteins from transport proteins and classifying categories of five complexes in electron transport proteins. In the first phase, the performances from PSSM with AAIndex feature set were successful in identifying electron transport proteins in transport proteins with achieved sensitivity of 73.2%, specificity of 94.1%, and accuracy of 91.3%, with MCC of 0.64 for independent data set. With the second phase, our method can approach a precise model for identifying of five complexes with different molecular functions in electron transport proteins. The PSSM with AAIndex properties in five complexes achieved MCC of 0.51, 0.47, 0.42, 0.74, and 1.00 for independent data set, respectively. We suggest that our study could be a power model for determining new proteins that belongs into which molecular function of electron transport proteins. Copyright © 2017 Elsevier Inc. All rights reserved.

MgH Rydberg series: Transition energies from electron propagator theory and oscillator strengths from the molecular quantum defect orbital method

Science.gov (United States)

Corzo, H. H.; Velasco, A. M.; Lavín, C.; Ortiz, J. V.

2018-02-01

Vertical excitation energies belonging to several Rydberg series of MgH have been inferred from 3+ electron-propagator calculations of the electron affinities of MgH+ and are in close agreement with experiment. Many electronically excited states with n > 3 are reported for the first time and new insight is given on the assignment of several Rydberg series. Valence and Rydberg excited states of MgH are distinguished respectively by high and low pole strengths corresponding to Dyson orbitals of electron attachment to the cation. By applying the Molecular Quantum Defect Orbital method, oscillator strengths for electronic transitions involving Rydberg states also have been determined.

Electrically Rotatable Polarizer Using One-Dimensional Photonic Crystal with a Nematic Liquid Crystal Defect Layer

Directory of Open Access Journals (Sweden)

Ryotaro Ozaki

2015-09-01

Full Text Available Polarization characteristics of defect mode peaks in a one-dimensional (1D photonic crystal (PC with a nematic liquid crystal (NLC defect layer have been investigated. Two different polarized defect modes are observed in a stop band. One group of defect modes is polarized along the long molecular axis of the NLC, whereas another group is polarized along its short axis. Polarizations of the defect modes can be tuned by field-induced in-plane reorientation of the NLC in the defect layer. The polarization properties of the 1D PC with the NLC defect layer is also investigated by the finite difference time domain (FDTD simulation.

Ion-irradiation-induced defects in bundles of carbon nanotubes

International Nuclear Information System (INIS)

Salonen, E.; Krasheninnikov, A.V.; Nordlund, K.

2002-01-01

We study the structure and formation yields of atomic-scale defects produced by low-dose Ar ion irradiation in bundles of single-wall carbon nanotubes. For this, we employ empirical potential molecular dynamics and simulate ion impact events over an energy range of 100-1000 eV. We show that the most common defects produced at all energies are vacancies on nanotube walls, which at low temperatures are metastable but long-lived defects. We further calculate the spatial distribution of the defects, which proved to be highly non-uniform. We also show that ion irradiation gives rise to the formations of inter-tube covalent bonds mediated by carbon recoils and nanotube lattice distortions due to dangling bond saturation. The number of inter-tube links, as well as the overall damage, linearly grows with the energy of incident ions

Quantitative Evaluation of Defect Based on Ultrasonic Guided Wave and CHMM

Directory of Open Access Journals (Sweden)

Chen Le

2016-01-01

Full Text Available The axial length of pipe defects is not linear with the reflection coefficient, which is difficult to identify the axial length of the defect by the reflection coefficient method. Continuous Hidden Markov Model (CHMM is proposed to accurately classify the axial length of defects, achieving the objective of preliminary quantitative evaluation. Firstly, wavelet packet decomposition method is used to extract the characteristic information of the guided wave signal, and Kernel Sliced Inverse Regression (KSIR method is used to reduce the dimension of feature set. Then, a variety of CHMM models are trained for classification. Finally, the trained models are used to identify the artificial corrosion defects on the outer surface of the pipe. The results show that the CHMM model has better robustness and can accurately identify the axial defects.

Cellular and Axonal Diversity in Molecular Layer Heterotopia of the Rat Cerebellar Vermis

Directory of Open Access Journals (Sweden)

Sarah E. Van Dine

2013-01-01

Full Text Available Molecular layer heterotopia of the cerebellar primary fissure are a characteristic of many rat strains and are hypothesized to result from defect of granule cells exiting the external granule cell layer during cerebellar development. However, the cellular and axonal constituents of these malformations remain poorly understood. In the present report, we use histochemistry and immunocytochemistry to identify neuronal, glial, and axonal classes in molecular layer heterotopia. In particular, we identify parvalbumin-expressing molecular layer interneurons in heterotopia as well as three glial cell types including Bergmann glia, Olig2-expressing oligodendrocytes, and Iba1-expressing microglia. In addition, we document the presence of myelinated, serotonergic, catecholaminergic, and cholinergic axons in heterotopia indicating possible spinal and brainstem afferent projections to heterotopic cells. These findings are relevant toward understanding the mechanisms of normal and abnormal cerebellar development.

Defect engineering of ZnO

Energy Technology Data Exchange (ETDEWEB)

Weber, M.H. [Center for Materials Research and Department of Physics and Astronomy, Washington State University, Pullman, WA 99164-2711 (United States)], E-mail: m_weber@wsu.edu; Selim, F.A.; Solodovnikov, D.; Lynn, K.G. [Center for Materials Research and Department of Physics and Astronomy, Washington State University, Pullman, WA 99164-2711 (United States)

2008-10-31

The defect responsible for the transparent to red color change of nominally undoped ZnO bulk single crystals is investigated. Upon annealing in the presence of metallic Zn as reported by Halliburton et al. and also Ti and Zr a native defect forms with an energy level about 0.7 eV below the conduction band. This change is reversible upon annealing in oxygen. Optical transmission data along with positron depth profiles and annealing studies are combined to identify the defect as oxygen vacancies. Vacancy clustering occurs at about 500 deg. C if isolated zinc and oxygen vacancies. In the absence of zinc vacancies, clusters form at about 800 deg. C.

Defect engineering of ZnO

International Nuclear Information System (INIS)

Weber, M.H.; Selim, F.A.; Solodovnikov, D.; Lynn, K.G.

2008-01-01

The defect responsible for the transparent to red color change of nominally undoped ZnO bulk single crystals is investigated. Upon annealing in the presence of metallic Zn as reported by Halliburton et al. and also Ti and Zr a native defect forms with an energy level about 0.7 eV below the conduction band. This change is reversible upon annealing in oxygen. Optical transmission data along with positron depth profiles and annealing studies are combined to identify the defect as oxygen vacancies. Vacancy clustering occurs at about 500 deg. C if isolated zinc and oxygen vacancies. In the absence of zinc vacancies, clusters form at about 800 deg. C

Primordial inhomogeneities from massive defects during inflation

Energy Technology Data Exchange (ETDEWEB)

Firouzjahi, Hassan; Karami, Asieh; Rostami, Tahereh, E-mail: firouz@ipm.ir, E-mail: karami@ipm.ir, E-mail: t.rostami@ipm.ir [School of Astronomy, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran (Iran, Islamic Republic of)

2016-10-01

We consider the imprints of local massive defects, such as a black hole or a massive monopole, during inflation. The massive defect breaks the background homogeneity. We consider the limit that the physical Schwarzschild radius of the defect is much smaller than the inflationary Hubble radius so a perturbative analysis is allowed. The inhomogeneities induced in scalar and gravitational wave power spectrum are calculated. We obtain the amplitudes of dipole, quadrupole and octupole anisotropies in curvature perturbation power spectrum and identify the relative configuration of the defect to CMB sphere in which large observable dipole asymmetry can be generated. We observe a curious reflection symmetry in which the configuration where the defect is inside the CMB comoving sphere has the same inhomogeneous variance as its mirror configuration where the defect is outside the CMB sphere.

Analysis of nano-sized irradiation-induced defects in Fe-base materials by means of small angle neutron scattering and molecular dynamics simulations

International Nuclear Information System (INIS)

Yu, G.

2008-12-01

of RAFM steels with Molecular Dynamics (MD) simulations of main expected nano-sized defects in irradiated pure Fe and Fe-He alloys, as model materials for RAFM steels, and simulations of their corresponding TEM images and SANS signals. In particular, the SANS signal of various types of defects was simulated for the first time. The methodology used in this work was the following: (i) SANS experiments were performed by applying a strong saturating magnetic field to unirradiated and irradiated specimens of three types of RAFM steels, namely the European EUROFER 97, the Japanese F82H and the Swiss OPTIMAX A steels. The available irradiated specimens included specimens which had been irradiated with 590 MeV protons in the Proton IRradiation EXperiment (PIREX) facility at the Paul Scherrer Institute (PSI) at temperatures in the range of 50-350 °C to doses in the range of 0.3-2.0 dpa. SANS spectra as well as values of the so-called A ratio, which represents the ratio of the total scattered intensity to the nuclear scattered intensity, were obtained for the various irradiation doses and temperatures investigated. (ii) MD simulations of atomic displacement cascades in pure Fe and in Fe-He alloys were performed using Embedded Atom Method (EAM) many-body interatomic potentials. The main nano-sized defects that should be produced in RAFM steels under irradiation were created by means of MD in pure Fe. These included dislocation loops of various types, voids, helium bubbles with various He concentration and Cr precipitates. (iii) TEM images of cascade damage and all the defects created by MD were simulated in the dark field/weak beam imaging modes by using the Electron Microscopy Software (EMS) developed by P.A. Stadelmann (EPFL) and analyzed in terms of variations of contrast intensities versus depth inside the specimen. (iv) The SANS signal provided by cascade damage and all the defects created by MD was simulated by using a slightly modified version of EMS, accounting for

Amino acids interacting with defected carbon nanotubes: ab initio calculations

Directory of Open Access Journals (Sweden)

M. Darvish Ganji

2016-09-01

Full Text Available The adsorption of a number of amino acids on a defected single-walled carbon nanotube (SWCNT is investigated by using the density-functional theory (DFT calculations. The adsorption energies and equilibrium distances are calculated for various configurations such as amino acid attaching to defect sites heptagon, pentagon and hexagon in defective tube and also for several molecular orientations with respect to the nanotube surface. The results showed that amino acids prefer to be physisorbed on the outer surface of the defected nanotube with different interaction strength following the hierarchy histidine > glycine > phenylalanine > cysteine. Comparing these findings with those obtained for perfect SWCNTs reveals that the adsorption energy of the amino acids increase for adsorption onto defected CNTs. The adsorption nature has also been evaluated by means of electronics structures analysis within the Mulliken population and DOS spectra for the interacting entities.

Defect Characterization of Pyroelectric Materials

National Research Council Canada - National Science Library

Keeble, David

2002-01-01

Two methods for identify point defects applicable to the study of technologically relevant pyroelectric oxide materials have been investigated, namely Positron Annihilation Lifetime Spectroscopy (PALS...

Transforming graphene nanoribbons into nanotubes by use of point defects.

Science.gov (United States)

Sgouros, A; Sigalas, M M; Papagelis, K; Kalosakas, G

2014-03-26

Using molecular dynamics simulations with semi-empirical potentials, we demonstrate a method to fabricate carbon nanotubes (CNTs) from graphene nanoribbons (GNRs), by periodically inserting appropriate structural defects into the GNR crystal structure. We have found that various defect types initiate the bending of GNRs and eventually lead to the formation of CNTs. All kinds of carbon nanotubes (armchair, zigzag, chiral) can be produced with this method. The structural characteristics of the resulting CNTs, and the dependence on the different type and distribution of the defects, were examined. The smallest (largest) CNT obtained had a diameter of ∼ 5 Å (∼ 39 Å). Proper manipulation of ribbon edges controls the chirality of the CNTs formed. Finally, the effect of randomly distributed defects on the ability of GNRs to transform into CNTs is considered.

Carbon Nanotubes: Molecular Electronic Components

Science.gov (United States)

Srivastava, Deepak; Saini, Subhash; Menon, Madhu

1997-01-01

The carbon Nanotube junctions have recently emerged as excellent candidates for use as the building blocks in the formation of nanoscale molecular electronic networks. While the simple joint of two dissimilar tubes can be generated by the introduction of a pair of heptagon-pentagon defects in an otherwise perfect hexagonal graphene sheet, more complex joints require other mechanisms. In this work we explore structural characteristics of complex 3-point junctions of carbon nanotubes using a generalized tight-binding molecular-dynamics scheme. The study of pi-electron local densities of states (LDOS) of these junctions reveal many interesting features, most prominent among them being the defect-induced states in the gap.

NEWLY IDENTIFIED EXTENDED GREEN OBJECTS (EGOs) FROM THE SPITZER GLIMPSE II SURVEY. II. MOLECULAR CLOUD ENVIRONMENTS

Energy Technology Data Exchange (ETDEWEB)

Chen Xi; Gan Conggui; Shen Zhiqiang [Key Laboratory for Research in Galaxies and Cosmology, Shanghai Astronomical Observatory, Chinese Academy of Sciences, Shanghai 200030 (China); Ellingsen, Simon P.; Titmarsh, Anita [School of Mathematics and Physics, University of Tasmania, Hobart, Tasmania (Australia); He Jinhua, E-mail: chenxi@shao.ac.cn [Key Laboratory for the Structure and Evolution of Celestial Objects, Yunnan Astronomical Observatory/National Astronomical Observatory, Chinese Academy of Sciences, P.O. Box 110, Kunming 650011, Yunnan Province (China)

2013-06-01

We have undertaken a survey of molecular lines in the 3 mm band toward 57 young stellar objects using the Australia Telescope National Facility Mopra 22 m radio telescope. The target sources were young stellar objects with active outflows (extended green objects (EGOs)) newly identified from the GLIMPSE II survey. We observe a high detection rate (50%) of broad line wing emission in the HNC and CS thermal lines, which combined with the high detection rate of class I methanol masers toward these sources (reported in Paper I) further demonstrates that the GLIMPSE II EGOs are associated with outflows. The physical and kinematic characteristics derived from the 3 mm molecular lines for these newly identified EGOs are consistent with these sources being massive young stellar objects with ongoing outflow activity and rapid accretion. These findings support our previous investigations of the mid-infrared properties of these sources and their association with other star formation tracers (e.g., infrared dark clouds, methanol masers and millimeter dust sources) presented in Paper I. The high detection rate (64%) of the hot core tracer CH{sub 3}CN reveals that the majority of these new EGOs have evolved to the hot molecular core stage. Comparison of the observed molecular column densities with predictions from hot core chemistry models reveals that the newly identified EGOs from the GLIMPSE II survey are members of the youngest hot core population, with an evolutionary time scale of the order of 10{sup 3} yr.

Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells.

Science.gov (United States)

Tsang, Jason C H; Yu, Yong; Burke, Shannon; Buettner, Florian; Wang, Cui; Kolodziejczyk, Aleksandra A; Teichmann, Sarah A; Lu, Liming; Liu, Pentao

2015-09-21

Hematopoietic stem cells (HSCs) are a rare cell type with the ability of long-term self-renewal and multipotency to reconstitute all blood lineages. HSCs are typically purified from the bone marrow using cell surface markers. Recent studies have identified significant cellular heterogeneities in the HSC compartment with subsets of HSCs displaying lineage bias. We previously discovered that the transcription factor Bcl11a has critical functions in the lymphoid development of the HSC compartment. In this report, we employ single-cell transcriptomic analysis to dissect the molecular heterogeneities in HSCs. We profile the transcriptomes of 180 highly purified HSCs (Bcl11a (+/+) and Bcl11a (-/-)). Detailed analysis of the RNA-seq data identifies cell cycle activity as the major source of transcriptomic variation in the HSC compartment, which allows reconstruction of HSC cell cycle progression in silico. Single-cell RNA-seq profiling of Bcl11a (-/-) HSCs reveals abnormal proliferative phenotypes. Analysis of lineage gene expression suggests that the Bcl11a (-/-) HSCs are constituted of two distinct myeloerythroid-restricted subpopulations. Remarkably, similar myeloid-restricted cells could also be detected in the wild-type HSC compartment, suggesting selective elimination of lymphoid-competent HSCs after Bcl11a deletion. These defects are experimentally validated in serial transplantation experiments where Bcl11a (-/-) HSCs are myeloerythroid-restricted and defective in self-renewal. Our study demonstrates the power of single-cell transcriptomics in dissecting cellular process and lineage heterogeneities in stem cell compartments, and further reveals the molecular and cellular defects in the Bcl11a-deficient HSC compartment.

Pluripotent cell models of fanconi anemia identify the early pathological defect in human hemoangiogenic progenitors.

Science.gov (United States)

Suzuki, Naoya M; Niwa, Akira; Yabe, Miharu; Hira, Asuka; Okada, Chihiro; Amano, Naoki; Watanabe, Akira; Watanabe, Ken-Ichiro; Heike, Toshio; Takata, Minoru; Nakahata, Tatsutoshi; Saito, Megumu K

2015-04-01

Fanconi anemia (FA) is a disorder of genomic instability characterized by progressive bone marrow failure (BMF), developmental abnormalities, and an increased susceptibility to cancer. Although various consequences in hematopoietic stem/progenitor cells have been attributed to FA-BMF, the quest to identify the initial pathological event is still ongoing. To address this issue, we established induced pluripotent stem cells (iPSCs) from fibroblasts of six patients with FA and FANCA mutations. An improved reprogramming method yielded iPSC-like colonies from all patients, and iPSC clones were propagated from two patients. Quantitative evaluation of the differentiation ability demonstrated that the differentiation propensity toward the hematopoietic and endothelial lineages is already defective in early hemoangiogenic progenitors. The expression levels of critical transcription factors were significantly downregulated in these progenitors. These data indicate that the hematopoietic consequences in FA patients originate from the early hematopoietic stage and highlight the potential usefulness of iPSC technology for elucidating the pathogenesis of FA-BMF. ©AlphaMed Press.

Defects and defect processes in nonmetallic solids

CERN Document Server

Hayes, W

2004-01-01

This extensive survey covers defects in nonmetals, emphasizing point defects and point-defect processes. It encompasses electronic, vibrational, and optical properties of defective solids, plus dislocations and grain boundaries. 1985 edition.

Exploring atomic defects in molybdenum disulphide monolayers

KAUST Repository

Hong, Jinhua; Hu, Zhixin; Probert, Matt; Li, Kun; Lv, Danhui; Yang, Xinan; Gu, Lin; Mao, Nannan; Feng, Qingliang; Xie, Liming; Zhang, Jin; Wu, Dianzhong; Zhang, Zhiyong; Jin, Chuanhong; Ji, Wei; Zhang, Xixiang; Yuan, Jun; Zhang, Ze

2015-01-01

Defects usually play an important role in tailoring various properties of two-dimensional materials. Defects in two-dimensional monolayer molybdenum disulphide may be responsible for large variation of electric and optical properties. Here we present a comprehensive joint experiment-theory investigation of point defects in monolayer molybdenum disulphide prepared by mechanical exfoliation, physical and chemical vapour deposition. Defect species are systematically identified and their concentrations determined by aberration-corrected scanning transmission electron microscopy, and also studied by ab-initio calculation. Defect density up to 3.5 × 10 13 cm '2 is found and the dominant category of defects changes from sulphur vacancy in mechanical exfoliation and chemical vapour deposition samples to molybdenum antisite in physical vapour deposition samples. Influence of defects on electronic structure and charge-carrier mobility are predicted by calculation and observed by electric transport measurement. In light of these results, the growth of ultra-high-quality monolayer molybdenum disulphide appears a primary task for the community pursuing high-performance electronic devices.

Exploring atomic defects in molybdenum disulphide monolayers

KAUST Repository

Hong, Jinhua

2015-02-19

Defects usually play an important role in tailoring various properties of two-dimensional materials. Defects in two-dimensional monolayer molybdenum disulphide may be responsible for large variation of electric and optical properties. Here we present a comprehensive joint experiment-theory investigation of point defects in monolayer molybdenum disulphide prepared by mechanical exfoliation, physical and chemical vapour deposition. Defect species are systematically identified and their concentrations determined by aberration-corrected scanning transmission electron microscopy, and also studied by ab-initio calculation. Defect density up to 3.5 × 10 13 cm \\'2 is found and the dominant category of defects changes from sulphur vacancy in mechanical exfoliation and chemical vapour deposition samples to molybdenum antisite in physical vapour deposition samples. Influence of defects on electronic structure and charge-carrier mobility are predicted by calculation and observed by electric transport measurement. In light of these results, the growth of ultra-high-quality monolayer molybdenum disulphide appears a primary task for the community pursuing high-performance electronic devices.

Mechanical properties of highly defective graphene: from brittle rupture to ductile fracture.

Science.gov (United States)

Xu, Lanqing; Wei, Ning; Zheng, Yongping

2013-12-20

Defects are generally believed to deteriorate the superlative performance of graphene-based devices but may also be useful when carefully engineered to tailor the local properties and achieve new functionalities. Central to most defect-associated applications is the defect coverage and arrangement. In this work, we investigate, by molecular dynamics simulations, the mechanical properties and fracture dynamics of graphene sheets with randomly distributed vacancies or Stone-Wales defects under tensile deformations over a wide defect coverage range. With defects presented, an sp-sp(2) bonding network and an sp-sp(2)-sp(3) bonding network are observed in vacancy-defected and Stone-Wales-defected graphene, respectively. The ultimate strength degrades gradually with increasing defect coverage and saturates in the high-ratio regime, whereas the fracture strain presents an unusual descending-saturating-improving trend. In the dense vacancy defect situation, the fracture becomes more plastic and super-ductility is observed. Further fracture dynamics analysis reveals that the crack trapping by sp-sp(2) and sp-sp(2)-sp(3) rings and the crack-tip blunting account for the ductile fracture, whereas geometric rearrangement on the entire sheet for vacancy defects and geometric rearrangement on the specific defect sites for Stone-Wales defects account for their distinctive rules of the evolution of the fracture strain.

The role of defects in laser damage of multilayer coatings

International Nuclear Information System (INIS)

Kozlowski, M.R.; Chow, R.

1993-01-01

Laser induced damage to optical coatings is generally a localized phenomenon associated with coating defects. The most common of the defect types are the well-known nodule defect. This paper reviews the use of experiments and modeling to understand the formation of these defects and their interaction with laser light. Of particular interest are efforts to identify which defects are most susceptible to laser damage. Also discussed are possible methods for stabilizing these defects (laser conditioning) or preventing their initiation (source stabilization, spatter particle trapping)

Defect analysis program for LOFT. Progress report, 1977

International Nuclear Information System (INIS)

Doyle, R.E.; Scoonover, T.M.

1978-03-01

In order to alleviate problems encountered while performing previous defect analyses on components of the LOFT system, regions of LOFT most likely to require defect analysis have been identified. A review of available documentation has been conducted to identify shapes, sizes, materials, and welding procedures and to compile mechanical property data. The LOFT Reactor Vessel Material Surveillance Program has also been reviewed, and a survey of available literature describing existing techniques for conducting elastic-plastic defect analysis was initiated. While large amounts of mechanical property data were obtained from the available documentation and the literature, much information was not available, especially for weld heat-affected zones. Therefore, a program of mechanical property testing is recommended for FY-78 as well as continued literature search. It is also recommended that fatigue-crack growth-rate data be sought from the literature and that evaluation of the various techniques of elastic-plastic defect analysis be continued. Review of additional regions of the LOFT system in the context of potential defect analysis will be conducted as time permits

Effect of sp3-hybridized defects on the oscillatory behavior of carbon nanotube oscillators

International Nuclear Information System (INIS)

Guo, Taiyu; Ding, Tony Weixi; Pei, Qing-Xiang; Zhang, Yong-Wei

2011-01-01

Using molecular dynamics simulations, we investigate the oscillatory behaviors of carbon nanotube oscillators containing sp 3 -hybridized defects formed by hydrogen chemisorption. It is found that the presence of these defects significantly affects the kinetic and potential energies of the nanotube systems, which in turn affects their oscillation periods and frequencies. We have also studied the oscillatory characteristics of the oscillators containing sp 3 -hybridized Stone-Wales defects. Our results show that it is possible to control the motion of the inner nanotube by introducing sp 3 -hybridized defects on the outer nanotube, which provides a potential way to tune the oscillatory behavior of nanotube oscillators. -- Highlights: → sp 3 -hybridized defects increase energy dissipation. → sp 3 -hybridized defects arranged in a row have stronger effect than that in a ring. → sp 3 -hybridized defects reduces the effect of SW defects.

Autism in Phenylketonuria Patients: From Clinical Presentation to Molecular Defects.

Science.gov (United States)

Khemir, Sameh; Halayem, Soumeyya; Azzouz, Hatem; Siala, Hajer; Ferchichi, Maherzia; Guedria, Asma; Bedoui, Amel; Abdelhak, Sonia; Messaoud, Taieb; Tebib, Neji; Belhaj, Ahlem; Kaabachi, Naziha

2016-06-01

Autism has been reported in untreated patients with phenylketonuria. The authors aimed to explore autism in 15 Tunisian and 4 Algerian phenylketonuria patients, and report their clinical, biochemical and molecular peculiarities. The Childhood Autism Rating Scale and the Autism Diagnostic Interview-Revised were used for the diagnosis of autism. Five exons of phenylalanine hydroxylase gene (7, 6, 10, 11, and 5) were amplified by polymerase chain reaction and directly sequenced. Among these patients, 15 were suffering from autism at the time of evaluation. Six mutations were identified: p.E280K, p.G352Vfs, IVS10nt11, p.I224T, p.R261Q, and p.R252W. There was no correlation between autism and mutations affecting the phenylalanine hydroxylase gene, but the age of diet onset was the determining factor in autistic symptoms' evolution. © The Author(s) 2016.

Fetal Alcohol Spectrum Disorder (FASD) Associated Neural Defects: Complex Mechanisms and Potential Therapeutic Targets.

Science.gov (United States)

Muralidharan, Pooja; Sarmah, Swapnalee; Zhou, Feng C; Marrs, James A

2013-06-19

Fetal alcohol spectrum disorder (FASD), caused by prenatal alcohol exposure, can result in craniofacial dysmorphism, cognitive impairment, sensory and motor disabilities among other defects. FASD incidences are as high as 2% to 5 % children born in the US, and prevalence is higher in low socioeconomic populations. Despite various mechanisms being proposed to explain the etiology of FASD, the molecular targets of ethanol toxicity during development are unknown. Proposed mechanisms include cell death, cell signaling defects and gene expression changes. More recently, the involvement of several other molecular pathways was explored, including non-coding RNA, epigenetic changes and specific vitamin deficiencies. These various pathways may interact, producing a wide spectrum of consequences. Detailed understanding of these various pathways and their interactions will facilitate the therapeutic target identification, leading to new clinical intervention, which may reduce the incidence and severity of these highly prevalent preventable birth defects. This review discusses manifestations of alcohol exposure on the developing central nervous system, including the neural crest cells and sensory neural placodes, focusing on molecular neurodevelopmental pathways as possible therapeutic targets for prevention or protection.

Fetal Alcohol Spectrum Disorder (FASD Associated Neural Defects: Complex Mechanisms and Potential Therapeutic Targets

Directory of Open Access Journals (Sweden)

James A. Marrs

2013-06-01

Full Text Available Fetal alcohol spectrum disorder (FASD, caused by prenatal alcohol exposure, can result in craniofacial dysmorphism, cognitive impairment, sensory and motor disabilities among other defects. FASD incidences are as high as 2% to 5 % children born in the US, and prevalence is higher in low socioeconomic populations. Despite various mechanisms being proposed to explain the etiology of FASD, the molecular targets of ethanol toxicity during development are unknown. Proposed mechanisms include cell death, cell signaling defects and gene expression changes. More recently, the involvement of several other molecular pathways was explored, including non-coding RNA, epigenetic changes and specific vitamin deficiencies. These various pathways may interact, producing a wide spectrum of consequences. Detailed understanding of these various pathways and their interactions will facilitate the therapeutic target identification, leading to new clinical intervention, which may reduce the incidence and severity of these highly prevalent preventable birth defects. This review discusses manifestations of alcohol exposure on the developing central nervous system, including the neural crest cells and sensory neural placodes, focusing on molecular neurodevelopmental pathways as possible therapeutic targets for prevention or protection.

Young's modulus of defective graphene sheet from intrinsic thermal vibrations

International Nuclear Information System (INIS)

Thomas, Siby; Mrudul, M S; Ajith, K M; Valsakumar, M C

2016-01-01

Classical molecular dynamics simulations have been performed to establish a relation between thermally excited ripples and Young's modulus of defective graphene sheet within a range of temperatures. The presence of the out-of-plane intrinsic ripples stabilizes the graphene membranes and the mechanical stability is analyzed by means of thermal mean square vibration amplitude in the long wavelength regime. We observed that the presence of vacancy and Stone-Wales (SW) defects reduces the Young's modulus of graphene sheets. Graphene sheet with vacancy defects possess superior Young's modulus to that of a sheet with Stone-Wales defects. The obtained room temperature Young's modulus of pristine and defective graphene sheet is ∼ 1 TPa, which is comparable to the results of earlier experimental and atomistic simulation studies. (paper)

ILT based defect simulation of inspection images accurately predicts mask defect printability on wafer

Science.gov (United States)

Deep, Prakash; Paninjath, Sankaranarayanan; Pereira, Mark; Buck, Peter

2016-05-01

printability of defects at wafer level and automates the process of defect dispositioning from images captured using high resolution inspection machine. It first eliminates false defects due to registration, focus errors, image capture errors and random noise caused during inspection. For the remaining real defects, actual mask-like contours are generated using the Calibre® ILT solution [1][2], which is enhanced to predict the actual mask contours from high resolution defect images. It enables accurate prediction of defect contours, which is not possible from images captured using inspection machine because some information is already lost due to optical effects. Calibre's simulation engine is used to generate images at wafer level using scanner optical conditions and mask-like contours as input. The tool then analyses simulated images and predicts defect printability. It automatically calculates maximum CD variation and decides which defects are severe to affect patterns on wafer. In this paper, we assess the printability of defects for the mask of advanced technology nodes. In particular, we will compare the recovered mask contours with contours extracted from SEM image of the mask and compare simulation results with AIMSTM for a variety of defects and patterns. The results of printability assessment and the accuracy of comparison are presented in this paper. We also suggest how this method can be extended to predict printability of defects identified on EUV photomasks.

Electrical fingerprint of pipeline defects

International Nuclear Information System (INIS)

Mica, Isabella; Polignano, Maria Luisa; Marco, Cinzia De

2004-01-01

Pipeline defects are dislocations that connect the source region of the transistor with the drain region. They were widely reported to occur in CMOS, BiCMOS devices and recently in SOI technologies. They can reduce device yield either by affecting the devices functionality or by increasing the current consumption under stand-by conditions. In this work the electrical fingerprint of these dislocations is studied, its purpose is to enable us to identify these defects as the ones responsible for device failure. It is shown that the pipeline defects are responsible for a leakage current from source to drain in the transistors. This leakage has a resistive characteristic and it is lightly modulated by the body bias. It is not sensitive to temperature; vice versa the off-current of a good transistor exhibits the well-known exponential dependence on 1/T. The emission spectrum of these defects was studied and compared with the spectrum of a good transistor. The paper aims to show that the spectrum of a defective transistor is quite peculiar; it shows well defined peaks, whereas the spectrum of a good transistor under saturation conditions is characterized by a broad spectral light emission distribution. Finally the deep-level transient spectroscopy (DLTS) is tried on defective diodes

Thermal conductivity of graphene with defects induced by electron beam irradiation

Science.gov (United States)

Malekpour, Hoda; Ramnani, Pankaj; Srinivasan, Srilok; Balasubramanian, Ganesh; Nika, Denis L.; Mulchandani, Ashok; Lake, Roger K.; Balandin, Alexander A.

2016-07-01

We investigate the thermal conductivity of suspended graphene as a function of the density of defects, ND, introduced in a controllable way. High-quality graphene layers are synthesized using chemical vapor deposition, transferred onto a transmission electron microscopy grid, and suspended over ~7.5 μm size square holes. Defects are induced by irradiation of graphene with the low-energy electron beam (20 keV) and quantified by the Raman D-to-G peak intensity ratio. As the defect density changes from 2.0 × 1010 cm-2 to 1.8 × 1011 cm-2 the thermal conductivity decreases from ~(1.8 +/- 0.2) × 103 W mK-1 to ~(4.0 +/- 0.2) × 102 W mK-1 near room temperature. At higher defect densities, the thermal conductivity reveals an intriguing saturation-type behavior at a relatively high value of ~400 W mK-1. The thermal conductivity dependence on the defect density is analyzed using the Boltzmann transport equation and molecular dynamics simulations. The results are important for understanding phonon - point defect scattering in two-dimensional systems and for practical applications of graphene in thermal management.We investigate the thermal conductivity of suspended graphene as a function of the density of defects, ND, introduced in a controllable way. High-quality graphene layers are synthesized using chemical vapor deposition, transferred onto a transmission electron microscopy grid, and suspended over ~7.5 μm size square holes. Defects are induced by irradiation of graphene with the low-energy electron beam (20 keV) and quantified by the Raman D-to-G peak intensity ratio. As the defect density changes from 2.0 × 1010 cm-2 to 1.8 × 1011 cm-2 the thermal conductivity decreases from ~(1.8 +/- 0.2) × 103 W mK-1 to ~(4.0 +/- 0.2) × 102 W mK-1 near room temperature. At higher defect densities, the thermal conductivity reveals an intriguing saturation-type behavior at a relatively high value of ~400 W mK-1. The thermal conductivity dependence on the defect density is

MicroRNA Expression Profiling Identifies Molecular Diagnostic Signatures for Anaplastic Large Cell Lymphoma

DEFF Research Database (Denmark)

Liu, Cuiling; Iqbal, Javeed; Teruya-Feldstein, Julie

2013-01-01

distinct clustering of ALCL, PTCL-NOS, and the AITL subtype of PTCL. Cases of ALK(+) ALCL and ALK(-) ALCL were interspersed in unsupervised analysis, suggesting a close relationship at the molecular level. We identified an miRNA signature of 7 miRNAs (5 upregulated: miR-512-3p, miR-886-5p, miR-886-3p, mi...

PAR1 deletions downstream of SHOX are the most frequent defect in a Spanish cohort of Léri-Weill dyschondrosteosis (LWD) probands.

Science.gov (United States)

Benito-Sanz, Sara; del Blanco, Darya Gorbenko; Aza-Carmona, Miriam; Magano, Luis F; Lapunzina, Pablo; Argente, Jesús; Campos-Barros, Angel; Heath, Karen E

2006-10-01

Léri-Weill dyschondrosteosis (LWD) is a skeletal dysplasia characterized by disproportionate short stature and Madelung deformity. Mutations or deletions of the SHOX gene have been previously identified as the main cause of LWD. We recently identified the existence of a second class of pseudoautosomal region 1 (PAR1) deletions which do not include SHOX, implicated in the etiopathogenesis of LWD. The deletions map at least 30-250 kb downstream of SHOX, are variable in size and clearly cosegregate with the LWD phenotype. In order to determine the frequency of this new type of deletions in the Spanish population we analyzed the distribution of PAR1 defects, including the screening of SHOX deletions, mutations, and PAR1 deletions downstream of SHOX, in a total of 26 LWD probands by a combination of MLPA, microsatellite analysis, SNP genotyping, dHPLC, and DNA sequencing. A molecular defect was identified in 16/26 LWD patients (61.5%): 10 PAR1 deletions downstream of SHOX, four SHOX encompassing deletions, and two SHOX mutations. No apparent phenotypic differences were observed between patients with SHOX defects and those with PAR1 deletions downstream of SHOX. In the examined cohort of Spanish LWD probands, PAR1 deletions downstream of SHOX represent the highest proportion of identified mutations (38%) compared to SHOX deletions (15%) and mutations (8%). As a consequence of our findings, the screening of this region should be included in the routine genetic testing of LWD. Also, LWD patients who tested negative for SHOX defects should be re-evaluated for PAR1 deletions downstream of SHOX.

Molecular Diagnostics of Copper-Transporting Protein Mutations Allows Early Onset Individual Therapy of Menkes Disease.

Science.gov (United States)

Králík, L; Flachsová, E; Hansíková, H; Saudek, V; Zeman, J; Martásek, P

2017-01-01

Menkes disease is a severe X-linked recessive disorder caused by a defect in the ATP7A gene, which encodes a membrane copper-transporting ATPase. Deficient activity of the ATP7A protein results in decreased intestinal absorption of copper, low copper level in serum and defective distribution of copper in tissues. The clinical symptoms are caused by decreased activities of copper-dependent enzymes and include neurodegeneration, connective tissue disorders, arterial changes and hair abnormalities. Without therapy, the disease is fatal in early infancy. Rapid diagnosis of Menkes disease and early start of copper therapy is critical for the effectiveness of treatment. We report a molecular biology-based strategy that allows early diagnosis of copper transport defects and implementation of individual therapies before the full development of pathological symptoms. Low serum copper and decreased activity of copperdependent mitochondrial cytochrome c oxidase in isolated platelets found in three patients indicated a possibility of functional defects in copper-transporting proteins, especially in the ATPA7 protein, a copper- transporting P-type ATPase. Rapid mutational screening of the ATP7A gene using high-resolution melting analysis of DNA indicated presence of mutations in the patients. Molecular investigation for mutations in the ATP7A gene revealed three nonsense mutations: c.2170C>T (p.Gln724Ter); c.3745G>T (p.Glu1249Ter); and c.3862C>T (p.Gln1288Ter). The mutation c.3745G>T (p.Glu1249Ter) has not been identified previously. Molecular analysis of the ATOX1 gene as a possible modulating factor of Menkes disease did not reveal presence of pathogenic mutations. Molecular diagnostics allowed early onset of individual therapies, adequate genetic counselling and prenatal diagnosis in the affected families.

Defect kinetics in novel detector materials

CERN Document Server

MacEvoy, B C

2000-01-01

Silicon particle detectors will be used extensively in experiments at the CERN Large Hadron Collider, where unprecedented particle fluences will cause significant atomic displacement damage. We present a model of the evolution of defect concentrations and consequent electrical behaviour in "novel" detector materials with various oxygen and carbon impurity concentrations. The divacancy-oxygen (V/sub 2/O) defect is identified as the cause of changes in device characteristics during /sup 60/Co gamma irradiation. In the case of hadron irradiation changes in detector doping concentration (N/sub eff/) are dominated by cluster defects, in particular the divacancy (V/sub 2/), which exchange charge directly via a non-Shockley-Read- Hall mechanism. The V/sub 2/O defect also contributes to Ne/sub eff/. This defect is more copiously produced during 24 GeV/c proton irradiation than during 1 MeV neutron irradiation on account of the higher vacancy introduction rate, hence the radiation hardness of materials is more sensiti...

Subsurface defects structural evolution in nano-cutting of single crystal copper

International Nuclear Information System (INIS)

Wang, Quanlong; Bai, Qingshun; Chen, Jiaxuan; Sun, Yazhou; Guo, Yongbo; Liang, Yingchun

2015-01-01

Highlights: • An innovative analysis method is adopted to analyze nano-cutting process accurately. • A characteristic SFT and stair-rod dislocation are found in subsurface defect layer. • The formation mechanism of stair-rod dislocation is investigated. • The local atomic structure of subsurface defects is introduced. - Abstract: In this work, molecular dynamics simulation is performed to study the subsurface defects structural distribution and its evolution during nano-cutting process of single crystal copper. The formation mechanism of chip and machined surface is interviewed by analyzing the dislocation evolution and atomic migration. The centro-symmetry parameter and spherical harmonics method are adopted to characterize the distribution and evolution of the subsurface defect structures and local atomic structures. The results show that stacking faults, dislocation loops, “V-shaped” dislocation loops, and plenty of point defects are formed during the machined surface being formed in shear-slip zone. In subsurface damage layers, stair-rod dislocation, stacking fault tetrahedra, atomic cluster defect, and vacancy defect are formed. And the formation mechanism of stair-rod dislocation is investigated by atomic-scale structure evolution. The local atomic structures of subsurface defects are icosahedrons, hexagonal close packed, body-centered cubic, and defect face center cubic, and the variations of local atomic structures are investigated

Subsurface defects structural evolution in nano-cutting of single crystal copper

Energy Technology Data Exchange (ETDEWEB)

Wang, Quanlong [School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001 (China); Center for Precision Engineering, Harbin Institute of Technology, Harbin 150001 (China); Bai, Qingshun [School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001 (China); Chen, Jiaxuan, E-mail: wangquanlong0@hit.edu.cn [Center for Precision Engineering, Harbin Institute of Technology, Harbin 150001 (China); Sun, Yazhou [School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001 (China); Guo, Yongbo [Center for Precision Engineering, Harbin Institute of Technology, Harbin 150001 (China); Liang, Yingchun [School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001 (China)

2015-07-30

Highlights: • An innovative analysis method is adopted to analyze nano-cutting process accurately. • A characteristic SFT and stair-rod dislocation are found in subsurface defect layer. • The formation mechanism of stair-rod dislocation is investigated. • The local atomic structure of subsurface defects is introduced. - Abstract: In this work, molecular dynamics simulation is performed to study the subsurface defects structural distribution and its evolution during nano-cutting process of single crystal copper. The formation mechanism of chip and machined surface is interviewed by analyzing the dislocation evolution and atomic migration. The centro-symmetry parameter and spherical harmonics method are adopted to characterize the distribution and evolution of the subsurface defect structures and local atomic structures. The results show that stacking faults, dislocation loops, “V-shaped” dislocation loops, and plenty of point defects are formed during the machined surface being formed in shear-slip zone. In subsurface damage layers, stair-rod dislocation, stacking fault tetrahedra, atomic cluster defect, and vacancy defect are formed. And the formation mechanism of stair-rod dislocation is investigated by atomic-scale structure evolution. The local atomic structures of subsurface defects are icosahedrons, hexagonal close packed, body-centered cubic, and defect face center cubic, and the variations of local atomic structures are investigated.

Early and long-standing rheumatoid arthritis: distinct molecular signatures identified by gene-expression profiling in synovia

Science.gov (United States)

Lequerré, Thierry; Bansard, Carine; Vittecoq, Olivier; Derambure, Céline; Hiron, Martine; Daveau, Maryvonne; Tron, François; Ayral, Xavier; Biga, Norman; Auquit-Auckbur, Isabelle; Chiocchia, Gilles; Le Loët, Xavier; Salier, Jean-Philippe

2009-01-01

Introduction Rheumatoid arthritis (RA) is a heterogeneous disease and its underlying molecular mechanisms are still poorly understood. Because previous microarray studies have only focused on long-standing (LS) RA compared to osteoarthritis, we aimed to compare the molecular profiles of early and LS RA versus control synovia. Methods Synovial biopsies were obtained by arthroscopy from 15 patients (4 early untreated RA, 4 treated LS RA and 7 controls, who had traumatic or mechanical lesions). Extracted mRNAs were used for large-scale gene-expression profiling. The different gene-expression combinations identified by comparison of profiles of early, LS RA and healthy synovia were linked to the biological processes involved in each situation. Results Three combinations of 719, 116 and 52 transcripts discriminated, respectively, early from LS RA, and early or LS RA from healthy synovia. We identified several gene clusters and distinct molecular signatures specifically expressed during early or LS RA, thereby suggesting the involvement of different pathophysiological mechanisms during the course of RA. Conclusions Early and LS RA have distinct molecular signatures with different biological processes participating at different times during the course of the disease. These results suggest that better knowledge of the main biological processes involved at a given RA stage might help to choose the most appropriate treatment. PMID:19563633

Automatic classification of blank substrate defects

Science.gov (United States)

Boettiger, Tom; Buck, Peter; Paninjath, Sankaranarayanan; Pereira, Mark; Ronald, Rob; Rost, Dan; Samir, Bhamidipati

2014-10-01

Mask preparation stages are crucial in mask manufacturing, since this mask is to later act as a template for considerable number of dies on wafer. Defects on the initial blank substrate, and subsequent cleaned and coated substrates, can have a profound impact on the usability of the finished mask. This emphasizes the need for early and accurate identification of blank substrate defects and the risk they pose to the patterned reticle. While Automatic Defect Classification (ADC) is a well-developed technology for inspection and analysis of defects on patterned wafers and masks in the semiconductors industry, ADC for mask blanks is still in the early stages of adoption and development. Calibre ADC is a powerful analysis tool for fast, accurate, consistent and automatic classification of defects on mask blanks. Accurate, automated classification of mask blanks leads to better usability of blanks by enabling defect avoidance technologies during mask writing. Detailed information on blank defects can help to select appropriate job-decks to be written on the mask by defect avoidance tools [1][4][5]. Smart algorithms separate critical defects from the potentially large number of non-critical defects or false defects detected at various stages during mask blank preparation. Mechanisms used by Calibre ADC to identify and characterize defects include defect location and size, signal polarity (dark, bright) in both transmitted and reflected review images, distinguishing defect signals from background noise in defect images. The Calibre ADC engine then uses a decision tree to translate this information into a defect classification code. Using this automated process improves classification accuracy, repeatability and speed, while avoiding the subjectivity of human judgment compared to the alternative of manual defect classification by trained personnel [2]. This paper focuses on the results from the evaluation of Automatic Defect Classification (ADC) product at MP Mask

Mechanical properties of highly defective graphene: from brittle rupture to ductile fracture

International Nuclear Information System (INIS)

Xu, Lanqing; Wei, Ning; Zheng, Yongping

2013-01-01

Defects are generally believed to deteriorate the superlative performance of graphene-based devices but may also be useful when carefully engineered to tailor the local properties and achieve new functionalities. Central to most defect-associated applications is the defect coverage and arrangement. In this work, we investigate, by molecular dynamics simulations, the mechanical properties and fracture dynamics of graphene sheets with randomly distributed vacancies or Stone–Wales defects under tensile deformations over a wide defect coverage range. With defects presented, an sp–sp 2 bonding network and an sp–sp 2 –sp 3 bonding network are observed in vacancy-defected and Stone–Wales-defected graphene, respectively. The ultimate strength degrades gradually with increasing defect coverage and saturates in the high-ratio regime, whereas the fracture strain presents an unusual descending–saturating–improving trend. In the dense vacancy defect situation, the fracture becomes more plastic and super-ductility is observed. Further fracture dynamics analysis reveals that the crack trapping by sp–sp 2 and sp–sp 2 –sp 3 rings and the crack-tip blunting account for the ductile fracture, whereas geometric rearrangement on the entire sheet for vacancy defects and geometric rearrangement on the specific defect sites for Stone–Wales defects account for their distinctive rules of the evolution of the fracture strain. (paper)

Reduction in Defect Content of ODS Alloys

Energy Technology Data Exchange (ETDEWEB)

Ritherdon, J

2001-05-15

The work detailed within this report is a continuation of earlier work carried out under contract number 1DX-SY382V. The earlier work comprises a literature review of the sources and types of defects found principally in Fe-based ODS alloys as well as experimental work designed to identify defects in the prototype ODS-Fe{sub 3}Al alloy, deduce their origins and to recommend methods of defect reduction. The present work is an extension of the experimental work already reported and concentrates on means of reduction of defects already identified rather than the search for new defect types. This report also includes results gathered during powder separation trials, conducted by the University of Groningen, Netherlands and coordinated by the University of Liverpool, involving the separation of different metallic powders in terms of their differing densities. The scope and objectives of the present work were laid out in the technical proposal ''Reduction in Defect Content in ODS Alloys-III''. All the work proposed in the ''Statement of Work'' section of the technical proposal has been carried out and all work extra to the ''Statement of Work'' falls within the context of an ODS-Fe{sub 3}Al alloy of improved overall quality and potential creep performance in the consolidated form. The outturn of the experimental work performed is reported in the following sections.

Defect identification for the AsGa family

International Nuclear Information System (INIS)

Overhof, H.; Spaeth, J.-M.

2003-01-01

The As Ga family consists of at least four distinctly different point defects including the technologically important EL2 defect. While the different members are easily distinguished from their MCDA spectra, the differences of the hf and shf interactions as derived from ODEPR and ODENDOR are rather small. We present ab initio calculations using the LMTO-ASA Green's function method for a variety of defect models that might be relevant for the identification of As Ga -related defects. We confirm the identification of the isolated As Ga and show that the {As Ga -X 2 } defect must be identified with the nearest-neighbor antistructure pair rather than with the {As Ga -V As } pair. For the {As Ga -X 1 } defect a distant antistructure pair is a likely candidate. For the EL2, the most important member of the As Ga family, we have not found a conclusive defect model. The recent ODENDOR data are similar to those of the distant orthorhombic {As Ga -V Ga } pair, which, however is a triple acceptor and not a donor

A novel inspection system for cosmetic defects

Science.gov (United States)

Hazra, S.; Roy, R.; Williams, D.; Aylmore, R.; Hollingdale, D.

2013-12-01

The appearance of automotive skin panels creates desirability for a product and differentiates it from the competition. Because of the importance of skin panels, considerable care is taken in minimizing defects such as the 'hollow' defect that occur around door-handle depressions. However, the inspection process is manual, subjective and time-consuming. This paper describes the development of an objective and inspection scheme for the 'hollow' defect. In this inspection process, the geometry of a panel is captured using a structured lighting system. The geometry data is subsequently analyzed by a purpose-built wavelet-based algorithm to identify the location of any defects that may be present and to estimate the perceived severity of the defects without user intervention. This paper describes and critically evaluates the behavior of this physically-based algorithm on an ideal and real geometry and compares its result to an actual audit. The results show that the algorithm is capable of objectively locating and classifying 'hollow' defects in actual panels.

Pollen developmental defects in ZD-CMS rice line explored by cytological, molecular and proteomic approaches.

Science.gov (United States)

Yan, Junjie; Tian, Han; Wang, Shuzhen; Shao, Jinzhen; Zheng, Yinzhen; Zhang, Hongyuan; Guo, Lin; Ding, Yi

2014-08-28

Cytoplasmic male sterility (CMS) is a widely observed phenomenon, which is especially useful in hybrid seed production. Meixiang A (MxA) is a new rice CMS line derived from a pollen-free sterile line named Yunnan ZidaoA (ZD-CMS). In this study, a homologous WA352 gene with variation in two nucleotides was identified in MxA. Cytological analysis revealed that MxA was aborted in the early uninucleate stage. The protein expression profiles of MxA and its maintainer line MeixiangB (MxB) were systematically compared using iTRAQ-based quantitative proteomics technology using young florets at the early uninucleate stage. A total of 688 proteins were quantified in both rice lines, and 45 of these proteins were found to be differentially expressed. Bioinformatics analysis indicated a large number of the proteins involved in carbohydrate metabolism or the stress response were downregulated in MxA, suggesting that these metabolic processes had been hindered during pollen development in MxA. The ROS (reactive oxygen species) level was increased in the mitochondrion of MxA, and further ultrastructural analysis showed the mitochondria with disrupted cristae in the rice CMS line MxA. These findings substantially contribute to our knowledge of pollen developmental defects in ZD-CMS rice line. MeixiangA (MxA) is a new type of rice CMS line, which is derived from pollen-free sterile line Yunnan ZidaoA. In this study, the cytological, molecular and proteomic approaches were used to study the characteristics of this new CMS line. Cytological study indicates the CMS line is aborted at the early uninucleate stage. A potential sterile gene ZD352 is identified in MxA, the protein product of which is mainly accumulated at the MMC/Meiotic stage. iTRAQ based proteomic analysis is performed to study the relevant proteins involved in the CMS occurance, 45 proteins are found to be significant differentially expressed and these proteins are involved in many cellular processes such as

Construction of a molecular clone of ovine enzootic nasal tumor virus.

Science.gov (United States)

Walsh, Scott R; Gerpe, María Carla Rosales; Wootton, Sarah K

2016-12-30

Enzootic nasal tumor virus (ENTV-1) is an ovine betaretrovirus that has been linked to enzootic nasal adenocarcinoma (ENA), a contagious tumor of the ethmoid turbinates of sheep. Transmission experiments performed using virus isolated from cell free nasal tumor homogenates suggest that ENTV-1 is the causative agent of ENA; however, this etiological relationship has not been conclusively proven due to the fact that the virus cannot be propagated in vitro nor is there an infectious molecular clone of the virus. Here we report construction of a molecular clone of ENTV-1 and demonstrate that transfection of this molecular clone into HEK 293T cells produces mature virus particles. Analysis of recombinant virus particles derived from the initial molecular clone revealed a defect in the proteolytic processing of Gag; however, this defect could be corrected by co-expression of the Gag-Pro-Pol polyprotein from the highly related Jaagsiekte sheep retrovirus (JSRV) suggesting that the polyprotein cleavage sites in the ENTV-1 molecular clone were functional. Mutagenesis of the molecular clone to correct amino acid variants identified within the pro gene did not restore proteolytic processing; whereas deletion of one proline residue from a polyproline tract located in variable region 1 (VR1) of the matrix resulted in production of CA protein of the mature (cleaved) size strongly suggesting that normal virion morphogenesis and polyprotein cleavage took place. Finally, electron microscopy revealed the presence of spherical virus particles with an eccentric capsid and an average diameter of about 100 nm. In summary, we have constructed the first molecular clone of ENTV-1 from which mature virus particles can be produced. Future experiments using virus produced from this molecular clone can now be conducted to fulfill Koch's postulates and demonstrate that ENTV-1 is necessary and sufficient to induce ENA in sheep.

Congenital Heart Defects and Receipt of Special Education Services.

Science.gov (United States)

Riehle-Colarusso, Tiffany; Autry, Andrew; Razzaghi, Hilda; Boyle, Coleen A; Mahle, William T; Van Naarden Braun, Kim; Correa, Adolfo

2015-09-01

We investigated the prevalence of receipt of special education services among children with congenital heart defects (CHDs) compared with children without birth defects. Children born from 1982 to 2004 in metropolitan Atlanta with CHDs (n = 3744) were identified from a population-based birth defect surveillance program; children without birth defects (n = 860 715) were identified from birth certificates. Cohorts were linked to special education files for the 1992-2012 school years to identify special education services. Children with noncardiac defects or genetic syndromes were excluded; children with CHDs were classified by presence or absence of critical CHDs (ie, CHDs requiring intervention by age one year). We evaluated the prevalence of receipt of special education services and prevalence rate ratios using children without birth defects as a reference. Compared with children without birth defects, children with CHDs were 50% more likely to receive special education services overall (adjusted prevalence rate ratio [aPRR] = 1.5; 95% confidence interval [CI]: 1.4-1.7). Specifically, they had higher prevalence of several special education categories including: intellectual disability (aPRR = 3.8; 95% CI: 2.8-5.1), sensory impairment (aPRR = 3.0; 95% CI: 1.8-5.0), other health impairment (aPRR = 2.8; 95% CI: 2.2-3.5), significant developmental delay (aPRR = 1.9; 95% CI: 1.3-2.8), and specific learning disability (aPRR = 1.4; 95% CI: 1.1-1.7). For most special education services, the excess prevalence did not vary by presence of critical CHDs. Children with CHDs received special education services more often than children without birth defects. These findings highlight the need for special education services and the importance of developmental screening for all children with CHDs. Copyright © 2015 by the American Academy of Pediatrics.

Defects in conformal field theory

International Nuclear Information System (INIS)

Billò, Marco; Gonçalves, Vasco; Lauria, Edoardo; Meineri, Marco

2016-01-01

We discuss consequences of the breaking of conformal symmetry by a flat or spherical extended operator. We adapt the embedding formalism to the study of correlation functions of symmetric traceless tensors in the presence of the defect. Two-point functions of a bulk and a defect primary are fixed by conformal invariance up to a set of OPE coefficients, and we identify the allowed tensor structures. A correlator of two bulk primaries depends on two cross-ratios, and we study its conformal block decomposition in the case of external scalars. The Casimir equation in the defect channel reduces to a hypergeometric equation, while the bulk channel blocks are recursively determined in the light-cone limit. In the special case of a defect of codimension two, we map the Casimir equation in the bulk channel to the one of a four-point function without defect. Finally, we analyze the contact terms of the stress-tensor with the extended operator, and we deduce constraints on the CFT data. In two dimensions, we relate the displacement operator, which appears among the contact terms, to the reflection coefficient of a conformal interface, and we find unitarity bounds for the latter.

Defects in conformal field theory

Energy Technology Data Exchange (ETDEWEB)

Billò, Marco [Dipartimento di Fisica, Università di Torino, and Istituto Nazionale di Fisica Nucleare - sezione di Torino,Via P. Giuria 1 I-10125 Torino (Italy); Gonçalves, Vasco [Centro de Física do Porto,Departamento de Física e Astronomia Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto (Portugal); ICTP South American Institute for Fundamental Research Instituto de Física Teórica,UNESP - University Estadual Paulista,Rua Dr. Bento T. Ferraz 271, 01140-070, São Paulo, SP (Brazil); Lauria, Edoardo [Institute for Theoretical Physics, KU Leuven, Celestijnenlaan 200D, B-3001 Leuven (Belgium); Meineri, Marco [Perimeter Institute for Theoretical Physics,Waterloo, Ontario, N2L 2Y5 (Canada); Scuola Normale Superiore, and Istituto Nazionale di Fisica Nucleare - sezione di Pisa,Piazza dei Cavalieri 7 I-56126 Pisa (Italy)

2016-04-15

We discuss consequences of the breaking of conformal symmetry by a flat or spherical extended operator. We adapt the embedding formalism to the study of correlation functions of symmetric traceless tensors in the presence of the defect. Two-point functions of a bulk and a defect primary are fixed by conformal invariance up to a set of OPE coefficients, and we identify the allowed tensor structures. A correlator of two bulk primaries depends on two cross-ratios, and we study its conformal block decomposition in the case of external scalars. The Casimir equation in the defect channel reduces to a hypergeometric equation, while the bulk channel blocks are recursively determined in the light-cone limit. In the special case of a defect of codimension two, we map the Casimir equation in the bulk channel to the one of a four-point function without defect. Finally, we analyze the contact terms of the stress-tensor with the extended operator, and we deduce constraints on the CFT data. In two dimensions, we relate the displacement operator, which appears among the contact terms, to the reflection coefficient of a conformal interface, and we find unitarity bounds for the latter.

Molecular Responses to the Zika Virus in Mosquitoes

Directory of Open Access Journals (Sweden)

Catalina Alfonso-Parra

2018-05-01

Full Text Available The Zika virus (ZIKV, originally discovered in 1947, did not become a major concern until the virus swept across the Pacific and into the Americas in the last decade, bringing with it news of neurological complications and birth defects in ZIKV affected areas. This prompted researchers to dissect the molecular interactions between ZIKV and the mosquito vector in an attempt to better understand not only the changes that occur upon infection, but to also identify molecules that may potentially enhance or suppress a mosquito’s ability to become infected and/or transmit the virus. Here, we review what is currently known regarding ZIKV-mosquito molecular interactions, focusing on ZIKV infection of Aedes aegypti and Aedes albopictus, the primary species implicated in transmitting ZIKV during the recent outbreaks.

SiC substrate defects and III-N heteroepitaxy

Energy Technology Data Exchange (ETDEWEB)

Poust, B D [Department of Materials Science and Engineering, University of California, Los Angeles, CA 90095 (United States); Koga, T S [Department of Materials Science and Engineering, University of California, Los Angeles, CA 90095 (United States); Sandhu, R [Department of Materials Science and Engineering, University of California, Los Angeles, CA 90095 (United States); Heying, B [Northrop Grumman Space Technology, Space and Electronics Group, Redondo Beach, CA 90278 (United States); Hsing, R [Northrop Grumman Space Technology, Space and Electronics Group, Redondo Beach, CA 90278 (United States); Wojtowicz, M [Northrop Grumman Space Technology, Space and Electronics Group, Redondo Beach, CA 90278 (United States); Khan, A [Department of Electrical Engineering, University of South Carolina, Columbia, SC (United States); Goorsky, M S [Department of Materials Science and Engineering, University of California, Los Angeles, CA 90095 (United States)

2003-05-21

This study addressed how defects in SiC substrates influence the crystallographic properties of AlGaN/GaN layers deposited by metallorganic vapour phase epitaxy and by molecular beam epitaxy. We employed double crystal reflection x-ray topography using symmetric (0008) and (00012) reflections with CuK{alpha} radiation ({lambda} = 1.54 A) to image dislocations, micropipes, and low angle boundaries in SiC substrates. Lattice strain near the core of a micropipe defect was estimated to be of the order of 10{sup -7}. The substrates investigated exhibited radial patterns of strain and, primarily, of tilt of the order of tens of arcsec. After deposition of the AlGaN and GaN layers, DCXRT images were generated from the substrate (0008) or (00012) and GaN epitaxial layer (0004) reflections. Full-width at half-maximum values ranging from {approx}100 to 300 arcsec were typical of the GaN reflections, while those of the 4H-SiC reflections were {approx}20-70 arcsec. Micropipes, tilt boundaries, and inclusions in the SiC were shown to produce structural defects in the GaN layers. A clear correlation between SiC substrate defects and GaN defects has been established.

SiC substrate defects and III-N heteroepitaxy

International Nuclear Information System (INIS)

Poust, B D; Koga, T S; Sandhu, R; Heying, B; Hsing, R; Wojtowicz, M; Khan, A; Goorsky, M S

2003-01-01

This study addressed how defects in SiC substrates influence the crystallographic properties of AlGaN/GaN layers deposited by metallorganic vapour phase epitaxy and by molecular beam epitaxy. We employed double crystal reflection x-ray topography using symmetric (0008) and (00012) reflections with CuKα radiation (λ = 1.54 A) to image dislocations, micropipes, and low angle boundaries in SiC substrates. Lattice strain near the core of a micropipe defect was estimated to be of the order of 10 -7 . The substrates investigated exhibited radial patterns of strain and, primarily, of tilt of the order of tens of arcsec. After deposition of the AlGaN and GaN layers, DCXRT images were generated from the substrate (0008) or (00012) and GaN epitaxial layer (0004) reflections. Full-width at half-maximum values ranging from ∼100 to 300 arcsec were typical of the GaN reflections, while those of the 4H-SiC reflections were ∼20-70 arcsec. Micropipes, tilt boundaries, and inclusions in the SiC were shown to produce structural defects in the GaN layers. A clear correlation between SiC substrate defects and GaN defects has been established

Early Retinal Defects in Fmr1-/y Mice: Toward a Critical Role of Visual Dys-Sensitivity in the Fragile X Syndrome Phenotype?

Science.gov (United States)

Perche, Olivier; Felgerolle, Chloé; Ardourel, Maryvonne; Bazinet, Audrey; Pâris, Arnaud; Rossignol, Rafaëlle; Meyer-Dilhet, Géraldine; Mausset-Bonnefont, Anne-Laure; Hébert, Betty; Laurenceau, David; Montécot-Dubourg, Céline; Menuet, Arnaud; Bizot, Jean-Charles; Pichon, Jacques; Ranchon-Cole, Isabelle; Briault, Sylvain

2018-01-01

Fragile X Syndrome (FXS) is caused by a deficiency in Fragile X Mental Retardation Protein (FMRP) leading to global sensorial abnormalities, among which visual defects represent a critical part. These visual defects are associated with cerebral neuron immaturity especially in the primary visual cortex. However, we recently demonstrated that retinas of adult Fmr1 -/y mice, the FXS murine model, present molecular, cellular and functional alterations. However, no data are currently available on the evolution pattern of such defects. As retinal stimulation through Eye Opening (EO) is a crucial signal for the cerebral visual system maturation, we questioned the precocity of molecular and functional retinal phenotype. To answer this question, we studied the retinal molecular phenotype of Fmr1 -/y mice before EO until adult age and the consequences of the retinal loss of Fmrp on retinal function in young and adult mice. We showed that retinal molecular defects are present before EO and remain stable at adult age, leading to electrophysiological impairments without any underlying structural changes. We underlined that loss of Fmrp leads to a wide range of defects in the retina, settled even before EO. Our work demonstrates a critical role of the sensorial dysfunction in the Fmr1 -/y mice overall phenotype, and provides evidence that altered peripheral perception is a component of the sensory processing defect in FXS conditions.

Defect phase diagram for doping of Ga2O3

Science.gov (United States)

Lany, Stephan

2018-04-01

For the case of n-type doping of β-Ga2O3 by group 14 dopants (C, Si, Ge, Sn), a defect phase diagram is constructed from defect equilibria calculated over a range of temperatures (T), O partial pressures (pO2), and dopant concentrations. The underlying defect levels and formation energies are determined from first-principles supercell calculations with GW bandgap corrections. Only Si is found to be a truly shallow donor, C is a deep DX-like (lattice relaxed donor) center, and Ge and Sn have defect levels close to the conduction band minimum. The thermodynamic modeling includes the effect of association of dopant-defect pairs and complexes, which causes the net doping to decline when exceeding a certain optimal dopant concentration. The optimal doping levels are surprisingly low, between about 0.01% and 1% of cation substitution, depending on the (T, pO2) conditions. Considering further the stability constraints due to sublimation of molecular Ga2O, specific predictions of optimized pO2 and Si dopant concentrations are given. The incomplete passivation of dopant-defect complexes in β-Ga2O3 suggests a design rule for metastable doping above the solubility limit.

Deficiency of RITA results in multiple mitotic defects by affecting microtubule dynamics.

Science.gov (United States)

Steinhäuser, K; Klöble, P; Kreis, N-N; Ritter, A; Friemel, A; Roth, S; Reichel, J M; Michaelis, J; Rieger, M A; Louwen, F; Oswald, F; Yuan, J

2017-04-01

Deregulation of mitotic microtubule (MT) dynamics results in defective spindle assembly and chromosome missegregation, leading further to chromosome instability, a hallmark of tumor cells. RBP-J interacting and tubulin-associated protein (RITA) has been identified as a negative regulator of the Notch signaling pathway. Intriguingly, deregulated RITA is involved in primary hepatocellular carcinoma and other malignant entities. We were interested in the potential molecular mechanisms behind its involvement. We show here that RITA binds to tubulin and localizes to various mitotic MT structures. RITA coats MTs and affects their structures in vitro as well as in vivo. Tumor cell lines deficient of RITA display increased acetylated α-tubulin, enhanced MT stability and reduced MT dynamics, accompanied by multiple mitotic defects, including chromosome misalignment and segregation errors. Re-expression of wild-type RITA, but not RITA Δtub ineffectively binding to tubulin, restores the phenotypes, suggesting that the role of RITA in MT modulation is mediated via its interaction with tubulin. Mechanistically, RITA interacts with tubulin/histone deacetylase 6 (HDAC6) and its suppression decreases the binding of the deacetylase HDAC6 to tubulin/MTs. Furthermore, the mitotic defects and increased MT stability are also observed in RITA -/- mouse embryonic fibroblasts. RITA has thus a novel role in modulating MT dynamics and its deregulation results in erroneous chromosome segregation, one of the major reasons for chromosome instability in tumor cells.

[Molecular basis of Fanconi's anemia].

Science.gov (United States)

Digweed, M

1999-01-01

Fanconi anaemia (FA) is an autosomal recessive genetic disorder characterised clinically by progressive bone marrow failure, skeletal deformities and a predisposition to neoplasia. Patient cells manifest an extreme chromosomal instability and hypersensitivity to polyfunctional alkylating agents. It is assumed that the basic defect is related to the repair of DNA damage, in particular that of so-called DNA crosslinks. Currently there are eight complementation groups in FA (FA-A-FA-H) which indicates that at least eight independent genes can lead to FA. Three of these genes have been identified: FANCA, FANCC and FANCG. In this review, the molecular biology and genetics of FA are presented and possible functions of the FANC proteins are discussed.

Identifying molecular subtypes in human colon cancer using gene expression and DNA methylation microarray data

OpenAIRE

REN, ZHONGLU; WANG, WENHUI; LI, JINMING

2015-01-01

Identifying colon cancer subtypes based on molecular signatures may allow for a more rational, patient-specific approach to therapy in the future. Classifications using gene expression data have been attempted before with little concordance between the different studies carried out. In this study we aimed to uncover subtypes of colon cancer that have distinct biological characteristics and identify a set of novel biomarkers which could best reflect the clinical and/or biological characteristi...

Molecular profiling of complete congenital stationary night blindness: a pilot study on an Indian cohort.

Science.gov (United States)

Malaichamy, Sivasankar; Sen, Parveen; Sachidanandam, Ramya; Arokiasamy, Tharigopala; Lancelot, Marie Elise; Audo, Isabelle; Zeitz, Christina; Soumittra, Nagasamy

2014-01-01

Congenital stationary night blindness (CSNB) is a non-progressive retinal disorder that shows genetic and clinical heterogeneity. CSNB is inherited as an autosomal recessive, autosomal dominant, or X-linked recessive trait and shows a good genotype-phenotype correlation. Clinically, CSNB is classified as the Riggs type and the Schubert-Bornschein type. The latter form is further sub-classified into complete and incomplete forms based on specific waveforms on the electroretinogram (ERG). There are no molecular genetic data for CSNB in the Indian population. Therefore, we present for the first time molecular profiling of eight families with complete CSNB (cCSNB). The index patients and their other affected family members were comprehensively evaluated for the phenotype, including complete ophthalmic evaluation, ERG, fundus autofluorescence, optical coherence tomography, and color vision test. The known gene defects for cCSNB, LRIT3, TRPM1, GRM6, GPR179, and NYX, were screened by PCR direct sequencing. Bioinformatic analyses were performed using SIFT and PolyPhen for the identified missense mutations. All eight affected index patients and affected family members were identified as having cCSNB based on their ERG waveforms. Mutations in the TRPM1 gene were identified in six index patients. The two remaining index patients each carried a GPR179 and GRM6 mutation. Seven of the patients revealed homozygous mutations, while one patient showed a compound heterozygous mutation. Six of the eight mutations identified are novel. This is the first report on molecular profiling of candidate genes in CSNB in an Indian cohort. As shown for other cohorts, TRPM1 seems to be a major gene defect in patients with cCSNB in India.

Precise design-based defect characterization and root cause analysis

Science.gov (United States)

Xie, Qian; Venkatachalam, Panneerselvam; Lee, Julie; Chen, Zhijin; Zafar, Khurram

2017-03-01

As semiconductor manufacturing continues its march towards more advanced technology nodes, it becomes increasingly important to identify and characterize design weak points, which is typically done using a combination of inline inspection data and the physical layout (or design). However, the employed methodologies have been somewhat imprecise, relying greatly on statistical techniques to signal excursions. For example, defect location error that is inherent to inspection tools prevents them from reporting the true locations of defects. Therefore, common operations such as background-based binning that are designed to identify frequently failing patterns cannot reliably identify specific weak patterns. They can only identify an approximate set of possible weak patterns, but within these sets there are many perfectly good patterns. Additionally, characterizing the failure rate of a known weak pattern based on inline inspection data also has a lot of fuzziness due to coordinate uncertainty. SEM (Scanning Electron Microscope) Review attempts to come to the rescue by capturing high resolution images of the regions surrounding the reported defect locations, but SEM images are reviewed by human operators and the weak patterns revealed in those images must be manually identified and classified. Compounding the problem is the fact that a single Review SEM image may contain multiple defective patterns and several of those patterns might not appear defective to the human eye. In this paper we describe a significantly improved methodology that brings advanced computer image processing and design-overlay techniques to better address the challenges posed by today's leading technology nodes. Specifically, new software techniques allow the computer to analyze Review SEM images in detail, to overlay those images with reference design to detect every defect that might be present in all regions of interest within the overlaid reference design (including several classes of defects

Computer Vision System For Locating And Identifying Defects In Hardwood Lumber

Science.gov (United States)

Conners, Richard W.; Ng, Chong T.; Cho, Tai-Hoon; McMillin, Charles W.

1989-03-01

This paper describes research aimed at developing an automatic cutup system for use in the rough mills of the hardwood furniture and fixture industry. In particular, this paper describes attempts to create the vision system that will power this automatic cutup system. There are a number of factors that make the development of such a vision system a challenge. First there is the innate variability of the wood material itself. No two species look exactly the same, in fact, they can have a significant visual difference in appearance among species. Yet a truly robust vision system must be able to handle a variety of such species, preferably with no operator intervention required when changing from one species to another. Secondly, there is a good deal of variability in the definition of what constitutes a removable defect. The hardwood furniture and fixture industry is diverse in the nature of the products that it makes. The products range from hardwood flooring to fancy hardwood furniture, from simple mill work to kitchen cabinets. Thus depending on the manufacturer, the product, and the quality of the product the nature of what constitutes a removable defect can and does vary. The vision system must be such that it can be tailored to meet each of these unique needs, preferably without any additional program modifications. This paper will describe the vision system that has been developed. It will assess the current system capabilities, and it will discuss the directions for future research. It will be argued that artificial intelligence methods provide a natural mechanism for attacking this computer vision application.

Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers

OpenAIRE

Girardot, Charles; Scholtalbers, Jelle; Sauer, Sajoscha; Su, Shu-Yi; Furlong, Eileen E.M.

2016-01-01

Background The yield obtained from next generation sequencers has increased almost exponentially in recent years, making sample multiplexing common practice. While barcodes (known sequences of fixed length) primarily encode the sample identity of sequenced DNA fragments, barcodes made of random sequences (Unique Molecular Identifier or UMIs) are often used to distinguish between PCR duplicates and transcript abundance in, for example, single-cell RNA sequencing (scRNA-seq). In paired-end sequ...

Slow Replication Fork Velocity of Homologous Recombination-Defective Cells Results from Endogenous Oxidative Stress

Science.gov (United States)

Magdalou, Indiana; Machon, Christelle; Dardillac, Elodie; Técher, Hervé; Guitton, Jérôme; Debatisse, Michelle; Lopez, Bernard S.

2016-01-01

Replications forks are routinely hindered by different endogenous stresses. Because homologous recombination plays a pivotal role in the reactivation of arrested replication forks, defects in homologous recombination reveal the initial endogenous stress(es). Homologous recombination-defective cells consistently exhibit a spontaneously reduced replication speed, leading to mitotic extra centrosomes. Here, we identify oxidative stress as a major endogenous source of replication speed deceleration in homologous recombination-defective cells. The treatment of homologous recombination-defective cells with the antioxidant N-acetyl-cysteine or the maintenance of the cells at low O2 levels (3%) rescues both the replication fork speed, as monitored by single-molecule analysis (molecular combing), and the associated mitotic extra centrosome frequency. Reciprocally, the exposure of wild-type cells to H2O2 reduces the replication fork speed and generates mitotic extra centrosomes. Supplying deoxynucleotide precursors to H2O2-exposed cells rescued the replication speed. Remarkably, treatment with N-acetyl-cysteine strongly expanded the nucleotide pool, accounting for the replication speed rescue. Remarkably, homologous recombination-defective cells exhibit a high level of endogenous reactive oxygen species. Consistently, homologous recombination-defective cells accumulate spontaneous γH2AX or XRCC1 foci that are abolished by treatment with N-acetyl-cysteine or maintenance at 3% O2. Finally, oxidative stress stimulated homologous recombination, which is suppressed by supplying deoxynucleotide precursors. Therefore, the cellular redox status strongly impacts genome duplication and transmission. Oxidative stress should generate replication stress through different mechanisms, including DNA damage and nucleotide pool imbalance. These data highlight the intricacy of endogenous replication and oxidative stresses, which are both evoked during tumorigenesis and senescence initiation

Slow Replication Fork Velocity of Homologous Recombination-Defective Cells Results from Endogenous Oxidative Stress.

Directory of Open Access Journals (Sweden)

Therese Wilhelm

2016-05-01

Full Text Available Replications forks are routinely hindered by different endogenous stresses. Because homologous recombination plays a pivotal role in the reactivation of arrested replication forks, defects in homologous recombination reveal the initial endogenous stress(es. Homologous recombination-defective cells consistently exhibit a spontaneously reduced replication speed, leading to mitotic extra centrosomes. Here, we identify oxidative stress as a major endogenous source of replication speed deceleration in homologous recombination-defective cells. The treatment of homologous recombination-defective cells with the antioxidant N-acetyl-cysteine or the maintenance of the cells at low O2 levels (3% rescues both the replication fork speed, as monitored by single-molecule analysis (molecular combing, and the associated mitotic extra centrosome frequency. Reciprocally, the exposure of wild-type cells to H2O2 reduces the replication fork speed and generates mitotic extra centrosomes. Supplying deoxynucleotide precursors to H2O2-exposed cells rescued the replication speed. Remarkably, treatment with N-acetyl-cysteine strongly expanded the nucleotide pool, accounting for the replication speed rescue. Remarkably, homologous recombination-defective cells exhibit a high level of endogenous reactive oxygen species. Consistently, homologous recombination-defective cells accumulate spontaneous γH2AX or XRCC1 foci that are abolished by treatment with N-acetyl-cysteine or maintenance at 3% O2. Finally, oxidative stress stimulated homologous recombination, which is suppressed by supplying deoxynucleotide precursors. Therefore, the cellular redox status strongly impacts genome duplication and transmission. Oxidative stress should generate replication stress through different mechanisms, including DNA damage and nucleotide pool imbalance. These data highlight the intricacy of endogenous replication and oxidative stresses, which are both evoked during tumorigenesis and

Slow Replication Fork Velocity of Homologous Recombination-Defective Cells Results from Endogenous Oxidative Stress.

Science.gov (United States)

Wilhelm, Therese; Ragu, Sandrine; Magdalou, Indiana; Machon, Christelle; Dardillac, Elodie; Técher, Hervé; Guitton, Jérôme; Debatisse, Michelle; Lopez, Bernard S

2016-05-01

Replications forks are routinely hindered by different endogenous stresses. Because homologous recombination plays a pivotal role in the reactivation of arrested replication forks, defects in homologous recombination reveal the initial endogenous stress(es). Homologous recombination-defective cells consistently exhibit a spontaneously reduced replication speed, leading to mitotic extra centrosomes. Here, we identify oxidative stress as a major endogenous source of replication speed deceleration in homologous recombination-defective cells. The treatment of homologous recombination-defective cells with the antioxidant N-acetyl-cysteine or the maintenance of the cells at low O2 levels (3%) rescues both the replication fork speed, as monitored by single-molecule analysis (molecular combing), and the associated mitotic extra centrosome frequency. Reciprocally, the exposure of wild-type cells to H2O2 reduces the replication fork speed and generates mitotic extra centrosomes. Supplying deoxynucleotide precursors to H2O2-exposed cells rescued the replication speed. Remarkably, treatment with N-acetyl-cysteine strongly expanded the nucleotide pool, accounting for the replication speed rescue. Remarkably, homologous recombination-defective cells exhibit a high level of endogenous reactive oxygen species. Consistently, homologous recombination-defective cells accumulate spontaneous γH2AX or XRCC1 foci that are abolished by treatment with N-acetyl-cysteine or maintenance at 3% O2. Finally, oxidative stress stimulated homologous recombination, which is suppressed by supplying deoxynucleotide precursors. Therefore, the cellular redox status strongly impacts genome duplication and transmission. Oxidative stress should generate replication stress through different mechanisms, including DNA damage and nucleotide pool imbalance. These data highlight the intricacy of endogenous replication and oxidative stresses, which are both evoked during tumorigenesis and senescence initiation

Thyroid Medication Use and Birth Defects in the National Birth Defects Prevention Study.

Science.gov (United States)

Howley, Meredith M; Fisher, Sarah C; Van Zutphen, Alissa R; Waller, Dorothy K; Carmichael, Suzan L; Browne, Marilyn L

2017-11-01

Thyroid disorders are common among reproductive-aged women, with hypothyroidism affecting 2 to 3% of pregnancies, and hyperthyroidism affecting an additional 0.1 to 1%. We examined associations between thyroid medications and individual birth defects using data from the National Birth Defects Prevention Study (NBDPS). The NBDPS is a multisite, population-based, case-control study that included pregnancies with estimated delivery dates from 1997 to 2011. We analyzed self-reported thyroid medication use from mothers of 31,409 birth defect cases and 11,536 unaffected controls. Adjusted odds ratios (ORs) and 95% confidence intervals (CIs) were estimated using logistic regression for birth defects with five or more exposed cases, controlling for maternal age, race/ethnicity, and study center. Crude ORs and exact 95% CIs were estimated for defects with 3 to 4 exposed cases. Thyroid hormone was used by 738 (2.3%) case and 237 (2.1%) control mothers, and was associated with anencephaly (OR = 1.68; 95% CI, 1.03-2.73), holoprosencephaly (OR = 2.48; 95% CI, 1.13-5.44), hydrocephaly (1.77; 95% CI, 1.07-2.95) and small intestinal atresia (OR = 1.81; 95% CI, 1.04-3.15). Anti-thyroid medication was used by 34 (0.1%) case and 10 (<0.1%) control mothers, and was associated with aortic valve stenosis (OR = 6.91; 95% CI, 1.21-27.0). While new associations were identified, our findings are relatively consistent with previous NBDPS analyses. Our findings suggest thyroid medication use is not associated with most birth defects studied in the NBDPS, but may be associated with some specific birth defects. These results should not be interpreted to suggest that medications used to treat thyroid disease are teratogens, as the observed associations may reflect effects of the underlying thyroid disease. Birth Defects Research 109:1471-1481, 2017.© 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

RNA sequencing of Populus x canadensis roots identifies key molecular mechanisms underlying physiological adaption to excess zinc.

Directory of Open Access Journals (Sweden)

Andrea Ariani

Full Text Available Populus x canadensis clone I-214 exhibits a general indicator phenotype in response to excess Zn, and a higher metal uptake in roots than in shoots with a reduced translocation to aerial parts under hydroponic conditions. This physiological adaptation seems mainly regulated by roots, although the molecular mechanisms that underlie these processes are still poorly understood. Here, differential expression analysis using RNA-sequencing technology was used to identify the molecular mechanisms involved in the response to excess Zn in root. In order to maximize specificity of detection of differentially expressed (DE genes, we consider the intersection of genes identified by three distinct statistical approaches (61 up- and 19 down-regulated and validate them by RT-qPCR, yielding an agreement of 93% between the two experimental techniques. Gene Ontology (GO terms related to oxidation-reduction processes, transport and cellular iron ion homeostasis were enriched among DE genes, highlighting the importance of metal homeostasis in adaptation to excess Zn by P. x canadensis clone I-214. We identified the up-regulation of two Populus metal transporters (ZIP2 and NRAMP1 probably involved in metal uptake, and the down-regulation of a NAS4 gene involved in metal translocation. We identified also four Fe-homeostasis transcription factors (two bHLH38 genes, FIT and BTS that were differentially expressed, probably for reducing Zn-induced Fe-deficiency. In particular, we suggest that the down-regulation of FIT transcription factor could be a mechanism to cope with Zn-induced Fe-deficiency in Populus. These results provide insight into the molecular mechanisms involved in adaption to excess Zn in Populus spp., but could also constitute a starting point for the identification and characterization of molecular markers or biotechnological targets for possible improvement of phytoremediation performances of poplar trees.

Early Retinal Defects in Fmr1−/y Mice: Toward a Critical Role of Visual Dys-Sensitivity in the Fragile X Syndrome Phenotype?

Science.gov (United States)

Perche, Olivier; Felgerolle, Chloé; Ardourel, Maryvonne; Bazinet, Audrey; Pâris, Arnaud; Rossignol, Rafaëlle; Meyer-Dilhet, Géraldine; Mausset-Bonnefont, Anne-Laure; Hébert, Betty; Laurenceau, David; Montécot-Dubourg, Céline; Menuet, Arnaud; Bizot, Jean-Charles; Pichon, Jacques; Ranchon-Cole, Isabelle; Briault, Sylvain

2018-01-01

Fragile X Syndrome (FXS) is caused by a deficiency in Fragile X Mental Retardation Protein (FMRP) leading to global sensorial abnormalities, among which visual defects represent a critical part. These visual defects are associated with cerebral neuron immaturity especially in the primary visual cortex. However, we recently demonstrated that retinas of adult Fmr1−/y mice, the FXS murine model, present molecular, cellular and functional alterations. However, no data are currently available on the evolution pattern of such defects. As retinal stimulation through Eye Opening (EO) is a crucial signal for the cerebral visual system maturation, we questioned the precocity of molecular and functional retinal phenotype. To answer this question, we studied the retinal molecular phenotype of Fmr1−/y mice before EO until adult age and the consequences of the retinal loss of Fmrp on retinal function in young and adult mice. We showed that retinal molecular defects are present before EO and remain stable at adult age, leading to electrophysiological impairments without any underlying structural changes. We underlined that loss of Fmrp leads to a wide range of defects in the retina, settled even before EO. Our work demonstrates a critical role of the sensorial dysfunction in the Fmr1−/y mice overall phenotype, and provides evidence that altered peripheral perception is a component of the sensory processing defect in FXS conditions. PMID:29681800

Early Retinal Defects in Fmr1−/y Mice: Toward a Critical Role of Visual Dys-Sensitivity in the Fragile X Syndrome Phenotype?

Directory of Open Access Journals (Sweden)

Olivier Perche

2018-04-01

Full Text Available Fragile X Syndrome (FXS is caused by a deficiency in Fragile X Mental Retardation Protein (FMRP leading to global sensorial abnormalities, among which visual defects represent a critical part. These visual defects are associated with cerebral neuron immaturity especially in the primary visual cortex. However, we recently demonstrated that retinas of adult Fmr1−/y mice, the FXS murine model, present molecular, cellular and functional alterations. However, no data are currently available on the evolution pattern of such defects. As retinal stimulation through Eye Opening (EO is a crucial signal for the cerebral visual system maturation, we questioned the precocity of molecular and functional retinal phenotype. To answer this question, we studied the retinal molecular phenotype of Fmr1−/y mice before EO until adult age and the consequences of the retinal loss of Fmrp on retinal function in young and adult mice. We showed that retinal molecular defects are present before EO and remain stable at adult age, leading to electrophysiological impairments without any underlying structural changes. We underlined that loss of Fmrp leads to a wide range of defects in the retina, settled even before EO. Our work demonstrates a critical role of the sensorial dysfunction in the Fmr1−/y mice overall phenotype, and provides evidence that altered peripheral perception is a component of the sensory processing defect in FXS conditions.

Reduced defect densities in the ZnO epilayer grown on Si substrates by laser-assisted molecular-beam epitaxy using a ZnS epitaxial buffer layer

International Nuclear Information System (INIS)

Onuma, T.; Chichibu, S.F.; Uedono, A.; Yoo, Y.-Z.; Chikyow, T.; Sota, T.; Kawasaki, M.; Koinuma, H.

2004-01-01

Nonradiative photoluminescence (PL) lifetime (τ nr ) and point defect density in the (0001) ZnO epilayer grown on (111) Si substrates by laser-assisted molecular-beam epitaxy (L-MBE) using a (0001) ZnS epitaxial buffer layer were compared with those in the ZnO films on (111) and (001) Si substrates prepared by direct transformation of ZnS epilayers on Si by thermal oxidation [Yoo et al., Appl. Phys. Lett. 78, 616 (2001)]. Both the ZnO films exhibited excitonic reflectance anomalies and corresponding PL peaks at low temperature, and the density or size of vacancy-type point defects (Zn vacancies), which were measured by the monoenergetic positron annihilation measurement, in the L-MBE epilayer was lower than that in the films prepared by the oxidation transformation. The ZnO epilayer grown on a (0001) ZnS epitaxial buffer on (111) Si exhibited longer τ nr of 105 ps at room temperature

A molecular dynamics study of thermal transport in nanoparticle doped Argon like solid

Energy Technology Data Exchange (ETDEWEB)

Shahadat, Muhammad Rubayat Bin, E-mail: rubayat37@gmail.com; Ahmed, Shafkat; Morshed, A. K. M. M. [Department of Mechanical Engineering Bangladesh University of Engineering and Technology (BUET) Dhaka (Bangladesh)

2016-07-12

Interfacial phenomena such as mass and type of the interstitial atom, nano scale material defect influence heat transfer and the effect become very significant with the reduction of the material size. Non Equilibrium Molecular Dynamics (NEMD) simulation was carried out in this study to investigate the effect of the interfacial phenomena on solid. Argon like solid was considered in this study and LJ potential was used for atomic interaction. Nanoparticles of different masses and different molecular defects were inserted inside the solid. From the molecular simulation, it was observed that a large interfacial mismatch due to change in mass in the homogenous solid causes distortion of the phonon frequency causing increase in thermal resistance. Position of the doped nanoparticles have more profound effect on the thermal conductivity of the solid whereas influence of the mass ratio is not very significant. Interstitial atom positioned perpendicular to the heat flow causes sharp reduction in thermal conductivity. Structural defect caused by the molecular defect (void) also observed to significantly affect the thermal conductivity of the solid.

Mechanical properties and fracture behaviour of defective phosphorene nanotubes under uniaxial tension

Science.gov (United States)

Liu, Ping; Pei, Qing-Xiang; Huang, Wei; Zhang, Yong-Wei

2017-12-01

The easy formation of vacancy defects and the asymmetry in the two sublayers of phosphorene nanotubes (PNTs) may result in brand new mechanical properties and failure behaviour. Herein, we investigate the mechanical properties and fracture behaviour of defective PNTs under uniaxial tension using molecular dynamics simulations. Our simulation results show that atomic vacancies cause local stress concentration and thus significantly reduce the fracture strength and fracture strain of PNTs. More specifically, a 1% defect concentration is able to reduce the fracture strength and fracture strain by as much as 50% and 66%, respectively. Interestingly, the reduction in the mechanical properties is found to depend on the defect location: a defect located in the outer sublayer has a stronger effect than one located in the inner layer, especially for PNTs with a small diameter. Temperature is also found to strongly influence the mechanical properties of both defect-free and defective PNTs. When the temperature is increased from 0 K to 400 K, the fracture strength and fracture strain of defective PNTs with a defect concentration of 1% are reduced further by 71% and 61%, respectively. These findings are of great importance for the structural design of PNTs as building blocks in nanodevices.

Investigation of a metal-organic interface. Realization and understanding of a molecular switch

Energy Technology Data Exchange (ETDEWEB)

Neucheva, Olga [Forschungszentrum Juelich (DE). Institute of Bio- and Nanosystems (IBN), Functional Nanostructures at Surfaces (IBN-3)

2010-07-01

The field of molecular organic electronics is an emerging and very dynamic area. The continued trend to miniaturisation, combined with increasing complexity and cost of production in conventional semiconductor electronics, forces companies to turn their attention to alternatives that promise the next levels of scale at significantly lower cost. After consumer electronic devices based on organic transistors, such as TVs and book readers, have already been presented, molecular electronics is expected to offer the next breakthrough in feature size. Unfortunately, most of the organic/metal interfaces contain intrinsic defects that break the homogeneity of the interface properties. In this thesis, the electronic and structural properties of such defects were examined in order to understand the influence of the inhomogeneities on the quality of the interface layer. However, the main focus of this work was the investigation of the local properties of a single molecule. Taking advantage of the Scanning Tunnelling Microscope's (STM's) ability to act as a local probe, a single molecular switch was realized and studied. Moreover, in close collaboration with theory groups, the underlying mechanism driving the switching process was identified and described. Besides the investigation of the switching process, the ability of the STM to build nanostructures of different shapes from large organic molecules was shown. Knowing the parameters for realization and control of the switching process and for building the molecular corrals, the results of this investigation enable the reconstruction of the studied molecular ensemble and its deployment in electric molecular circuits, constituting a next step towards further miniaturization of electronic devices. (orig.)

Mobility of point defects induced by subthreshold collisions

International Nuclear Information System (INIS)

Tenenbaum, A.; Nguyen Van Doan

1976-01-01

The effect of thermal vibrations on atomic collision focusing was studied with the view to demonstrate that such collisions may induce point defect migration through the crystal. The persistence of the phenomenon of focused atomic collisions in a crystal at thermal equilibrium was studied, using a computer simulation by the Molecular Dynamics Technique. In the temperature range (0 to 500K) matter and momentum transfers in c.f.c. crystals proceed mainly by focused collisions along and directions. Their contribution to the induced migration of radiation defects was determined from the threshold energy of every primary able to be involved in the process. As an example, the quantitative model is applied to electron irradiation along the crystallographic directions [fr

An inherited immunoglobulin class-switch recombination deficiency associated with a defect in the INO80 chromatin remodeling complex.

Science.gov (United States)

Kracker, Sven; Di Virgilio, Michela; Schwartzentruber, Jeremy; Cuenin, Cyrille; Forveille, Monique; Deau, Marie-Céline; McBride, Kevin M; Majewski, Jacek; Gazumyan, Anna; Seneviratne, Suranjith; Grimbacher, Bodo; Kutukculer, Necil; Herceg, Zdenko; Cavazzana, Marina; Jabado, Nada; Nussenzweig, Michel C; Fischer, Alain; Durandy, Anne

2015-04-01

Immunoglobulin class-switch recombination defects (CSR-D) are rare primary immunodeficiencies characterized by impaired production of switched immunoglobulin isotypes and normal or elevated IgM levels. They are caused by impaired T:B cooperation or intrinsic B cell defects. However, many immunoglobulin CSR-Ds are still undefined at the molecular level. This study's objective was to delineate new causes of immunoglobulin CSR-Ds and thus gain further insights into the process of immunoglobulin class-switch recombination (CSR). Exome sequencing in 2 immunoglobulin CSR-D patients identified variations in the INO80 gene. Functional experiments were performed to assess the function of INO80 on immunoglobulin CSR. We identified recessive, nonsynonymous coding variations in the INO80 gene in 2 patients affected by defective immunoglobulin CSR. Expression of wild-type INO80 in patients' fibroblastic cells corrected their hypersensitivity to high doses of γ-irradiation. In murine CH12-F3 cells, the INO80 complex accumulates at Sα and Eμ regions of the IgH locus, and downregulation of INO80 as well as its partners Reptin and Pontin impaired CSR. In addition, Reptin and Pontin were shown to interact with activation-induced cytidine deaminase. Finally, an abnormal separation of sister chromatids was observed upon INO80 downregulation in CH12-F3 cells, pinpointing its role in cohesin activity. INO80 deficiency appears to be associated with defective immunoglobulin CSR. We propose that the INO80 complex modulates cohesin function that may be required during immunoglobulin switch region synapsis. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Cytogenetic and molecular cytogenetic methods in hemato-oncology

International Nuclear Information System (INIS)

Novakova, P.; Ilencikova, D.

2010-01-01

Cancer, either sporadic or hereditary, is a genetic disease that develops through multiple genetic changes. Specific genetic defects have been found to be associated non randomly with the predisposition, genesis, progression, and metastasis of various kinds of neoplasia. Cytogenetics in haematological malignancy to aid in diagnosis and in identifying recurrent chromosomal rearrangements, an essential prerequisite to identifying genes involved in leukaemia and lymphoma pathogenesis. In the late 1980s, a series of technologies based around fluorescence in situ hybridisation (FISH) revolutionised the field. FISH technology, a combination of molecular and conventional cytogenetic techniques, has brought modern cytogenetics to a new era with significantly higher resolutions and much wider testing spectrum. Since then, numerous new FISH-based technologies have been emerging, from metaphase FISH to interphase FISH, from single-color FISH to multicolor FISH, from comparative gnenomic hybridisation (CGH) to array CGH, and so on. In this review the advantages and limitations of each of the various types of conventional and molecular cytogenetic methodologies are discussed with regard to their application in human neoplasia. (author)

Effect of triangular vacancy defect on thermal conductivity and thermal rectification in graphene nanoribbons

Energy Technology Data Exchange (ETDEWEB)

Yang, Ping, E-mail: yangpingdm@ujs.edu.cn [Laboratory of Advanced Manufacturing and Reliability for MEMS/NEMS/OEDS, Jiangsu University, Zhenjiang 212013 (China); Li, Xialong; Zhao, Yanfan [Laboratory of Advanced Manufacturing and Reliability for MEMS/NEMS/OEDS, Jiangsu University, Zhenjiang 212013 (China); Yang, Haiying [School of Materials Science and Engineering, Jiangsu University, Zhenjiang 212013 (China); Wang, Shuting, E-mail: wangst@mail.hust.edu.cn [School of Mechanical Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China)

2013-11-01

We investigate the thermal transport properties of armchair graphene nanoribbons (AGNRs) possessing various sizes of triangular vacancy defect within a temperature range of 200–600 K by using classical molecular dynamics simulation. The results show that the thermal conductivities of the graphene nanoribbons decrease with increasing sizes of triangular vacancy defects in both directions across the whole temperature range tested, and the presence of the defect can decrease the thermal conductivity by more than 40% as the number of removed cluster atoms is increased to 25 (1.56% for vacancy concentration) owing to the effect of phonon–defect scattering. In the meantime, we find the thermal conductivity of defective graphene nanoribbons is insensitive to the temperature change at higher vacancy concentrations. Furthermore, the dependence of temperatures and various sizes of triangular vacancy defect for the thermal rectification ration are also detected. This work implies a possible route to achieve thermal rectifier for 2D materials by defect engineering.

Hydrogen molecule defect in proton-conductive SrTiO3 Perovskite

Science.gov (United States)

Onishi, Taku

2017-11-01

In proton-conductive SrTiO3 perovskite, no hydrogen molecule defect ideally exists. However, the unforeseen chemical reaction is often observed after the use of fuel cell. From the viewpoint of battery safety, we have investigated the effect of hydrogen molecule defect by molecular orbital analysis. When counter cation vacancy exists, the activation energy for hydrogen molecule migration was 1.39 - 1.50 eV, which is much smaller than the dissociation energy of hydrogen molecule. It implies that hydrogen molecule may migrate without its dissociation.

Parent stress across molecular subtypes of children with Angelman syndrome.

Science.gov (United States)

Miodrag, N; Peters, S

2015-09-01

Parenting stress has been consistently reported among parents of children with developmental disabilities. However, to date, no studies have investigated the impact of a molecular subtype of Angelman syndrome (AS) on parent stress, despite distinct phenotypic differences among subtypes. Data for 124 families of children with three subtypes of AS: class I and II deletions (n = 99), imprinting centre defects (IC defects; n = 11) and paternal uniparental disomy (UPD; n = 14) were drawn from the AS Rare Diseases Clinical Research Network (RDCRN) database and collected from five research sites across the Unites States. The AS study at the RDCRN gathered health information to understand how the syndrome develops and how to treat it. Parents completed questionnaires on their perceived psychological stress, the severity of children's aberrant behaviour and children's sleep patterns. Children's adaptive functioning and developmental levels were clinically evaluated. Child-related stress reached clinical levels for 40% of parents of children with deletions, 100% for IC defects and 64.3% for UPD. Sleep difficulties were similar and elevated across subtypes. There were no differences between molecular subtypes for overall child and parent-related stress. However, results showed greater isolation and lack of perceived parenting skills for parents of children with UPD compared with deletions. Better overall cognition for children with deletions was significantly related to more child-related stress while their poorer adaptive functioning was associated with more child-related stress. For all three groups, the severity of children's inappropriate behaviour was positively related to different aspects of stress. How parents react to stress depends, in part, on children's AS molecular subtype. Despite falling under the larger umbrella term of AS, it is important to acknowledge the unique aspects associated with children's molecular subtype. Identifying these factors can

Defect phase diagram for doping of Ga2O3

Directory of Open Access Journals (Sweden)

Stephan Lany

2018-04-01

Full Text Available For the case of n-type doping of β-Ga2O3 by group 14 dopants (C, Si, Ge, Sn, a defect phase diagram is constructed from defect equilibria calculated over a range of temperatures (T, O partial pressures (pO2, and dopant concentrations. The underlying defect levels and formation energies are determined from first-principles supercell calculations with GW bandgap corrections. Only Si is found to be a truly shallow donor, C is a deep DX-like (lattice relaxed donor center, and Ge and Sn have defect levels close to the conduction band minimum. The thermodynamic modeling includes the effect of association of dopant-defect pairs and complexes, which causes the net doping to decline when exceeding a certain optimal dopant concentration. The optimal doping levels are surprisingly low, between about 0.01% and 1% of cation substitution, depending on the (T, pO2 conditions. Considering further the stability constraints due to sublimation of molecular Ga2O, specific predictions of optimized pO2 and Si dopant concentrations are given. The incomplete passivation of dopant-defect complexes in β-Ga2O3 suggests a design rule for metastable doping above the solubility limit.

Defect sizing using automated ultrasonic inspection techniques at RNL

International Nuclear Information System (INIS)

Rogerson, A.; Highmore, P.J.; Poulter, L.N.J.

1983-10-01

RNL has developed and applied automated wide-beam pulse-echo and time-of-flight techniques with synthetic aperture processing for sizing defects in clad thick-section weldments and nozzle corner regions. These techniques were amongst those used in the four test plate inspections making up the UKAEA Defect Detection Trials. In this report a critical appraisal is given of the sizing procedures adopted by RNL in these inspections. Several factors influencing sizing accuracy are discussed and results from particular defects highlighted. The time-of-flight technique with colour graphics data display is shown to be highly effective in imaging near-vertical buried defects and underclad defects of height greater than 5 mm. Early characterisation of any identified defect from its ultrasonic response under pulse-echo inspection is seen as a desirable aid to the selection of an appropriate advanced sizing technique for buried defects. (author)

Vertebral defect, anal atresia, cardiac defect, tracheoesophageal fistula/esophageal atresia, renal defect, and limb defect association with Mayer-Rokitansky-Küster-Hauser syndrome in co-occurrence

DEFF Research Database (Denmark)

Bjørsum-Meyer, Thomas; Herlin, Morten; Qvist, Niels

2016-01-01

Background: The vertebral defect, anal atresia, cardiac defect, tracheoesophageal fistula/esophageal atresia, renal defect, and limb defect association and Mayer-Rokitansky-Küster-Hauser syndrome are rare conditions. We aimed to present two cases with the vertebral defect, anal atresia, cardiac...... defect, tracheoesophageal fistula/esophageal atresia, renal defect, and limb defect association and Mayer-Rokitansky-Küster-Hauser co-occurrence from our local surgical center and through a systematic literature search detect published cases. Furthermore, we aimed to collect existing knowledge...... in the embryopathogenesis and genetics in order to discuss a possible link between the vertebral defect, anal atresia, cardiac defect, tracheoesophageal fistula/esophageal atresia, renal defect, and limb defect association and Mayer-Rokitansky-Küster-Hauser syndrome. Case presentation: Our first case was a white girl...

Molecular subtypes of osteosarcoma identified by reducing tumor heterogeneity through an interspecies comparative approach

Science.gov (United States)

Scott, Milcah C.; Sarver, Aaron L.; Gavin, Katherine J.; Thayanithy, Venugopal; Getzy, David M.; Newman, Robert A.; Cutter, Gary R.; Lindblad-Toh, Kerstin; Kisseberth, William C.; Hunter, Lawrence E.; Subramanian, Subbaya; Breen, Matthew; Modiano, Jaime F.

2011-01-01

The heterogeneous and chaotic nature of osteosarcoma has confounded accurate molecular classification, prognosis, and prediction for this tumor. The occurrence of spontaneous osteosarcoma is largely confined to humans and dogs. While the clinical features are remarkably similar in both species, the organization of dogs into defined breeds provides a more homogeneous genetic background that may increase the likelihood to uncover molecular subtypes for this complex disease. We thus hypothesized that molecular profiles derived from canine osteosarcoma would aid in molecular subclassification of this disease when applied to humans. To test the hypothesis, we performed genome wide gene expression profiling in a cohort of dogs with osteosarcoma, primarily from high-risk breeds. To further reduce inter-sample heterogeneity, we assessed tumor-intrinsic properties through use of an extensive panel of osteosarcoma-derived cell lines. We observed strong differential gene expression that segregated samples into two groups with differential survival probabilities. Groupings were characterized by the inversely correlated expression of genes associated with G2/M transition and DNA damage checkpoint and microenvironment-interaction categories. This signature was preserved in data from whole tumor samples of three independent dog osteosarcoma cohorts, with stratification into the two expected groups. Significantly, this restricted signature partially overlapped a previously defined, predictive signature for soft tissue sarcomas, and it unmasked orthologous molecular subtypes and their corresponding natural histories in five independent data sets from human patients with osteosarcoma. Our results indicate that the narrower genetic diversity of dogs can be utilized to group complex human osteosarcoma into biologically and clinically relevant molecular subtypes. This in turn may enhance prognosis and prediction, and identify relevant therapeutic targets. PMID:21621658

Transformation between divacancy defects induced by an energy pulse in graphene.

Science.gov (United States)

Xia, Jun; Liu, XiaoYi; Zhou, Wei; Wang, FengChao; Wu, HengAn

2016-07-08

The mutual transformations among the four typical divacancy defects induced by a high-energy pulse were studied via molecular dynamics simulation. Our study revealed all six possible mutual transformations and found that defects transformed by absorbing energy to overcome the energy barrier with bonding, debonding, and bond rotations. The reversibility of defect transformations was also investigated by potential energy analysis. The energy difference was found to greatly influence the transformation reversibility. The direct transformation path was irreversible if the energy difference was too large. We also studied the correlation between the transformation probability and the input energy. It was found that the transformation probability had a local maxima at an optimal input energy. The introduction of defects and their structural evolutions are important for tailoring the exceptional properties and thereby performances of graphene-based devices, such as nanoporous membranes for the filtration and desalination of water.

Molecular ions, Rydberg spectroscopy and dynamics

International Nuclear Information System (INIS)

Jungen, Ch.

2015-01-01

Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering

Molecular ions, Rydberg spectroscopy and dynamics

Energy Technology Data Exchange (ETDEWEB)

Jungen, Ch. [Laboratoire Aimé Cotton, Université de Paris-Sud, 91405 Orsay (France)

2015-01-22

Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering.

Dislocation defect interaction in irradiated Cu

International Nuclear Information System (INIS)

Schaeublin, R.; Yao, Z.; Spaetig, P.; Victoria, M.

2005-01-01

Pure Cu single crystals irradiated at room temperature to low doses with 590 MeV protons have been deformed in situ in a transmission electron microscope in order to identify the basic mechanisms at the origin of hardening. Cu irradiated to 10 -4 dpa shows at room temperature a yield shear stress of 13.7 MPa to be compared to the 8.8 MPa of the unirradiated Cu. Irradiation induced damage consists at 90% of 2 nm stacking fault tetrahedra, the remaining being dislocation loops and unidentified defects. In-situ deformation reveals that dislocation-defect interaction can take several forms. Usually, dislocations pinned by defects bow out under the applied stress and escape without leaving any visible defect. From the escape angles obtained at 183 K, an average critical stress of 100 MPa is deduced. In some cases, the pinning of dislocations leads to debris that are about 20 nm long, which formation could be recorded during the in situ experiment

RNA-based mutation analysis identifies an unusual MSH6 splicing defect and circumvents PMS2 pseudogene interference.

Science.gov (United States)

Etzler, J; Peyrl, A; Zatkova, A; Schildhaus, H-U; Ficek, A; Merkelbach-Bruse, S; Kratz, C P; Attarbaschi, A; Hainfellner, J A; Yao, S; Messiaen, L; Slavc, I; Wimmer, K

2008-02-01

Heterozygous germline mutations in one of the mismatch repair (MMR) genes MLH1, MSH2, MSH6, and PMS2 cause hereditary nonpolyposis colorectal cancer (HNPCC) or Lynch syndrome, a dominantly inherited cancer susceptibility syndrome. Recent reports provide evidence for a novel recessively inherited cancer syndrome with constitutive MMR deficiency due to biallelic germline mutations in one of the MMR genes. MMR-deficiency (MMR-D) syndrome is characterized by childhood brain tumors, hematological and/or gastrointestinal malignancies, and signs of neurofibromatosis type 1 (NF1). We established an RNA-based mutation detection assay for the four MMR genes, since 1) a number of splicing defects may escape detection by the analysis of genomic DNA, and 2) DNA-based mutation detection in the PMS2 gene is severely hampered by the presence of multiple highly similar pseudogenes, including PMS2CL. Using this assay, which is based on direct cDNA sequencing of RT-PCR products, we investigated two families with children suspected to suffer from MMR-D syndrome. We identified a homozygous complex MSH6 splicing alteration in the index patients of the first family and a novel homozygous PMS2 mutation (c.182delA) in the index patient of the second family. Furthermore, we demonstrate, by the analysis of a PMS2/PMS2CL "hybrid" allele carrier, that RNA-based PMS2 testing effectively avoids the caveats of genomic DNA amplification approaches; i.e., pseudogene coamplification as well as allelic dropout, and will, thus, allow more sensitive mutation analysis in MMR deficiency and in HNPCC patients with PMS2 defects. (c) 2007 Wiley-Liss, Inc.

Mutations in the newly identified RAX regulatory sequence are not a frequent cause of micro/anophthalmia.

Science.gov (United States)

Chassaing, Nicolas; Vigouroux, Adeline; Calvas, Patrick

2009-06-01

Microphthalmia and anophthalmia are at the severe end of the spectrum of abnormalities in ocular development. A few genes (SOX2, OTX2, RAX, and CHX10) have been implicated in isolated micro/anophthalmia, but causative mutations of these genes explain less than a quarter of these developmental defects. A specifically conserved SOX2/OTX2-mediated RAX expression regulatory sequence has recently been identified. We postulated that mutations in this sequence could lead to micro/anophthalmia, and thus we performed molecular screening of this regulatory element in patients suffering from micro/anophthalmia. Fifty-one patients suffering from nonsyndromic microphthalmia (n = 40) or anophthalmia (n = 11) were included in this study after negative molecular screening for SOX2, OTX2, RAX, and CHX10 mutations. Mutation screening of the RAX regulatory sequence was performed by direct sequencing for these patients. No mutations were identified in the highly conserved RAX regulatory sequence in any of the 51 patients. Mutations in the newly identified RAX regulatory sequence do not represent a frequent cause of nonsyndromic micro/anophthalmia.

Using molecular tools to identify the geographical origin of a case of human brucellosis.

Science.gov (United States)

Muchowski, J K; Koylass, M S; Dainty, A C; Stack, J A; Perrett, L; Whatmore, A M; Perrier, C; Chircop, S; Demicoli, N; Gatt, A B; Caruana, P A; Gopaul, K K

2015-10-01

Although Malta is historically linked with the zoonosis brucellosis, there had not been a case of the disease in either the human or livestock population for several years. However, in July 2013 a case of human brucellosis was identified on the island. To determine whether this recent case originated in Malta, four isolates from this case were subjected to molecular analysis. Molecular profiles generated using multilocus sequence analysis and multilocus variable number tandem repeat for the recent human case isolates and 11 Brucella melitensis strains of known Maltese origin were compared with others held on in-house and global databases. While the 11 isolates of Maltese origin formed a distinct cluster, the recent human isolation was not associated with these strains but instead clustered with isolates originating from the Horn of Africa. These data was congruent with epidemiological trace-back showed that the individual had travelled to Malta from Eritrea. This work highlights the potential of using molecular typing data to aid in epidemiological trace-back of Brucella isolations and assist in monitoring of the effectiveness of brucellosis control schemes.

Influence of defects on the thermal conductivity of compressed LiF

Science.gov (United States)

Jones, R. E.; Ward, D. K.

2018-02-01

Defect formation in LiF, which is used as an observation window in ramp and shock experiments, has significant effects on its transmission properties. Given the extreme conditions of the experiments it is hard to measure the change in transmission directly. Using molecular dynamics, we estimate the change in conductivity as a function of the concentration of likely point and extended defects using a Green-Kubo technique with careful treatment of size effects. With this data, we form a model of the mean behavior and its estimated error; then, we use this model to predict the conductivity of a large sample of defective LiF resulting from a direct simulation of ramp compression as a demonstration of the accuracy of its predictions. Given estimates of defect densities in a LiF window used in an experiment, the model can be used to correct the observations of thermal energy through the window. In addition, the methodology we develop is extensible to modeling, with quantified uncertainty, the effects of a variety of defects on the thermal conductivity of solid materials.

Study of irradiation induced defects in silicon

International Nuclear Information System (INIS)

Pal, Gayatri; Sebastian, K.C.; Somayajulu, D.R.S.; Chintalapudi, S.N.

2000-01-01

Pure high resistivity (6000 ohm-cm) silicon wafers were recoil implanted with 1.8 MeV 111 In ions. As-irradiated wafers showed a 13 MHz quadrupole interaction frequency, which was not observed earlier. The annealing behaviour of these defects in the implanted wafers was studied between room temperature and 1073 K. At different annealing temperatures two more interaction frequencies corresponding to defect complexes D2 and D3 are observed. Even though the experimental conditions were different, these are identical to the earlier reported ones. Based on an empirical point charge model calculation, an attempt is made to identify the configuration of these defect complexes. (author)

Developmental defects in zebrafish for classification of EGF pathway inhibitors

Energy Technology Data Exchange (ETDEWEB)

Pruvot, Benoist; Curé, Yoann; Djiotsa, Joachim; Voncken, Audrey; Muller, Marc, E-mail: m.muller@ulg.ac.be

2014-01-15

One of the major challenges when testing drug candidates targeted at a specific pathway in whole animals is the discrimination between specific effects and unwanted, off-target effects. Here we used the zebrafish to define several developmental defects caused by impairment of Egf signaling, a major pathway of interest in tumor biology. We inactivated Egf signaling by genetically blocking Egf expression or using specific inhibitors of the Egf receptor function. We show that the combined occurrence of defects in cartilage formation, disturbance of blood flow in the trunk and a decrease of myelin basic protein expression represent good indicators for impairment of Egf signaling. Finally, we present a classification of known tyrosine kinase inhibitors according to their specificity for the Egf pathway. In conclusion, we show that developmental indicators can help to discriminate between specific effects on the target pathway from off-target effects in molecularly targeted drug screening experiments in whole animal systems. - Highlights: • We analyze the functions of Egf signaling on zebrafish development. • Genetic blocking of Egf expression causes cartilage, myelin and circulatory defects. • Chemical inhibition of Egf receptor function causes similar defects. • Developmental defects can reveal the specificity of Egf pathway inhibitors.

Developmental defects in zebrafish for classification of EGF pathway inhibitors

International Nuclear Information System (INIS)

Pruvot, Benoist; Curé, Yoann; Djiotsa, Joachim; Voncken, Audrey; Muller, Marc

2014-01-01

One of the major challenges when testing drug candidates targeted at a specific pathway in whole animals is the discrimination between specific effects and unwanted, off-target effects. Here we used the zebrafish to define several developmental defects caused by impairment of Egf signaling, a major pathway of interest in tumor biology. We inactivated Egf signaling by genetically blocking Egf expression or using specific inhibitors of the Egf receptor function. We show that the combined occurrence of defects in cartilage formation, disturbance of blood flow in the trunk and a decrease of myelin basic protein expression represent good indicators for impairment of Egf signaling. Finally, we present a classification of known tyrosine kinase inhibitors according to their specificity for the Egf pathway. In conclusion, we show that developmental indicators can help to discriminate between specific effects on the target pathway from off-target effects in molecularly targeted drug screening experiments in whole animal systems. - Highlights: • We analyze the functions of Egf signaling on zebrafish development. • Genetic blocking of Egf expression causes cartilage, myelin and circulatory defects. • Chemical inhibition of Egf receptor function causes similar defects. • Developmental defects can reveal the specificity of Egf pathway inhibitors

Birth Defects

Science.gov (United States)

A birth defect is a problem that happens while a baby is developing in the mother's body. Most birth defects happen during the first 3 months of ... in the United States is born with a birth defect. A birth defect may affect how the ...

Cytoskeletal defects in Bmpr2-associated pulmonary arterial hypertension.

Science.gov (United States)

Johnson, Jennifer A; Hemnes, Anna R; Perrien, Daniel S; Schuster, Manfred; Robinson, Linda J; Gladson, Santhi; Loibner, Hans; Bai, Susan; Blackwell, Tom R; Tada, Yuji; Harral, Julie W; Talati, Megha; Lane, Kirk B; Fagan, Karen A; West, James

2012-03-01

The heritable form of pulmonary arterial hypertension (PAH) is typically caused by a mutation in bone morphogenic protein receptor type 2 (BMPR2), and mice expressing Bmpr2 mutations develop PAH with features similar to human disease. BMPR2 is known to interact with the cytoskeleton, and human array studies in PAH patients confirm alterations in cytoskeletal pathways. The goal of this study was to evaluate cytoskeletal defects in BMPR2-associated PAH. Expression arrays on our Bmpr2 mutant mouse lungs revealed cytoskeletal defects as a prominent molecular consequence of universal expression of a Bmpr2 mutation (Rosa26-Bmpr2(R899X)). Pulmonary microvascular endothelial cells cultured from these mice have histological and functional cytoskeletal defects. Stable transfection of different BMPR2 mutations into pulmonary microvascular endothelial cells revealed that cytoskeletal defects are common to multiple BMPR2 mutations and are associated with activation of the Rho GTPase, Rac1. Rac1 defects are corrected in cell culture and in vivo through administration of exogenous recombinant human angiotensin-converting enzyme 2 (rhACE2). rhACE2 reverses 77% of gene expression changes in Rosa26-Bmpr2(R899X) transgenic mice, in particular, correcting defects in cytoskeletal function. Administration of rhACE2 to Rosa26-Bmpr2(R899X) mice with established PAH normalizes pulmonary pressures. Together, these findings suggest that cytoskeletal function is central to the development of BMPR2-associated PAH and that intervention against cytoskeletal defects may reverse established disease.

Primary cellular meningeal defects cause neocortical dysplasia and dyslamination

Science.gov (United States)

Hecht, Jonathan H.; Siegenthaler, Julie A.; Patterson, Katelin P.; Pleasure, Samuel J.

2010-01-01

Objective Cortical malformations are important causes of neurological morbidity, but in many cases their etiology is poorly understood. Mice with Foxc1 mutations have cellular defects in meningeal development. We use hypomorphic and null alleles of Foxc1 to study the effect of meningeal defects on neocortical organization. Methods Embryos with loss of Foxc1 activity were generated using the hypomorphic Foxc1hith allele and the null Foxc1lacZ allele. Immunohistologic analysis was used to assess cerebral basement membrane integrity, marginal zone heterotopia formation, neuronal overmigration, meningeal defects, and changes in basement membrane composition. Dysplasia severity was quantified using two measures. Results Cortical dysplasia resembling cobblestone cortex, with basement membrane breakdown and lamination defects, is seen in Foxc1 mutants. As Foxc1 activity was reduced, abnormalities in basement membrane integrity, heterotopia formation, neuronal overmigration, and meningeal development appeared earlier in gestation and were more severe. Surprisingly, the basement membrane appeared intact at early stages of development in the face of severe deficits in meningeal development. Prominent defects in basement membrane integrity appeared as development proceeded. Molecular analysis of basement membrane laminin subunits demonstrated that loss of the meninges led to changes in basement membrane composition. Interpretation Cortical dysplasia can be caused by cellular defects in the meninges. The meninges are not required for basement membrane establishment but are needed for remodeling as the brain expands. Specific changes in basement membrane composition may contribute to subsequent breakdown. Our study raises the possibility that primary meningeal defects may cortical dysplasia in some cases. PMID:20976766

Genetic Defects Underlie the Non-syndromic Autosomal Recessive Intellectual Disability (NS-ARID

Directory of Open Access Journals (Sweden)

Saleha Shamim

2017-05-01

Full Text Available Intellectual disability (ID is a neurodevelopmental disorder which appears frequently as the result of genetic mutations and may be syndromic (S-ID or non-syndromic (NS-ID. ID causes an important economic burden, for patient's family, health systems, and society. Identifying genes that cause S-ID can easily be evaluated due to the clinical symptoms or physical anomalies. However, in the case of NS-ID due to the absence of co-morbid features, the latest molecular genetic techniques can be used to understand the genetic defects that underlie it. Recent studies have shown that non-syndromic autosomal recessive (NS-ARID is extremely heterogeneous and contributes much more than X-linked ID. However, very little is known about the genes and loci involved in NS-ARID relative to X-linked ID, and whose complete genetic etiology remains obscure. In this review article, the known genetic etiology of NS-ARID and possible relationships between genes and the associated molecular pathways of their encoded proteins has been reviewed which will enhance our understanding about the underlying genes and mechanisms in NS-ARID.

Nonlinear defect localized modes and composite gray and anti-gray solitons in one-dimensional waveguide arrays with dual-flip defects

Science.gov (United States)

Liu, Yan; Guan, Yefeng; Li, Hai; Luo, Zhihuan; Mai, Zhijie

2017-08-01

We study families of stationary nonlinear localized modes and composite gray and anti-gray solitons in a one-dimensional linear waveguide array with dual phase-flip nonlinear point defects. Unstaggered fundamental and dipole bright modes are studied when the defect nonlinearity is self-focusing. For the fundamental modes, symmetric and asymmetric nonlinear modes are found. Their stable areas are studied using different defect coefficients and their total power. For the nonlinear dipole modes, the stability conditions of this type of mode are also identified by different defect coefficients and the total power. When the defect nonlinearity is replaced by the self-defocusing one, staggered fundamental and dipole bright modes are created. Finally, if we replace the linear waveguide with a full nonlinear waveguide, a new type of gray and anti-gray solitons, which are constructed by a kink and anti-kink pair, can be supported by such dual phase-flip defects. In contrast to the usual gray and anti-gray solitons formed by a single kink, their backgrounds on either side of the gray hole or bright hump have the same phase.

CT Image Sequence Processing For Wood Defect Recognition

Science.gov (United States)

Dongping Zhu; R.W. Conners; Philip A. Araman

1991-01-01

The research reported in this paper explores a non-destructive testing application of x-ray computed tomography (CT) in the forest products industry. This application involves a computer vision system that uses CT to locate and identify internal defects in hardwood logs. The knowledge of log defects is critical in deciding whether to veneer or to saw up a log, and how...

Cancer in silico drug discovery: a systems biology tool for identifying candidate drugs to target specific molecular tumor subtypes.

Science.gov (United States)

San Lucas, F Anthony; Fowler, Jerry; Chang, Kyle; Kopetz, Scott; Vilar, Eduardo; Scheet, Paul

2014-12-01

Large-scale cancer datasets such as The Cancer Genome Atlas (TCGA) allow researchers to profile tumors based on a wide range of clinical and molecular characteristics. Subsequently, TCGA-derived gene expression profiles can be analyzed with the Connectivity Map (CMap) to find candidate drugs to target tumors with specific clinical phenotypes or molecular characteristics. This represents a powerful computational approach for candidate drug identification, but due to the complexity of TCGA and technology differences between CMap and TCGA experiments, such analyses are challenging to conduct and reproduce. We present Cancer in silico Drug Discovery (CiDD; scheet.org/software), a computational drug discovery platform that addresses these challenges. CiDD integrates data from TCGA, CMap, and Cancer Cell Line Encyclopedia (CCLE) to perform computational drug discovery experiments, generating hypotheses for the following three general problems: (i) determining whether specific clinical phenotypes or molecular characteristics are associated with unique gene expression signatures; (ii) finding candidate drugs to repress these expression signatures; and (iii) identifying cell lines that resemble the tumors being studied for subsequent in vitro experiments. The primary input to CiDD is a clinical or molecular characteristic. The output is a biologically annotated list of candidate drugs and a list of cell lines for in vitro experimentation. We applied CiDD to identify candidate drugs to treat colorectal cancers harboring mutations in BRAF. CiDD identified EGFR and proteasome inhibitors, while proposing five cell lines for in vitro testing. CiDD facilitates phenotype-driven, systematic drug discovery based on clinical and molecular data from TCGA. ©2014 American Association for Cancer Research.

Comprehensive expression profiling of tumor cell lines identifies molecular signatures of melanoma progression.

Directory of Open Access Journals (Sweden)

Byungwoo Ryu

2007-07-01

Full Text Available Gene expression profiling has revolutionized our ability to molecularly classify primary human tumors and significantly enhanced the development of novel tumor markers and therapies; however, progress in the diagnosis and treatment of melanoma over the past 3 decades has been limited, and there is currently no approved therapy that significantly extends lifespan in patients with advanced disease. Profiling studies of melanoma to date have been inconsistent due to the heterogeneous nature of this malignancy and the limited availability of informative tissue specimens from early stages of disease.In order to gain an improved understanding of the molecular basis of melanoma progression, we have compared gene expression profiles from a series of melanoma cell lines representing discrete stages of malignant progression that recapitulate critical characteristics of the primary lesions from which they were derived. Here we describe the unsupervised hierarchical clustering of profiling data from melanoma cell lines and melanocytes. This clustering identifies two distinctive molecular subclasses of melanoma segregating aggressive metastatic tumor cell lines from less-aggressive primary tumor cell lines. Further analysis of expression signatures associated with melanoma progression using functional annotations categorized these transcripts into three classes of genes: 1 Upregulation of activators of cell cycle progression, DNA replication and repair (CDCA2, NCAPH, NCAPG, NCAPG2, PBK, NUSAP1, BIRC5, ESCO2, HELLS, MELK, GINS1, GINS4, RAD54L, TYMS, and DHFR, 2 Loss of genes associated with cellular adhesion and melanocyte differentiation (CDH3, CDH1, c-KIT, PAX3, CITED1/MSG-1, TYR, MELANA, MC1R, and OCA2, 3 Upregulation of genes associated with resistance to apoptosis (BIRC5/survivin. While these broad classes of transcripts have previously been implicated in the progression of melanoma and other malignancies, the specific genes identified within each class

Oxygen defects in amorphous Al{sub 2}O{sub 3}: A hybrid functional study

Energy Technology Data Exchange (ETDEWEB)

Guo, Zhendong, E-mail: zhendong.guo@epfl.ch; Ambrosio, Francesco; Pasquarello, Alfredo [Chaire de Simulation à l' Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne (Switzerland)

2016-08-08

The electronic properties of the oxygen vacancy and interstitial in amorphous Al{sub 2}O{sub 3} are studied via ab initio molecular dynamics simulations and hybrid functional calculations. Our results indicate that these defects do not occur in amorphous Al{sub 2}O{sub 3}, due to structural rearrangements which assimilate the defect structure and cause a delocalization of the associated defect levels. The imbalance of oxygen leads to a nonstoichiometric compound in which the oxygen occurs in the form of O{sup 2–} ions. Intrinsic oxygen defects are found to be unable to trap excess electrons. For low Fermi energies, the formation of peroxy linkages is found to be favored leading to the capture of holes. The relative +2/0 defect levels occur at 2.5 eV from the valence band.

Molecular dynamics study on the relaxation properties of bilayered ...

Indian Academy of Sciences (India)

2017-08-31

Aug 31, 2017 ... Abstract. The influence of defects on the relaxation properties of bilayered graphene (BLG) has been studied by molecular dynamics simulation in nanometre sizes. Type and position of defects were taken into account in the calculated model. The results show that great changes begin to occur in the ...

Dual approaches for defects condensation

Energy Technology Data Exchange (ETDEWEB)

Rougemont, Romulo; Grigorio, Leonardo de Souza; Wotzasek, Clovis [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil); Guimaraes, Marcelo Santos [Universidade do Estado do Rio de Janeiro (UERJ), RJ (Brazil)

2009-07-01

Full text. Due to the fact that the QCD running coupling constant becomes larger as we go into the low energy (or large distance) limit of the theory, a perturbative treatment of its infrared (IR) region is impossible. In particular, a formal mathematical demonstration of color confinement and a complete physical understanding of the exact mechanism that confines quarks and gluons are two missing points in our current knowledge of the IR-QCD. It was known that due to the Meissner effect of expulsion of magnetic fields in a electric condensate that usual superconductors should confine magnetic monopoles. That point led to the conjecture that the QCD vacuum could be a condensate of chromomagnetic monopoles, a dual superconductor (DSC). Such a chromomagnetic condensate should be responsible for the dual Meissner effect which is expected to lead to the confinement of color charges immersed in this medium. In dual superconductor models of color confinement, magnetic monopoles appear as topological defects in points of the space where the abelian projection becomes singular. Also, condensation of other kinds of defects such as vortices in superfluids and line-like defects in solids are responsible for a great variety of phase transitions, which once more proves the relevance of the subject. In the present work we review two methods that allow us to approach the condensation of defects: the Kleinert Mechanism (KM) and the Julia-Toulouse Mechanism (JTM). We show that in the limit where the vortex gauge field goes to zero, which we identify as the signature of the condensation of defects in the dual picture, these are two equivalent dual prescriptions for obtaining an effective theory for a phase where defects are condensed, starting from the fundamental theory defined in the normal phase where defects are diluted. (author)

Direct Observation of Radiation Defects: Experiment and Interpretation

International Nuclear Information System (INIS)

Dudarev, S.L.

2012-01-01

at low cost in comparison with the mock-up tests, offer scientific insight and make it possible to perform, in combination with experimental information derived from fission and ion-beam irradiation experiments, the preliminary assessment of power plant operating scenarios. Defining the limits of visibility of small defect clusters and dislocation loops, and optimal diffraction conditions for electron microscope imaging, remains one of the central problems of electron microscopy of irradiated materials. Using computer image simulations based on the propagation- interpolation algorithm for solving the Howie-Basinski equations, it is possible to investigate the relation between the actual and the 'observed' size of small loops, the part played by many-beam dynamical diffraction effects, and limitations of electron microscope imaging in identifying the structure of small defects. A particularly impressive and useful application of electron microscopy is given by recent in situ electron microscope observations, providing real-time visualization of dynamics of defects produced by ultra-high-energy electron irradiation, or showing microstructural evolution occurring under ion beam irradiation. Such observations have revolutionized our understanding of how properties of metals and alloys change in the extreme radiation and thermal environments of a fission or a fusion power plant. The key feature of in situ electron microscopy is its ability to exhibit the time-dependent dynamics of migration, interaction, and transformation of radiation defects, and to visualize the entire complexity of evolving defect and dislocation networks. For example, in situ electron microscope observations provided evidence of violation of the Burgers vector conservation law for dislocations on the nanoscale. This gave a vital clue needed for modeling microscopic processes responsible for the formation of unusual high temperature dislocation structures in iron, and for explaining the origin of the

On the origin and elimination of macroscopic defects in MBE films

Science.gov (United States)

Wood, C. E. C.; Rathbun, L.; Ohno, H.; DeSimone, D.

1981-02-01

Spitting of group III metal droplets from Knudsen type effusion cells has been found culpable for a genre of problematical macroscopic surface topographical defects observed in the growth of semiconductor films by molecular beam epitaxy. Successful precautions are described which virtually eliminate the problem.

Many-Body Theory of Proton-Generated Point Defects for Losses of Electron Energy and Photons in Quantum Wells

Science.gov (United States)

Huang, Danhong; Iurov, Andrii; Gao, Fei; Gumbs, Godfrey; Cardimona, D. A.

2018-02-01

The effects of point defects on the loss of either energies of ballistic electron beams or incident photons are studied by using a many-body theory in a multi-quantum-well system. This theory includes the defect-induced vertex correction to a bare polarization function of electrons within the ladder approximation, and the intralayer and interlayer screening of defect-electron interactions is also taken into account in the random-phase approximation. The numerical results of defect effects on both energy-loss and optical-absorption spectra are presented and analyzed for various defect densities, numbers of quantum wells, and wave vectors. The diffusion-reaction equation is employed for calculating distributions of point defects in a layered structure. For completeness, the production rate for Frenkel-pair defects and their initial concentration are obtained based on atomic-level molecular-dynamics simulations. By combining the defect-effect, diffusion-reaction, and molecular-dynamics models with an available space-weather-forecast model, it will be possible in the future to enable specific designing for electronic and optoelectronic quantum devices that will be operated in space with radiation-hardening protection and, therefore, effectively extend the lifetime of these satellite onboard electronic and optoelectronic devices. Specifically, this theory can lead to a better characterization of quantum-well photodetectors not only for high quantum efficiency and low dark current density but also for radiation tolerance or mitigating the effects of the radiation.

Disparate peroxisome-related defects in Arabidopsis pex6 and pex26 mutants link peroxisomal retrotranslocation and oil body utilization.

Science.gov (United States)

Gonzalez, Kim L; Fleming, Wendell A; Kao, Yun-Ting; Wright, Zachary J; Venkova, Savina V; Ventura, Meredith J; Bartel, Bonnie

2017-10-01

Catabolism of fatty acids stored in oil bodies is essential for seed germination and seedling development in Arabidopsis. This fatty acid breakdown occurs in peroxisomes, organelles that sequester oxidative reactions. Import of peroxisomal enzymes is facilitated by peroxins including PEX5, a receptor that delivers cargo proteins from the cytosol to the peroxisomal matrix. After cargo delivery, a complex of the PEX1 and PEX6 ATPases and the PEX26 tail-anchored membrane protein removes ubiquitinated PEX5 from the peroxisomal membrane. We identified Arabidopsis pex6 and pex26 mutants by screening for inefficient seedling β-oxidation phenotypes. The mutants displayed distinct defects in growth, response to a peroxisomally metabolized auxin precursor, and peroxisomal protein import. The low PEX5 levels in these mutants were increased by treatment with a proteasome inhibitor or by combining pex26 with peroxisome-associated ubiquitination machinery mutants, suggesting that ubiquitinated PEX5 is degraded by the proteasome when the function of PEX6 or PEX26 is reduced. Combining pex26 with mutations that increase PEX5 levels either worsened or improved pex26 physiological and molecular defects, depending on the introduced lesion. Moreover, elevating PEX5 levels via a 35S:PEX5 transgene exacerbated pex26 defects and ameliorated the defects of only a subset of pex6 alleles, implying that decreased PEX5 is not the sole molecular deficiency in these mutants. We found peroxisomes clustered around persisting oil bodies in pex6 and pex26 seedlings, suggesting a role for peroxisomal retrotranslocation machinery in oil body utilization. The disparate phenotypes of these pex alleles may reflect unanticipated functions of the peroxisomal ATPase complex. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Synthetic lethality between gene defects affecting a single non-essential molecular pathway with reversible steps.

Directory of Open Access Journals (Sweden)

Andrei Zinovyev

2013-04-01

Full Text Available Systematic analysis of synthetic lethality (SL constitutes a critical tool for systems biology to decipher molecular pathways. The most accepted mechanistic explanation of SL is that the two genes function in parallel, mutually compensatory pathways, known as between-pathway SL. However, recent genome-wide analyses in yeast identified a significant number of within-pathway negative genetic interactions. The molecular mechanisms leading to within-pathway SL are not fully understood. Here, we propose a novel mechanism leading to within-pathway SL involving two genes functioning in a single non-essential pathway. This type of SL termed within-reversible-pathway SL involves reversible pathway steps, catalyzed by different enzymes in the forward and backward directions, and kinetic trapping of a potentially toxic intermediate. Experimental data with recombinational DNA repair genes validate the concept. Mathematical modeling recapitulates the possibility of kinetic trapping and revealed the potential contributions of synthetic, dosage-lethal interactions in such a genetic system as well as the possibility of within-pathway positive masking interactions. Analysis of yeast gene interaction and pathway data suggests broad applicability of this novel concept. These observations extend the canonical interpretation of synthetic-lethal or synthetic-sick interactions with direct implications to reconstruct molecular pathways and improve therapeutic approaches to diseases such as cancer.

Identification of biochemical features of defective Coffea arabica L. beans.

Science.gov (United States)

Casas, María I; Vaughan, Michael J; Bonello, Pierluigi; McSpadden Gardener, Brian; Grotewold, Erich; Alonso, Ana P

2017-05-01

Coffee organoleptic properties are based in part on the quality and chemical composition of coffee beans. The presence of defective beans during processing and roasting contribute to off flavors and reduce overall cup quality. A multipronged approach was undertaken to identify specific biochemical markers for defective beans. To this end, beans were split into defective and non-defective fractions and biochemically profiled in both green and roasted states. A set of 17 compounds in green beans, including organic acids, amino acids and reducing sugars; and 35 compounds in roasted beans, dominated by volatile compounds, organic acids, sugars and sugar alcohols, were sufficient to separate the defective and non-defective fractions. Unsorted coffee was examined for the presence of the biochemical markers to test their utility in detecting defective beans. Although the green coffee marker compounds were found in all fractions, three of the roasted coffee marker compounds (1-methylpyrrole, 5-methyl- 2-furfurylfuran, and 2-methylfuran) were uniquely present in defective fractions. Published by Elsevier Ltd.

Helium bubbles aggravated defects production in self-irradiated copper

Science.gov (United States)

Wu, FengChao; Zhu, YinBo; Wu, Qiang; Li, XinZhu; Wang, Pei; Wu, HengAn

2017-12-01

Under the environment of high radiation, materials used in fission and fusion reactors will internally accumulate numerous lattice defects and bubbles. With extensive studies focused on bubble resolution under irradiation, the mutually effects between helium bubbles and displacement cascades in irradiated materials remain unaddressed. Therefore, the defects production and microstructure evolution under self-irradiation events in vicinity of helium bubbles are investigated by preforming large scale molecular dynamics simulations in single-crystal copper. When subjected to displacement cascades, distinguished bubble resolution categories dependent on bubble size are observed. With the existence of bubbles, radiation damage is aggravated with the increasing bubble size, represented as the promotion of point defects and dislocations. The atomic mechanisms of heterogeneous dislocation structures are attributed to different helium-vacancy cluster modes, transforming from the resolved gas trapped with vacancies to the biased absorption of vacancies by the over-pressured bubble. In both cases, helium impedes the recombination of point defects, leading to the accelerated formation of interstitial loops. The results and insight obtained here might contribute to understand the underlying mechanism of transmutant solute on the long-term evolution of irradiated materials.

The effects of self-interstitial clusters on cascade defect evolution beyond the primary damage state

Energy Technology Data Exchange (ETDEWEB)

Heinisch, H.L. [Pacific Northwest National Lab., Richland, WA (United States)

1997-04-01

The intracascade evolution of the defect distributions of cascades in copper is investigated using stochastic annealing simulations applied to cascades generated with molecular dynamics (MD). The temperature and energy dependencies of annihilation, clustering and free defect production are determined for individual cascades. The annealing simulation results illustrate the strong influence on intracascade evolution of the defect configuration existing in the primary damage state. Another factor significantly affecting the evolution of the defect distribution is the rapid one-dimensional diffusion of small, glissile interstitial loops produced directly in cascades. This phenomenon introduces a cascade energy dependence of defect evolution that is apparent only beyond the primary damage state, amplifying the need for further study of the annealing phase of cascade evolution and for performing many more MD cascade simulations at higher energies.

The effects of self-interstitial clusters on cascade defect evolution beyond the primary damage state

International Nuclear Information System (INIS)

Heinisch, H.L.

1997-01-01

The intracascade evolution of the defect distributions of cascades in copper is investigated using stochastic annealing simulations applied to cascades generated with molecular dynamics (MD). The temperature and energy dependencies of annihilation, clustering and free defect production are determined for individual cascades. The annealing simulation results illustrate the strong influence on intracascade evolution of the defect configuration existing in the primary damage state. Another factor significantly affecting the evolution of the defect distribution is the rapid one-dimensional diffusion of small, glissile interstitial loops produced directly in cascades. This phenomenon introduces a cascade energy dependence of defect evolution that is apparent only beyond the primary damage state, amplifying the need for further study of the annealing phase of cascade evolution and for performing many more MD cascade simulations at higher energies

Classification of maxillectomy defects: a systematic review and criteria necessary for a universal description.

Science.gov (United States)

Bidra, Avinash S; Jacob, Rhonda F; Taylor, Thomas D

2012-04-01

Maxillectomy defects are complex and involve a number of anatomic structures. Several maxillectomy defect classifications have been proposed with no universal acceptance among surgeons and prosthodontists. Established criteria for describing the maxillectomy defect are lacking. This systematic review aimed to evaluate classification systems in the available literature, to provide a critical appraisal, and to identify the criteria necessary for a universal description of maxillectomy and midfacial defects. An electronic search of the English language literature between the periods of 1974 and June 2011 was performed by using PubMed, Scopus, and Cochrane databases with predetermined inclusion criteria. Key terms included in the search were maxillectomy classification, maxillary resection classification, maxillary removal classification, maxillary reconstruction classification, midfacial defect classification, and midfacial reconstruction classification. This was supplemented by a manual search of selected journals. After application of predetermined exclusion criteria, the final list of articles was reviewed in-depth to provide a critical appraisal and identify criteria for a universal description of a maxillectomy defect. The electronic database search yielded 261 titles. Systematic application of inclusion and exclusion criteria resulted in identification of 14 maxillectomy and midfacial defect classification systems. From these articles, 6 different criteria were identified as necessary for a universal description of a maxillectomy defect. Multiple deficiencies were noted in each classification system. Though most articles described the superior-inferior extent of the defect, only a small number of articles described the anterior-posterior and medial-lateral extent of the defect. Few articles listed dental status and soft palate involvement when describing maxillectomy defects. No classification system has accurately described the maxillectomy defect, based on

Chemotaxis-defective mutants of the nematode Caenorhabditis elegans.

Science.gov (United States)

Dusenbery, D B; Sheridan, R E; Russell, R L

1975-06-01

The technique of countercurrent separation has been used to isolate 17 independent chemotaxis-defective mutants of the nematode Caenorhabditis elegans. The mutants, selected to be relatively insensitive to the normally attractive salt NaCl, show varying degrees of residual sensitivity; some are actually weakly repelled by NaCl. The mutants are due to single gene defects, are autosomal and recessive, and identify at least five complementation groups.

The molecular mechanism and physiological role of cytoplasmic streaming.

Science.gov (United States)

Tominaga, Motoki; Ito, Kohji

2015-10-01

Cytoplasmic streaming occurs widely in plants ranging from algae to angiosperms. However, the molecular mechanism and physiological role of cytoplasmic streaming have long remained unelucidated. Recent molecular genetic approaches have identified specific myosin members (XI-2 and XI-K as major and XI-1, XI-B, and XI-I as minor motive forces) for the generation of cytoplasmic streaming among 13 myosin XIs in Arabidopsis thaliana. Simultaneous knockout of these myosin XI members led to a reduced velocity of cytoplasmic streaming and marked defects of plant development. Furthermore, the artificial modifications of myosin XI-2 velocity changed plant and cell sizes along with the velocity of cytoplasmic streaming. Therefore, we assume that cytoplasmic streaming is one of the key regulators in determining plant size. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Defect reduction of patterned media templates and disks

Science.gov (United States)

Luo, Kang; Ha, Steven; Fretwell, John; Ramos, Rick; Ye, Zhengmao; Schmid, Gerard; LaBrake, Dwayne; Resnick, Douglas J.; Sreenivasan, S. V.

2010-05-01

Imprint lithography has been shown to be an effective technique for the replication of nano-scale features. Acceptance of imprint lithography for manufacturing will require a demonstration of defect levels commensurate with cost-effective device production. This work summarizes the results of defect inspections of hard disks patterned using Jet and Flash Imprint Lithography (J-FILTM). Inspections were performed with optical based automated inspection tools. For the hard drive market, it is important to understand the defectivity of both the template and the imprinted disk. This work presents a methodology for automated pattern inspection and defect classification for imprint-patterned media. Candela CS20 and 6120 tools from KLA-Tencor map the optical properties of the disk surface, producing highresolution grayscale images of surface reflectivity and scattered light. Defects that have been identified in this manner are further characterized according to the morphology. The imprint process was tested after optimizing both the disk cleaning and adhesion layers processes that precede imprinting. An extended imprint run was performed and both the defect types and trends are reported.

[Molecular characterization of heterozygous beta-thalassemia in Lanzarote, Spain].

Science.gov (United States)

Calvo-Villas, José Manuel; de la Iglesia Iñigo, Silvia; Ropero Gradilla, Paloma; Zapata Ramos, María Francisca; Cuesta Tovar, Jorge; Sicilia Guillén, Francisco

2008-04-05

The aim of this study was to determine the molecular defects of heterozygous beta thalassaemia and to ascertain their distribution in Lanzarote. Molecular characterization was achieved by real time polymerase chain reaction (RT-PCR LightCycler, Roche), PCR-ARMS (PCR-amplification reaction mutations system) and DNA sequencing on an automated DNA sequencer. Two hundred forty-three heterozygous beta thalassaemia carriers were included between July 1991 and February 2007. RT-PCR detected the molecular defect in 81% of the beta thalassaemia chromosomes analyzed [113 codon CD 39 (C --> T); 41 IVS-1-nt-110 (G --> A), 25 IVS 1-nt-1 (G --> A) and 19 IVS 1-nt-6 (T --> C)]. The remaining 12 molecular defects included the deletion 619 bp (7.8%) and the mutations -28 (A --> G), IVS1-nt-2 (T --> G), CD 41/42 (-TTCT), CD 8/9 (+G), CD 51 (-C), CD 22 (G --> T) and CD 24 (T --> A), CD 67 (-TG) and the novel mutation CD 20/21-TGGA. The distribution of the mutations is similar to that found in the Mediterranean area. The increasing migratory flow received in the Canary Islands may explain the emergence of new mutations not reported before in our area.

Reduction in Defect Content in ODS Alloys

Energy Technology Data Exchange (ETDEWEB)

Ritherdon, J.; Jones, A.R.

2000-02-01

The work detailed within this report is a continuation of earlier work that was carried out under contract number IDX-SY382V. The earlier work comprised a literature review of the sources and types of defects found principally in Fe-based ODS alloys together with a series of experiments designed to identify defects in ODS Fe{sub 3}Al material and recommend methods of defect reduction. Defects found in the Mechanically Alloyed (MA) ODS Fe{sub 3}Al included regions of incomplete MA, porosity, intrusions and fine-grained stringers. Some defects tended to be found in association with one another e.g. intrusions and fine-grained stringers. Preliminary powder separation experiments were also performed. The scope and objectives of the present work were laid out in the technical proposal ``Reduction in Defect Content in ODS Alloys--II'' which formed the basis of amendment 3 of the current contract. The current studies were devised in the context of the preceding work with a view to extending and concluding certain experiments while exploring new avenues of investigation of defect control and reduction where appropriate. All work proposed was within the context of achieving an ODS Fe{sub 3}Al alloy of improved overall quality and potential creep performance (particularly) in the consolidated, release condition. The interim outturn of the experimental work performed is also reported.

Defect- and dopant-controlled carbon nanotubes fabricated by self-assembly of graphene nanoribbons

Institute of Scientific and Technical Information of China (English)

Cun Zhang and Shaohua Chen

2015-01-01

Molecular dynamics simulations showed that a basal carbon nanotube can activate and guide the fabrication of single-walled carbon nanotubes （CNTs） on its internal surface by self-assembly of edge-unpassivated graphene nanoribbons with defects. Furthermore, the distribution of defects on self-assembled CNTs is controllable. The system temperature and defect fraction are two main factors that influence the success of self-assembly. Due to possible joint flaws formed at the boundaries under a relatively high constant temperature, a technique based on increasing the temperature is adopted. Self-assembly is always successful for graphene nanoribbons with relatively small defect fractions, while it will fail in cases with relatively large ones. Similar to the self-assembly of graphene nanoribbons with defects, graphene nanoribbons with different types of dopants can also be self-assembled into carbon nanotubes. The finding provides a possible fabrication technique not only for carbon nanotubes with metallic or semi-con- ductive properties but also for carbon nanotubes with electromagnetic induction characteristics.

Calibrating a multi-model approach to defect production in high energy collision cascades

International Nuclear Information System (INIS)

Heinisch, H.L.; Singh, B.N.; Diaz de la Rubia, T.

1994-01-01

A multi-model approach to simulating defect production processes at the atomic scale is described that incorporates molecular dynamics (MD), binary collision approximation (BCA) calculations and stochastic annealing simulations. The central hypothesis is that the simple, fast computer codes capable of simulating large numbers of high energy cascades (e.g., BCA codes) can be made to yield the correct defect configurations when their parameters are calibrated using the results of the more physically realistic MD simulations. The calibration procedure is investigated using results of MD simulations of 25 keV cascades in copper. The configurations of point defects are extracted from the MD cascade simulations at the end of the collisional phase, thus providing information similar to that obtained with a binary collision model. The MD collisional phase defect configurations are used as input to the ALSOME annealing simulation code, and values of the ALSOME quenching parameters are determined that yield the best fit to the post-quenching defect configurations of the MD simulations. ((orig.))

Designing topological defects in 2D materials using scanning probe microscopy and a self-healing mechanism: a density functional-based molecular dynamics study

Science.gov (United States)

Popov, Igor; Đurišić, Ivana; Belić, Milivoj R.

2017-12-01

Engineering of materials at the atomic level is one of the most important aims of nanotechnology. The unprecedented ability of scanning probe microscopy to address individual atoms opened up the possibilities for nanomanipulation and nanolitography of surfaces and later on of two-dimensional materials. While the state-of-the-art scanning probe lithographic methods include, primarily, adsorption, desorption and repositioning of adatoms and molecules on substrates or tailoring nanoribbons by etching of trenches, the precise modification of the intrinsic atomic structure of materials is yet to be advanced. Here we introduce a new concept, scanning probe microscopy with a rotating tip, for engineering of the atomic structure of membranes based on two-dimensional materials. In order to indicate the viability of the concept, we present our theoretical research, which includes atomistic modeling, molecular dynamics simulations, Fourier analysis and electronic transport calculations. While stretching can be employed for fabrication of atomic chains only, our comprehensive molecular dynamics simulations indicate that nanomanipulation by scanning probe microscopy with a rotating tip is capable of assembling a wide range of topological defects in two-dimensional materials in a rather controllable and reproducible manner. We analyze two possibilities. In the first case the probe tip is retracted from the membrane while in the second case the tip is released beneath the membrane allowing graphene to freely relax and self-heal the pore made by the tip. The former approach with the tip rotation can be achieved experimentally by rotation of the sample, which is equivalent to rotation of the tip, whereas irradiation of the membrane by nanoclusters can be utilized for the latter approach. The latter one has the potential to yield a yet richer diversity of topological defects on account of a lesser determinacy. If successfully realized experimentally the concept proposed here could

Assessment of structures and stabilities of defect clusters and surface energies predicted by nine interatomic potentials for UO{sub 2}

Energy Technology Data Exchange (ETDEWEB)

Taller, Stephen A. [School of Nuclear Engineering, Purdue University, West Lafayette, IN 47907 (United States); Bai, Xian-Ming, E-mail: xianming.bai@inl.gov [Fuels Modeling and Simulation Department, Idaho National Laboratory, Idaho Falls, ID 83415 (United States)

2013-11-15

The irradiation in nuclear reactors creates many point defects and defect clusters in uranium dioxide (UO{sub 2}) and their evolution severely degrades the thermal and mechanical properties of the nuclear fuels. Previously many empirical interatomic potentials have been developed for modeling defect production and evolution in UO{sub 2}. However, the properties of defect clusters and extended defects are usually not fitted into these potentials. In this work nine interatomic potentials for UO{sub 2} are examined by using molecular statics and molecular dynamics to assess their applicability in predicting the properties of various types of defect clusters in UO{sub 2}. The binding energies and structures for these defect clusters have been evaluated for each potential. In addition, the surface energies of voids of different radii and (1 1 0) flat surfaces predicted by these potentials are also evaluated. It is found that both good agreement and significant discrepancies exist for these potentials in predicting these properties. For oxygen interstitial clusters, these potentials predict significantly different defect cluster structures and stabilities; For defect clusters consisting of both uranium and oxygen defects, the prediction is in better agreement; The surface energies predicted by these potentials have significant discrepancies, and some of them are much higher than the experimentally measured values. The results from this work can provide insight on interpreting the outcome of atomistic modeling of defect production using these potentials and may provide guidelines for choosing appropriate potential models to study problems of interest in UO{sub 2}.

Radiation defects in lithium fluoride induced by heavy ions

Energy Technology Data Exchange (ETDEWEB)

Trautmann, C.; Schwartz, K.; Steckenreiter, T. [Gesellschaft fuer Schwerionenforschung mbH, Darmstadt (Germany); Costantini, J.M. [CEA Centre d`Etudes de Bruyeres-le-Chatel, 91 (France). DPTA/SPMC; Toulemonde, M. [Centre Interdisciplinaire de Recherches avec les Ions Lourds (CIRIL), 14 - Caen (France)

1998-07-01

Single crystals of lithium fluoride were irradiated with various species of heavy ions in the energy regime between 1 and 30 MeV/u. The induced radiation damage was studied with techniques such as optical absorption spectroscopy, small-angle x-ray scattering, chemical etching and profilometry, complemented by annealing experiments. Clear evidence is given for a complex track structure and defect morphology. Single defects such as F-centers are produced in a large halo of several tens of nanometers around the ion trajectory. The defect creation in this zone is similar to that under conventional radiation. For heavy ions above a critical energy loss of 10 keV/nm, new effects occur within a very small core region of 2-4 nm in diameter. The damage in this zone is responsible for chemical etching and for a characteristic anisotropic x-ray scattering. It is assumed that in this core, complex defect aggregates (e.g., cluster of color centers, molecular anions and vacancies) are created. Their formation is only slightly influenced by the irradiation temperature and takes place even at 15 K where diffusion processes of primary defects are frozen. Furthermore, irradiation with heavy ions leads to pronounced swelling effects which can be related to an intermediate zone of around 10 nm around the ion path. (orig.) 40 refs.

Identifying molecular subtypes in human colon cancer using gene expression and DNA methylation microarray data.

Science.gov (United States)

Ren, Zhonglu; Wang, Wenhui; Li, Jinming

2016-02-01

Identifying colon cancer subtypes based on molecular signatures may allow for a more rational, patient-specific approach to therapy in the future. Classifications using gene expression data have been attempted before with little concordance between the different studies carried out. In this study we aimed to uncover subtypes of colon cancer that have distinct biological characteristics and identify a set of novel biomarkers which could best reflect the clinical and/or biological characteristics of each subtype. Clustering analysis and discriminant analysis were utilized to discover the subtypes in two different molecular levels on 153 colon cancer samples from The Cancer Genome Atlas (TCGA) Data Portal. At gene expression level, we identified two major subtypes, ECL1 (expression cluster 1) and ECL2 (expression cluster 2) and a list of signature genes. Due to the heterogeneity of colon cancer, the subtype ECL1 can be further subdivided into three nested subclasses, and HOTAIR were found upregulated in subclass 2. At DNA methylation level, we uncovered three major subtypes, MCL1 (methylation cluster 1), MCL2 (methylation cluster 2) and MCL3 (methylation cluster 3). We found only three subtypes of CpG island methylator phenotype (CIMP) in colon cancer instead of the four subtypes in the previous reports, and we found no sufficient evidence to subdivide MCL3 into two distinct subgroups.

Shock-induced spall in copper: the effects of anisotropy, temperature, loading pulse and defect

Energy Technology Data Exchange (ETDEWEB)

Luo, Shengnian [Los Alamos National Laboratory; Germann, Timothy C [Los Alamos National Laboratory; An, Qi [Los Alamos National Laboratory; Han, Li - Bo [USTC

2009-07-28

Shock-induced spall in Cu is investigated with molecular dynamics simulations. We examine spallation in initially perfect crystals and defective solids with grain boundaries (columnar bicrystals), stacking faults or vacancies, as well as the effect of temperature and loading pulses. Spall in single crystal Cu is anisotropic, and defects and high temperature may reduce the spall strength. Taylor-wave (triangular shock-release wave) loading is explored in comparison with square wave shock loading.

Targeted exome sequencing identified novel USH2A mutations in Usher syndrome families.

Directory of Open Access Journals (Sweden)

Xiu-Feng Huang

Full Text Available Usher syndrome (USH is a leading cause of deaf-blindness in autosomal recessive trait. Phenotypic and genetic heterogeneities in USH make molecular diagnosis much difficult. This is a pilot study aiming to develop an approach based on next-generation sequencing to determine the genetic defects in patients with USH or allied diseases precisely and effectively. Eight affected patients and twelve unaffected relatives from five unrelated Chinese USH families, including 2 pseudo-dominant ones, were recruited. A total of 144 known genes of inherited retinal diseases were selected for deep exome resequencing. Through systematic data analysis using established bioinformatics pipeline and segregation analysis, a number of genetic variants were released. Eleven mutations, eight of them were novel, in the USH2A gene were identified. Biparental mutations in USH2A were revealed in 2 families with pseudo-dominant inheritance. A proband was found to have triple mutations, two of them were supposed to locate in the same chromosome. In conclusion, this study revealed the genetic defects in the USH2A gene and demonstrated the robustness of targeted exome sequencing to precisely and rapidly determine genetic defects. The methodology provides a reliable strategy for routine gene diagnosis of USH.

The effect of topological defects and oxygen adsorption on the electronic transport properties of single-walled carbon-nanotubes

International Nuclear Information System (INIS)

Grujicic, M.; Cao, G.; Singh, R.

2003-01-01

Ab initio density functional theory (DFT) calculations of the interactions between isolated infinitely-long semiconducting zig-zag (10, 0) or isolated infinitely-long metallic arm-chair (5, 5) single-walled carbon-nanotubes (SWCNTs) and single oxygen-molecules are carried out in order to determine the character of molecular-oxygen adsorption and its effect on electronic transport properties of these SWCNTs. A Green's function method combined with a nearest-neighbor tight-binding Hamiltonian in a non-orthogonal basis is used to compute the electrical conductance of SWCNTs and its dependence on the presence of topological defects in SWCNTs and of molecular-oxygen adsorbates. The computational results obtained show that in both semiconducting and metallic SWCNTs, oxygen-molecules are physisorbed to the defect-free nanotube walls, but when such walls contain topological defects, oxygen-molecules become strongly chemisorbed. In semiconducting (10, 0) SWCNTs, physisorbed O 2 -molecules are found to significantly increase electrical conductance while the effect of 7-5-5-7 defects is practically annulled by chemisorbed O 2 -molecules. In metallic (5, 5) SWCNTs, both O 2 adsorbates and 7-5-5-7 defects are found to have a relatively small effect on electrical conductance of these nanotubes

Subjects with molecularly defined familial hypercholesterolemia or familial defective apoB-100 are not being adequately treated.

Directory of Open Access Journals (Sweden)

Trond P Leren

2011-02-01

Full Text Available To study whether subjects with a molecular genetic diagnosis of familial hypercholesterolemia (FH or familial defective apoB-100 (FDB are being adequately treated.A questionnaire regarding medical history was sent to 2611 subjects who had been provided with a molecular genetic diagnosis of FH or FDB, and a blood sample was obtained for lipid measurements.956 (36.6% of the 2611 subjects participated. The mean age for starting lipid-lowering therapy was 33.4 (±12.1 years. Among those below 18 years of age, only 20.4% were on lipid-lowering drugs, whereas 89.1% of those aged 18 and above were on lipid-lowering drugs. The mean levels of total serum cholesterol and LDL-cholesterol were 5.7 (±1.5 mmol/l and 3.9 (±1.3 mmol/l, respectively. Among those who were on lipid-lowering drugs, 29.0% and 12.2% had levels of LDL cholesterol below 3.0 mmol/l and 2.6 mmol/l, respectively. Only 47.3% of the 956 subjects were considered as being adequately treated largely due to a failure to titrate their drug regimens. From the use of cholesterol-years score, lipid-lowering therapy must start before the age of 20 in order to prevent the subjects from contracting premature coronary heart disease.The majority of FH/FDB subjects are being diagnosed late in life and are not being adequately treated. In order to prevent them from contracting premature coronary heart disease, it is key that levels of LDL cholesterol are normalized from a young age and that sufficient doses of lipid-lowering drugs are being used.

Molecular dynamics growth modeling of InAs1-xSbx-based type-II superlattice

Science.gov (United States)

Ciani, Anthony J.; Grein, Christoph H.; Irick, Barry; Miao, Maosheng; Kioussis, Nicholas

2017-09-01

Type-II strained-layer superlattices (T2SL) based on InAs1-xSbx are a promising photovoltaic detector material technology for thermal imaging; however, Shockley-Read-Hall recombination and generation rates are still too high for thermal imagers based on InAs1-xSbx T2SL to reach their ideal performance. Molecular dynamics simulations using the Stillinger-Weber (SW) empirical potentials are a useful tool to study the growth of tetrahedral coordinated crystals and the nonequilibrium formation of defects within them, including the long-range effects of strain. SW potentials for the possible atomic interactions among {Ga, In, As, Sb} were developed by fitting to ab initio calculations of elastically distorted zinc blende and diamond unit cells. The SW potentials were tested against experimental observations of molecular beam epitaxial (MBE) growth and then used to simulate the MBE growth of InAs/InAs0.5Sb0.5 T2SL on GaSb substrates over a range of processes parameters. The simulations showed and helped to explain Sb cross-incorporation into the InAs T2SL layers, Sb segregation within the InAsSb layers, and identified medium-range defect clusters involving interstitials and their induction of interstitial-vacancy pairs. Defect formation was also found to be affected by growth temperature and flux stoichiometry.

A harmonic transition state theory model for defect initiation in crystals

International Nuclear Information System (INIS)

Delph, T J; Cao, P; Park, H S; Zimmerman, J A

2013-01-01

We outline here a model for the initiation of defects in crystals based upon harmonic transition state theory (hTST). This model combines a previously developed model for zero-temperature defect initiation with a multi-dimensional hTST model that is capable of accurately predicting the effects of temperature and loading rate upon defect initiation. The model has several features that set it apart from previous efforts along these lines, most notably a straightforward method of determining the energy barrier between adjacent equilibrium states that does not depend upon a priori information concerning the nature of the defect. We apply the model to two examples, triaxial stretching of a perfect fcc crystal and nanoindentation of a gold substrate. Very good agreement is found between the predictions of the model and independent molecular dynamics (MD) simulations. Among other things, the model predicts a strong dependence of the defect initiation behavior upon the loading parameter. A very attractive feature of this model is that it is valid for arbitrarily slow loading rates, in particular loading rates achievable in the laboratory, and suffers from none of the limitations in this regard inherent in MD simulations. (paper)

Repair of massively defected hemi-joints using demineralized osteoarticular allografts with protected cartilage.

Science.gov (United States)

Li, Siming; Yang, Xiaohong; Tang, Shenghui; Zhang, Xunmeng; Feng, Zhencheng; Cui, Shuliang

2015-08-01

Surgical replacement of massively defected joints necessarily relies on osteochondral grafts effective to both of bone and cartilage. Demineralized bone matrix (DBM) retains the osteoconductivity but destroys viable chondrocytes in the cartilage portion essential for successful restoration of defected joints. This study prepared osteochondral grafts of DBM with protected cartilage. Protected cartilage portions was characterized by cellular and molecular biology and the grafts were allogenically used for grafting. Protected cartilage showed similar histomorphological structure and protected proteins estimated by total proteins and cartilage specific proteins as in those of fresh controls when DBMs were generated in bone portions. Such grafts were successfully used for simultaneously repair of bone and cartilage in massively defected osteoarticular joints within 16 weeks post-surgery. These results present an allograft with clinical potential for simultaneous restoration of bone and cartilage in defected joints.

Tuning thermal conductivity in homoepitaxial SrTiO{sub 3} films via defects

Energy Technology Data Exchange (ETDEWEB)

Brooks, Charles M. [Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853-1501 (United States); Department of Materials Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802 (United States); Wilson, Richard B.; Cahill, David G. [Department of Materials Science and Engineering and Materials Research Laboratory, University of Illinois, Urbana, Illinois 61801 (United States); Schäfer, Anna; Schubert, Jürgen [Peter Grünberg Institute (PGI9-IT), JARA-Fundamentals of Future Information Technology, Research Centre Jülich, D-52425 Jülich (Germany); Mundy, Julia A.; Holtz, Megan E. [School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853 (United States); Muller, David A. [School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853 (United States); Kavli Institute at Cornell for Nanoscale Science, Ithaca, New York 14853 (United States); Schlom, Darrell G. [Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853-1501 (United States); Kavli Institute at Cornell for Nanoscale Science, Ithaca, New York 14853 (United States)

2015-08-03

We demonstrate the ability to tune the thermal conductivity of homoepitaxial SrTiO{sub 3} films deposited by reactive molecular-beam epitaxy by varying growth temperature, oxidation environment, and cation stoichiometry. Both point defects and planar defects decrease the longitudinal thermal conductivity (k{sub 33}), with the greatest decrease in films of the same composition observed for films containing planar defects oriented perpendicular to the direction of heat flow. The longitudinal thermal conductivity can be modified by as much as 80%—from 11.5 W m{sup −1}K{sup −1} for stoichiometric homoepitaxial SrTiO{sub 3} to 2 W m{sup −1}K{sup −1} for strontium-rich homoepitaxial Sr{sub 1+δ}TiO{sub x} films—by incorporating (SrO){sub 2} Ruddlesden-Popper planar defects.

A suite of molecular markers for identifying species, detecting introgression and describing population structure in spadefoot toads (Spea spp.).

Science.gov (United States)

Pfennig, Karin S; Allenby, Ashley; Martin, Ryan A; Monroy, Anaïs; Jones, Corbin D

2012-09-01

Two congeneric species of spadefoot toad, Spea multiplicata and Spea bombifrons, have been the focus of hybridization studies since the 1970s. Because complex hybrids are not readily distinguished phenotypically, genetic markers are needed to identify introgressed individuals. We therefore developed a set of molecular markers (amplified fragment length polymorphism, polymerase chain reaction-restriction fragment length polymorphism and single nucleotide polymorphism) for identifying pure-species, F1 hybrids and more complex introgressed types. To do so, we tested a series of markers across both species and known hybrids using populations in both allopatry and sympatry. We retained those markers that differentiated the two pure-species and also consistently identified known species hybrids. These markers are well suited for identifying hybrids between these species. Moreover, those markers that show variation within each species can be used in conjunction with existing molecular markers in studies of population structure and gene flow. © 2012 Blackwell Publishing Ltd.

Power spectrum analysis for defect screening in integrated circuit devices

Science.gov (United States)

Tangyunyong, Paiboon; Cole Jr., Edward I.; Stein, David J.

2011-12-01

A device sample is screened for defects using its power spectrum in response to a dynamic stimulus. The device sample receives a time-varying electrical signal. The power spectrum of the device sample is measured at one of the pins of the device sample. A defect in the device sample can be identified based on results of comparing the power spectrum with one or more power spectra of the device that have a known defect status.

A 6-gene signature identifies four molecular subgroups of neuroblastoma

Science.gov (United States)

2011-01-01

Background There are currently three postulated genomic subtypes of the childhood tumour neuroblastoma (NB); Type 1, Type 2A, and Type 2B. The most aggressive forms of NB are characterized by amplification of the oncogene MYCN (MNA) and low expression of the favourable marker NTRK1. Recently, mutations or high expression of the familial predisposition gene Anaplastic Lymphoma Kinase (ALK) was associated to unfavourable biology of sporadic NB. Also, various other genes have been linked to NB pathogenesis. Results The present study explores subgroup discrimination by gene expression profiling using three published microarray studies on NB (47 samples). Four distinct clusters were identified by Principal Components Analysis (PCA) in two separate data sets, which could be verified by an unsupervised hierarchical clustering in a third independent data set (101 NB samples) using a set of 74 discriminative genes. The expression signature of six NB-associated genes ALK, BIRC5, CCND1, MYCN, NTRK1, and PHOX2B, significantly discriminated the four clusters (p INSS stage 4 and/or dead of disease, p < 0.05, Fisher's exact test). Conclusions Based on expression profiling we have identified four molecular subgroups of neuroblastoma, which can be distinguished by a 6-gene signature. The fourth subgroup has not been described elsewhere, and efforts are currently made to further investigate this group's specific characteristics. PMID:21492432

An Mcm10 Mutant Defective in ssDNA Binding Shows Defects in DNA Replication Initiation.

Science.gov (United States)

Perez-Arnaiz, Patricia; Kaplan, Daniel L

2016-11-20

Mcm10 is an essential protein that functions to initiate DNA replication after the formation of the replication fork helicase. In this manuscript, we identified a budding yeast Mcm10 mutant (Mcm10-m2,3,4) that is defective in DNA binding in vitro. Moreover, this Mcm10-m2,3,4 mutant does not stimulate the phosphorylation of Mcm2 by Dbf4-dependent kinase (DDK) in vitro. When we expressed wild-type levels of mcm10-m2,3,4 in budding yeast cells, we observed a severe growth defect and a substantially decreased DNA replication. We also observed a substantially reduced replication protein A- chromatin immunoprecipitation signal at origins of replication, reduced levels of DDK-phosphorylated Mcm2, and diminished Go, Ichi, Ni, and San (GINS) association with Mcm2-7 in vivo. mcm5-bob1 bypasses the growth defect conferred by DDK-phosphodead Mcm2 in budding yeast. However, the growth defect observed by expressing mcm10-m2,3,4 is not bypassed by the mcm5-bob1 mutation. Furthermore, origin melting and GINS association with Mcm2-7 are substantially decreased for cells expressing mcm10-m2,3,4 in the mcm5-bob1 background. Thus, the origin melting and GINS-Mcm2-7 interaction defects we observed for mcm10-m2,3,4 are not explained by decreased Mcm2 phosphorylation by DDK, since the defects persist in an mcm5-bob1 background. These data suggest that DNA binding by Mcm10 is essential for the initiation of DNA replication. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molecular subtype classification of urothelial carcinoma in Lynch syndrome.

Science.gov (United States)

Therkildsen, Christina; Eriksson, Pontus; Höglund, Mattias; Jönsson, Mats; Sjödahl, Gottfrid; Nilbert, Mef; Liedberg, Fredrik

2018-05-23

Lynch syndrome confers an increased risk for urothelial carcinoma (UC). Molecular subtypes may be relevant to prognosis and therapeutic possibilities, but have to date not been defined in Lynch syndrome-associated urothelial cancer. We aimed to provide a molecular description of Lynch syndrome-associated UC. Thus, Lynch syndrome-associated UC of the upper urinary tract and the urinary bladder were identified in the Danish hereditary non-polyposis colorectal cancer (HNPCC) register and were transcriptionally and immunohistochemically profiled and further related to data from 307 sporadic urothelial carcinomas. Whole genome mRNA expression profiles of 41 tumors and immunohistochemical stainings against FGFR3, KRT5, CCNB1, RB1, and CDKN2A (p16) of 37 tumors from Lynch syndrome patients were generated. Pathological data, microsatellite instability, anatomic location, and overall survival data was analyzed and compared with sporadic bladder cancer. The 41 Lynch syndrome-associated UC developed at a mean age of 61 years with 59% women. mRNA expression profiling and immunostaining classified the majority of the Lynch syndrome-associated UC as Urothelial-like tumors with only 20% being Genomically Unstable, Basal/SCC-like or other subtypes. The subtypes were associated with stage, grade, and microsatellite instability. Comparison to larger data sets revealed that Lynch syndrome-associated UC share molecular similarities with sporadic UC. In conclusion, transcriptomic and immunohistochemical profiling identifies a predominance of the Urothelial-like molecular subtype in Lynch syndrome and reveals that the molecular subtypes of sporadic bladder cancer are relevant also within this hereditary, mismatch-repair defective subset. This article is protected by copyright. All rights reserved. Molecular Oncology (2018) © 2018 The Authors. Published by FEBS Press and John Wiley & Sons Ltd.

Comprehensive profiling of DNA repair defects in breast cancer identifies a novel class of endocrine therapy resistance drivers.

Science.gov (United States)

Anurag, Meenakshi; Punturi, Nindo; Hoog, Jeremy; Bainbridge, Matthew N; Ellis, Matthew J; Haricharan, Svasti

2018-05-23

This study was undertaken to conduct a comprehensive investigation of the role of DNA damage repair (DDR) defects in poor outcome ER+ disease. Expression and mutational status of DDR genes in ER+ breast tumors were correlated with proliferative response in neoadjuvant aromatase inhibitor therapy trials (discovery data set), with outcomes in METABRIC, TCGA and Loi data sets (validation data sets), and in patient derived xenografts. A causal relationship between candidate DDR genes and endocrine treatment response, and the underlying mechanism, was then tested in ER+ breast cancer cell lines. Correlations between loss of expression of three genes: CETN2 (p<0.001) and ERCC1 (p=0.01) from the nucleotide excision repair (NER) and NEIL2 (p=0.04) from the base excision repair (BER) pathways were associated with endocrine treatment resistance in discovery data sets, and subsequently validated in independent patient cohorts. Complementary mutation analysis supported associations between mutations in NER and BER pathways and reduced endocrine treatment response. A causal role for CETN2, NEIL2 and ERCC1 loss in intrinsic endocrine resistance was experimentally validated in ER+ breast cancer cell lines, and in ER+ patient-derived xenograft models. Loss of CETN2, NEIL2 or ERCC1 induced endocrine treatment response by dysregulating G1/S transition, and therefore, increased sensitivity to CDK4/6 inhibitors. A combined DDR signature score was developed that predicted poor outcome in multiple patient cohorts. This report identifies DDR defects as a new class of endocrine treatment resistance drivers and indicates new avenues for predicting efficacy of CDK4/6 inhibition in the adjuvant treatment setting. Copyright ©2018, American Association for Cancer Research.

Xenon Defects in Uranium Dioxide From First Principles and Interatomic Potentials

Science.gov (United States)

Thompson, Alexander

In this thesis, we examine the defect energetics and migration energies of xenon atoms in uranium dioxide (UO2) from first principles and interatomic potentials. We also parameterize new, accurate interatomic potentials for xenon and uranium dioxide. To achieve accurate energetics and provide a foundation for subsequent calculations, we address difficulties in finding consistent energetics within Hubbard U corrected density functional theory (DFT+U). We propose a method of slowly ramping the U parameter in order to guide the calculation into low energy orbital occupations. We find that this method is successful for a variety of materials. We then examine the defect energetics of several noble gas atoms in UO2 for several different defect sites. We show that the energy to incorporate large noble gas atoms into interstitial sites is so large that it is energetically favorable for a Schottky defect cluster to be created to relieve the strain. We find that, thermodynamically, xenon will rarely ever be in the interstitial site of UO2. To study larger defects associated with the migration of xenon in UO 2, we turn to interatomic potentials. We benchmark several previously published potentials against DFT+U defect energetics and migration barriers. Using a combination of molecular dynamics and nudged elastic band calculations, we find a new, low energy migration pathway for xenon in UO2. We create a new potential for xenon that yields accurate defect energetics. We fit this new potential with a method we call Iterative Potential Refinement that parameterizes potentials to first principles data via a genetic algorithm. The potential finds accurate energetics for defects with relatively low amounts of strain (xenon in defect clusters). It is important to find accurate energetics for these sorts of low-strain defects because they essentially represent small xenon bubbles. Finally, we parameterize a new UO2 potential that simultaneously yields accurate vibrational properties

Defects introduced by Ar plasma exposure in GaAs probed by monoenergetic positron beam

Energy Technology Data Exchange (ETDEWEB)

Uedono, Akira; Tanigawa, Shoichiro [Tsukuba Univ., Ibaraki (Japan). Inst. of Materials Science; Kawano, Takao; Wada, Kazumi; Nakanishi, Hideo

1994-10-01

Ar-plasma-induced defects in n-type GaAs were probed by a monoenergetic positron beam. The depth distribution of the defects was obtained from measurements of Doppler broadening profiles of the annihilation radiation as a function of incident positron energy. The damaged layer induced by the exposure was found to extend far beyond the stopping range of Ar ions, and the dominant defects were identified as interstitial-type defects. After 100degC annealing, such defects were annealed. Instead, vacancy-type defects were found to be the dominant defects in the subsurface region. (author).

Characterization of point defects in CdTe by positron annihilation spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Elsharkawy, M. R. M. [Carnegie Laboratory of Physics, SUPA, School of Science and Engineering, University of Dundee, Dundee DD1 4HN (United Kingdom); Physics Department, Faculty of Science, Minia University, P.O. Box 61519, Minia (Egypt); Kanda, G. S.; Keeble, D. J., E-mail: d.j.keeble@dundee.ac.uk [Carnegie Laboratory of Physics, SUPA, School of Science and Engineering, University of Dundee, Dundee DD1 4HN (United Kingdom); Abdel-Hady, E. E. [Physics Department, Faculty of Science, Minia University, P.O. Box 61519, Minia (Egypt)

2016-06-13

Positron lifetime measurements on CdTe 0.15% Zn-doped by weight are presented, trapping to monovacancy defects is observed. At low temperatures, localization at shallow binding energy positron traps dominates. To aid defect identification density functional theory, calculated positron lifetimes and momentum distributions are obtained using relaxed geometry configurations of the monovacancy defects and the Te antisite. These calculations provide evidence that combined positron lifetime and coincidence Doppler spectroscopy measurements have the capability to identify neutral or negative charge states of the monovacancies, the Te antisite, A-centers, and divacancy defects in CdTe.

Ab initio R-matrix/Multi-channel Quantum Defect Theory applied to Molecular Core Excitation and Ionization

International Nuclear Information System (INIS)

Hiyama, M.; Kosugi, N.

2004-01-01

Full text: Ab initio R-matrix/MQDT approach, which is a combination of ab initio R-matrix techniques and the multi channel quantum defect theory (MQDT), has recently been developed by one of the present authors (MH) and Child, to successfully obtain the potential energy curves of Rydberg states converging to not only the lowest but also the higher ionized states. This approach is also applied to estimate the valence state interaction with Rydberg and continuum (ionization) channels. Very recently we have made an original ab initio polyatomic R-matrix/MQDT program package, GSCF4R based on Gaussian type basis functions for the bound and continuum states, to extensively study molecular excitation and ionization in the X-ray region as well as in the VUV region. We are going to report the results for core excitation and ionization of diatomic molecules such as NO and O 2 to show that the R-matrix/MQDT method is indispensable to describe the core-to-Rydberg states with the higher quantum number and the continuum states. These results lead us to the conclusion that the close-coupling approximation augmented with the correlation term within the R-matrix/MQDT formalism is powerful to calculate the Rydberg-valence mixing and the interchannel coupling between several core-ionized states

Deep level transient spectroscopic investigation of phosphorus-doped silicon by self-assembled molecular monolayers.

Science.gov (United States)

Gao, Xuejiao; Guan, Bin; Mesli, Abdelmadjid; Chen, Kaixiang; Dan, Yaping

2018-01-09

It is known that self-assembled molecular monolayer doping technique has the advantages of forming ultra-shallow junctions and introducing minimal defects in semiconductors. In this paper, we report however the formation of carbon-related defects in the molecular monolayer-doped silicon as detected by deep-level transient spectroscopy and low-temperature Hall measurements. The molecular monolayer doping process is performed by modifying silicon substrate with phosphorus-containing molecules and annealing at high temperature. The subsequent rapid thermal annealing drives phosphorus dopants along with carbon contaminants into the silicon substrate, resulting in a dramatic decrease of sheet resistance for the intrinsic silicon substrate. Low-temperature Hall measurements and secondary ion mass spectrometry indicate that phosphorus is the only electrically active dopant after the molecular monolayer doping. However, during this process, at least 20% of the phosphorus dopants are electrically deactivated. The deep-level transient spectroscopy shows that carbon-related defects are responsible for such deactivation.

Quantitative proteomics identify molecular targets that are crucial in larval settlement and metamorphosis of bugula neritina

KAUST Repository

Zhang, Huoming

2011-01-07

The marine invertebrate Bugula neritina has a biphasic life cycle that consists of a swimming larval stage and a sessile juvenile and adult stage. The attachment of larvae to the substratum and their subsequent metamorphosis have crucial ecological consequences. Despite many studies on this species, little is known about the molecular mechanism of these processes. Here, we report a comparative study of swimming larvae and metamorphosing individuals at 4 and 24 h postattachment using label-free quantitative proteomics. We identified more than 1100 proteins at each stage, 61 of which were differentially expressed. Specifically, proteins involved in energy metabolism and structural molecules were generally down-regulated, whereas proteins involved in transcription and translation, the extracellular matrix, and calcification were strongly up-regulated during metamorphosis. Many tightly regulated novel proteins were also identified. Subsequent analysis of the temporal and spatial expressions of some of the proteins and an assay of their functions indicated that they may have key roles in metamorphosis of B. neritina. These findings not only provide molecular evidence with which to elucidate the substantial changes in morphology and physiology that occur during larval attachment and metamorphosis but also identify potential targets for antifouling treatment. © 2011 American Chemical Society.

The effect of temperature on primary defect formation in Ni–Fe alloy

Energy Technology Data Exchange (ETDEWEB)

Wang, Chengbin, E-mail: wangchengbin@sinap.ac.cn [Key Laboratory of Interfacial Physics and Technology, Chinese Academy of Sciences, Shanghai 201800 (China); Zhang, Wei; Ren, Cuilan [Key Laboratory of Interfacial Physics and Technology, Chinese Academy of Sciences, Shanghai 201800 (China); Huai, Ping [Key Laboratory of Nuclear Radiation and Nuclear Energy Technology, Chinese Academy of Sciences, Shanghai 201800 (China); Zhu, Zhiyuan [Key Laboratory of Interfacial Physics and Technology, Chinese Academy of Sciences, Shanghai 201800 (China)

2014-02-15

Molecular dynamics (MD) simulations have been used to study the influence of temperature on defect generation and evolution in nickel and Ni–Fe alloy (with 15% and 50% Fe content) with a 10-keV primary knock-on atom (PKA) at six different temperatures from 0 to 1500 K. The recently available Ni–Fe potential is used with its repulsive part modified by Vörtler. The temporal evolution and temperature dependence of stable defect formation and in-cascade clustering processes are analysed. The number of stable defect and the interstitial clustering fraction are found to increase with temperature whereas the vacancy clustering fraction decreases with temperature. The alloy composition dependence of the stable defect number is also found for the PKA energy considered here. Additionally, a study of the temperature influence on the cluster size distribution is performed, revealing a systematic change in the cluster size distributions, with higher temperature cascades producing larger interstitial clusters.

Optimization of Soft Tissue Management, Spacer Design, and Grafting Strategies for Large Segmental Bone Defects using the Chronic Caprine Tibial Defect Model

Science.gov (United States)

2015-12-01

for this animal revealed an abscess at the defect site with cultures identifying Staphylococcus aureus infection . Another animal (15G11) developed...foreign body reaction and expose a bleeding vascular surface significantly increased bone formation in the defect site. Adding texture to a smooth...ACHIEVEMENTS: Nothing to report 10. REFERENCES: 1. Johnson, E.N., et al., Infectious complications of open type III tibial fractures among combat

Immobile defects in ferroelastic walls: Wall nucleation at defect sites

Science.gov (United States)

He, X.; Salje, E. K. H.; Ding, X.; Sun, J.

2018-02-01

Randomly distributed, static defects are enriched in ferroelastic domain walls. The relative concentration of defects in walls, Nd, follows a power law distribution as a function of the total defect concentration C: N d ˜ C α with α = 0.4 . The enrichment Nd/C ranges from ˜50 times when C = 10 ppm to ˜3 times when C = 1000 ppm. The resulting enrichment is due to nucleation at defect sites as observed in large scale MD simulations. The dynamics of domain nucleation and switching is dependent on the defect concentration. Their energy distribution follows the power law with exponents during yield between ɛ ˜ 1.82 and 2.0 when the defect concentration increases. The power law exponent is ɛ ≈ 2.7 in the plastic regime, independent of the defect concentration.

Molecular dissection of Norrie disease.

Science.gov (United States)

Berger, W

1998-01-01

Norrie disease (ND) is a severe form of congenital blindness accompanied by mental retardation and/or deafness in at least one third of the patients. This article summarizes advances in the molecular genetic analysis of this disease during the last 13 years, including mapping and cloning of the human gene and the generation and characterization of a mouse model. Genetic linkage studies and physical mapping strategies have assigned the ND locus to the proximal short arm of the human X chromosome. The identification of chromosomal rearrangements in several patients, such as microdeletions, enabled the isolation of the ND gene by a positional cloning approach. Numerous point mutations in this gene have been identified in three distinct clinical entities: (1) ND, (2) familial and sporadic exudative vitreoretinopathy, and (3) retinopathy of prematurity. The gene encodes a relatively small protein, consisting of 133 amino acids. The function of the gene product is yet unknown, although homologies with known proteins and molecular modelling data suggest a role in the regulation of cell interaction or differentiation processes. A mouse model has been generated to shed more light on early pathogenic events involved in ND and allelic disorders. The mouse homologous protein is highly identical (94%) to the human polypeptide. The gene is expressed in the neuronal layers of the mouse retina, the cerebellum and olfactory epithelium. Mutant mice show snowflake-like opacities within the vitreous, dysgenesis of the ganglion cell layer and occasionally degeneration of photoreceptor cells. The mouse phenotype does not include phthisis bulbi and, overall, resembles a mild form of ND. Electrophysiological studies revealed a severely altered electroretinogram b-wave. These results suggest a primary defect in the inner neuronal layers of the retina. Defects in the vitreous and photoreceptor cell layer are most likely secondary effects. Further histological, functional and molecular

Strong Coupling between Nanofluidic Transport and Interfacial Chemistry: How Defect Reactivity Controls Liquid-Solid Friction through Hydrogen Bonding.

Science.gov (United States)

Joly, Laurent; Tocci, Gabriele; Merabia, Samy; Michaelides, Angelos

2016-04-07

Defects are inevitably present in nanofluidic systems, yet the role they play in nanofluidic transport remains poorly understood. Here, we report ab initio molecular dynamics (AIMD) simulations of the friction of liquid water on defective graphene and boron nitride sheets. We show that water dissociates at certain defects and that these "reactive" defects lead to much larger friction than the "nonreactive" defects at which water molecules remain intact. Furthermore, we find that friction is extremely sensitive to the chemical structure of reactive defects and to the number of hydrogen bonds they can partake in with the liquid. Finally, we discuss how the insight obtained from AIMD can be used to quantify the influence of defects on friction in nanofluidic devices for water treatment and sustainable energy harvesting. Overall, we provide new insight into the role of interfacial chemistry on nanofluidic transport in real, defective systems.

Identifying self-interstitials of bcc and fcc crystals in molecular dynamics

Science.gov (United States)

Bukkuru, S.; Bhardwaj, U.; Warrier, M.; Rao, A. D. P.; Valsakumar, M. C.

2017-02-01

Identification of self-interstitials in molecular dynamics (MD) simulations is of critical importance. There exist several criteria for identifying the self-interstitial. Most of the existing methods use an assumed cut-off value for the displacement of an atom from its lattice position to identify the self-interstitial. The results obtained are affected by the chosen cut-off value. Moreover, these chosen cut-off values are independent of temperature. We have developed a novel unsupervised learning algorithm called Max-Space Clustering (MSC) to identify an appropriate cut-off value and its dependence on temperature. This method is compared with some widely used methods such as effective sphere (ES) method and nearest neighbor sphere (NNS) method. The cut-off radius obtained using our method shows a linear variation with temperature. The value of cut-off radius and its temperature dependence is derived for five bcc (Cr, Fe, Mo, Nb, W) and six fcc (Ag, Au, Cu, Ni, Pd, Pt) crystals. It is seen that the ratio of the cut-off values "r" to the lattice constant "a" lies between 0.23 and 0.3 at 300 K and this ratio is on an average smaller for the fcc crystals. Collision cascade simulations are carried out for Primary knock-on Atom (PKA) energies of 5 keV in Fe (at 300 K and 1000 K) and W (at 300 K and 2500 K) and the results are compared using the various methods.

Modification of ferromagnetic nanostripe dynamic behavior by edge defects

Science.gov (United States)

Hu, Bo; Zhao, Chunwang; Li, Yulian

2018-03-01

The dynamic spectra of ferromagnetic nanostripes with different edge defects are investigated using the three-dimensional object-oriented micromagnetic framework code. Two main resonance peaks are found in nanostripes due to nonuniformity of the static magnetization patterns. The higher peak can be identified by the precession of magnetization in the middle part of the nanostripes. The lower one can be identified by the sample end part. The values of two precession frequencies and linewidths can be modified using the edge defect to tune the magnetization of different parts of samples, which is important and useful in magnetic storage devices.

Defect Characterization in Semiconductors with Positron Annihilation Spectroscopy

Science.gov (United States)

Tuomisto, Filip

Positron annihilation spectroscopy is an experimental technique that allows the selective detection of vacancy defects in semiconductors, providing a means to both identify and quantify them. This chapter gives an introduction to the principles of the positron annihilation techniques and then discusses the physics of some interesting observations on vacancy defects related to growth and doping of semiconductors. Illustrative examples are selected from studies performed in silicon, III-nitrides, and ZnO.

Dissecting molecular stress networks: identifying nodes of divergence between life-history phenotypes.

Science.gov (United States)

Schwartz, Tonia S; Bronikowski, Anne M

2013-02-01

The complex molecular network that underlies physiological stress response is comprised of nodes (proteins, metabolites, mRNAs, etc.) whose connections span cells, tissues and organs. Variable nodes are points in the network upon which natural selection may act. Thus, identifying variable nodes will reveal how this molecular stress network may evolve among populations in different habitats and how it might impact life-history evolution. Here, we use physiological and genetic assays to test whether laboratory-born juveniles from natural populations of garter snakes (Thamnophis elegans), which have diverged in their life-history phenotypes, vary concomitantly at candidate nodes of the stress response network, (i) under unstressed conditions and (ii) in response to an induced stress. We found that two common measures of stress (plasma corticosterone and liver gene expression of heat shock proteins) increased under stress in both life-history phenotypes. In contrast, the phenotypes diverged at four nodes both under unstressed conditions and in response to stress: circulating levels of reactive oxygen species (superoxide, H(2)O(2)); liver gene expression of GPX1 and erythrocyte DNA damage. Additionally, allele frequencies for SOD2 diverge from neutral markers, suggesting diversifying selection on SOD2 alleles. This study supports the hypothesis that these life-history phenotypes have diverged at the molecular level in how they respond to stress, particularly in nodes regulating oxidative stress. Furthermore, the differences between the life-history phenotypes were more pronounced in females. We discuss the responses to stress in the context of the associated life-history phenotype and the evolutionary pressures thought to be responsible for divergence between the phenotypes. © 2012 Blackwell Publishing Ltd.

A REVIEW OF FACTORS AFFECTING BUILDING DEFECTS IN SINGAPORE

Directory of Open Access Journals (Sweden)

Po Seng Kian

2001-01-01

Full Text Available In developing countries, building maintenance technology is currently vastly underrated and ignored by owners, managers, and professionals. The building and construction authority of Singapore (BCA has identified that the complaints about building defects have gone up in recent years with common problems such as leaky roof and walls, floor defect, and improper outlet pipe. This paper presents a brief description on building defect in use for commercial building as well as residential buildings in Singapore. The main objective is to highlight the important problems and suggest a greater participation of professionals in building maintenance. It also provides some site investigations photographs of various defects, which is expected to be useful for builders, architects, and others who deal with building materials.

Electron damage and defects in organic crystals

International Nuclear Information System (INIS)

Howitt, D.G.

1976-06-01

The nature of the defects discernable from and the radiation damage that is induced by high resolution electron microscopy is reported. The structural aspects of the radiation damage process can be correlated to the expected radiochemical decomposition of these materials and these effects identified. The types of local defect formed by radiation damage are often clearly distinguishable, in high resolution images, from those inherent in the microstructure. Techniques used in this type of electron microscopy and the limitations imposed by radiation damage are described as are the relevant radiochemical characteristics of these processes. In copper pthalocyanine, microstructural features distinct from those induced by radiation damage were identified which are consistent with those predicted and described by other workers in similar materials. The high resolution studies indicate that some of the microstructures observed are caused by structural rearrangements that can account, to some extent, for additional crystallographic forms that have been identified in this material and the photochemical behaviour of related structures

Investigation on the effect of atomic defects on the breaking behaviors of gold nanowires

International Nuclear Information System (INIS)

Wang Fenying; Sun Wei; Wang Hongbo; Zhao Jianwei; Kiguchi, Manabu; Sun Changqing

2012-01-01

The mechanical properties and breaking behaviors of the [100]-oriented single-crystal gold nanowires containing a set of defect ratios have been studied at different temperatures using molecular dynamics simulations. The size of the nanowire is 10a × 10a × 30a (a stands for lattice constant, 0.408 nm for gold). The mechanical strengths of the nanowires decrease with the increasing temperature. However, the defects that enhance the local thermal energy have improved the nanowire mechanical strength under a wide range of temperature. Comparing to the single-crystal nanowire, the existence of the atomic defects extends the elastic deformation showing a larger yield strain. By summarizing 300 samples at each temperature, the statistical breaking position distribution shows that the nanowire breaking behavior is sensitive to the atomic defects when the defect ratio is 5 % at 100 K, whereas the ratio is 1 % when temperatures are 300 and 500 K.

Point defects and irradiation in oxides: simulations at the atomic scale

International Nuclear Information System (INIS)

Crocombette, J.P.

2005-12-01

The studies done by Jean-Paul Crocombette between 1996 and 2005 in the Service de Recherches de Metallurgie Physique of the Direction de l'Energie Nucleaire in Saclay are presented in this Habilitation thesis. These works were part of the material science researches on the ageing, especially under irradiation, of oxides of interest for the nuclear industry. In this context simulation studies at the atomic scale were performed on two elementary components of ageing under irradiation : point defects and displacement cascades ; using two complementary simulation techniques : ab initio electronic structure calculations and empirical potential molecular dynamics. The first part deals with point defects : self defects (vacancies or interstitials) or hetero-atomic dopants. One first recalls the energetics of such defects in oxides, the specific features of defects calculations and the expected accuracy of these calculations. Then one presents the results obtained on uranium dioxide, oxygen in silver and amorphous silica. The second part tackles the modelling of disintegration recoil nuclei in various?displacement cascades created by crystalline matrices for actinide waste disposal. Cascade calculations give access to the amorphization mechanisms under irradiation of these materials. One thus predicts that the amorphization in zircon takes place directly in the tracks whereas in lanthanum zirconate, the amorphization proceeds through the accumulation of point defects. Finally the prospects of these studies are discussed. (author)

Novel rattling of K atoms in aluminium-doped defect pyrochlore tungstate

International Nuclear Information System (INIS)

Shoko, Elvis; Kearley, Gordon J; Peterson, Vanessa K; Thorogood, Gordon J; Mutka, Hannu; Koza, Michael M; Yamaura, Jun-ichi; Hiroi, Zenji

2014-01-01

Rattling dynamics have been identified as fundamental to superconductivity in defect pyrochlore osmates and aluminium vanadium intermetallics, as well as low thermal conductivity in clathrates and filled skutterudites. Combining inelastic neutron scattering (INS) measurements and ab initio molecular dynamics (MD) simulations, we use a new approach to investigate rattling in the Al-doped defect pyrochlore tungstates: AAl 0.33 W 1.67 O 6 (A = K, Rb, Cs). We find that although all the alkali metals rattle, the rattling of the K atoms is unique, not only among the tungstates but also among the analogous defect osmates, KOs 2 O 6 and RbOs 2 O 6 . Detailed analysis of the MD trajectories reveals that two unique features set the K dynamics apart from the rest, namely, (1) quasi one-dimensional local diffusion within a cage, and (2) vibration at a range of frequencies. The local diffusion is driven by strongly anharmonic local potentials around the K atoms exhibiting a double-well structure in the direction of maximum displacement, which is also the direction of local diffusion. On the other hand, vibration at a range of frequencies is a consequence of the strong anisotropy in the local potentials around the K atoms as revealed by directional magnitude spectra. We present evidence to show that it is the smaller size rather than the smaller mass of the K rattler which leads to the unusual dynamics. Finally, we suggest that the occurrence of local diffusion and vibration at a range of frequencies in the dynamics of a single rattler, as found here for the K atoms, may open new possibilities for phonon engineering in thermoelectric materials. (paper)

Fundamental investigation of point defect interactions in FE-CR alloys

International Nuclear Information System (INIS)

Wirth, B.D.; Lee, H.J.; Wong, K.

2008-01-01

Full text of publication follows. Fe-Cr alloys are a leading candidate material for structural applications in Generation TV and fusion reactors, and there is a relatively large database on their irradiation performance. However, complete understanding of the response of Fe-Cr alloys to intermediate-to-high temperature irradiation, including the radiation induced segregation of Cr, requires knowledge of point defect and point defect cluster interactions with Cr solute atoms and impurities. We present results from a hierarchical multi-scale modelling approach of defect cluster behaviour in Fe-Cr alloys. The modelling includes ab initio electronic structure calculations performed using the VASP code with projector-augmented electron wave functions using PBE pseudo-potentials and a collinear treatment of magnetic spins, molecular dynamics using semi-empirical Finnic-Sinclair type potentials, and kinetic Monte Carlo simulations of coupled defect and Cr transport responsible for microstructural evolution. The modelling results are compared to experimental observations in both binary Fe-Cr and more complex ferritic-martensitic alloys, and provide a basis for understanding a dislocation loop evolution and the observations of Cr enrichment and depletion at grain boundaries in various irradiation experiments. (authors)

Edge dislocations as sinks for sub-nanometric radiation induced defects in α-iron

Science.gov (United States)

Anento, N.; Malerba, L.; Serra, A.

2018-01-01

The role of edge dislocations as sinks for small radiation induced defects in bcc-Fe is investigated by means of atomistic computer simulation. In this work we investigate by Molecular Statics (T = 0K) the interaction between an immobile dislocation line and defect clusters of small sizes invisible experimentally. The study highlights in particular the anisotropy of the interaction and distinguishes between absorbed and trapped defects. When the considered defect intersects the dislocation glide plane and the distance from the dislocation line to the defect is on the range between 2 nm and 4 nm, either total or partial absorption of the cluster takes place leading to the formation of jogs. Residual defects produced during partial absorption pin the dislocation. By the calculation of stress-strain curves we have assessed the strength of those residues as obstacles for the motion of the dislocation, which is reflected on the unpinning stresses and the binding energies obtained. When the defect is outside this range, but on planes close to the dislocation glide plane, instead of absorption we have observed a capture process. Finally, with a view to introducing explicitly in kinetic Monte Carlo models a sink with the shape of a dislocation line, we have summarized our findings on a table presenting the most relevant parameters, which define the interaction of the dislocation with the defects considered.

Actinic inspection of multilayer defects on EUV masks

International Nuclear Information System (INIS)

Barty, A; Liu, Y; Gullikson, E; Taylor, J S; Wood, O

2005-01-01

The production of defect-free mask blanks, and the development of techniques for inspecting and qualifying EUV mask blanks, remains a key challenge for EUV lithography. In order to ensure a reliable supply of defect-free mask blanks, it is necessary to develop techniques to reliably and accurately detect defects on un-patterned mask blanks. These inspection tools must be able to accurately detect all critical defects whilst simultaneously having the minimum possible false-positive detection rate. There continues to be improvement in high-speed non-actinic mask blank inspection tools, and it is anticipated that these tools can and will be used by industry to qualify EUV mask blanks. However, the outstanding question remains one of validating that non-actinic inspection techniques are capable of detecting all printable EUV defects. To qualify the performance of non-actinic inspection tools, a unique dual-mode EUV mask inspection system has been installed at the Advanced Light Source (ALS) synchrotron at Lawrence Berkeley National Laboratory. In high-speed inspection mode, whole mask blanks are scanned for defects using 13.5-nm wavelength light to identify and map all locations on the mask that scatter a significant amount of EUV light. In imaging, or defect review mode, a zone plate is placed in the reflected beam path to image a region of interest onto a CCD detector with an effective resolution on the mask of 100-nm or better. Combining the capabilities of the two inspection tools into one system provides the unique capability to determine the coordinates of native defects that can be used to compare actinic defect inspection with visible light defect inspection tools under commercial development, and to provide data for comparing scattering models for EUV mask defects

Defect structure in proton-irradiated copper and nickel

International Nuclear Information System (INIS)

Tsukuda, Noboru; Ehrhart, P.; Jaeger, W.; Schilling, W.; Dworschak, F.; Gadalla, A.A.

1987-01-01

This single crystals of copper or nickel with a thickness of about 10 μm are irradiated with 3 MeV protons at room temperature and the structures of resultant defects are investigated based on measurements of the effects of irradiation on the electrical resistivity, length, lattice constants, x-ray diffraction line profile and electron microscopic observations. The measurements show that the electrical resistivity increases with irradiation dose, while leveling off at high dose due to overlapping of irradiation cascades. The lattice constants decreases, indicating that many vacancies still remain while most of the interstitial stoms are eliminated, absorbed or consumed for dislocation loop formation. The x-ray line profile undergoes broadening, which is the result of dislocation loops, dislocation networks and SFT's introduced by the proton irradiation. Various defects have different effects though they cannot be identified separately from the profile alone. A satellite peak appears at a low angle, which seems to arise from periodic defect structures that are found in electron microscopic observations. In both copper and nickel, such periodic defect structures are seen over a wide range from high to low dose. Defect-free and defect-rich domains (defect walls), 0.5 to several μm in size, are alingned parallel to the {001} plane at intervals of 60 nm. The defect walls, which consist of dislocations, dislocation loops and SFT's, is 20 - 40 nm thick. (Nogami, K.)

Intrinsic and extrinsic contributors to defective CD8+ T cell responses with aging.

Science.gov (United States)

Jergović, Mladen; Smithey, Megan J; Nikolich-Žugich, Janko

2018-05-01

Aging has a profound effect on the immune system, and both innate and adaptive arms of the immune system show functional decline with age. In response to infection with intracellular microorganisms, old animals mobilize decreased numbers of antigen-specific CD8+ T cells with reduced production of effector molecules and impaired cytolytic activity. However, the CD8+ T cell-intrinsic contribution to, and molecular mechanisms behind, these defects remain unclear. In this review we will discuss the mechanistic contributions of age related changes in the CD8+ T cell pool and the relative roles of intrinsic functional defects in aged CD8+ T cells vs. defects in the aged environment initiating the CD8+ T cell response. Copyright © 2018 Elsevier Inc. All rights reserved.

Studies of defects and defect agglomerates by positron annihilation spectroscopy

DEFF Research Database (Denmark)

Eldrup, Morten Mostgaard; Singh, B.N.

1997-01-01

A brief introduction to positron annihilation spectroscopy (PAS), and in particular lo its use for defect studies in metals is given. Positrons injected into a metal may become trapped in defects such as vacancies, vacancy clusters, voids, bubbles and dislocations and subsequently annihilate from...... the trapped state iri the defect. The annihilation characteristics (e.g., the lifetime of the positron) can be measured and provide information about the nature of the defect (e.g., size, density, morphology). The technique is sensitive to both defect size (in the range from monovacancies up to cavities...

THE BUILDER?S LIABILITY BEYOND THE DEFECTS LIABILITY

Directory of Open Access Journals (Sweden)

Johnson I IKPO

2005-01-01

Full Text Available This paper reviews the obligations of a builder after the expiration of the contracted defects liability period using relevant decided cases. The common areas identified as forming the bedrock of litigation pertain to structural and dimensional stability, freedom from damp, durability, adequate drainage, good waste disposal works, and effective service installations. Particular reference is made to walls, roofs, and services, which from the pilot study account for about 46%, 23%, and 17% respectively of the total defects attributable to the builder. It is concluded that the builder is responsible for defects arising from his product till the effluxion of reasonable time, except he establishes an element of contributory negligence.

Sirenomelia: an epidemiologic study in a large dataset from the International Clearinghouse of Birth Defects Surveillance and Research, and literature review.

Science.gov (United States)

Orioli, Iêda M; Amar, Emmanuelle; Arteaga-Vazquez, Jazmin; Bakker, Marian K; Bianca, Sebastiano; Botto, Lorenzo D; Clementi, Maurizio; Correa, Adolfo; Csaky-Szunyogh, Melinda; Leoncini, Emanuele; Li, Zhu; López-Camelo, Jorge S; Lowry, R Brian; Marengo, Lisa; Martínez-Frías, María-Luisa; Mastroiacovo, Pierpaolo; Morgan, Margery; Pierini, Anna; Ritvanen, Annukka; Scarano, Gioacchino; Szabova, Elena; Castilla, Eduardo E

2011-11-15

Sirenomelia is a very rare limb anomaly in which the normally paired lower limbs are replaced by a single midline limb. This study describes the prevalence, associated malformations, and maternal characteristics among cases with sirenomelia. Data originated from 19 birth defect surveillance system members of the International Clearinghouse for Birth Defects Surveillance and Research, and were reported according to a single pre-established protocol. Cases were clinically evaluated locally and reviewed centrally. A total of 249 cases with sirenomelia were identified among 25,290,172 births, for a prevalence of 0.98 per 100,000, with higher prevalence in the Mexican registry. An increase of sirenomelia prevalence with maternal age less than 20 years was statistically significant. The proportion of twinning was 9%, higher than the 1% expected. Sex was ambiguous in 47% of cases, and no different from expectation in the rest. The proportion of cases born alive, premature, and weighting less than 2,500 g were 47%, 71.2%, and 88.2%, respectively. Half of the cases with sirenomelia also presented with genital, large bowel, and urinary defects. About 10-15% of the cases had lower spinal column defects, single or anomalous umbilical artery, upper limb, cardiac, and central nervous system defects. There was a greater than expected association of sirenomelia with other very rare defects such as bladder exstrophy, cyclopia/holoprosencephaly, and acardia-acephalus. The application of the new biological network analysis approach, including molecular results, to these associated very rare diseases is suggested for future studies. Copyright © 2011 Wiley Periodicals, Inc.

Defect modelling

International Nuclear Information System (INIS)

Norgett, M.J.

1980-01-01

Calculations, drawing principally on developments at AERE Harwell, of the relaxation about lattice defects are reviewed with emphasis on the techniques required for such calculations. The principles of defect modelling are outlined and various programs developed for defect simulations are discussed. Particular calculations for metals, ionic crystals and oxides, are considered. (UK)

Scanning tip measurement for identification of point defects

Directory of Open Access Journals (Sweden)

Raineri Vito

2011-01-01

Full Text Available Abstract Self-assembled iron-silicide nanostructures were prepared by reactive deposition epitaxy of Fe onto silicon. Capacitance-voltage, current-voltage, and deep level transient spectroscopy (DLTS were used to measure the electrical properties of Au/silicon Schottky junctions. Spreading resistance and scanning probe capacitance microscopy (SCM were applied to measure local electrical properties. Using a preamplifier the sensitivity of DLTS was increased satisfactorily to measure transients of the scanning tip semiconductor junction. In the Fe-deposited area, Fe-related defects dominate the surface layer in about 0.5 μm depth. These defects deteriorated the Schottky junction characteristic. Outside the Fe-deposited area, Fe-related defect concentration was identified in a thin layer near the surface. The defect transients in this area were measured both in macroscopic Schottky junctions and by scanning tip DLTS and were detected by bias modulation frequency dependence in SCM.

Fanconi Anemia Proteins and Their Interacting Partners: A Molecular Puzzle

Science.gov (United States)

Kaddar, Tagrid; Carreau, Madeleine

2012-01-01

In recent years, Fanconi anemia (FA) has been the subject of intense investigations, primarily in the DNA repair research field. Many discoveries have led to the notion of a canonical pathway, termed the FA pathway, where all FA proteins function sequentially in different protein complexes to repair DNA cross-link damages. Although a detailed architecture of this DNA cross-link repair pathway is emerging, the question of how a defective DNA cross-link repair process translates into the disease phenotype is unresolved. Other areas of research including oxidative metabolism, cell cycle progression, apoptosis, and transcriptional regulation have been studied in the context of FA, and some of these areas were investigated before the fervent enthusiasm in the DNA repair field. These other molecular mechanisms may also play an important role in the pathogenesis of this disease. In addition, several FA-interacting proteins have been identified with roles in these “other” nonrepair molecular functions. Thus, the goal of this paper is to revisit old ideas and to discuss protein-protein interactions related to other FA-related molecular functions to try to give the reader a wider perspective of the FA molecular puzzle. PMID:22737580

A comprehensive molecular study on Coffin-Siris and Nicolaides-Baraitser syndromes identifies a broad molecular and clinical spectrum converging on altered chromatin remodeling.

Science.gov (United States)

Wieczorek, Dagmar; Bögershausen, Nina; Beleggia, Filippo; Steiner-Haldenstätt, Sabine; Pohl, Esther; Li, Yun; Milz, Esther; Martin, Marcel; Thiele, Holger; Altmüller, Janine; Alanay, Yasemin; Kayserili, Hülya; Klein-Hitpass, Ludger; Böhringer, Stefan; Wollstein, Andreas; Albrecht, Beate; Boduroglu, Koray; Caliebe, Almuth; Chrzanowska, Krystyna; Cogulu, Ozgur; Cristofoli, Francesca; Czeschik, Johanna Christina; Devriendt, Koenraad; Dotti, Maria Teresa; Elcioglu, Nursel; Gener, Blanca; Goecke, Timm O; Krajewska-Walasek, Malgorzata; Guillén-Navarro, Encarnación; Hayek, Joussef; Houge, Gunnar; Kilic, Esra; Simsek-Kiper, Pelin Özlem; López-González, Vanesa; Kuechler, Alma; Lyonnet, Stanislas; Mari, Francesca; Marozza, Annabella; Mathieu Dramard, Michèle; Mikat, Barbara; Morin, Gilles; Morice-Picard, Fanny; Ozkinay, Ferda; Rauch, Anita; Renieri, Alessandra; Tinschert, Sigrid; Utine, G Eda; Vilain, Catheline; Vivarelli, Rossella; Zweier, Christiane; Nürnberg, Peter; Rahmann, Sven; Vermeesch, Joris; Lüdecke, Hermann-Josef; Zeschnigk, Michael; Wollnik, Bernd

2013-12-20

Chromatin remodeling complexes are known to modify chemical marks on histones or to induce conformational changes in the chromatin in order to regulate transcription. De novo dominant mutations in different members of the SWI/SNF chromatin remodeling complex have recently been described in individuals with Coffin-Siris (CSS) and Nicolaides-Baraitser (NCBRS) syndromes. Using a combination of whole-exome sequencing, NGS-based sequencing of 23 SWI/SNF complex genes, and molecular karyotyping in 46 previously undescribed individuals with CSS and NCBRS, we identified a de novo 1-bp deletion (c.677delG, p.Gly226Glufs*53) and a de novo missense mutation (c.914G>T, p.Cys305Phe) in PHF6 in two individuals diagnosed with CSS. PHF6 interacts with the nucleosome remodeling and deacetylation (NuRD) complex implicating dysfunction of a second chromatin remodeling complex in the pathogenesis of CSS-like phenotypes. Altogether, we identified mutations in 60% of the studied individuals (28/46), located in the genes ARID1A, ARID1B, SMARCB1, SMARCE1, SMARCA2, and PHF6. We show that mutations in ARID1B are the main cause of CSS, accounting for 76% of identified mutations. ARID1B and SMARCB1 mutations were also found in individuals with the initial diagnosis of NCBRS. These individuals apparently belong to a small subset who display an intermediate CSS/NCBRS phenotype. Our proposed genotype-phenotype correlations are important for molecular screening strategies.

On the law of interaction between charged defects in ionic crystals

International Nuclear Information System (INIS)

Varaksin, A.N.; Kolmogorov, Yu.N.

1990-01-01

Values of E int PC (R 12 ) interaction energy between dominant defects in NaCl- and CaF 2 -type crystals are calculated using Mott-Littleton method in harmonic approximation. It is shown, that interaction between cationic and anionic vacancies in NaCl type crystals is described using Coulomb law for charge interaction in dielectric up till R 12 smallest distances between vacancies. Good conformity of E int PC R 12 values with calculation made using Coulomb formula should be expected for Frenkel anionic pair in CaF 2 type crystals. Deviations from Coulomb law are possible for other defects at R 12 small distances; deviation degree depends on lattice type, defect type and on relative polarizability of crystal cationic and anionic sublattices. Calculations of E int PC (R 12 ) values using Mott-Littleton method are compared with calculations conducted by MOLSTAT program using molecular static method

Identifying self-interstitials of bcc and fcc crystals in molecular dynamics

International Nuclear Information System (INIS)

Bukkuru, S.; Bhardwaj, U.; Warrier, M.; Rao, A.D.P.; Valsakumar, M.C.

2017-01-01

Identification of self-interstitials in molecular dynamics (MD) simulations is of critical importance. There exist several criteria for identifying the self-interstitial. Most of the existing methods use an assumed cut-off value for the displacement of an atom from its lattice position to identify the self-interstitial. The results obtained are affected by the chosen cut-off value. Moreover, these chosen cut-off values are independent of temperature. We have developed a novel unsupervised learning algorithm called Max-Space Clustering (MSC) to identify an appropriate cut-off value and its dependence on temperature. This method is compared with some widely used methods such as effective sphere (ES) method and nearest neighbor sphere (NNS) method. The cut-off radius obtained using our method shows a linear variation with temperature. The value of cut-off radius and its temperature dependence is derived for five bcc (Cr, Fe, Mo, Nb, W) and six fcc (Ag, Au, Cu, Ni, Pd, Pt) crystals. It is seen that the ratio of the cut-off values “r” to the lattice constant “a” lies between 0.23 and 0.3 at 300 K and this ratio is on an average smaller for the fcc crystals. Collision cascade simulations are carried out for Primary knock-on Atom (PKA) energies of 5 keV in Fe (at 300 K and 1000 K) and W (at 300 K and 2500 K) and the results are compared using the various methods. - Highlights: • Max-Space Clustering (MSC) method is developed to identify interstitials in crystals. • MSC provides a structured way to identify the temperature dependent cut-off radius. • It is compared with widely used sphere methods and found to be better. • MSC coupled with graph tree optimization can be used to obtain diffusion trajectory. • Cascade simulations of Fe, W are carried out and results are compared with various methods.

Identifying self-interstitials of bcc and fcc crystals in molecular dynamics

Energy Technology Data Exchange (ETDEWEB)

Bukkuru, S., E-mail: srinivasaraobukkuru@gmail.com [Dept. of Nuclear Physics, Andhra University, Visakhapatnam 530003 (India); Bhardwaj, U., E-mail: haptork@gmail.com [Computational Analysis Division, BARC, Visakhapatnam 530012, Andhra Pradesh (India); Warrier, M., E-mail: manoj.warrier@gmail.com [Computational Analysis Division, BARC, Visakhapatnam 530012, Andhra Pradesh (India); Rao, A.D.P., E-mail: adp_rao_99@yahoo.com [Dept. of Nuclear Physics, Andhra University, Visakhapatnam 530003 (India); Valsakumar, M.C., E-mail: mc.valsakumar@gmail.com [IIT Palakkad, Kozhippara P.O., Palakkad 678557, Kerala (India)

2017-02-15

Identification of self-interstitials in molecular dynamics (MD) simulations is of critical importance. There exist several criteria for identifying the self-interstitial. Most of the existing methods use an assumed cut-off value for the displacement of an atom from its lattice position to identify the self-interstitial. The results obtained are affected by the chosen cut-off value. Moreover, these chosen cut-off values are independent of temperature. We have developed a novel unsupervised learning algorithm called Max-Space Clustering (MSC) to identify an appropriate cut-off value and its dependence on temperature. This method is compared with some widely used methods such as effective sphere (ES) method and nearest neighbor sphere (NNS) method. The cut-off radius obtained using our method shows a linear variation with temperature. The value of cut-off radius and its temperature dependence is derived for five bcc (Cr, Fe, Mo, Nb, W) and six fcc (Ag, Au, Cu, Ni, Pd, Pt) crystals. It is seen that the ratio of the cut-off values “r” to the lattice constant “a” lies between 0.23 and 0.3 at 300 K and this ratio is on an average smaller for the fcc crystals. Collision cascade simulations are carried out for Primary knock-on Atom (PKA) energies of 5 keV in Fe (at 300 K and 1000 K) and W (at 300 K and 2500 K) and the results are compared using the various methods. - Highlights: • Max-Space Clustering (MSC) method is developed to identify interstitials in crystals. • MSC provides a structured way to identify the temperature dependent cut-off radius. • It is compared with widely used sphere methods and found to be better. • MSC coupled with graph tree optimization can be used to obtain diffusion trajectory. • Cascade simulations of Fe, W are carried out and results are compared with various methods.

Minimization of Defective Products in The Department of Press Bridge & Rib Through Six Sigma DMAIC Phases

Science.gov (United States)

Rochman, YA; Agustin, A.

2017-06-01

This study proposes the DMAIC Six Sigma approach of Define, Measure, Analyze, Improve/Implement and Control (DMAIC) to minimizing the number of defective products in the bridge & rib department. There are 5 types of defects were the most dominant are broken rib, broken sound board, strained rib, rib sliding and sound board minori. The imperative objective is to improve the quality through the DMAIC phases. In the define phase, the critical to quality (CTQ) parameters was identified minimization of product defects through the pareto chart and FMEA. In this phase, to identify waste based on the current value stream mapping. In the measure phase, the specified control limits product used to maintain the variations of the product, the calculation of the value of DPMO (Defect Per Million Opportunities) and the calculation of the value of sigma level. In analyze phase, determine the type of defect of the most dominant and identify the causes of defective products. In the improve phase, the existing design was modified through various alternative solutions by conducting brainstorming sessions. In this phase, the solution was identified based on the results of FMEA. Improvements were made to the seven priority causes of disability based on the highest RPN value. In the control phase, focusing on improvements to be made. Proposed improvements include making and define standard operating procedures, improving the quality and eliminate waste defective products.

[Molecular updates on Usher syndrome].

Science.gov (United States)

Roux, A-F

2005-01-01

Usher syndrome (USH) is an autosomal recessive disorder characterized by the association of sensorineural hearing loss and retinitis pigmentosa (RP). Usher syndrome is both clinically and genetically heterogeneous. Three clinical subtypes are defined with respect to vestibular dysfunction and the degree of hearing loss. Type I (USH1) patients have profound hearing loss and vestibular dysfunction from birth. Type II (USH2) is the most frequent and patients tend to have less severe hearing impairment and normal vestibular response. Type III (USH3) is characterized by a progressive loss of hearing and is found more frequently among Finnish patients. Recently, major breakthroughs have been made in the molecular genetics of Usher syndrome as a number of chromosomal loci and causative genes have been identified in each clinical subtype. Twelve loci are known and the corresponding genes have been cloned for six of them. Although their functions are not always clearly established, a common role is emerging for the proteins identified within each subtype. As a result, each subtype could emanate from defects affecting distinct cellular mechanisms.

Defects and Disorder in the Drosophila Eye

Science.gov (United States)

Kim, Sangwoo; Carthew, Richard; Hilgenfeldt, Sascha

Cell division and differentiation tightly control the regular pattern in the normal eye of the Drosophila fruit fly while certain genetic mutations introduce disorder in the form of topological defects. Analyzing data from pupal retinas, we develop a model based on Voronoi construction that explains the defect statistics as a consequence of area variation of individual facets (ommatidia). The analysis reveals a previously unknown systematic long-range area variation that spans the entire eye, with distinct effects on topological disorder compared to local fluctuations. The internal structure of the ommatidia and the stiffness of their interior cells also plays a crucial role in the defect generation. Accurate predictions of the correlation between the area variation and the defect density in both normal and mutant animals are obtained without free parameters. This approach can potentially be applied to cellular systems in many other contexts to identify size-topology correlations near the onset of symmetry breaking. This work has been supported by the NIH (GM098077) and the NSF (Grant No. 1504301).

THE SENSORY CHARACTERISTIC DEFECT OF "CACHAÇA" DISTILLED IN ABSENCE OF COOPER

Directory of Open Access Journals (Sweden)

JOãO BOSCO FARIA

2009-07-01

Full Text Available

Sugar cane spirit or "cachaça", the most popular Brazilian beverage, is made by distilling fermented sugar cane juice. When distilled in equipment build without copper, that beverage, may present a particular sulfury sensory defect. In order to identify the compound(s responsable for this defect, paired samples of "cachaça" from the same wine, but distilled in presence and absence of copper, were compared. Based on the composition of the headspace samples determined by HRGC-MS, on sensory characteristic of each component, evaluated by sniffing the GC column effluents and on sensory analysis results, dimethyl sulfide was identified as the main responsable for the sensory defect of cachaça distilled in absence of copper. Results also indicate 4.3-5.2 mg/L of dimethyl sulfide as limit for causing this sensory defect. KEYWORDS: "Cachaça"; dimethyl sulfide; sensory defect; copper and stainless steel distillers.

First-principles engineering of charged defects for two-dimensional quantum technologies

Science.gov (United States)

Wu, Feng; Galatas, Andrew; Sundararaman, Ravishankar; Rocca, Dario; Ping, Yuan

2017-12-01

Charged defects in two-dimensional (2D) materials have emerging applications in quantum technologies such as quantum emitters and quantum computation. The advancement of these technologies requires a rational design of ideal defect centers, demanding reliable computation methods for the quantitatively accurate prediction of defect properties. We present an accurate, parameter-free, and efficient procedure to evaluate the quasiparticle defect states and thermodynamic charge transition levels of defects in 2D materials. Importantly, we solve critical issues that stem from the strongly anisotropic screening in 2D materials, that have so far precluded the accurate prediction of charge transition levels in these materials. Using this procedure, we investigate various defects in monolayer hexagonal boron nitride (h -BN ) for their charge transition levels, stable spin states, and optical excitations. We identify CBVN (nitrogen vacancy adjacent to carbon substitution of boron) to be the most promising defect candidate for scalable quantum bit and emitter applications.

An optimization method for defects reduction in fiber laser keyhole welding

Science.gov (United States)

Ai, Yuewei; Jiang, Ping; Shao, Xinyu; Wang, Chunming; Li, Peigen; Mi, Gaoyang; Liu, Yang; Liu, Wei

2016-01-01

Laser welding has been widely used in automotive, power, chemical, nuclear and aerospace industries. The quality of welded joints is closely related to the existing defects which are primarily determined by the welding process parameters. This paper proposes a defects optimization method that takes the formation mechanism of welding defects and weld geometric features into consideration. The analysis of welding defects formation mechanism aims to investigate the relationship between welding defects and process parameters, and weld features are considered to identify the optimal process parameters for the desired welded joints with minimum defects. The improved back-propagation neural network possessing good modeling for nonlinear problems is adopted to establish the mathematical model and the obtained model is solved by genetic algorithm. The proposed method is validated by macroweld profile, microstructure and microhardness in the confirmation tests. The results show that the proposed method is effective at reducing welding defects and obtaining high-quality joints for fiber laser keyhole welding in practical production.

Drought Tolerance in Pinus halepensis Seed Sources As Identified by Distinctive Physiological and Molecular Markers

OpenAIRE

Taïbi, Khaled; Campo, Antonio D. del; Vilagrosa Carmona, Alberto; Bellés, José M.; López-Gresa, María Pilar; Pla, Davinia; Calvete, Juan J.; López-Nicolás, José M.; Mulet, José M.

2017-01-01

Drought is one of the main constraints determining forest species growth, survival and productivity, and therefore one of the main limitations for reforestation or afforestation. The aim of this study is to characterize the drought response at the physiological and molecular level of different Pinus halepensis (common name Aleppo pine) seed sources, previously characterized in field trials as drought-sensitive or drought-tolerant. This approach aims to identify different traits capable of pre...

Influence of point defects on the near edge structure of hexagonal boron nitride

Science.gov (United States)

McDougall, Nicholas L.; Partridge, Jim G.; Nicholls, Rebecca J.; Russo, Salvy P.; McCulloch, Dougal G.

2017-10-01

Hexagonal boron nitride (hBN) is a wide-band-gap semiconductor with applications including gate insulation layers in graphene transistors, far-ultraviolet light emitting devices and as hydrogen storage media. Due to its complex microstructure, defects in hBN are challenging to identify. Here, we combine x-ray absorption near edge structure (XANES) spectroscopy with ab initio theoretical modeling to identify energetically favorable defects. Following annealing of hBN samples in vacuum and oxygen, the B and N K edges exhibited angular-dependent peak modifications consistent with in-plane defects. Theoretical calculations showed that the energetically favorable defects all produce signature features in XANES. Comparing these calculations with experiments, the principle defects were attributed to substitutional oxygen at the nitrogen site, substitutional carbon at the boron site, and hydrogen passivated boron vacancies. Hydrogen passivation of defects was found to significantly affect the formation energies, electronic states, and XANES. In the B K edge, multiple peaks above the major 1 s to π* peak occur as a result of these defects and the hydrogen passivated boron vacancy produces the frequently observed doublet in the 1 s to σ* transition. While the N K edge is less sensitive to defects, features attributable to substitutional C at the B site were observed. This defect was also calculated to have mid-gap states in its band structure that may be responsible for the 4.1-eV ultraviolet emission frequently observed from this material.

The cardiac proteome in patients with congenital ventricular septal defect: A comparative study between right atria and right ventricles.

Science.gov (United States)

Bond, A R; Iacobazzi, D; Abdul-Ghani, S; Ghorbel, M T; Heesom, K J; George, S J; Caputo, M; Suleiman, M-S; Tulloh, R M

2018-03-20

Right ventricle (RV) remodelling occurs in neonatal patients born with ventricular septal defect (VSD). The presence of a defect between the two ventricles allows for shunting of blood from the left to right side. The resulting RV hypertrophy leads to molecular remodelling which has thus far been largely investigated using right atrial (RA) tissue. In this study we used proteomic and phosphoproteomic analysis in order to determine any difference between the proteomes for RA and RV. Samples were therefore taken from the RA and RV of five infants (0.34 ± 0.05 years, mean ± SEM) with VSD who were undergoing cardiac surgery to repair the defect. Significant differences in protein expression between RV and RA were seen. 150 protein accession numbers were identified which were significantly lower in the atria, whereas none were significantly higher in the atria compared to the ventricle. 19 phosphorylation sites (representing 19 phosphoproteins) were also lower in RA. This work has identified differences in the proteome between RA and RV which reflect differences in contractile activity and metabolism. As such, caution should be used when drawing conclusions based on analysis of the RA and extrapolating to the hypertrophied RV. RV hypertrophy occurs in neonatal patients born with VSD. Very little is known about how the atria responds to RV hypertrophy, especially at the protein level. Access to tissue from age-matched groups of patients is very rare, and we are in the unique position of being able to get tissue from both the atria and ventricle during reparative surgery of these infants. Our findings will be beneficial to future research into heart chamber malformations in congenital heart defects. Copyright © 2018. Published by Elsevier B.V.

Bi-allelic Mutations in PKD1L1 Are Associated with Laterality Defects in Humans.

Science.gov (United States)

Vetrini, Francesco; D'Alessandro, Lisa C A; Akdemir, Zeynep C; Braxton, Alicia; Azamian, Mahshid S; Eldomery, Mohammad K; Miller, Kathryn; Kois, Chelsea; Sack, Virginia; Shur, Natasha; Rijhsinghani, Asha; Chandarana, Jignesh; Ding, Yan; Holtzman, Judy; Jhangiani, Shalini N; Muzny, Donna M; Gibbs, Richard A; Eng, Christine M; Hanchard, Neil A; Harel, Tamar; Rosenfeld, Jill A; Belmont, John W; Lupski, James R; Yang, Yaping

2016-10-06

Disruption of the establishment of left-right (L-R) asymmetry leads to situs anomalies ranging from situs inversus totalis (SIT) to situs ambiguus (heterotaxy). The genetic causes of laterality defects in humans are highly heterogeneous. Via whole-exome sequencing (WES), we identified homozygous mutations in PKD1L1 from three affected individuals in two unrelated families. PKD1L1 encodes a polycystin-1-like protein and its loss of function is known to cause laterality defects in mouse and medaka fish models. Family 1 had one fetus and one deceased child with heterotaxy and complex congenital heart malformations. WES identified a homozygous splicing mutation, c.6473+2_6473+3delTG, which disrupts the invariant splice donor site in intron 42, in both affected individuals. In the second family, a homozygous c.5072G>C (p.Cys1691Ser) missense mutation was detected in an individual with SIT and congenital heart disease. The p.Cys1691Ser substitution affects a highly conserved cysteine residue and is predicted by molecular modeling to disrupt a disulfide bridge essential for the proper folding of the G protein-coupled receptor proteolytic site (GPS) motif. Damaging effects associated with substitutions of this conserved cysteine residue in the GPS motif have also been reported in other genes, namely GPR56, BAI3, and PKD1 in human and lat-1 in C. elegans, further supporting the likely pathogenicity of p.Cys1691Ser in PKD1L1. The identification of bi-allelic PKD1L1 mutations recapitulates previous findings regarding phenotypic consequences of loss of function of the orthologous genes in mice and medaka fish and further expands our understanding of genetic contributions to laterality defects in humans. Copyright © 2016 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Exome sequencing in 32 patients with anophthalmia/microphthalmia and developmental eye defects.

Science.gov (United States)

Slavotinek, A M; Garcia, S T; Chandratillake, G; Bardakjian, T; Ullah, E; Wu, D; Umeda, K; Lao, R; Tang, P L-F; Wan, E; Madireddy, L; Lyalina, S; Mendelsohn, B A; Dugan, S; Tirch, J; Tischler, R; Harris, J; Clark, M J; Chervitz, S; Patwardhan, A; West, J M; Ursell, P; de Alba Campomanes, A; Schneider, A; Kwok, P-Y; Baranzini, S; Chen, R O

2015-11-01

Anophthalmia/microphthalmia (A/M) is a genetically heterogeneous birth defect for which the etiology is unknown in more than 50% of patients. We used exome sequencing with the ACE Exome(TM) (Personalis, Inc; 18 cases) and UCSF Genomics Core (21 cases) to sequence 28 patients with A/M and four patients with varied developmental eye defects. In the 28 patients with A/M, we identified de novo mutations in three patients (OTX2, p.(Gln91His), RARB, p.Arg387Cys and GDF6, p.Ala249Glu) and inherited mutations in STRA6 in two patients. In patients with developmental eye defects, a female with cataracts and cardiomyopathy had a de novo COL4A1 mutation, p.(Gly773Arg), expanding the phenotype associated with COL4A1 to include cardiomyopathy. A male with a chorioretinal defect, microcephaly, seizures and sensorineural deafness had two PNPT1 mutations, p.(Ala507Ser) and c.401-1G>A, and we describe eye defects associated with this gene for the first time. Exome sequencing was efficient for identifying mutations in pathogenic genes for which there is no clinical testing available and for identifying cases that expand phenotypic spectra, such as the PNPT1 and COL4A1-associated disorders described here. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Anisotropic frictional heating and defect generation in cyclotrimethylene-trinitramine molecular crystals

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Rajak, Pankaj; Mishra, Ankit; Sheng, Chunyang; Tiwari, Subodh; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

2018-05-01

Anisotropic frictional response and corresponding heating in cyclotrimethylene-trinitramine molecular crystals are studied using molecular dynamics simulations. The nature of damage and temperature rise due to frictional forces is monitored along different sliding directions on the primary slip plane, (010), and on non-slip planes, (100) and (001). Correlations between the friction coefficient, deformation, and frictional heating are established. We find that the friction coefficients on slip planes are smaller than those on non-slip planes. In response to sliding on a slip plane, the crystal deforms easily via dislocation generation and shows less heating. On non-slip planes, due to the inability of the crystal to deform via dislocation generation, a large damage zone is formed just below the contact area, accompanied by the change in the molecular ring conformation from chair to boat/half-boat. This in turn leads to a large temperature rise below the contact area.

Dirichlet topological defects

International Nuclear Information System (INIS)

Carroll, S.M.; Trodden, M.

1998-01-01

We propose a class of field theories featuring solitonic solutions in which topological defects can end when they intersect other defects of equal or higher dimensionality. Such configurations may be termed open-quotes Dirichlet topological defects,close quotes in analogy with the D-branes of string theory. Our discussion focuses on defects in scalar field theories with either gauge or global symmetries, in 3+1 dimensions; the types of defects considered include walls ending on walls, strings on walls, and strings on strings. copyright 1998 The American Physical Society

Molecular Dynamics Simulations of displacement cascades in metallic systems

International Nuclear Information System (INIS)

Doan, N.V.; Tietze, H.

1995-01-01

We use Molecular Dynamics Computer Simulations to investigate defect production induced by energetic displacement cascades up to 10 keV in pure metals (Cu, Ni) and in ordered intermetallic alloys NiAl, Ni 3 Al. Various model potentials were employed to describe the many-body nature of the interactions: the RGL (Rosato-Guillope-Legrand) model was used in pure Cu and Ni simulations; the modified version of the Vitek, Ackland and Cserti potentials (due to Gao, Bacon and Ackland) in Ni 3 Al and the EAM potentials of Foiles and Daw modified by Rubini and Ballone in NiAl, Ni 3 Al were used in alloy simulations. Atomic mixing and disordering were studied into details owing to imaging techniques and determined at different phases of the cascades. Some mixing mechanisms were identified. Our results were compared with existing data and those obtained by similar Molecular Dynamics Simulations available in the literature. (orig.)

Intra-articular injection of synovium-derived mesenchymal stem cells and hyaluronic acid promote regeneration of massive cartilage defects in rabbits

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Vyacheslav Ogay

2014-01-01

Full Text Available Introduction: The purpose of this study was to investigate whether intra-articular injection of synovium-derived mesenchymal stem cells (SD MSCs with low molecular weight hyaluronic acid (HA could promote regeneration of massive cartilage in rabbits. Material and methods: The SD MSCs were harvested from the knees of 10 Flemish giant rabbits, expanded in culture, and characterized. A reproducible 4-mm cylindrical defect was created in the intercondylar groove area using a kit for the mosaic chondroplasty of femoral condyle COR (De Puy, Mitek. The defect was made within the cartilage layer without destruction of subchondral bone. Two weeks after the cartilage defect, SD MSCs (2 × 106 cell/0.15 ml were suspended in 0.5% low molecular weight HA (0.15 ml and injected into the left knee, and HA solution (0.30 ml alone was placed into the right knee. Cartilage regeneration in the experimental and control groups were evaluated by macroscopically and histologically at 10, 30, and 60 days. Results: On day 10, after intra-articular injection of SD MSCs, we observed an early process of cartilage regeneration in the defect area. Histological studies revealed that cartilage defect was covered by a thin layer of spindle-shaped undifferentiated cells and proliferated chodroblasts. In contrast, an injection of HA did not induce reparation of cartilage in the defect area. At 30 days, macroscopic observation showed that the size of cartilage defect after SD MSC injection was significantly smaller than after HA injection. Histological score was also better in the MSC- treated intercondylar defect. At 60 days after MSC treatment, cartilage defect was nearly nonexistent and looked similar to an intact cartilage. Conclusion: Thus, intra-articular injection of SD MSCs can adhere to the defect in the intercondylar area, and promote cartilage regeneration in rabbits.

Links between environmental geochemistry and rate of birth defects: Shanxi Province, China

Energy Technology Data Exchange (ETDEWEB)

Yu Haiying [State Key Laboratory of Earth Surface Processes and Resource Ecology, School of Geography, Beijing Normal University, Beijing 100875 (China); College of Resources and Environmental Sciences, Sichuan Agricultural University, Ya' an, Sichuan 625014 (China); Zhang Keli, E-mail: keli@bnu.edu.cn [State Key Laboratory of Earth Surface Processes and Resource Ecology, School of Geography, Beijing Normal University, Beijing 100875 (China)

2011-01-01

The rate of birth defects in Shanxi Province is among the highest worldwide. In order to identify the impacts of geochemical and environmental factors on birth defect risk, samples of soil, water and food were collected from an area with an unusually high rate of birth defects (study area) and an area with a low rate of birth defects (control area) in Shanxi Province, China. Element contents were determined by ICP-OES, and the results were analyzed using a non-parametric test and stepwise regression. Differences in the level and distribution of 14 geochemical elements, namely arsenic (As), selenium (Se), molybdenum (Mo), zinc (Zn), strontium (Sr), iron (Fe), tin (Sn), magnesium (Mg), vanadium (V), calcium (Ca), copper (Cu), aluminum (Al), potassium (K) and sulfur (S) were thus compared between the study and control areas. The results reveal that the geochemical element contents in soil, water and food show a significant difference between the study area and control area, and suggest that the study area was characterized by higher S and lower Sr and Al contents. These findings, based on statistical analysis, may be useful in directing further epidemiological investigations identifying the leading causes of birth defects. - Research Highlights: {yields} Environmental geochemistry has an significant impact on birth defects in the regions with an unusually high rate of birth defects. {yields} An excess of S and deficiency of Sr and Al are the distinctive environmental features associated with the high rate of birth defects in the Shanxi Province of China. {yields} Geochemical anomalies is a non-medical basis for effective prevention and cure of birth defects.

Links between environmental geochemistry and rate of birth defects: Shanxi Province, China

International Nuclear Information System (INIS)

Yu Haiying; Zhang Keli

2011-01-01

The rate of birth defects in Shanxi Province is among the highest worldwide. In order to identify the impacts of geochemical and environmental factors on birth defect risk, samples of soil, water and food were collected from an area with an unusually high rate of birth defects (study area) and an area with a low rate of birth defects (control area) in Shanxi Province, China. Element contents were determined by ICP-OES, and the results were analyzed using a non-parametric test and stepwise regression. Differences in the level and distribution of 14 geochemical elements, namely arsenic (As), selenium (Se), molybdenum (Mo), zinc (Zn), strontium (Sr), iron (Fe), tin (Sn), magnesium (Mg), vanadium (V), calcium (Ca), copper (Cu), aluminum (Al), potassium (K) and sulfur (S) were thus compared between the study and control areas. The results reveal that the geochemical element contents in soil, water and food show a significant difference between the study area and control area, and suggest that the study area was characterized by higher S and lower Sr and Al contents. These findings, based on statistical analysis, may be useful in directing further epidemiological investigations identifying the leading causes of birth defects. - Research Highlights: → Environmental geochemistry has an significant impact on birth defects in the regions with an unusually high rate of birth defects. → An excess of S and deficiency of Sr and Al are the distinctive environmental features associated with the high rate of birth defects in the Shanxi Province of China. → Geochemical anomalies is a non-medical basis for effective prevention and cure of birth defects.

Identifying molecular targets of lifestyle modifications in colon cancer prevention

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Molly Marie Derry

2013-05-01

Full Text Available One in four deaths in the United States is cancer-related, and colorectal cancer (CRC is the second leading cause of cancer-associated deaths. Screening strategies are utilized but have not reduced disease incidence or mortality. In this regard, there is an interest in cancer preventive strategies focusing on lifestyle intervention, where specific etiologic factors involved in cancer initiation, promotion, and progression could be targeted. For example, exposure to dietary carcinogens, such as nitrosamines and polycyclic aromatic hydrocarbons influences colon carcinogenesis. Furthermore, dietary deficiencies could alter sensitivity to genetic damage and influence carcinogen metabolism contributing to CRC. High alcohol consumption increases the risk of mutations including the fact that acetaldehyde, an ethanol metabolite, is classified as a group 1 carcinogen. Tobacco smoke exposure is also a risk factor for cancer development; ~20% of CRCs are associated with smoking. Additionally, obese patients have a higher risk of cancer development, which is further supported by the fact that physical activity decreases CRC risk by 55%. Similarly, chronic inflammatory conditions also increase the risk of CRC development. Moreover, the circadian clock alters digestion and regulates other biochemical, physiological and behavioral processes that could positively influence CRC. Taken together, colon carcinogenesis involves a number of etiological factors, and therefore, to create effective preventive strategies, molecular targets need to be identified and beleaguered prior to disease progression. With this in mind, the following is a comprehensive review identifying downstream target proteins of the above lifestyle risk factors, which are modulated during colon carcinogenesis and could be targeted for CRC prevention by novel agents including phytochemicals.

A 6-gene signature identifies four molecular subgroups of neuroblastoma

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Kogner Per

2011-04-01

Full Text Available Abstract Background There are currently three postulated genomic subtypes of the childhood tumour neuroblastoma (NB; Type 1, Type 2A, and Type 2B. The most aggressive forms of NB are characterized by amplification of the oncogene MYCN (MNA and low expression of the favourable marker NTRK1. Recently, mutations or high expression of the familial predisposition gene Anaplastic Lymphoma Kinase (ALK was associated to unfavourable biology of sporadic NB. Also, various other genes have been linked to NB pathogenesis. Results The present study explores subgroup discrimination by gene expression profiling using three published microarray studies on NB (47 samples. Four distinct clusters were identified by Principal Components Analysis (PCA in two separate data sets, which could be verified by an unsupervised hierarchical clustering in a third independent data set (101 NB samples using a set of 74 discriminative genes. The expression signature of six NB-associated genes ALK, BIRC5, CCND1, MYCN, NTRK1, and PHOX2B, significantly discriminated the four clusters (p ALK, BIRC5, and PHOX2B, and was significantly associated with higher tumour stage, poor outcome and poor survival compared to the Type 1-corresponding favourable group (INSS stage 4 and/or dead of disease, p Conclusions Based on expression profiling we have identified four molecular subgroups of neuroblastoma, which can be distinguished by a 6-gene signature. The fourth subgroup has not been described elsewhere, and efforts are currently made to further investigate this group's specific characteristics.

Altered surfactant homeostasis and recurrent respiratory failure secondary to TTF-1 nuclear targeting defect.

Science.gov (United States)

Peca, Donatella; Petrini, Stefania; Tzialla, Chryssoula; Boldrini, Renata; Morini, Francesco; Stronati, Mauro; Carnielli, Virgilio P; Cogo, Paola E; Danhaive, Olivier

2011-08-25

Mutations of genes affecting surfactant homeostasis, such as SFTPB, SFTPC and ABCA3, lead to diffuse lung disease in neonates and children. Haploinsufficiency of NKX2.1, the gene encoding the thyroid transcription factor-1 (TTF-1)--critical for lung, thyroid and central nervous system morphogenesis and function--causes a rare form of progressive respiratory failure designated brain-lung-thyroid syndrome. Molecular mechanisms involved in this syndrome are heterogeneous and poorly explored. We report a novel TTF-1 molecular defect causing recurrent respiratory failure episodes in an infant. The subject was an infant with severe neonatal respiratory distress syndrome followed by recurrent respiratory failure episodes, hypopituitarism and neurological abnormalities. Lung histology and ultrastructure were assessed by surgical biopsy. Surfactant-related genes were studied by direct genomic DNA sequencing and array chromatine genomic hybridization (aCGH). Surfactant protein expression in lung tissue was analyzed by confocal immunofluorescence microscopy. For kinetics studies, surfactant protein B and disaturated phosphatidylcholine (DSPC) were isolated from serial tracheal aspirates after intravenous administration of stable isotope-labeled (2)H(2)O and (13)C-leucine; fractional synthetic rate was derived from gas chromatography/mass spectrometry (2)H and (13)C enrichment curves. Six intubated infants with no primary lung disease were used as controls. Lung biopsy showed desquamative interstitial pneumonitis and lamellar body abnormalities suggestive of genetic surfactant deficiency. Genetic studies identified a heterozygous ABCA3 mutation, L941P, previously unreported. No SFTPB, SFTPC or NKX2.1 mutations or deletions were found. However, immunofluorescence studies showed TTF-1 prevalently expressed in type II cell cytoplasm instead of nucleus, indicating defective nuclear targeting. This pattern has not been reported in human and was not found in two healthy controls and

Altered surfactant homeostasis and recurrent respiratory failure secondary to TTF-1 nuclear targeting defect

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Carnielli Virgilio P

2011-08-01

Full Text Available Abstract Background Mutations of genes affecting surfactant homeostasis, such as SFTPB, SFTPC and ABCA3, lead to diffuse lung disease in neonates and children. Haploinsufficiency of NKX2.1, the gene encoding the thyroid transcription factor-1 (TTF-1 - critical for lung, thyroid and central nervous system morphogenesis and function - causes a rare form of progressive respiratory failure designated brain-lung-thyroid syndrome. Molecular mechanisms involved in this syndrome are heterogeneous and poorly explored. We report a novel TTF-1 molecular defect causing recurrent respiratory failure episodes in an infant. Methods The subject was an infant with severe neonatal respiratory distress syndrome followed by recurrent respiratory failure episodes, hypopituitarism and neurological abnormalities. Lung histology and ultrastructure were assessed by surgical biopsy. Surfactant-related genes were studied by direct genomic DNA sequencing and array chromatine genomic hybridization (aCGH. Surfactant protein expression in lung tissue was analyzed by confocal immunofluorescence microscopy. For kinetics studies, surfactant protein B and disaturated phosphatidylcholine (DSPC were isolated from serial tracheal aspirates after intravenous administration of stable isotope-labeled 2H2O and 13C-leucine; fractional synthetic rate was derived from gas chromatography/mass spectrometry 2H and 13C enrichment curves. Six intubated infants with no primary lung disease were used as controls. Results Lung biopsy showed desquamative interstitial pneumonitis and lamellar body abnormalities suggestive of genetic surfactant deficiency. Genetic studies identified a heterozygous ABCA3 mutation, L941P, previously unreported. No SFTPB, SFTPC or NKX2.1 mutations or deletions were found. However, immunofluorescence studies showed TTF-1 prevalently expressed in type II cell cytoplasm instead of nucleus, indicating defective nuclear targeting. This pattern has not been reported in human

First Trimester Influenza Vaccination and Risks for Major Structural Birth Defects in Offspring.

Science.gov (United States)

Kharbanda, Elyse Olshen; Vazquez-Benitez, Gabriela; Romitti, Paul A; Naleway, Allison L; Cheetham, T Craig; Lipkind, Heather S; Klein, Nicola P; Lee, Grace; Jackson, Michael L; Hambidge, Simon J; McCarthy, Natalie; DeStefano, Frank; Nordin, James D

2017-08-01

To examine risks for major structural birth defects in infants after first trimester inactivated influenza vaccine (IIV) exposures. In this observational study, we used electronic health data from 7 Vaccine Safety Datalink sites to examine risks for selected major structural defects in infants after maternal IIV exposure. Vaccine exposures for women with continuous insurance enrollment through pregnancy who delivered singleton live births between 2004 and 2013 were identified from standardized files. Infants with continuous insurance enrollment were followed to 1 year of age. We excluded mother-infant pairs with other exposures that potentially increased their background risk for birth defects. Selected cardiac, orofacial or respiratory, neurologic, ophthalmologic or otologic, gastrointestinal, genitourinary and muscular or limb defects were identified from diagnostic codes in infant medical records using validated algorithms. Propensity score adjusted generalized estimating equations were used to estimate prevalence ratios (PRs). We identified 52 856 infants with maternal first trimester IIV exposure and 373 088 infants whose mothers were unexposed to IIV during first trimester. Prevalence (per 100 live births) for selected major structural birth defects was 1.6 among first trimester IIV exposed versus 1.5 among unexposed mothers. The adjusted PR was 1.02 (95% CI 0.94-1.10). Organ system-specific PRs were similar to the overall PR. First trimester maternal IIV exposure was not associated with an increased risk for selected major structural birth defects in this large cohort of singleton live births. Copyright © 2017 Elsevier Inc. All rights reserved.

Effect of hydrogen adsorption on the formation and annealing of Stone-Wales defects in graphene

Science.gov (United States)

Podlivaev, A. I.; Openov, L. A.

2015-12-01

The heights of energy barriers preventing the formation and annealing of Stone-Wales defects in graphene with a hydrogen atom adsorbed on the defect or in its immediate vicinity have been calculated using the atomistic computer simulation. It has been shown that, in the presence of hydrogen, both barriers are significantly lower than those in the absence of hydrogen. Based on the analysis of the potential energy surface, the frequency factors have been calculated for two different paths of the Stone-Wales transformation, and the temperature dependences of the corresponding annealing times of the defects have been found. The results obtained have been compared with the first-principles calculations and molecular dynamics data.

Single nickel-related defects in molecular-sized nanodiamonds for multicolor bioimaging: an ab initio study

Science.gov (United States)

Thiering, Gergő; Londero, Elisa; Gali, Adam

2014-09-01

Fluorescent nanodiamonds constitute an outstanding alternative to semiconductor quantum dots and dye molecules for in vivo biomarker applications, where the fluorescence comes from optically active point defects acting as color centers in the nanodiamonds. For practical purposes, these color centers should be photostable as a function of the laser power or the surface termination of nanodiamonds. Furthermore, they should exhibit a sharp and nearly temperature-independent zero-phonon line. In this study, we show by hybrid density functional theory calculations that nickel doped nanodiamonds exhibit the desired properties, thus opening the avenue to practical applications. In particular, harnessing the strong quantum confinement effect in molecule-sized nanodiamonds is very promising for achieving multicolor imaging by single nickel-related defects.

Single nickel-related defects in molecular-sized nanodiamonds for multicolor bioimaging: an ab initio study.

Science.gov (United States)

Thiering, Gergő; Londero, Elisa; Gali, Adam

2014-10-21

Fluorescent nanodiamonds constitute an outstanding alternative to semiconductor quantum dots and dye molecules for in vivo biomarker applications, where the fluorescence comes from optically active point defects acting as color centers in the nanodiamonds. For practical purposes, these color centers should be photostable as a function of the laser power or the surface termination of nanodiamonds. Furthermore, they should exhibit a sharp and nearly temperature-independent zero-phonon line. In this study, we show by hybrid density functional theory calculations that nickel doped nanodiamonds exhibit the desired properties, thus opening the avenue to practical applications. In particular, harnessing the strong quantum confinement effect in molecule-sized nanodiamonds is very promising for achieving multicolor imaging by single nickel-related defects.

Defect forces, defect couples and path integrals in fracture mechanics

International Nuclear Information System (INIS)

Roche, R.L.

1979-07-01

In this work, it is shown that the path integrals can be introduced without any reference to the material behavior. The method is based on the definition in a continuous medium of a set of vectors and couples having the dimension of a force or a moment. More precisely, definitions are given of volume defect forces, surface defect forces, volume defect couples, and surface defect couples. This is done with the help of the stress working variation of a particule moving through the solid. The most important result is: the resultant of all the defect forces included in a volume V is the J integral on the surface surrounding V and the moment resultant is the L integral. So these integrals are defined without any assumption on the material constitutive equation. Another result is the material form of the virtual work principle - defect forces are acting like conventional forces in the conventional principles of virtual work. This lead to the introduction of the energy momentum tensor and of the associated couple stress. Application of this method is made to fracture mechanics in studying the defect forces distribution around a crack [fr

Electron and molecular ion collisions relevant to divertor plasma

International Nuclear Information System (INIS)

Takagi, H.

2005-01-01

We introduce the concept of the multi-channel quantum defect theory (MQDT) and show the outline of the MQDT newly extended to include the dissociative states. We investigate some molecular processes relevant to the divertor plasma by using the MQDT: the dissociative recombination, dissociative excitation, and rotation-vibrational transition in the hydrogen molecular ion and electron collisions. (author)

Neural Tube Defects

Science.gov (United States)

Neural tube defects are birth defects of the brain, spine, or spinal cord. They happen in the ... that she is pregnant. The two most common neural tube defects are spina bifida and anencephaly. In ...

Sigma models in the presence of dynamical point-like defects

International Nuclear Information System (INIS)

Doikou, Anastasia; Karaiskos, Nikos

2013-01-01

Point-like Liouville integrable dynamical defects are introduced in the context of the Landau–Lifshitz and Principal Chiral (Faddeev–Reshetikhin) models. Based primarily on the underlying quadratic algebra we identify the first local integrals of motion, the associated Lax pairs as well as the relevant sewing conditions around the defect point. The involution of the integrals of motion is shown taking into account the sewing conditions.

Characteristics Associated With Active Defects in Juvenile Spondylolysis.

Science.gov (United States)

Gum, Jeffrey L; Crawford, Charles H; Collis, Philip C; Carreon, Leah Y

2015-10-01

Diagnosis is crucial in early-stage lumbar spondylolysis, as osseous healing can occur with conservative treatment. Single-photon emission computed tomography (SPECT) traditionally has been the most sensitive modality for diagnosing active (early) spondylolysis. More recently, high signal change (HSC) in the pedicle or pars interarticularis on fluid-specific (T2) magnetic resonance imaging (MRI) has been shown to be important in the diagnosis of early spondylolysis. We conducted a study to determine the clinical and radiographic characteristics associated with the diagnosis of early or active spondylolysis. Fifty-seven patients with a total of 108 pars defects and a mean age of 14.6 years were retrospectively identified. Defects with a positive SPECT or HSC on T2 MRI were classified as active. There were 49 active and 59 inactive defects. The active and inactive groups did not differ in age, body mass index, symptom duration, lumbar lordosis, pelvic incidence, slip percentage, or laterality. There was a difference in sex (35 vs 19 males; P spondylolysis appears to be associated with male patients and the absence of listhesis, which may be important in identifying patients with a higher potential to experience osseous healing with nonoperative treatment.

High defect stage, contralateral defects, and poor flexibility are negative predictive factors of bone union in pediatric and adolescent athletes with spondylolysis.

Science.gov (United States)

Yamazaki, Kazufumi; Kota, Shintaro; Oikawa, Daisuke; Suzuki, Yoshiji

2018-01-01

To identify predisposition to spondylolysis and physical characteristics associated with "bone union" following conservative spondylolysis treatment among pediatric and adolescent athletes. We retrospectively analyzed pediatric and adolescent athletes with spondylolysis who underwent conservative treatment and rehabilitation for three or more consecutive months following sports activity cessation. Patients with terminal spondylolysis or who did not discontinue sports activities were excluded. We compared physical fitness factors in the union and nonunion groups and examined the association between bone union and spondylolysis severity by logistic regression analysis. Of 183 patients with spondylolysis who underwent rehabilitation over a four-year period, 127 patients with 227 defects were included in the final analysis. Bone union was achieved in 66.5% (151/227) of the pars interarticularis defects and 70.1% (89/127) of the patients. On multivariate analysis, stage of pars interarticularis defect (odds ratio [OR], 0.26;p = 0.0027), stage of contralateral pars interarticularis defect (OR, 0.51;p = 0.00026), and straight leg-raising test (OR, 1.06;p = 0.028) were significantly associated with bone union. High defect stage, stage of the contralateral pars interarticularis defect, and poor flexibility were negative prognostic factors of bone healing in athletes with spondylolysis. J. Med. Invest. 65:126-130, February, 2018.

Computational modeling of the behavior of nuclear materials (2). Molecular simulations for nuclear materials. Current situation and future perspective

International Nuclear Information System (INIS)

Okita, Taira; Itakura, Mitsuhiro

2017-01-01

Molecular simulations for nuclear materials aim to reproduce atomistic-scale phenomena induced by irradiation and infer the change in material properties. In the present work, recent progress in this field is presented. In particular, the following three topics are explained: (1) Quantification of lattice defects formation process induced by fast neutron collision. (2) Identification of dislocation-channeling mechanism induced by interactions between defect clusters and dislocations. (3) Modeling of the three dimensional movement of defect clusters using molecular dynamics and kinetic Monte Carlo simulations. (author)

Paternal uniparental isodisomy of the entire chromosome 20 as a molecular cause of pseudohypoparathyroidism type Ib (PHP-Ib).

Science.gov (United States)

Bastepe, Murat; Altug-Teber, Ozge; Agarwal, Chhavi; Oberfield, Sharon E; Bonin, Michael; Jüppner, Harald

2011-03-01

Pseudohypoparathyoridism type Ib (PHP-Ib) typically defines the presence of end-organ resistance to parathyroid hormone in the absence of Albright's hereditary osteodystrophy. Patients affected by this disorder present with imprinting defects in the complex GNAS locus. Microdeletions within STX16 or GNAS have been identified in familial cases with PHP-Ib, but the molecular cause of the GNAS imprinting defects in sporadic PHP-Ib cases remains poorly defined. We now report a case with sporadic PHP-Ib for whom a SNPlex analysis revealed loss of the maternal GNAS allele. Further analysis of the entire genome with a 100K SNP chip identified a paternal uniparental isodisomy affecting the entire chromosome 20 without evidence for another chromosomal abnormality. Our findings explain the observed GNAS methylation changes and the patient's hormone resistance, and furthermore suggest that chromosome 20 harbors, besides GNAS, no additional imprinted region that contributes to the clinical and laboratory phenotype. Copyright © 2010 Elsevier Inc. All rights reserved.

New technique of identifying the hierarchy of dynamic domains in proteins using a method of molecular dynamics simulations

Directory of Open Access Journals (Sweden)

Yesylevskyy S. O.

2010-04-01

Full Text Available Aim. Despite a large number of existing domain identification techniques there is no universally accepted method, which identifies the hierarchy of dynamic domains using the data of molecular dynamics (MD simulations. The goal of this work is to develop such technique. Methods. The dynamic domains are identified by eliminating systematic motions from MD trajectories recursively in a model-free manner. Results. The technique called the Hierarchical Domain-Wise Alignment (HDWA to identify hierarchically organized dynamic domains in proteins using the MD trajectories has been developed. Conclusion. A new method of domain identification in proteins is proposed

Probing molecular mechanisms of the Hsp90 chaperone: biophysical modeling identifies key regulators of functional dynamics.

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Anshuman Dixit

Full Text Available Deciphering functional mechanisms of the Hsp90 chaperone machinery is an important objective in cancer biology aiming to facilitate discovery of targeted anti-cancer therapies. Despite significant advances in understanding structure and function of molecular chaperones, organizing molecular principles that control the relationship between conformational diversity and functional mechanisms of the Hsp90 activity lack a sufficient quantitative characterization. We combined molecular dynamics simulations, principal component analysis, the energy landscape model and structure-functional analysis of Hsp90 regulatory interactions to systematically investigate functional dynamics of the molecular chaperone. This approach has identified a network of conserved regions common to the Hsp90 chaperones that could play a universal role in coordinating functional dynamics, principal collective motions and allosteric signaling of Hsp90. We have found that these functional motifs may be utilized by the molecular chaperone machinery to act collectively as central regulators of Hsp90 dynamics and activity, including the inter-domain communications, control of ATP hydrolysis, and protein client binding. These findings have provided support to a long-standing assertion that allosteric regulation and catalysis may have emerged via common evolutionary routes. The interaction networks regulating functional motions of Hsp90 may be determined by the inherent structural architecture of the molecular chaperone. At the same time, the thermodynamics-based "conformational selection" of functional states is likely to be activated based on the nature of the binding partner. This mechanistic model of Hsp90 dynamics and function is consistent with the notion that allosteric networks orchestrating cooperative protein motions can be formed by evolutionary conserved and sparsely connected residue clusters. Hence, allosteric signaling through a small network of distantly connected

Radiographic detection of artificial intra-bony defects in the edentulous area.

Science.gov (United States)

Van Assche, N; Jacobs, R; Coucke, W; van Steenberghe, D; Quirynen, M

2009-03-01

Since intra-bony pathologies might jeopardize implant outcome, their preoperative detection is crucial. In sixteen human cadaver bloc sections from upper and lower jaws, artificial defects with progressively increasing size (n=7) have been created. From each respective defect, analogue and digital intra-oral radiographs were taken, the latter processed via a periodontal filter and afterwards presented in black-white as well as in colour, resulting in three sets of 7 images per bloc section. Eight observers were asked to diagnosis an eventual defect on randomly presented radiographs, and at another occasion to rank each set based on the defect size. The clinicians were only able to identify a defect, when the junctional area was involved, except for bony pieces with a very homogeneous structure. For longitudinal evaluation of healing bone (e.g. after tooth extraction), colour digital images can be recommended. These observations indicate that intra-oral radiographs are not always reliable for the detection of any intra-bony defect.

Ferromagnetically coupled local moments along an extended line defect in graphene

Science.gov (United States)

White, Carter T.; Vasudevan, Smitha; Gunlycke, Daniel

2011-03-01

Recently an extended line defect was observed composed of octagonal and pentagonal carbon rings embedded in a graphene sheet [Nat. Nanotech. 5, 326 (2010)]. We report results of studies we have made of this defect using both first-principles and semi-empirical methods. Two types of boundary-localized states arising from the defect are identified. The first (second) type has eigenstates with wavefunctions that are anti- symmetric (symmetric) with respect to a mirror plane that is perpendicular to the graphene sheet and passes through the line defect center line. The boundary-localized anti-symmetric states are shown to be intimately connected to the zigzag edge states of semi-infinite graphene. They exhibit little dispersion along the defect line and lie close to the Fermi level giving rise to a spontaneous spin polarization along the defect once electron-electron interactions are included at the level of a mean field approximation to a Hubbard Model. Within this approach, symmetry requires that the principal moments couple ferromagnetically both along and across the line defect leading to approximately 2/3 more up than down spin electrons per defect repeat unit. This work was supported by ONR, directly and through NRL.

Characterization of structural defects in SnSe2 thin films grown by molecular beam epitaxy on GaAs (111)B substrates

Science.gov (United States)

Tracy, Brian D.; Li, Xiang; Liu, Xinyu; Furdyna, Jacek; Dobrowolska, Margaret; Smith, David J.

2016-11-01

Tin selenide thin films have been grown by molecular beam epitaxy on GaAs (111)B substrates at a growth temperature of 150 °C, and a microstructural study has been carried out, primarily using the technique of transmission electron microscopy. The Se:Sn flux ratio during growth was systematically varied and found to have a strong impact on the resultant crystal structure and quality. Low flux ratios (Se:Sn=3:1) led to defective films consisting primarily of SnSe, whereas high flux ratios (Se:Sn>10:1) gave higher quality, single-phase SnSe2. The structure of the monoselenide films was found to be consistent with the Space Group Pnma with the epitaxial growth relationship of [011]SnSe// [ 1 1 bar 0 ] GaAs, while the diselenide films were consistent with the Space Group P 3 bar m1 , and had the epitaxial growth relationship [ 2 1 bar 1 bar 0 ]SnSe2// [ 1 1 bar 0 ] GaAs.

Eisenmenger ventricular septal defect in a Humboldt penguin (Spheniscus humboldti).

Science.gov (United States)

Laughlin, D S; Ialeggio, D M; Trupkiewicz, J G; Sleeper, M M

2016-09-01

The Eisenmenger ventricular septal defect is an uncommon type of ventricular septal defect characterised in humans by a traditionally perimembranous ventricular septal defect, anterior deviation (cranioventral deviation in small animal patients) of the muscular outlet septum causing malalignment relative to the remainder of the muscular septum, and overriding of the aortic valve. This anomaly is reported infrequently in human patients and was identified in a 45-day-old Humboldt Penguin, Spheniscus humboldti, with signs of poor growth and a cardiac murmur. This case report describes the findings in this penguin and summarises the anatomy and classification of this cardiac anomaly. To the authors' knowledge this is the first report of an Eisenmenger ventricular septal defect in a veterinary patient. Copyright © 2016 Elsevier B.V. All rights reserved.

Revealing the properties of defects formed by CH3NH2 molecules in organic-inorganic hybrid perovskite MAPbBr3

Science.gov (United States)

Wang, Ji; Zhang, Ao; Yan, Jun; Li, Dan; Chen, Yunlin

2017-03-01

The properties of defects in organic-inorganic hybrid perovskite are widely studied from the first-principles calculation. However, the defects of methylamine (methylamine = CH3NH2), which would be easily formed during the preparation of the organic-inorganic hybrid perovskite, are rarely investigated. Thermodynamic properties as well as defect states of methylamine embedded MAPbX3 (MA = methyl-ammonium = CH3NH3, X = Br, I) are studied based on first-principles calculations of density functional theory. It was found that there is a shallow defect level near the highest occupied molecular orbital, which induced by the interstitial methylamine defect in MAPbBr3, will lead to an increase of photoluminescence. The calculation results showed that interstitial defect states of methylamine may move deeper due to the interaction between methylamine molecules and methyl-ammonium cations. It was also showed that the interstitial methylamine defect is stable at room temperature, and the defect can be removed easily by annealing.

Defect evolution in a Ni−Mo−Cr−Fe alloy subjected to high-dose Kr ion irradiation at elevated temperature

Energy Technology Data Exchange (ETDEWEB)

Reyes, Massey de los [Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, 2234 (Australia); Nuclear Fuel Cycle Royal Commission (NFCRC), 50 Grenfell Street Adelaide South Australia, 5000 (Australia); Voskoboinikov, Roman [The National Research Centre ‘Kurchatov Institute’, Kurchatov Sq 1, Moscow 123182 (Russian Federation); Kirk, Marquis A. [Nuclear Engineering Division, Argonne National Laboratory, Argonne, IL 60439 (United States); Huang, Hefei [Shanghai Institute of Applied Physics, Chinese Academy of Science (CAS), 2019 Jialuo Road, Jiading District, Shanghai 201800 (China); Lumpkin, Greg [Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, 2234 (Australia); Bhattacharyya, Dhriti, E-mail: dhriti.bhattacharyya@ansto.gov.au [Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, 2234 (Australia)

2016-06-15

A candidate Ni−Mo−Cr−Fe alloy (GH3535) for application as a structural material in a molten salt nuclear reactor was irradiated with 1 MeV Kr{sup 2+} ions (723 K, max dose of 100 dpa) at the IVEM-Tandem facility. The evolution of defects like dislocation loops and vacancy- and self-interstitial clusters was examined in-situ. For obtaining a deeper insight into the true nature of these defects, the irradiated sample was further analysed under a TEM post-facto. The results show that there is a range of different types of defects formed under irradiation. Interaction of radiation defects with each other and with pre-existing defects, e.g., linear dislocations, leads to the formation of complex microstructures. Molecular dynamics simulations used to obtain a greater understanding of these defect transformations showed that the interaction between linear dislocations and radiation induced dislocation loops could form faulted structures that explain the fringed contrast of these defects observed in TEM.

The electronic and optical properties of amorphous silica with hydrogen defects by ab initio calculations

Science.gov (United States)

Ren, Dahua; Xiang, Baoyan; Hu, Cheng; Qian, Kai; Cheng, Xinlu

2018-04-01

Hydrogen can be trapped in the bulk materials in four forms: interstitial molecular H2, interstitial atom H, O‑H+(2Si=O–H)+, Si‑H‑( {{4O}}\\bar \\equiv {{Si&x2212H}})‑ to affect the electronic and optical properties of amorphous silica. Therefore, the electronic and optical properties of defect-free and hydrogen defects in amorphous silica were performed within the scheme of density functional theory. Initially, the negative charged states hydrogen defects introduced new defect level between the valence band top and conduction band bottom. However, the neutral and positive charged state hydrogen defects made both the valence band and conduction band transfer to the lower energy. Subsequently, the optical properties such as absorption spectra, conductivity and loss functions were analyzed. It is indicated that the negative hydrogen defects caused the absorption peak ranging from 0 to 2.0 eV while the positive states produced absorption peaks at lower energy and two strong absorption peaks arose at 6.9 and 9.0 eV. However, the neutral hydrogen defects just improved the intensity of absorption spectrum. This may give insights into understanding the mechanism of laser-induced damage for optical materials. Project supported by the Science and Technology of Hubei Provincial Department of Education (No. B2017098).

Computer simulations of liquid crystals: Defects, deformations and dynamics

Science.gov (United States)

Billeter, Jeffrey Lee

1999-11-01

Computer simulations play an increasingly important role in investigating fundamental issues in the physics of liquid crystals. Presented here are the results of three projects which utilize the unique power of simulations to probe questions which neither theory nor experiment can adequately answer. Throughout, we use the (generalized) Gay-Berne model, a widely-used phenomenological potential which captures the essential features of the anisotropic mesogen shapes and interactions. First, we used a Molecular Dynamics simulation with 65536 Gay-Berne particles to study the behaviors of topological defects in a quench from the isotropic to the nematic phase. Twist disclination loops were the dominant defects, and we saw evidence for dynamical scaling. We observed the loops separating, combining and collapsing, and we also observed numerous non-singular type-1 lines which appeared to be intimately involved with many of the loop processes. Second, we used a Molecular Dynamics simulation of a sphere embedded in a system of 2048 Gay-Berne particles to study the effects of radial anchoring of the molecules at the sphere's surface. A saturn ring defect configuration was observed, and the ring caused a driven sphere (modelling the falling ball experiment) to experience an increased resistance as it moved through the nematic. Deviations from a linear relationship between the driving force and the terminal speed are attributed to distortions of the saturn ring which we observed. The existence of the saturn ring confirms theoretical predictions for small spheres. Finally, we constructed a model for wedge-shaped molecules and used a linear response approach in a Monte Carlo simulation to investigate the flexoelectric behavior of a system of 256 such wedges. Novel potential models as well as novel analytical and visualization techniques were developed for these projects. Once again, the emphasis throughout was to investigate questions which simulations alone can adequately answer.

On holographic defect entropy

International Nuclear Information System (INIS)

Estes, John; Jensen, Kristan; O’Bannon, Andy; Tsatis, Efstratios; Wrase, Timm

2014-01-01

We study a number of (3+1)- and (2+1)-dimensional defect and boundary conformal field theories holographically dual to supergravity theories. In all cases the defects or boundaries are planar, and the defects are codimension-one. Using holography, we compute the entanglement entropy of a (hemi-)spherical region centered on the defect (boundary). We define defect and boundary entropies from the entanglement entropy by an appropriate background subtraction. For some (3+1)-dimensional theories we find evidence that the defect/boundary entropy changes monotonically under certain renormalization group flows triggered by operators localized at the defect or boundary. This provides evidence that the g-theorem of (1+1)-dimensional field theories generalizes to higher dimensions

Defects in Nicotinamide-adenine Dinucleotide Phosphate Oxidase Genes NOX1 and DUOX2 in Very Early Onset Inflammatory Bowel DiseaseSummary

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Patti Hayes

2015-09-01

Full Text Available Background & Aims: Defects in intestinal innate defense systems predispose patients to inflammatory bowel disease (IBD. Reactive oxygen species (ROS generated by nicotinamide-adenine dinucleotide phosphate (NADPH oxidases in the mucosal barrier maintain gut homeostasis and defend against pathogenic attack. We hypothesized that molecular genetic defects in intestinal NADPH oxidases might be present in children with IBD. Methods: After targeted exome sequencing of epithelial NADPH oxidases NOX1 and DUOX2 on 59 children with very early onset inflammatory bowel disease (VEOIBD, the identified mutations were validated using Sanger Sequencing. A structural analysis of NOX1 and DUOX2 variants was performed by homology in silico modeling. The functional characterization included ROS generation in model cell lines and in in vivo transduced murine crypts, protein expression, intracellular localization, and cell-based infection studies with the enteric pathogens Campylobacter jejuni and enteropathogenic Escherichia coli. Results: We identified missense mutations in NOX1 (c.988G>A, p.Pro330Ser; c.967G>A, p.Asp360Asn and DUOX2 (c.4474G>A, p.Arg1211Cys; c.3631C>T, p.Arg1492Cys in 5 of 209 VEOIBD patients. The NOX1 p.Asp360Asn variant was replicated in a male Ashkenazi Jewish ulcerative colitis cohort. Patients with both NOX1 and DUOX2 variants showed abnormal Paneth cell metaplasia. All NOX1 and DUOX2 variants showed reduced ROS production compared with wild-type enzymes. Despite appropriate cellular localization and comparable pathogen-stimulated translocation of altered oxidases, cells harboring NOX1 or DUOX2 variants had defective host resistance to infection with C. jejuni. Conclusions: This study identifies the first inactivating missense variants in NOX1 and DUOX2 associated with VEOIBD. Defective ROS production from intestinal epithelial cells constitutes a risk factor for developing VEOIBD. Keywords: Inflammatory Bowel Disease, NADPH Oxidase

Evaluation of condyle defects using different reconstruction protocols of cone-beam computed tomography

International Nuclear Information System (INIS)

Bastos, Luana Costa; Campos, Paulo Sergio Flores; Ramos-Perez, Flavia Maria de Moraes; Pontual, Andrea dos Anjos; Almeida, Solange Maria

2013-01-01

This study was conducted to investigate how well cone-beam computed tomography (CBCT) can detect simulated cavitary defects in condyles, and to test the influence of the reconstruction protocols. Defects were created with spherical diamond burs (numbers 1013, 1016, 3017) in superior and / or posterior surfaces of twenty condyles. The condyles were scanned, and cross-sectional reconstructions were performed with nine different protocols, based on slice thickness (0.2, 0.6, 1.0 mm) and on the filters (original image, Sharpen Mild, S9) used. Two observers evaluated the defects, determining their presence and location. Statistical analysis was carried out using simple Kappa coefficient and McNemar’s test to check inter- and intra-rater reliability. The chi-square test was used to compare the rater accuracy. Analysis of variance (Tukey's test) assessed the effect of the protocols used. Kappa values for inter- and intra-rater reliability demonstrate almost perfect agreement. The proportion of correct answers was significantly higher than that of errors for cavitary defects on both condyle surfaces (p < 0.01). Only in identifying the defects located on the posterior surface was it possible to observe the influence of the 1.0 mm protocol thickness and no filter, which showed a significantly lower value. Based on the results of the current study, the technique used was valid for identifying the existence of cavities in the condyle surface. However, the protocol of a 1.0 mm-thick slice and no filter proved to be the worst method for identifying the defects on the posterior surface. (author)

Intrinsic and extrinsic defects in a family of coal-derived graphene quantum dots

Science.gov (United States)

Singamaneni, Srinivasa Rao; van Tol, Johan; Ye, Ruquan; Tour, James M.

2015-11-01

In this letter, we report on the high frequency (239.2 and 336 GHz) electron spin resonance (ESR) studies performed on graphene quantum dots (GQDs), prepared through a wet chemistry route from three types of coal: (a) bituminous, (b) anthracite, and (c) coke; and from non-coal derived GQDs. The microwave frequency-, power-, and temperature-dependent ESR spectra coupled with computer-aided simulations reveal four distinct magnetic defect centers. In bituminous- and anthracite-derived GQDs, we have identified two of them as intrinsic carbon-centered magnetic defect centers (a broad signal of peak to peak width = 697 (10-4 T), g = 2.0023; and a narrow signal of peak to peak width = 60 (10-4 T), g = 2.003). The third defect center is Mn2+ (6S5/2, 3d5) (signal width = 61 (10-4 T), g = 2.0023, Aiso = 93(10-4 T)), and the fourth defect is identified as Cu2+ (2D5/2, 3d9) (g⊥ = 2.048 and g‖ = 2.279), previously undetected. Coke-derived and non-coal derived GQDs show Mn2+ and two-carbon related signals, and no Cu2+ signal. The extrinsic impurities most likely originate from the starting coal. Furthermore, Raman, photoluminescence, and ESR measurements detected no noticeable changes in the properties of the bituminous GQDs after one year. This study highlights the importance of employing high frequency ESR spectroscopy in identifying the (magnetic) defects, which are roadblocks for spin relaxation times of graphene-based materials. These defects would not have been possible to probe by other spin transport measurements.

Evaluation of condyle defects using different reconstruction protocols of cone-beam computed tomography

Energy Technology Data Exchange (ETDEWEB)

Bastos, Luana Costa; Campos, Paulo Sergio Flores, E-mail: bastosluana@ymail.com [Universidade Federal da Bahia (UFBA), Salvador, BA (Brazil). Fac. de Odontologia. Dept. de Radiologia Oral e Maxilofacial; Ramos-Perez, Flavia Maria de Moraes [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Fac. de Odontologia. Dept. de Clinica e Odontologia Preventiva; Pontual, Andrea dos Anjos [Universidade Federal de Pernambuco (UFPE), Camaragibe, PE (Brazil). Fac. de Odontologia. Dept. de Radiologia Oral; Almeida, Solange Maria [Universidade Estadual de Campinas (UNICAMP), Piracicaba, SP (Brazil). Fac. de Odontologia. Dept. de Radiologia Oral

2013-11-15

This study was conducted to investigate how well cone-beam computed tomography (CBCT) can detect simulated cavitary defects in condyles, and to test the influence of the reconstruction protocols. Defects were created with spherical diamond burs (numbers 1013, 1016, 3017) in superior and / or posterior surfaces of twenty condyles. The condyles were scanned, and cross-sectional reconstructions were performed with nine different protocols, based on slice thickness (0.2, 0.6, 1.0 mm) and on the filters (original image, Sharpen Mild, S9) used. Two observers evaluated the defects, determining their presence and location. Statistical analysis was carried out using simple Kappa coefficient and McNemar’s test to check inter- and intra-rater reliability. The chi-square test was used to compare the rater accuracy. Analysis of variance (Tukey's test) assessed the effect of the protocols used. Kappa values for inter- and intra-rater reliability demonstrate almost perfect agreement. The proportion of correct answers was significantly higher than that of errors for cavitary defects on both condyle surfaces (p < 0.01). Only in identifying the defects located on the posterior surface was it possible to observe the influence of the 1.0 mm protocol thickness and no filter, which showed a significantly lower value. Based on the results of the current study, the technique used was valid for identifying the existence of cavities in the condyle surface. However, the protocol of a 1.0 mm-thick slice and no filter proved to be the worst method for identifying the defects on the posterior surface. (author)

Derivation of kinetic coefficients by atomistic methods for studying defect behavior in Mo

International Nuclear Information System (INIS)

Insepov, Z.; Rest, J.; Yacout, A.M.; Kuksin, A.Yu.; Norman, G.E.; Stegailov, V.V.; Starikov, S.V.; Yanilkin, A.V.

2012-01-01

Highlights: ► A multiscale concept couples molecular dynamics (MD) with ab initio and kinetic rate theory. ► Evolution of a system of self-interstitial atoms and vacancies in Mo is studied by MD. ► Formation of di-SIA clusters and SIA–vacancy recombination is analyzed. ► 1D diffusion of self-interstitials at various temperature and defect concentrations were studied. ► This paper provides a powerful predictive tool for simulating irradiation of nuclear materials. - Abstract: A multiscale concept for irradiated materials simulation is formulated based on coupling molecular dynamics simulations (MD) where the potential was obtained from ab initio data of energies of the basic defect structures, with kinetic mesoscale models. The evolution of a system containing self-interstitial atoms (SIAs) and vacancies in crystalline molybdenum is investigated by means of MD. The kinetics of formation of di-SIA clusters and SIA–vacancy recombination is analyzed via approaches used in the kinetic theory of radiation ageing. The effects of 1D diffusion of SIAs, temperature, and defect concentrations on the reaction rates are also studied. This approach can validate both the kinetic mechanisms and the appropriate kinetic coefficients, offering the potential to significantly reduce the uncertainty of the kinetic methodology and providing a powerful predictive tool for simulating irradiation behavior of nuclear materials.

Seed defective reduction in automotive Electro-Deposition Coating Process of truck cabin

Science.gov (United States)

Sonthilug, Aekkalag; Chutima, Parames

2018-02-01

The case study company is one of players in Thailand’s Automotive Industry who manufacturing truck and bus for both domestic and international market. This research focuses on a product quality problem about seed defects occurred in the Electro-Deposition Coating Process of truck cabin. The 5-phase of Six Sigma methodology including D-Define, M-Measure, A-Analyze, I-Improve, and C-Control is applied to this research to identify root causes of problem for setting new parameters of each significant factor. After the improvement, seed defects in this process is reduced from 9,178 defects per unit to 876 defects per unit (90% improvement)

Neuron-specific knockdown of the Drosophila fat induces reduction of life span, deficient locomotive ability, shortening of motoneuron terminal branches and defects in axonal targeting.

Science.gov (United States)

Nakamura, Aya; Tanaka, Ryo; Morishita, Kazushige; Yoshida, Hideki; Higuchi, Yujiro; Takashima, Hiroshi; Yamaguchi, Masamitsu

2017-07-01

Mutations in FAT4 gene, one of the human FAT family genes, have been identified in Van Maldergem syndrome (VMS) and Hennekam lymphangiectasia-lymphedema syndrome (HS). The FAT4 gene encodes a large protein with extracellular cadherin repeats, EGF-like domains and Laminin G-like domains. FAT4 plays a role in tumor suppression and planar cell polarity. Drosophila contains a human FAT4 homologue, fat. Drosophila fat has been mainly studied with Drosophila eye and wing systems. Here, we specially knocked down Drosophila fat in nerve system. Neuron-specific knockdown of fat shortened the life span and induced the defect in locomotive abilities of adult flies. In consistent with these phenotypes, defects in synapse structure at neuromuscular junction were observed in neuron-specific fat-knockdown flies. In addition, aberrations in axonal targeting of photoreceptor neuron in third-instar larvae were also observed, suggesting that fat involves in axonal targeting. Taken together, the results indicate that Drosophila fat plays an essential role in formation and/or maintenance of neuron. Both VMS and HS show mental retardation and neuronal defects. We therefore consider that these two rare human diseases could possibly be caused by the defect in FAT4 function in neuronal cells. © 2017 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.

Die Defects and Die Corrections in Metal Extrusion

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Sayyad Zahid Qamar

2018-05-01

Full Text Available Extrusion is a very popular and multi-faceted manufacturing process. A large number of products for the automotive, aerospace, and construction sectors are produced through aluminum extrusion. Many defects in the extruded products occur because of the conditions of the dies and tooling. The problems in dies can be due to material issues, design and manufacturing, or severe usage. They can be avoided by maintaining the billet quality, by controlling the extrusion process parameters, and through routine maintenance. Die problems that occur on a day-to-day basis are mostly repairable and are rectified through various types of die correction operations. These defects and repair operations have not been reported in detail in the published literature. The current paper presents an in-depth description of repairable die defects and related die correction operations in metal extrusion. All major die defects are defined and classified, and their causes, preventive measures, and die correction operations are described. A brief frequency-based statistical study of die defects is also carried out to identify the most frequent die corrections. This work can be of direct benefit to plant engineers and operators and to researchers and academics in the field of metal extrusion.

Assessment of defects in ferromagnetic metals with eddy currents

OpenAIRE

Oaten, Susan Rosemary

1989-01-01

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University. A study was made to identify and size surface breaking defects in ferromagnetic materials with eddy currents, whilst eliminating unwanted signals due to changes in magnetic permeability and probe lift-off. The former was overcome by the use of high frequencies and the latter by utilising the lift-off to characterise the defects. The lift- off or "touch" method was shown to be advantageous in ...

Optical coherence tomography use in the diagnosis of enamel defects

Science.gov (United States)

Al-Azri, Khalifa; Melita, Lucia N.; Strange, Adam P.; Festy, Frederic; Al-Jawad, Maisoon; Cook, Richard; Parekh, Susan; Bozec, Laurent

2016-03-01

Molar incisor hypomineralization (MIH) affects the permanent incisors and molars, whose undermineralized matrix is evidenced by lesions ranging from white to yellow/brown opacities to crumbling enamel lesions incapable of withstanding normal occlusal forces and function. Diagnosing the condition involves clinical and radiographic examination of these teeth, with known limitations in determining the depth extent of the enamel defects in particular. Optical coherence tomography (OCT) is an emerging hard and soft tissue imaging technique, which was investigated as a new potential diagnostic method in dentistry. A comparison between the diagnostic potential of the conventional methods and OCT was conducted. Compared to conventional imaging methods, OCT gave more information on the structure of the enamel defects as well as the depth extent of the defects into the enamel structure. Different types of enamel defects were compared, each type presenting a unique identifiable pattern when imaged using OCT. Additionally, advanced methods of OCT image analysis including backscattered light intensity profile analysis and enface reconstruction were performed. Both methods confirmed the potential of OCT in enamel defects diagnosis. In conclusion, OCT imaging enabled the identification of the type of enamel defect and the determination of the extent of the enamel defects in MIH with the advantage of being a radiation free diagnostic technique.

Deep level defects in Ge-doped (010) β-Ga2O3 layers grown by plasma-assisted molecular beam epitaxy

Science.gov (United States)

Farzana, Esmat; Ahmadi, Elaheh; Speck, James S.; Arehart, Aaron R.; Ringel, Steven A.

2018-04-01

Deep level defects were characterized in Ge-doped (010) β-Ga2O3 layers grown by plasma-assisted molecular beam epitaxy (PAMBE) using deep level optical spectroscopy (DLOS) and deep level transient (thermal) spectroscopy (DLTS) applied to Ni/β-Ga2O3:Ge (010) Schottky diodes that displayed Schottky barrier heights of 1.50 eV. DLOS revealed states at EC - 2.00 eV, EC - 3.25 eV, and EC - 4.37 eV with concentrations on the order of 1016 cm-3, and a lower concentration level at EC - 1.27 eV. In contrast to these states within the middle and lower parts of the bandgap probed by DLOS, DLTS measurements revealed much lower concentrations of states within the upper bandgap region at EC - 0.1 - 0.2 eV and EC - 0.98 eV. There was no evidence of the commonly observed trap state at ˜EC - 0.82 eV that has been reported to dominate the DLTS spectrum in substrate materials synthesized by melt-based growth methods such as edge defined film fed growth (EFG) and Czochralski methods [Zhang et al., Appl. Phys. Lett. 108, 052105 (2016) and Irmscher et al., J. Appl. Phys. 110, 063720 (2011)]. This strong sensitivity of defect incorporation on crystal growth method and conditions is unsurprising, which for PAMBE-grown β-Ga2O3:Ge manifests as a relatively "clean" upper part of the bandgap. However, the states at ˜EC - 0.98 eV, EC - 2.00 eV, and EC - 4.37 eV are reminiscent of similar findings from these earlier results on EFG-grown materials, suggesting that possible common sources might also be present irrespective of growth method.

Genome-wide DNA methylation analysis of pseudohypoparathyroidism patients with GNAS imprinting defects.

Science.gov (United States)

Rochtus, Anne; Martin-Trujillo, Alejandro; Izzi, Benedetta; Elli, Francesca; Garin, Intza; Linglart, Agnes; Mantovani, Giovanna; Perez de Nanclares, Guiomar; Thiele, Suzanne; Decallonne, Brigitte; Van Geet, Chris; Monk, David; Freson, Kathleen

2016-01-01

Pseudohypoparathyroidism (PHP) is caused by (epi)genetic defects in the imprinted GNAS cluster. Current classification of PHP patients is hampered by clinical and molecular diagnostic overlaps. The European Consortium for the study of PHP designed a genome-wide methylation study to improve molecular diagnosis. The HumanMethylation 450K BeadChip was used to analyze genome-wide methylation in 24 PHP patients with parathyroid hormone resistance and 20 age- and gender-matched controls. Patients were previously diagnosed with GNAS-specific differentially methylated regions (DMRs) and include 6 patients with known STX16 deletion (PHP(Δstx16)) and 18 without deletion (PHP(neg)). The array demonstrated that PHP patients do not show DNA methylation differences at the whole-genome level. Unsupervised clustering of GNAS-specific DMRs divides PHP(Δstx16) versus PHP(neg) patients. Interestingly, in contrast to the notion that all PHP patients share methylation defects in the A/B DMR while only PHP(Δstx16) patients have normal NESP, GNAS-AS1 and XL methylation, we found a novel DMR (named GNAS-AS2) in the GNAS-AS1 region that is significantly different in both PHP(Δstx16) and PHP(neg), as validated by Sequenom EpiTYPER in a larger PHP cohort. The analysis of 58 DMRs revealed that 8/18 PHP(neg) and 1/6 PHP(Δstx16) patients have multi-locus methylation defects. Validation was performed for FANCC and SVOPL DMRs. This is the first genome-wide methylation study for PHP patients that confirmed that GNAS is the most significant DMR, and the presence of STX16 deletion divides PHP patients in two groups. Moreover, a novel GNAS-AS2 DMR affects all PHP patients, and PHP patients seem sensitive to multi-locus methylation defects.

Test and Diagnosis for Small-Delay Defects

CERN Document Server

Tehranipoor, Mohammad; Chakrabarty, Krishnendu

2012-01-01

This book introduces new techniques for detecting and diagnosing small-delay defects (SDD) in integrated circuits. Although this sort of timing defect is commonly found in integrated circuits manufactured with nanometer technology, this will be the first book to introduce effective and scalable methodologies for screening and diagnosing small-delay defects, including important parameters such as process variations, crosstalk, and power supply noise. This book presents new techniques and methodologies to improve overall SDD detection with very small pattern sets. These methods can result in pattern counts as low as a traditional 1-detect pattern set and long path sensitization and SDD detection similar to or even better than n-detect or timing-aware pattern sets. The important design parameters and pattern-induced noises such as process variations,power supply noise (PSN) and crosstalk are taken into account in the methodologies presented. A diagnostic flow is also presented to identify whether the failure is ...

Molecular-resolution imaging of pentacene on KCl(001

Directory of Open Access Journals (Sweden)

Julia L. Neff

2012-02-01

Full Text Available The growth of pentacene on KCl(001 at submonolayer coverage was studied by dynamic scanning force microscopy. At coverages below one monolayer pentacene was found to arrange in islands with an upright configuration. The molecular arrangement was resolved in high-resolution images. In these images two different types of patterns were observed, which switch repeatedly. In addition, defects were found, such as a molecular vacancy and domain boundaries.

[Treatment of acute full-thickness chondral defects with high molecular weight hyaluronic acid; an experimental model].

Science.gov (United States)

Figueroa, D; Espinosa, M; Calvo, R; Scheu, M; Valderrama, J J; Gallegos, M; Conget, P

2014-01-01

To evaluate the effect of 2 different protocols of intra-articular hyaluronic acid (HA, hylan G-F20) to articular cartilage regeneration in acute full-thickness chondral defects. Full-thickness chondral defects of 3 x 6 mm were performed into the lateral femoral condyles of New Zealand rabbits, treated with a single or three doses of HA. The animals were sacrified at 12 weeks and the regenerated tissue was evaluated by direct observation and histology with the ICRS scale. Macroscopically, in both groups treated with HA the defects were filled with irregular tissue with areas similar to hyaline cartilage and others in which depressed areas with exposed subchondral bone were observed. Histological analysis showed in both groups treated with HA a hyaline-like cartilage compared to control group. However, the score of the International Cartilage Repair Society (ICRS) scale did not show differences between the groups treated with HA. The use of single dose or 3 doses of AH in acute chondral lesions has a limited and similar benefit in articular cartilage regeneration. Copyright © 2014 SECOT. Published by Elsevier Espana. All rights reserved.

Defects in semiconductors

CERN Document Server

Romano, Lucia; Jagadish, Chennupati

2015-01-01

This volume, number 91 in the Semiconductor and Semimetals series, focuses on defects in semiconductors. Defects in semiconductors help to explain several phenomena, from diffusion to getter, and to draw theories on materials' behavior in response to electrical or mechanical fields. The volume includes chapters focusing specifically on electron and proton irradiation of silicon, point defects in zinc oxide and gallium nitride, ion implantation defects and shallow junctions in silicon and germanium, and much more. It will help support students and scientists in their experimental and theoret

Defect Detection in Superconducting Radiofrequency Cavity Surface Using C + + and OpenCV

Science.gov (United States)

Oswald, Samantha; Thomas Jefferson National Accelerator Facility Collaboration

2014-03-01

Thomas Jefferson National Accelerator Facility (TJNAF) uses superconducting radiofrequency (SRF) cavities to accelerate an electron beam. If theses cavities have a small particle or defect, it can degrade the performance of the cavity. The problem at hand is inspecting the cavity for defects, little bubbles of niobium on the surface of the cavity. Thousands of pictures have to be taken of a single cavity and then looked through to see how many defects were found. A C + + program with Open Source Computer Vision (OpenCV) was constructed to reduce the number of hours searching through the images and finds all the defects. Using this code, the SRF group is now able to use the code to identify defects in on-going tests of SRF cavities. Real time detection is the next step so that instead of taking pictures when looking at the cavity, the camera will detect all the defects.

Point defects in cubic boron nitride after neutron irradiation

International Nuclear Information System (INIS)

Atobe, Kozo; Honda, Makoto; Ide, Munetoshi; Yamaji, Hiromichi; Matsukawa, Tokuo; Fukuoka, Noboru; Okada, Moritami; Nakagawa, Masuo.

1993-01-01

The production of point defects induced by reactor neutrons and the thermal behavior of defects in sintered cubic boron nitride are investigated using the optical absorption and electron spin resonance (ESR) methods. A strong structureless absorption over the visible region was observed after fast neutron irradiation to a dose of 5.3 x 10 16 n/cm 2 (E > 0.1 MeV) at 25 K. This specimen also shows an ESR signal with g-value 2.006 ± 0.001, which can be tentatively identified as an electron trapped in a nitrogen vacancy. On examination of the thermal decay of the signal, the activation energy for recovery of the defects was determined to be about 1.79 eV. (author)

Reliability-Limiting Defects in GaN/AlGaN High Electron Mobility Transistors

Science.gov (United States)

2011-12-01

GaN grown by plasma-assisted molecular beam epitaxy”, Appl. Phys. Lett., vol. 77, no. 18, pp. 2885- 2887, 2000. [24] A. Hierro , A. R. Arehart, B...defects and impurities: Applications to III-nitrides”, J. Appl. Phys., vol. 95, pp.3851-3879, 2004. [43] A. Hierro , S. A. Ringel, M. Hansen, J. S

Unbalanced atrioventricular septal defect: definition and decision making.

Science.gov (United States)

Overman, David M; Baffa, Jeanne M; Cohen, Meryl S; Mertens, Luc; Gremmels, David B; Jegatheeswaram, Anusha; McCrindle, Brian W; Blackstone, Eugene H; Morell, Victor O; Caldarone, Christopher; Williams, William G; Pizarro, Christian

2010-04-01

Unbalanced atrioventricular septal defect is an uncommon lesion with widely varying anatomic manifestations. When unbalance is severe, diagnosis and treatment is straightforward, directed toward single-ventricle palliation. Milder forms, however, pose a challenge to current diagnostic and therapeutic approaches. The transition from anatomies that are capable of sustaining biventricular physiology to those that cannot is obscure, resulting in uneven application of surgical strategy and excess mortality. Imprecise assessments of ventricular competence have dominated clinical decision making in this regard. Malalignment of the atrioventricular junction and its attendant derangement of inflow physiology is a critical factor in determining the feasibility of biventricular repair in the setting of unbalanced atrioventricular septal defect. The atrioventricular valve index accurately identifies unbalanced atrioventricular septal defect and also brings into focus a zone of transition from anatomies that can support a biventricular end state and those that cannot.

Investigation of point defects diffusion in bcc uranium and U–Mo alloys

International Nuclear Information System (INIS)

Smirnova, D.E.; Kuksin, A.Yu.; Starikov, S.V.

2015-01-01

We present results of investigation of point defects formation and diffusion in pure γ-U and γ-U–Mo fuel alloys. The study was performed using molecular dynamics simulation with the different interatomic potentials. The point defects formation and migration energies were estimated for bcc γ-U and U–9 wt.%Mo alloy. The calculated diffusivities of atoms via defects are provided for pure γ-U and for the alloy components. Analysis of simulation results shows that self-interstitial atoms play a leading role in the self-diffusion processes in the materials studied. This fact can explain a remarkably high self-diffusion mobility observed experimentally for γ-U. The self-diffusion coefficients in γ-U calculated in this assumption agree with the data measured experimentally. It is shown that alloying of γ-U with Mo increase formation energy for self-interstitial atoms and decelerate their mobility. These changes lead to decrease of self-diffusion coefficients in U–Mo alloy compared to pure U

Study of prevalence & risk factors of congenital heart defect (Review Article

Directory of Open Access Journals (Sweden)

ali dehghani

2017-09-01

Full Text Available Abstract Background: Congenital heart defects are known as the state that comes from birth and influences on structure and function of baby's heart, The different types of defects can range from mild (e.g., a small hole between the heart chambers to hard (like a flaw or weakness in a part of the heart. Method: This article is a review article in which the articles published in Farsi and English that the bases valid as Medline, Google Scholar, Pubmed, Springer, SID index has been used, as well as for the study of keywords associated with the use of MESH keywords in identifying and no time limit listed in the databases were searched. Result The prevalence of congenital heart defect, in general, less than one per cent in newborn. The ventricular wall abnormalities defect (VSD, atrial septal defect of (ASD, patent ductus arteriosus (PDA and tetralogy of Fallot (TOF Top among the most types of congenital heart anomalies. Factors such as the age of the parents at conception, maternal risk of diabetes, influenza and febrile illness during pregnancy, drug use during pregnancy and taking a multivitamin before and during the Pregnancy were influenced of newborns with congenital heart defects. Conclusion: According to studies need to be conducted in the presence of multiple risk factors for these disorders, seem to have a detailed plan to Study of More about the factors that affect the risk of developing these disorders, as well as interventions to reduce risk factors identified particularly during pregnancy.

Accelerated carrier recombination by grain boundary/edge defects in MBE grown transition metal dichalcogenides

Science.gov (United States)

Chen, Ke; Roy, Anupam; Rai, Amritesh; Movva, Hema C. P.; Meng, Xianghai; He, Feng; Banerjee, Sanjay K.; Wang, Yaguo

2018-05-01

Defect-carrier interaction in transition metal dichalcogenides (TMDs) plays important roles in carrier relaxation dynamics and carrier transport, which determines the performance of electronic devices. With femtosecond laser time-resolved spectroscopy, we investigated the effect of grain boundary/edge defects on the ultrafast dynamics of photoexcited carrier in molecular beam epitaxy (MBE)-grown MoTe2 and MoSe2. We found that, comparing with exfoliated samples, the carrier recombination rate in MBE-grown samples accelerates by about 50 times. We attribute this striking difference to the existence of abundant grain boundary/edge defects in MBE-grown samples, which can serve as effective recombination centers for the photoexcited carriers. We also observed coherent acoustic phonons in both exfoliated and MBE-grown MoTe2, indicating strong electron-phonon coupling in this materials. Our measured sound velocity agrees well with the previously reported result of theoretical calculation. Our findings provide a useful reference for the fundamental parameters: carrier lifetime and sound velocity and reveal the undiscovered carrier recombination effect of grain boundary/edge defects, both of which will facilitate the defect engineering in TMD materials for high speed opto-electronics.

Accelerated carrier recombination by grain boundary/edge defects in MBE grown transition metal dichalcogenides

Directory of Open Access Journals (Sweden)

Ke Chen

2018-05-01

Full Text Available Defect-carrier interaction in transition metal dichalcogenides (TMDs plays important roles in carrier relaxation dynamics and carrier transport, which determines the performance of electronic devices. With femtosecond laser time-resolved spectroscopy, we investigated the effect of grain boundary/edge defects on the ultrafast dynamics of photoexcited carrier in molecular beam epitaxy (MBE-grown MoTe2 and MoSe2. We found that, comparing with exfoliated samples, the carrier recombination rate in MBE-grown samples accelerates by about 50 times. We attribute this striking difference to the existence of abundant grain boundary/edge defects in MBE-grown samples, which can serve as effective recombination centers for the photoexcited carriers. We also observed coherent acoustic phonons in both exfoliated and MBE-grown MoTe2, indicating strong electron-phonon coupling in this materials. Our measured sound velocity agrees well with the previously reported result of theoretical calculation. Our findings provide a useful reference for the fundamental parameters: carrier lifetime and sound velocity and reveal the undiscovered carrier recombination effect of grain boundary/edge defects, both of which will facilitate the defect engineering in TMD materials for high speed opto-electronics.

Mitochondrial fatty acid oxidation defects--remaining challenges

DEFF Research Database (Denmark)

Gregersen, Niels; Andresen, Brage S; Pedersen, Christina B

2008-01-01

Mitochondrial fatty acid oxidation defects have been recognized since the early 1970s. The discovery rate has been rather constant, with 3-4 'new' disorders identified every decade and with the most recent example, ACAD9 deficiency, reported in 2007. In this presentation we will focus on three...

Thermal evolution of defects in undoped zinc oxide grown by pulsed laser deposition

Energy Technology Data Exchange (ETDEWEB)

Wang, Zilan; Su, Shichen; Ling, Francis Chi-Chung, E-mail: ccling@hku.hk [Department of Physics, The University of Hong Kong, Pokfulam Road, Hong Kong (China); Anwand, W.; Wagner, A. [Institute of Radiation Physics, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstr. 400, 01328 Dresden (Germany)

2014-07-21

Undoped ZnO films are grown by pulsed laser deposition on c-plane sapphire with different oxygen pressures. Thermal evolutions of defects in the ZnO films are studied by secondary ion mass spectroscopy (SIMS), Raman spectroscopy, and positron annihilation spectroscopy (PAS), and with the electrical properties characterized by the room temperature Hall measurement. Oxygen deficient defect related Raman lines 560 cm{sup −1} and 584 cm{sup −1} are identified and their origins are discussed. Thermal annealing induces extensive Zn out-diffusion at the ZnO/sapphire interface and leaves out Zn-vacancy in the ZnO film. Two types of Zn-vacancy related defects with different microstructures are identified in the films. One of them dominates in the samples grown without oxygen. Annealing the sample grown without oxygen or growing the samples in oxygen would favor the Zn-vacancy with another microstructure, and this Zn-vacancy defect persists after 1100 °C annealing.

Thermal evolution of defects in undoped zinc oxide grown by pulsed laser deposition

Science.gov (United States)

Wang, Zilan; Su, Shichen; Ling, Francis Chi-Chung; Anwand, W.; Wagner, A.

2014-07-01

Undoped ZnO films are grown by pulsed laser deposition on c-plane sapphire with different oxygen pressures. Thermal evolutions of defects in the ZnO films are studied by secondary ion mass spectroscopy (SIMS), Raman spectroscopy, and positron annihilation spectroscopy (PAS), and with the electrical properties characterized by the room temperature Hall measurement. Oxygen deficient defect related Raman lines 560 cm-1 and 584 cm-1 are identified and their origins are discussed. Thermal annealing induces extensive Zn out-diffusion at the ZnO/sapphire interface and leaves out Zn-vacancy in the ZnO film. Two types of Zn-vacancy related defects with different microstructures are identified in the films. One of them dominates in the samples grown without oxygen. Annealing the sample grown without oxygen or growing the samples in oxygen would favor the Zn-vacancy with another microstructure, and this Zn-vacancy defect persists after 1100 °C annealing.

Thermal evolution of defects in undoped zinc oxide grown by pulsed laser deposition

International Nuclear Information System (INIS)

Wang, Zilan; Su, Shichen; Ling, Francis Chi-Chung; Anwand, W.; Wagner, A.

2014-01-01

Undoped ZnO films are grown by pulsed laser deposition on c-plane sapphire with different oxygen pressures. Thermal evolutions of defects in the ZnO films are studied by secondary ion mass spectroscopy (SIMS), Raman spectroscopy, and positron annihilation spectroscopy (PAS), and with the electrical properties characterized by the room temperature Hall measurement. Oxygen deficient defect related Raman lines 560 cm −1 and 584 cm −1 are identified and their origins are discussed. Thermal annealing induces extensive Zn out-diffusion at the ZnO/sapphire interface and leaves out Zn-vacancy in the ZnO film. Two types of Zn-vacancy related defects with different microstructures are identified in the films. One of them dominates in the samples grown without oxygen. Annealing the sample grown without oxygen or growing the samples in oxygen would favor the Zn-vacancy with another microstructure, and this Zn-vacancy defect persists after 1100 °C annealing.

Congenital tracheal defects: embryonic development and animal models

Directory of Open Access Journals (Sweden)

Zenab Arooj Sher

2016-03-01

Full Text Available Tracheal anomalies are potentially catastrophic congenital defects. As a newborn begins to breathe, the trachea needs to maintain an appropriate balance of elasticity and rigidity. If the tracheal cartilages are disorganized or structurally weak, the airways can collapse, obstructing breathing. Cartilage rings that are too small or too rigid can also obstruct breathing. These anomalies are frequently associated with craniofacial syndromes, and, despite the importance, are poorly understood. In this review, we summarize the spectrum of pathological phenotypes of the trachea and correlate them with the molecular events uncovered in mouse models.

A Hybrid Instance Selection Using Nearest-Neighbor for Cross-Project Defect Prediction

Institute of Scientific and Technical Information of China (English)

Duksan Ryu; Jong-In Jang; Jongmoon Baik; Member; ACM; IEEE

2015-01-01

Software defect prediction (SDP) is an active research field in software engineering to identify defect-prone modules. Thanks to SDP, limited testing resources can be effectively allocated to defect-prone modules. Although SDP requires suffcient local data within a company, there are cases where local data are not available, e.g., pilot projects. Companies without local data can employ cross-project defect prediction (CPDP) using external data to build classifiers. The major challenge of CPDP is different distributions between training and test data. To tackle this, instances of source data similar to target data are selected to build classifiers. Software datasets have a class imbalance problem meaning the ratio of defective class to clean class is far low. It usually lowers the performance of classifiers. We propose a Hybrid Instance Selection Using Nearest-Neighbor (HISNN) method that performs a hybrid classification selectively learning local knowledge (via k-nearest neighbor) and global knowledge (via na¨ıve Bayes). Instances having strong local knowledge are identified via nearest-neighbors with the same class label. Previous studies showed low PD (probability of detection) or high PF (probability of false alarm) which is impractical to use. The experimental results show that HISNN produces high overall performance as well as high PD and low PF.

Identification of the DNA repair defects in a case of Dubowitz syndrome.

Directory of Open Access Journals (Sweden)

Jingyin Yue

Full Text Available Dubowitz Syndrome is an autosomal recessive disorder with a unique set of clinical features including microcephaly and susceptibility to tumor formation. Although more than 140 cases of Dubowitz syndrome have been reported since 1965, the genetic defects of this disease has not been identified. In this study, we systematically analyzed the DNA damage response and repair capability of fibroblasts established from a Dubowitz Syndrome patient. Dubowitz syndrome fibroblasts are hypersensitive to ionizing radiation, bleomycin, and doxorubicin. However, they have relatively normal sensitivities to mitomycin-C, cisplatin, and camptothecin. Dubowitz syndrome fibroblasts also have normal DNA damage signaling and cell cycle checkpoint activations after DNA damage. These data implicate a defect in repair of DNA double strand break (DSB likely due to defective non-homologous end joining (NHEJ. We further sequenced several genes involved in NHEJ, and identified a pair of novel compound mutations in the DNA Ligase IV gene. Furthermore, expression of wild type DNA ligase IV completely complement the DNA repair defects in Dubowitz syndrome fibroblasts, suggesting that the DNA ligase IV mutation is solely responsible for the DNA repair defects. These data suggests that at least subset of Dubowitz syndrome can be attributed to DNA ligase IV mutations.

Revisiting the reasons for contact fatigue defects in rails

Directory of Open Access Journals (Sweden)

Darenskiy Alexander

2017-01-01

Full Text Available As it is known rail is one of the most significant elements of the whole railway construction. Operation under alternating loads from wheels of the rolling stock and different ambient temperatures lead to appearance and development of rail defects and damages. A great variety of operational factors (freight traffic density, axial loads, traffic speeds, track layout and profile as well as special features of manufacturing and thermal treatment of rails create certain difficulties while identifying reasons for defects and damages. The article deals with an attempt to estimate influence of track layout and lateral forces on appearance of defects and damages in rails on the base of long-term observations of rail operation in Kharkiv Metro. On the basis of the vehicle/track mathematical model which considers structural features of both rolling stock and permanent way in underground systems, the level of lateral forces in curves was calculated. The coefficients of correlation between the track curvature, the level of forces and the amount of defected rails removed were later obtained, that made it possible to determine the dominant factor which may lead to appearance and development of contact fatigue defects in rails laid in curves.

Medium-Chain Acyl-CoA Deficiency: Outlines from Newborn Screening, In Silico Predictions, and Molecular Studies

Directory of Open Access Journals (Sweden)

Serena Catarzi

2013-01-01

Full Text Available Medium-chain acyl-CoA dehydrogenase deficiency (MCADD is a disorder of fatty acid oxidation characterized by hypoglycemic crisis under fasting or during stress conditions, leading to lethargy, seizures, brain damage, or even death. Biochemical acylcarnitines data obtained through newborn screening by liquid chromatography-tandem mass spectrometry (LC-MS/MS were confirmed by molecular analysis of the medium-chain acyl-CoA dehydrogenase (ACADM gene. Out of 324.000 newborns screened, we identified 14 MCADD patients, in whom, by molecular analysis, we found a new nonsense c.823G>T (p.Gly275* and two new missense mutations: c.253G>C (p.Gly85Arg and c.356T>A (p.Val119Asp. Bioinformatics predictions based on both phylogenetic conservation and functional/structural software were used to characterize the new identified variants. Our findings confirm the rising incidence of MCADD whose existence is increasingly recognized due to the efficacy of an expanded newborn screening panel by LC-MS/MS making possible early specific therapies that can prevent possible crises in at-risk infants. We noticed that the “common” p.Lys329Glu mutation only accounted for 32% of the defective alleles, while, in clinically diagnosed patients, this mutation accounted for 90% of defective alleles. Unclassified variants (UVs or VUSs are especially critical when considering screening programs. The functional and pathogenic characterization of genetic variants presented here is required to predict their medical consequences in newborns.

Medium-Chain Acyl-CoA Deficiency: Outlines from Newborn Screening, In Silico Predictions, and Molecular Studies

Science.gov (United States)

Catarzi, Serena; Caciotti, Anna; Thusberg, Janita; Tonin, Rodolfo; Malvagia, Sabrina; la Marca, Giancarlo; Pasquini, Elisabetta; Cavicchi, Catia; Ferri, Lorenzo; Donati, Maria A.; Baronio, Federico; Guerrini, Renzo; Mooney, Sean D.; Morrone, Amelia

2013-01-01

Medium-chain acyl-CoA dehydrogenase deficiency (MCADD) is a disorder of fatty acid oxidation characterized by hypoglycemic crisis under fasting or during stress conditions, leading to lethargy, seizures, brain damage, or even death. Biochemical acylcarnitines data obtained through newborn screening by liquid chromatography-tandem mass spectrometry (LC-MS/MS) were confirmed by molecular analysis of the medium-chain acyl-CoA dehydrogenase (ACADM) gene. Out of 324.000 newborns screened, we identified 14 MCADD patients, in whom, by molecular analysis, we found a new nonsense c.823G>T (p.Gly275∗) and two new missense mutations: c.253G>C (p.Gly85Arg) and c.356T>A (p.Val119Asp). Bioinformatics predictions based on both phylogenetic conservation and functional/structural software were used to characterize the new identified variants. Our findings confirm the rising incidence of MCADD whose existence is increasingly recognized due to the efficacy of an expanded newborn screening panel by LC-MS/MS making possible early specific therapies that can prevent possible crises in at-risk infants. We noticed that the “common” p.Lys329Glu mutation only accounted for 32% of the defective alleles, while, in clinically diagnosed patients, this mutation accounted for 90% of defective alleles. Unclassified variants (UVs or VUSs) are especially critical when considering screening programs. The functional and pathogenic characterization of genetic variants presented here is required to predict their medical consequences in newborns. PMID:24294134

Fibrous metaphyseal defects

International Nuclear Information System (INIS)

Ritschl, P.; Hajek, P.C.; Pechmann, U.

1989-01-01

Sixteen patients with fibrous metaphyseal defects were examined with both plain radiography and magnetic resonance (MR) imaging. Depending on the age of the fibrous metaphyseal defects, characteristic radiomorphologic changes were found which correlated well with MR images. Following intravenous Gadolinium-DTPA injection, fibrous metaphyseal defects invariably exhibited a hyperintense border and signal enhancement. (orig./GDG)

Exotic Non-Abelian Topological Defects in Lattice Fractional Quantum Hall States

Science.gov (United States)

Liu, Zhao; Möller, Gunnar; Bergholtz, Emil J.

2017-09-01

We investigate extrinsic wormholelike twist defects that effectively increase the genus of space in lattice versions of multicomponent fractional quantum Hall systems. Although the original band structure is distorted by these defects, leading to localized midgap states, we find that a new lowest flat band representing a higher genus system can be engineered by tuning local single-particle potentials. Remarkably, once local many-body interactions in this new band are switched on, we identify various Abelian and non-Abelian fractional quantum Hall states, whose ground-state degeneracy increases with the number of defects, i.e, with the genus of space. This sensitivity of topological degeneracy to defects provides a "proof of concept" demonstration that genons, predicted by topological field theory as exotic non-Abelian defects tied to a varying topology of space, do exist in realistic microscopic models. Specifically, our results indicate that genons could be created in the laboratory by combining the physics of artificial gauge fields in cold atom systems with already existing holographic beam shaping methods for creating twist defects.

Shp2 knockdown and Noonan/LEOPARD mutant Shp2-induced gastrulation defects.

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Chris Jopling

2007-12-01

Full Text Available Shp2 is a cytoplasmic protein-tyrosine phosphatase that is essential for normal development. Activating and inactivating mutations have been identified in humans to cause the related Noonan and LEOPARD syndromes, respectively. The cell biological cause of these syndromes remains to be determined. We have used the zebrafish to assess the role of Shp2 in early development. Here, we report that morpholino-mediated knockdown of Shp2 in zebrafish resulted in defects during gastrulation. Cell tracing experiments demonstrated that Shp2 knockdown induced defects in convergence and extension cell movements. In situ hybridization using a panel of markers indicated that cell fate was not affected by Shp2 knock down. The Shp2 knockdown-induced defects were rescued by active Fyn and Yes and by active RhoA. We generated mutants of Shp2 with mutations that were identified in human patients with Noonan or LEOPARD Syndrome and established that Noonan Shp2 was activated and LEOPARD Shp2 lacked catalytic protein-tyrosine phosphatase activity. Expression of Noonan or LEOPARD mutant Shp2 in zebrafish embryos induced convergence and extension cell movement defects without affecting cell fate. Moreover, these embryos displayed craniofacial and cardiac defects, reminiscent of human symptoms. Noonan and LEOPARD mutant Shp2s were not additive nor synergistic, consistent with the mutant Shp2s having activating and inactivating roles in the same signaling pathway. Our results demonstrate that Shp2 is required for normal convergence and extension cell movements during gastrulation and that Src family kinases and RhoA were downstream of Shp2. Expression of Noonan or LEOPARD Shp2 phenocopied the craniofacial and cardiac defects of human patients. The finding that defective Shp2 signaling induced cell movement defects as early as gastrulation may have implications for the monitoring and diagnosis of Noonan and LEOPARD syndrome.

Vertebral defect, anal atresia, cardiac defect, tracheoesophageal fistula/esophageal atresia, renal defect, and limb defect association with Mayer-Rokitansky-Küster-Hauser syndrome in co-occurrence: two case reports and a review of the literature.

Science.gov (United States)

Bjørsum-Meyer, Thomas; Herlin, Morten; Qvist, Niels; Petersen, Michael B

2016-12-21

The vertebral defect, anal atresia, cardiac defect, tracheoesophageal fistula/esophageal atresia, renal defect, and limb defect association and Mayer-Rokitansky-Küster-Hauser syndrome are rare conditions. We aimed to present two cases with the vertebral defect, anal atresia, cardiac defect, tracheoesophageal fistula/esophageal atresia, renal defect, and limb defect association and Mayer-Rokitansky-Küster-Hauser co-occurrence from our local surgical center and through a systematic literature search detect published cases. Furthermore, we aimed to collect existing knowledge in the embryopathogenesis and genetics in order to discuss a possible link between the vertebral defect, anal atresia, cardiac defect, tracheoesophageal fistula/esophageal atresia, renal defect, and limb defect association and Mayer-Rokitansky-Küster-Hauser syndrome. Our first case was a white girl delivered by caesarean section at 37 weeks of gestation; our second case was a white girl born at a gestational age of 40 weeks. A co-occurrence of vertebral defect, anal atresia, cardiac defect, tracheoesophageal fistula/esophageal atresia, renal defect, and limb defect association and Mayer-Rokitansky-Küster-Hauser syndrome was diagnosed in both cases. We performed a systematic literature search in PubMed ((VACTERL) OR (VATER)) AND ((MRKH) OR (Mayer-Rokitansky-Küster-Hauser) OR (mullerian agenesis) OR (mullerian aplasia) OR (MURCS)) without limitations. A similar search was performed in Embase and the Cochrane library. We added two cases from our local center. All cases (n = 9) presented with anal atresia and renal defect. Vertebral defects were present in eight patients. Rectovestibular fistula was confirmed in seven patients. Along with the uterovaginal agenesis, fallopian tube aplasia appeared in five of nine cases and in two cases ovarian involvement also existed. The co-occurrence of the vertebral defect, anal atresia, cardiac defect, tracheoesophageal fistula/esophageal atresia, renal

Deficiency of the vestibular spine in atrioventricular septal defects in human fetuses with down syndrome

NARCIS (Netherlands)

Blom, Nico A.; Ottenkamp, Jaap; Wenink, Arnold G. C.; Gittenberger-de Groot, Adriana C.

2003-01-01

Data on the morphogenesis of atrioventricular septal defect (AVSD) in Down syndrome are lacking to support molecular studies on Down syndrome heart critical region. Therefore, we studied the development of complete AVSD in human embryos and fetuses with trisomy 21 using 3-dimensional graphic

A 6-gene signature identifies four molecular subgroups of neuroblastoma

LENUS (Irish Health Repository)

Abel, Frida

2011-04-14

Abstract Background There are currently three postulated genomic subtypes of the childhood tumour neuroblastoma (NB); Type 1, Type 2A, and Type 2B. The most aggressive forms of NB are characterized by amplification of the oncogene MYCN (MNA) and low expression of the favourable marker NTRK1. Recently, mutations or high expression of the familial predisposition gene Anaplastic Lymphoma Kinase (ALK) was associated to unfavourable biology of sporadic NB. Also, various other genes have been linked to NB pathogenesis. Results The present study explores subgroup discrimination by gene expression profiling using three published microarray studies on NB (47 samples). Four distinct clusters were identified by Principal Components Analysis (PCA) in two separate data sets, which could be verified by an unsupervised hierarchical clustering in a third independent data set (101 NB samples) using a set of 74 discriminative genes. The expression signature of six NB-associated genes ALK, BIRC5, CCND1, MYCN, NTRK1, and PHOX2B, significantly discriminated the four clusters (p < 0.05, one-way ANOVA test). PCA clusters p1, p2, and p3 were found to correspond well to the postulated subtypes 1, 2A, and 2B, respectively. Remarkably, a fourth novel cluster was detected in all three independent data sets. This cluster comprised mainly 11q-deleted MNA-negative tumours with low expression of ALK, BIRC5, and PHOX2B, and was significantly associated with higher tumour stage, poor outcome and poor survival compared to the Type 1-corresponding favourable group (INSS stage 4 and\\/or dead of disease, p < 0.05, Fisher\\'s exact test). Conclusions Based on expression profiling we have identified four molecular subgroups of neuroblastoma, which can be distinguished by a 6-gene signature. The fourth subgroup has not been described elsewhere, and efforts are currently made to further investigate this group\\'s specific characteristics.

Mutation update of transcription factor genes FOXE3, HSF4, MAF, and PITX3 causing cataracts and other developmental ocular defects.

Science.gov (United States)

Anand, Deepti; Agrawal, Smriti A; Slavotinek, Anne; Lachke, Salil A

2018-04-01

Mutations in the transcription factor genes FOXE3, HSF4, MAF, and PITX3 cause congenital lens defects including cataracts that may be accompanied by defects in other components of the eye or in nonocular tissues. We comprehensively describe here all the variants in FOXE3, HSF4, MAF, and PITX3 genes linked to human developmental defects. A total of 52 variants for FOXE3, 18 variants for HSF4, 20 variants for MAF, and 19 variants for PITX3 identified so far in isolated cases or within families are documented. This effort reveals FOXE3, HSF4, MAF, and PITX3 to have 33, 16, 18, and 7 unique causal mutations, respectively. Loss-of-function mutant animals for these genes have served to model the pathobiology of the associated human defects, and we discuss the currently known molecular function of these genes, particularly with emphasis on their role in ocular development. Finally, we make the detailed FOXE3, HSF4, MAF, and PITX3 variant information available in the Leiden Online Variation Database (LOVD) platform at https://www.LOVD.nl/FOXE3, https://www.LOVD.nl/HSF4, https://www.LOVD.nl/MAF, and https://www.LOVD.nl/PITX3. Thus, this article informs on key variants in transcription factor genes linked to cataract, aphakia, corneal opacity, glaucoma, microcornea, microphthalmia, anterior segment mesenchymal dysgenesis, and Ayme-Gripp syndrome, and facilitates their access through Web-based databases. © 2018 Wiley Periodicals, Inc.

Defect detection based on extreme edge of defective region histogram

Directory of Open Access Journals (Sweden)

Zouhir Wakaf

2018-01-01

Full Text Available Automatic thresholding has been used by many applications in image processing and pattern recognition systems. Specific attention was given during inspection for quality control purposes in various industries like steel processing and textile manufacturing. Automatic thresholding problem has been addressed well by the commonly used Otsu method, which provides suitable results for thresholding images based on a histogram of bimodal distribution. However, the Otsu method fails when the histogram is unimodal or close to unimodal. Defects have different shapes and sizes, ranging from very small to large. The gray-level distributions of the image histogram can vary between unimodal and multimodal. Furthermore, Otsu-revised methods, like the valley-emphasis method and the background histogram mode extents, which overcome the drawbacks of the Otsu method, require preprocessing steps and fail to use the general threshold for multimodal defects. This study proposes a new automatic thresholding algorithm based on the acquisition of the defective region histogram and the selection of its extreme edge as the threshold value to segment all defective objects in the foreground from the image background. To evaluate the proposed defect-detection method, common standard images for experimentation were used. Experimental results of the proposed method show that the proposed method outperforms the current methods in terms of defect detection.

Folic Acid and Birth Defects: A Case Study (Iran

Directory of Open Access Journals (Sweden)

Mohammad Bager Hosseini

2011-01-01

Full Text Available The aim of this study was to evaluate the impact of folic acid use in pregnancy for the reduction of neural tube defects (NTDs in the northwest region of Iran. We studied 243 women with pregnancies complicated by some forms of birth defect(s. These patients were identified by medical diagnostic tests as having a fetus with some types of congenital anomalies. The prevalence of NTDs among pregnant women who were referred for therapeutic termination of pregnancy was 24.7 percent. Consumption of folic acid prevented NTDs by 79 percent (Odds Ratio = 0.21, CI 95%: 0.12–0.40 and 94 percent (Odds Ratio = 0.06, CI 95%: 0.03–0.15 compared to pregnancies complicated by other anomalies and normal pregnancies, respectively. Hydrops fetalis, hydrocephaly, Down syndrome, and limb anomalies did not have any significant association with the folic acid use. Along with the advice for the consumption of folic acid for pregnant women, they should be offered prenatal screening or diagnostic tests to identify fetal abnormalities for possible termination of pregnancy.

The role of the sonic hedgehog signalling pathway in patients with midline defects and congenital hypopituitarism.

Science.gov (United States)

Gregory, L C; Gaston-Massuet, C; Andoniadou, C L; Carreno, G; Webb, E A; Kelberman, D; McCabe, M J; Panagiotakopoulos, L; Saldanha, J W; Spoudeas, H A; Torpiano, J; Rossi, M; Raine, J; Canham, N; Martinez-Barbera, J P; Dattani, M T

2015-05-01

The Gli family of zinc finger (GLI) transcription factors mediates the sonic hedgehog signalling pathway (HH) essential for CNS, early pituitary and ventral forebrain development in mice. Human mutations in this pathway have been described in patients with holoprosencephaly (HPE), isolated congenital hypopituitarism (CH) and cranial/midline facial abnormalities. Mutations in Sonic hedgehog (SHH) have been associated with HPE but not CH, despite murine studies indicating involvement in pituitary development. We aimed to establish the role of the HH pathway in the aetiology of hypothalamo-pituitary disorders by screening our cohort of patients with midline defects and/or CH for mutations in SHH, GLI2, Shh brain enhancer 2 (SBE2) and growth-arrest specific 1 (GAS1). Two variants and a deletion of GLI2 were identified in three patients. A novel variant at a highly conserved residue in the zinc finger DNA-binding domain, c.1552G > A [pE518K], was identified in a patient with growth hormone deficiency and low normal free T4. A nonsynonymous variant, c.2159G > A [p.R720H], was identified in a patient with a short neck, cleft palate and hypogonadotrophic hypogonadism. A 26·6 Mb deletion, 2q12·3-q21·3, encompassing GLI2 and 77 other genes, was identified in a patient with short stature and impaired growth. Human embryonic expression studies and molecular characterisation of the GLI2 mutant p.E518K support the potential pathogenicity of GLI2 mutations. No mutations were identified in GAS1 or SBE2. A novel SHH variant, c.1295T>A [p.I432N], was identified in two siblings with variable midline defects but normal pituitary function. Our data suggest that mutations in SHH, GAS1 and SBE2 are not associated with hypopituitarism, although GLI2 is an important candidate for CH. © 2014 John Wiley & Sons Ltd.

Electrically active defects in p-type silicon after alpha-particle irradiation

Science.gov (United States)

Danga, Helga T.; Auret, F. Danie; Tunhuma, Shandirai M.; Omotoso, Ezekiel; Igumbor, Emmanuel; Meyer, Walter E.

2018-04-01

In this work, we investigated the defects introduced when boron (B) doped silicon (Si) was irradiated by making use of a 5.4 MeV americium (Am) 241 foil radioactive source with a fluence rate of 7×106 cm-2 s-1 at room temperature. Deep level transient spectroscopy (DLTS) and Laplace-DLTS measurements were used to investigate the electronic properties of the introduced defects. After exposure at a fluence of 5.1×1010 cm-2, the energy levels of the hole traps measured were: H(0.10), H(0.16), H(0.33) and H(0.52) The defect level H(0.10) was tri-vacancy related. H(0.33) was identified as the interstitial carbon (Ci) related defect which was a result of radiation induced damage. H(0.52) was a B-related defect. Explicit deductions about the origin of H(0.16) have not yet been achieved.

Synthetic Defects for Vibrothermography

Science.gov (United States)

Renshaw, Jeremy; Holland, Stephen D.; Thompson, R. Bruce; Eisenmann, David J.

2010-02-01

Synthetic defects are an important tool used for characterizing the performance of nondestructive evaluation techniques. Viscous material-filled synthetic defects were developed for use in vibrothermography (also known as sonic IR) as a tool to improve inspection accuracy and reliability. This paper describes how the heat-generation response of these VMF synthetic defects is similar to the response of real defects. It also shows how VMF defects can be applied to improve inspection accuracy for complex industrial parts and presents a study of their application in an aircraft engine stator vane.

Vacancy-type defects induced by grinding of Si wafers studied by monoenergetic positron beams

Energy Technology Data Exchange (ETDEWEB)

Uedono, Akira; Yoshihara, Nakaaki [Division of Applied Physics, Faculty of Pure and Applied Science, University of Tsukuba, Tsukuba, Ibaraki 305-8573 (Japan); Mizushima, Yoriko [Devices and Materials Labs Fujitsu Laboratories Ltd., Atsugi, Kanagawa 243-0197 (Japan); ICE Cube Center, Tokyo Institute of Technology, Yokohama 226-8503 (Japan); Kim, Youngsuk [ICE Cube Center, Tokyo Institute of Technology, Yokohama 226-8503 (Japan); Disco Corporation, Ota, Tokyo 143-8580 (Japan); Nakamura, Tomoji [Devices and Materials Labs Fujitsu Laboratories Ltd., Atsugi, Kanagawa 243-0197 (Japan); Ohba, Takayuki [ICE Cube Center, Tokyo Institute of Technology, Yokohama 226-8503 (Japan); Oshima, Nagayasu; Suzuki, Ryoichi [Research Institute of Instrumentation Frontier, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8568 (Japan)

2014-10-07

Vacancy-type defects introduced by the grinding of Czochralski-grown Si wafers were studied using monoenergetic positron beams. Measurements of Doppler broadening spectra of the annihilation radiation and the lifetime spectra of positrons showed that vacancy-type defects were introduced in the surface region (<98 nm), and the major defect species were identified as (i) relatively small vacancies incorporated in dislocations and (ii) large vacancy clusters. Annealing experiments showed that the defect concentration decreased with increasing annealing temperature in the range between 100 and 500°C. After 600–700°C annealing, the defect-rich region expanded up to about 170 nm, which was attributed to rearrangements of dislocation networks, and a resultant emission of point defects toward the inside of the sample. Above 800°C, the stability limit of those vacancies was reached and they started to disappear. After the vacancies were annealed out (900°C), oxygen-related defects were the major point defects and they were located at <25 nm.

Defective TiO2 with oxygen vacancies: synthesis, properties and photocatalytic applications

Science.gov (United States)

Pan, Xiaoyang; Yang, Min-Quan; Fu, Xianzhi; Zhang, Nan; Xu, Yi-Jun

2013-04-01

Titanium dioxide (TiO2), as an important semiconductor metal oxide, has been widely investigated in the field of photocatalysis. The properties of TiO2, including its light absorption, charge transport and surface adsorption, are closely related to its defect disorder, which in turn plays a significant role in the photocatalytic performance of TiO2. Among all the defects identified in TiO2, oxygen vacancy is one of the most important and is supposed to be the prevalent defect in many metal oxides, which has been widely investigated both by theoretical calculations and experimental characterizations. Here, we give a short review on the existing strategies for the synthesis of defective TiO2 with oxygen vacancies, and the defect related properties of TiO2 including structural, electronic, optical, dissociative adsorption and reductive properties, which are intimately related to the photocatalytic performance of TiO2. In particular, photocatalytic applications with regard to defective TiO2 are outlined. In addition, we offer some perspectives on the challenge and new direction for future research in this field. We hope that this tutorial minireview would provide some useful contribution to the future design and fabrication of defective semiconductor-based nanomaterials for diverse photocatalytic applications.Titanium dioxide (TiO2), as an important semiconductor metal oxide, has been widely investigated in the field of photocatalysis. The properties of TiO2, including its light absorption, charge transport and surface adsorption, are closely related to its defect disorder, which in turn plays a significant role in the photocatalytic performance of TiO2. Among all the defects identified in TiO2, oxygen vacancy is one of the most important and is supposed to be the prevalent defect in many metal oxides, which has been widely investigated both by theoretical calculations and experimental characterizations. Here, we give a short review on the existing strategies for the

Stability and mobility of defect clusters and dislocation loops in metals

DEFF Research Database (Denmark)

Osetsky, Y.N.; Bacon, D.J.; Serra, A.

2000-01-01

has been observed in the computer simulation of small vacancy loops in alpha-Fe. In the present paper we summarise results obtained by molecular dynamics simulations of defect clusters and small dislocation loops in alpha-Fe(bcc) and Cu(fcc). The structure and stability of vacancy and interstitial......According to the production bias model, glissile defect clusters and small dislocation loops play an important role in the microstructural evolution during irradiation under cascade damage conditions. The atomic scale computer simulations carried out in recent years have clarified many questions...... loops are reviewed, and the dynamics of glissile clusters assessed. The relevance and importance of these results in establishing a better understanding of the observed differences in the damage accumulation behaviour between bcc and fee metals irradiated under cascade damage conditions are pointed out...

Defect kinetics and resistance to amorphization in zirconium carbide

International Nuclear Information System (INIS)

Zheng, Ming-Jie; Szlufarska, Izabela; Morgan, Dane

2015-01-01

To better understand the radiation response of zirconium carbide (ZrC), and in particular its excellent resistance to amorphization, we have used density functional theory methods to study the kinetics of point defects in ZrC. The migration barriers and recombination barriers of the simple point defects are calculated using the ab initio molecular dynamics simulation and the nudged elastic band method. These barriers are used to estimate C and Zr interstitial and vacancy diffusion and Frenkel pair recombination rates. A significant barrier for C Frenkel pair recombination is found but it is shown that a large concentration of C vacancies reduces this barrier dramatically, allowing facile healing of radiation damage. The mechanisms underlying high resistance to amorphization of ZrC were analyzed from the perspectives of structural, thermodynamic, chemical and kinetic properties. This study provides insights into the amorphization resistance of ZrC as well as a foundation for understanding general radiation damage in this material

The Co-Occurrence of Autism and Birth Defects: Prevalence and Risk in a Population-Based Cohort

Science.gov (United States)

Schendel, Diana E.; Autry, Andrew; Wines, Roberta; Moore, Cynthia

2009-01-01

Aim: To estimate the prevalence of major birth defects among children with autism, the prevalence of autism in children with birth defects, and the risk for autism associated with having birth defects. Method: Retrospective cohort including all children born in Atlanta, GA, USA, 1986 to 1993, who survived to age 3 years and were identified through…

Drought Tolerance in Pinus halepensis Seed Sources As Identified by Distinctive Physiological and Molecular Markers.

Science.gov (United States)

Taïbi, Khaled; Del Campo, Antonio D; Vilagrosa, Alberto; Bellés, José M; López-Gresa, María Pilar; Pla, Davinia; Calvete, Juan J; López-Nicolás, José M; Mulet, José M

2017-01-01

Drought is one of the main constraints determining forest species growth, survival and productivity, and therefore one of the main limitations for reforestation or afforestation. The aim of this study is to characterize the drought response at the physiological and molecular level of different Pinus halepensis (common name Aleppo pine) seed sources, previously characterized in field trials as drought-sensitive or drought-tolerant. This approach aims to identify different traits capable of predicting the ability of formerly uncharacterized seedlings to cope with drought stress. Gas-exchange, water potential, photosynthetic pigments, soluble sugars, free amino acids, glutathione and proteomic analyses were carried out on control and drought-stressed seedlings in greenhouse conditions. Gas-exchange determinations were also assessed in field-planted seedlings in order to validate the greenhouse experimental conditions. Drought-tolerant seed sources presented higher values of photosynthetic rates, water use efficiency, photosynthetic pigments and soluble carbohydrates concentrations. We observed the same pattern of variation of photosynthesis rate and maximal efficiency of PSII in field. Interestingly drought-tolerant seed sources exhibited increased levels of glutathione, methionine and cysteine. The proteomic profile of drought tolerant seedlings identified two heat shock proteins and an enzyme related to methionine biosynthesis that were not present in drought sensitive seedlings, pointing to the synthesis of sulfur amino acids as a limiting factor for drought tolerance in Pinus halepensis . Our results established physiological and molecular traits useful as distinctive markers to predict drought tolerance in Pinus halepensis provenances that could be reliably used in reforestation programs in drought prone areas.

Drought Tolerance in Pinus halepensis Seed Sources As Identified by Distinctive Physiological and Molecular Markers

Directory of Open Access Journals (Sweden)

Khaled Taïbi

2017-07-01

Full Text Available Drought is one of the main constraints determining forest species growth, survival and productivity, and therefore one of the main limitations for reforestation or afforestation. The aim of this study is to characterize the drought response at the physiological and molecular level of different Pinus halepensis (common name Aleppo pine seed sources, previously characterized in field trials as drought-sensitive or drought-tolerant. This approach aims to identify different traits capable of predicting the ability of formerly uncharacterized seedlings to cope with drought stress. Gas-exchange, water potential, photosynthetic pigments, soluble sugars, free amino acids, glutathione and proteomic analyses were carried out on control and drought-stressed seedlings in greenhouse conditions. Gas-exchange determinations were also assessed in field-planted seedlings in order to validate the greenhouse experimental conditions. Drought-tolerant seed sources presented higher values of photosynthetic rates, water use efficiency, photosynthetic pigments and soluble carbohydrates concentrations. We observed the same pattern of variation of photosynthesis rate and maximal efficiency of PSII in field. Interestingly drought-tolerant seed sources exhibited increased levels of glutathione, methionine and cysteine. The proteomic profile of drought tolerant seedlings identified two heat shock proteins and an enzyme related to methionine biosynthesis that were not present in drought sensitive seedlings, pointing to the synthesis of sulfur amino acids as a limiting factor for drought tolerance in Pinus halepensis. Our results established physiological and molecular traits useful as distinctive markers to predict drought tolerance in Pinus halepensis provenances that could be reliably used in reforestation programs in drought prone areas.

Related Structure Characters and Stability of Structural Defects in a Metallic Glass.

Science.gov (United States)

Niu, Xiaofeng; Feng, Shidong; Pan, Shaopeng

2018-03-22

Structural defects were investigated by a recently proposed structural parameter, quasi-nearest atom (QNA), in a modeled Zr 50 Cu 50 metallic glass through molecular dynamics simulations. More QNAs around an atom usually means that more defects are located near the atom. Structural analysis reveals that the spatial distribution of the numbers of QNAs displays to be clearly heterogeneous. Furthermore, QNA is closely correlated with cluster connections, especially four-atom cluster connections. Atoms with larger coordination numbers usually have less QNAs. When two atoms have the same coordination number, the atom with larger five-fold symmetry has less QNAs. The number of QNAs around an atom changes rather frequently and the change of QNAs might be correlated with the fast relaxation metallic glasses.

Related Structure Characters and Stability of Structural Defects in a Metallic Glass

Science.gov (United States)

Niu, Xiaofeng; Feng, Shidong; Pan, Shaopeng

2018-01-01

Structural defects were investigated by a recently proposed structural parameter, quasi-nearest atom (QNA), in a modeled Zr50Cu50 metallic glass through molecular dynamics simulations. More QNAs around an atom usually means that more defects are located near the atom. Structural analysis reveals that the spatial distribution of the numbers of QNAs displays to be clearly heterogeneous. Furthermore, QNA is closely correlated with cluster connections, especially four-atom cluster connections. Atoms with larger coordination numbers usually have less QNAs. When two atoms have the same coordination number, the atom with larger five-fold symmetry has less QNAs. The number of QNAs around an atom changes rather frequently and the change of QNAs might be correlated with the fast relaxation metallic glasses. PMID:29565298

Influence of ion irradiation induced defects on mechanical properties of copper nanowires

International Nuclear Information System (INIS)

Li, Weina; Sun, Lixin; Xue, Jianming; Wang, Jianxiang; Duan, Huiling

2013-01-01

The mechanical properties of copper nanowires irradiated with energetic ions have been investigated by using molecular dynamics simulations. The Cu ions with energies ranging from 0.2 to 8.0 keV are used in our simulation, and both the elastic properties and yields under tension and compression are analyzed. The results show that two kinds of defects, namely point defects and stacking faults, appear in the irradiated nanowires depending on the incident ion energy. The Young modulus is significantly reduced by the ion irradiation, and the reduction magnitude depends on the vacancy number, which is determined by the ion energy. Moreover, the irradiated nanowires yield at a smaller strain, compared with the unirradiated nanowire. The mechanism for these changes are also discussed

A systems biology pipeline identifies new immune and disease related molecular signatures and networks in human cells during microgravity exposure.

Science.gov (United States)

Mukhopadhyay, Sayak; Saha, Rohini; Palanisamy, Anbarasi; Ghosh, Madhurima; Biswas, Anupriya; Roy, Saheli; Pal, Arijit; Sarkar, Kathakali; Bagh, Sangram

2016-05-17

Microgravity is a prominent health hazard for astronauts, yet we understand little about its effect at the molecular systems level. In this study, we have integrated a set of systems-biology tools and databases and have analysed more than 8000 molecular pathways on published global gene expression datasets of human cells in microgravity. Hundreds of new pathways have been identified with statistical confidence for each dataset and despite the difference in cell types and experiments, around 100 of the new pathways are appeared common across the datasets. They are related to reduced inflammation, autoimmunity, diabetes and asthma. We have identified downregulation of NfκB pathway via Notch1 signalling as new pathway for reduced immunity in microgravity. Induction of few cancer types including liver cancer and leukaemia and increased drug response to cancer in microgravity are also found. Increase in olfactory signal transduction is also identified. Genes, based on their expression pattern, are clustered and mathematically stable clusters are identified. The network mapping of genes within a cluster indicates the plausible functional connections in microgravity. This pipeline gives a new systems level picture of human cells under microgravity, generates testable hypothesis and may help estimating risk and developing medicine for space missions.

A systems biology pipeline identifies new immune and disease related molecular signatures and networks in human cells during microgravity exposure

Science.gov (United States)

Mukhopadhyay, Sayak; Saha, Rohini; Palanisamy, Anbarasi; Ghosh, Madhurima; Biswas, Anupriya; Roy, Saheli; Pal, Arijit; Sarkar, Kathakali; Bagh, Sangram

2016-05-01

Microgravity is a prominent health hazard for astronauts, yet we understand little about its effect at the molecular systems level. In this study, we have integrated a set of systems-biology tools and databases and have analysed more than 8000 molecular pathways on published global gene expression datasets of human cells in microgravity. Hundreds of new pathways have been identified with statistical confidence for each dataset and despite the difference in cell types and experiments, around 100 of the new pathways are appeared common across the datasets. They are related to reduced inflammation, autoimmunity, diabetes and asthma. We have identified downregulation of NfκB pathway via Notch1 signalling as new pathway for reduced immunity in microgravity. Induction of few cancer types including liver cancer and leukaemia and increased drug response to cancer in microgravity are also found. Increase in olfactory signal transduction is also identified. Genes, based on their expression pattern, are clustered and mathematically stable clusters are identified. The network mapping of genes within a cluster indicates the plausible functional connections in microgravity. This pipeline gives a new systems level picture of human cells under microgravity, generates testable hypothesis and may help estimating risk and developing medicine for space missions.

Computed tomography angiography intraluminal filling defect is predictive of internal carotid artery free-floating thrombus

Energy Technology Data Exchange (ETDEWEB)

Jaberi, A.; Lum, C.; Stefanski, P.; Iancu, D. [University of Ottawa, Faculty of Medicine, Ottawa, Ontario (Canada); The Ottawa Hospital, Department of Radiology, Neuroradiology Section, Ottawa, Ontario (Canada); Thornhill, R. [Neurosciences and Clinical Epidemiology Program/Methods Centre, Ottawa Hospital Research Institute, Ottawa, Ontario (Canada); The Ottawa Hospital, Department of Radiology, Neuroradiology Section, Ottawa, Ontario (Canada); Petrcich, W. [Neurosciences and Clinical Epidemiology Program/Methods Centre, Ottawa Hospital Research Institute, Ottawa, Ontario (Canada); Momoli, F. [Children' s Hospital of Eastern Ontario Research Institute, Ottawa, Ontario (Canada); University of Ottawa, Department of Epidemiology and Community Medicine, Ottawa, Ontario (Canada); Torres, C.; Dowlatshahi, D. [University of Ottawa, Faculty of Medicine, Ottawa, Ontario (Canada); University of Ottawa, Division of Neurology, Department of Medicine, Ottawa, Ontario (Canada)

2014-01-15

Filling defects at the internal carotid artery (ICA) origin in the work-up of stroke or transient ischemic attack may be an ulcerated plaque or free-floating thrombus (FFT). This may be challenging to distinguish, as they can appear morphologically similar. This is an important distinction as FFT can potentially embolize distally, and its management differs. We describe a series of patients with suspected FFT and evaluate its imaging appearance, clinical features, and evolution with therapy. Between 2008 and 2013, we prospectively collected consecutive patients with proximal ICA filling defects in the axial plane surrounded by contrast on CT/MR angiography. We defined FFT as a filling defect that resolved on follow-up imaging. We assessed the cranial-caudal dimension of the filling defect and receiver operating characteristics to identify clinical and radiological variables that distinguished FFT from complex ulcerated plaque. Intraluminal filling defects were identified in 32 patients. Filling defects and resolved or decreased in 25 patients (78 %) and felt to be FFT; there was no change in 7 (22 %). Resolved defects and those that decreased in size extended more cranially than those that remained unchanged: 7.3 mm (4.2-15.9) versus 3.1 mm (2.7-3.7; p = 0.0038). Receiver operating characteristic analysis established a threshold of 3.8 mm (filling defect length), sensitivity of 88 %, specificity of 86 %, and area under the curve of 0.86 (p < 0.0001) for distinguishing FFT from plaque. Filling defects in the proximal ICA extending cranially >3.8 mm were more likely to be FFT than complex ulcerated plaque. Further studies evaluating filling defect length as a predictor for FFT are warranted. (orig.)

Application of artificial neural networks to evaluate weld defects of nuclear components

International Nuclear Information System (INIS)

Amin, E.S.

2007-01-01

Artificial neural networks (ANNs) are computational representations based on the biological neural architecture of the brain. ANNs have been successfully applied to a wide range of engineering and scientific applications, such as signal, image processing and data analysis. Although Radiographic testing is widely used for welding defects, it is unsuccessful in identifying some welding defects because of the nature of image formation and quality. Neoteric algorithms have been used for the purpose of weld defects identifications in radiographic images to replace the expert knowledge. The application of artificial neural networks in noise detection of radiographic films is used. Radial Basis (RB) and learning vector quantization (LVQ) were applied. The method shows good performance in weld defects recognition and classification problems.

Facts about Birth Defects

Science.gov (United States)

... label> Information For… Media Policy Makers Facts about Birth Defects Language: English (US) Español (Spanish) Recommend on ... having a baby born without a birth defect. Birth Defects Are Common Every 4 ½ minutes, a ...

Intrinsic and extrinsic defects in a family of coal-derived graphene quantum dots

Energy Technology Data Exchange (ETDEWEB)

Singamaneni, Srinivasa Rao, E-mail: ssingam@ncsu.edu, E-mail: tour@rice.edu [Materials Science Division, Army Research Office, Research Triangle Park, North Carolina 27709 (United States); Department of Material Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695 (United States); Tol, Johan van [National High Magnetic Field Laboratory, Florida State University, 1800 E. Paul Dirac Drive, Tallahassee, Florida 32310 (United States); Ye, Ruquan [Department of Chemistry, Rice University, MS-222, 6100 Main Street, Houston, Texas 77005 (United States); Tour, James M., E-mail: ssingam@ncsu.edu, E-mail: tour@rice.edu [Department of Chemistry, Rice University, MS-222, 6100 Main Street, Houston, Texas 77005 (United States); Department of Materials Science and NanoEngineering, Rice University, MS-222, 6100 Main Street, Houston, Texas 77005 (United States); Smalley Institute for Nanoscale Science and Technology, Rice University, MS-222, 6100 Main Street, Houston, Texas 77005 (United States)

2015-11-23

In this letter, we report on the high frequency (239.2 and 336 GHz) electron spin resonance (ESR) studies performed on graphene quantum dots (GQDs), prepared through a wet chemistry route from three types of coal: (a) bituminous, (b) anthracite, and (c) coke; and from non-coal derived GQDs. The microwave frequency-, power-, and temperature-dependent ESR spectra coupled with computer-aided simulations reveal four distinct magnetic defect centers. In bituminous- and anthracite-derived GQDs, we have identified two of them as intrinsic carbon-centered magnetic defect centers (a broad signal of peak to peak width = 697 (10{sup −4} T), g = 2.0023; and a narrow signal of peak to peak width = 60 (10{sup −4} T), g = 2.003). The third defect center is Mn{sup 2+} ({sup 6}S{sub 5/2}, 3d{sup 5}) (signal width = 61 (10{sup −4} T), g = 2.0023, A{sub iso} = 93(10{sup −4} T)), and the fourth defect is identified as Cu{sup 2+} ({sup 2}D{sub 5/2}, 3d{sup 9}) (g{sub ⊥} = 2.048 and g{sub ‖} = 2.279), previously undetected. Coke-derived and non-coal derived GQDs show Mn{sup 2+} and two-carbon related signals, and no Cu{sup 2+} signal. The extrinsic impurities most likely originate from the starting coal. Furthermore, Raman, photoluminescence, and ESR measurements detected no noticeable changes in the properties of the bituminous GQDs after one year. This study highlights the importance of employing high frequency ESR spectroscopy in identifying the (magnetic) defects, which are roadblocks for spin relaxation times of graphene-based materials. These defects would not have been possible to probe by other spin transport measurements.

PNPLA1 Deficiency in Mice and Humans Leads to a Defect in the Synthesis of Omega-O-Acylceramides

Science.gov (United States)

Grond, Susanne; Eichmann, Thomas O.; Dubrac, Sandrine; Kolb, Dagmar; Schmuth, Matthias; Fischer, Judith; Crumrine, Debra; Elias, Peter M.; Haemmerle, Guenter; Zechner, Rudolf; Lass, Achim; Radner, Franz P.W.

2017-01-01

Mutations in PNPLA1 have been identified as causative for autosomal recessive congenital ichthyosis in humans and dogs. So far, the underlying molecular mechanisms are unknown. In this study, we generated and characterized PNPLA1-deficient mice and found that PNPLA1 is crucial for epidermal sphingolipid synthesis. The absence of functional PNPLA1 in mice impaired the formation of omega-O-acylceramides and led to an accumulation of nonesterified omega-hydroxy-ceramides. As a consequence, PNPLA1-deficient mice lacked a functional corneocyte-bound lipid envelope leading to a severe skin barrier defect and premature death of newborn animals. Functional analyses of differentiated keratinocytes from a patient with mutated PNPLA1 demonstrated an identical defect in omega-O-acylceramide synthesis in human cells, indicating that PNPLA1 function is conserved among mammals and indispensable for normal skin physiology. Notably, topical application of epidermal lipids from wild-type onto Pnpla1-mutant mice promoted rebuilding of the corneocyte-bound lipid envelope, indicating that supplementation of ichthyotic skin with omega-O-acylceramides might be a therapeutic approach for the treatment of skin symptoms in individuals affected by omega-O-acylceramide deficiency. PMID:27751867

Molecular dynamics simulations of irradiation cascades in alpha-zirconium under macroscopic strain

Energy Technology Data Exchange (ETDEWEB)

Di, Sali [Department of Mechanical and Materials Engineering, Queen’s University, Kingston, ON, Canada K7L 3N6 (Canada); Yao, Zhongwen, E-mail: yaoz@me.queensu.ca [Department of Mechanical and Materials Engineering, Queen’s University, Kingston, ON, Canada K7L 3N6 (Canada); Daymond, Mark R. [Department of Mechanical and Materials Engineering, Queen’s University, Kingston, ON, Canada K7L 3N6 (Canada); Gao, Fei [Pacific Northwest National Laboratory, Richland, WA 99352 (United States)

2013-05-15

Numerous computer simulation studies have been performed on the radiation damage of zirconium. In contrast to most of the work in the literature which has focused on the effects of temperature and recoil energy on defect production and defect clustering, we have developed a computational model to consider the influence of elastic strain field on the formation of defects and their clusters, as strain is commonly present in a real reactor environment. In this work, irradiation induced displacement cascades in alpha-zirconium experiencing a macroscopic strain have been studied by molecular dynamics (MD) simulations using a many-body interatomic potential. The external strain mainly affects the size of defect clusters rather than the total number of defects. The sizes of interstitial and vacancy clusters respond differently to the external strain conditions.