Oscillation of Branching Ratios Between the D (2 s )+D (1 s ) and the D (2 p )+D (1 s ) Channels in Direct Photodissociation of D2

NASA Astrophysics Data System (ADS)

Wang, Jie; Meng, Qingnan; Mo, Yuxiang

2017-08-01

The direct photodissociation of D2 at excitation energies above 14.76 eV occurs via two channels, D (2 s )+D (1 s ) and D (2 p )+D (1 s ) . The branching ratios between the two have been measured from the dissociation threshold to 3200 cm-1 above it, and it is found that they show cosine oscillations as a function of the fragment wave vector magnitudes. The oscillation is due to an interference effect and can be simulated using the phase difference between the wave functions of the two channels, analogous to Young's double-slit experiment. By fitting the measured branching ratios, we have determined the depths and widths of the effective spherical potential wells related to the two channels, which are in agreement with the effective depths and widths of the ab initio interaction potentials. The results of this Letter illustrate the importance of the relative phase between the fragments in controlling the branching ratios of the photodissociation channels.

Note: Coherent resonances observed in the dissociative electron attachment to carbon monoxide

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

Wang, Xu-Dong; Xuan, Chuan-Jin; Tian, Shan Xi, E-mail: sxtian@ustc.edu.cn

Succeeding our previous finding about coherent interference of the resonant states of CO{sup −} formed by the low-energy electron attachment [Tian et al. Phys. Rev. A 88, 012708 (2013)], here we provide further evidence of the coherent interference. The completely backward distributions of the O{sup −} fragment of the temporary CO{sup −} are observed with anion velocity map imaging technique in an electron energy range of 11.3–12.6 eV and explained as the results of the coherent interferences of three resonant states. Furthermore, the state configuration of the interference is changed with the increase of electron attachment energy.

Quantification of Lysine Acetylation and Succinylation Stoichiometry in Proteins Using Mass Spectrometric Data-Independent Acquisitions (SWATH)

DOE PAGES

Meyer, Jesse G.; D’Souza, Alexandria K.; Sorensen, Dylan J.; ...

2016-09-02

Post-translational modification of lysine residues by N ε-acylation is an important regulator of protein function. Many large-scale protein acylation studies have assessed relative changes of lysine acylation sites after antibody enrichment using mass spectrometry-based proteomics. Although relative acylation fold-changes are important, this does not reveal site occupancy, or stoichiometry, of individual modification sites, which is critical to understand functional consequences. Recently, methods for determining lysine acetylation stoichiometry have been proposed based on ratiometric analysis of endogenous levels to those introduced after quantitative per-acetylation of proteins using stable isotope-labeled acetic anhydride. However, in our hands, we find that these methods canmore » overestimate acetylation stoichiometries because of signal interferences when endogenous levels of acylation are very low, which is especially problematic when using MS1 scans for quantification. In this study, we sought to improve the accuracy of determining acylation stoichiometry using data-independent acquisition (DIA). Specifically, we use SWATH acquisition to comprehensively collect both precursor and fragment ion intensity data. The use of fragment ions for stoichiometry quantification not only reduces interferences but also allows for determination of site-level stoichiometry from peptides with multiple lysine residues. We also demonstrate the novel extension of this method to measurements of succinylation stoichiometry using deuterium-labeled succinic anhydride. Proof of principle SWATH acquisition studies were first performed using bovine serum albumin for both acetylation and succinylation occupancy measurements, followed by the analysis of more complex samples of E. coli cell lysates. Although overall site occupancy was low (<1%), some proteins contained lysines with relatively high acetylation occupancy.« less

Amplified fragment length polymorphism analysis to assess crossover interference and homozygosity in gynogenetic diploid Pacific abalone (Haliotis discus hannai).

PubMed

Nie, H-T; Li, Q; Kong, L-F

2014-06-01

Recombination analysis in gynogenetic diploids is a powerful tool for assessing the degree of inbreeding, investigating crossover events and understanding chiasma interference during meiosis. To estimate the marker-centromere recombination rate, the inheritance pattern of 654 amplified fragment length polymorphism (AFLP) markers was examined in the 72-h veliger larvae of two meiogynogenetic diploid families in the Pacific abalone (Haliotis discus hannai). The second-division segregation frequency (y) of the AFLP loci ranged from 0.00 to 0.96, with 23.9% of loci showing y-values higher than 0.67, evidencing the existence of interference. The average recombination frequency across the 654 AFLP loci was 0.45, allowing estimation of the fixation index of 0.55, indicating that meiotic gynogenesis could provide an effective means of rapid inbreeding in the Pacific abalone. The AFLP loci have a small proportion (4.4%) of y-values greater than 0.90, suggesting that a relatively low or intermediate degree of chiasma interference occurred in the abalone chromosomes. The information obtained in this study will enhance our understanding of the abalone genome and will be useful for genetic studies in the species. © 2014 Stichting International Foundation for Animal Genetics.

Activation of different split functionalities upon re-association of RNA-DNA hybrids

PubMed Central

Afonin, Kirill A.; Viard, Mathias; Martins, Angelica N.; Lockett, Stephen J.; Maciag, Anna E.; Freed, Eric O.; Heldman, Eliahu; Jaeger, Luc; Blumenthal, Robert; Shapiro, Bruce A.

2013-01-01

Split-protein systems, an approach that relies on fragmentation of proteins with their further conditional re-association to form functional complexes, are increasingly used for various biomedical applications. This approach offers tight control of the protein functions and improved detection sensitivity. Here we show a similar technique based on a pair of RNA-DNA hybrids that can be generally used for triggering different split functionalities. Individually, each hybrid is inactive but when two cognate hybrids re-associate, different functionalities are triggered inside mammalian cells. As a proof of concept this work is mainly focused on activation of RNA interference; however the release of other functionalities (resonance energy transfer and RNA aptamer) is also shown. Furthermore, in vivo studies demonstrate a significant uptake of the hybrids by tumors together with specific gene silencing. This split-functionality approach presents a new route in the development of “smart” nucleic acids based nanoparticles and switches for various biomedical applications. PMID:23542902

Identification of E-cadherin signature motifs functioning as cleavage sites for Helicobacter pylori HtrA

NASA Astrophysics Data System (ADS)

Schmidt, Thomas P.; Perna, Anna M.; Fugmann, Tim; Böhm, Manja; Jan Hiss; Haller, Sarah; Götz, Camilla; Tegtmeyer, Nicole; Hoy, Benjamin; Rau, Tilman T.; Neri, Dario; Backert, Steffen; Schneider, Gisbert; Wessler, Silja

2016-03-01

The cell adhesion protein and tumour suppressor E-cadherin exhibits important functions in the prevention of gastric cancer. As a class-I carcinogen, Helicobacter pylori (H. pylori) has developed a unique strategy to interfere with E-cadherin functions. In previous studies, we have demonstrated that H. pylori secretes the protease high temperature requirement A (HtrA) which cleaves off the E-cadherin ectodomain (NTF) on epithelial cells. This opens cell-to-cell junctions, allowing bacterial transmigration across the polarised epithelium. Here, we investigated the molecular mechanism of the HtrA-E-cadherin interaction and identified E-cadherin cleavage sites for HtrA. Mass-spectrometry-based proteomics and Edman degradation revealed three signature motifs containing the [VITA]-[VITA]-x-x-D-[DN] sequence pattern, which were preferentially cleaved by HtrA. Based on these sites, we developed a substrate-derived peptide inhibitor that selectively bound and inhibited HtrA, thereby blocking transmigration of H. pylori. The discovery of HtrA-targeted signature sites might further explain why we detected a stable 90 kDa NTF fragment during H. pylori infection, but also additional E-cadherin fragments ranging from 105 kDa to 48 kDa in in vitro cleavage experiments. In conclusion, HtrA targets E-cadherin signature sites that are accessible in in vitro reactions, but might be partially masked on epithelial cells through functional homophilic E-cadherin interactions.

Pre-stressor cognitive control is related to intrusive cognition of a stressful film.

PubMed

Wessel, Ineke; Overwijk, Sippie; Verwoerd, Johan; de Vrieze, Nienke

2008-04-01

It has been suggested that relatively weak cognitive control existing prior to a stressful event may be associated with intrusive memories of that stressor afterwards. We explored this in two analog studies employing unselected participants who saw an emotional film fragment and completed behavioral (i.e., color-naming interference [CNI]) and self-report indices of intrusions. Prior to film presentation, several cognitive control tests were administered. Study 1 showed that better updating/monitoring was linked to less CNI from negative film-related words. However, better updating/monitoring was associated with more diary reports of intrusive memories. Study 2 showed that a better resistance to pro-active interference (PI) predicted less self-reported film-related intrusive cognition after 24h. However, after this delay, both self-reported intrusions and CNI were not related to updating/monitoring. Taken together, the results suggest that a specific pre-existing cognitive control function (i.e., resistance to PI) may be involved in the regulation of post-stressor intrusive memory phenomena.

Organelle targeting during bacterial infection: insights from Listeria.

PubMed

Lebreton, Alice; Stavru, Fabrizia; Cossart, Pascale

2015-06-01

Listeria monocytogenes, a facultative intracellular bacterium responsible for severe foodborne infections, is now recognized as a multifaceted model in infection biology. Comprehensive studies of the molecular and cellular basis of the infection have unraveled how the bacterium crosses the intestinal and feto-placental barriers, invades several cell types in which it multiplies and moves, and spreads from cell to cell. Interestingly, although Listeria does not actively invade host cell organelles, it can interfere with their function. We discuss the effect of Listeria on the endoplasmic reticulum (ER) and the mechanisms leading to the fragmentation of the mitochondrial network and its consequences, and review the strategies used by Listeria to subvert nuclear functions, more precisely to control host gene expression at the chromatin level. Copyright © 2015 Elsevier Ltd. All rights reserved.

Different molecular mechanisms involved in spontaneous and oxidative stress-induced mitochondrial fragmentation in tripeptidyl peptidase-1 (TPP-1)-deficient fibroblasts

PubMed Central

Van Beersel, Guillaume; Tihon, Eliane; Demine, Stéphane; Hamer, Isabelle; Jadot, Michel; Arnould, Thierry

2012-01-01

NCLs (neuronal ceroid lipofuscinoses) form a group of eight inherited autosomal recessive diseases characterized by the intralysosomal accumulation of autofluorescent pigments, called ceroids. Recent data suggest that the pathogenesis of NCL is associated with the appearance of fragmented mitochondria with altered functions. However, even if an impairement in the autophagic pathway has often been evoked, the molecular mechanisms leading to mitochondrial fragmentation in response to a lysosomal dysfunction are still poorly understood. In this study, we show that fibroblasts that are deficient for the TPP-1 (tripeptidyl peptidase-1), a lysosomal hydrolase encoded by the gene mutated in the LINCL (late infantile NCL, CLN2 form) also exhibit a fragmented mitochondrial network. This morphological alteration is accompanied by an increase in the expression of the protein BNIP3 (Bcl2/adenovirus E1B 19 kDa interacting protein 3) as well as a decrease in the abundance of mitofusins 1 and 2, two proteins involved in mitochondrial fusion. Using RNAi (RNA interference) and quantitative analysis of the mitochondrial morphology, we show that the inhibition of BNIP3 expression does not result in an increase in the reticulation of the mitochondrial population in LINCL cells. However, this protein seems to play a key role in cell response to mitochondrial oxidative stress as it sensitizes mitochondria to antimycin A-induced fragmentation. To our knowledge, our results bring the first evidence of a mechanism that links TPP-1 deficiency and oxidative stress-induced changes in mitochondrial morphology. PMID:23249249

Identification and characterization of glycation adducts on osteocalcin

PubMed Central

Thomas, Corinne J.; Cleland, Timothy P.; Zhang, Sheng; Gundberg, Caren M.; Vashishth, Deepak

2017-01-01

Osteocalcin is an important extracellular matrix bone protein that contributes to the structural properties of bone through its interactions with hydroxyapatite mineral and with collagen I. This role may be affected by glycation, a labile modification the levels of which has been shown to correlate with bone fragility. Glycation starts with the spontaneous addition of a sugar onto a free amine group on a protein, forming an Amadori product, and then proceeds through several environment-dependent stages resulting in the formation of an advanced glycation end product. Here, we induce the first step of this modification on synthetic osteocalcin, and then use multiple mass spectrometry fragmentation techniques to determine the location of this modification. Collision-induced dissociation resulted in spectra dominated by neutral loss, and was unable to identify Amadori products. Electron-transfer dissociation showed that the Amadori product formed solely on osteocalcin’s N-terminus. This suggests that the glycation of osteocalcin is unlikely to interfere with osteocalcin’s interaction with hydroxyapatite. Instead, glycation may interfere with its interaction with collagen I or another bone protein, osteopontin. Potentially, the levels of glycated osteocalcin fragments released from bone during bone resorption could be used to assess bone quality, should the N-terminal fragments be targeted. PMID:28237256

Sperm DNA fragmentation affects epigenetic feature in human male pronucleus.

PubMed

Rajabi, H; Mohseni-Kouchesfehani, H; Eslami-Arshaghi, T; Salehi, M

2018-02-01

To evaluate whether the sperm DNA fragmentation affects male pronucleus epigenetic factors, semen analysis was performed and DNA fragmentation was assessed by the method of sperm chromatin structure assay (SCSA). Human-mouse interspecies fertilisation was used to create human male pronucleus. Male pronucleus DNA methylation and H4K12 acetylation were evaluated by immunostaining. Results showed a significant positive correlation between the level of sperm DNA fragmentation and DNA methylation in male pronuclei. In other words, an increase in DNA damage caused an upsurge in DNA methylation. In the case of H4K12 acetylation, no correlation was detected between DNA damage and the level of histone acetylation in the normal group, but results for the group in which male pronuclei were derived from sperm cells with DNA fragmentation, increased DNA damage led to a decreased acetylation level. Sperm DNA fragmentation interferes with the active demethylation process and disrupts the insertion of histones into the male chromatin in the male pronucleus, following fertilisation. © 2017 Blackwell Verlag GmbH.

Structural analysis of binding functionality of folic acid-PEG dendrimers against folate receptor.

PubMed

Sampogna-Mireles, Diana; Araya-Durán, Ingrid D; Márquez-Miranda, Valeria; Valencia-Gallegos, Jesús A; González-Nilo, Fernando D

2017-03-01

Dendrimers functionalized with folic acid (FA) are drug delivery systems that can selectively target cancer cells with folate receptors (FR-α) overexpression. Incorporation of polyethylene glycol (PEG) can enhance dendrimers solubility and pharmacokinetics, but ligand-receptor binding must not be affected. In this work we characterized, at atomic level, the binding functionality of conventional site-specific dendrimers conjugated with FA with PEG 750 or PEG 3350 as a linker. After Molecular Dynamics simulation, we observed that both PEG's did not interfere over ligand-receptor binding functionality. Although binding kinetics could be notably affected, the folate fragment from both dendrimers remained exposed to the solvent before approaching selectively to FR-α. PEG 3350 provided better solubility and protection from enzymatic degradation to the dendrimer than PEG 750. Also, FA-PEG3350 dendrimer showed a slightly better interaction with FR-α than FA-PEG750 dendrimer. Therefore, theoretical evidence supports that both dendrimers are suitable as drug delivery systems for cancer therapies. Copyright © 2017 Elsevier Inc. All rights reserved.

Pathogen effector protein screening in yeast identifies Legionella factors that interfere with membrane trafficking.

PubMed

Shohdy, Nadim; Efe, Jem A; Emr, Scott D; Shuman, Howard A

2005-03-29

Legionella pneumophila invades and replicates intracellularly in human and protozoan hosts. The bacteria use the Icm/Dot type IVB secretion system to translocate effectors that inhibit phagosome maturation and modulate host vesicle trafficking pathways. To understand how L. pneumophila modulates organelle trafficking in host cells, we carried out pathogen effector protein screening in yeast, identifying L. pneumophila genes that produced membrane trafficking [vacuole protein sorting (VPS)] defects in yeast. We identified four L. pneumophila DNA fragments that perturb sorting of vacuolar proteins. Three encode ORFs of unknown function that are translocated via the Icm/Dot transporter from Legionella into macrophages. VPS inhibitor protein (Vip) A is a coiled-coil protein, VipD is a patatin domain-containing protein, and VipF contains an acetyltransferase domain. Processing studies in yeast indicate that VipA, VipD, and VipF inhibit lysosomal protein trafficking by different mechanisms; overexpressing VipA has an effect on carboxypeptidase Y trafficking, whereas VipD interferes with multivesicular body formation at the late endosome and endoplasmic reticulum-to-Golgi body transport. Such differences highlight the multiple strategies L. pneumophila effectors use to subvert host trafficking processes. Using yeast as an effector gene discovery tool allows for a powerful, genetic approach to both the identification of virulence factors and the study of their function.

Cas4 Facilitates PAM-Compatible Spacer Selection during CRISPR Adaptation.

PubMed

Kieper, Sebastian N; Almendros, Cristóbal; Behler, Juliane; McKenzie, Rebecca E; Nobrega, Franklin L; Haagsma, Anna C; Vink, Jochem N A; Hess, Wolfgang R; Brouns, Stan J J

2018-03-27

CRISPR-Cas systems adapt their immunological memory against their invaders by integrating short DNA fragments into clustered regularly interspaced short palindromic repeat (CRISPR) loci. While Cas1 and Cas2 make up the core machinery of the CRISPR integration process, various class I and II CRISPR-Cas systems encode Cas4 proteins for which the role is unknown. Here, we introduced the CRISPR adaptation genes cas1, cas2, and cas4 from the type I-D CRISPR-Cas system of Synechocystis sp. 6803 into Escherichia coli and observed that cas4 is strictly required for the selection of targets with protospacer adjacent motifs (PAMs) conferring I-D CRISPR interference in the native host Synechocystis. We propose a model in which Cas4 assists the CRISPR adaptation complex Cas1-2 by providing DNA substrates tailored for the correct PAM. Introducing functional spacers that target DNA sequences with the correct PAM is key to successful CRISPR interference, providing a better chance of surviving infection by mobile genetic elements. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Absence of furrowing activity following regional cortical tension reduction in sand dollar blastomere and fertilized egg fragment surfaces.

PubMed

Rappaport, R

1999-08-01

The purpose of the present investigation was to test experimentally the possibility that division mechanism establishment at the equator of sand dollar eggs may be a consequence of cortical tension gradients between the equator and the poles. Cytochalasin has been shown to decrease tension at the sea urchin egg surface. The concave ends of cytochalasin D-containing agarose cylinders were held against regions of the surface of Echinarachnius parma blastomeres and enucleated fertilized egg fragments. The ability to interfere with normal furrowing activity was used as a biological indicator of the effectiveness of cytochalasin. When agarose containing 2 microg/mL cytochalasin contacted the equatorial region of the blastomeres resulting from the first cleavage, or the equatorial surfaces of nucleated fertilized egg halves, furrowing was blocked, stalled or delayed, indicating that the concentration of cytochalasin was effective. When the same concentration of cytochalasin was applied to the poles, the cells and nucleated fertilized egg fragments divided in the same way as the controls, indicating that the effectiveness of the cytochalasin did not spread from the poles to the equator and that bisection did not interfere with the division of nucleated fertilized egg fragments. When the same concentration of cytochalasin was applied to diametrically opposed surfaces of enucleated, spherical egg fragments, there was no evidence of furrowing activity between the areas that contacted the cytochalasin or in any other part of the surface. Because of the tension-reducing effect of cytochalasin, a tension gradient existed between the regions affected and unaffected by cytochalasin. The results strongly suggest that establishment of the division mechanism by simple gradients of tension at the surface is unlikely.

Silencing the HaHR3 Gene by Transgenic Plant-mediated RNAi to Disrupt Helicoverpa armigera Development

PubMed Central

Xiong, Yehui; Zeng, Hongmei; Zhang, Yuliang; Xu, Dawei; Qiu, Dewen

2013-01-01

RNA interference (RNAi) caused by exogenous double-stranded RNA (dsRNA) has developed into a powerful technique in functional genomics, and to date it is widely used to down-regulate crucial physiology-related genes to control pest insects. A molt-regulating transcription factor gene, HaHR3, of cotton bollworm (Helicoverpa armigera) was selected as the target gene. Four different fragments covering the coding sequence (CDS) of HaHR3 were cloned into vector L4440 to express dsRNAs in Escherichia coli. The most effective silencing fragment was then cloned into a plant over-expression vector to express a hairpin RNA (hpRNA) in transgenic tobacco (Nicotiana tabacum). When H. armigera larvae were fed the E. coli or transgenic plants, the HaHR3 mRNA and protein levels dramatically decreased, resulting developmental deformity and larval lethality. The results demonstrate that both recombinant bacteria and transgenic plants could induce HaHR3 silence to disrupt H. armigera development, transgenic plant-mediated RNAi is emerging as a powerful approach for controlling insect pests. PMID:23630449

Tryptic digestion of human GPIIIa. Isolation and biochemical characterization of the 23 kDa N-terminal glycopeptide carrying the antigenic determinant for a monoclonal antibody (P37) which inhibits platelet aggregation.

PubMed Central

Calvete, J J; Rivas, G; Maruri, M; Alvarez, M V; McGregor, J L; Hew, C L; Gonzalez-Rodriguez, J

1988-01-01

Early digestion of pure human platelet glycoprotein IIIa (GPIIIa) leads to a single cleavage of the molecule at 23 kDa far from one of the terminal amino acids. Automated Edman degradation demonstrates that GPIIIa and the smaller (23 kDa) tryptic fragment share the same N-terminal amino acid sequence. A further cleavage occurs in the larger fragment (80 kDa), reducing its apparent molecular mass by 10 kDa. The 23 kDa fragment remains attached to the larger ones in unreduced samples. Stepwise reduction of early digested GPIIIa with dithioerythritol selectively reduces the single disulphide bond joining the smaller (23 kDa) to the larger (80/70 kDa) fragments. Two fractions were obtained by size-exclusion chromatography of early digested GPIIIa after partial or full reduction and alkylation. The larger-size fraction contains the 80/70 kDa fragments, while the 23 kDa fragment is isolated in the smaller. The amino acid compositions of these fractions do not differ very significantly from the composition of GPIIIa; however the 23 kDa fragment contains only 10.2% by weight of sugars and is richer in neuraminic acid. Disulphide bonds are distributed four in the 23 kDa glycopeptide and 20-21 in the 80/70 kDa glycopeptide. The epitope for P37, a monoclonal antibody which inhibits platelet aggregation [Melero & González-Rodríguez (1984) Eur. J. Biochem. 141, 421-427] is situated within the first 17 kDa of the N-terminal region of GPIIIa, which gives a special functional interest to this extracellular region of GPIIIa. On the other hand, the epitopes for GPIIIa-specific monoclonal antibodies, P6, P35, P40 and P97, which do not interfere with platelet aggregation, are located within the larger tryptic fragment (80/70 kDa). Thus, the antigenic areas available in the extracellular surface of GPIIIa for these five monoclonal antibodies are now more precisely delineated. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. PMID:2455507

The human T-cell leukemia virus type 1 p13II protein: effects on mitochondrial function and cell growth

PubMed Central

D’Agostino, DM; Silic-Benussi, M; Hiraragi, H; Lairmore, MD; Ciminale, V

2011-01-01

p13II of human T-cell leukemia virus type 1 (HTLV-1) is an 87-amino-acid protein that is targeted to the inner mitochondrial membrane. p13II alters mitochondrial membrane permeability, producing a rapid, membrane potential-dependent influx of K+. These changes result in increased mitochondrial matrix volume and fragmentation and may lead to depolarization and alterations in mitochondrial Ca2+ uptake/retention capacity. At the cellular level, p13II has been found to interfere with cell proliferation and transformation and to promote apoptosis induced by ceramide and Fas ligand. Assays carried out in T cells (the major targets of HTLV-1 infection in vivo) demonstrate that p13II-mediated sensitization to Fas ligand-induced apoptosis can be blocked by an inhibitor of Ras farnesylation, thus implicating Ras signaling as a downstream target of p13II function. PMID:15761473

Carrier-envelope phase control over pathway interference in strong-field dissociation of H2+.

PubMed

Kling, Nora G; Betsch, K J; Zohrabi, M; Zeng, S; Anis, F; Ablikim, U; Jochim, Bethany; Wang, Z; Kübel, M; Kling, M F; Carnes, K D; Esry, B D; Ben-Itzhak, I

2013-10-18

The dissociation of an H2+ molecular-ion beam by linearly polarized, carrier-envelope-phase-tagged 5 fs pulses at 4×10(14) W/cm2 with a central wavelength of 730 nm was studied using a coincidence 3D momentum imaging technique. Carrier-envelope-phase-dependent asymmetries in the emission direction of H+ fragments relative to the laser polarization were observed. These asymmetries are caused by interference of odd and even photon number pathways, where net zero-photon and one-photon interference predominantly contributes at H+ + H kinetic energy releases of 0.2-0.45 eV, and net two-photon and one-photon interference contributes at 1.65-1.9 eV. These measurements of the benchmark H2+ molecule offer the distinct advantage that they can be quantitatively compared with ab initio theory to confirm our understanding of strong-field coherent control via the carrier-envelope phase.

A vision of the environmental and occupational noise pollution in Malaysia.

PubMed

Yuen, Foo Keng

2014-01-01

Environmental noise remains a complex and fragmented interplay between industrialization, population growth, technological developments, and the living environment. Next to the circulatory diseases and cancer, noise pollution has been cited as the third epidemic cause of psychological and physiological disorders internationally. A reliable and firm relationship between the cumulative health implications with the traffic annoyance and occupational noise has been established. This agenda has called for an integrated, coordinated, and participatory approach to the reliable protection of noise interference. Despite several fragmented policies, legislation and global efforts have been addressed; the noise pollution complaints have been traditionally neglected in developing countries, especially in Malaysia. This paper was undertaken to postulate an initial platform to address the dynamic pressures, gigantic challenges, and tremendous impacts of noise pollution scenario in Malaysia. The emphasis is speculated on the traffic interference and assessment of industrial and occupational noise. The fundamental importance of noise monitoring and modeling is proposed. Additionally, the confronting conservation program and control measure for noise pollution control are laconically elucidated.

Msh2-Msh3 Interferes with Okazaki Fragment Processing to Promote Trinucleotide Repeat Expansions

PubMed Central

Kantartzis, Athena; Williams, Gregory M.; Balakrishnan, Lata; Roberts, Rick L.; Surtees, Jennifer A.; Bambara, Robert A.

2012-01-01

Summary Trinucleotide repeat (TNR) expansions are the underlying cause of more than forty neurodegenerative and neuromuscular diseases, including myotonic dystrophy and Huntington’s disease. Although genetic evidence has attributed the cause of these diseases to errors in DNA replication and/or repair, clear molecular mechanisms have not been described. We have focused on the role of the mismatch repair complex Msh2-Msh3 in promoting TNR expansions. We demonstrate that Msh2-Msh3 promotes CTG and CAG repeat expansions in vivo in Saccharomyces cerevisiae. We further provide biochemical evidence that Msh2-Msh3 directly interferes with normal Okazaki fragment processing by flap endonuclease1 (Rad27) and DNA Ligase I (Cdc9) in the presence of TNR sequences, thereby producing small, incremental expansion events. We believe that this is the first mechanistic evidence showing the interplay of replication and repair proteins in the expansion of sequences during lagging strand DNA replication. PMID:22938864

Msh2-Msh3 interferes with Okazaki fragment processing to promote trinucleotide repeat expansions.

PubMed

Kantartzis, Athena; Williams, Gregory M; Balakrishnan, Lata; Roberts, Rick L; Surtees, Jennifer A; Bambara, Robert A

2012-08-30

Trinucleotide repeat (TNR) expansions are the underlying cause of more than 40 neurodegenerative and neuromuscular diseases, including myotonic dystrophy and Huntington's disease. Although genetic evidence points to errors in DNA replication and/or repair as the cause of these diseases, clear molecular mechanisms have not been described. Here, we focused on the role of the mismatch repair complex Msh2-Msh3 in promoting TNR expansions. We demonstrate that Msh2-Msh3 promotes CTG and CAG repeat expansions in vivo in Saccharomyces cerevisiae. Furthermore, we provide biochemical evidence that Msh2-Msh3 directly interferes with normal Okazaki fragment processing by flap endonuclease1 (Rad27) and DNA ligase I (Cdc9) in the presence of TNR sequences, thereby producing small, incremental expansion events. We believe that this is the first mechanistic evidence showing the interplay of replication and repair proteins in the expansion of sequences during lagging-strand DNA replication. Copyright © 2012 The Authors. Published by Elsevier Inc. All rights reserved.

On the drag of model dendrite fragments at low Reynolds number

NASA Technical Reports Server (NTRS)

Zakhem, R.; Weidman, P. D.; Degroh, H. C., III

1993-01-01

An experimental study of low Reynolds number drag on laboratory models of dendrite fragments has been conducted. The terminal velocities of the dendrites undergoing free fall along their axis of symmetry were measured in a large Stokes flow facility. Corrections for wall interference give nearly linear drag vs Reynolds number curves. Corrections for both wall interference and inertia effects show that the dendrite Stokes settling velocities are always less than that of a sphere of equal mass and volume. In the Stokes limit, the settling speed ratio is found to correlate well with primary dendrite arm aspect ratio and a second dimensionless shape paremeter which serves as a measure of the fractal-like nature of the dendrite models. These results can be used to estimate equiaxed grain velocities and distance of travel in metal castings. The drag measurements may be used in numerical codes to calculate the movement of grains in a convecting melt in an effort to determine macrosegregation patterns caused by the sink/float mechanism.

Does vector-free gravity simulate microgravity? Functional and morphologic attributes of clinorotated nerve and muscle grown in cell culture

NASA Technical Reports Server (NTRS)

Gruener, Raphael; Hoeger, Glenn

1988-01-01

Cocultured Xenopus neurons and myocytes were subjected to nonvectorial gravity by clinostat rotation to determine the effects of microgravity on cell development and communications. Observed effects included increases in the myocyte and its nuclear area, fragmentation of nucleoli, the appearance of neuritic aneurysms, decreased growth in the presence of trophic factors, and decreased yolk utilization. These effects were most notable at 1-10 rpm and depended on the onset and duration of rotation. It is found that, in microgravity, cell differentiation is altered by interference with cytoskeleton-related mechanisms. It is suggested that the alteration of the distribution of acetylcholine receptor aggregates on myocytes which occurs might indicate that microgravity affects brain development.

Complementary online aerosol mass spectrometry and offline FT-IR spectroscopy measurements: Prospects and challenges for the analysis of anthropogenic aerosol particle emissions

NASA Astrophysics Data System (ADS)

Faber, Peter; Drewnick, Frank; Bierl, Reinhard; Borrmann, Stephan

2017-10-01

The aerosol mass spectrometer (AMS) is well established in investigating highly time-resolved dynamics of submicron aerosol chemical composition including organic aerosol (OA). However, interpretation of mass spectra on molecular level is limited due to strong fragmentation of organic substances and potential reactions inside the AMS ion chamber. Results from complementary filter-based FT-IR absorption measurements were used to explain features in high-resolution AMS mass spectra of different types of OA (e.g. cooking OA, cigarette smoking OA, wood burning OA). Using this approach some AMS fragment ions were validated in this study as appropriate and rather specific markers for a certain class of organic compounds for all particle types under investigation. These markers can therefore be used to get deeper insights in the chemical composition of OA based on AMS mass spectra in upcoming studies. However, the specificity of other fragment ions such as C2H4O2+ (m/z 60.02114) remains ambiguous. In such cases, complementary FT-IR measurements allow the interpretation of highly time-resolved AMS mass spectra at the level of molecular functional groups. Furthermore, this study discusses the challenges in reducing inorganic interferences (e.g. from water and ammonium salts) in FT-IR spectra of atmospheric aerosols to decrease spectral uncertainties for better comparisons and, thus, to get more robust results.

nanos function is essential for development and regeneration of planarian germ cells.

PubMed

Wang, Yuying; Zayas, Ricardo M; Guo, Tingxia; Newmark, Phillip A

2007-04-03

Germ cells are required for the successful propagation of sexually reproducing species. Understanding the mechanisms by which these cells are specified and how their totipotency is established and maintained has important biomedical and evolutionary implications. Freshwater planarians serve as fascinating models for studying these questions. They can regenerate germ cells from fragments of adult tissues that lack reproductive structures, suggesting that inductive signaling is involved in planarian germ cell specification. To study the development and regeneration of planarian germ cells, we have functionally characterized an ortholog of nanos, a gene required for germ cell development in diverse organisms, from Schmidtea mediterranea. In the hermaphroditic strain of this species, Smed-nanos mRNA is detected in developing, regenerating, and mature ovaries and testes. However, it is not detected in the vast majority of newly hatched planarians or in small tissue fragments that will ultimately regenerate germ cells, consistent with an epigenetic origin of germ cells. We show that Smed-nanos RNA interference (RNAi) results in failure to develop, regenerate, or maintain gonads in sexual planarians. Unexpectedly, Smed-nanos mRNA is also detected in presumptive testes primordia of asexual individuals that reproduce strictly by fission. These presumptive germ cells are lost after Smed-nanos RNAi, suggesting that asexual planarians specify germ cells, but their differentiation is blocked downstream of Smed-nanos function. Our results reveal a conserved function of nanos in germ cell development in planarians and suggest that these animals will serve as useful models for dissecting the molecular basis of epigenetic germ cell specification.

Inferring Resilience to Fragmentation-Induced Changes in Plant Communities in a Semi-Arid Mediterranean Ecosystem

PubMed Central

de Frutos, Ángel; Navarro, Teresa; Pueyo, Yolanda; Alados, Concepción L.

2015-01-01

Predicting the capacity of ecosystems to absorb impacts from disturbance events (resilience), including land-use intensification and landscape fragmentation, is challenging in the face of global change. Little is known about the impacts of fragmentation on ecosystem functioning from a multi-dimensional perspective (multiple traits). This study used 58 500-m linear transects to quantify changes in the functional composition and resilience of vascular plant communities in response to an increase in landscape fragmentation in 18 natural scrubland fragments embedded within a matrix of abandoned crop fields in Cabo de Gata-Níjar Natural Park, Almería, Spain. Changes in functional community composition were measured using functional diversity indices (functional richness and functional dispersion) that were based on 12 plant traits. Resilience was evaluated using the functional redundancy and response diversity from the perspective of plant dispersal, which is important, particularly, in fragmented landscapes. Scrubland fragmentation was measured using the Integral Index of Connectivity (IIC). The functional richness of the plant communities was higher in the most fragmented scrubland. Conversely, the functional dispersion (i.e., spread) of trait values among species in the functional trait space was lower at the most fragmented sites; consequently, the ecological tolerance of the vegetation to scrubland fragmentation decreased. Classifying the plant species into four functional groups indicated that fragmentation favoured an increase in functional redundancy in the ‘short basal annual forbs and perennial forbs’ group, most of which are species adapted to degraded soils. An assessment based on the traits associated with plant dispersal indicated that the resilience of ‘woody plants’, an important component in the Mediterranean scrubland, and habitat fragmentation were negatively correlated; however, the correlation was positive in the ‘short basal annual forbs and perennial forbs’ and the ‘grasses’ groups. PMID:25790432

The threshold signal:noise ratio in the perception of fragmented figures.

PubMed

Merkul'ev, A V; Pronin, S V; Semenov, L A; Foreman, N; Chikhman, V N; Shelepin, Yu E

2006-01-01

Perception thresholds were measured for fragmented outline figures (the Gollin test). A new approach to the question of the perception of incomplete images was developed. In this approach, figure fragmentation consisted of masking with multiplicative texture-like noise--this interference was termed "invisible" masking. The first series of studies established that the "similarity" between the amplitude-frequency spectra of test figures and "invisible" masks, expressed as a linear correlation coefficient, had significant effects on the recognition thresholds of these figures. The second series of experiments showed that progressing formation of the figures was accompanied by increases in the correlation between their spatial-frequency characteristics and the corresponding characteristics of the incomplete figure, while the correlation with the "invisible" mask decreased. It is suggested that the ratio of the correlation coefficients, characterizing the "similarity" of the fragmented figure with the intact figure and the "invisible" mask, corresponds to the signal:noise ratio. The psychophysical recognition threshold for figures for naive subjects not familiar with the test image alphabet was reached after the particular level of fragmentation at which this ratio was unity.

Conformation-driven quantum interference effects mediated by through-space conjugation in self-assembled monolayers

NASA Astrophysics Data System (ADS)

Carlotti, Marco; Kovalchuk, Andrii; Wächter, Tobias; Qiu, Xinkai; Zharnikov, Michael; Chiechi, Ryan C.

2016-12-01

Tunnelling currents through tunnelling junctions comprising molecules with cross-conjugation are markedly lower than for their linearly conjugated analogues. This effect has been shown experimentally and theoretically to arise from destructive quantum interference, which is understood to be an intrinsic, electronic property of molecules. Here we show experimental evidence of conformation-driven interference effects by examining through-space conjugation in which π-conjugated fragments are arranged face-on or edge-on in sufficiently close proximity to interact through space. Observing these effects in the latter requires trapping molecules in a non-equilibrium conformation closely resembling the X-ray crystal structure, which we accomplish using self-assembled monolayers to construct bottom-up, large-area tunnelling junctions. In contrast, interference effects are completely absent in zero-bias simulations on the equilibrium, gas-phase conformation, establishing through-space conjugation as both of fundamental interest and as a potential tool for tuning tunnelling charge-transport in large-area, solid-state molecular-electronic devices.

Single chain variable fragment antibodies block aggregation and toxicity induced by familial ALS-linked mutant forms of SOD1.

PubMed

Ghadge, Ghanashyam D; Pavlovic, John D; Koduvayur, Sujatha P; Kay, Brian K; Roos, Raymond P

2013-08-01

Approximately 10% of amyotrophic lateral sclerosis (ALS) cases are familial (known as FALS) with an autosomal dominant inheritance pattern, and ~25% of FALS cases are caused by mutations in Cu/Zn superoxide dismutase (SOD1). There is convincing evidence that mutant SOD1 (mtSOD1) kills motor neurons (MNs) because of a gain-of-function toxicity, most likely related to aggregation of mtSOD1. A number of recent reports have suggested that antibodies can be used to treat mtSOD1-induced FALS. To follow up on the use of antibodies as potential therapeutics, we generated single chain fragments of variable region antibodies (scFvs) against SOD1, and then expressed them as 'intrabodies' within a motor neuron cell line. In the present study, we describe isolation of human scFvs that interfere with mtSOD1 in vitro aggregation and toxicity. These scFvs may have therapeutic potential in sporadic ALS, as well as FALS, given that sporadic ALS may also involve abnormalities in the SOD1 protein or activity. Copyright © 2013 Elsevier Inc. All rights reserved.

Individual differences in executive processing predict susceptibility to interference in verbal working memory.

PubMed

Hedden, Trey; Yoon, Carolyn

2006-09-01

Recent theories have suggested that resistance to interference is a unifying principle of executive function and that individual differences in interference may be explained by executive function (M. J. Kane & R. W. Engle, 2002). Measures of executive function, memory, and perceptual speed were obtained from 121 older adults (ages 63-82). We used structural equation modeling to investigate the relationships of these constructs with interference in a working memory task. Executive function was best described as two related subcomponent processes: shifting and updating goal-relevant representations and inhibition of proactive interference. These subcomponents were distinct from verbal and visual memory and speed. Individual differences in interference susceptibility and recollection were best predicted by shifting and updating and by resistance to proactive interference, and variability in familiarity was predicted by resistance to proactive interference and speed. ((c) 2006 APA, all rights reserved).

Regulatory functions of trehalose-6-phosphate synthase in the chitin biosynthesis pathway in Tribolium castaneum (Coleoptera: Tenebrionidae) revealed by RNA interference.

PubMed

Chen, Q W; Jin, S; Zhang, L; Shen, Q D; Wei, P; Wei, Z M; Wang, S G; Tang, B

2018-06-01

RNA interference (RNAi) is a very effective technique for studying gene function and may be an efficient method for controlling pests. Trehalose-6-phosphate synthase (TPS), which plays a key role in the synthesis of trehalose and insect development, was cloned in Tribolium castaneum (Herbst) (TcTPS) and the putative functions were studied using RNAi via the injection of double-stranded RNA (dsRNA) corresponding to conserved TPS and trehalose-6-phosphate phosphatase domains. Expression analyses show that TcTPS is expressed higher in the fat body, while quantitative real-time polymerase chain reaction results show that the expression of four trehalase isoforms was significantly suppressed by dsTPS injection. Additionally, the expression of six chitin synthesis-related genes, such as hexokinase 2 and glutamine-fructose-6-phosphate aminotransferase, was suppressed at 48 and 72 h post-dsTPS-1 and dsTPS-2 RNA injection, which were two dsTPS fragments that had been designed for two different locations in TcTPS open reading frame, and that trehalose content and trehalase 1 activity decreased significantly at 72 h post-dsRNA injection. Furthermore, T. castaneum injected with dsTPS-1 and dsTPS-2 RNA displayed significantly lower levels of chitin and could not complete the molting process from larvae to pupae, revealing abnormal molting phenotypes. These results demonstrate that silencing TPS gene leads to molting deformities and high mortality rates via regulation of gene expression in the chitin biosynthetic pathway, and may be a promising approach for pest control in the future.

Metabolic Enhancer Piracetam Attenuates the Translocation of Mitochondrion-Specific Proteins of Caspase-Independent Pathway, Poly [ADP-Ribose] Polymerase 1 Up-regulation and Oxidative DNA Fragmentation.

PubMed

Verma, Dinesh Kumar; Gupta, Sonam; Biswas, Joyshree; Joshi, Neeraj; Sivarama Raju, K; Wahajuddin, Mu; Singh, Sarika

2018-03-12

Piracetam, a nootropic drug, has been clinically used for decades; however, its mechanism of action still remains enigmatic. The present study was undertaken to evaluate the role of mitochondrion-specific factors of caspase-independent pathway like apoptotic-inducing factor (AIF) and endonuclease-G (endo-G) in piracetam-induced neuroprotection. N2A cells treated with lipopolysaccharide (LPS) exhibited significant cytotoxicity, impaired mitochondrial activity, and reactive oxygen species generation which was significantly attenuated with piracetam co-treatment. Cells co-treated with LPS and piracetam exhibited significant uptake of piracetam in comparison to only piracetam-treated cells as estimated by liquid chromatography-mass spectrometry (LC-MSMS). LPS treatment caused significant translocation of AIF and endonuclease-G in neuronal N2A cells which were significantly attenuated with piracetam co-treatment. Significant over-expression of proinflammatory cytokines was also observed after treatment of LPS to cells which was inhibited with piracetam co-treatment demonstrating its anti-inflammatory property. LPS-treated cells exhibited significant oxidative DNA fragmentation and poly [ADP-ribose] polymerase-1 (PARP-1) up-regulation in nucleus, both of which were attenuated with piracetam treatment. Antioxidant melatonin but not z-VAD offered the inhibited LPS-induced DNA fragmentation indicating the involvement of oxidative DNA fragmentation. Further, we did not observe the altered caspase-3 level after LPS treatment initially while at a later time point, significantly augmented level of caspase-3 was observed which was not inhibited with piracetam treatment. In total, our findings indicate the interference of piracetam in mitochondrion-mediated caspase-independent pathway, as well as its anti-inflammatory and antioxidative properties. Graphical Abstract Graphical abstract indicating the novel interference of metabolic enhancer piracetam (P) in neuronal death mechanisms.

Small RNA populations revealed by blocking rRNA fragments in Drosophila melanogaster reproductive tissues

PubMed Central

Dalmay, Tamas

2018-01-01

RNA interference (RNAi) is a complex and highly conserved regulatory mechanism mediated via small RNAs (sRNAs). Recent technical advances in high throughput sequencing have enabled an increasingly detailed analysis of sRNA abundances and profiles in specific body parts and tissues. This enables investigations of the localized roles of microRNAs (miRNAs) and small interfering RNAs (siRNAs). However, variation in the proportions of non-coding RNAs in the samples being compared can hinder these analyses. Specific tissues may vary significantly in the proportions of fragments of longer non-coding RNAs (such as ribosomal RNA or transfer RNA) present, potentially reflecting tissue-specific differences in biological functions. For example, in Drosophila, some tissues contain a highly abundant 30nt rRNA fragment (the 2S rRNA) as well as abundant 5’ and 3’ terminal rRNA fragments. These can pose difficulties for the construction of sRNA libraries as they can swamp the sequencing space and obscure sRNA abundances. Here we addressed this problem and present a modified “rRNA blocking” protocol for the construction of high-definition (HD) adapter sRNA libraries, in D. melanogaster reproductive tissues. The results showed that 2S rRNAs targeted by blocking oligos were reduced from >80% to < 0.01% total reads. In addition, the use of multiple rRNA blocking oligos to bind the most abundant rRNA fragments allowed us to reveal the underlying sRNA populations at increased resolution. Side-by-side comparisons of sequencing libraries of blocked and non-blocked samples revealed that rRNA blocking did not change the miRNA populations present, but instead enhanced their abundances. We suggest that this rRNA blocking procedure offers the potential to improve the in-depth analysis of differentially expressed sRNAs within and across different tissues. PMID:29474379

Modulation of chaperone function and cochaperone interaction by novobiocin in the C-terminal domain of Hsp90: evidence that coumarin antibiotics disrupt Hsp90 dimerization.

PubMed

Allan, Rudi K; Mok, Danny; Ward, Bryan K; Ratajczak, Thomas

2006-03-17

The C-terminal domain of Hsp90 displays independent chaperone activity, mediates dimerization, and contains the MEEVD motif essential for interaction with tetratricopeptide repeat-containing immunophilin cochaperones assembled in mature steroid receptor complexes. An alpha-helical region, upstream of the MEEVD peptide, helps form the dimerization interface and includes a hydrophobic microdomain that contributes to the Hsp90 interaction with the immunophilin cochaperones and corresponds to the binding site for novobiocin, a coumarin-related Hsp90 inhibitor. Mutation of selected residues within the hydrophobic microdomain significantly impacted the chaperone function of a recombinant C-terminal Hsp90 fragment and novobiocin inhibited wild-type chaperone activity. Prior incubation of the Hsp90 fragment with novobiocin led to a direct blockade of immunophilin cochaperone binding. However, the drug had little influence on the pre-formed Hsp90-immunophilin complex, suggesting that bound cochaperones mask the novobiocin-binding site. We observed a differential effect of the drug on Hsp90-immunophilin interaction, suggesting that the immunophilins make distinct contacts within the C-terminal domain to specifically modulate Hsp90 function. Novobiocin also precluded the interaction of full-length Hsp90 with the p50(cdc37) cochaperone, which targets the N-terminal nucleotide-binding domain, and is prevalent in Hsp90 complexes with protein kinase substrates. Novobiocin therefore acts locally and allosterically to induce conformational changes within multiple regions of the Hsp90 protein. We provide evidence that coumermycin A1, a coumarin structurally related to novobiocin, interferes with dimerization of the Hsp90 C-terminal domain. Coumarin-based inhibitors then may antagonize Hsp90 function by inducing a conformation favoring separation of the C-terminal domains and release of substrate.

Constitutive Endocytosis of VEGFR2 Protects the Receptor against Shedding.

PubMed

Basagiannis, Dimitris; Christoforidis, Savvas

2016-08-05

VEGFR2 plays a fundamental role in blood vessel formation and in life threatening diseases, such as cancer angiogenesis and cardiovascular disorders. Although inactive growth factor receptors are mainly localized at the plasma membrane, VEGFR2 undergoes constitutive endocytosis (in the absence of ligand) and recycling. Intriguingly, the significance of these futile transport cycles of VEGFR2 remains unclear. Here we found that, unexpectedly, the function of constitutive endocytosis of VEGFR2 is to protect the receptor against plasma membrane cleavage (shedding), thereby preserving the functional state of the receptor until the time of activation by VEGF. Inhibition of constitutive endocytosis of VEGFR2, by interference with the function of clathrin, dynamin, or Rab5, increases dramatically the cleavage/shedding of VEGFR2. Shedding of VEGFR2 produces an N-terminal soluble fragment (100 kDa, s100), which is released in the extracellular space, and a residual C-terminal part (130 kDa, p130) that remains integrated at the plasma membrane. The released soluble fragment (s100) co-immunoprecipitates with VEGF, in line with the topology of the VEGF-binding domain at the N terminus of VEGFR2. Increased shedding of VEGFR2 (via inhibition of constitutive endocytosis) results in reduced response to VEGF, consistently with the loss of the VEGF-binding domain from the membrane remnant of VEGFR2. These data suggest that constitutive internalization of VEGFR2 protects the receptor against shedding and provides evidence for an unprecedented mechanism via which endocytosis can regulate the fate and activity of growth factor receptors. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Constitutive Endocytosis of VEGFR2 Protects the Receptor against Shedding*

PubMed Central

Basagiannis, Dimitris; Christoforidis, Savvas

2016-01-01

VEGFR2 plays a fundamental role in blood vessel formation and in life threatening diseases, such as cancer angiogenesis and cardiovascular disorders. Although inactive growth factor receptors are mainly localized at the plasma membrane, VEGFR2 undergoes constitutive endocytosis (in the absence of ligand) and recycling. Intriguingly, the significance of these futile transport cycles of VEGFR2 remains unclear. Here we found that, unexpectedly, the function of constitutive endocytosis of VEGFR2 is to protect the receptor against plasma membrane cleavage (shedding), thereby preserving the functional state of the receptor until the time of activation by VEGF. Inhibition of constitutive endocytosis of VEGFR2, by interference with the function of clathrin, dynamin, or Rab5, increases dramatically the cleavage/shedding of VEGFR2. Shedding of VEGFR2 produces an N-terminal soluble fragment (100 kDa, s100), which is released in the extracellular space, and a residual C-terminal part (130 kDa, p130) that remains integrated at the plasma membrane. The released soluble fragment (s100) co-immunoprecipitates with VEGF, in line with the topology of the VEGF-binding domain at the N terminus of VEGFR2. Increased shedding of VEGFR2 (via inhibition of constitutive endocytosis) results in reduced response to VEGF, consistently with the loss of the VEGF-binding domain from the membrane remnant of VEGFR2. These data suggest that constitutive internalization of VEGFR2 protects the receptor against shedding and provides evidence for an unprecedented mechanism via which endocytosis can regulate the fate and activity of growth factor receptors. PMID:27298320

Plasmid P1 replication: negative control by repeated DNA sequences.

PubMed Central

Chattoraj, D; Cordes, K; Abeles, A

1984-01-01

The incompatibility locus, incA, of the unit-copy plasmid P1 is contained within a fragment that is essentially a set of nine 19-base-pair repeats. One or more copies of the fragment destabilizes the plasmid when present in trans. Here we show that extra copies of incA interfere with plasmid DNA replication and that a deletion of most of incA increases plasmid copy number. Thus, incA is not essential for replication but is required for its control. When cloned in a high-copy-number vector, pieces of the incA fragment that each contain only three repeats destabilize P1 plasmids efficiently. This result makes it unlikely that incA specifies a regulatory product. Our in vivo results suggest that the repeating DNA sequence itself negatively controls replication by titrating a P1-determined protein, RepA, that is essential for replication. Consistent with this hypothesis is the observation that the RepA protein binds to the incA fragment in vitro. Images PMID:6387706

PxAPN5 serves as a functional receptor of Cry2Ab in Plutella xylostella (L.) and its binding domain analysis.

PubMed

Pan, Zhi-Zhen; Xu, Lian; Liu, Bo; Zhang, Jing; Chen, Zheng; Chen, Qing-Xi; Zhu, Yu-Jing

2017-12-01

Lepidopteran midgut aminopeptidases N (APNs) are widely studied for their potential roles as one of the receptors for Bacillus thuringiensis (Bt) crystal toxins. In the present study, a loss of function analyses by RNAi (RNA interference) silencing of the Plutella xylostella APN5 (PxAPN5), a binding protein of Bt crystal toxin Cry2Ab, were performed. The knocking down of PxAPN5 in P. xylostella larvae greatly reduced their susceptibility to Cry2Ab and led to a decrease of Cry2Ab binding to P. xylostella midgut. Four truncated fragments of PxAPN5 were further constructed and expressed in Escherichia coli (E.coli) to find the binding region of PxAPN5 to Cry2Ab. The ligand blot result indicated that D1 domain (residues 1-262) and D3 domain (residues 510-620) of PxAPN5 could specially bind to Cry2Ab. Copyright © 2017 Elsevier B.V. All rights reserved.

Quark fragmentation functions in NJL-jet model

NASA Astrophysics Data System (ADS)

Bentz, Wolfgang; Matevosyan, Hrayr; Thomas, Anthony

2014-09-01

We report on our studies of quark fragmentation functions in the Nambu-Jona-Lasinio (NJL) - jet model. The results of Monte-Carlo simulations for the fragmentation functions to mesons and nucleons, as well as to pion and kaon pairs (dihadron fragmentation functions) are presented. The important role of intermediate vector meson resonances for those semi-inclusive deep inelastic production processes is emphasized. Our studies are very relevant for the extraction of transverse momentum dependent quark distribution functions from measured scattering cross sections. We report on our studies of quark fragmentation functions in the Nambu-Jona-Lasinio (NJL) - jet model. The results of Monte-Carlo simulations for the fragmentation functions to mesons and nucleons, as well as to pion and kaon pairs (dihadron fragmentation functions) are presented. The important role of intermediate vector meson resonances for those semi-inclusive deep inelastic production processes is emphasized. Our studies are very relevant for the extraction of transverse momentum dependent quark distribution functions from measured scattering cross sections. Supported by Grant in Aid for Scientific Research, Japanese Ministry of Education, Culture, Sports, Science and Technology, Project No. 20168769.

Effect of amphiphilic additives on the behavior of water-based acrylic pressure-sensitive adhesives during paper recycling

Treesearch

Jihui Guo; Steven J. Severtson; Larry E. Gwin; Carl J. Houtman

2008-01-01

Pressure-sensitive adhesives (PSAs) in recovered paper reduce efficiency and increase operating costs for paper recycling mills. Increased PSA fragmentation during pulping and the corresponding reduction in screening efficiency are indications that a PSA will likely interfere with paper recycling. Water-based PSAs, which dominate the label market, have complex...

Development and validation of a high-content bimolecular fluorescence complementation assay for small-molecule inhibitors of HIV-1 Nef dimerization.

PubMed

Poe, Jerrod A; Vollmer, Laura; Vogt, Andreas; Smithgall, Thomas E

2014-04-01

Nef is a human immunodeficiency virus 1 (HIV-1) accessory factor essential for viral pathogenesis and AIDS progression. Many Nef functions require dimerization, and small molecules that block Nef dimerization may represent antiretroviral drug leads. Here we describe a cell-based assay for Nef dimerization inhibitors based on bimolecular fluorescence complementation (BiFC). Nef was fused to nonfluorescent, complementary fragments of yellow fluorescent protein (YFP) and coexpressed in the same cell population. Dimerization of Nef resulted in juxtaposition of the YFP fragments and reconstitution of the fluorophore. For automation, the Nef-YFP fusion proteins plus a monomeric red fluorescent protein (mRFP) reporter were expressed from a single vector, separated by picornavirus "2A" linker peptides to permit equivalent translation of all three proteins. Validation studies revealed a critical role for gating on the mRFP-positive subpopulation of transfected cells, as well as use of the mRFP signal to normalize the Nef-BiFC signal. Nef-BiFC/mRFP ratios resulting from cells expressing wild-type versus dimerization-defective Nef were very clearly separated, with Z factors consistently in the 0.6 to 0.7 range. A fully automated pilot screen of the National Cancer Institute Diversity Set III identified several hit compounds that reproducibly blocked Nef dimerization in the low micromolar range. This BiFC-based assay has the potential to identify cell-active small molecules that directly interfere with Nef dimerization and function.

Development and Validation of a High-Content Bimolecular Fluorescence Complementation Assay for Small Molecule Inhibitors of HIV-1 Nef Dimerization

PubMed Central

Poe, Jerrod A.; Vollmer, Laura; Vogt, Andreas; Smithgall, Thomas E.

2014-01-01

Nef is an HIV-1 accessory factor essential for viral pathogenesis and AIDS progression. Many Nef functions require dimerization, and small molecules that block Nef dimerization may represent antiretroviral drug leads. Here we describe a cell-based assay for Nef dimerization inhibitors based on bimolecular fluorescence complementation (BiFC). Nef was fused to non-fluorescent, complementary fragments of YFP and co-expressed in the same cell population. Dimerization of Nef resulted in juxtaposition of the YFP fragments and reconstitution of the fluorophore. For automation, the Nef-YFP fusion proteins plus an mRFP reporter were expressed from a single vector, separated by picornavirus ‘2A’ linker peptides to permit equivalent translation of all three proteins. Validation studies revealed a critical role for gating on the mRFP-positive subpopulation of transfected cells, as well as use of the mRFP signal to normalize the Nef-BiFC signal. Nef-BiFC/mRFP ratios resulting from cells expressing wild-type vs. dimerization-defective Nef were very clearly separated, with Z-factors consistently in the 0.6–0.7 range. A fully automated pilot screen of the NIH Diversity Set III identified several hit compounds that reproducibly blocked Nef dimerization in the low micromolar range. This BiFC-based assay has the potential to identify cell-active small molecules that directly interfere with Nef dimerization and function. PMID:24282155

[Improvement and the mechanism of cardiac function by knockdown of ADAM10 in adriamycin-induced cardiomyopathy rats].

PubMed

Li, Xiaoou; Xie, Lili; He, Bing; Huang, Wei

2018-01-01

Objective To study the role of a disintegrin and metalloproteinase10 (ADAM10) in shedding neural cadherin (N-cadherin) and develop an approach to interfere the process of ventricular remodeling in adriamycin-induced cardiomyopathy (ACM) rats. Methods In a rat model of ACM, the effects of intraperitoneal injection of the lentiviral RNAi vector of ADAM10 on the morphology of cardiomyocytes and contractile function were observed by HE staining and color Doppler echocardiography. The expressions of N-cadherin and C-terminal fragment 1 (CTF1) were detected by Western blotting and immunohistochemistry. Results In the in vivo experiment, a large amount of fluorescence was seen in the isolated primary cardiomyocytes, which indicated that the transfection in the rat model was successful. In the treatment group, the morphology of cardiomyocytes and function of the heart were evidently improved, N-cadherin protein expression was remarkably up-regulated and CTF1 protein was obviously down-regulated compared with the model group. Conclusion Knock-down of ADAM10 increases N-cadherin expression and decreases CTF1 expression, thus improves cardiac function in the rat model of ACM.

RGD and polyhistidine tumor homing peptides potentiates the action of human Maspin as an antineoplastic candidate.

PubMed

Yin, Runting; Guo, Le; Zhang, Jie; Liu, Guangzhao; Yao, Wenjuan; Zhu, Hongyan; Xu, Xiaole; Zhang, Wei

2016-07-01

Maspin, a non-inhibitory member of serine protease family, acts as an effective tumor suppressor by inhibiting cell inhesion and mobility. We found that exogenous wild-type rMaspin had a low effect on tumor growth in vivo. However, when the peptide Arg-Gly-Asp-hexahistidine (RGD-6His) was introduced into rMaspin, the modified rMaspin showed significant inhibitory activity in angiogenic assays and tumor-bearing animal models. Overall, our data suggested that both the RGD and hexahistidine fragments contributed to improve the fusion protein activity and polyhistidine peptide could be considered as flexible linker to separate RGD and Maspin moieties to avoid function interference. Besides, it is an efficient tag to achieve purified recombinant proteins. Furthermore, rMaspin fusing with RGD and hexahistidine could be a viable anticancer candidate.

Fluorescent hydroxylamine derived from the fragmentation of PAMAM dendrimers for intracellular hypochlorite recognition.

PubMed

Wu, Te-Haw; Liu, Ching-Ping; Chien, Chih-Te; Lin, Shu-Yi

2013-08-26

Herein, a promising sensing approach based on the structure fragmentation of poly(amidoamine) (PAMAM) dendrimers for the selective detection of intracellular hypochlorite (OCl(-)) is reported. PAMAM dendrimers were easily disrupted by a cascade of oxidations in the tertiary amines of the dendritic core to produce an unsaturated hydroxylamine with blue fluorescence. Specially, the novel fluorophore was only sensitive to OCl(-), one of reactive oxygen species (ROS), resulting in an irreversible fluorescence turn-off. The fluorescent hydroxylamine was selectively oxidised by OCl(-) to form a labile oxoammonium cation that underwent further degradation. Without using any troublesomely synthetic steps, the novel sensing platform based on the fragmentation of PAMAM dendrimers, can be applied to detect OCl(-) in macrophage cells. The results suggest that the sensing approach may be useful for the detection of intracellular OCl(-) with minimal interference from biological matrixes. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Jet production and fragmentation properties in deep inelastic muon scattering

NASA Astrophysics Data System (ADS)

Arneodo, M.; Arvidson, A.; Aubert, J. J.; Badelek, B.; Beaufays, J.; Bee, C. P.; Benchouk, C.; Berghoff, G.; Bird, I.; Blum, D.; Böhm, E.; de Bouard, X.; Brasse, F. W.; Braun, H.; Broll, C.; Brown, S.; Brück, H.; Calen, H.; Chima, J. S.; Ciborowski, J.; Clifft, R.; Coignet, G.; Combley, F.; Conrad, J.; Coughlan, J.; D'Agostini, G.; Dahlgren, S.; Dengler, F.; Derado, I.; Dreyer, T.; Drees, J.; Drobnitzki, M.; Düren, M.; Eckardt, V.; Edwards, A.; Edwards, M.; Ernst, T.; Eszes, G.; Favier, J.; Ferrero, M. I.; Figiel, J.; Flauger, W.; Foster, J.; Ftàčnik, J.; Gabathuler, E.; Gajewski, J.; Gamet, R.; Gayler, J.; Geddes, N.; Grafström, P.; Grard, F.; Haas, J.; Hagberg, E.; Hasert, F. J.; Hayman, P.; Heusse, P.; Jaffre, M.; Jacholkowska, A.; Janata, F.; Jancso, G.; Johnson, A. S.; Kabuss, E. M.; Kellner, G.; Korbel, V.; Krüger, A.; Krüger, J.; Kullander, S.; Landgraf, U.; Lanske, D.; Loken, J.; Long, K.; Maire, M.; Malecki, P.; Manz, A.; Maselli, S.; Mohr, W.; Montanet, F.; Montgomery, H. E.; Nagy, E.; Nassalski, J.; Norton, P. R.; Oakham, F. G.; Osborne, A. M.; Pascaud, C.; Pawlik, B.; Payre, P.; Peroni, C.; Peschel, H.; Pessard, H.; Pettingale, J.; Pietrzyk, B.; Pietrzyk, U.; Pönsgen, B.; Pötsch, M.; Renton, P.; Ribarics, P.; Rith, K.; Rondio, E.; Sandacz, A.; Scheer, M.; Schlabböhmer, A.; Schiemann, H.; Schmitz, N.; Schneegans, M.; Scholz, M.; Schröder, T.; Schultze, K.; Sloan, T.; Stier, H. E.; Studt, M.; Taylor, G. N.; Thénard, J. M.; Thompson, J. C.; de La Torre, A.; Toth, J.; Urban, L.; Urban, L.; Wallucks, W.; Whalley, M.; Wheeler, S.; Williams, W. S. C.; Wimpenny, S. J.; Windmolders, R.; Wolf, G.; Ziemons, K.

1987-12-01

Results are presented from a study of deep inelastic 280 GeV muon-nucleon interactions on the transverse momenta and jet properties of the final state hadrons. The results are analysed in a way which attempts to separate the contributions of hard and soft QCD effects from those that arise from the fragmentation process. The fragmentation models with which the data are compared are the Lund string model, the independent jet model, the QCD parton shower model including soft gluon interference effects, and the firestring model. The discrimination between these models is discussed. Various methods of analysis of the data in terms of hard QCD processes are presented. From a study of the properties of the jet profiles a value of α s , to leading order, is determined using the Lund string model, namely α s =0.29±0.01 (stat.) ±0.02 (syst.), for Q 2˜20 GeV2.

43 CFR 423.22 - Interference with agency functions and disorderly conduct.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false Interference with agency functions and..., AND WATERBODIES Rules of Conduct § 423.22 Interference with agency functions and disorderly conduct... behavior; (2) Language, utterance, gesture, display, or act that is obscene, physically threatening or...

Analytical interference of 4-hydroxy-3-methoxymethamphetamine with the measurement of plasma free normetanephrine by ultra-high pressure liquid chromatography-tandem mass spectrometry.

PubMed

Dunand, Marielle; Donzelli, Massimiliano; Rickli, Anna; Hysek, Cédric M; Liechti, Matthias E; Grouzmann, Eric

2014-08-01

The diagnosis of pheochromocytoma relies on the measurement of plasma free metanephrines assay whose reliability has been considerably improved by ultra-high pressure liquid chromatography tandem mass spectrometry (UHPLC-MS/MS). Here we report an analytical interference occurring between 4-hydroxy-3-methoxymethamphetamine (HMMA), a metabolite of 3,4-methylenedioxymethamphetamine (MDMA, "Ecstasy"), and normetanephrine (NMN) since they share a common pharmacophore resulting in the same product ion after fragmentation. Synthetic HMMA was spiked into plasma samples containing various concentrations of NMN and the intensity of the interference was determined by UPLC-MS/MS before and after improvement of the analytical method. Using a careful adjustment of chromatographic conditions including the change of the UPLC analytical column, we were able to distinguish both compounds. HMMA interference for NMN determination should be seriously considered since MDMA activates the sympathetic nervous system and if confounded with NMN may lead to false-positive tests when performing a differential diagnostic of pheochromocytoma. Copyright © 2014 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Low functional richness and redundancy of a predator assemblage in native forest fragments of Chiloe island, Chile.

PubMed

Farias, Ariel A; Jaksic, Fabian M

2011-07-01

1. Changes in land use and habitat fragmentation are major drivers of global change, and studying their effects on biodiversity constitutes a major research programme. However, biodiversity is a multifaceted concept, with a functional component linking species richness to ecosystem function. Currently, the interaction between functional and taxonomic components of biodiversity under realistic scenarios of habitat degradation is poorly understood. 2. The expected functional richness (FR)-species richness relationship (FRSR) is positive, and attenuated for functional redundancy in species-rich assemblages. Further, environmental filters are expected to flatten that association by sorting species with similar traits. Thus, analysing FRSR can inform about the response of biodiversity to environmental gradients and habitat fragmentation, and its expected functional consequences. 3. Top predators affect ecosystem functioning through prey consumption and are particularly vulnerable to changes in land use and habitat fragmentation, being good indicators of ecosystem health and suitable models for assessing the effects of habitat fragmentation on their FR. 4. Thus, this study analyses the functional redundancy of a vertebrate predator assemblage at temperate forest fragments in a rural landscape of Chiloe island (Chile), testing the existence of environmental filters by contrasting an empirically derived FRSR against those predicted from null models, and testing the association between biodiversity components and the structure of forest fragments. 5. Overall, contrasts against null models indicate that regional factors determine low levels of FR and redundancy for the vertebrate predator assemblage studied, while recorded linear FRSR indicates proportional responses of the two biodiversity components to the structure of forest fragments. Further, most species were positively associated with either fragment size or shape complexity, which are highly correlated. This, and the absence of ecological filters at the single-fragment scale, rendered taxonomically and functionally richer predator assemblages at large complex-shaped fragments. 6. These results predict strong effects of deforestation on both components of biodiversity, potentially affecting the functioning of remnants of native temperate forest ecosystems. Thus, the present study assesses general responses of functional and taxonomic components of biodiversity to a specific human-driven process. © 2011 The Authors. Journal of Animal Ecology © 2011 British Ecological Society.

Direct connection between the different QCD orders for parton distribution and fragmentation functions

NASA Astrophysics Data System (ADS)

Shevchenko, O. Yu.

2013-06-01

The formulas directly connecting parton distribution functions and fragmentation functions at the next-to-leading-order QCD with the same quantities at the leading order are derived. These formulas are universal, i.e., have the same form for all kinds of parton distribution functions and fragmentation functions, differing only in the respective splitting functions entering there.

The rotary gallstone lithotrite to aid gallbladder extraction in laparoscopic cholecystectomy.

PubMed

Sackier, J M; Hunter, J G; Paz-Partlow, M; Cuschieri, A

1992-01-01

During laparoscopic cholecystectomy, a large stone burden may cause difficulty when extracting the gallbladder through the abdominal wall. Currently, the alternatives available to the surgeon include increasing the incision, removing stones singly, or utilizing complex fragmentation techniques like the pulsed dye laser. We have employed an electromechanical rotary gallstone lithotrite (RGL) to fragment stones to an aspiratable size. Initially, cholesterol spheres were pulverized in a latex balloon to demonstrate the efficacy of the device. Then, human gallstones were placed in the balloon and reduced to fragments less than or equal to 1 mm from initial sizes of 4-24 mm. Human stones were then inserted in ex vivo porcine gallbladders in a controlled experiment and treated with the device. Ten out of 12 tests were completed within 30 s; one test required 49 s and one 105 s to achieve complete fragmentation. Blinded histological evaluation demonstrated that tissue abrasion caused by use of the device would not interfere with the diagnosis of unsuspected malignancy. Clinical trials have now commenced under the auspices of the hospital ethical committee.

Effects of perturbations on space debris in supersynchronous storage orbits

NASA Astrophysics Data System (ADS)

Luu, Khanh Kim

1998-12-01

Accumulation of space debris in the geosynchronous region (GEO) has raised attention among spacefaring nations. The current mitigation measure supported is to boost satellites into supersynchronous orbits in the time before station-keeping fuel is expected to be exhausted. Because this solution does not remove mass from space, debris generation by fragmentation events remains a possibility. The collision hazard between inactive satellites in the supersynchronous region raises questions about the consequences of collisions in this regime and possible interaction with GEO. In considering the use of supersynchronous orbits for satellite disposal, the first concern is to determine the minimum safe distance above GEO such that objects in the disposal orbits will not interfere with the GEO population in the future. This involves defining the useful GEO area and studying the perturbation effects on objects in supersynchronous orbits. Thus far, research has focused on propagating the orbits of intact objects. However, in the aftermath of a collision, pieces of varying sizes and shapes can be found in orbits quite different from the parent objects' orbits. This document summarizes background information on debris in the GEO region, sources and management strategies, and then addresses the problem: Will orbits of fragments from a collision in a storage orbit occupy GEO altitudes at some time after the collision? If so, at what altitude should the storage orbit occupy such that collision fragments will not interfere with the GEO population? The methods and tools by which the effects of collisions in the supersynchronous region can be analyzed are discussed. A low-velocity collision model is employed to provide delta-velocities imparted to the fragments. An analytical study of perturbation effects, including solar and lunar third body gravitation, Earth oblateness through degree and order four, and solar radiation pressure, follows in order to evaluate the magnitude of these disturbing forces on the fragmentation debris. Validation of these results by numerical analysis using proven numerical and semianalytical orbit propagators is discussed. The results show that currently practiced reorbiting distances above GEO do not isolate debris from GEO after the occurrence of collisions in the storage orbit.

Anthropogenic Matrices Favor Homogenization of Tree Reproductive Functions in a Highly Fragmented Landscape.

PubMed

Carneiro, Magda Silva; Campos, Caroline Cambraia Furtado; Beijo, Luiz Alberto; Ramos, Flavio Nunes

2016-01-01

Species homogenization or floristic differentiation are two possible consequences of the fragmentation process in plant communities. Despite the few studies, it seems clear that fragments with low forest cover inserted in anthropogenic matrices are more likely to experience floristic homogenization. However, the homogenization process has two other components, genetic and functional, which have not been investigated. The purpose of this study was to verify whether there was homogenization of tree reproductive functions in a fragmented landscape and, if found, to determine how the process was influenced by landscape composition. The study was conducted in eight fragments in southwest Brazil. The study was conducted in eight fragments in southwestern Brazil. In each fragment, all individual trees were sampled that had a diameter at breast height ≥3 cm, in ten plots (0.2 ha) and, classified within 26 reproductive functional types (RFTs). The process of functional homogenization was evaluated using additive partitioning of diversity. Additionally, the effect of landscape composition on functional diversity and on the number of individuals within each RFT was evaluated using a generalized linear mixed model. appeared to be in a process of functional homogenization (dominance of RFTs, alpha diversity lower than expected by chance and and low beta diversity). More than 50% of the RFTs and the functional diversity were affected by the landscape parameters. In general, the percentage of forest cover has a positive effect on RFTs while the percentage of coffee matrix has a negative one. The process of functional homogenization has serious consequences for biodiversity conservation because some functions may disappear that, in the long term, would threaten the fragments. This study contributes to a better understanding of how landscape changes affect the functional diversity, abundance of individuals in RFTs and the process of functional homogenization, as well as how to manage fragmented landscapes.

Anthropogenic Matrices Favor Homogenization of Tree Reproductive Functions in a Highly Fragmented Landscape

PubMed Central

2016-01-01

Species homogenization or floristic differentiation are two possible consequences of the fragmentation process in plant communities. Despite the few studies, it seems clear that fragments with low forest cover inserted in anthropogenic matrices are more likely to experience floristic homogenization. However, the homogenization process has two other components, genetic and functional, which have not been investigated. The purpose of this study was to verify whether there was homogenization of tree reproductive functions in a fragmented landscape and, if found, to determine how the process was influenced by landscape composition. The study was conducted in eight fragments in southwest Brazil. The study was conducted in eight fragments in southwestern Brazil. In each fragment, all individual trees were sampled that had a diameter at breast height ≥3 cm, in ten plots (0.2 ha) and, classified within 26 reproductive functional types (RFTs). The process of functional homogenization was evaluated using additive partitioning of diversity. Additionally, the effect of landscape composition on functional diversity and on the number of individuals within each RFT was evaluated using a generalized linear mixed model. appeared to be in a process of functional homogenization (dominance of RFTs, alpha diversity lower than expected by chance and and low beta diversity). More than 50% of the RFTs and the functional diversity were affected by the landscape parameters. In general, the percentage of forest cover has a positive effect on RFTs while the percentage of coffee matrix has a negative one. The process of functional homogenization has serious consequences for biodiversity conservation because some functions may disappear that, in the long term, would threaten the fragments. This study contributes to a better understanding of how landscape changes affect the functional diversity, abundance of individuals in RFTs and the process of functional homogenization, as well as how to manage fragmented landscapes. PMID:27760218

Screening of a Novel Fragment Library with Functional Complexity against Mycobacterium tuberculosis InhA.

PubMed

Prati, Federica; Zuccotto, Fabio; Fletcher, Daniel; Convery, Maire A; Fernandez-Menendez, Raquel; Bates, Robert; Encinas, Lourdes; Zeng, Jingkun; Chung, Chun-Wa; De Dios Anton, Paco; Mendoza-Losana, Alfonso; Mackenzie, Claire; Green, Simon R; Huggett, Margaret; Barros, David; Wyatt, Paul G; Ray, Peter C

2018-04-06

Our findings reported herein provide support for the benefits of including functional group complexity (FGC) within fragments when screening against protein targets such as Mycobacterium tuberculosis InhA. We show that InhA fragment actives with FGC maintained their binding pose during elaboration. Furthermore, weak fragment hits with functional group handles also allowed for facile fragment elaboration to afford novel and potent InhA inhibitors with good ligand efficiency metrics for optimization. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Changes in Tree Reproductive Traits Reduce Functional Diversity in a Fragmented Atlantic Forest Landscape

PubMed Central

Girão, Luciana Coe; Lopes, Ariadna Valentina; Tabarelli, Marcelo; Bruna, Emilio M.

2007-01-01

Functional diversity has been postulated to be critical for the maintenance of ecosystem functioning, but the way it can be disrupted by human-related disturbances remains poorly investigated. Here we test the hypothesis that habitat fragmentation changes the relative contribution of tree species within categories of reproductive traits (frequency of traits) and reduces the functional diversity of tree assemblages. The study was carried out in an old and severely fragmented landscape of the Brazilian Atlantic forest. We used published information and field observations to obtain the frequency of tree species and individuals within 50 categories of reproductive traits (distributed in four major classes: pollination systems, floral biology, sexual systems, and reproductive systems) in 10 fragments and 10 tracts of forest interior (control plots). As hypothesized, populations in fragments and control plots differed substantially in the representation of the four major classes of reproductive traits (more than 50% of the categories investigated). The most conspicuous differences were the lack of three pollination systems in fragments-pollination by birds, flies and non-flying mammals-and that fragments had a higher frequency of both species and individuals pollinated by generalist vectors. Hermaphroditic species predominate in both habitats, although their relative abundances were higher in fragments. On the contrary, self-incompatible species were underrepresented in fragments. Moreover, fragments showed lower functional diversity (H' scores) for pollination systems (−30.3%), floral types (−23.6%), and floral sizes (−20.8%) in comparison to control plots. In contrast to the overwhelming effect of fragmentation, patch and landscape metrics such as patch size and forest cover played a minor role on the frequency of traits. Our results suggest that habitat fragmentation promotes a marked shift in the relative abundance of tree reproductive traits and greatly reduces the functional diversity of tree assemblages in fragmented landscapes. PMID:17878943

ANTAGONISTIC EFFECTS OF 6-MERCAPTOPURINE AND COENZYME A ON MITOCHONDRIA AND MITOSIS IN TISSUE CULTURE

PubMed Central

Biesele, John J.

1955-01-01

The partial mitotic inhibition caused by 6-mercaptopurine in tissue cultures of Crocker mouse sarcoma 180 and embryonic mouse skin is blocked by co-enzyme A. 6-Mercaptopurine and coenzyme A also have opposite effects on mitochondrial morphology. Mitochondria in cells treated with 6-mercaptopurine become thin and fragmented. Coenzyme A blocks this effect, and alone coenzyme A makes for longer and thicker mitochondria. 6-Mercaptopurine inhibits lipogenesis in embryo skin fibroblasts, and this inhibition is partly counteracted by coenzyme A, which by itself makes for a greater accumulation of lipid droplets in the cytoplasm. It is suggested that at least one part of the action by which 6-mercaptopurine decreases mitotic incidence in tissue cultures may be an interference on the part of 6-mercaptopurine, acting as an antimetabolite of coenzyme A, in mitochondrial function related to cell division. PMID:14381434

Functional association of Sun1 with nuclear pore complexes

PubMed Central

Liu, Qian; Pante, Nelly; Misteli, Tom; Elsagga, Mohamed; Crisp, Melissa; Hodzic, Didier; Burke, Brian; Roux, Kyle J.

2007-01-01

Sun1 and 2 are A-type lamin-binding proteins that, in association with nesprins, form a link between the inner nuclear membranes (INMs) and outer nuclear membranes of mammalian nuclear envelopes. Both immunofluorescence and immunoelectron microscopy reveal that Sun1 but not Sun2 is intimately associated with nuclear pore complexes (NPCs). Topological analyses indicate that Sun1 is a type II integral protein of the INM. Localization of Sun1 to the INM is defined by at least two discrete regions within its nucleoplasmic domain. However, association with NPCs is dependent on the synergy of both nucleoplasmic and lumenal domains. Cells that are either depleted of Sun1 by RNA interference or that overexpress dominant-negative Sun1 fragments exhibit clustering of NPCs. The implication is that Sun1 represents an important determinant of NPC distribution across the nuclear surface. PMID:17724119

Negative Impacts of Human Land Use on Dung Beetle Functional Diversity

PubMed Central

Barragán, Felipe; Moreno, Claudia E.; Escobar, Federico; Halffter, Gonzalo; Navarrete, Dario

2011-01-01

The loss of biodiversity caused by human activity is assumed to alter ecosystem functioning. However our understanding of the magnitude of the effect of these changes on functional diversity and their impact on the dynamics of ecological processes is still limited. We analyzed the functional diversity of copro-necrophagous beetles under different conditions of land use in three Mexican biosphere reserves. In Montes Azules pastures, forest fragments and continuous rainforest were analyzed, in Los Tuxtlas rainforest fragments of different sizes were analyzed and in Barranca de Metztitlán two types of xerophile scrub with different degrees of disturbance from grazing were analyzed. We assigned dung beetle species to functional groups based on food relocation, beetle size, daily activity period and food preferences, and as measures of functional diversity we used estimates based on multivariate methods. In Montes Azules functional richness was lower in the pastures than in continuous rainforest and rainforest fragments, but fragments and continuous forest include functionally redundant species. In small rainforest fragments (<5 ha) in Los Tuxtlas, dung beetle functional richness was lower than in large rainforest fragments (>20 ha). Functional evenness and functional dispersion did not vary among habitat types or fragment size in these reserves. In contrast, in Metztitlán, functional richness and functional dispersion were different among the vegetation types, but differences were not related to the degree of disturbance by grazing. More redundant species were found in submontane than in crassicaule scrub. For the first time, a decrease in the functional diversity in communities of copro-necrophagous beetles resulting from changes in land use is documented, the potential implications for ecosystem functioning are discussed and a series of variables that could improve the evaluation of functional diversity for this biological group is proposed. PMID:21448292

Negative impacts of human land use on dung beetle functional diversity.

PubMed

Barragán, Felipe; Moreno, Claudia E; Escobar, Federico; Halffter, Gonzalo; Navarrete, Dario

2011-03-23

The loss of biodiversity caused by human activity is assumed to alter ecosystem functioning. However our understanding of the magnitude of the effect of these changes on functional diversity and their impact on the dynamics of ecological processes is still limited. We analyzed the functional diversity of copro-necrophagous beetles under different conditions of land use in three Mexican biosphere reserves. In Montes Azules pastures, forest fragments and continuous rainforest were analyzed, in Los Tuxtlas rainforest fragments of different sizes were analyzed and in Barranca de Metztitlán two types of xerophile scrub with different degrees of disturbance from grazing were analyzed. We assigned dung beetle species to functional groups based on food relocation, beetle size, daily activity period and food preferences, and as measures of functional diversity we used estimates based on multivariate methods. In Montes Azules functional richness was lower in the pastures than in continuous rainforest and rainforest fragments, but fragments and continuous forest include functionally redundant species. In small rainforest fragments (<5 ha) in Los Tuxtlas, dung beetle functional richness was lower than in large rainforest fragments (>20 ha). Functional evenness and functional dispersion did not vary among habitat types or fragment size in these reserves. In contrast, in Metztitlán, functional richness and functional dispersion were different among the vegetation types, but differences were not related to the degree of disturbance by grazing. More redundant species were found in submontane than in crassicaule scrub. For the first time, a decrease in the functional diversity in communities of copro-necrophagous beetles resulting from changes in land use is documented, the potential implications for ecosystem functioning are discussed and a series of variables that could improve the evaluation of functional diversity for this biological group is proposed.

Does an attention bias to appetitive and aversive words modulate interference control in youth with ADHD?

PubMed

Ma, Ili; Mies, Gabry W; Lambregts-Rommelse, Nanda N J; Buitelaar, Jan K; Cillessen, Antonius H N; Scheres, Anouk

2018-05-01

Interference control refers to the ability to selectively attend to certain information while ignoring distracting information. This ability can vary as a function of distractor relevance. Distractors that are particularly relevant to an individual may attract more attention than less relevant distractors. This is referred to as attention bias. Weak interference control and altered reward sensitivity are both important features of attention deficit hyperactivity disorder (ADHD). However, interference control is typically studied in isolation. This study integrates both. Youths (aged 9 to 17 years) with ADHD (n = 37, 25 boys) and typically-developing controls (n = 38, 20 boys) completed a Stroop task using appetitive words and matched neutral words to assess whether appetitive distractors diminished interference control more in youths with ADHD than controls. In order to test for specificity, aversive words were also included. As expected, appetitive words disrupted interference control but this effect was not stronger for youths with ADHD than the controls. Aversive words, on the other hand, facilitated interference control. Dimensional analyses revealed that this facilitation effect increased substantially as a function of ADHD symptom severity. Possible mechanisms for this effect include up-regulation of interference control as a function of induced negative mood, or as a function of increased effort. In conclusion, appetitive words do not lead to worse interference control in youths with ADHD compared with controls. Interference control was modulated in a valence-specific manner, concurrent with mood-induced effects on cognitive control.

Fragment-Based Optimization of Small Molecule CXCL12 Inhibitors for Antagonizing the CXCL12/CXCR4 Interaction

PubMed Central

Ziarek, Joshua J.; Liu, Yan; Smith, Emmanuel; Zhang, Guolin; Peterson, Francis C.; Chen, Jun; Yu, Yongping; Chen, Yu; Volkman, Brian F.; Li, Rongshi

2013-01-01

The chemokine CXCL12 and its G protein-coupled receptor (GPCR) CXCR4 are high-priority clinical targets because of their involvement in metastatic cancers (also implicated in autoimmune disease and cardiovascular disease). Because chemokines interact with two distinct sites to bind and activate their receptors, both the GPCRs and chemokines are potential targets for small molecule inhibition. A number of chemokines have been validated as targets for drug development, but virtually all drug discovery efforts focus on the GPCRs. However, all CXCR4 receptor antagonists with the exception of MSX-122 have failed in clinical trials due to unmanageable toxicities, emphasizing the need for alternative strategies to interfere with CXCL12/CXCR4-guided metastatic homing. Although targeting the relatively featureless surface of CXCL12 was presumed to be challenging, focusing efforts at the sulfotyrosine (sY) binding pockets proved successful for procuring initial hits. Using a hybrid structure-based in silico/NMR screening strategy, we recently identified a ligand that occludes the receptor recognition site. From this initial hit, we designed a small fragment library containing only nine tetrazole derivatives using a fragment-based and bioisostere approach to target the sY binding sites of CXCL12. Compound binding modes and affinities were studied by 2D NMR spectroscopy, X-ray crystallography, molecular docking and cell-based functional assays. Our results demonstrate that the sY binding sites are conducive to the development of high affinity inhibitors with better ligand efficiency (LE) than typical protein-protein interaction inhibitors (LE ≤ 0.24). Our novel tetrazole-based fragment 18 was identified to bind the sY21 site with a Kd of 24 μM (LE = 0.30). Optimization of 18 yielded compound 25 which specifically inhibits CXCL12-induced migration with an improvement in potency over the initial hit 9. The fragment from this library that exhibited the highest affinity and ligand efficiency (11: Kd = 13 μM, LE = 0.33) may serve as a starting point for development of inhibitors targeting the sY12 site. PMID:23368099

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

PubMed Central

2010-01-01

Background Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. Description RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics) is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. RNA FRABASE 2.0 is freely available at http://rnafrabase.cs.put.poznan.pl. Conclusions RNA FRABASE 2.0 provides a novel database and powerful search engine which is equipped with new data and functionalities that are unavailable elsewhere. Our intention is that this advanced version of the RNA FRABASE will be of interest to all researchers working in the RNA field. PMID:20459631

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures.

PubMed

Popenda, Mariusz; Szachniuk, Marta; Blazewicz, Marek; Wasik, Szymon; Burke, Edmund K; Blazewicz, Jacek; Adamiak, Ryszard W

2010-05-06

Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics) is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. RNA FRABASE 2.0 is freely available at http://rnafrabase.cs.put.poznan.pl. RNA FRABASE 2.0 provides a novel database and powerful search engine which is equipped with new data and functionalities that are unavailable elsewhere. Our intention is that this advanced version of the RNA FRABASE will be of interest to all researchers working in the RNA field.

Compact Two-step Laser Time-of-Flight Mass Spectrometer for in Situ Analyses of Aromatic Organics on Planetary Missions

NASA Technical Reports Server (NTRS)

Getty, Stephanie; Brickerhoff, William; Cornish, Timothy; Ecelberger, Scott; Floyd, Melissa

2012-01-01

RATIONALE A miniature time-of-flight mass spectrometer has been adapted to demonstrate two-step laser desorption-ionization (LOI) in a compact instrument package for enhanced organics detection. Two-step LDI decouples the desorption and ionization processes, relative to traditional laser ionization-desorption, in order to produce low-fragmentation conditions for complex organic analytes. Tuning UV ionization laser energy allowed control ofthe degree of fragmentation, which may enable better identification of constituent species. METHODS A reflectron time-of-flight mass spectrometer prototype measuring 20 cm in length was adapted to a two-laser configuration, with IR (1064 nm) desorption followed by UV (266 nm) postionization. A relatively low ion extraction voltage of 5 kV was applied at the sample inlet. Instrument capabilities and performance were demonstrated with analysis of a model polycyclic aromatic hydrocarbon, representing a class of compounds important to the fields of Earth and planetary science. RESULTS L2MS analysis of a model PAH standard, pyrene, has been demonstrated, including parent mass identification and the onset o(tunable fragmentation as a function of ionizing laser energy. Mass resolution m/llm = 380 at full width at half-maximum was achieved which is notable for gas-phase ionization of desorbed neutrals in a highly-compact mass analyzer. CONCLUSIONS Achieving two-step laser mass spectrometry (L2MS) in a highly-miniature instrument enables a powerful approach to the detection and characterization of aromatic organics in remote terrestrial and planetary applications. Tunable detection of parent and fragment ions with high mass resolution, diagnostic of molecular structure, is possible on such a compact L2MS instrument. Selectivity of L2MS against low-mass inorganic salt interferences is a key advantage when working with unprocessed, natural samples, and a mechanism for the observed selectivity is presented.

Towards optimized methods to study viral impacts on soil microbial carbon cycling

NASA Astrophysics Data System (ADS)

Trubl, G. G.; Roux, S.; Jang, H. B.; Solonenko, N.; Sullivan, M. B.; Rich, V. I.

2016-12-01

Permafrost contains 50% of global soil carbon and is rapidly thawing. While the fate of this carbon is currently unknown, it will undoubtedly be shaped by microbes and their associated viruses, which modulate host activities via mortality and metabolic control. However, little is known about soil viruses generally and their impact on terrestrial biogeochemistry; this is partially due to the presence of inhibitory substances (e.g. humic acids) in soils that interfere with sample processing and sequence-based metagenomics surveys. To address this problem, we examined viral populations in three different peat soils along a permafrost thaw gradient. These samples yielded low viral DNA recoveries, and shallow metagenomic sequencing, but still resulted in the recovery of 40 viral genome fragments. Genome- and network-based classification suggested that these new references represented 11 viral clusters, and ecological patterns (based upon non-redundant fragment recruitment) showed that viral populations were distinct in each habitat. Although only 31% of the genes could be functionally classified, pairwise genome comparisons classified 63% of the viruses taxonomically. Additionally, comparison of the 40 viral genome fragments to 53 previously recovered fragments from the same site showed no overlap, suggesting only a small portion of the resident viral community has been sampled. A follow-up experiment was performed to remove more humics during extraction and thereby obtain better viral metagenomes. Three DNA extraction protocols were tested (CTAB, PowerSoil, and Wizard columns) and the DNA was further purified with an AMPure clean-up. The PowerSoil kit maximized DNA yield (3x CTAB and 6x Wizard), and yielded the purest DNA (based on NanoDrop 260:230 ratio). Given the important roles of viruses in biogeochemical cycles in better-studied systems, further research and humic-removal optimization on these thawing permafrost-associated viral communities is needed to clarify their involvement in carbon cycle feedbacks.

Using hadron-in-jet data in a global analysis of D* fragmentation functions

NASA Astrophysics Data System (ADS)

Anderle, Daniele P.; Kaufmann, Tom; Stratmann, Marco; Ringer, Felix; Vitev, Ivan

2017-08-01

We present a novel global QCD analysis of charged D*-meson fragmentation functions at next-to-leading order accuracy. This is achieved by making use of the available data for single-inclusive D*-meson production in electron-positron annihilation, hadron-hadron collisions, and, for the first time, in-jet fragmentation in proton-proton scattering. It is shown how to include all relevant processes efficiently and without approximations within the Mellin moment technique, specifically for the in-jet fragmentation cross section. The presented technical framework is generic and can be straightforwardly applied to future analyses of fragmentation functions for other hadron species, as soon as more in-jet fragmentation data become available. We choose to work within the zero mass variable flavor number scheme which is applicable for sufficiently high energies and transverse momenta. The obtained optimum set of parton-to-D* fragmentation functions is accompanied by Hessian uncertainty sets which allow one to propagate hadronization uncertainties to other processes of interest.

Water channel in the binding site of a high affinity anti-methotrexate antibody.

PubMed

Gayda, Susan; Longenecker, Kenton L; Manoj, Sharmila; Judge, Russell A; Saldana, Sylvia C; Ruan, Qiaoqiao; Swift, Kerry M; Tetin, Sergey Y

2014-06-17

In the present study, we report the structure of the free and drug-bound Fab fragment of a high affinity anti-methotrexate antibody and perform a thermodynamic analysis of the binding process. The anti-methotrexate Fab fragment features a remarkably rigid tunnel-like binding site that extends into a water channel serving as a specialized route to move solvent out and into the site upon ligand binding and dissociation. This new finding in antibody structure-function relationships directly relates to the fast association (1 × 10⁷ M⁻¹ s⁻¹) and slow dissociation (4 × 10⁻⁵ s⁻¹) rates determined for mAb ADD056, resulting in a very strong binding with a K(D) ~ 3.6 pM at 20 °C. As follows from the X-ray data analysis, the methotrexate-antibody complex is stabilized by an extended network of hydrogen bonds and stacking interactions. The analysis also shows structural involvement of the CDR H3 in formation of the water channel revealing another important role of this hypervariable region. This suggests a new direction in natural affinity maturation and opens a new possibility in antibody engineering. Methotrexate is a widely used therapeutic agent for many malignant diseases and inflammatory disorders. Unfortunately, it may also interfere with central aspects of metabolism and thereby cause inevitable side effects. Therefore, methotrexate therapy requires careful monitoring of drug blood levels, which is traditionally done by immunoassays. An understanding of the structure-function properties of antibodies selected for drug monitoring substantiates the performance and robustness of such tests.

The mixture of "ecstasy" and its metabolites impairs mitochondrial fusion/fission equilibrium and trafficking in hippocampal neurons, at in vivo relevant concentrations.

PubMed

Barbosa, Daniel José; Serrat, Romàn; Mirra, Serena; Quevedo, Martí; de Barreda, Elena Goméz; Àvila, Jesús; Ferreira, Luísa Maria; Branco, Paula Sério; Fernandes, Eduarda; Lourdes Bastos, Maria de; Capela, João Paulo; Soriano, Eduardo; Carvalho, Félix

2014-06-01

3,4-Methylenedioxymethamphetamine (MDMA; "ecstasy") is a potentially neurotoxic recreational drug of abuse. Though the mechanisms involved are still not completely understood, formation of reactive metabolites and mitochondrial dysfunction contribute to MDMA-related neurotoxicity. Neuronal mitochondrial trafficking, and their targeting to synapses, is essential for proper neuronal function and survival, rendering neurons particularly vulnerable to mitochondrial dysfunction. Indeed, MDMA-associated disruption of Ca(2+) homeostasis and ATP depletion have been described in neurons, thus suggesting possible MDMA interference on mitochondrial dynamics. In this study, we performed real-time functional experiments of mitochondrial trafficking to explore the role of in situ mitochondrial dysfunction in MDMA's neurotoxic actions. We show that the mixture of MDMA and six of its major in vivo metabolites, each compound at 10μM, impaired mitochondrial trafficking and increased the fragmentation of axonal mitochondria in cultured hippocampal neurons. Furthermore, the overexpression of mitofusin 2 (Mfn2) or dynamin-related protein 1 (Drp1) K38A constructs almost completely rescued the trafficking deficits caused by this mixture. Finally, in hippocampal neurons overexpressing a Mfn2 mutant, Mfn2 R94Q, with impaired fusion and transport properties, it was confirmed that a dysregulation of mitochondrial fission/fusion events greatly contributed to the reported trafficking phenotype. In conclusion, our study demonstrated, for the first time, that the mixture of MDMA and its metabolites, at concentrations relevant to the in vivo scenario, impaired mitochondrial trafficking and increased mitochondrial fragmentation in hippocampal neurons, thus providing a new insight in the context of "ecstasy"-induced neuronal injury.

BcL-xL Conformational Changes upon Fragment Binding Revealed by NMR

PubMed Central

Aguirre, Clémentine; ten Brink, Tim; Walker, Olivier; Guillière, Florence; Davesne, Dany; Krimm, Isabelle

2013-01-01

Protein-protein interactions represent difficult but increasingly important targets for the design of therapeutic compounds able to interfere with biological processes. Recently, fragment-based strategies have been proposed as attractive approaches for the elaboration of protein-protein surface inhibitors from fragment-like molecules. One major challenge in targeting protein-protein interactions is related to the structural adaptation of the protein surface upon molecular recognition. Methods capable of identifying subtle conformational changes of proteins upon fragment binding are therefore required at the early steps of the drug design process. In this report we present a fast NMR method able to probe subtle conformational changes upon fragment binding. The approach relies on the comparison of experimental fragment-induced Chemical Shift Perturbation (CSP) of amine protons to CSP simulated for a set of docked fragment poses, considering the ring-current effect from fragment binding. We illustrate the method by the retrospective analysis of the complex between the anti-apoptotic Bcl-xL protein and the fragment 4′-fluoro-[1,1′-biphenyl]-4-carboxylic acid that was previously shown to bind one of the Bcl-xL hot spots. The CSP-based approach shows that the protein undergoes a subtle conformational rearrangement upon interaction, for residues located in helices 2, 3 and the very beginning of 5. Our observations are corroborated by residual dipolar coupling measurements performed on the free and fragment-bound forms of the Bcl-xL protein. These NMR-based results are in total agreement with previous molecular dynamic calculations that evidenced a high flexibility of Bcl-xL around the binding site. Here we show that CSP of protein amine protons are useful and reliable structural probes. Therefore, we propose to use CSP simulation to assess protein conformational changes upon ligand binding in the fragment-based drug design approach. PMID:23717610

Dissociating interference-control processes between memory and response.

PubMed

Bissett, Patrick G; Nee, Derek Evan; Jonides, John

2009-09-01

The ability to mitigate interference is of central importance to cognition. Previous research has provided conflicting accounts about whether operations that resolve interference are singular in character or form a family of functions. Here, the authors examined the relationship between interference-resolution processes acting on working memory representations versus responses. The authors combined multiple forms of interference into a single paradigm by merging a directed-forgetting task, which induces proactive interference, with a stop-signal task, which taps response inhibition processes. The results demonstrated that proactive interference and response inhibition produced distinct behavioral signatures that did not interact. By contrast, combining two different measures of response inhibition by merging a go/no-go task variant and a stop signal produced overadditive behavioral interference, demonstrating that different forms of response inhibition tap the same processes. However, not all forms of response conflict interacted, suggesting that inhibition-related functions acting on response selection are dissociable from those acting on response inhibition. These results suggest that inhibition-related functions for memory and responses are dissociable. (c) 2009 APA, all rights reserved.

Interference susceptibility measurements for an MSK satellite communication link

NASA Technical Reports Server (NTRS)

Kerczewski, Robert J.; Fujikawa, Gene

1992-01-01

The results are presented of measurements of the degradation of an MSK satellite link due to modulated and CW (unmodulated) interference. These measurements were made using a hardware based satellite communication link simulator at NASA-Lewis. The results indicate the amount of bit error rate degradation caused by CW interference as a function of frequency and power level, and the degradation caused by adjacent channel and cochannel modulated interference as a function of interference power level. Results were obtained for both the uplink case (including satellite nonlinearity) and the downlink case (linear channel).

Nuclear interference in the Coulomb explosion of H2+ in short vuv laser fields.

PubMed

Førre, Morten; Barmaki, Samira; Bachau, Henri

2009-03-27

We report ab initio calculations of H2+ three-photon ionization by vuv/fs 10(12) W/cm(2) laser pulses including electronic and vibrational degrees of freedom in the Born-Oppenheimer approximation. The initial nuclear wave packet of H2+(1ssigma(g)) is assumed to be equal to the H2 vibrational ground state. For pulse durations longer than 10 fs, we find an unexpected modulation in the kinetic energy spectra of the correlated fragments (H++H+). It is shown that the structures in the spectra originate from the interference between a direct and a sequential dissociation channel. While the first channel is open even for relatively short pulses, the sequential one only opens for pulse durations longer than 10 fs. In the latter case we show that interference between the two components results in a modulated kinetic energy release spectrum in the dissociation channel 3dsigma(g), which is reflected in the ionization spectrum.

Inorganic Salt Interference on CO2+ in Aerodyne AMS and ACSM Organic Aerosol Composition Studies.

PubMed

Pieber, Simone M; El Haddad, Imad; Slowik, Jay G; Canagaratna, Manjula R; Jayne, John T; Platt, Stephen M; Bozzetti, Carlo; Daellenbach, Kaspar R; Fröhlich, Roman; Vlachou, Athanasia; Klein, Felix; Dommen, Josef; Miljevic, Branka; Jiménez, José L; Worsnop, Douglas R; Baltensperger, Urs; Prévôt, André S H

2016-10-04

Aerodyne aerosol mass spectrometer (AMS) and Aerodyne aerosol chemical speciation monitor (ACSM) mass spectra are widely used to quantify organic aerosol (OA) elemental composition, oxidation state, and major environmental sources. The OA CO 2 + fragment is among the most important measurements for such analyses. Here, we show that a non-OA CO 2 + signal can arise from reactions on the particle vaporizer, ion chamber, or both, induced by thermal decomposition products of inorganic salts. In our tests (eight instruments, n = 29), ammonium nitrate (NH 4 NO 3 ) causes a median CO 2 + interference signal of +3.4% relative to nitrate. This interference is highly variable between instruments and with measurement history (percentiles P 10-90 = +0.4 to +10.2%). Other semi-refractory nitrate salts showed 2-10 times enhanced interference compared to that of NH 4 NO 3 , while the ammonium sulfate ((NH 4 ) 2 SO 4 ) induced interference was 3-10 times lower. Propagation of the CO 2 + interference to other ions during standard AMS and ACSM data analysis affects the calculated OA mass, mass spectra, molecular oxygen-to-carbon ratio (O/C), and f 44 . The resulting bias may be trivial for most ambient data sets but can be significant for aerosol with higher inorganic fractions (>50%), e.g., for low ambient temperatures, or laboratory experiments. The large variation between instruments makes it imperative to regularly quantify this effect on individual AMS and ACSM systems.

A study of coherence of soft gluons in hadron jets

NASA Astrophysics Data System (ADS)

Akrawy, M. Z.; Alexander, G.; Allison, J.; Allport, P. P.; Anderson, K. J.; Armitage, J. C.; Arnison, G. T. J.; Ashton, P.; Azuelos, G.; Baines, J. T. M.; Ball, A. H.; Banks, J.; Barker, G. J.; Barlow, R. J.; Batley, J. R.; Becker, J.; Behnke, T.; Bell, K. W.; Bella, G.; Bethke, S.; Biebel, O.; Binder, U.; Bloodworth, I. J.; Bock, P.; Breuker, H.; Brown, R. M.; Brun, R.; Buijs, A.; Burckhart, H. J.; Capiluppi, P.; Carnegie, R. K.; Carter, A. A.; Carter, J. R.; Chang, C. Y.; Charlton, D. G.; Chrin, J. T. M.; Clarke, P. E. L.; Cohen, I.; Collins, W. J.; Conboy, J. E.; Couch, M.; Coupland, M.; Cuffiani, M.; Dado, S.; Dallavalle, G. M.; Debu, P.; Deninno, M. M.; Dieckmann, A.; Dittmar, M.; Dixit, M. S.; Duchovni, E.; Duerdoth, I. P.; Dumas, D. J. P.; El Mamouni, H.; Elcombe, P. A.; Estabrooks, P. G.; Etzion, E.; Fabbri, F.; Farthouat, P.; Fischer, H. M.; Fong, D. G.; French, M. T.; Fukunaga, C.; Gaidot, A.; Ganel, O.; Gary, J. W.; Gascon, J.; Geddes, N. I.; Gee, C. N. P.; Geich-Gimbel, C.; Gensler, S. W.; Gentit, F. X.; Giacomelli, G.; Gibson, V.; Gibson, W. R.; Gillies, J. D.; Goldberg, J.; Goodrick, M. J.; Gorn, W.; Granite, D.; Gross, E.; Grunhaus, J.; Hagedorn, H.; Hagemann, J.; Hansroul, M.; Hargrove, C. K.; Harrus, I.; Hart, J.; Hattersley, P. M.; Hauschild, M.; Hawkes, C. M.; Heflin, E.; Hemingway, R. J.; Heuer, R. D.; Hill, J. C.; Hillier, S. J.; Ho, C.; Hobbs, J. D.; Hobson, P. R.; Hochman, D.; Holl, B.; Homer, R. J.; Hou, S. R.; Howarth, C. P.; Hughes-Jones, R. E.; Humbert, R.; Igo-Kemenes, P.; Ihssen, H.; Imrie, D. C.; Jawahery, A.; Jeffreys, P. W.; Jeremie, H.; Jimack, M.; Jobes, M.; Jones, R. W. L.; Jovanovic, P.; Karlen, D.; Kawagoe, K.; Kawamoto, T.; Kellogg, R. G.; Kennedy, B. W.; Kleinwort, C.; Klem, D. E.; Knop, G.; Kobayashi, T.; Kokott, T. P.; Köpke, L.; Kowalewski, R.; Kreutzmann, H.; Kroll, J.; Kuwano, M.; Kyberd, P.; Lafferty, G. D.; Lamarche, F.; Larson, W. J.; Layter, J. G.; Le Du, P.; Leblanc, P.; Lee, A. M.; Lehto, M. H.; Lellouch, D.; Lennert, P.; Lessard, L.; Levinson, L.; Lloyd, S. L.; Loebinger, F. K.; Lorah, J. M.; Lorazo, B.; Losty, M. J.; Ludwig, J.; Ma, J.; Macbeth, A. A.; Mannelli, M.; Marcellini, S.; Maringer, G.; Martin, A. J.; Martin, J. P.; Mashimo, T.; Mättig, P.; Maur, U.; McMahon, T. J.; McNutt, J. R.; McPherson, A. C.; Meijers, F.; Menszner, D.; Merritt, F. S.; Mes, H.; Michelini, A.; Middleton, R. P.; Mikenberg, G.; Miller, D. J.; Milstene, C.; Minowa, M.; Mohr, W.; Montanari, A.; Mori, T.; Moss, M. W.; Murphy, P. G.; Murray, W. J.; Nellen, B.; Nguyen, H. H.; Nozaki, M.; O'Dowd, A. J. P.; O'Neale, S. W.; O'Neill, B. P.; Oakham, F. G.; Odorici, F.; Ogg, M.; Oh, H.; Oreglia, M. J.; Orito, S.; Pansart, J. P.; Patrick, G. N.; Pawley, S. J.; Pfister, P.; Pilcher, J. E.; Pinfold, J. L.; Plane, D. E.; Poli, B.; Pouladdej, A.; Pritchard, T. W.; Quast, G.; Raab, J.; Redmond, M. W.; Rees, D. L.; Regimbald, M.; Riles, K.; Roach, C. M.; Robins, S. A.; Rollnik, A.; Roney, J. M.; Rossberg, S.; Rossi, A. M.; Routenburg, P.; Runge, K.; Runolfsson, O.; Sanghera, S.; Sansum, R. A.; Sasaki, M.; Saunders, B. J.; Schaile, A. D.; Schaile, O.; Schappert, W.; Scharff-Hansen, P.; Schreiber, S.; Schwarz, J.; Shapira, A.; Shen, B. C.; Sherwood, P.; Simon, A.; Singh, P.; Siroli, G. P.; Skuia, A.; Smith, A. M.; Smith, T. J.; Snow, G. A.; Springer, R. W.; Sproston, M.; Stephens, K.; Stier, H. E.; Ströhmer, R.; Strom, D.; Takeda, H.; Takeshita, T.; Tsukamoto, T.; Turner, M. F.; Tysarczyk-Niemeyer, G.; Van den plas, D.; VanDalen, G. J.; Vasseur, G.; Virtue, C. J.; von der Schmitt, H.; von Krogh, J.; Wagner, A.; Wahl, C.; Ward, C. P.; Ward, D. R.; Waterhouse, J.; Watkins, P. M.; Watson, A. T.; Watson, N. K.; Weber, M.; Weisz, S.; Wells, P. S.; Wermes, N.; Weymann, M.; Wilson, G. W.; Wilson, J. A.; Wingerter, I.; Winterer, V.-H.; Wood, N. C.; Wotton, S.; Wuensch, B.; Wyatt, T. R.; Yaari, R.; Yang, Y.; Yekutieli, G.; Yoshida, T.; Zeuner, W.; Zorn, G. T.; OPAL Collaboration

1990-09-01

We study the inclusive momentum distribution of charged particles in multihadronic events produced in e +e - annihilations at ECM∼ M(Z 0). We find agreement with the analytical formulae for gluon production that include the phenomena of soft gluon interference. Using data from CM energies between 14 and 91 GeV, we study the dependence of the inclusive momentum distribution on the centre of momentum energy. We find that the analytical formulae describe the data over the entire energy range. Both the momentum distribution at a fixed energy and the change with energy are described by QCD shower Monte Carlo's which include either coherent gluon branchings or string fragmentation. Simple incoherent models with independent fragmentation fail to reproduce the energy dependence and momentum spectra.

The Relations Among Inhibition and Interference Control Functions: A Latent-Variable Analysis

ERIC Educational Resources Information Center

Friedman, Naomi P.; Miyake, Akira

2004-01-01

This study used data from 220 adults to examine the relations among 3 inhibition-related functions. Confirmatory factor analysis suggested that Prepotent Response Inhibition and Resistance to Distractor Interference were closely related, but both were unrelated to Resistance to Proactive Interference. Structural equation modeling, which combined…

Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data-independent Acquisition Mass Spectrometry (MS) using SWATHProphet*

PubMed Central

Keller, Andrew; Bader, Samuel L.; Shteynberg, David; Hood, Leroy; Moritz, Robert L.

2015-01-01

Proteomics by mass spectrometry technology is widely used for identifying and quantifying peptides and proteins. The breadth and sensitivity of peptide detection have been advanced by the advent of data-independent acquisition mass spectrometry. Analysis of such data, however, is challenging due to the complexity of fragment ion spectra that have contributions from multiple co-eluting precursor ions. We present SWATHProphet software that identifies and quantifies peptide fragment ion traces in data-independent acquisition data, provides accurate probabilities to ensure results are correct, and automatically detects and removes contributions to quantitation originating from interfering precursor ions. Integration in the widely used open source Trans-Proteomic Pipeline facilitates subsequent analyses such as combining results of multiple data sets together for improved discrimination using iProphet and inferring sample proteins using ProteinProphet. This novel development should greatly help make data-independent acquisition mass spectrometry accessible to large numbers of users. PMID:25713123

Strategy to improve the quantitative LC-MS analysis of molecular ions resistant to gas-phase collision induced dissociation: application to disulfide-rich cyclic peptides.

PubMed

Ciccimaro, Eugene; Ranasinghe, Asoka; D'Arienzo, Celia; Xu, Carrie; Onorato, Joelle; Drexler, Dieter M; Josephs, Jonathan L; Poss, Michael; Olah, Timothy

2014-12-02

Due to observed collision induced dissociation (CID) fragmentation inefficiency, developing sensitive liquid chromatography tandem mass spectrometry (LC-MS/MS) assays for CID resistant compounds is especially challenging. As an alternative to traditional LC-MS/MS, we present here a methodology that preserves the intact analyte ion for quantification by selectively filtering ions while reducing chemical noise. Utilizing a quadrupole-Orbitrap MS, the target ion is selectively isolated while interfering matrix components undergo MS/MS fragmentation by CID, allowing noise-free detection of the analyte's surviving molecular ion. In this manner, CID affords additional selectivity during high resolution accurate mass analysis by elimination of isobaric interferences, a fundamentally different concept than the traditional approach of monitoring a target analyte's unique fragment following CID. This survivor-selected ion monitoring (survivor-SIM) approach has allowed sensitive and specific detection of disulfide-rich cyclic peptides extracted from plasma.

A DS-UWB Cognitive Radio System Based on Bridge Function Smart Codes

NASA Astrophysics Data System (ADS)

Xu, Yafei; Hong, Sheng; Zhao, Guodong; Zhang, Fengyuan; di, Jinshan; Zhang, Qishan

This paper proposes a direct-sequence UWB Gaussian pulse of cognitive radio systems based on bridge function smart sequence matrix and the Gaussian pulse. As the system uses the spreading sequence code, that is the bridge function smart code sequence, the zero correlation zones (ZCZs) which the bridge function sequences' auto-correlation functions had, could reduce multipath fading of the pulse interference. The Modulated channel signal was sent into the IEEE 802.15.3a UWB channel. We analysis the ZCZs's inhibition to the interference multipath interference (MPI), as one of the main system sources interferences. The simulation in SIMULINK/MATLAB is described in detail. The result shows the system has better performance by comparison with that employing Walsh sequence square matrix, and it was verified by the formula in principle.

Ramsey Interference in One-Dimensional Systems: The Full Distribution Function of Fringe Contrast as a Probe of Many-Body Dynamics

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

Kitagawa, Takuya; Pielawa, Susanne; Demler, Eugene

2010-06-25

We theoretically analyze Ramsey interference experiments in one-dimensional quasicondensates and obtain explicit expressions for the time evolution of full distribution functions of fringe contrast. We show that distribution functions contain unique signatures of the many-body mechanism of decoherence. We argue that Ramsey interference experiments provide a powerful tool for analyzing strongly correlated nature of 1D interacting systems.

First Monte Carlo analysis of fragmentation functions from single-inclusive e + e - annihilation

DOE PAGES

Sato, Nobuo; Ethier, J. J.; Melnitchouk, W.; ...

2016-12-02

Here, we perform the first iterative Monte Carlo (IMC) analysis of fragmentation functions constrained by all available data from single-inclusive $e^+ e^-$ annihilation into pions and kaons. The IMC method eliminates potential bias in traditional analyses based on single fits introduced by fixing parameters not well contrained by the data, and provides a statistically rigorous determination of uncertainties. Our analysis reveals specific features of fragmentation functions using the new IMC methodology and those obtained from previous analyses, especially for light quarks and for strange quark fragmentation to kaons.

The plant G box promoter sequence activates transcription in Saccharomyces cerevisiae and is bound in vitro by a yeast activity similar to GBF, the plant G box binding factor.

PubMed Central

Donald, R G; Schindler, U; Batschauer, A; Cashmore, A R

1990-01-01

G box and I box sequences of the Arabidopsis thaliana ribulose-bisphosphate-1,5-carboxylase small subunit (RBCS) promoter are required for expression mediated by the Arabidopsis rbcS-1A promoter in transgenic tobacco plants and are bound in vitro by factors from plant nuclear extracts termed GBF and GA-1, respectively. We show here that a -390 to -60 rbcS-1A promoter fragment containing the G box and two I boxes activates transcription from a truncated iso-1-cytochrome c (CYC1) gene promoter in Saccharomyces cerevisiae. Mutagenesis of either the rbcS-1A G box or both I box sequences eliminated the expression mediated by this fragment. When polymerized, I box oligonucleotides were also capable of enhancing expression from the truncated CYC1 promoter. Single-copy G box sequences from the Arabidopsis rbcS-1A, Arabidopsis Adh and tomato rbcS-3A promoters were more potent activators and were used in mobility shift assays to identify a DNA binding activity in yeast functionally similar to GBF. In methylation interference experiments, the binding specificity of the yeast protein was indistinguishable from that obtained with plant nuclear extracts. Images Fig. 3. Fig. 4. Fig. 5. Fig. 6. PMID:2161333

G-Quadruplex-based DNAzyme for colorimetric detection of cocaine: using magnetic nanoparticles as the separation and amplification element.

PubMed

Du, Yan; Li, Bingling; Guo, Shaojun; Zhou, Zhixue; Zhou, Ming; Wang, Erkang; Dong, Shaojun

2011-02-07

The appearance of the aptamer provides good recognition elements for small molecules, especially for drugs. In this work, by combining the advantages of magnetic nanoparticles (MNPs) with colorimetric drug detection using hemin-G-quadruplex complex as the sensing element, we report a simple and sensitive DNAzyme-based colorimetric sensor for cocaine detection in a 3,3,5,5-tetramethylbenzidine sulfate (TMB)-H(2)O(2) reaction system. The whole experimental processes are simplified. Cocaine aptamer fragments, SH-C2, are covalently labeled onto the amine-functionalized MNPs. When the target cocaine and another cocaine aptamer fragments (C1) grafted with G-riched strand AG4 (i.e. C1-AG4) are present simultaneously, the C2 layer on MNPs hybridizes partly with C1-AG4 to bind the cocaine. The C1-AG4 can be combinded with hemin to form DNAzyme which can effectively catalyze the H(2)O(2)-mediated oxidation of TMB, giving rise to a change in solution color. Importantly, using MNPs as the separation and amplification elements could effectively reduce the background signal and the interference from the real samples. A linear response from 0.1 μM to 20 μM is obtained for cocaine and a detection limit of 50 nM is achieved, which provides high sensitivity and selectivity to detect cocaine.

Pain and Cognitive Function Among Older Adults Living in the Community

PubMed Central

van der Leeuw, Guusje; Eggermont, Laura H. P.; Shi, Ling; Milberg, William P.; Gross, Alden L.; Hausdorff, Jeffrey M.; Bean, Jonathan F.

2016-01-01

Background. Pain related to many age-related chronic conditions is a burdensome problem in elderly adults and may also interfere with cognitive functioning. The purpose of this study was to examine the cross-sectional relationship between measures of pain severity and pain interference and cognitive performance in community-living older adults. Methods. We studied 765 participants in the Maintenance of Balance Independent Living Intellect and Zest (MOBILIZE) Boston Study, a population-based study of persons aged 70 and older. Global pain severity and interference were measured using the Brief Pain Inventory subscales. The neuropsychological battery included measures of attentional capacity (Trail Making Test A, WORLD Test), executive function (Trail Making Test B and Delta, Clock-in-a-Box, Letter Fluency), memory (Hopkins Verbal Learning Test), and a global composite measure of cognitive function. Multivariable linear regression models were used to analyze the relationship between pain and cognitive functioning. Results. Elderly adults with more severe pain or more pain interference had poorer performance on memory tests and executive functioning compared to elders with none or less pain. Pain interference was also associated with impaired attentional capacity. Additional adjustment for chronic conditions, behaviors, and psychiatric medication resulted in attenuation of many of the observed associations. However, the association between pain interference and general cognitive function persisted. Conclusions. Our findings point to the need for further research to understand how chronic pain may contribute to decline in cognitive function and to determine strategies that may help in preventing or managing these potential consequences of pain on cognitive function in older adults. PMID:26433218

Biosensor-based small molecule fragment screening with biolayer interferometry

NASA Astrophysics Data System (ADS)

Wartchow, Charles A.; Podlaski, Frank; Li, Shirley; Rowan, Karen; Zhang, Xiaolei; Mark, David; Huang, Kuo-Sen

2011-07-01

Biosensor-based fragment screening is a valuable tool in the drug discovery process. This method is advantageous over many biochemical methods because primary hits can be distinguished from non-specific or non-ideal interactions by examining binding profiles and responses, resulting in reduced false-positive rates. Biolayer interferometry (BLI), a technique that measures changes in an interference pattern generated from visible light reflected from an optical layer and a biolayer containing proteins of interest, is a relatively new method for monitoring small molecule interactions. The BLI format is based on a disposable sensor that is immersed in 96-well or 384-well plates. BLI has been validated for small molecule detection and fragment screening with model systems and well-characterized targets where affinity constants and binding profiles are generally similar to those obtained with surface plasmon resonsance (SPR). Screens with challenging targets involved in protein-protein interactions including BCL-2, JNK1, and eIF4E were performed with a fragment library of 6,500 compounds, and hit rates were compared for these targets. For eIF4E, a protein containing a PPI site and a nucleotide binding site, results from a BLI fragment screen were compared to results obtained in biochemical HTS screens. Overlapping hits were observed for the PPI site, and hits unique to the BLI screen were identified. Hit assessments with SPR and BLI are described.

Agonistic and Antagonistic Roles for TNIK and MINK in Non-Canonical and Canonical Wnt Signalling

PubMed Central

Mikryukov, Alexander; Moss, Tom

2012-01-01

Wnt signalling is a key regulatory factor in animal development and homeostasis and plays an important role in the establishment and progression of cancer. Wnt signals are predominantly transduced via the Frizzled family of serpentine receptors to two distinct pathways, the canonical ß-catenin pathway and a non-canonical pathway controlling planar cell polarity and convergent extension. Interference between these pathways is an important determinant of cellular and phenotypic responses, but is poorly understood. Here we show that TNIK (Traf2 and Nck-interacting kinase) and MINK (Misshapen/NIKs-related kinase) MAP4K signalling kinases are integral components of both canonical and non-canonical pathways in Xenopus. xTNIK and xMINK interact and are proteolytically cleaved in vivo to generate Kinase domain fragments that are active in signal transduction, and Citron-NIK-Homology (CNH) Domain fragments that are suppressive. The catalytic activity of the Kinase domain fragments of both xTNIK and xMINK mediate non-canonical signalling. However, while the Kinase domain fragments of xTNIK also mediate canonical signalling, the analogous fragments derived from xMINK strongly antagonize this signalling. Our data suggest that the proteolytic cleavage of xTNIK and xMINK determines their respective activities and is an important factor in controlling the balance between canonical and non-canonical Wnt signalling in vivo. PMID:22984420

Stochastic weighted particle methods for population balance equations with coagulation, fragmentation and spatial inhomogeneity

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

Lee, Kok Foong; Patterson, Robert I.A.; Wagner, Wolfgang

2015-12-15

Graphical abstract: -- Highlights: •Problems concerning multi-compartment population balance equations are studied. •A class of fragmentation weight transfer functions is presented. •Three stochastic weighted algorithms are compared against the direct simulation algorithm. •The numerical errors of the stochastic solutions are assessed as a function of fragmentation rate. •The algorithms are applied to a multi-dimensional granulation model. -- Abstract: This paper introduces stochastic weighted particle algorithms for the solution of multi-compartment population balance equations. In particular, it presents a class of fragmentation weight transfer functions which are constructed such that the number of computational particles stays constant during fragmentation events. Themore » weight transfer functions are constructed based on systems of weighted computational particles and each of it leads to a stochastic particle algorithm for the numerical treatment of population balance equations. Besides fragmentation, the algorithms also consider physical processes such as coagulation and the exchange of mass with the surroundings. The numerical properties of the algorithms are compared to the direct simulation algorithm and an existing method for the fragmentation of weighted particles. It is found that the new algorithms show better numerical performance over the two existing methods especially for systems with significant amount of large particles and high fragmentation rates.« less

The development of performance-monitoring function in the posterior medial frontal cortex

PubMed Central

Fitzgerald, Kate Dimond; Perkins, Suzanne C.; Angstadt, Mike; Johnson, Timothy; Stern, Emily R.; Welsh, Robert C.; Taylor, Stephan F.

2009-01-01

Background Despite its critical role in performance-monitoring, the development of posterior medial prefrontal cortex (pMFC) in goal-directed behaviors remains poorly understood. Performance monitoring depends on distinct, but related functions that may differentially activate the pMFC, such as monitoring response conflict and detecting errors. Developmental differences in conflict- and error-related activations, coupled with age-related changes in behavioral performance, may confound attempts to map the maturation of pMFC functions. To characterize the development of pMFC-based performance monitoring functions, we segregated interference and error-processing, while statistically controlling for performance. Methods Twenty-one adults and 23 youth performed an event-related version of the Multi-Source Interference Task during functional magnetic resonance imaging (fMRI). Linear modeling of interference and error contrast estimates derived from the pMFC were regressed on age, while covarying for performance. Results Interference- and error-processing were associated with robust activation of the pMFC in both youth and adults. Among youth, interference- and error-related activation of the pMFC increased with age, independent of performance. Greater accuracy associated with greater pMFC activity during error commission in both groups. Discussion Increasing pMFC response to interference and errors occurs with age, likely contributing to the improvement of performance monitoring capacity during development. PMID:19913101

To what extent does urbanisation affect fragmented grassland functioning?

PubMed

van der Walt, L; Cilliers, S S; Kellner, K; Du Toit, M J; Tongway, D

2015-03-15

Urbanisation creates altered environments characterised by increased human habitation, impermeable surfaces, artificial structures, landscape fragmentation, habitat loss, resulting in different resource loss pathways. The vulnerable Rand Highveld Grassland vegetation unit in the Tlokwe Municipal area, South Africa, has been extensively affected and transformed by urbanisation, agriculture, and mining. Grassland fragments in urban areas are often considered to be less species rich and less functional than in the more untransformed or "natural" exurban environments, and are therefore seldom a priority for conservation. Furthermore, urban grassland fragments are often being more intensely managed than exurban areas, such as consistent mowing in open urban areas. Four urbanisation measures acting as indicators for patterns and processes associated with urban areas were calculated for matrix areas surrounding each selected grassland fragment to quantify the position of each grassland remnant along an urbanisation gradient. The grassland fragments were objectively classified into two classes of urbanisation, namely "exurban" and "urban" based on the urbanisation measure values. Grazing was recorded in some exurban grasslands and mowing in some urban grassland fragments. Unmanaged grassland fragments were present in both urban and exurban areas. Fine-scale biophysical landscape function was determined by executing the Landscape Function Analysis (LFA) method. LFA assesses fine-scale landscape patchiness (entailing resource conserving potential and erosion resistance) and 11 soil surface indicators to produce three main LFA parameters (stability, infiltration, and nutrient cycling), which indicates how well a system is functioning in terms of fine-scale biophysical soil processes and characteristics. The aim of this study was to determine the effects of urbanisation and associated management practices on fine-scale biophysical landscape function of urban and exurban grassland fragments, as well as to determine the potential for the use of LFA in decision-making involving the conservation of grassland fragments. The results indicated that the occurrence, size and characteristics of vegetated patches, and especially the presence of litter abundances, were the main factors determining differences in the LFA indices. Furthermore, mowing resulted in the overall fine-scale biophysical indices being higher for some of the urban grassland fragments. This implied that it is not necessarily the influence of urbanisation entailing high or low resource conserving patchiness and patch quality, but rather the management practices associated with urban and exurban areas. Therefore, from a conservation point of view, the grassland fragments in the City of Potchefstroom are just as conservable (on a biophysical function level involving soil processes) than the more "natural" exurban grassland fragments. Copyright © 2014 Elsevier Ltd. All rights reserved.

Too big or too narrow? Disturbance characteristics determine the functional resilience in virtual microbial ecosystems

NASA Astrophysics Data System (ADS)

König, Sara; Firle, Anouk-Letizia; Koehnke, Merlin; Banitz, Thomas; Frank, Karin

2017-04-01

In general ecology, there is an ongoing debate about the influence of fragmentation on extinction thresholds. Whether this influence is positive or negative depends on the considered type of fragmentation: whereas habitat fragmentation often has a negative influence on population extinction thresholds, spatially fragmented disturbances are observed to have mostly positive effects on the extinction probability. Besides preventing population extinction, in soil systems ecology we are interested in analyzing how ecosystem functions are maintained despite disturbance events. Here, we analyzed the influence of disturbance size and fragmentation on the functional resilience of a microbial soil ecosystem. As soil is a highly heterogeneous environment exposed to disturbances of different spatial configurations, the identification of critical disturbance characteristics for maintaining its functions is crucial. We used the numerical simulation model eColony considering bacterial growth, degradation and dispersal for analyzing the dynamic response of biodegradation examplary for an important microbial ecosystem service to disturbance events of different spatial configurations. We systematically varied the size and the degree of fragmentation of the affected area (disturbance pattern). We found that the influence of the disturbance size on functional recovery and biodegradation performance highly depends on the spatial fragmentation of the disturbance. Generally, biodegradation performance decreases with increasing clumpedness and increasing size of the affected area. After spatially correlated disturbance events, biodegradation performance decreases linear with increasing disturbance size. After spatially fragmented disturbance events, on the other hand, an increase in disturbance size has no influence on the biodegradation performance until a critical disturbance size is reached. Is the affected area bigger than this critical size, the functional performance decreases dramatically. Under recurrent disturbance events, this threshold is shifted to lower disturbance sizes. The more frequent disturbances are recurring, the lower is the critical disturbance size. Our simulation results indicate the importance of spatial characteristics of disturbance events for the functional resilience of microbial ecosystems. Critical values for disturbance size and fragmentation emerge from an interplay between both characteristics. In consequence, a precise definition of the specific disturbance regime is necessary for analysing functional resilience. With this study, we show that we need to consider the influence of fragmentation in terrestrial environments not only on population extincions but also on the resilience of ecosystem functions. Moreover, spatial disturbance characteristics - which are widely discussed on landscape scale - are an important factor on smaller scales, too.

RNA interference for functional genomics and improvement of cotton (Gossypium species)

USDA-ARS?s Scientific Manuscript database

RNA interference (RNAi), is a powerful new technology in the discovery of genetic sequence functions, and has become a valuable tool for functional genomics of cotton (Gossypium ssp.). The rapid adoption of RNAi has replaced previous antisense technology. RNAi has aided in the discovery of function ...

Foreign Subtitles Help but Native-Language Subtitles Harm Foreign Speech Perception

PubMed Central

Mitterer, Holger; McQueen, James M.

2009-01-01

Understanding foreign speech is difficult, in part because of unusual mappings between sounds and words. It is known that listeners in their native language can use lexical knowledge (about how words ought to sound) to learn how to interpret unusual speech-sounds. We therefore investigated whether subtitles, which provide lexical information, support perceptual learning about foreign speech. Dutch participants, unfamiliar with Scottish and Australian regional accents of English, watched Scottish or Australian English videos with Dutch, English or no subtitles, and then repeated audio fragments of both accents. Repetition of novel fragments was worse after Dutch-subtitle exposure but better after English-subtitle exposure. Native-language subtitles appear to create lexical interference, but foreign-language subtitles assist speech learning by indicating which words (and hence sounds) are being spoken. PMID:19918371

The right posterior paravermis and the control of language interference.

PubMed

Filippi, Roberto; Richardson, Fiona M; Dick, Frederic; Leech, Robert; Green, David W; Thomas, Michael S C; Price, Cathy J

2011-07-20

Auditory and written language in humans' comprehension necessitates attention to the message of interest and suppression of interference from distracting sources. Investigating the brain areas associated with the control of interference is challenging because it is inevitable that activation of the brain regions that control interference co-occurs with activation related to interference per se. To isolate the mechanisms that control verbal interference, we used a combination of structural and functional imaging techniques in Italian and German participants who spoke English as a second language. First, we searched structural MRI images of Italian participants for brain regions in which brain structure correlated with the ability to suppress interference from the unattended dominant language (Italian) while processing heard sentences in their weaker language (English). This revealed an area in the posterior paravermis of the right cerebellum in which gray matter density was higher in individuals who were better at controlling verbal interference. Second, we found functional activation in the same region when our German participants made semantic decisions on written English words in the presence of interference from unrelated words in their dominant language (German). This combination of structural and functional imaging therefore highlights the contribution of the right posterior paravermis to the control of verbal interference. We suggest that the importance of this region for language processing has previously been missed because most fMRI studies limit the field of view to increase sensitivity, with the lower part of the cerebellum being the region most likely to be excluded.

Evaluating the effect of aging on interference resolution with time-varying complex networks analysis

PubMed Central

Ariza, Pedro; Solesio-Jofre, Elena; Martínez, Johann H.; Pineda-Pardo, José A.; Niso, Guiomar; Maestú, Fernando; Buldú, Javier M.

2015-01-01

In this study we used graph theory analysis to investigate age-related reorganization of functional networks during the active maintenance of information that is interrupted by external interference. Additionally, we sought to investigate network differences before and after averaging network parameters between both maintenance and interference windows. We compared young and older adults by measuring their magnetoencephalographic recordings during an interference-based working memory task restricted to successful recognitions. Data analysis focused on the topology/temporal evolution of functional networks during both the maintenance and interference windows. We observed that: (a) Older adults require higher synchronization between cortical brain sites in order to achieve a successful recognition, (b) The main differences between age groups arise during the interference window, (c) Older adults show reduced ability to reorganize network topology when interference is introduced, and (d) Averaging network parameters leads to a loss of sensitivity to detect age differences. PMID:26029079

Gluon fragmentation into quarkonium at next-to-leading order

DOE PAGES

Artoisenet, Pierre; Braaten, Eric

2015-04-22

Here, we present the first calculation at next-to-leading order (NLO) in α s of a fragmentation function into quarkonium whose form at leading order is a nontrivial function of z, namely the fragmentation function for a gluon into a spin-singlet S-wave state at leading order in the relative velocity. To calculate the real NLO corrections, we introduce a new subtraction scheme that allows the phase-space integrals to be evaluated in 4 dimensions. We extract all ultraviolet and infrared divergences in the real NLO corrections analytically by calculating the phase-space integrals of the subtraction terms in 4 – 2ϵ dimensions. Wemore » also extract the divergences in the virtual NLO corrections analytically, and detail the cancellation of all divergences after renormalization. The NLO corrections have a dramatic effect on the shape of the fragmentation function, and they significantly increase the fragmentation probability.« less

Exogenous Thyropin from p41 Invariant Chain Diminishes Cysteine Protease Activity and Affects IL-12 Secretion during Maturation of Human Dendritic Cells

PubMed Central

Zavašnik-Bergant, Tina; Bergant Marušič, Martina

2016-01-01

Dendritic cells (DC) play a pivotal role as antigen presenting cells (APC) and their maturation is crucial for effectively eliciting an antigen-specific immune response. The p41 splice variant of MHC class II-associated chaperone, called invariant chain p41 Ii, contains an amino acid sequence, the p41 fragment, which is a thyropin-type inhibitor of proteolytic enzymes. The effects of exogenous p41 fragment and related thyropin inhibitors acting on human immune cells have not been reported yet. In this study we demonstrate that exogenous p41 fragment can enter the endocytic pathway of targeted human immature DC. Internalized p41 fragment has contributed to the total amount of the immunogold labelled p41 Ii-specific epitope, as quantified by transmission electron microscopy, in particular in late endocytic compartments with multivesicular morphology where antigen processing and binding to MHC II take place. In cell lysates of treated immature DC, diminished enzymatic activity of cysteine proteases has been confirmed. Internalized exogenous p41 fragment did not affect the perinuclear clustering of acidic cathepsin S-positive vesicles typical of mature DC. p41 fragment is shown to interfere with the nuclear translocation of NF-κB p65 subunit in LPS-stimulated DC. p41 fragment is also shown to reduce the secretion of interleukin-12 (IL-12/p70) during the subsequent maturation of treated DC. The inhibition of proteolytic activity of lysosomal cysteine proteases in immature DC and the diminished capability of DC to produce IL-12 upon their subsequent maturation support the immunomodulatory potential of the examined thyropin from p41 Ii. PMID:26960148

XRN2 is required for the degradation of target RNAs by RNase H1-dependent antisense oligonucleotides

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

Hori, Shin-Ichiro; Yamamoto, Tsuyoshi; Obika, Satoshi, E-mail: obika@phs.osaka-u.ac.jp

Antisense oligonucleotides (ASOs) can suppress the expression of a target gene by cleaving pre-mRNA and/or mature mRNA via RNase H1. Following the initial endonucleolytic cleavage by RNase H1, the target RNAs are degraded by a mechanism that is poorly understood. To better understand this degradation pathway, we depleted the expression of two major 5′ to 3′ exoribonucleases (XRNs), named XRN1 and XRN2, and analyzed the levels of 3′ fragments of the target RNAs in vitro. We found that the 3′ fragments of target pre-mRNA generated by ASO were almost completely degraded from their 5′ ends by nuclear XRN2 after RNase H1-mediatedmore » cleavage, whereas the 3′ fragments of mature mRNA were partially degraded by XRN2. In contrast to ASO, small interference RNA (siRNA) could reduce the expression level of only mature mRNA, and the 3′ fragment was degraded by cytoplasmic XRN1. Our findings indicate that the RNAs targeted by RNase H1-dependent ASO are rapidly degraded in the nucleus, contrary to the cytoplasmic degradation pathway mediated by siRNA. - Highlights: • We compared the degradation mechanism of the transcript targeted by ASO and siRNA. • We focused on two 5′ to 3′ exoribonucleases, cytoplasmic XRN1, and nuclear XRN2. • The 3′ fragment of target pre-mRNA generated by ASO was degraded by XRN2. • The 3′ fragment of target mRNA generated by ASO was partially degraded by XRN2. • XRN1 depletion promoted accumulation of the 3′ fragment of mRNA generated by siRNA.« less

How to Be Proactive About Interference: Lessons From Animal Memory

PubMed Central

Wright, Anthony A.; Katz, Jeffrey S.; Ma, Wei Ji

2015-01-01

Processes of proactive interference were explored using the pigeon as a model system of memory. This study shows that proactive interference extends back in time at least 16 trials (and as many minutes), revealing a continuum of interference and providing a framework for studying memory. Pigeons were tested in a delayed same/different task containing trial-unique pictures. On interference trials, sample pictures from previous trials reappeared as test pictures on different trials. Proactive-interference functions showed greatest interference from the most recent trial and with the longer of two delays (10 s vs. 1 s). These interference functions are accounted for by a time-estimation model based on signal detection theory. The model predicts that accuracy at test is determined solely by the ratio of the elapsed time since the offset of the current-trial sample to the elapsed time since the offset of the interfering sample. Implications for comparing memory of different species and different types of memory (e.g., familiarity vs. recollection) are discussed. PMID:22491142

How to be proactive about interference: lessons from animal memory.

PubMed

Wright, Anthony A; Katz, Jeffrey S; Ma, Wei Ji

2012-05-01

Processes of proactive interference were explored using the pigeon as a model system of memory. This study shows that proactive interference extends back in time at least 16 trials (and as many minutes), revealing a continuum of interference and providing a framework for studying memory. Pigeons were tested in a delayed same/different task containing trial-unique pictures. On interference trials, sample pictures from previous trials reappeared as test pictures on different trials. Proactive-interference functions showed greatest interference from the most recent trial and with the longer of two delays (10 s vs. 1 s). These interference functions are accounted for by a time-estimation model based on signal detection theory. The model predicts that accuracy at test is determined solely by the ratio of the elapsed time since the offset of the current-trial sample to the elapsed time since the offset of the interfering sample. Implications for comparing memory of different species and different types of memory (e.g., familiarity vs. recollection) are discussed.

Thermostability promotes the cooperative function of split adenylate kinases.

PubMed

Nguyen, Peter Q; Liu, Shirley; Thompson, Jeremy C; Silberg, Jonathan J

2008-05-01

Proteins can often be cleaved to create inactive polypeptides that associate into functional complexes through non-covalent interactions, but little is known about what influences the cooperative function of the ensuing protein fragments. Here, we examine whether protein thermostability affects protein fragment complementation by characterizing the function of split adenylate kinases from the mesophile Bacillus subtilis (AKBs) and the hyperthermophile Thermotoga neapolitana (AKTn). Complementation studies revealed that the split AKTn supported the growth of Escherichia coli with a temperature-sensitive AK, but not the fragmented AKBs. However, weak complementation occurred when the AKBs fragments were fused to polypeptides that strongly associate, and this was enhanced by a Q16L mutation that thermostabilizes the full-length protein. To examine how the split AK homologs differ in structure and function, their catalytic activity, zinc content, and circular dichroism spectra were characterized. The reconstituted AKTn had higher levels of zinc, greater secondary structure, and >10(3)-fold more activity than the AKBs pair, albeit 17-fold less active than full-length AKTn. These findings provide evidence that the design of protein fragments that cooperatively function can be improved by choosing proteins with the greatest thermostability for bisection, and they suggest that this arises because hyperthermophilic protein fragments exhibit greater residual structure compared to their mesophilic counterparts.

RNAi-mediated endogene silencing in strawberry fruit: detection of primary and secondary siRNAs by deep sequencing.

PubMed

Härtl, Katja; Kalinowski, Gregor; Hoffmann, Thomas; Preuss, Anja; Schwab, Wilfried

2017-05-01

RNA interference (RNAi) has been exploited as a reverse genetic tool for functional genomics in the nonmodel species strawberry (Fragaria × ananassa) since 2006. Here, we analysed for the first time different but overlapping nucleotide sections (>200 nt) of two endogenous genes, FaCHS (chalcone synthase) and FaOMT (O-methyltransferase), as inducer sequences and a transitive vector system to compare their gene silencing efficiencies. In total, ten vectors were assembled each containing the nucleotide sequence of one fragment in sense and corresponding antisense orientation separated by an intron (inverted hairpin construct, ihp). All sequence fragments along the full lengths of both target genes resulted in a significant down-regulation of the respective gene expression and related metabolite levels. Quantitative PCR data and successful application of a transitive vector system coinciding with a phenotypic change suggested propagation of the silencing signal. The spreading of the signal in strawberry fruit in the 3' direction was shown for the first time by the detection of secondary small interfering RNAs (siRNAs) outside of the primary targets by deep sequencing. Down-regulation of endogenes by the transitive method was less effective than silencing by ihp constructs probably because the numbers of primary siRNAs exceeded the quantity of secondary siRNAs by three orders of magnitude. Besides, we observed consistent hotspots of primary and secondary siRNA formation along the target sequence which fall within a distance of less than 200 nt. Thus, ihp vectors seem to be superior over the transitive vector system for functional genomics in strawberry fruit. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Intracellular Domain Fragment of CD44 Alters CD44 Function in Chondrocytes*

PubMed Central

Mellor, Liliana; Knudson, Cheryl B.; Hida, Daisuke; Askew, Emily B.; Knudson, Warren

2013-01-01

The hyaluronan receptor CD44 undergoes sequential proteolytic cleavage at the cell surface. The initial cleavage of the CD44 extracellular domain is followed by a second intramembranous cleavage of the residual CD44 fragment, liberating the C-terminal cytoplasmic tail of CD44. In this study conditions that promote CD44 cleavage resulted in a diminished capacity to assemble and retain pericellular matrices even though sufficient non-degraded full-length CD44 remained. Using stable and transient overexpression of the cytoplasmic domain of CD44, we determined that the intracellular domain interfered with anchoring of the full-length CD44 to the cytoskeleton and disrupted the ability of the cells to bind hyaluronan and assemble a pericellular matrix. Co-immunoprecipitation assays were used to determine whether the mechanism of this interference was due to competition with actin adaptor proteins. CD44 of control chondrocytes was found to interact and co-immunoprecipitate with both the 65- and 130-kDa isoforms of ankyrin-3. Moreover, this interaction with ankyrin-3 proteins was diminished in cells overexpressing the CD44 intracellular domain. Mutating the putative ankyrin binding site of the transiently transfected CD44 intracellular domain diminished the inhibitory effects of this protein on matrix retention. Although CD44 in other cells types has been shown to interact with members of the ezrin/radixin/moesin (ERM) family of adaptor proteins, only modest interactions between CD44 and moesin could be demonstrated in chondrocytes. The data suggest that release of the CD44 intracellular domain into the cytoplasm of cells such as chondrocytes exerts a competitive or dominant-negative effect on the function of full-length CD44. PMID:23884413

Pain and Cognitive Function Among Older Adults Living in the Community.

PubMed

van der Leeuw, Guusje; Eggermont, Laura H P; Shi, Ling; Milberg, William P; Gross, Alden L; Hausdorff, Jeffrey M; Bean, Jonathan F; Leveille, Suzanne G

2016-03-01

Pain related to many age-related chronic conditions is a burdensome problem in elderly adults and may also interfere with cognitive functioning. The purpose of this study was to examine the cross-sectional relationship between measures of pain severity and pain interference and cognitive performance in community-living older adults. We studied 765 participants in the Maintenance of Balance Independent Living Intellect and Zest (MOBILIZE) Boston Study, a population-based study of persons aged 70 and older. Global pain severity and interference were measured using the Brief Pain Inventory subscales. The neuropsychological battery included measures of attentional capacity (Trail Making Test A, WORLD Test), executive function (Trail Making Test B and Delta, Clock-in-a-Box, Letter Fluency), memory (Hopkins Verbal Learning Test), and a global composite measure of cognitive function. Multivariable linear regression models were used to analyze the relationship between pain and cognitive functioning. Elderly adults with more severe pain or more pain interference had poorer performance on memory tests and executive functioning compared to elders with none or less pain. Pain interference was also associated with impaired attentional capacity. Additional adjustment for chronic conditions, behaviors, and psychiatric medication resulted in attenuation of many of the observed associations. However, the association between pain interference and general cognitive function persisted. Our findings point to the need for further research to understand how chronic pain may contribute to decline in cognitive function and to determine strategies that may help in preventing or managing these potential consequences of pain on cognitive function in older adults. © The Author 2015. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Dissociating Interference-Control Processes between Memory and Response

ERIC Educational Resources Information Center

Bissett, Patrick G.; Nee, Derek Evan; Jonides, John

2009-01-01

The ability to mitigate interference is of central importance to cognition. Previous research has provided conflicting accounts about whether operations that resolve interference are singular in character or form a family of functions. Here, the authors examined the relationship between interference-resolution processes acting on working memory…

Links between plant and fungal diversity in habitat fragments of coastal shrubland

DOE PAGES

Maltz, Mia R.; Treseder, Kathleen K.; McGuire, Krista L.

2017-09-19

Habitat fragmentation is widespread across ecosystems, detrimentally affecting biodiversity. Although most habitat fragmentation studies have been conducted on macroscopic organisms, microbial communities and fungal processes may also be threatened by fragmentation. This study investigated whether fragmentation, and the effects of fragmentation on plants, altered fungal diversity and function within a fragmented shrubland in southern California. Using fluorimetric techniques, we assayed enzymes from plant litter collected from fragments of varying sizes to investigate enzymatic responses to fragmentation. To isolate the effects of plant richness from those of fragment size on fungi, we deployed litter bags containing different levels of plant littermore » diversity into the largest fragment and incubated in the field for one year. Following field incubation, we determined litter mass loss and conducted molecular analyses of fungal communities. We found that leaf-litter enzyme activity declined in smaller habitat fragments with less diverse vegetation. Moreover, we detected greater litter mass loss in litter bags containing more diverse plant litter. Additionally, bags with greater plant litter diversity harbored greater numbers of fungal taxa. These findings suggest that both plant litter resources and fungal function may be affected by habitat fragmentation's constraints on plants, possibly because plant species differ chemically, and may thus decompose at different rates. Diverse plant assemblages may produce a greater variety of litter resources and provide more ecological niche space, which may support greater numbers of fungal taxa. Thus, reduced plant diversity may constrain both fungal taxa richness and decomposition in fragmented coastal shrublands. Altogether, our findings provide evidence that even fungi may be affected by human-driven habitat fragmentation via direct effects of fragmentation on plants. Our findings underscore the importance of restoring diverse vegetation communities within larger coastal sage scrub fragments and suggest that this may be an effective way to improve the functional capacity of degraded sites.« less

Links between plant and fungal diversity in habitat fragments of coastal shrubland

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

Maltz, Mia R.; Treseder, Kathleen K.; McGuire, Krista L.

Habitat fragmentation is widespread across ecosystems, detrimentally affecting biodiversity. Although most habitat fragmentation studies have been conducted on macroscopic organisms, microbial communities and fungal processes may also be threatened by fragmentation. This study investigated whether fragmentation, and the effects of fragmentation on plants, altered fungal diversity and function within a fragmented shrubland in southern California. Using fluorimetric techniques, we assayed enzymes from plant litter collected from fragments of varying sizes to investigate enzymatic responses to fragmentation. To isolate the effects of plant richness from those of fragment size on fungi, we deployed litter bags containing different levels of plant littermore » diversity into the largest fragment and incubated in the field for one year. Following field incubation, we determined litter mass loss and conducted molecular analyses of fungal communities. We found that leaf-litter enzyme activity declined in smaller habitat fragments with less diverse vegetation. Moreover, we detected greater litter mass loss in litter bags containing more diverse plant litter. Additionally, bags with greater plant litter diversity harbored greater numbers of fungal taxa. These findings suggest that both plant litter resources and fungal function may be affected by habitat fragmentation's constraints on plants, possibly because plant species differ chemically, and may thus decompose at different rates. Diverse plant assemblages may produce a greater variety of litter resources and provide more ecological niche space, which may support greater numbers of fungal taxa. Thus, reduced plant diversity may constrain both fungal taxa richness and decomposition in fragmented coastal shrublands. Altogether, our findings provide evidence that even fungi may be affected by human-driven habitat fragmentation via direct effects of fragmentation on plants. Our findings underscore the importance of restoring diverse vegetation communities within larger coastal sage scrub fragments and suggest that this may be an effective way to improve the functional capacity of degraded sites.« less

PROCEEDINGS OF RIKEN/BNL RESEARCH CENTER WORKSHOP FUTURE TRANSVERSITY MEASUREMENTS (VOLUME 29).

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

Boer, D.; Grosse Perdekamp, M.

2001-01-02

The RIKEN-BNL Research Center workshop on ''Future Transversity Measurements'' was held at BNL from September 18-20, 2000. The main goal of the workshop was to explore future measurements of transversity distributions. This issue is of importance to the RHIC experiments, which will study polarized proton-proton collisions with great precision. One of the workshop's goals was to enhance interactions between the DIS community at HERA and the spin community at RHIC in this field. The workshop has been well received by the participants; the number of 69 registered participants demonstrates broad interest in the workshop's topics. The program contained 35 talksmore » and there was ample time for lively discussions. The program covered all recent work in the field and in addition some very elucidating educational talks were given. At the workshop the present status of the field was discussed and it has succeeded in stimulating new experimental and theoretical studies (e.g. model calculations for interference fragmentation functions (IFF), IFF analysis at DELPHI). It also functioned to focus attention on the open questions that need to be resolved for near future experiments. In general, the conclusions were optimistic, i.e. measuring the transversity functions seems to be possible, although some new experimental hurdles will have to be taken.« less

Photoionization and Photofragmentation of the Endohedral Xe C60+ Molecular Ion

NASA Astrophysics Data System (ADS)

Aryal, Nagendra Bahadur

An experimental study of photoionization and fragmentation of the Xe C 60+ endohedral molecular ion is presented in the photon energy range of the well-known Xe 4d giant resonance, and evidence of redistribution of the Xe 4d oscillator strength in photon energy due to multipath interference is reported. Experiments were conducted at undulator beamline 10.0.1 of the Advanced Light Source (ALS) using the merged-beams technique. Prior to these measurements, macroscopic samples containing endohedral Xe C60 were prepared using a setup developed at the ALS. Endohedral Xe C60 yields as high as 2.5x10 -4 were synthesized and a pure Xe C60+ ion beam current of up to 5.5 pA was obtained for the merged-beams experiments. Cross sections were measured in the photon energy range 60 - 150 eV in 0.5 eV steps for single, double, and triple photoionization of endohedral Xe C 60+ accompanied by the loss of n pairs of carbon atoms yielding Xe C60-2n2+ (n = 0, 1), Xe C60-2n 3+ (n = 0, 1, 2, 3), and Xe C584+ photoion products. Reference absolute cross-section measurements were made for empty C60+ for the corresponding reaction channels. The spectroscopic measurements with Xe C60+ were placed onto an absolute scale by normalization to the reference cross sections for C60+ in ranges of photon energies where the Xe 4d contributions were negligible. Results for single photoionization and fragmentation of Xe C60+ show no evidence of the presence of the caged Xe atom. The measurements of double and triple photoionization with fragmentation of Xe C60+ exhibit prominent signatures of the Xe 4d resonance and together account for 6.6 +/- 1.5 of the total Xe 4d oscillator strength of 10. Compared to that for a free Xe atom, the Xe oscillator strength in Xe C60+ is redistributed in photon energy due to multipath interference of outgoing Xe 4d photoelectron waves that may be transmitted or reflected by the spherical C60+ molecular cage, yielding so-called confinement resonances. The experimental data are compared with numerous theoretical predictions for this novel single-molecule photoelectron interferometer system. The comparison indicates that the interference structure is sensitive to the geometry of the molecular cage.

Functional Interference Clusters in Cancer Patients With Bone Metastases: A Secondary Analysis of RTOG 9714

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

Chow, Edward, E-mail: Edward.Chow@sunnybrook.c; James, Jennifer; Barsevick, Andrea

Purpose: To explore the relationships (clusters) among the functional interference items in the Brief Pain Inventory (BPI) in patients with bone metastases. Methods: Patients enrolled in the Radiation Therapy Oncology Group (RTOG) 9714 bone metastases study were eligible. Patients were assessed at baseline and 4, 8, and 12 weeks after randomization for the palliative radiotherapy with the BPI, which consists of seven functional items: general activity, mood, walking ability, normal work, relations with others, sleep, and enjoyment of life. Principal component analysis with varimax rotation was used to determine the clusters between the functional items at baseline and the follow-up.more » Cronbach's alpha was used to determine the consistency and reliability of each cluster at baseline and follow-up. Results: There were 448 male and 461 female patients, with a median age of 67 years. There were two functional interference clusters at baseline, which accounted for 71% of the total variance. The first cluster (physical interference) included normal work and walking ability, which accounted for 58% of the total variance. The second cluster (psychosocial interference) included relations with others and sleep, which accounted for 13% of the total variance. The Cronbach's alpha statistics were 0.83 and 0.80, respectively. The functional clusters changed at week 12 in responders but persisted through week 12 in nonresponders. Conclusion: Palliative radiotherapy is effective in reducing bone pain. Functional interference component clusters exist in patients treated for bone metastases. These clusters changed over time in this study, possibly attributable to treatment. Further research is needed to examine these effects.« less

A determination of the fragmentation functions of u-quarks into charged pions

NASA Astrophysics Data System (ADS)

Aubert, J. J.; Bassompierre, G.; Becks, K. H.; Benchouk, C.; Best, C.; Böhm, E.; De Bouard, X.; Brasse, F. W.; Broll, C.; Brown, S.; Carr, J.; Clifft, R.; Cobb, J. H.; Coignet, G.; Combley, F.; Court, G. R.; D'Agostini, G.; Dau, W. D.; Davies, J. K.; Déclais, Y.; Dosselli, U.; Drees, J.; Edwards, A.; Edwards, M.; Favier, J.; Ferrero, M. I.; Flauger, W.; Forsbach, H.; Gabathuler, E.; Gamet, R.; Gayler, J.; Gerhardt, V.; Gössling, C.; Haas, J.; Hamacher, K.; Hayman, P.; Henckes, M.; Korbel, V.; Korzen, B.; Landgraf, U.; Leenen, M.; Maire, M.; Mohr, W.; Montgomery, H. E.; Moser, K.; Mount, R. P.; Nagy, E.; Nassalski, J.; Norton, P. R.; McNicholas, J.; Osborne, A. M.; Payre, P.; Peroni, C.; Peschel, H.; Pessard, H.; Pietrzyk, U.; Rith, K.; Schneegans, M.; Schneider, A.; Sloan, T.; Stier, H. E.; Stockhausen, W.; Thénard, J. M.; Thompson, J. C.; Urban, L.; Villers, M.; Wahlen, H.; Whalley, M.; Williams, D.; Williams, W. S. C.; Williamson, J.; Wimpenny, S. J.; European Muon Collaboration (EMC)

1985-10-01

The fragmentation functions of u-quarks into positive and negative pions are determined from an analysis of identified pions produced in deep inelastic muon-deuterium scattering. The method adopted is not sensitive to the knowledge of the primary quark distribution functions. The fragmentation of u quarks to positive pions is found to fall less steeply in z than that to negative pions as expected in the quark parton model.

Digital music players cause interference with interrogation telemetry for pacemakers and implantable cardioverter-defibrillators without affecting device function.

PubMed

Webster, Gregory; Jordao, Ligia; Martuscello, Maria; Mahajan, Tarun; Alexander, Mark E; Cecchin, Frank; Triedman, John K; Walsh, Edward P; Berul, Charles I

2008-04-01

Concern exists regarding the potential electromagnetic interaction between pacemakers, implantable cardioverter-defibrillators (ICDs) and digital music players (DMPs). A preliminary study reported interference in 50% of patients whose devices were interrogated near Apple iPods. Given the high prevalence of DMP use among young patients, we sought to define the nature of interference from iPods and evaluate other DMPs. Four DMPs (Apple Nano, Apple Video, SanDisk Sansa and Microsoft Zune) were evaluated against pacemakers and ICDs (PM/ICD). Along with continuous monitoring, we recorded a baseline ECG strip, sensing parameters and lead impedance at baseline and for each device. Among 51 patients evaluated (age 6 to 60 years, median 22), there was no interference with intrinsic device function. Interference with the programmer occurred in 41% of the patients. All four DMPs caused programmer interference, including disabled communication between the PM/ICD and programmer, noise in the ECG channel, and lost marker channel indicators. Sensing parameters and lead impedances exhibited no more than baseline variability. When the DMPs were removed six inches, there were no further programmer telemetry interactions. Contrary to a prior report, we did not identify any evidence for electromagnetic interference between a selection of DMPs and intrinsic function of PM/ICDs. The DMPs did sometimes interfere with device-programmer communication, but not in a way that compromised device function. Therefore, we recommend that DMPs not be used during device interrogation, but suggest that there is reassuring counterevidence to mitigate the current high level of concern for interactions between DMPs and implantable cardiac rhythm devices.

Apparent hyperthyroidism caused by biotin-like interference from IgM anti-streptavidin antibodies.

PubMed

Lam, Leo; Bagg, Warwick; Smith, Geoff; Chiu, Weldon; Middleditch, Martin James; Lim, Julie Ching-Hsia; Kyle, Campbell Vance

2018-05-29

Exclusion of analytical interference is important when there is discrepancy between clinical and laboratory findings. However, interferences on immunoassays are often mistaken as isolated laboratory artefacts. We characterized and report the mechanism of a rare cause of interference in two patients that caused erroneous thyroid function tests, and also affects many other biotin dependent immunoassays. Patient 1 was a 77 y female with worsening fatigue while taking carbimazole over several years. Her thyroid function tests however, were not suggestive of hypothyroidism. Patient 2 was a 25 y female also prescribed carbimazole for apparent primary hyperthyroidism. Despite an elevated FT4, the lowest TSH on record was 0.17mIU/L. In both cases, thyroid function tests performed by an alternative method were markedly different. Further characterization of both patients' serum demonstrated analytical interference on many immunoassays using the biotin-streptavidin interaction. Sandwich assays (e.g. TSH, FSH, TNT, beta-HCG) were falsely low, while competitive assays (e.g. FT4, FT3, TBII) were falsely high. Pre-incubation of serum with streptavidin microparticles removed the analytical interference, initially suggesting the cause of interference was biotin, however, neither patient had been taking biotin. Instead, a ~100kDa IgM immunoglobulin with high affinity to streptavidin was isolated from each patient's serum. The findings confirm IgM anti-streptavidin antibodies as the cause of analytical interference. We describe two patients with apparent hyperthyroidism as a result of analytical interference caused by IgM anti-streptavidin antibodies. Analytical interference identified on one immunoassay should raise the possibility of other affected results. Characterization of interference may help to identify other potentially affected immunoassays. In the case of anti-streptavidin antibodies, the pattern of interference mimics that due to biotin ingestion; however, the degree of interference varies between individual assays and between patients.

Relativistic corrections to heavy quark fragmentation to S-wave heavy mesons

NASA Astrophysics Data System (ADS)

Sang, Wen-Long; Yang, Lan-Fei; Chen, Yu-Qi

2009-07-01

The relativistic corrections of order v2 to the fragmentation functions for the heavy quark to S-wave heavy quarkonia are calculated in the framework of the nonrelativistic quantum chromodynamics factorization formula. We derive the fragmentation functions by using the Collins-Soper definition in both the Feynman gauge and the axial gauge. We also extract them through the process Z0→Hq qmacr in the limit MZ/m→∞. We find that all results obtained by these two different methods and in different gauges are the same. We estimate the relative size of the relativistic corrections to the fragmentation functions.

Relativistic corrections to heavy quark fragmentation to S-wave heavy mesons

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

Sang Wenlong; Yang Lanfei; Chen Yuqi

The relativistic corrections of order v{sup 2} to the fragmentation functions for the heavy quark to S-wave heavy quarkonia are calculated in the framework of the nonrelativistic quantum chromodynamics factorization formula. We derive the fragmentation functions by using the Collins-Soper definition in both the Feynman gauge and the axial gauge. We also extract them through the process Z{sup 0}{yields}Hqq in the limit M{sub Z}/m{yields}{infinity}. We find that all results obtained by these two different methods and in different gauges are the same. We estimate the relative size of the relativistic corrections to the fragmentation functions.

Meteoroid head echo polarization features studied by numerical electromagnetics modeling

NASA Astrophysics Data System (ADS)

Vertatschitsch, L. E.; Sahr, J. D.; Colestock, P.; Close, S.

2011-12-01

Meteoroid head echoes are radar returns associated with scatter from the dense plasma surrounding meteoroids striking the Earth's atmosphere. Such echoes are detected by high power, large aperture (HPLA) radars. Frequently such detections show large variations in signal strength that suggest constructive and destructive interference. Using the ARPA Long-Range Tracking and Instrumentation Radar (ALTAIR) we can also observe the polarization of the returns. Usually, scatter from head echoes resembles scatter from a small sphere; when transmitting right circular polarization (RC), the received signal consists entirely of left circular polarization (LC). For some detections, power is also received in the RC channel, which indicates the presence of a more complicated scattering process. Radar returns of a fragmenting meteoroid are simulated using a hard-sphere scattering model numerically evaluated in the resonant region of Mie scatter. The cross- and co-polar scattering cross-sections are computed for pairs of spheres lying within a few wavelengths, simulating the earliest stages of fragmentation upon atmospheric impact. The likelihood of detecting this sort of idealized fragmentation event is small, but this demonstrates the measurements that would result from such an event would display RC power comparable to LC power, matching the anomalous data. The resulting computations show that fragmentation is a consistent interpretation for these head echo radar returns.

Predictors of Upper-Extremity Physical Function in Older Adults.

PubMed

Hermanussen, Hugo H; Menendez, Mariano E; Chen, Neal C; Ring, David; Vranceanu, Ana-Maria

2016-10-01

Little is known about the influence of habitual participation in physical exercise and diet on upper-extremity physical function in older adults. To assess the relationship of general physical exercise and diet to upper-extremity physical function and pain intensity in older adults. A cohort of 111 patients 50 or older completed a sociodemographic survey, the Rapid Assessment of Physical Activity (RAPA), an 11-point ordinal pain intensity scale, a Mediterranean diet questionnaire, and three Patient- Reported Outcomes Measurement Information System (PROMIS) based questionnaires: Pain Interference to measure inability to engage in activities due to pain, Upper-Extremity Physical Function, and Depression. Multivariable linear regression modeling was used to characterize the association of physical activity, diet, depression, and pain interference to pain intensity and upper-extremity function. Higher general physical activity was associated with higher PROMIS Upper-Extremity Physical Function and lower pain intensity in bivariate analyses. Adherence to the Mediterranean diet did not correlate with PROMIS Upper-Extremity Physical Function or pain intensity in bivariate analysis. In multivariable analyses factors associated with higher PROMIS Upper-Extremity Physical Function were male sex, non-traumatic diagnosis and PROMIS Pain Interference, with the latter accounting for most of the observed variability (37%). Factors associated with greater pain intensity in multivariable analyses included fewer years of education and higher PROMIS Pain Interference. General physical activity and diet do not seem to be as strongly or directly associated with upper-extremity physical function as pain interference.

Production of functional sperm by subcutaneous auto-grafting of immature testes in rainbow trout.

PubMed

Hayashi, Makoto; Sakuma, Daika; Yoshizaki, Goro

2018-02-01

Sexually mature individuals are indispensable for breeding programs. Salmonids require a long period before reaching sexual maturity, so we aimed to shorten the period required to obtain functional sperm by grafting immature testicular fragments into mature recipients, which we predicted would allow the grafted testicular fragments to skip the long pre-pubertal period. First, we demonstrated successful subcutaneous auto-grafting of testicular fragments in rainbow trout. Unilateral testectomy was performed, and the isolated immature testicular fragment was auto-grafted into the subcutaneous space along the back of recipient fish. The grafted testicular fragments developed synchronously with the recipients' testis remaining in its body cavity, and both eventually produced functional sperm. Next, immature testicular fragments were auto-grafted into the subcutaneous space of sexually mature males. We achieved this, without immune rejection, by isolating and cryopreserving testes from immature fish, and rearing these unilaterally testectomized fish until sexual maturity. The cryopreserved testes were then auto-grafted into the original, now spermiating fish. The grated immature testicular fragments differentiated and produced functional sperm within 5 months after grafting. By combining this grafting method with a technique to avoid immune rejection, we expect to develop a practical method for producing sperm in a shorter period in salmonids. © 2017 Wiley Periodicals, Inc.

Nucleon localization and fragment formation in nuclear fission

DOE PAGES

Zhang, C. L.; Schuetrumpf, B.; Nazarewicz, W.

2016-12-27

An electron localization measure was originally introduced to characterize chemical bond structures in molecules. Recently, a nucleon localization based on Hartree-Fock densities has been introduced to investigate α-cluster structures in light nuclei. Compared to the local nucleonic densities, the nucleon localization function has been shown to be an excellent indicator of shell effects and cluster correlations. In this work, using the spatial nucleon localization measure, we investigated the emergence of fragments in fissioning heavy nuclei using the self-consistent energy density functional method with a quantified energy density functional optimized for fission studies. We studied the particle densities and spatial nucleonmore » localization distributions along the fission pathways of 264Fm, 232Th, and 240Pu. We demonstrated that the fission fragments were formed fairly early in the evolution, well before scission. To illustrate the usefulness of the localization measure, we showed how the hyperdeformed state of 232Th could be understood in terms of a quasimolecular state made of 132Sn and 100Zr fragments. Compared to nucleonic distributions, the nucleon localization function more effectively quantifies nucleonic clustering: its characteristic oscillating pattern, traced back to shell effects, is a clear fingerprint of cluster/fragment configurations. This is of particular interest for studies of fragment formation and fragment identification in fissioning nuclei.« less

Localizing text in scene images by boundary clustering, stroke segmentation, and string fragment classification.

PubMed

Yi, Chucai; Tian, Yingli

2012-09-01

In this paper, we propose a novel framework to extract text regions from scene images with complex backgrounds and multiple text appearances. This framework consists of three main steps: boundary clustering (BC), stroke segmentation, and string fragment classification. In BC, we propose a new bigram-color-uniformity-based method to model both text and attachment surface, and cluster edge pixels based on color pairs and spatial positions into boundary layers. Then, stroke segmentation is performed at each boundary layer by color assignment to extract character candidates. We propose two algorithms to combine the structural analysis of text stroke with color assignment and filter out background interferences. Further, we design a robust string fragment classification based on Gabor-based text features. The features are obtained from feature maps of gradient, stroke distribution, and stroke width. The proposed framework of text localization is evaluated on scene images, born-digital images, broadcast video images, and images of handheld objects captured by blind persons. Experimental results on respective datasets demonstrate that the framework outperforms state-of-the-art localization algorithms.

Pain and pain-related interference in adults with lower-limb amputation: comparison of knee-disarticulation, transtibial, and transfemoral surgical sites.

PubMed

Behr, James; Friedly, Janna; Molton, Ivan; Morgenroth, David; Jensen, Mark P; Smith, Douglas G

2009-01-01

Pain and pain-related interference with physical function have not been thoroughly studied in individuals who have undergone knee-disarticulation amputations. The principal aim of this study was to determine whether individuals with knee-disarticulation amputations have worse pain and pain-related interference with physical function than do individuals with transtibial or transfemoral amputations. We analyzed cross-sectional survey data provided by 42 adults with lower-limb amputations. These individuals consisted of 14 adults reporting knee-disarticulation amputation in one limb and best-matched cases (14 reporting transfemoral amputation and 14 reporting transtibial amputation) from a larger cross-sectional sample of 472 individuals. Participants were rigorously matched based on time since amputation, reason for amputation, age, sex, diabetes diagnosis, and pain before amputation. Continuous outcome variables were analyzed by one-way analysis of variance. Categorical outcomes were analyzed by Pearson chi-square statistic. Given the relatively small sample size and power concerns, mean differences were also described by estimated effect size (Cohen's d). Of the 42 participants, 83% were male. They ranged in age from 36 to 85 (median = 55.1, standard deviation = 11.0). Most amputations were of traumatic origin (74%), and participants were on average 12.4 years from their amputations at the time of the survey. Individuals with transtibial amputation reported significantly more prosthesis use than did individuals with knee-disarticulation amputation. Amputation levels did not significantly differ in phantom limb pain, residual limb pain, back pain, and pain-related interference with physical function. Estimates of effect size, however, indicated that participants with knee-disarticulation amputation reported less phantom limb pain, phantom limb pain-related interference with physical function, residual limb pain, residual limb pain-related interference with physical function, and back pain-related interference with physical function than did participants with transtibial or transfemoral amputations. This study demonstrated that patients with knee-disarticulation amputation used prostheses significantly less than did patients with transtibial amputation. However, no evidence was found that patients with knee-disarticulation amputation have worse outcomes in terms of pain and pain-related interference with physical function; in fact, they may have more favorable long-term outcomes.

Phosphorylation of XPB helicase regulates TFIIH nucleotide excision repair activity

PubMed Central

Coin, Frédéric; Auriol, Jérome; Tapias, Angel; Clivio, Pascale; Vermeulen, Wim; Egly, Jean-Marc

2004-01-01

Nucleotide excision repair (NER) removes damage from DNA in a tightly regulated multiprotein process. The xeroderma pigmentosum group B (XPB) helicase subunit of TFIIH functions in NER and transcription. The serine 751 (S751) residue of XPB was found to be phosphorylated in vivo. This phosphorylation inhibits NER and the microinjection of a phosphomimicking XPB-S751E mutant is unable to correct the NER defect of XP-B cells. Conversely, XPB-S751 dephosphorylation or its substitution with alanine (S751A) restores NER both in vivo and in vitro. Surprisingly, phospho/dephosphorylation of S751 spares TFIIH-dependent transcription. Finally, the phosphorylation of XPB-S751 does not impair the TFIIH unwinding of the DNA around the lesion, but rather prevents the 5′ incision triggered by the ERCC1-XPF endonuclease. These data support an additional role for XPB in promoting the incision of the damaged fragment and reveal a point of NER regulation on TFIIH without interference in its transcription activity. PMID:15549133

[Public health stewardship and governance regarding the Colombian healthcare system, 2012-2013].

PubMed

Roth-Deubel, André N; Molina-Marín, Gloria

2013-01-01

Analysing decision-making concerning public health issues regarding the Colombian healthcare system from a market economy-based approach. This study involved applying Glaser and Strauss's grounded theory in six Colombian cities during 2012: Bogotá, Barranquilla, Bucaramanga, Leticia, Medellin and Pasto. 120 individual interviews were conducted with professionals involved in decision-making, running public healthcare programmes and making policy within public and private institutions. Fourteen focus groups were held with community organisation leaders. The findings suggested national and municipal health authorities' weak stewardship and ineffective governance regarding public healthcare policy and programmes, related to a lack of staff trained in public health management issues. In turn, this was related to political parties' interference and private insurers' particular interests and the structural fragmentation of functions and actors within the health system, thereby limiting public health development. A new axiology is necessary for achieving effective governance (I.e. cooperation between Colombian Healthcare Social Security System actors) to overcome current incompetence and financial self-interest predominating within the Colombian healthcare system.

Lens-free imaging of magnetic particles in DNA assays.

PubMed

Colle, Frederik; Vercruysse, Dries; Peeters, Sara; Liu, Chengxun; Stakenborg, Tim; Lagae, Liesbet; Del-Favero, Jurgen

2013-11-07

We present a novel opto-magnetic system for the fast and sensitive detection of nucleic acids. The system is based on a lens-free imaging approach resulting in a compact and cheap optical readout of surface hybridized DNA fragments. In our system magnetic particles are attracted towards the detection surface thereby completing the labeling step in less than 1 min. An optimized surface functionalization combined with magnetic manipulation was used to remove all nonspecifically bound magnetic particles from the detection surface. A lens-free image of the specifically bound magnetic particles on the detection surface was recorded by a CMOS imager. This recorded interference pattern was reconstructed in software, to represent the particle image at the focal distance, using little computational power. As a result we were able to detect DNA concentrations down to 10 pM with single particle sensitivity. The possibility of integrated sample preparation by manipulation of magnetic particles, combined with the cheap and highly compact lens-free detection makes our system an ideal candidate for point-of-care diagnostic applications.

Establishment of a tissue-specific RNAi system in C. elegans.

PubMed

Qadota, Hiroshi; Inoue, Makiko; Hikita, Takao; Köppen, Mathias; Hardin, Jeffrey D; Amano, Mutsuki; Moerman, Donald G; Kaibuchi, Kozo

2007-10-01

In C. elegans, mosaic analysis is a powerful genetic tool for determining in which tissue or specific cells a gene of interest is required. For traditional mosaic analysis, a loss-of-function mutant and a genomic fragment that can rescue the mutant phenotype are required. Here we establish an easy and rapid mosaic system using RNAi (RNA mediated interference), using a rde-1 mutant that is resistant to RNAi. Tissue-specific expression of the wild type rde-1 cDNA in rde-1 mutants limits RNAi sensitivity to a specific tissue. We established hypodermal-and muscle-specific RNAi systems by expressing rde-1 cDNA under the control of the lin-26 and hlh-1 promoters, respectively. We confirmed tissue-specific RNAi using two assays: (1) tissue-specific knockdown of GFP expression, and (2) phenocopy of mutations in essential genes that were previously known to function in a tissue-specific manner. We also applied this system to an essential gene, ajm-1, expressed in hypodermis and gut, and show that lethality in ajm-1 mutants is due to loss of expression in hypodermal cells. Although we demonstrate tissue-specific RNAi in hypodermis and muscle, this method could be easily applied to other tissues.

Establishment of a tissue-specific RNAi system in C. elegans

PubMed Central

Qadota, Hiroshi; Inoue, Makiko; Hikita, Takao; Köppen, Mathias; Hardin, Jeffrey D.; Amano, Mutsuki; Moerman, Donald G.; Kaibuchi, Kozo

2011-01-01

In C. elegans, mosaic analysis is a powerful genetic tool for determining in which tissue or specific cells a gene of interest is required. For traditional mosaic analysis, a loss-of-function mutant and a genomic fragment that can rescue the mutant phenotype are required. Here we establish an easy and rapid mosaic system using RNAi (RNA mediated interference), using a rde-1 mutant that is resistant to RNAi. Tissue-specific expression of the wild type rde-1 cDNA in rde-1 mutants limits RNAi sensitivity to a specific tissue. We established hypodermal- and muscle-specific RNAi systems by expressing rde-1 cDNA under the control of the lin-26 and hlh-1 promoters, respectively. We confirmed tissue-specific RNAi using two assays: (1) tissue-specific knockdown of GFP expression, and (2) phenocopy of mutations in essential genes that were previously known to function in a tissue-specific manner. We also applied this system to an essential gene, ajm-1, expressed in hypodermis and gut, and show that lethality in ajm-1 mutants is due to loss of expression in hypodermal cells. Although we demonstrate tissue-specific RNAi in hypodermis and muscle, this method could be easily applied to other tissues. PMID:17681718

Effective field theory approach to heavy quark fragmentation

DOE PAGES

Fickinger, Michael; Fleming, Sean; Kim, Chul; ...

2016-11-17

Using an approach based on Soft Collinear Effective Theory (SCET) and Heavy Quark Effective Theory (HQET) we determine the b-quark fragmentation function from electron-positron annihilation data at the Z-boson peak at next-to-next-to leading order with next-to-next-to leading log resummation of DGLAP logarithms, and next-to-next-to-next-to leading log resummation of endpoint logarithms. This analysis improves, by one order, the previous extraction of the b-quark fragmentation function. We find that while the addition of the next order in the calculation does not much shift the extracted form of the fragmentation function, it does reduce theoretical errors indicating that the expansion is converging. Usingmore » an approach based on effective field theory allows us to systematically control theoretical errors. Furthermore, while the fits of theory to data are generally good, the fits seem to be hinting that higher order correction from HQET may be needed to explain the b-quark fragmentation function at smaller values of momentum fraction.« less

Detection of Listeria monocytogenes with short peptide fragments from class IIa bacteriocins as recognition elements.

PubMed

Azmi, Sarfuddin; Jiang, Keren; Stiles, Michael; Thundat, Thomas; Kaur, Kamaljit

2015-03-09

We employed a direct peptide-bacteria binding assay to screen peptide fragments for high and specific binding to Listeria monocytogenes. Peptides were screened from a peptide array library synthesized on cellulose membrane. Twenty four peptide fragments (each a 14-mer) were derived from three potent anti-listerial peptides, Leucocin A, Pediocin PA1, and Curvacin A, that belong to class IIa bacteriocins. Fragment Leu10 (GEAFSAGVHRLANG), derived from the C-terminal region of Leucocin A, displayed the highest binding among all of the library fragments toward several pathogenic Gram-positive bacteria, including L. monocytogenes, Enterococcus faecalis, and Staphylococcus aureus. The specific binding of Leu10 to L. monocytogenes was further validated using microcantilever (MCL) experiments. Microcantilevers coated with gold were functionalized with peptides by chemical conjugation using a cysteamine linker to yield a peptide density of ∼4.8×10(-3) μmol/cm2 for different peptide fragments. Leu10 (14-mer) functionalized MCL was able to detect Listeria with same sensitivity as that of Leucocin A (37-mer) functionalized MCL, validating the use of short peptide fragments in bacterial detection platforms. Fragment Leu10 folded into a helical conformation in solution, like that of native Leucocin A, suggesting that both Leu10 and Leucocin A may employ a similar mechanism for binding target bacteria. The results show that peptide-conjugated microcantilevers can function as highly sensitive platforms for Listeria detection and hold potential to be developed as biosensors for pathogenic bacteria.

Hypervelocity Impact Test Fragment Modeling: Modifications to the Fragment Rotation Analysis and Lightcurve Code

NASA Technical Reports Server (NTRS)

Gouge, Michael F.

2011-01-01

Hypervelocity impact tests on test satellites are performed by members of the orbital debris scientific community in order to understand and typify the on-orbit collision breakup process. By analysis of these test satellite fragments, the fragment size and mass distributions are derived and incorporated into various orbital debris models. These same fragments are currently being put to new use using emerging technologies. Digital models of these fragments are created using a laser scanner. A group of computer programs referred to as the Fragment Rotation Analysis and Lightcurve code uses these digital representations in a multitude of ways that describe, measure, and model on-orbit fragments and fragment behavior. The Dynamic Rotation subroutine generates all of the possible reflected intensities from a scanned fragment as if it were observed to rotate dynamically while in orbit about the Earth. This calls an additional subroutine that graphically displays the intensities and the resulting frequency of those intensities as a range of solar phase angles in a Probability Density Function plot. This document reports the additions and modifications to the subset of the Fragment Rotation Analysis and Lightcurve concerned with the Dynamic Rotation and Probability Density Function plotting subroutines.

Fragment-based 13C nuclear magnetic resonance chemical shift predictions in molecular crystals: An alternative to planewave methods

NASA Astrophysics Data System (ADS)

Hartman, Joshua D.; Monaco, Stephen; Schatschneider, Bohdan; Beran, Gregory J. O.

2015-09-01

We assess the quality of fragment-based ab initio isotropic 13C chemical shift predictions for a collection of 25 molecular crystals with eight different density functionals. We explore the relative performance of cluster, two-body fragment, combined cluster/fragment, and the planewave gauge-including projector augmented wave (GIPAW) models relative to experiment. When electrostatic embedding is employed to capture many-body polarization effects, the simple and computationally inexpensive two-body fragment model predicts both isotropic 13C chemical shifts and the chemical shielding tensors as well as both cluster models and the GIPAW approach. Unlike the GIPAW approach, hybrid density functionals can be used readily in a fragment model, and all four hybrid functionals tested here (PBE0, B3LYP, B3PW91, and B97-2) predict chemical shifts in noticeably better agreement with experiment than the four generalized gradient approximation (GGA) functionals considered (PBE, OPBE, BLYP, and BP86). A set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided based on these benchmark calculations. Statistical cross-validation procedures are used to demonstrate the robustness of these fits.

Fragment-based (13)C nuclear magnetic resonance chemical shift predictions in molecular crystals: An alternative to planewave methods.

PubMed

Hartman, Joshua D; Monaco, Stephen; Schatschneider, Bohdan; Beran, Gregory J O

2015-09-14

We assess the quality of fragment-based ab initio isotropic (13)C chemical shift predictions for a collection of 25 molecular crystals with eight different density functionals. We explore the relative performance of cluster, two-body fragment, combined cluster/fragment, and the planewave gauge-including projector augmented wave (GIPAW) models relative to experiment. When electrostatic embedding is employed to capture many-body polarization effects, the simple and computationally inexpensive two-body fragment model predicts both isotropic (13)C chemical shifts and the chemical shielding tensors as well as both cluster models and the GIPAW approach. Unlike the GIPAW approach, hybrid density functionals can be used readily in a fragment model, and all four hybrid functionals tested here (PBE0, B3LYP, B3PW91, and B97-2) predict chemical shifts in noticeably better agreement with experiment than the four generalized gradient approximation (GGA) functionals considered (PBE, OPBE, BLYP, and BP86). A set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided based on these benchmark calculations. Statistical cross-validation procedures are used to demonstrate the robustness of these fits.

Augmented generation of protein fragments during wakefulness as the molecular cause of sleep: a hypothesis

PubMed Central

Varshavsky, Alexander

2012-01-01

Despite extensive understanding of sleep regulation, the molecular-level cause and function of sleep are unknown. I suggest that they originate in individual neurons and stem from increased production of protein fragments during wakefulness. These fragments are transient parts of protein complexes in which the fragments were generated. Neuronal Ca2+ fluxes are higher during wakefulness than during sleep. Subunits of transmembrane channels and other proteins are cleaved by Ca2+-activated calpains and by other nonprocessive proteases, including caspases and secretases. In the proposed concept, termed the fragment generation (FG) hypothesis, sleep is a state during which the production of fragments is decreased (owing to lower Ca2+ transients) while fragment-destroying pathways are upregulated. These changes facilitate the elimination of fragments and the remodeling of protein complexes in which the fragments resided. The FG hypothesis posits that a proteolytic cleavage, which produces two fragments, can have both deleterious effects and fitness-increasing functions. This (previously not considered) dichotomy can explain both the conservation of cleavage sites in proteins and the evolutionary persistence of sleep, because sleep would counteract deleterious aspects of protein fragments. The FG hypothesis leads to new explanations of sleep phenomena, including a longer sleep after sleep deprivation. Studies in the 1970s showed that ethanol-induced sleep in mice can be strikingly prolonged by intracerebroventricular injections of either Ca2+ alone or Ca2+ and its ionophore (Erickson et al., Science 1978;199:1219–1221; Harris, Pharmacol Biochem Behav 1979;10:527–534; Erickson et al., Pharmacol Biochem Behav 1980;12:651–656). These results, which were never interpreted in connection to protein fragments or the function of sleep, may be accounted for by the FG hypothesis about molecular causation of sleep. PMID:22930402

Sodium Solute Symporter and Cadherin Proteins Act as Bacillus thuringiensis Cry3Ba Toxin Functional Receptors in Tribolium castaneum*

PubMed Central

Contreras, Estefanía; Schoppmeier, Michael; Real, M. Dolores; Rausell, Carolina

2013-01-01

Understanding how Bacillus thuringiensis (Bt) toxins interact with proteins in the midgut of susceptible coleopteran insects is crucial to fully explain the molecular bases of Bt specificity and insecticidal action. In this work, aminopeptidase N (TcAPN-I), E-cadherin (TcCad1), and sodium solute symporter (TcSSS) have been identified by ligand blot as putative Cry3Ba toxin-binding proteins in Tribolium castaneum (Tc) larvae. RNA interference knockdown of TcCad1 or TcSSS proteins resulted in decreased susceptibility to Cry3Ba toxin, demonstrating the Cry toxin receptor functionality for these proteins. In contrast, TcAPN-I silencing had no effect on Cry3Ba larval toxicity, suggesting that this protein is not relevant in the Cry3Ba toxin mode of action in Tc. Remarkable features of TcSSS protein were the presence of cadherin repeats in its amino acid sequence and that a TcSSS peptide fragment containing a sequence homologous to a binding epitope found in Manduca sexta and Tenebrio molitor Bt cadherin functional receptors enhanced Cry3Ba toxicity. This is the first time that the involvement of a sodium solute symporter protein as a Bt functional receptor has been demonstrated. The role of this novel receptor in Bt toxicity against coleopteran insects together with the lack of receptor functionality of aminopeptidase N proteins might account for some of the differences in toxin specificity between Lepidoptera and Coleoptera insect orders. PMID:23645668

Central coherence in adolescents with bulimia nervosa spectrum eating disorders.

PubMed

Darcy, Alison M; Fitzpatrick, Kathleen Kara; Manasse, Stephanie M; Datta, Nandini; Klabunde, Megan; Colborn, Danielle; Aspen, Vandana; Stiles-Shields, Colleen; Labuschagne, Zandre; Le Grange, Daniel; Lock, James

2015-07-01

Weak central coherence-a tendency to process details at the expense of the gestalt-has been observed among adults with bulimia nervosa (BN) and is a potential candidate endophenotype for eating disorders (EDs). However, as BN behaviors typically onset during adolescence it is important to assess central coherence in this younger age group to determine whether the findings in adults are likely a result of BN or present earlier in the evolution of the disorder. This study examines whether the detail-oriented and fragmented cognitive inefficiency observed among adults with BN is observable among adolescents with shorter illness duration, relative to healthy controls. The Rey-Osterrieth Complex Figure Test (RCFT) was administered to a total of 47 adolescents with DSM5 BN, 42 with purging disorder (PD), and 25 healthy controls (HC). Performance on this measure was compared across the three groups. Those with BN and PD demonstrated significantly worse accuracy scores compared to controls in the copy and delayed recall condition with a moderate effect size. These findings were exacerbated when symptoms of BN increased. Poorer accuracy scores reflect a fragmented and piecemeal strategy that interferes with visual-spatial integration in BN spectrum disorders. This cognitive inefficiency likely contributes to broad difficulties in executive functioning in this population especially in the context of worsening bulimic symptoms. The findings of this study support the hypothesis that poor global integration may constitute a cognitive endophenotype for BN. © 2014 Wiley Periodicals, Inc.

The effects of characteristics of substituents on toxicity of the nitroaromatics: HiT QSAR study

NASA Astrophysics Data System (ADS)

Kuz'min, Victor E.; Muratov, Eugene N.; Artemenko, Anatoly G.; Gorb, Leonid; Qasim, Mohammad; Leszczynski, Jerzy

2008-10-01

The present study applies the Hierarchical Technology for Quantitative Structure-Activity Relationships (HiT QSAR) for (i) evaluation of the influence of the characteristics of 28 nitroaromatic compounds (some of which belong to a widely known class of explosives) as to their toxicity; (ii) prediction of toxicity for new nitroaromatic derivatives; (iii) analysis of the effects of substituents in nitroaromatic compounds on their toxicity in vivo. The 50% lethal dose concentration for rats (LD50) was used to develop the QSAR models based on simplex representation of molecular structure. The preliminary 1D QSAR results show that even the information on the composition of molecules reveals the main tendencies of changes in toxicity. The statistic characteristics for partial least squares 2D QSAR models are quite satisfactory ( R 2 = 0.96-0.98; Q 2 = 0.91-0.93; R 2 test = 0.89-0.92), which allows us to carry out the prediction of activity for 41 novel compounds designed by the application of new combinations of substituents represented in the training set. The comprehensive analysis of toxicity changes as a function of substituent position and nature was carried out. Molecular fragments that promote and interfere with toxicity were defined on the basis of the obtained models. It was shown that the mutual influence of substituents in the benzene ring plays a crucial role regarding toxicity. The influence of different substituents on toxicity can be mediated via different C-H fragments of the aromatic ring.

Activity interference and noise annoyance

NASA Astrophysics Data System (ADS)

Hall, F. L.; Taylor, S. M.; Birnie, S. E.

1985-11-01

Debate continues over differences in the dose-response functions used to predict the annoyance at different sources of transportation noise. This debate reflects the lack of an accepted model of noise annoyance in residential communities. In this paper a model is proposed which is focussed on activity interference as a central component mediating the relationship between noise exposure and annoyance. This model represents a departure from earlier models in two important respects. First, single event noise levels (e.g., maximum levels, sound exposure level) constitute the noise exposure variables in place of long-term energy equivalent measures (e.g., 24-hour Leq or Ldn). Second, the relationships within the model are expressed as probabilistic rather than deterministic equations. The model has been tested by using acoustical and social survey data collected at 57 sites in the Toronto region exposed to aircraft, road traffic or train noise. Logit analysis was used to estimate two sets of equations. The first predicts the probability of activity interference as a function of event noise level. Four types of interference are included: indoor speech, outdoor speech, difficulty getting to sleep and awakening. The second set predicts the probability of annoyance as a function of the combination of activity interferences. From the first set of equations, it was possible to estimate a function for indoor speech interference only. In this case, the maximum event level was the strongest predictor. The lack of significant results for the other types of interference is explained by the limitations of the data. The same function predicts indoor speech interference for all three sources—road, rail and aircraft noise. The results for the second set of equations show strong relationships between activity interference and the probability of annoyance. Again, the parameters of the logit equations are similar for the three sources. A trial application of the model predicts a higher probability of annoyance for aircraft than for road traffic situations with the same 24-hour Leq. This result suggests that the model may account for previously reported source differences in annoyance.

Homo-trimerization is essential for the transcription factor function of Myrf for oligodendrocyte differentiation.

PubMed

Kim, Dongkyeong; Choi, Jin-Ok; Fan, Chuandong; Shearer, Randall S; Sharif, Mohamed; Busch, Patrick; Park, Yungki

2017-05-19

Myrf is a key transcription factor for oligodendrocyte differentiation and central nervous system myelination. We and others have previously shown that Myrf is generated as a membrane protein in the endoplasmic reticulum (ER), and that it undergoes auto-processing to release its N-terminal fragment from the ER, which enters the nucleus to work as a transcription factor. These previous studies allow a glimpse into the unusual complexity behind the biogenesis and function of the transcription factor domain of Myrf. Here, we report that Myrf N-terminal fragments assemble into stable homo-trimers before ER release. Consequently, Myrf N-terminal fragments are released from the ER only as homo-trimers. Our re-analysis of a previous genetic screening result in Caenorhabditis elegans shows that homo-trimerization is essential for the biological functions of Myrf N-terminal fragment, and that the region adjacent to the DNA-binding domain is pivotal to its homo-trimerization. Further, our computational analysis uncovered a novel homo-trimeric DNA motif that mediates the homo-trimeric DNA binding of Myrf N-terminal fragments. Importantly, we found that homo-trimerization defines the DNA binding specificity of Myrf N-terminal fragments. In sum, our study elucidates the molecular mechanism governing the biogenesis and function of Myrf N-terminal fragments and its physiological significance. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Empty Sella Syndrome

MedlinePlus

... hormone prolactin, which can interfere with the normal function of the testicles and ovaries. Primary ESS is most common in adults and women, ... hormone prolactin, which can interfere with the normal function of the testicles and ovaries. Primary ESS is most common in adults and women, ...

Postfragmentation density function for bacterial aggregates in laminar flow

PubMed Central

Byrne, Erin; Dzul, Steve; Solomon, Michael; Younger, John

2014-01-01

The postfragmentation probability density of daughter flocs is one of the least well-understood aspects of modeling flocculation. We use three-dimensional positional data of Klebsiella pneumoniae bacterial flocs in suspension and the knowledge of hydrodynamic properties of a laminar flow field to construct a probability density function of floc volumes after a fragmentation event. We provide computational results which predict that the primary fragmentation mechanism for large flocs is erosion. The postfragmentation probability density function has a strong dependence on the size of the original floc and indicates that most fragmentation events result in clumps of one to three bacteria eroding from the original floc. We also provide numerical evidence that exhaustive fragmentation yields a limiting density inconsistent with the log-normal density predicted in the literature, most likely due to the heterogeneous nature of K. pneumoniae flocs. To support our conclusions, artificial flocs were generated and display similar postfragmentation density and exhaustive fragmentation. PMID:21599205

Two techniques for eliminating luminol interference material and flow system configurations for luminol and firefly luciferase systems

NASA Technical Reports Server (NTRS)

Thomas, R. R.

1976-01-01

Two methods for eliminating luminol interference materials are described. One method eliminates interference from organic material by pre-reacting a sample with dilute hydrogen peroxide. The reaction rate resolution method for eliminating inorganic forms of interference is also described. The combination of the two methods makes the luminol system more specific for bacteria. Flow system designs for both the firefly luciferase and luminol bacteria detection systems are described. The firefly luciferase flow system incorporating nitric acid extraction and optimal dilutions has a functional sensitivity of 3 x 100,000 E. coli/ml. The luminol flow system incorporates the hydrogen peroxide pretreatment and the reaction rate resolution techniques for eliminating interference. The functional sensitivity of the luminol flow system is 1 x 10,000 E. coli/ml.

Reassembly of a bioluminescent protein Renilla luciferase directed through DNA hybridization.

PubMed

Cissell, Kyle A; Rahimi, Yasmeen; Shrestha, Suresh; Deo, Sapna K

2009-01-01

Reassembly of split reporter proteins, also referred to as protein complementation, is utilized in the detection of protein-protein or protein-nucleic acid interactions. In this strategy, a reporter protein is fragmented into two inactive polypeptides to which interacting/binding partners are fused. The interaction between fused partners leads to the formation of a reassembled, active reporter. In this Communication, we have presented a proof-of-concept for the detection of a target nucleic acid sequence based on the reassembly of the bioluminescent reporter Renilla luciferase (Rluc), which is driven by DNA hybridization. Although, reassembly of Rluc though protein interactions has been demonstrated by others, the Rluc reassembly through DNA hybridization has not been shown yet, which is the novelty of this work. It is well established that bioluminescence detection offers significant advantages due to the absence of any background signal. In our study, two rationally designed fragments of Rluc were conjugated to complementary oligonucleotide probes. Hybridization of the two probes with fused Rluc fragments resulted in the reassembly of the fragments, generating active Rluc, measurable by the intensity of light given off upon addition of coelenterazine. Our study also shows that the reassembly of Rluc can be inhibited by an oligonucleotide probe that competes to bind to the hybridized probe-Rluc fragment complex, indicating a potential strategy for the quantitative detection of target nucleic acid. We were able to achieve the reassembly of Rluc fused to oligonucleotide probes using femtomole amounts of the probe-fragment protein conjugate. This concentration is approximately 4 orders of magnitude less than that reported using green fluorescent protein (GFP) as the reporter. A DNA-driven Rluc reassembly study performed in a cellular matrix did not show any interference from the matrix.

A predator-prey model with a holling type I functional response including a predator mutual interference

USGS Publications Warehouse

Seo, G.; DeAngelis, D.L.

2011-01-01

The most widely used functional response in describing predator-prey relationships is the Holling type II functional response, where per capita predation is a smooth, increasing, and saturating function of prey density. Beddington and DeAngelis modified the Holling type II response to include interference of predators that increases with predator density. Here we introduce a predator-interference term into a Holling type I functional response. We explain the ecological rationale for the response and note that the phase plane configuration of the predator and prey isoclines differs greatly from that of the Beddington-DeAngelis response; for example, in having three possible interior equilibria rather than one. In fact, this new functional response seems to be quite unique. We used analytical and numerical methods to show that the resulting system shows a much richer dynamical behavior than the Beddington-DeAngelis response, or other typically used functional responses. For example, cyclic-fold, saddle-fold, homoclinic saddle connection, and multiple crossing bifurcations can all occur. We then use a smooth approximation to the Holling type I functional response with predator mutual interference to show that these dynamical properties do not result from the lack of smoothness, but rather from subtle differences in the functional responses. ?? 2011 Springer Science+Business Media, LLC.

Testing complex animal cognition: Concept learning, proactive interference, and list memory.

PubMed

Wright, Anthony A

2018-01-01

This article describes an approach for assessing and comparing complex cognition in rhesus monkeys and pigeons by training them in a sequence of synergistic tasks, each yielding a whole function for enhanced comparisons. These species were trained in similar same/different tasks with expanding training sets (8, 16, 32, 64, 128 … 1024 pictures) followed by novel-stimulus transfer eventually resulting in full abstract-concept learning. Concept-learning functions revealed better rhesus transfer throughout and full concept learning at the 128 set, versus pigeons at the 256 set. They were then tested in delayed same/different tasks for proactive interference by inserting occasional tests within trial-unique sessions where the test stimulus matched a previous sample stimulus (1, 2, 4, 8, 16 trials prior). Proactive-interference functions revealed time-based interference for pigeons (1, 10 s delays), but event-based interference for rhesus (no effect of 1, 10, 20 s delays). They were then tested in list-memory tasks by expanding the sample to four samples in trial-unique sessions (minimizing proactive interference). The four-item, list-memory functions revealed strong recency memory at short delays, gradually changing to strong primacy memory at long delays over 30 s for rhesus, and 10 s for pigeons. Other species comparisons and future directions are discussed. © 2018 Society for the Experimental Analysis of Behavior.

Matrix interference from Fc-Fc interactions in immunoassays for detecting human IgG4 therapeutics.

PubMed

Partridge, Michael A; Karayusuf, Elif Kabuloglu; Dhulipala, Gangadhar; Dreyer, Robert; Daly, Thomas; Sumner, Giane; Pyles, Erica; Torri, Albert

2015-01-01

An assay measuring an IgG4 biotherapeutic in human serum used a drug-specific monoclonal antibody (mAb) capture reagent and an antihuman IgG4 mAb as detection reagent. However, serum IgG4 binding to the capture mAb via Fc-interactions was detected by the anti-IgG4 mAb, causing high background. Two approaches were developed to minimize background; incorporating a mild acid sample preparation step or using the Fab of the capture antibody. Either strategy improved signal:noise dramatically, increasing assay sensitivity >20-fold. Biophysical analyses of antibody domains indicated that noncovalent Fc oligomers could inhibit the background. Matrix interference from human IgG4 binding to the capture mAb was reduced with a Fab fragment of the drug-specific capture antibody or by incorporating a mild acid sample treatment into the assay.

Inhibitor of MYC identified in a Kröhnke pyridine library

PubMed Central

Hart, Jonathan R.; Garner, Amanda L.; Yu, Jing; Ito, Yoshihiro; Sun, Minghao; Ueno, Lynn; Rhee, Jin-Kyu; Baksh, Michael M.; Stefan, Eduard; Hartl, Markus; Bister, Klaus; Vogt, Peter K.; Janda, Kim D.

2014-01-01

In a fluorescence polarization screen for the MYC–MAX interaction, we have identified a novel small-molecule inhibitor of MYC, KJ-Pyr-9, from a Kröhnke pyridine library. The Kd of KJ-Pyr-9 for MYC in vitro is 6.5 ± 1.0 nM, as determined by backscattering interferometry; KJ-Pyr-9 also interferes with MYC–MAX complex formation in the cell, as shown in a protein fragment complementation assay. KJ-Pyr-9 specifically inhibits MYC-induced oncogenic transformation in cell culture; it has no or only weak effects on the oncogenic activity of several unrelated oncoproteins. KJ-Pyr-9 preferentially interferes with the proliferation of MYC-overexpressing human and avian cells and specifically reduces the MYC-driven transcriptional signature. In vivo, KJ-Pyr-9 effectively blocks the growth of a xenotransplant of MYC-amplified human cancer cells. PMID:25114221

Incorporation of charge transfer into the explicit polarization fragment method by grand canonical density functional theory.

PubMed

Isegawa, Miho; Gao, Jiali; Truhlar, Donald G

2011-08-28

Molecular fragmentation algorithms provide a powerful approach to extending electronic structure methods to very large systems. Here we present a method for including charge transfer between molecular fragments in the explicit polarization (X-Pol) fragment method for calculating potential energy surfaces. In the conventional X-Pol method, the total charge of each fragment is preserved, and charge transfer between fragments is not allowed. The description of charge transfer is made possible by treating each fragment as an open system with respect to the number of electrons. To achieve this, we applied Mermin's finite temperature method to the X-Pol wave function. In the application of this method to X-Pol, the fragments are open systems that partially equilibrate their number of electrons through a quasithermodynamics electron reservoir. The number of electrons in a given fragment can take a fractional value, and the electrons of each fragment obey the Fermi-Dirac distribution. The equilibrium state for the electrons is determined by electronegativity equalization with conservation of the total number of electrons. The amount of charge transfer is controlled by re-interpreting the temperature parameter in the Fermi-Dirac distribution function as a coupling strength parameter. We determined this coupling parameter so as to reproduce the charge transfer energy obtained by block localized energy decomposition analysis. We apply the new method to ten systems, and we show that it can yield reasonable approximations to potential energy profiles, to charge transfer stabilization energies, and to the direction and amount of charge transferred. © 2011 American Institute of Physics

Incorporation of charge transfer into the explicit polarization fragment method by grand canonical density functional theory

PubMed Central

Isegawa, Miho; Gao, Jiali; Truhlar, Donald G.

2011-01-01

Molecular fragmentation algorithms provide a powerful approach to extending electronic structure methods to very large systems. Here we present a method for including charge transfer between molecular fragments in the explicit polarization (X-Pol) fragment method for calculating potential energy surfaces. In the conventional X-Pol method, the total charge of each fragment is preserved, and charge transfer between fragments is not allowed. The description of charge transfer is made possible by treating each fragment as an open system with respect to the number of electrons. To achieve this, we applied Mermin's finite temperature method to the X-Pol wave function. In the application of this method to X-Pol, the fragments are open systems that partially equilibrate their number of electrons through a quasithermodynamics electron reservoir. The number of electrons in a given fragment can take a fractional value, and the electrons of each fragment obey the Fermi–Dirac distribution. The equilibrium state for the electrons is determined by electronegativity equalization with conservation of the total number of electrons. The amount of charge transfer is controlled by re-interpreting the temperature parameter in the Fermi–Dirac distribution function as a coupling strength parameter. We determined this coupling parameter so as to reproduce the charge transfer energy obtained by block localized energy decomposition analysis. We apply the new method to ten systems, and we show that it can yield reasonable approximations to potential energy profiles, to charge transfer stabilization energies, and to the direction and amount of charge transferred. PMID:21895159

Tracking Eye Movements to Localize Stroop Interference in Naming: Word Planning versus Articulatory Buffering

ERIC Educational Resources Information Center

Roelofs, Ardi

2014-01-01

Investigators have found no agreement on the functional locus of Stroop interference in vocal naming. Whereas it has long been assumed that the interference arises during spoken word planning, more recently some investigators have revived an account from the 1960s and 1970s holding that the interference occurs in an articulatory buffer after word…

Female Partners of Men With Peyronie's Disease Have Impaired Sexual Function, Satisfaction, and Mood, While Degree of Sexual Interference Is Associated With Worse Outcomes.

PubMed

Davis, Seth N P; Ferrar, Saskia; Sadikaj, Gentiana; Gerard, Marina; Binik, Yitzchak M; Carrier, Serge

2016-07-01

Peyronie's disease (PD) causes penile deformity and can result in sexual dysfunction and psychological distress. Currently, nothing is known about the psychosexual impact on the partners of men with PD. Research carried out on the partners of men with other chronic illnesses suggests that the partners of men with PD might have increased rates of sexual dysfunction and decreased sexual satisfaction. To examine (i) sexual functioning, sexual satisfaction, negative affect, and relationship satisfaction of men with PD and their female partners and (ii) the effect of male-perceived sexual interference on partners' outcomes. Forty-four men diagnosed with PD and their female partners completed a questionnaire package. Each partner filled out the Revised Dyadic Adjustment Scale, the Positive and Negative Affect Scale, the Global Measure of Sexual Satisfaction, and the Female Sexual Function Index (women) or the International Index of Erectile Function (men). Overall, partners of men with PD were found to have decreased sexual function, sexual satisfaction, and mood compared with population-based norms. Men and their partners showed non-distressed levels of relationship satisfaction. The degree to which PD interfered with sexual activity was an important correlate of outcomes. Increased sexual interference was associated with lower sexual function and satisfaction for the person experiencing interference. Sexual interference also was associated with negative affect and relationship satisfaction in partners and the person experiencing interference. PD is associated with negative psychosexual and psychosocial effects on those with the disease and their partners. As a result, assessment and intervention should include the two members of the couple. Copyright © 2016 International Society for Sexual Medicine. Published by Elsevier Inc. All rights reserved.

Selective inhibition and naming performance in semantic blocking, picture-word interference, and color-word Stroop tasks.

PubMed

Shao, Zeshu; Roelofs, Ardi; Martin, Randi C; Meyer, Antje S

2015-11-01

In 2 studies, we examined whether explicit distractors are necessary and sufficient to evoke selective inhibition in 3 naming tasks: the semantic blocking, picture-word interference, and color-word Stroop task. Delta plots were used to quantify the size of the interference effects as a function of reaction time (RT). Selective inhibition was operationalized as the decrease in the size of the interference effect as a function of naming RT. For all naming tasks, mean naming RTs were significantly longer in the interference condition than in the control condition. The slopes of the interference effects for the longest naming RTs correlated with the magnitude of the mean interference effect in both the semantic blocking task and the picture-word interference task, suggesting that selective inhibition was involved to reduce the interference from strong semantic competitors either invoked by a single explicit competitor or strong implicit competitors in picture naming. However, there was no correlation between the slopes and the mean interference effect in the Stroop task, suggesting less importance of selective inhibition in this task despite explicit distractors. Whereas the results of the semantic blocking task suggest that an explicit distractor is not necessary for triggering inhibition, the results of the Stroop task suggest that such a distractor is not sufficient for evoking inhibition either. (c) 2015 APA, all rights reserved).

Patient-reported outcomes of pain and physical functioning in neurofibromatosis clinical trials.

PubMed

Wolters, Pamela L; Martin, Staci; Merker, Vanessa L; Tonsgard, James H; Solomon, Sondra E; Baldwin, Andrea; Bergner, Amanda L; Walsh, Karin; Thompson, Heather L; Gardner, Kathy L; Hingtgen, Cynthia M; Schorry, Elizabeth; Dudley, William N; Franklin, Barbara

2016-08-16

Tumors and other disease complications of neurofibromatosis (NF) can cause pain and negatively affect physical functioning. To document the clinical benefit of treatment in NF trials targeting these manifestations, patient-reported outcomes (PROs) assessing pain and physical functioning should be included as study endpoints. Currently, there is no consensus on the selection and use of such measures in the NF population. This article presents the recommendations of the PRO group of the Response Evaluation in Neurofibromatosis and Schwannomatosis (REiNS) International Collaboration for assessing the domains of pain and physical functioning for NF clinical trials. The REiNS PRO group reviewed and rated existing PRO measures assessing pain intensity, pain interference, and physical functioning using their systematic method. Final recommendations are based primarily on 4 main criteria: patient characteristics, item content, psychometric properties, and feasibility for clinical trials. The REiNS PRO group chose the Numeric Rating Scale-11 (≥8 years) to assess pain intensity, the Pain Interference Index (6-24 years) and the Patient-Reported Outcome Measurement Information System (PROMIS) Pain Interference Scale (≥18 years) to evaluate pain interference, and the PROMIS Physical Functioning Scale to measure upper extremity function and mobility (≥5 years) for NF clinical trials. The REiNS Collaboration currently recommends these PRO measures to assess the domains of pain and physical functioning for NF clinical trials; however, further research is needed to evaluate their use in individuals with NF. A final consensus recommendation for the pain interference measure will be disseminated in a future publication based on findings from additional published research. © 2016 American Academy of Neurology.

An unusual fragmentation of oxetane-embedded tetracyclic ketal systems.

PubMed

Rao, G Hari Mangeswara; Khan, Faiz Ahmed

2013-11-01

An unusual route for the synthesis of functionalized cyclobutane derivatives starting from functionalized norbornane derivatives is reported. Base-induced fragmentation of an oxetanol-type moiety embedded in a tetracyclic norbornyl ketal leads to a cyclobutane-fused derivative as the major or exclusive product. The fragmentation reaction for bridgehead-bromine-substituted derivatives was much faster than for the corresponding chlorine-substituted substrates. The functionalized cyclobutane product was formed exclusively in high yield in the former case, while the latter furnished a minor uncyclized side product in varying yields.

Fragment-based {sup 13}C nuclear magnetic resonance chemical shift predictions in molecular crystals: An alternative to planewave methods

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

Hartman, Joshua D.; Beran, Gregory J. O., E-mail: gregory.beran@ucr.edu; Monaco, Stephen

2015-09-14

We assess the quality of fragment-based ab initio isotropic {sup 13}C chemical shift predictions for a collection of 25 molecular crystals with eight different density functionals. We explore the relative performance of cluster, two-body fragment, combined cluster/fragment, and the planewave gauge-including projector augmented wave (GIPAW) models relative to experiment. When electrostatic embedding is employed to capture many-body polarization effects, the simple and computationally inexpensive two-body fragment model predicts both isotropic {sup 13}C chemical shifts and the chemical shielding tensors as well as both cluster models and the GIPAW approach. Unlike the GIPAW approach, hybrid density functionals can be used readilymore » in a fragment model, and all four hybrid functionals tested here (PBE0, B3LYP, B3PW91, and B97-2) predict chemical shifts in noticeably better agreement with experiment than the four generalized gradient approximation (GGA) functionals considered (PBE, OPBE, BLYP, and BP86). A set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided based on these benchmark calculations. Statistical cross-validation procedures are used to demonstrate the robustness of these fits.« less

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

Zhang, C. L.; Schuetrumpf, B.; Nazarewicz, W.

An electron localization measure was originally introduced to characterize chemical bond structures in molecules. Recently, a nucleon localization based on Hartree-Fock densities has been introduced to investigate α-cluster structures in light nuclei. Compared to the local nucleonic densities, the nucleon localization function has been shown to be an excellent indicator of shell effects and cluster correlations. In this work, using the spatial nucleon localization measure, we investigated the emergence of fragments in fissioning heavy nuclei using the self-consistent energy density functional method with a quantified energy density functional optimized for fission studies. We studied the particle densities and spatial nucleonmore » localization distributions along the fission pathways of 264Fm, 232Th, and 240Pu. We demonstrated that the fission fragments were formed fairly early in the evolution, well before scission. To illustrate the usefulness of the localization measure, we showed how the hyperdeformed state of 232Th could be understood in terms of a quasimolecular state made of 132Sn and 100Zr fragments. Compared to nucleonic distributions, the nucleon localization function more effectively quantifies nucleonic clustering: its characteristic oscillating pattern, traced back to shell effects, is a clear fingerprint of cluster/fragment configurations. This is of particular interest for studies of fragment formation and fragment identification in fissioning nuclei.« less

BIOTIN INTERFERENCE WITH ROUTINE CLINICAL IMMUNOASSAYS: UNDERSTAND THE CAUSES AND MITIGATE THE RISKS.

PubMed

Samarasinghe, Shanika; Meah, Farah; Singh, Vinita; Basit, Arshi; Emanuele, Nicholas; Emanuele, Mary Ann; Mazhari, Alaleh; Holmes, Earle W

2017-08-01

The objectives of this report are to review the mechanisms of biotin interference with streptavidin/biotin-based immunoassays, identify automated immunoassay systems vulnerable to biotin interference, describe how to estimate and minimize the risk of biotin interference in vulnerable assays, and review the literature pertaining to biotin interference in endocrine function tests. The data in the manufacturer's "Instructions for Use" for each of the methods utilized by seven immunoassay system were evaluated. We also conducted a systematic search of PubMed/MEDLINE for articles containing terms associated with biotin interference. Available original reports and case series were reviewed. Abstracts from recent scientific meetings were also identified and reviewed. The recent, marked, increase in the use of over-the-counter, high-dose biotin supplements has been accompanied by a steady increase in the number of reports of analytical interference by exogenous biotin in the immunoassays used to evaluate endocrine function. Since immunoassay methods of similar design are also used for the diagnosis and management of anemia, malignancies, autoimmune and infectious diseases, cardiac damage, etc., biotin-related analytical interference is a problem that touches every area of internal medicine. It is important for healthcare personnel to become more aware of immunoassay methods that are vulnerable to biotin interference and to consider biotin supplements as potential sources of falsely increased or decreased test results, especially in cases where a lab result does not correlate with the clinical scenario. FDA = U.S. Food & Drug Administration FT3 = free tri-iodothyronine FT4 = free thyroxine IFUs = instructions for use LH = luteinizing hormone PTH = parathyroid hormone SA/B = streptavidin/biotin TFT = thyroid function test TSH = thyroid-stimulating hormone.

An overview of learning disabilities: psychoeducational perspectives.

PubMed

Johnson, D J

1995-01-01

In general, people with learning disabilities are a heterogeneous population that require a multidisciplinary evaluation and careful, well-planned intervention. Despite this heterogeneity, patterns of problems often co-occur. Therefore, diagnosticians and educators should look beyond single areas of achievement such as reading or arithmetic. In addition, problems in one area of learning typically have secondary impacts on higher levels of learning. That is, comprehension problems typically interfere with expression. Every effort should be made to examine patterns of problems and to avoid fragmentation of services so that each area of underachievement is not treated separately. Although learning disabilities usually interfere with school performance, they are not simply academic handicaps. They interfere with certain social activities as well as occupational pursuits. In many instances, they impact on mental health and self-esteem. Therefore, students need multiple services. And, as emphasized throughout this journal issue, learning disabled individuals may have comorbid conditions such as attention deficit disorder, depression, and neurologic problems. Furthermore, the problems may change over time. Children may first be identified because of language comprehension problems but later have reading or mathematics difficulty. With intervention, oral expressive problems may be alleviated but may be manifested later in written language.

Examination of tear film smoothness on corneae after refractive surgeries using a noninvasive interferometric method

NASA Astrophysics Data System (ADS)

Szczesna, Dorota H.; Kulas, Zbigniew; Kasprzak, Henryk T.; Stenevi, Ulf

2009-11-01

A lateral shearing interferometer was used to examine the smoothness of the tear film. The information about the distribution and stability of the precorneal tear film is carried out by the wavefront reflected from the surface of tears and coded in interference fringes. Smooth and regular fringes indicate a smooth tear film surface. On corneae after laser in situ keratomileusis (LASIK) or radial keratotomy (RK) surgery, the interference fringes are seldom regular. The fringes are bent on bright lines, which are interpreted as tear film breakups. The high-intensity pattern seems to appear in similar location on the corneal surface after refractive surgery. Our purpose was to extract information about the pattern existing under the interference fringes and calculate its shape reproducibility over time and following eye blinks. A low-pass filter was applied and correlation coefficient was calculated to compare a selected fragment of the template image to each of the following frames in the recorded sequence. High values of the correlation coefficient suggest that irregularities of the corneal epithelium might influence tear film instability and that tear film breakup may be associated with local irregularities of the corneal topography created after the LASIK and RK surgeries.

Changes in Orchid Bee Communities Across Forest-Agroecosystem Boundaries in Brazilian Atlantic Forest Landscapes.

PubMed

De Aguiar, Willian Moura; Sofia, Silvia H; Melo, Gabriel A R; Gaglianone, Maria Cristina

2015-12-01

Deforestation has dramatically reduced the extent of Atlantic Forest cover in Brazil. Orchid bees are key pollinators in neotropical forest, and many species are sensitive to anthropogenic interference. In this sense understanding the matrix permeability for these bees is important for maintaining genetic diversity and pollination services. Our main objective was to assess whether the composition, abundance, and diversity of orchid bees in matrices differed from those in Atlantic forest. To do this we sampled orchid bees at 4-mo intervals from 2007 to 2009 in remnants of Atlantic Forest, and in the surrounding pasture and eucalyptus matrices. The abundance, richness, and diversity of orchid bees diminished significantly from the forest fragment toward the matrix points in the eucalyptus and pasture. Some common or intermediate species in the forest areas, such as Eulaema cingulata (F.) and Euglossa fimbriata Moure, respectively, become rare species in the matrices. Our results show that the orchid bee community is affected by the matrices surrounding the forest fragments. They also suggest that connections between forest fragments need to be improved using friendly matrices that can provide more favorable conditions for bees and increase their dispersal between fragments. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Design and implementation of bimolecular fluorescence complementation (BiFC) assays for the visualization of protein interactions in living cells.

PubMed

Kerppola, Tom K

2006-01-01

Bimolecular fluorescence complementation (BiFC) analysis enables direct visualization of protein interactions in living cells. The BiFC assay is based on the discoveries that two non-fluorescent fragments of a fluorescent protein can form a fluorescent complex and that the association of the fragments can be facilitated when they are fused to two proteins that interact with each other. BiFC must be confirmed by parallel analysis of proteins in which the interaction interface has been mutated. It is not necessary for the interaction partners to juxtapose the fragments within a specific distance of each other because they can associate when they are tethered to a complex with flexible linkers. It is also not necessary for the interaction partners to form a complex with a long half-life or a high occupancy since the fragments can associate in a transient complex and un-associated fusion proteins do not interfere with detection of the complex. Many interactions can be visualized when the fusion proteins are expressed at levels comparable to their endogenous counterparts. The BiFC assay has been used for the visualization of interactions between many types of proteins in different subcellular locations and in different cell types and organisms. It is technically straightforward and can be performed using a regular fluorescence microscope and standard molecular biology and cell culture reagents.

Measurement of the jet fragmentation function and transverse profile in proton–proton collisions at a center-of-mass energy of 7 TeV with the ATLAS detector

DOE PAGES

Aad, G.; Abbott, B.; Abdallah, J.; ...

2011-11-30

The jet fragmentation function and transverse profile for jets with 25 GeV < p Tjet < 500 GeV and |η jet| < 1.2 produced in proton–proton collisions with a center-of-mass energy of 7 TeV are presented. The measurement is performed using data with an integrated luminosity of 36 pb –1. Jets are reconstructed and their momentum measured using calorimetric information. The momenta of the charged particle constituents are measured using the tracking system. The distributions corrected for detector effects are compared with various Monte Carlo event generators and generator tunes. Several of these choices show good agreement with the measuredmore » fragmentation function. Furthermore, none of these choices reproduce both the transverse profile and fragmentation function over the full kinematic range of the measurement.« less

Double Parton Fragmentation Function and its Evolution in Quarkonium Production

NASA Astrophysics Data System (ADS)

Kang, Zhong-Bo

2014-01-01

We summarize the results of a recent study on a new perturbative QCD factorization formalism for the production of heavy quarkonia of large transverse momentum pT at collider energies. Such a new factorization formalism includes both the leading power (LP) and next-to-leading power (NLP) contributions to the cross section in the mQ2/p_T^2 expansion for heavy quark mass mQ. For the NLP contribution, the so-called double parton fragmentation functions are involved, whose evolution equations have been derived. We estimate fragmentation functions in the non-relativistic QCD formalism, and found that their contribution reproduce the bulk of the large enhancement found in explicit NLO calculations in the color singlet model. Heavy quarkonia produced from NLP channels prefer longitudinal polarization, in contrast to the single parton fragmentation function. This might shed some light on the heavy quarkonium polarization puzzle.

Matter-wave diffraction approaching limits predicted by Feynman path integrals for multipath interference

NASA Astrophysics Data System (ADS)

Barnea, A. Ronny; Cheshnovsky, Ori; Even, Uzi

2018-02-01

Interference experiments have been paramount in our understanding of quantum mechanics and are frequently the basis of testing the superposition principle in the framework of quantum theory. In recent years, several studies have challenged the nature of wave-function interference from the perspective of Born's rule—namely, the manifestation of so-called high-order interference terms in a superposition generated by diffraction of the wave functions. Here we present an experimental test of multipath interference in the diffraction of metastable helium atoms, with large-number counting statistics, comparable to photon-based experiments. We use a variation of the original triple-slit experiment and accurate single-event counting techniques to provide a new experimental bound of 2.9 ×10-5 on the statistical deviation from the commonly approximated null third-order interference term in Born's rule for matter waves. Our value is on the order of the maximal contribution predicted for multipath trajectories by Feynman path integrals.

Neural mechanisms of proactive interference-resolution.

PubMed

Nee, Derek Evan; Jonides, John; Berman, Marc G

2007-12-01

The ability to mitigate interference from information that was previously relevant, but is no longer relevant, is central to successful cognition. Several studies have implicated left ventrolateral prefrontal cortex (VLPFC) as a region tied to this ability, but it is unclear whether this result generalizes across different tasks. In addition, it has been suggested that left anterior prefrontal cortex (APFC) also plays a role in proactive interference-resolution although support for this claim has been limited. The present study used event-related functional magnetic resonance imaging (fMRI) to investigate the role of these regions in resolving proactive-interference across two different tasks performed on the same subjects. Results indicate that both left VLPFC and left APFC are involved in the resolution of proactive interference across tasks. However, different functional networks related to each region suggest dissociable roles for the two regions. Additionally, regions of the posterior cingulate gyrus demonstrated unique involvement in facilitation when short- and long-term memory converged. This pattern of results serves to further specify models of proactive interference-resolution.

MS/MS analysis and imaging of lipids across Drosophila brain using secondary ion mass spectrometry.

PubMed

Phan, Nhu T N; Munem, Marwa; Ewing, Andrew G; Fletcher, John S

2017-06-01

Lipids are abundant biomolecules performing central roles to maintain proper functioning of cells and biological bodies. Due to their highly complex composition, it is critical to obtain information of lipid structures in order to identify particular lipids which are relevant for a biological process or metabolic pathway under study. Among currently available molecular identification techniques, MS/MS in secondary ion mass spectrometry (SIMS) imaging has been of high interest in the bioanalytical community as it allows visualization of intact molecules in biological samples as well as elucidation of their chemical structures. However, there have been few applications using SIMS and MS/MS owing to instrumental challenges for this capability. We performed MS and MS/MS imaging to study the lipid structures of Drosophila brain using the J105 and 40-keV Ar 4000 + gas cluster ion source, with the novelty being the use of MS/MS SIMS analysis of intact lipids in the fly brain. Glycerophospholipids were identified by MS/MS profiling. MS/MS was also used to characterize diglyceride fragment ions and to identify them as triacylglyceride fragments. Moreover, MS/MS imaging offers a unique possibility for detailed elucidation of biomolecular distribution with high accuracy based on the ion images of its fragments. This is particularly useful in the presence of interferences which disturb the interpretation of biomolecular localization. Graphical abstract MS/MS was performed during time-of-flight secondary ion mass spectrometry (ToF-SIMS) analysis of Drosophila melongaster (fruit fly) to elucidate the structure and origin of different chemical species in the brain including a range of different phospholipid classes (PC, PI, PE) and di- and triacylglycerides (DAG & TAG) species where reference MS/MS spectra provided a potential means of discriminating between the isobaric [M-OH] + ion of DAGs and the [M-RCO] + ion of TAGs.

Constructive and Destructive Interference in Nonadiabatic Tunneling via Conical Intersections

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

Xie, Changjian; Kendrick, Brian K.; Yarkony, David R.

As a manifestation of the molecular Aharonov–Bohm effect, tunneling-facilitated dissociation under a conical intersection (CI) requires the inclusion of the geometric phase (GP) to ensure a single-valued adiabatic wave function encircling the CI. Here, we demonstrate using a simple two-dimensional model that the GP induces destructive interference for vibrational states with even quanta in the coupling mode, but it leads to constructive interference for those with odd quanta. The interference patterns are manifested in tunneling wave functions and clearly affect the tunneling lifetime. Furthermore, we show that the inclusion of the diagonal Born–Oppenheimer correction is necessary for agreement with exactmore » results.« less

Constructive and Destructive Interference in Nonadiabatic Tunneling via Conical Intersections

DOE PAGES

Xie, Changjian; Kendrick, Brian K.; Yarkony, David R.; ...

2017-03-31

As a manifestation of the molecular Aharonov–Bohm effect, tunneling-facilitated dissociation under a conical intersection (CI) requires the inclusion of the geometric phase (GP) to ensure a single-valued adiabatic wave function encircling the CI. Here, we demonstrate using a simple two-dimensional model that the GP induces destructive interference for vibrational states with even quanta in the coupling mode, but it leads to constructive interference for those with odd quanta. The interference patterns are manifested in tunneling wave functions and clearly affect the tunneling lifetime. Furthermore, we show that the inclusion of the diagonal Born–Oppenheimer correction is necessary for agreement with exactmore » results.« less

General interference law for nonstationary, separable optical fields.

PubMed

Manea, Vladimir

2009-09-01

An approach to the theory of partial coherence for nonstationary optical fields is presented. Starting with a spectral representation, a favorable decomposition of the optical signals is discussed that supports a natural extension of the mathematical formalism. The coherence functions are redefined, but still as temporal correlation functions, allowing the obtaining of a more general form of the interference law for partially coherent optical signals. The general theory is applied in some relevant particular cases of nonstationary interference, namely, with quasi-monochromatic beams of different frequencies and with phase-modulated quasi-monochromatic beams of similar frequency spectra. All the results of the general treatment are reducible to the ones given in the literature for the case of stationary interference.

Temporal change in fragmentation of continental US forests

Treesearch

James D. Wickham; Kurt H. Riitters; Timothy G. Wade; Collin Homer

2008-01-01

Changes in forest ecosystem function and condition arise from changes in forest fragmentation. Previous studies estimated forest fragmentation for the continental United States (US). In this study, new temporal land-cover data from the National Land Cover Database (NLCD) were used to estimate changes in forest fragmentation at multiple scales for the continental US....

Augmented generation of protein fragments during wakefulness as the molecular cause of sleep: a hypothesis.

PubMed

Varshavsky, Alexander

2012-11-01

Despite extensive understanding of sleep regulation, the molecular-level cause and function of sleep are unknown. I suggest that they originate in individual neurons and stem from increased production of protein fragments during wakefulness. These fragments are transient parts of protein complexes in which the fragments were generated. Neuronal Ca²⁺ fluxes are higher during wakefulness than during sleep. Subunits of transmembrane channels and other proteins are cleaved by Ca²⁺-activated calpains and by other nonprocessive proteases, including caspases and secretases. In the proposed concept, termed the fragment generation (FG) hypothesis, sleep is a state during which the production of fragments is decreased (owing to lower Ca²⁺ transients) while fragment-destroying pathways are upregulated. These changes facilitate the elimination of fragments and the remodeling of protein complexes in which the fragments resided. The FG hypothesis posits that a proteolytic cleavage, which produces two fragments, can have both deleterious effects and fitness-increasing functions. This (previously not considered) dichotomy can explain both the conservation of cleavage sites in proteins and the evolutionary persistence of sleep, because sleep would counteract deleterious aspects of protein fragments. The FG hypothesis leads to new explanations of sleep phenomena, including a longer sleep after sleep deprivation. Studies in the 1970s showed that ethanol-induced sleep in mice can be strikingly prolonged by intracerebroventricular injections of either Ca²⁺ alone or Ca²⁺ and its ionophore (Erickson et al., Science 1978;199:1219-1221; Harris, Pharmacol Biochem Behav 1979;10:527-534; Erickson et al., Pharmacol Biochem Behav 1980;12:651-656). These results, which were never interpreted in connection to protein fragments or the function of sleep, may be accounted for by the FG hypothesis about molecular causation of sleep. Copyright © 2012 The Protein Society.

Distinctive amygdala subregions involved in emotion-modulated Stroop interference

PubMed Central

Han, Hyun Jung; Lee, Kanghee; Kim, Hyun Taek; Kim, Hackjin

2014-01-01

Despite the well-known role of the amygdala in mediating emotional interference during tasks requiring cognitive resources, no definite conclusion has yet been reached regarding the differential roles of functionally and anatomically distinctive subcomponents of the amygdala in such processes. In this study, we examined female participants and attempted to separate the neural processes for the detection of emotional information from those for the regulation of cognitive interference from emotional distractors by adding a temporal gap between emotional stimuli and a subsequent cognitive Stroop task. Reaction time data showed a significantly increased Stroop interference effect following emotionally negative stimuli compared with neutral stimuli, and functional magnetic resonance imaging data revealed that the anterior ventral amygdala (avAMYG) showed greater responses to negative stimuli compared with neutral stimuli. In addition, individuals who scored high in neuroticism showed greater posterior dorsal amygdala (pdAMYG) responses to incongruent compared with congruent Stroop trials following negative stimuli, but not following neutral stimuli. Taken together, the findings of this study demonstrated functionally distinctive contributions of the avAMYG and pdAMYG to the emotion-modulated Stroop interference effect and suggested that the avAMYG encodes associative values of emotional stimuli whereas the pdAMYG resolves cognitive interference from emotional distractors. PMID:23543193

Reverse transcription of phage RNA and its fragment directed by synthetic heteropolymeric primers

PubMed Central

Frolova, L. Yu.; Metelyev, V. G.; Ratmanova, K. I.; Smirnov, V. D.; Shabarova, Z. A.; Prokofyev, M. A.; Berzin, V. M.; Jansone, I. V.; Gren, E. J.; Kisselev, L. L.

1977-01-01

DNA synthesis catalysed by RNA-directed DNA-polymerase (reverse transcriptase) was found to proceed on the RNA template of an MS2 phage in the presence of heteropolymeric synthetic octa- and nonadeoxyribonucleotide primers complementary to the intercistronic region (coat protein binding site) and the region of the coat protein cistron, respectively. The product of synthesis consists of discrete DNA fractions of different length, including transcripts longer than 1,000 nucleotides. The coat protein inhibits DNA synthesis if it is initiated at its binding site, but has no effect on DNA synthesis initiated at the coat protein cistron. It has been suggested that, in this system, the initiation of DNA synthesis by synthetic primers is topographically specific. The MS2 coat protein binding site (an RNA fragment of 59 nucleotides) serves as a template for polydeoxyribonucleotide synthesis in the presence of octanucleotide primer and reverse transcriptase. The product of synthesis is homogenous and its length corresponds to the length of the template. The effective and complete copying of the fragment having a distinct secondary structure proves that the secondary structure does not interfere, in principle, with RNA being a template in the system of reverse transcription. PMID:71713

The effect of electromagnetic interference from mobile communication on the performance of intensive care ventilators.

PubMed

Jones, R P; Conway, D H

2005-08-01

Electromagnetic interference produced by wireless communication can affect medical devices and hospital policies exist to address this risk. During the transfer of ventilated patients, these policies may be compromised by essential communication between base and receiving hospitals. Local wireless networks (e.g. Bluetooth) may reduce the 'spaghetti syndrome' of wires and cables seen on intensive care units, but also generate electromagnetic interference. The aim of this study was to investigate these effects on displayed and actual ventilator performance. Five ventilators were tested: Drager Oxylog 2000, BREAS LTV-1000, Respironics BiPAP VISION, Puritan Bennett 7200 and 840. Electromagnetic interference was generated by three devices: Simoco 8020 radio handset, Nokia 7210 and Nokia 6230 mobile phone, Nokia 6230 communicating via Bluetooth with a Palm Tungsten T Personal Digital Assistant. We followed the American National Standard Recommended Practice for On-Site, Ad Hoc Testing (ANSI C63) for electromagnetic interference. We used a ventilator tester, to simulate healthy adult lungs and measure ventilator performance. The communication device under test was moved in towards each ventilator from a distance of 1 m in six axes. Alarms or error codes on the ventilator were recorded, as was ventilator performance. All ventilators tested, except for the Respironics VISION, showed a display error when subjected to electromagnetic interference from the Nokia phones and Simoco radio. Ventilator performance was only affected by the radio which caused the Puritan Bennett 840 to stop functioning completely. The transfer ventilators' performance were not affected by radio or mobile phone, although the mobile phone did trigger a low-power alarm. Effects on intensive care ventilators included display reset, with the ventilator restoring normal display function within 2 s, and low-power/low-pressure alarms. Bluetooth transmission had no effect on the function of all the ventilators tested. In a clinical setting, high-power-output devices such as a two-way radio may cause significant interference in ventilator function. Medium-power-output devices such as mobile phones may cause minor alarm triggers. Low-power-output devices such as Bluetooth appear to cause no interference with ventilator function.

Corridors restore animal-mediated pollination in fragmented tropical forest landscapes

PubMed Central

Kormann, Urs; Scherber, Christoph; Tscharntke, Teja; Klein, Nadja; Larbig, Manuel; Valente, Jonathon J.; Hadley, Adam S.; Betts, Matthew G.

2016-01-01

Tropical biodiversity and associated ecosystem functions have become heavily eroded through habitat loss. Animal-mediated pollination is required in more than 94% of higher tropical plant species and 75% of the world's leading food crops, but it remains unclear if corridors avert deforestation-driven pollination breakdown in fragmented tropical landscapes. Here, we used manipulative resource experiments and field observations to show that corridors functionally connect neotropical forest fragments for forest-associated hummingbirds and increase pollen transfer. Further, corridors boosted forest-associated pollinator availability in fragments by 14.3 times compared with unconnected equivalents, increasing overall pollination success. Plants in patches without corridors showed pollination rates equal to bagged control flowers, indicating pollination failure in isolated fragments. This indicates, for the first time, that corridors benefit tropical forest ecosystems beyond boosting local species richness, by functionally connecting mutualistic network partners. We conclude that small-scale adjustments to landscape configuration safeguard native pollinators and associated pollination services in tropical forest landscapes. PMID:26817765

Highly efficient recovery of functional single-chain Fv fragments from inclusion bodies overexpressed in Escherichia coli by controlled introduction of oxidizing reagent--application to a human single-chain Fv fragment.

PubMed

Tsumoto, K; Shinoki, K; Kondo, H; Uchikawa, M; Juji, T; Kumagai, I

1998-10-01

An improved and efficient refolding system for a single-chain antibody fragment (scFv) from inclusion bodies expressed in Escherichia coli was developed. Stepwise removal of denaturing reagent and controlled addition of oxidizing reagent were found to be the most effective conditions to achieve for almost complete recovery of functional monomeric scFv from inclusion bodies. Adding L-arginine to the refolding solution also increased the yield of refolded functional scFv. The single-chain Fv fragments of both a mouse anti-lysozyme monoclonal antibody, HyHEL10, and a human monoclonal antibody against the D antigen of the Rh blood group, D10, in solubilized inclusion bodies could be refolded under these conditions with yields of up to 95%. The refolding procedures developed in this study will contribute to providing a stable supply of large amounts of human single-chain Fv fragments.

Postfragmentation density function for bacterial aggregates in laminar flow.

PubMed

Byrne, Erin; Dzul, Steve; Solomon, Michael; Younger, John; Bortz, David M

2011-04-01

The postfragmentation probability density of daughter flocs is one of the least well-understood aspects of modeling flocculation. We use three-dimensional positional data of Klebsiella pneumoniae bacterial flocs in suspension and the knowledge of hydrodynamic properties of a laminar flow field to construct a probability density function of floc volumes after a fragmentation event. We provide computational results which predict that the primary fragmentation mechanism for large flocs is erosion. The postfragmentation probability density function has a strong dependence on the size of the original floc and indicates that most fragmentation events result in clumps of one to three bacteria eroding from the original floc. We also provide numerical evidence that exhaustive fragmentation yields a limiting density inconsistent with the log-normal density predicted in the literature, most likely due to the heterogeneous nature of K. pneumoniae flocs. To support our conclusions, artificial flocs were generated and display similar postfragmentation density and exhaustive fragmentation. ©2011 American Physical Society

Endogenous sterol biosynthesis is important for mitochondrial function and cell morphology in procyclic forms of Trypanosoma brucei.

PubMed

Pérez-Moreno, Guiomar; Sealey-Cardona, Marco; Rodrigues-Poveda, Carlos; Gelb, Michael H; Ruiz-Pérez, Luis Miguel; Castillo-Acosta, Víctor; Urbina, Julio A; González-Pacanowska, Dolores

2012-10-01

Sterol biosynthesis inhibitors are promising entities for the treatment of trypanosomal diseases. Insect forms of Trypanosoma brucei, the causative agent of sleeping sickness, synthesize ergosterol and other 24-alkylated sterols, yet also incorporate cholesterol from the medium. While sterol function has been investigated by pharmacological manipulation of sterol biosynthesis, molecular mechanisms by which endogenous sterols influence cellular processes remain largely unknown in trypanosomes. Here we analyse by RNA interference, the effects of a perturbation of three specific steps of endogenous sterol biosynthesis in order to dissect the role of specific intermediates in proliferation, mitochondrial function and cellular morphology in procyclic cells. A decrease in the levels of squalene synthase and squalene epoxidase resulted in a depletion of cellular sterol intermediates and end products, impaired cell growth and led to aberrant morphologies, DNA fragmentation and a profound modification of mitochondrial structure and function. In contrast, cells deficient in sterol methyl transferase, the enzyme involved in 24-alkylation, exhibited a normal growth phenotype in spite of a complete abolition of the synthesis and content of 24-alkyl sterols. Thus, the data provided indicates that while the depletion of squalene and post-squalene endogenous sterol metabolites results in profound cellular defects, bulk 24-alkyl sterols are not strictly required to support growth in insect forms of T. brucei in vitro. Copyright © 2012 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Association of Pain With Physical Function, Depressive Symptoms, Fatigue, and Sleep Quality Among Veteran and non-Veteran Postmenopausal Women

PubMed Central

Patel, Kushang V.; Cochrane, Barbara B.; Turk, Dennis C.; Bastian, Lori A.; Haskell, Sally G.; Woods, Nancy F.; Zaslavsky, Oleg; Wallace, Robert B.; Kerns, Robert D.

2016-01-01

Abstract Purpose of Study: To characterize the prevalence and longitudinal effects of pain in older Veteran and non-Veteran women. Design and Methods: Data on 144,956 participants in the Women’s Health Initiative were analyzed. At baseline, Veteran status, pain severity, and pain interference with activity were assessed. Outcomes of physical function, depressive symptoms, fatigue, and sleep quality were reported at baseline by all study participants and longitudinally on two follow-up occasions (3 years and 13–18 years after baseline) in the observational study participants ( n = 87,336). Results: At baseline, a total of 3,687 (2.5%) had a history of military service and 22,813 (15.8%) reported that pain limited their activity level moderately to extremely during the past 4 weeks. Prevalence of pain interference did not differ in Veterans and non-Veterans (16.8% and 15.7%, respectively; p = .09). At baseline, women with moderate-to-extreme pain interference had substantially worse physical function and greater symptoms of depression, fatigue, and insomnia than those with less pain ( p < .001 for all comparisons), adjusting for several social, behavioral, and health related factors. There were no significant military service by pain interference interactions for any of the outcomes ( p > .2), indicating that the effect of pain interference on outcomes at baseline did not vary between Veterans and non-Veterans. Moderate-to-extreme pain interference was associated with a greater rate of decline in physical function over time ( p < .001) and higher incidence of limited physical functioning ( p < .001), but these effects did not vary by Veteran status. Similar results were observed with pain severity as the exposure variable. Implications: As the Veteran population ages and the number of women exposed to combat operations grows, there will be an increased need for health care services that address not only pain severity and interference but also other disabling comorbid symptoms. PMID:26768395

Trajectory description of the quantum–classical transition for wave packet interference

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

Chou, Chia-Chun, E-mail: ccchou@mx.nthu.edu.tw

2016-08-15

The quantum–classical transition for wave packet interference is investigated using a hydrodynamic description. A nonlinear quantum–classical transition equation is obtained by introducing a degree of quantumness ranging from zero to one into the classical time-dependent Schrödinger equation. This equation provides a continuous description for the transition process of physical systems from purely quantum to purely classical regimes. In this study, the transition trajectory formalism is developed to provide a hydrodynamic description for the quantum–classical transition. The flow momentum of transition trajectories is defined by the gradient of the action function in the transition wave function and these trajectories follow themore » main features of the evolving probability density. Then, the transition trajectory formalism is employed to analyze the quantum–classical transition of wave packet interference. For the collision-like wave packet interference where the propagation velocity is faster than the spreading speed of the wave packet, the interference process remains collision-like for all the degree of quantumness. However, the interference features demonstrated by transition trajectories gradually disappear when the degree of quantumness approaches zero. For the diffraction-like wave packet interference, the interference process changes continuously from a diffraction-like to collision-like case when the degree of quantumness gradually decreases. This study provides an insightful trajectory interpretation for the quantum–classical transition of wave packet interference.« less

When and how to operate the posterior malleolus fragment in trimalleolar fractures: a systematic literature review.

PubMed

Verhage, Samuel Marinus; Hoogendoorn, Jochem Maarten; Krijnen, Pieta; Schipper, Inger Birgitta

2018-05-12

Whether or not and how to fixate the posterior malleolus fracture seems to depend on the fracture fragment size and its amount of dislocation, but clear guidelines for daily practice are lacking. In this review, we summarize the literature on preferred treatment of the posterior fragment in trimalleolar fractures. A systematic review of publications between January 1995 and April 30 2017 on this topic in the PubMed, Embase, and Cochrane databases was performed according to the PRISMA statement. Seventeen (2 prospective and 15 retrospective) of the 180 identified studies were included. Six studies report on indications for fixation of posterior malleolus fracture fragments. Eleven studies compare different fixation approaches and techniques for the posterior fragment. Meta-analysis was not possible due to varying fixation criteria and outcomes. There was no clear association between posterior fragment size and functional outcome or development of osteoarthritis. The non-anatomical reduction of the fragment was of more influence on outcome. Radiological and functional outcome was better after open reduction and internal fixation via the posterolateral approach than after percutaneous anterior-to-posterior screw fixation. The posterior fragment size is not a clear indication for its fixation. A step-off, however, seems an important indicator for developing posttraumatic osteoarthritis and worse functional outcome. Posterior fragments involving the intra-articular surface need to be reduced and fixated to prevent postoperative persisting step-off. Furthermore, fixation of the posterior malleolus via an open posterolateral approach seems superior to percutaneous anterior-to-posterior fixation. However, these results need to be confirmed in a prospective comparative trial. Therapeutic level II.

Habitat Fragmentation can Modulate Drought Effects on the Plant-soil-microbial System in Mediterranean Holm Oak (Quercus ilex) Forests.

PubMed

Flores-Rentería, Dulce; Curiel Yuste, Jorge; Rincón, Ana; Brearley, Francis Q; García-Gil, Juan Carlos; Valladares, Fernando

2015-05-01

Ecological transformations derived from habitat fragmentation have led to increased threats to above-ground biodiversity. However, the impacts of forest fragmentation on soils and their microbial communities are not well understood. We examined the effects of contrasting fragment sizes on the structure and functioning of soil microbial communities from holm oak forest patches in two bioclimatically different regions of Spain. We used a microcosm approach to simulate the annual summer drought cycle and first autumn rainfall (rewetting), evaluating the functional response of a plant-soil-microbial system. Forest fragment size had a significant effect on physicochemical characteristics and microbial functioning of soils, although the diversity and structure of microbial communities were not affected. The response of our plant-soil-microbial systems to drought was strongly modulated by the bioclimatic conditions and the fragment size from where the soils were obtained. Decreasing fragment size modulated the effects of drought by improving local environmental conditions with higher water and nutrient availability. However, this modulation was stronger for plant-soil-microbial systems built with soils from the northern region (colder and wetter) than for those built with soils from the southern region (warmer and drier) suggesting that the responsiveness of the soil-plant-microbial system to habitat fragmentation was strongly dependent on both the physicochemical characteristics of soils and the historical adaptation of soil microbial communities to specific bioclimatic conditions. This interaction challenges our understanding of future global change scenarios in Mediterranean ecosystems involving drier conditions and increased frequency of forest fragmentation.

Site-specific fab fragment biotinylation at the conserved nucleotide binding site for enhanced Ebola detection.

PubMed

Mustafaoglu, Nur; Alves, Nathan J; Bilgicer, Basar

2015-07-01

The nucleotide binding site (NBS) is a highly conserved region between the variable light and heavy chains at the Fab domains of all antibodies, and a small molecule that we identified, indole-3-butyric acid (IBA), binds specifically to this site. Fab fragment, with its small size and simple production methods compared to intact antibody, is good candidate for use in miniaturized diagnostic devices and targeted therapeutic applications. However, commonly used modification techniques are not well suited for Fab fragments as they are often more delicate than intact antibodies. Fab fragments are of particular interest for sensor surface functionalization but immobilization results in damage to the antigen binding site and greatly reduced activity due to their truncated size that allows only a small area that can bind to surfaces without impeding antigen binding. In this study, we describe an NBS-UV photocrosslinking functionalization method (UV-NBS(Biotin) in which a Fab fragment is site-specifically biotinylated with an IBA-EG11-Biotin linker via UV energy exposure (1 J/cm(2)) without affecting its antigen binding activity. This study demonstrates successful immobilization of biotinylated Ebola detecting Fab fragment (KZ52 Fab fragment) via the UV-NBS(Biotin) method yielding 1031-fold and 2-fold better antigen detection sensitivity compared to commonly used immobilization methods: direct physical adsorption and NHS-Biotin functionalization, respectively. Utilization of the UV-NBS(Biotin) method for site-specific conjugation to Fab fragment represents a proof of concept use of Fab fragment for various diagnostic and therapeutic applications with numerous fluorescent probes, affinity molecules and peptides. © 2015 Wiley Periodicals, Inc.

The interrelations between spiritual well-being, pain interference and depressive symptoms in patients with multiple sclerosis.

PubMed

Nsamenang, Sheri A; Hirsch, Jameson K; Topciu, Raluca; Goodman, Andrew D; Duberstein, Paul R

2016-04-01

Depressive symptoms are common in individuals with multiple sclerosis (MS), and are frequently exacerbated by pain; however, spiritual well-being may allow persons with MS to more effectively cope with pain-related deficits in physical and role functioning. We explored the associations between spiritual well-being, pain interference and depressive symptoms, assessing each as a potential mediator, in eighty-one patients being treated for MS, who completed self-report measures: Functional Assessment of Chronic Illness Therapy-Spiritual Well-Being Scale, Pain Effects Scale, and Center for Epidemiologic Studies Depression Scale Revised. At the bivariate level, spiritual well-being and its subscale of meaning and peace were negatively associated with depression and pain interference. In mediation models, depression was not related to pain interference via spiritual well-being, or to spiritual well-being via pain interference. Pain interference was related to depression via spiritual well-being and meaning/peace, and to spiritual well-being and meaning/peace via depressive symptoms. Finally, spiritual well-being and meaning/peace were related to depression via pain interference, and to pain interference via depressive symptoms. For patients with MS, a multi-faceted approach to treatment that includes pain reduction and promotion of spiritual well-being may be beneficial, although amelioration of depression remains a critical task.

Amide I vibrational circular dichroism of dipeptide: Conformation dependence and fragment analysis

NASA Astrophysics Data System (ADS)

Choi, Jun-Ho; Cho, Minhaeng

2004-03-01

The amide I vibrational circular dichroic response of alanine dipeptide analog (ADA) was theoretically investigated and the density functional theory calculation and fragment analysis results are presented. A variety of vibrational spectroscopic properties, local and normal mode frequencies, coupling constant, dipole, and rotational strengths, are calculated by varying two dihedral angles determining the three-dimensional ADA conformation. Considering two monopeptide fragments separately, we show that the amide I vibrational circular dichroism of the ADA can be quantitatively predicted. For several representative conformations of the model ADA, vibrational circular dichroism spectra are calculated by using both the density functional theory calculation and fragment analysis methods.

Generalized Boltzmann-Type Equations for Aggregation in Gases

NASA Astrophysics Data System (ADS)

Adzhiev, S. Z.; Vedenyapin, V. V.; Volkov, Yu. A.; Melikhov, I. V.

2017-12-01

The coalescence and fragmentation of particles in a dispersion system are investigated by applying kinetic theory methods, namely, by generalizing the Boltzmann kinetic equation to coalescence and fragmentation processes. Dynamic equations for the particle concentrations in the system are derived using the kinetic equations of motion. For particle coalescence and fragmentation, equations for the particle momentum, coordinate, and mass distribution functions are obtained and the coalescence and fragmentation coefficients are calculated. The equilibrium mass and velocity distribution functions of the particles in the dispersion system are found in the approximation of an active terminal group (Becker-Döring-type equation). The transition to a continuum description is performed.

CRISPR interference and priming varies with individual spacer sequences

PubMed Central

Xue, Chaoyou; Seetharam, Arun S.; Musharova, Olga; Severinov, Konstantin; J. Brouns, Stan J.; Severin, Andrew J.; Sashital, Dipali G.

2015-01-01

CRISPR–Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems allow bacteria to adapt to infection by acquiring ‘spacer’ sequences from invader DNA into genomic CRISPR loci. Cas proteins use RNAs derived from these loci to target cognate sequences for destruction through CRISPR interference. Mutations in the protospacer adjacent motif (PAM) and seed regions block interference but promote rapid ‘primed’ adaptation. Here, we use multiple spacer sequences to reexamine the PAM and seed sequence requirements for interference and priming in the Escherichia coli Type I-E CRISPR–Cas system. Surprisingly, CRISPR interference is far more tolerant of mutations in the seed and the PAM than previously reported, and this mutational tolerance, as well as priming activity, is highly dependent on spacer sequence. We identify a large number of functional PAMs that can promote interference, priming or both activities, depending on the associated spacer sequence. Functional PAMs are preferentially acquired during unprimed ‘naïve’ adaptation, leading to a rapid priming response following infection. Our results provide numerous insights into the importance of both spacer and target sequences for interference and priming, and reveal that priming is a major pathway for adaptation during initial infection. PMID:26586800

Critical Features of Fragment Libraries for Protein Structure Prediction

PubMed Central

dos Santos, Karina Baptista

2017-01-01

The use of fragment libraries is a popular approach among protein structure prediction methods and has proven to substantially improve the quality of predicted structures. However, some vital aspects of a fragment library that influence the accuracy of modeling a native structure remain to be determined. This study investigates some of these features. Particularly, we analyze the effect of using secondary structure prediction guiding fragments selection, different fragments sizes and the effect of structural clustering of fragments within libraries. To have a clearer view of how these factors affect protein structure prediction, we isolated the process of model building by fragment assembly from some common limitations associated with prediction methods, e.g., imprecise energy functions and optimization algorithms, by employing an exact structure-based objective function under a greedy algorithm. Our results indicate that shorter fragments reproduce the native structure more accurately than the longer. Libraries composed of multiple fragment lengths generate even better structures, where longer fragments show to be more useful at the beginning of the simulations. The use of many different fragment sizes shows little improvement when compared to predictions carried out with libraries that comprise only three different fragment sizes. Models obtained from libraries built using only sequence similarity are, on average, better than those built with a secondary structure prediction bias. However, we found that the use of secondary structure prediction allows greater reduction of the search space, which is invaluable for prediction methods. The results of this study can be critical guidelines for the use of fragment libraries in protein structure prediction. PMID:28085928

Critical Features of Fragment Libraries for Protein Structure Prediction.

PubMed

Trevizani, Raphael; Custódio, Fábio Lima; Dos Santos, Karina Baptista; Dardenne, Laurent Emmanuel

2017-01-01

The use of fragment libraries is a popular approach among protein structure prediction methods and has proven to substantially improve the quality of predicted structures. However, some vital aspects of a fragment library that influence the accuracy of modeling a native structure remain to be determined. This study investigates some of these features. Particularly, we analyze the effect of using secondary structure prediction guiding fragments selection, different fragments sizes and the effect of structural clustering of fragments within libraries. To have a clearer view of how these factors affect protein structure prediction, we isolated the process of model building by fragment assembly from some common limitations associated with prediction methods, e.g., imprecise energy functions and optimization algorithms, by employing an exact structure-based objective function under a greedy algorithm. Our results indicate that shorter fragments reproduce the native structure more accurately than the longer. Libraries composed of multiple fragment lengths generate even better structures, where longer fragments show to be more useful at the beginning of the simulations. The use of many different fragment sizes shows little improvement when compared to predictions carried out with libraries that comprise only three different fragment sizes. Models obtained from libraries built using only sequence similarity are, on average, better than those built with a secondary structure prediction bias. However, we found that the use of secondary structure prediction allows greater reduction of the search space, which is invaluable for prediction methods. The results of this study can be critical guidelines for the use of fragment libraries in protein structure prediction.

Core RNAi machinery and gene knockdown in the emerald ash borer (Agrilus planipennis).

PubMed

Zhao, Chaoyang; Alvarez Gonzales, Miguel A; Poland, Therese M; Mittapalli, Omprakash

2015-01-01

The RNA interference (RNAi) technology has been widely used in insect functional genomics research and provides an alternative approach for insect pest management. To understand whether the emerald ash borer (Agrilus planipennis), an invasive and destructive coleopteran insect pest of ash tree (Fraxinus spp.), possesses a strong RNAi machinery that is capable of degrading target mRNA as a response to exogenous double-stranded RNA (dsRNA) induction, we identified three RNAi pathway core component genes, Dicer-2, Argonaute-2 and R2D2, from the A. planipennis genome sequence. Characterization of these core components revealed that they contain conserved domains essential for the proteins to function in the RNAi pathway. Phylogenetic analyses showed that they are closely related to homologs derived from other coleopteran species. We also delivered the dsRNA fragment of AplaScrB-2, a β-fructofuranosidase-encoding gene horizontally acquired by A. planipennis as we reported previously, into A. planipennis adults through microinjection. Quantitative real-time PCR analysis on the dsRNA-treated beetles demonstrated a significantly decreased gene expression level of AplaScrB-2 appearing on day 2 and lasting until at least day 6. This study is the first record of RNAi applied in A. planipennis. Copyright © 2015 Elsevier Ltd. All rights reserved.

Decontaminating Solar Wind Samples with the Genesis Ultra-Pure Water Megasonic Wafer Spin Cleaner

NASA Technical Reports Server (NTRS)

Calaway, Michael J.; Rodriquez, M. C.; Allton, J. H.; Stansbery, E. K.

2009-01-01

The Genesis sample return capsule, though broken during the landing impact, contained most of the shattered ultra-pure solar wind collectors comprised of silicon and other semiconductor wafers materials. Post-flight analysis revealed that all wafer fragments were littered with surface particle contamination from spacecraft debris as well as soil from the impact site. This particulate contamination interferes with some analyses of solar wind. In early 2005, the Genesis science team decided to investigate methods for removing the surface particle contamination prior to solar wind analysis.

Event-based proactive interference in rhesus monkeys.

PubMed

Devkar, Deepna T; Wright, Anthony A

2016-10-01

Three rhesus monkeys (Macaca mulatta) were tested in a same/different memory task for proactive interference (PI) from prior trials. PI occurs when a previous sample stimulus appears as a test stimulus on a later trial, does not match the current sample stimulus, and the wrong response "same" is made. Trial-unique pictures (scenes, objects, animals, etc.) were used on most trials, except on trials where the test stimulus matched potentially interfering sample stimulus from a prior trial (1, 2, 4, 8, or 16 trials prior). Greater interference occurred when fewer trials separated interference and test. PI functions showed a continuum of interference. Delays between sample and test stimuli and intertrial intervals were manipulated to test how PI might vary as a function of elapsed time. Contrary to a similar study with pigeons, these time manipulations had no discernable effect on the monkey's PI, as shown by compete overlap of PI functions with no statistical differences or interactions. These results suggested that interference was strictly based upon the number of intervening events (trials with other pictures) without regard to elapsed time. The monkeys' apparent event-based interference was further supported by retesting with a novel set of 1,024 pictures. PI from novel pictures 1 or 2 trials prior was greater than from familiar pictures, a familiar set of 1,024 pictures. Moreover, when potentially interfering novel stimuli were 16 trials prior, performance accuracy was actually greater than accuracy on baseline trials (no interference), suggesting that remembering stimuli from 16 trials prior was a cue that this stimulus was not the sample stimulus on the current trial-a somewhat surprising conclusion particularly given monkeys.

Preserved Proactive Interference in Autism Spectrum Disorder

ERIC Educational Resources Information Center

Carmo, Joana C.; Duarte, Elsa; Pinho, Sandra; Filipe, Carlos N.; Marques, J. Frederico

2016-01-01

In this study, we aimed to evaluate further the functioning and structuring of the semantic system in autism spectrum disorders (ASD). We analyzed the performance of 19 high-functioning young adults with ASD and a group of 20 age-, verbal IQ- and education-matched individuals with the Proactive Interference (PI) Paradigm to evaluate semantic…

The electromagnetic interference of mobile phones on the function of a γ-camera.

PubMed

Javadi, Hamid; Azizmohammadi, Zahra; Mahmoud Pashazadeh, Ali; Neshandar Asli, Isa; Moazzeni, Taleb; Baharfar, Nastaran; Shafiei, Babak; Nabipour, Iraj; Assadi, Majid

2014-03-01

The aim of the present study is to evaluate whether or not the electromagnetic field generated by mobile phones interferes with the function of a SPECT γ-camera during data acquisition. We tested the effects of 7 models of mobile phones on 1 SPECT γ-camera. The mobile phones were tested when making a call, in ringing mode, and in standby mode. The γ-camera function was assessed during data acquisition from a planar source and a point source of Tc with activities of 10 mCi and 3 mCi, respectively. A significant visual decrease in count number was considered to be electromagnetic interference (EMI). The percentage of induced EMI with the γ-camera per mobile phone was in the range of 0% to 100%. The incidence of EMI was mainly observed in the first seconds of ringing and then mitigated in the following frames. Mobile phones are portable sources of electromagnetic radiation, and there is interference potential with the function of SPECT γ-cameras leading to adverse effects on the quality of the acquired images.

Distinct compartmentalization of dentin matrix protein 1 fragments in mineralized tissues and cells.

PubMed

Maciejewska, Izabela; Qin, Disheng; Huang, Bingzhen; Sun, Yao; Mues, Gabrielle; Svoboda, Kathy; Bonewald, Lynda; Butler, William T; Feng, Jerry Q; Qin, Chunlin

2009-01-01

Dentin matrix protein 1 (DMP1) has been shown to be critical for the formation of dentin and bone. However, the precise pathway by which DMP1 participates in dentinogenesis and osteogenesis remains to be clarified. DMP1 is present in the extracellular matrix of dentin and bone as processed NH(2)- and COOH-terminal fragments. The NH(2)-terminal fragment occurs as a proteoglycan, whereas the COOH-terminal fragment is highly phosphorylated. The differences in biochemical properties suggest that these fragments may have different tissue and cell distribution in association with distinct functions. In this study, we analyzed the distribution of the NH(2)- and COOH-terminal fragments of DMP1 in tooth, bone, osteocytes as well as MC3T3-E1 and HEK-293 cells. Immunohistochemical analyses were performed using antibodies specific to the NH(2)- or COOH-terminal region of DMP1. Clear differences in the distribution of these fragments were observed. In the teeth and bone, the NH(2)-terminal fragment was primarily located in the nonmineralized predentin and cartilage of the growth plate, while the COOH-terminal fragment accumulated in the mineralized zones. In osteocytes, the NH(2)-terminal fragment appeared more abundant along cell membrane and processes of osteocytes, while the COOH-terminal fragment was often found in the nuclei. This pattern of distribution in cellular compartments was further confirmed by analyses on MC3T3-E1 and HEK-293 cells transfected with a construct containing DMP1 cDNA. In these cell lines, the COOH-terminal fragment accumulated in cell nuclei, while the NH(2)-terminal fragment was in the cytosol. The different distribution of DMP1 fragments indicates that these DMP1 variants must perform distinct functions. Copyright 2008 S. Karger AG, Basel.

DNA fragment sizing and sorting by laser-induced fluorescence

DOEpatents

Hammond, Mark L.; Jett, James H.; Keller, Richard A.; Marrone, Babetta L.; Martin, John C.

1996-01-01

A method is provided for sizing DNA fragments using high speed detection systems, such as flow cytometry to determine unique characteristics of DNA pieces from a sample. In one characterization the DNA piece is fragmented at preselected sites to produce a plurality of DNA fragments. The DNA piece or the resulting DNA fragments are treated with a dye effective to stain stoichiometrically the DNA piece or the DNA fragments. The fluorescence from the dye in the stained fragments is then examined to generate an output functionally related to the number of nucleotides in each one of the DNA fragments. In one embodiment, the intensity of the fluorescence emissions from each fragment is linearly related to the fragment length. The distribution of DNA fragment sizes forms a characterization of the DNA piece for use in forensic and research applications.

Impact and explosion crater ejecta, fragment size, and velocity

NASA Technical Reports Server (NTRS)

Okeefe, J. D.; Ahrens, T. J.

1983-01-01

A model was developed for the mass distribution of fragments that are ejected at a given velocity for impact and explosion craters. The model is semi-empirical in nature and is derived from (1) numerical calculations of cratering and the resultant mass versus ejection velocity, (2) observed ejecta blanket particle size distributions, (3) an empirical relationship between maximum ejecta fragment size and crater diameter and an assumption on the functional form for the distribution of fragements ejected at a given velocity. This model implies that for planetary impacts into competent rock, the distribution of fragments ejected at a given velocity are nearly monodisperse, e.g., 20% of the mass of the ejecta at a given velocity contain fragments having a mass less than 0.1 times a mass of the largest fragment moving at that velocity. Using this model, the largest fragment that can be ejected from asteroids, the moon, Mars, and Earth is calculated as a function of crater diameter. In addition, the internal energy of ejecta versus ejecta velocity is found. The internal energy of fragments having velocities exceeding the escape velocity of the moon will exceed the energy required for incipient melting for solid silicates and thus, constrains the maximum ejected solid fragment size.

Generation and Nuclear Translocation of Sumoylated Transmembrane Fragment of Cell Adhesion Molecule L1

PubMed Central

Lutz, David; Wolters-Eisfeld, Gerrit; Joshi, Gunjan; Djogo, Nevena; Jakovcevski, Igor; Schachner, Melitta; Kleene, Ralf

2012-01-01

The functions of the cell adhesion molecule L1 in the developing and adult nervous system are triggered by homophilic and heterophilic interactions that stimulate signal transductions that activate cellular responses. Here, we show that stimulation of signaling by function-triggering L1 antibodies or L1-Fc leads to serine protease-dependent cleavage of full-length L1 at the plasma membrane and generation of a sumoylated transmembrane 70-kDa fragment comprising the intracellular and transmembrane domains and part of the extracellular domain. The 70-kDa transmembrane fragment is transported from the plasma membrane to a late endosomal compartment, released from endosomal membranes into the cytoplasm, and transferred from there into the nucleus by a pathway that depends on importin and chromatin-modifying protein 1. Mutation of the sumoylation site at Lys1172 or of the nuclear localization signal at Lys1147 abolished L1-stimulated generation or nuclear import of the 70-kDa fragment, respectively. Nuclear import of the 70-kDa fragment may activate cellular responses in parallel or in association with phosphorylation-dependent signaling pathways. Alterations in the levels of the 70-kDa fragment during development and in the adult after spinal cord injury or in a mouse model of Alzheimer disease suggest that this fragment is functionally implicated in development, regeneration, neurodegeneration, tumorigenesis, and possibly synaptic plasticity in the mature nervous system. PMID:22431726

Individuals with knee impairments identify items in need of clarification in the Patient Reported Outcomes Measurement Information System (PROMIS®) pain interference and physical function item banks - a qualitative study.

PubMed

Lynch, Andrew D; Dodds, Nathan E; Yu, Lan; Pilkonis, Paul A; Irrgang, James J

2016-05-11

The content and wording of the Patient Reported Outcome Measurement Information System (PROMIS) Physical Function and Pain Interference item banks have not been qualitatively assessed by individuals with knee joint impairments. The purpose of this investigation was to identify items in the PROMIS Physical Function and Pain Interference Item Banks that are irrelevant, unclear, or otherwise difficult to respond to for individuals with impairment of the knee and to suggest modifications based on cognitive interviews. Twenty-nine individuals with knee joint impairments qualitatively assessed items in the Pain Interference and Physical Function Item Banks in a mixed-methods cognitive interview. Field notes were analyzed to identify themes and frequency counts were calculated to identify items not relevant to individuals with knee joint impairments. Issues with clarity were identified in 23 items in the Physical Function Item Bank, resulting in the creation of 43 new or modified items, typically changing words within the item to be clearer. Interpretation issues included whether or not the knee joint played a significant role in overall health and age/gender differences in items. One quarter of the original items (31 of 124) in the Physical Function Item Bank were identified as irrelevant to the knee joint. All 41 items in the Pain Interference Item Bank were identified as clear, although individuals without significant pain substituted other symptoms which interfered with their life. The Physical Function Item Bank would benefit from additional items that are relevant to individuals with knee joint impairments and, by extension, to other lower extremity impairments. Several issues in clarity were identified that are likely to be present in other patient cohorts as well.

The dual role of fragments in fragment-assembly methods for de novo protein structure prediction

PubMed Central

Handl, Julia; Knowles, Joshua; Vernon, Robert; Baker, David; Lovell, Simon C.

2013-01-01

In fragment-assembly techniques for protein structure prediction, models of protein structure are assembled from fragments of known protein structures. This process is typically guided by a knowledge-based energy function and uses a heuristic optimization method. The fragments play two important roles in this process: they define the set of structural parameters available, and they also assume the role of the main variation operators that are used by the optimiser. Previous analysis has typically focused on the first of these roles. In particular, the relationship between local amino acid sequence and local protein structure has been studied by a range of authors. The correlation between the two has been shown to vary with the window length considered, and the results of these analyses have informed directly the choice of fragment length in state-of-the-art prediction techniques. Here, we focus on the second role of fragments and aim to determine the effect of fragment length from an optimization perspective. We use theoretical analyses to reveal how the size and structure of the search space changes as a function of insertion length. Furthermore, empirical analyses are used to explore additional ways in which the size of the fragment insertion influences the search both in a simulation model and for the fragment-assembly technique, Rosetta. PMID:22095594

A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments

PubMed Central

Cao, Chen; Wang, Guishen; Liu, An; Xu, Shutan; Wang, Lincong; Zou, Shuxue

2016-01-01

The assignment of secondary structure elements in proteins is a key step in the analysis of their structures and functions. We have developed an algorithm, SACF (secondary structure assignment based on Cα fragments), for secondary structure element (SSE) assignment based on the alignment of Cα backbone fragments with central poses derived by clustering known SSE fragments. The assignment algorithm consists of three steps: First, the outlier fragments on known SSEs are detected. Next, the remaining fragments are clustered to obtain the central fragments for each cluster. Finally, the central fragments are used as a template to make assignments. Following a large-scale comparison of 11 secondary structure assignment methods, SACF, KAKSI and PROSS are found to have similar agreement with DSSP, while PCASSO agrees with DSSP best. SACF and PCASSO show preference to reducing residues in N and C cap regions, whereas KAKSI, P-SEA and SEGNO tend to add residues to the terminals when DSSP assignment is taken as standard. Moreover, our algorithm is able to assign subtle helices (310-helix, π-helix and left-handed helix) and make uniform assignments, as well as to detect rare SSEs in β-sheets or long helices as outlier fragments from other programs. The structural uniformity should be useful for protein structure classification and prediction, while outlier fragments underlie the structure–function relationship. PMID:26978354

Statistical against dynamical PLF fission as seen by the IMF-IMF correlation functions and comparisons with CoMD model

NASA Astrophysics Data System (ADS)

Pagano, E. V.; Acosta, L.; Auditore, L.; Cap, T.; Cardella, G.; Colonna, M.; De Filippo, E.; Geraci, E.; Gnoffo, B.; Lanzalone, G.; Maiolino, C.; Martorana, N.; Pagano, A.; Papa, M.; Piasecki, E.; Pirrone, S.; Politi, G.; Porto, F.; Quattrocchi, L.; Rizzo, F.; Russotto, P.; Trifiro’, A.; Trimarchi, M.; Siwek-Wilczynska, K.

2018-05-01

In nuclear reactions at Fermi energies two and multi particles intensity interferometry correlation methods are powerful tools in order to pin down the characteristic time scale of the emission processes. In this paper we summarize an improved application of the fragment-fragment correlation function in the specific physics case of heavy projectile-like (PLF) binary massive splitting in two fragments of intermediate mass(IMF). Results are shown for the reverse kinematics reaction 124 Sn+64 Ni at 35 AMeV that has been investigated by using the forward part of CHIMERA multi-detector. The analysis was performed as a function of the charge asymmetry of the observed couples of IMF. We show a coexistence of dynamical and statistical components as a function of the charge asymmetry. Transport CoMD simulations are compared with the data in order to pin down the timescale of the fragments production and the relevant ingredients of the in medium effective interaction used in the transport calculations.

47 CFR 25.274 - Procedures to be followed in the event of harmful interference.

Code of Federal Regulations, 2013 CFR

2013-10-01

... in the event of harmful interference. (a) The earth station operator whose transmission is suffering harmful interference shall first check the earth station equipment to ensure that the equipment is functioning properly. (b) The earth station operator shall then check all other earth stations in the licensee...

47 CFR 25.274 - Procedures to be followed in the event of harmful interference.

Code of Federal Regulations, 2010 CFR

2010-10-01

... in the event of harmful interference. (a) The earth station operator whose transmission is suffering harmful interference shall first check the earth station equipment to ensure that the equipment is functioning properly. (b) The earth station operator shall then check all other earth stations in the licensee...

47 CFR 25.274 - Procedures to be followed in the event of harmful interference.

Code of Federal Regulations, 2012 CFR

2012-10-01

... in the event of harmful interference. (a) The earth station operator whose transmission is suffering harmful interference shall first check the earth station equipment to ensure that the equipment is functioning properly. (b) The earth station operator shall then check all other earth stations in the licensee...

47 CFR 25.274 - Procedures to be followed in the event of harmful interference.

Code of Federal Regulations, 2014 CFR

2014-10-01

... in the event of harmful interference. (a) The earth station operator whose transmission is suffering harmful interference shall first check the earth station equipment to ensure that the equipment is functioning properly. (b) The earth station operator shall then check all other earth stations in the licensee...

47 CFR 25.274 - Procedures to be followed in the event of harmful interference.

Code of Federal Regulations, 2011 CFR

2011-10-01

... in the event of harmful interference. (a) The earth station operator whose transmission is suffering harmful interference shall first check the earth station equipment to ensure that the equipment is functioning properly. (b) The earth station operator shall then check all other earth stations in the licensee...

Toward a General Approach for RNA-Templated Hierarchical Assembly of Split-Proteins

PubMed Central

Furman, Jennifer L.; Badran, Ahmed H.; Ajulo, Oluyomi; Porter, Jason R.; Stains, Cliff I.; Segal, David J.; Ghosh, Indraneel

2010-01-01

The ability to conditionally turn on a signal or induce a function in the presence of a user-defined RNA target has potential applications in medicine and synthetic biology. Although sequence-specific pumilio repeat proteins can target a limited set of ssRNA sequences, there are no general methods for targeting ssRNA with designed proteins. As a first step toward RNA recognition, we utilized the RNA binding domain of argonaute, implicated in RNA interference, for specifically targeting generic 2-nucleotide, 3' overhangs of any dsRNA. We tested the reassembly of a split-luciferase enzyme guided by argonaute-mediated recognition of newly generated nucleotide overhangs when ssRNA is targeted by a designed complementary guide sequence. This approach was successful when argonaute was utilized in conjunction with a pumilio repeat and expanded the scope of potential ssRNA targets. However, targeting any desired ssRNA remained elusive as two argonaute domains provided minimal reassembled split-luciferase. We next designed and tested a second hierarchical assembly, wherein ssDNA guides are appended to DNA hairpins that serve as a scaffold for high affinity zinc fingers attached to split-luciferase. In the presence of a ssRNA target containing adjacent sequences complementary to the guides, the hairpins are brought into proximity, allowing for zinc finger binding and concomitant reassembly of the fragmented luciferase. The scope of this new approach was validated by specifically targeting RNA encoding VEGF, hDM2, and HER2. These approaches provide potentially general design paradigms for the conditional reassembly of fragmented proteins in the presence of any desired ssRNA target. PMID:20681585

Interference of Photons from a Weak Laser and a Quantum Dot

NASA Astrophysics Data System (ADS)

Ritchie, David; Bennett, Anthony; Patel, Raj; Nicoll, Christine; Shields, Andrew

2010-03-01

We demonstrate two-photon interference from two unsynchronized sources operating via different physical processes [1]. One source is spontaneous emission from the X^- state of an electrically-driven InAs/GaAs single quantum dot with μeV linewidth, the other stimulated emission from a laser with a neV linewidth. We mix the emission from these sources on a balanced non-polarising beam splitter and measure correlations in the photons that exit using Si-avalanche photodiodes and a time-correlated counting card. By periodically switching the polarisation state of the weak laser we simultaneously measure the correlation for parallel and orthogonally polarised sources, corresponding to maximum and minimum degrees of interference. When the two sources have the same intensity, a reduction in the correlation function at time zero for the case of parallel photon sources clearly indicates this interference effect. To quantify the degree of interference, we develop a theory that predicts the correlation function. Data and experiment are then compared for a range of intensity ratios. Based on this analysis we infer a wave-function overlap of 91%, which is remarkable given the fundamental differences between the two sources. [1] Bennett A. J et al Nature Physics, 5, 715--717 (2009).

Does vector-free gravity simulate microgravity? Functional and morphologic attributes of clinorotated nerve and muscle grown in cell culture

NASA Technical Reports Server (NTRS)

Gruener, R.; Hoeger, G.

1988-01-01

Cocultured Xenopus neurons and myocytes were subjected to non-vectorial gravity by clinostat rotation to determine if microgravity, during space flights, may affect cell development and communications. Clinorotated cells showed changes consistent with the hypothesis that cell differentiation, in microgravity, is altered by interference with cytoskeleton-related mechanisms. We found: increases in the myocyte and its nuclear area, "fragmentation" of nucleoli, appearance of neuritic "aneurysms", decreased growth in the presence of "trophic" factors, and decreased yolk utilization. The effects were most notable at 1-10 rpm and depended on the onset and duration of rotation. Some parameters returned to near control values within 48 hrs after cessation of rotation. Cells from cultures rotated at higher speeds (>50 rpm) appeared comparable to controls. Compensation by centrifugal forces may account for this finding. Our data are consistent, in principle, with effects on other, flighted cells and suggest that "vector-free" gravity may simulate certain aspects of microgravity. The distribution of acetylcholine receptor aggregates, on myocytes, was also altered. This indicates that brain development, in microgravity, may also be affected.

Estimating functional connectivity of wildlife habitat and its relevance to ecological risk assessment

USGS Publications Warehouse

Johnson, A.R.; Allen, Craig R.; Simpson, K.A.N.; Kapustka, Lawrence; Biddinger, Gregory R.; Luxon, Matthew; Galbraith, Hector

2004-01-01

Habitat fragmentation is a major threat to the viability of wildlife populations and the maintenance of biodiversity. Fragmentation relates to the sub-division of habitat into disjunct patches. Usually coincident with fragmentation per se is loss of habitat, a reduction in the size of the remnant patches, and increasing distance between patches. Natural and anthropogenic processes leading to habitat fragmentation occur at many spatial scales, and their impacts on wildlife depend on the scales at which species interact with the landscape. The concept of functional connectivity captures this organism-based view of the relative ease of movement or degree of exchange between physically disjunct habitat patches. Functional connectivity of a given habitat arrangement for a given wildlife species depends on details of the organism's life history and behavioral ecology, but, for broad categories of species, quantities such as home range size and dispersal distance scale allometrically with body mass. These relationships can be incorporated into spatial analyses of functional connectivity, which can be quantified by indices or displayed graphically in maps. We review indices and GIS-based approaches to estimating functional connectivity, presenting examples from the literature and our own work on mammalian distributions. Such analyses can be readily incorporated within an ecological risk framework. Estimates of functional connectivity may be useful in a screening-level assessment of the impact of habitat fragmentation relative to other stressors, and may be crucial in detailed population modeling and viability analysis.

RNA Interference Therapies for an HIV-1 Functional Cure.

PubMed

Scarborough, Robert J; Gatignol, Anne

2017-12-27

HIV-1 drug therapies can prevent disease progression but cannot eliminate HIV-1 viruses from an infected individual. While there is hope that elimination of HIV-1 can be achieved, several approaches to reach a functional cure (control of HIV-1 replication in the absence of drug therapy) are also under investigation. One of these approaches is the transplant of HIV-1 resistant cells expressing anti-HIV-1 RNAs, proteins or peptides. Small RNAs that use RNA interference pathways to target HIV-1 replication have emerged as competitive candidates for cell transplant therapy and have been included in all gene combinations that have so far entered clinical trials. Here, we review RNA interference pathways in mammalian cells and the design of therapeutic small RNAs that use these pathways to target pathogenic RNA sequences. Studies that have been performed to identify anti-HIV-1 RNA interference therapeutics are also reviewed and perspectives on their use in combination gene therapy to functionally cure HIV-1 infection are provided.

A kernel function method for computing steady and oscillatory supersonic aerodynamics with interference.

NASA Technical Reports Server (NTRS)

Cunningham, A. M., Jr.

1973-01-01

The method presented uses a collocation technique with the nonplanar kernel function to solve supersonic lifting surface problems with and without interference. A set of pressure functions are developed based on conical flow theory solutions which account for discontinuities in the supersonic pressure distributions. These functions permit faster solution convergence than is possible with conventional supersonic pressure functions. An improper integral of a 3/2 power singularity along the Mach hyperbola of the nonplanar supersonic kernel function is described and treated. The method is compared with other theories and experiment for a variety of cases.

The Functional Determinants of Short-Term Memory: Evidence from Perceptual-Motor Interference in Verbal Serial Recall

ERIC Educational Resources Information Center

Hughes, Robert W.; Marsh, John E.

2017-01-01

A functional, perceptual-motor, account of serial short-term memory (STM) is examined by investigating the way in which an irrelevant spoken sequence interferes with verbal serial recall. Even with visual list-presentation, verbal serial recall is particularly susceptible to disruption by irrelevant spoken stimuli that have the same identity…

Neural systems and time course of proactive interference in working memory.

PubMed

Du, Yingchun; Zhang, John X; Xiao, Zhuangwei; Wu, Renhua

2007-01-01

The storage of information in working memory suffers as a function of proactive interference. Many works using neuroimaging technique have been done to reveal the brain mechanism of interference resolution. However, less is yet known about the time course of this process. Event-related potential method(ERP) and standardized Low Resolution Brain Electromagnetic Tomography method (sLORETA) were used in this study to discover the time course of interference resolution in working memory. The anterior P2 was thought to reflect interference resolution and if so, this process occurred earlier in working memory than in long-term memory.

Tsallis Entropy and the Transition to Scaling in Fragmentation

NASA Astrophysics Data System (ADS)

Sotolongo-Costa, Oscar; Rodriguez, Arezky H.; Rodgers, G. J.

2000-12-01

By using the maximum entropy principle with Tsallis entropy we obtain a fragment size distribution function which undergoes a transition to scaling. This distribution function reduces to those obtained by other authors using Shannon entropy. The treatment is easily generalisable to any process of fractioning with suitable constraints.

Forest fragmentation and selective logging have inconsistent effects on multiple animal-mediated ecosystem processes in a tropical forest.

PubMed

Schleuning, Matthias; Farwig, Nina; Peters, Marcell K; Bergsdorf, Thomas; Bleher, Bärbel; Brandl, Roland; Dalitz, Helmut; Fischer, Georg; Freund, Wolfram; Gikungu, Mary W; Hagen, Melanie; Garcia, Francisco Hita; Kagezi, Godfrey H; Kaib, Manfred; Kraemer, Manfred; Lung, Tobias; Naumann, Clas M; Schaab, Gertrud; Templin, Mathias; Uster, Dana; Wägele, J Wolfgang; Böhning-Gaese, Katrin

2011-01-01

Forest fragmentation and selective logging are two main drivers of global environmental change and modify biodiversity and environmental conditions in many tropical forests. The consequences of these changes for the functioning of tropical forest ecosystems have rarely been explored in a comprehensive approach. In a Kenyan rainforest, we studied six animal-mediated ecosystem processes and recorded species richness and community composition of all animal taxa involved in these processes. We used linear models and a formal meta-analysis to test whether forest fragmentation and selective logging affected ecosystem processes and biodiversity and used structural equation models to disentangle direct from biodiversity-related indirect effects of human disturbance on multiple ecosystem processes. Fragmentation increased decomposition and reduced antbird predation, while selective logging consistently increased pollination, seed dispersal and army-ant raiding. Fragmentation modified species richness or community composition of five taxa, whereas selective logging did not affect any component of biodiversity. Changes in the abundance of functionally important species were related to lower predation by antbirds and higher decomposition rates in small forest fragments. The positive effects of selective logging on bee pollination, bird seed dispersal and army-ant raiding were direct, i.e. not related to changes in biodiversity, and were probably due to behavioural changes of these highly mobile animal taxa. We conclude that animal-mediated ecosystem processes respond in distinct ways to different types of human disturbance in Kakamega Forest. Our findings suggest that forest fragmentation affects ecosystem processes indirectly by changes in biodiversity, whereas selective logging influences processes directly by modifying local environmental conditions and resource distributions. The positive to neutral effects of selective logging on ecosystem processes show that the functionality of tropical forests can be maintained in moderately disturbed forest fragments. Conservation concepts for tropical forests should thus include not only remaining pristine forests but also functionally viable forest remnants.

Forest Fragmentation and Selective Logging Have Inconsistent Effects on Multiple Animal-Mediated Ecosystem Processes in a Tropical Forest

PubMed Central

Schleuning, Matthias; Farwig, Nina; Peters, Marcell K.; Bergsdorf, Thomas; Bleher, Bärbel; Brandl, Roland; Dalitz, Helmut; Fischer, Georg; Freund, Wolfram; Gikungu, Mary W.; Hagen, Melanie; Garcia, Francisco Hita; Kagezi, Godfrey H.; Kaib, Manfred; Kraemer, Manfred; Lung, Tobias; Schaab, Gertrud; Templin, Mathias; Uster, Dana; Wägele, J. Wolfgang; Böhning-Gaese, Katrin

2011-01-01

Forest fragmentation and selective logging are two main drivers of global environmental change and modify biodiversity and environmental conditions in many tropical forests. The consequences of these changes for the functioning of tropical forest ecosystems have rarely been explored in a comprehensive approach. In a Kenyan rainforest, we studied six animal-mediated ecosystem processes and recorded species richness and community composition of all animal taxa involved in these processes. We used linear models and a formal meta-analysis to test whether forest fragmentation and selective logging affected ecosystem processes and biodiversity and used structural equation models to disentangle direct from biodiversity-related indirect effects of human disturbance on multiple ecosystem processes. Fragmentation increased decomposition and reduced antbird predation, while selective logging consistently increased pollination, seed dispersal and army-ant raiding. Fragmentation modified species richness or community composition of five taxa, whereas selective logging did not affect any component of biodiversity. Changes in the abundance of functionally important species were related to lower predation by antbirds and higher decomposition rates in small forest fragments. The positive effects of selective logging on bee pollination, bird seed dispersal and army-ant raiding were direct, i.e. not related to changes in biodiversity, and were probably due to behavioural changes of these highly mobile animal taxa. We conclude that animal-mediated ecosystem processes respond in distinct ways to different types of human disturbance in Kakamega Forest. Our findings suggest that forest fragmentation affects ecosystem processes indirectly by changes in biodiversity, whereas selective logging influences processes directly by modifying local environmental conditions and resource distributions. The positive to neutral effects of selective logging on ecosystem processes show that the functionality of tropical forests can be maintained in moderately disturbed forest fragments. Conservation concepts for tropical forests should thus include not only remaining pristine forests but also functionally viable forest remnants. PMID:22114695

Rostro-caudal and dorso-ventral gradients in medial and lateral prefrontal cortex during cognitive control of affective and cognitive interference.

PubMed

Rahm, Christoffer; Liberg, Benny; Wiberg-Kristoffersen, Maria; Aspelin, Peter; Msghina, Mussie

2013-04-01

Characterizing the anatomical substrates of major brain functions such as cognition and emotion is of utmost importance to the ongoing efforts of understanding the nature of psychiatric ailments and their potential treatment. The aim of our study was to investigate how the brain handles affective and cognitive interferences on cognitive processes. Functional magnetic resonance imaging investigation was performed on healthy individuals, comparing the brain oxygenation level dependent activation patterns during affective and cognitive counting Stroop tasks. The affective Stroop task activated rostral parts of medial prefrontal cortex (PFC) and rostral and ventral parts of lateral PFC, while cognitive Stroop activated caudal parts of medial PFC and caudal and dorsal parts of lateral PFC. Our findings suggest that the brain may handle affective and cognitive interference on cognitive processes differentially, with affective interference preferentially activating rostral and ventral PFC networks and cognitive interference activating caudal and dorsal PFC networks. © 2013 The Authors. Scandinavian Journal of Psychology © 2013 The Scandinavian Psychological Associations.

Fab fragment labeled with ICG-derivative for detecting digestive tract cancer.

PubMed

Yano, Hiromi; Muguruma, Naoki; Ito, Susumu; Aoyagi, Eriko; Kimura, Tetsuo; Imoto, Yoshitaka; Cao, Jianxin; Inoue, Shohei; Sano, Shigeki; Nagao, Yoshimitsu; Kido, Hiroshi

2006-09-01

In previous studies, we generated infrared ray fluorescence-labeled monoclonal antibodies and developed an infrared ray fluorescence endoscope capable of detecting the monoclonal antibodies to establish a novel diagnostic technique for gastrointestinal cancer. Although the whole IgG molecule has commonly been used for preparation of labeled antibodies, labeled IgG displays insufficient sensitivity and specificity, probably resulting from non-specific binding of the Fc fragment to target cells or interference between fluorochromes on the identical labeled antibody, which might be caused by molecular structure. In this in vitro study, we characterized an Fc-free fluorescence-labeled Fab fragment, which was expected to yield more specific binding to target cells than the whole IgG molecule. An anti-mucin antibody and ICG-ATT, an ICG derivative, were used as the labeled antibody and labeling compound, respectively. Paraffin sections of excised gastric cancer tissues were subjected to staining. The labeled whole IgG molecule (ICG-ATT-labeled IgG) and the labeled Fab fragment (ICG-ATT-labeled Fab) were prepared according to a previous report, and the fluorescence properties, antibody activities, and features of fluorescence microscope images obtained from paraffin sections were compared. Both ICG-ATT-labeled Fab and ICG-ATT-labeled IgG were excited by a near infrared ray of 766nm, and maximum emission occurred at 804nm. Antibody activities of ICG-ATT-labeled Fab were shown to be similar to those of unlabeled anti-MUC1 antibody. The fluorescence intensity obtained from paraffin sections of excised gastric cancer tissues revealed a tendency to be greater with ICG-ATT-labeled Fab than with ICG-ATT-labeled IgG. The infrared ray fluorescence-labeled Fab fragment was likely to be more specific than the conventionally labeled antibodies. Fragmentation of antibodies is considered to contribute to improved sensitivity and specificity of labeled antibodies for detection of micro gastrointestinal cancers.

Revisiting the co-existence of Attention-Deficit/Hyperactivity Disorder and Chronic Tic Disorder in childhood-The case of colour discrimination, sustained attention and interference control.

PubMed

Uebel-von Sandersleben, Henrik; Albrecht, Björn; Rothenberger, Aribert; Fillmer-Heise, Anke; Roessner, Veit; Sergeant, Joseph; Tannock, Rosemary; Banaschewski, Tobias

2017-01-01

Attention Deficit / Hyperactivity Disorder (ADHD) and Chronic Tic Disorder (CTD) are two common and frequently co-existing disorders, probably following an additive model. But this is not yet clear for the basic sensory function of colour processing sensitive to dopaminergic functioning in the retina and higher cognitive functions like attention and interference control. The latter two reflect important aspects for psychoeducation and behavioural treatment approaches. Colour discrimination using the Farnsworth-Munsell 100-hue Test, sustained attention during the Frankfurt Attention Inventory (FAIR), and interference liability during Colour- and Counting-Stroop-Tests were assessed to further clarify the cognitive profile of the co-existence of ADHD and CTD. Altogether 69 children were classified into four groups: ADHD (N = 14), CTD (N = 20), ADHD+CTD (N = 20) and healthy Controls (N = 15) and compared in cognitive functioning in a 2×2-factorial statistical model. Difficulties with colour discrimination were associated with both ADHD and CTD factors following an additive model, but in ADHD these difficulties tended to be more pronounced on the blue-yellow axis. Attention problems were characteristic for ADHD but not CTD. Interference load was significant in both Colour- and Counting-Stroop-Tests and unrelated to colour discrimination. Compared to Controls, interference load in the Colour-Stroop was higher in pure ADHD and in pure CTD, but not in ADHD+CTD, following a sub-additive model. In contrast, interference load in the Counting-Stroop did not reveal ADHD or CTD effects. The co-existence of ADHD and CTD is characterized by additive as well as sub-additive performance impairments, suggesting that their co-existence may show simple additive characteristics of both disorders or a more complex interaction, depending on demand. The equivocal findings on interference control may indicate limited validity of the Stroop-Paradigm for clinical assessments.

Revisiting the co-existence of Attention-Deficit/Hyperactivity Disorder and Chronic Tic Disorder in childhood—The case of colour discrimination, sustained attention and interference control

PubMed Central

Rothenberger, Aribert; Fillmer-Heise, Anke; Roessner, Veit; Sergeant, Joseph; Tannock, Rosemary; Banaschewski, Tobias

2017-01-01

Objective Attention Deficit / Hyperactivity Disorder (ADHD) and Chronic Tic Disorder (CTD) are two common and frequently co-existing disorders, probably following an additive model. But this is not yet clear for the basic sensory function of colour processing sensitive to dopaminergic functioning in the retina and higher cognitive functions like attention and interference control. The latter two reflect important aspects for psychoeducation and behavioural treatment approaches. Methods Colour discrimination using the Farnsworth-Munsell 100-hue Test, sustained attention during the Frankfurt Attention Inventory (FAIR), and interference liability during Colour- and Counting-Stroop-Tests were assessed to further clarify the cognitive profile of the co-existence of ADHD and CTD. Altogether 69 children were classified into four groups: ADHD (N = 14), CTD (N = 20), ADHD+CTD (N = 20) and healthy Controls (N = 15) and compared in cognitive functioning in a 2×2-factorial statistical model. Results Difficulties with colour discrimination were associated with both ADHD and CTD factors following an additive model, but in ADHD these difficulties tended to be more pronounced on the blue-yellow axis. Attention problems were characteristic for ADHD but not CTD. Interference load was significant in both Colour- and Counting-Stroop-Tests and unrelated to colour discrimination. Compared to Controls, interference load in the Colour-Stroop was higher in pure ADHD and in pure CTD, but not in ADHD+CTD, following a sub-additive model. In contrast, interference load in the Counting-Stroop did not reveal ADHD or CTD effects. Conclusion The co-existence of ADHD and CTD is characterized by additive as well as sub-additive performance impairments, suggesting that their co-existence may show simple additive characteristics of both disorders or a more complex interaction, depending on demand. The equivocal findings on interference control may indicate limited validity of the Stroop-Paradigm for clinical assessments. PMID:28594866

Two different kinds of rogue waves in weakly crossing sea states

NASA Astrophysics Data System (ADS)

Ruban, V. P.

2009-06-01

Formation of giant waves in sea states with two spectral maxima centered at close wave vectors k0±Δk/2 in the Fourier plane is numerically simulated using the fully nonlinear model for long-crested water waves [V. P. Ruban, Phys. Rev. E 71, 055303(R) (2005)]. Depending on an angle θ between the vectors k0 and Δk , which determines a typical orientation of interference stripes in the physical plane, rogue waves arise having different spatial structure. If θ≲arctan(1/2) , then typical giant waves are relatively long fragments of essentially two-dimensional (2D) ridges, separated by wide valleys and consisting of alternating oblique crests and troughs. At nearly perpendicular k0 and Δk , the interference minima develop to coherent structures similar to the dark solitons of the nonlinear Schrodinger equation, and a 2D freak wave looks much as a piece of a one-dimensional freak wave bounded in the transversal direction by two such dark solitons.

Fast antibody fragment motion: flexible linkers act as entropic spring

PubMed Central

Stingaciu, Laura R.; Ivanova, Oxana; Ohl, Michael; Biehl, Ralf; Richter, Dieter

2016-01-01

A flexible linker region between three fragments allows antibodies to adjust their binding sites to an antigen or receptor. Using Neutron Spin Echo Spectroscopy we observed fragment motion on a timescale of 7 ns with motional amplitudes of about 1 nm relative to each other. The mechanistic complexity of the linker region can be described by a spring model with Brownian motion of the fragments in a harmonic potential. Displacements, timescale, friction and force constant of the underlying dynamics are accessed. The force constant exhibits a similar strength to an entropic spring, with friction of the fragment matching the unbound state. The observed fast motions are fluctuations in pre-existing equilibrium configurations. The Brownian motion of domains in a harmonic potential is the appropriate model to examine functional hinge motions dependent on the structural topology and highlights the role of internal forces and friction to function. PMID:27020739

Fast antibody fragment motion: flexible linkers act as entropic spring

DOE PAGES

Stingaciu, Laura R.; Ivanova, Oxana; Ohl, Michael; ...

2016-03-29

A flexible linker region between three fragments allows antibodies to adjust their binding sites to an antigen or receptor. Using Neutron Spin Echo Spectroscopy we observed fragment motion on a timescale of 7 ns with motional amplitudes of about 1 nm relative to each other. The mechanistic complexity of the linker region can be described by a spring model with Brownian motion of the fragments in a harmonic potential. Displacements, timescale, friction and force constant of the underlying dynamics are accessed. The force constant exhibits a similar strength to an entropic spring, with friction of the fragment matching the unboundmore » state. The observed fast motions are fluctuations in pre-existing equilibrium configurations. In conclusion, the Brownian motion of domains in a harmonic potential is the appropriate model to examine functional hinge motions dependent on the structural topology and highlights the role of internal forces and friction to function.« less

Fast antibody fragment motion: flexible linkers act as entropic spring.

PubMed

Stingaciu, Laura R; Ivanova, Oxana; Ohl, Michael; Biehl, Ralf; Richter, Dieter

2016-03-29

A flexible linker region between three fragments allows antibodies to adjust their binding sites to an antigen or receptor. Using Neutron Spin Echo Spectroscopy we observed fragment motion on a timescale of 7 ns with motional amplitudes of about 1 nm relative to each other. The mechanistic complexity of the linker region can be described by a spring model with Brownian motion of the fragments in a harmonic potential. Displacements, timescale, friction and force constant of the underlying dynamics are accessed. The force constant exhibits a similar strength to an entropic spring, with friction of the fragment matching the unbound state. The observed fast motions are fluctuations in pre-existing equilibrium configurations. The Brownian motion of domains in a harmonic potential is the appropriate model to examine functional hinge motions dependent on the structural topology and highlights the role of internal forces and friction to function.

Scaling invariance of spherical projectile fragmentation upon high-velocity impact on a thin continuous shield

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

Myagkov, N. N., E-mail: nn-myagkov@mail.ru

The problem of aluminum projectile fragmentation upon high-velocity impact on a thin aluminum shield is considered. A distinctive feature of this description is that the fragmentation has been numerically simulated using the complete system of equations of deformed solid mechanics by a method of smoothed particle hydrodynamics in three-dimensional setting. The transition from damage to fragmentation is analyzed and scaling relations are derived in terms of the impact velocity (V), ratio of shield thickness to projectile diameter (h/D), and ultimate strength (σ{sub p}) in the criterion of projectile and shield fracture. Analysis shows that the critical impact velocity V{sub c}more » (separating the damage and fragmentation regions) is a power function of σ{sub p} and h/D. In the supercritical region (V > V{sub c}), the weight-average fragment mass asymptotically tends to a power function of the impact velocity with exponent independent of h/D and σ{sub p}. Mean cumulative fragment mass distributions at the critical point are scale-invariant with respect to parameters h/D and σ{sub p}. Average masses of the largest fragments are also scale-invariant at V > V{sub c}, but only with respect to variable parameter σ{sub p}.« less

Geometry analysis for landscape fragmentation in coastal areas of China

NASA Astrophysics Data System (ADS)

Zhang, Tianhai; Yu, Ning; Mu, Hongdu; Tuo, Tao

2017-08-01

In recent years, the continuous expansion of urban-transport networks in China has aggravated the fragmentation of regional landscapes and led to the degradation of multiple ecological functions. In this study, Geographic Information System (GIS) techniques, patch size of fragmentation geometry were used to identify and monitor spatial distribution patterns of landscape fragmentation due to urban-transport networks in Fujian Province. This network has caused serious damage to regional ecological functions, and risks to the persistence of animal populations and biodiversity. This analysis revealed that the smallest patch class (0-15 km2) occurred with a much greater frequency than all other larger patch sizes. In the coastal cities of Xiamen, Zhangzhou and Quanzhou, the percentage of the number of patches less than 300 km2 was higher than in the western cities of Nanping, Sanming and Longyan, and the percentage of the area of patches less than 300 km2 was also higher. Based on a holistic identification of the structure of the network and its landscape division, we found that: Fujian Province has a spatial pattern of landscape fragmentation, with less fragmentation in western and northern regions, and most fragmentation in southern and eastern regions. Coastal regions and areas close to the main transport routes were more seriously fragmented and contained most of the small patches.

Interference of functional monomers with polymerization efficiency of adhesives.

PubMed

Hanabusa, Masao; Yoshihara, Kumiko; Yoshida, Yasuhiro; Okihara, Takumi; Yamamoto, Takatsugu; Momoi, Yasuko; Van Meerbeek, Bart

2016-04-01

The degree of conversion (DC) of camphorquinone/amine-based adhesives is affected by acidic functional monomers as a result of inactivation of the amine co-initiator through an acid-base reaction. During bonding, functional monomers of self-etch adhesives chemically interact with hydroxyapatite (HAp). Here, we tested in how far the latter interaction of functional monomers with HAp counteracts the expected reduction in DC of camphorquinone/amine-based adhesives. The DC of three experimental adhesive formulations, containing either of the two functional monomers [10-methacryloyloxydecyl dihydrogen phosphate (10-MDP) or 4-methacryloxyethyl trimellitic acid anhydride (4-META)] or no functional monomer (no-FM; control), was measured with and without HAp powder added to the adhesive formulations. Both the variables 'functional monomer' and 'HAp' were found to be significant, with the functional monomer reducing the DC and HAp counteracting this effect. It is concluded that the functional monomers 10-MDP and 4-META interfere with the polymerization efficiency of adhesives. This interference is less prominent in the presence of HAp, which would clinically correspond to when these two functional monomers of the adhesive simultaneously interact with HAp in tooth tissue. © 2016 Eur J Oral Sci.

A multivariate analysis of age-related differences in functional networks supporting conflict resolution.

PubMed

Salami, Alireza; Rieckmann, Anna; Fischer, Håkan; Bäckman, Lars

2014-02-01

Functional neuroimaging studies demonstrate age-related differences in recruitment of a large-scale attentional network during interference resolution, especially within dorsolateral prefrontal cortex (DLPFC) and anterior cingulate cortex (ACC). These alterations in functional responses have been frequently observed despite equivalent task performance, suggesting age-related reallocation of neural resources, although direct evidence for a facilitating effect in aging is sparse. We used the multi-source interference task and multivariate partial-least-squares to investigate age-related differences in the neuronal signature of conflict resolution, and their behavioral implications in younger and older adults. There were interference-related increases in activity, involving fronto-parietal and basal ganglia networks that generalized across age. In addition an age-by-task interaction was observed within a distributed network, including DLPFC and ACC, with greater activity during interference in the old. Next, we combined brain-behavior and functional connectivity analyses to investigate whether compensatory brain changes were present in older adults, using DLPFC and ACC as regions of interest (i.e. seed regions). This analysis revealed two networks differentially related to performance across age groups. A structural analysis revealed age-related gray-matter losses in regions facilitating performance in the young, suggesting that functional reorganization may partly reflect structural alterations in aging. Collectively, these findings suggest that age-related structural changes contribute to reductions in the efficient recruitment of a youth-like interference network, which cascades into instantiation of a different network facilitating conflict resolution in elderly people. © 2013. Published by Elsevier Inc. All rights reserved.

Homogeneous versus heterogeneous probes for microbial ecological microarrays.

PubMed

Bae, Jin-Woo; Park, Yong-Ha

2006-07-01

Microbial ecological microarrays have been developed for investigating the composition and functions of microorganism communities in environmental niches. These arrays include microbial identification microarrays, which use oligonucleotides, gene fragments or microbial genomes as probes. In this article, the advantages and disadvantages of each type of probe are reviewed. Oligonucleotide probes are currently useful for probing uncultivated bacteria that are not amenable to gene fragment probing, whereas the functional gene fragments amplified randomly from microbial genomes require phylogenetic and hierarchical categorization before use as microbial identification probes, despite their high resolution for both specificity and sensitivity. Until more bacteria are sequenced and gene fragment probes are thoroughly validated, heterogeneous bacterial genome probes will provide a simple, sensitive and quantitative tool for exploring the ecosystem structure.

Modified stochastic fragmentation of an interval as an ageing process

NASA Astrophysics Data System (ADS)

Fortin, Jean-Yves

2018-02-01

We study a stochastic model based on modified fragmentation of a finite interval. The mechanism consists of cutting the interval at a random location and substituting a unique fragment on the right of the cut to regenerate and preserve the interval length. This leads to a set of segments of random sizes, with the accumulation of small fragments near the origin. This model is an example of record dynamics, with the presence of ‘quakes’ and slow dynamics. The fragment size distribution is a universal inverse power law with logarithmic corrections. The exact distribution for the fragment number as function of time is simply related to the unsigned Stirling numbers of the first kind. Two-time correlation functions are defined, and computed exactly. They satisfy scaling relations, and exhibit aging phenomena. In particular, the probability that the same number of fragments is found at two different times t>s is asymptotically equal to [4πlog(s)]-1/2 when s\\gg 1 and the ratio t/s is fixed, in agreement with the numerical simulations. The same process with a reset impedes the aging phenomenon-beyond a typical time scale defined by the reset parameter.

Molecularly Imprinted Polymers with DNA Aptamer Fragments as Macromonomers.

PubMed

Zhang, Zijie; Liu, Juewen

2016-03-01

Molecularly imprinted polymers (MIPs) are produced in the presence of a template molecule. After removing the template, the cavity can selectively rebind the template. MIPs are attractive functional materials with a low cost and high stability, but traditional MIPs often suffer from low binding affinity. This study employs DNA aptamer fragments as macromonomers to improve MIPs. The DNA aptamer for adenosine was first split into two halves, fluorescently labeled, and copolymerized into MIPs. With a fluorescence quenching assay, the importance of imprinting was confirmed. Further studies were carried out using isothermal titration calorimetry (ITC). Compared to the mixture of the free aptamer fragments, their MIPs doubled the binding affinity. Each free aptamer fragment alone cannot bind adenosine, whereas MIPs containing each fragment are effective binders. We further shortened one of the aptamer fragments, and the DNA length was pushed to as short as six nucleotides, yielding MIPs with a dissociation constant of 27 μM adenosine. This study provides a new method for preparing functional MIP materials by combining high-affinity biopolymer fragments with low-cost synthetic monomers, allowing higher binding affinity and providing a method for signaling binding based on DNA chemistry.

Transverse momentum dependent fragmenting jet functions with applications to quarkonium production

DOE PAGES

Bain, Reggie; Makris, Yiannis; Mehen, Thomas

2016-11-23

We introduce the transverse momentum dependent fragmenting jet function (TMDFJF), which appears in factorization theorems for cross sections for jets with an identified hadron. These are functions of z, the hadron’s longitudinal momentum fraction, and transverse momentum, p ⊥, relative to the jet axis. In the framework of Soft-Collinear Effective Theory (SCET) we derive the TMDFJF from both a factorized SCET cross section and the TMD fragmentation function defined in the literature. The TMDFJFs are factorized into distinct collinear and soft-collinear modes by matching onto SCET +. As TMD calculations contain rapidity divergences, both the renormalization group (RG) and rapiditymore » renormalization group (RRG) must be used to provide resummed calculations with next-to-leading-logarithm prime (NLL’) accuracy. We apply our formalism to the production of J/ψ within jets initiated by gluons. In this case the TMDFJF can be calculated in terms of NRQCD (Non-relativistic quantum chromodynamics) fragmentation functions. We find that when the J/ψ carries a significant fraction of the jet energy, the p T and z distributions differ for different NRQCD production mechanisms. Another observable with discriminating power is the average angle that the J/ψ makes with the jet axis.« less

Decay of mRNAs targeted by RISC requires XRN1, the Ski complex, and the exosome

PubMed Central

ORBAN, TAMAS I.; IZAURRALDE, ELISA

2005-01-01

RNA interference (RNAi) is a conserved RNA silencing pathway that leads to sequence-specific mRNA decay in response to the presence of double-stranded RNA (dsRNA). Long dsRNA molecules are first processed by Dicer into 21–22-nucleotide small interfering RNAs (siRNAs). The siRNAs are incorporated into a multimeric RNA-induced silencing complex (RISC) that cleaves mRNAs at a site determined by complementarity with the siRNAs. Following this initial endonucleolytic cleavage, the mRNA is degraded by a mechanism that is not completely understood. We investigated the decay pathway of mRNAs targeted by RISC in Drosophila cells. We show that 5′ mRNA fragments generated by RISC cleavage are rapidly degraded from their 3′ ends by the exosome, whereas the 3′ fragments are degraded from their 5′ ends by XRN1. Exosome-mediated decay of the 5′ fragments requires the Drosophila homologs of yeast Ski2p, Ski3p, and Ski8p, suggesting that their role as regulators of exosome activity is conserved. Our findings indicate that mRNAs targeted by siRNAs are degraded from the ends generated by RISC cleavage, without undergoing decapping or deadenylation. PMID:15703439

Selective Inhibition and Naming Performance in Semantic Blocking, Picture-Word Interference, and Color-Word Stroop Tasks

ERIC Educational Resources Information Center

Shao, Zeshu; Roelofs, Ardi; Martin, Randi C.; Meyer, Antje S.

2015-01-01

In 2 studies, we examined whether explicit distractors are necessary and sufficient to evoke selective inhibition in 3 naming tasks: the semantic blocking, picture-word interference, and color-word Stroop task. Delta plots were used to quantify the size of the interference effects as a function of reaction time (RT). Selective inhibition was…

Ribonucleic acid interference (RNAi) and control of citrus pests

USDA-ARS?s Scientific Manuscript database

Ribonucleic acid interference, RNAi, applications and function are described for the non-scientist to bring a better understanding of how this emerging technology is providing environmentally friendly, non-transgenic, insect pest control. ...

The rde-1 gene, RNA interference, and transposon silencing in C. elegans.

PubMed

Tabara, H; Sarkissian, M; Kelly, W G; Fleenor, J; Grishok, A; Timmons, L; Fire, A; Mello, C C

1999-10-15

Double-stranded (ds) RNA can induce sequence-specific inhibition of gene function in several organisms. However, both the mechanism and the physiological role of the interference process remain mysterious. In order to study the interference process, we have selected C. elegans mutants resistant to dsRNA-mediated interference (RNAi). Two loci, rde-1 and rde-4, are defined by mutants strongly resistant to RNAi but with no obvious defects in growth or development. We show that rde-1 is a member of the piwi/sting/argonaute/zwille/eIF2C gene family conserved from plants to vertebrates. Interestingly, several, but not all, RNAi-deficient strains exhibit mobilization of the endogenous transposons. We discuss implications for the mechanism of RNAi and the possibility that one natural function of RNAi is transposon silencing.

Reversible Disruption of Neuronal Mitochondria by Ischemic and Traumatic Injury Revealed by Quantitative Two-Photon Imaging in the Neocortex of Anesthetized Mice

PubMed Central

Kislin, Mikhail; Sword, Jeremy; Fomitcheva, Ioulia V.; Croom, Deborah; Pryazhnikov, Evgeny; Lihavainen, Eero; Toptunov, Dmytro; Rauvala, Heikki; Ribeiro, Andre S.

2017-01-01

Mitochondria play a variety of functional roles in cortical neurons, from metabolic support and neuroprotection to the release of cytokines that trigger apoptosis. In dendrites, mitochondrial structure is closely linked to their function, and fragmentation (fission) of the normally elongated mitochondria indicates loss of their function under pathological conditions, such as stroke and brain trauma. Using in vivo two-photon microscopy in mouse brain, we quantified mitochondrial fragmentation in a full spectrum of cortical injuries, ranging from severe to mild. Severe global ischemic injury was induced by bilateral common carotid artery occlusion, whereas severe focal stroke injury was induced by Rose Bengal photosensitization. The moderate and mild traumatic injury was inflicted by focal laser lesion and by mild photo-damage, respectively. Dendritic and mitochondrial structural changes were tracked longitudinally using transgenic mice expressing fluorescent proteins localized either in cytosol or in mitochondrial matrix. In response to severe injury, mitochondrial fragmentation developed in parallel with dendritic damage signified by dendritic beading. Reconstruction from serial section electron microscopy confirmed mitochondrial fragmentation. Unlike dendritic beading, fragmentation spread beyond the injury core in focal stroke and focal laser lesion models. In moderate and mild injury, mitochondrial fragmentation was reversible with full recovery of structural integrity after 1–2 weeks. The transient fragmentation observed in the mild photo-damage model was associated with changes in dendritic spine density without any signs of dendritic damage. Our findings indicate that alterations in neuronal mitochondria structure are very sensitive to the tissue damage and can be reversible in ischemic and traumatic injuries. SIGNIFICANCE STATEMENT During ischemic stroke or brain trauma, mitochondria can either protect neurons by supplying ATP and adsorbing excessive Ca2+, or kill neurons by releasing proapoptotic factors. Mitochondrial function is tightly linked to their morphology: healthy mitochondria are thin and long; dysfunctional mitochondria are thick (swollen) and short (fragmented). To date, fragmentation of mitochondria was studied either in dissociated cultured neurons or in brain slices, but not in the intact living brain. Using real-time in vivo two-photon microscopy, we quantified mitochondrial fragmentation during acute pathological conditions that mimic severe, moderate, and mild brain injury. We demonstrated that alterations in neuronal mitochondria structural integrity can be reversible in traumatic and ischemic injuries, highlighting mitochondria as a potential target for therapeutic interventions. PMID:28077713

A measurement of the b quark fragmentation function at {radical}Q{sup 2} = 45.6 GeV

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

Church, E.D.

1996-06-01

Presented here is a measurement of the b quark fragmentation function D{sub b}(X), taken from a sample of 504 semi-leptonic B decays which were selected from the 150,000 Z{sup 0} decays collected between 1993 and 1995 at the SLD at SLAC. The energy of each tagged B hadron is reconstructed using missing jet energy, based on the information from the lepton and a partially-reconstructed charm-decay vertex. Account is taken of the effect of primary orbitally excited mesons (B**s). An iterative unfolding procedure is used which serves to effectively extract the true fragmentation function from the reconstructed B energy spectrum. Themore » final result is shown to be compatible with many theoretical models. A comparison is made with other b fragmentation function measurements at 45.6 GeV, and this measurement is shown to be consistent with those results. The average scaled energy is found to be (x{sub E}) = 0.697{+-} 0.017(stat) {+-} 0.034(sys).« less

NMR screening in fragment-based drug design: a practical guide.

PubMed

Kim, Hai-Young; Wyss, Daniel F

2015-01-01

Fragment-based drug design (FBDD) comprises both fragment-based screening (FBS) to find hits and elaboration of these hits to lead compounds. Typical fragment hits have lower molecular weight (<300-350 Da) and lower initial potency but higher ligand efficiency when compared to those from high-throughput screening. NMR spectroscopy has been widely used for FBDD since it identifies and localizes the binding site of weakly interacting hits on the target protein. Here we describe ligand-based NMR methods for hit identification from fragment libraries and for functional cross-validation of primary hits.

Signatures of Hong-Ou-Mandel interference at microwave frequencies

NASA Astrophysics Data System (ADS)

Woolley, M. J.; Lang, C.; Eichler, C.; Wallraff, A.; Blais, A.

2013-10-01

Two-photon quantum interference at a beam splitter, commonly known as Hong-Ou-Mandel interference, is a fundamental demonstration of the quantum mechanical nature of electromagnetic fields and a key component of various quantum information processing protocols. The phenomenon was recently demonstrated with microwave-frequency photons by Lang et al (2013 Nature Phys. 9 345-8). This experiment employed circuit QED systems as sources of microwave photons, and was based on the measurement of second-order cross-correlation and auto-correlation functions of the microwave fields at the outputs of the beam splitter using linear detectors. Here we present the calculation of these correlation functions for the cases of inputs corresponding to: (i) trains of pulsed Gaussian or Lorentzian single microwave photons and (ii) resonant fluorescent microwave fields from continuously driven circuit QED systems. In both cases, the signature of two-photon quantum interference is a suppression of the second-order cross-correlation function for small delays. The experiment described in Lang et al (2013) was performed with trains of Lorentzian single photons, and very good agreement with experimental data is obtained. The results are relevant not only to interference experiments using circuit QED systems, but any such setup with highly controllable sources and time-resolved detection.

Measurements of the u valence quark distribution function in the proton and u quark fragmentation functions

NASA Astrophysics Data System (ADS)

Arneodo, M.; Arvidson, A.; Aubert, J. J.; Badelek, B.; Beaufays, J.; Bee, C. P.; Benchouk, C.; Berghoff, G.; Bird, I. G.; Blum, D.; Böhm, E.; De Bouard, X.; Brasse, F. W.; Braun, H.; Broll, C.; Brown, S. C.; Brück, H.; Calen, H.; Chima, J. S.; Ciborowski, J.; Clifft, R.; Coignet, G.; Combley, F.; Coughlan, J.; D'Agostini, G.; Dahlgren, S.; Dengler, F.; Derado, I.; Dreyer, T.; Drees, J.; Düren, M.; Eckardt, V.; Edwards, A.; Edwards, M.; Ernst, T.; Eszes, G.; Favier, J.; Ferrero, M. I.; Figiel, J.; Flauger, W.; Foster, J.; Gabathuler, E.; Gajewski, J.; Gamet, R.; Gayler, J.; Geddes, N.; Grafström, P.; Grard, F.; Haas, J.; Hagberg, E.; Hasert, F. J.; Hayman, P.; Heusse, P.; Jaffre, M.; Jacholkowska, A.; Janata, F.; Jancso, G.; Johnson, A. S.; Kabuss, E. M.; Kellner, G.; Korbel, V.; Krüger, A.; Krüger, J.; Kullander, S.; Landgraf, U.; Lanske, D.; Loken, J.; Long, K.; Maire, M.; Malecki, P.; Manz, A.; Maselli, S.; Mohr, W.; Montanet, F.; Montgomery, H. E.; Nagy, E.; Nassalski, J.; Norton, P. R.; Oakham, F. G.; Osborne, A. M.; Pascaud, C.; Pawlik, B.; Payre, P.; Peroni, C.; Peschel, H.; Pessard, H.; Pettingale, J.; Pietrzyk, B.; Poensgen, B.; Pötsch, M.; Renton, P.; Ribarics, P.; Rith, K.; Rondio, E.; Sandacz, A.; Scheer, M.; Schlagböhmer, A.; Schiemann, H.; Schmitz, N.; Schneegans, M.; Scholz, M.; Schouten, M.; Schröder, T.; Schultze, K.; Sloan, T.; Stier, H. E.; Studt, M.; Taylor, G. N.; Thenard, J. M.; Thompson, J. C.; De la Torre, A.; Toth, J.; Urban, L.; Urban, L.; Wallucks, W.; Whalley, M.; Wheeler, S.; Williams, W. S. C.; Wimpenny, S. J.; Windmolders, R.; Wolf, G.; European Muon Collaboration

1989-07-01

A new determination of the u valence quark distribution function in the proton is obtained from the analysis of identified charged pions, kaons, protons and antiprotons produced in muon-proton and muon-deuteron scattering. The comparison with results obtained in inclusive deep inelastic lepton-nucleon scattering provides a further test of the quark-parton model. The u quark fragmentation functions into positive and negative pions, kaons, protons and antiprotons are also measured.

The promises and pitfalls of RNA-interference-based therapeutics

PubMed Central

Castanotto, Daniela; Rossi, John J.

2009-01-01

The discovery that gene expression can be controlled by the Watson–Crick base-pairing of small RNAs with messenger RNAs containing complementary sequence — a process known as RNA interference — has markedly advanced our understanding of eukaryotic gene regulation and function. The ability of short RNA sequences to modulate gene expression has provided a powerful tool with which to study gene function and is set to revolutionize the treatment of disease. Remarkably, despite being just one decade from its discovery, the phenomenon is already being used therapeutically in human clinical trials, and biotechnology companies that focus on RNA-interference-based therapeutics are already publicly traded. PMID:19158789

Mapping the core mass function to the initial mass function

NASA Astrophysics Data System (ADS)

Guszejnov, Dávid; Hopkins, Philip F.

2015-07-01

It has been shown that fragmentation within self-gravitating, turbulent molecular clouds (`turbulent fragmentation') can naturally explain the observed properties of protostellar cores, including the core mass function (CMF). Here, we extend recently developed analytic models for turbulent fragmentation to follow the time-dependent hierarchical fragmentation of self-gravitating cores, until they reach effectively infinite density (and form stars). We show that turbulent fragmentation robustly predicts two key features of the initial mass function (IMF). First, a high-mass power-law scaling very close to the Salpeter slope, which is a generic consequence of the scale-free nature of turbulence and self-gravity. We predict the IMF slope (-2.3) is slightly steeper than the CMF slope (-2.1), owing to the slower collapse and easier fragmentation of large cores. Secondly, a turnover mass, which is set by a combination of the CMF turnover mass (a couple solar masses, determined by the `sonic scale' of galactic turbulence, and so weakly dependent on galaxy properties), and the equation of state (EOS). A `soft' EOS with polytropic index γ < 1.0 predicts that the IMF slope becomes `shallow' below the sonic scale, but fails to produce the full turnover observed. An EOS, which becomes `stiff' at sufficiently low surface densities Σgas ˜ 5000 M⊙ pc-2, and/or models, where each collapsing core is able to heat and effectively stiffen the EOS of a modest mass (˜0.02 M⊙) of surrounding gas, are able to reproduce the observed turnover. Such features are likely a consequence of more detailed chemistry and radiative feedback.

CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli

PubMed Central

Díez-Villaseñor, César; Guzmán, Noemí M.; Almendros, Cristóbal; García-Martínez, Jesús; Mojica, Francisco J.M.

2013-01-01

Prokaryotes immunize themselves against transmissible genetic elements by the integration (acquisition) in clustered regularly interspaced short palindromic repeats (CRISPR) loci of spacers homologous to invader nucleic acids, defined as protospacers. Following acquisition, mono-spacer CRISPR RNAs (termed crRNAs) guide CRISPR-associated (Cas) proteins to degrade (interference) protospacers flanked by an adjacent motif in extrachomosomal DNA. During acquisition, selection of spacer-precursors adjoining the protospacer motif and proper orientation of the integrated fragment with respect to the leader (sequence leading transcription of the flanking CRISPR array) grant efficient interference by at least some CRISPR-Cas systems. This adaptive stage of the CRISPR action is poorly characterized, mainly due to the lack of appropriate genetic strategies to address its study and, at least in Escherichia coli, the need of Cas overproduction for insertion detection. In this work, we describe the development and application in Escherichia coli strains of an interference-independent assay based on engineered selectable CRISPR-spacer integration reporter plasmids. By using this tool without the constraint of interference or cas overexpression, we confirmed fundamental aspects of this process such as the critical requirement of Cas1 and Cas2 and the identity of the CTT protospacer motif for the E. coli K12 system. In addition, we defined the CWT motif for a non-K12 CRISPR-Cas variant, and obtained data supporting the implication of the leader in spacer orientation, the preferred acquisition from plasmids harboring cas genes and the occurrence of a sequential cleavage at the insertion site by a ruler mechanism. PMID:23445770

CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli.

PubMed

Díez-Villaseñor, César; Guzmán, Noemí M; Almendros, Cristóbal; García-Martínez, Jesús; Mojica, Francisco J M

2013-05-01

Prokaryotes immunize themselves against transmissible genetic elements by the integration (acquisition) in clustered regularly interspaced short palindromic repeats (CRISPR) loci of spacers homologous to invader nucleic acids, defined as protospacers. Following acquisition, mono-spacer CRISPR RNAs (termed crRNAs) guide CRISPR-associated (Cas) proteins to degrade (interference) protospacers flanked by an adjacent motif in extrachomosomal DNA. During acquisition, selection of spacer-precursors adjoining the protospacer motif and proper orientation of the integrated fragment with respect to the leader (sequence leading transcription of the flanking CRISPR array) grant efficient interference by at least some CRISPR-Cas systems. This adaptive stage of the CRISPR action is poorly characterized, mainly due to the lack of appropriate genetic strategies to address its study and, at least in Escherichia coli, the need of Cas overproduction for insertion detection. In this work, we describe the development and application in Escherichia coli strains of an interference-independent assay based on engineered selectable CRISPR-spacer integration reporter plasmids. By using this tool without the constraint of interference or cas overexpression, we confirmed fundamental aspects of this process such as the critical requirement of Cas1 and Cas2 and the identity of the CTT protospacer motif for the E. coli K12 system. In addition, we defined the CWT motif for a non-K12 CRISPR-Cas variant, and obtained data supporting the implication of the leader in spacer orientation, the preferred acquisition from plasmids harboring cas genes and the occurrence of a sequential cleavage at the insertion site by a ruler mechanism.

Kinematics of current region fragmentation in semi-inclusive deeply inelastic scattering

DOE PAGES

Boglione, M.; Collins, J.; Gamberg, L.; ...

2017-01-16

Different kinematical regions of semi-inclusive deeply inelastic scattering (SIDIS) processes correspond to different underlying partonic pictures, and it is important to understand the transition between them. We find criteria in semi-inclusive deeply inelastic scattering (SIDIS) for identifying the current fragmentation region — the kinematical region where a factorization picture with fragmentation functions is appropriate, especially for studies of transverse-momentum-dependent (TMD) functions. This region is distinguished from the central (soft) and target fragmentation regions. The basis of our argument is in the errors in approximations used in deriving factorization. As compared with previous work, we show that it is essential tomore » take account of the transverse momentum of the detected hadron, and we find a much more restricted range for genuine current fragmentation. As a result, we show that it is important to develop an extended factorization formulation to treat hadronization in the central region, as well as the current and target fragmentation regions, and to obtain a unified formalism spanning all rapidities for the detected hadron.« less

Is chronic insomnia a precursor to major depression? Epidemiological and biological findings.

PubMed

Baglioni, Chiara; Riemann, Dieter

2012-10-01

Insomnia has been found to be a clinical predictor of subsequent depression. Nevertheless the biological processes underlying this causal relationship are yet not fully understood. Both conditions share a common imbalance of the arousal system. Patients with insomnia present fragmented REM sleep, which probably interferes with basal processes of emotion regulation. The interaction between the arousal and the affective system with the persistence of the disorder could slowly alter also the cognitive system and lead to depression. Although preliminary results seem to support this hypothesis, data are still too few to make valid conclusions.

Short Lingual Osteotomy Using a Piezosurgery Ultrasonic Bone-Cutting Device During Sagittal Split Ramus Osteotomy.

PubMed

Kawase-Koga, Yoko; Mori, Yoshiyuki; Kanno, Yuki; Hoshi, Kazuto; Takato, Tsuyoshi

2015-10-01

Short lingual osteotomy is a useful method for the performance of sagittal split ramus osteotomy involving interference between the proximal and distal bone fragments when lateral differences exist in the setback distance. However, this procedure occasionally results in abnormal fracture and nerve injury; expert surgical skill is thus required. We herein describe a novel technique involving the use of an ultrasonic bone-cutting device (Piezosurgery; Mectron Medical Technology, Carasco, Italy) for vertical osteotomy posterior to the mandibular foramen. Successful short lingual osteotomy was performed using this technique with avoidance of abnormal fracture and neurovascular bundle damage.

Responsiveness and Minimally Important Differences for 4 Patient-Reported Outcomes Measurement Information System Short Forms: Physical Function, Pain Interference, Depression, and Anxiety in Knee Osteoarthritis.

PubMed

Lee, Augustine C; Driban, Jeffrey B; Price, Lori Lyn; Harvey, William F; Rodday, Angie Mae; Wang, Chenchen

2017-09-01

Patient-Reported Outcomes Measurement Information System (PROMIS) instruments can provide valid, interpretable measures of health status among adults with osteoarthritis (OA). However, their ability to detect meaningful change over time is unknown. We evaluated the responsiveness and minimally important differences (MIDs) for 4 PROMIS Short Forms: Physical Function, Pain Interference, Depression, and Anxiety. We analyzed adults with symptomatic knee OA from our randomized trial comparing Tai Chi and physical therapy. Using baseline and 12-week scores, responsiveness was evaluated according to consensus standards by testing 6 a priori hypotheses of the correlations between PROMIS and legacy change scores. Responsiveness was considered high if ≥5 hypotheses were confirmed, and moderate if 3 or 4 were confirmed. MIDs were evaluated according to prospective change for people achieving previously-established MID on legacy comparators. The lowest and highest MIDs meeting a priori quality criteria formed a MID range for each PROMIS Short Form. Among 165 predominantly female (70%) and white (57%) participants, mean age was 61 years and body mass index was 33. PROMIS Physical Function had 5 confirmed hypotheses and Pain Interference, Depression, and Anxiety had 3 or 4. MID ranges were: Depression = 3.0 to 3.1; Anxiety = 2.3 to 3.4; Physical Function = 1.9 to 2.2; and Pain Interference = 2.35 to 2.4. PROMIS Physical Function has high responsiveness, and Depression, Anxiety, and Pain Interference have moderate responsiveness among adults with knee OA. We established the first MIDs for PROMIS in this population, and provided an important standard of reference to better apply or interpret PROMIS in future trials or clinical practice. This study examined whether PROMIS Short Form instruments (Physical Function, Pain Interference, Depression, and Anxiety) were able to detect change over time among adults with knee OA, and provided minimally important change estimates for each measure. This standard of reference can help apply or interpret these instruments in the future. Copyright © 2017. Published by Elsevier Inc.

Baculovirus display of functional antibody Fab fragments.

PubMed

Takada, Shinya; Ogawa, Takafumi; Matsui, Kazusa; Suzuki, Tasuku; Katsuda, Tomohisa; Yamaji, Hideki

2015-08-01

The generation of a recombinant baculovirus that displays antibody Fab fragments on the surface was investigated. A recombinant baculovirus was engineered so that the heavy chain (Hc; Fd fragment) of a mouse Fab fragment was expressed as a fusion to the N-terminus of baculovirus gp64, while the light chain of the Fab fragment was simultaneously expressed as a secretory protein. Following infection of Sf9 insect cells with the recombinant baculovirus, the culture supernatant was analyzed by enzyme-linked immunosorbent assay using antigen-coated microplates and either an anti-mouse IgG or an anti-gp64 antibody. A relatively strong signal was obtained in each case, showing antigen-binding activity in the culture supernatant. In western blot analysis of the culture supernatant using the anti-gp64 antibody, specific protein bands were detected at an electrophoretic mobility that coincided with the molecular weight of the Hc-gp64 fusion protein as well as that of gp64. Flow cytometry using a fluorescein isothiocyanate-conjugated antibody specific to mouse IgG successfully detected the Fab fragments on the surface of the Sf9 cells. These results suggest that immunologically functional antibody Fab fragments can be displayed on the surface of baculovirus particles, and that a fluorescence-activated cell sorter with a fluorescence-labeled antigen can isolate baculoviruses displaying specific Fab fragments. This successful baculovirus display of antibody Fab fragments may offer a novel approach for the efficient selection of specific antibodies.

Coherent molecular transistor: control through variation of the gate wave function.

PubMed

Ernzerhof, Matthias

2014-03-21

In quantum interference transistors (QUITs), the current through the device is controlled by variation of the gate component of the wave function that interferes with the wave function component joining the source and the sink. Initially, mesoscopic QUITs have been studied and more recently, QUITs at the molecular scale have been proposed and implemented. Typically, in these devices the gate lead is subjected to externally adjustable physical parameters that permit interference control through modifications of the gate wave function. Here, we present an alternative model of a molecular QUIT in which the gate wave function is directly considered as a variable and the transistor operation is discussed in terms of this variable. This implies that we specify the gate current as well as the phase of the gate wave function component and calculate the resulting current through the source-sink channel. Thus, we extend on prior works that focus on the phase of the gate wave function component as a control parameter while having zero or certain discrete values of the current. We address a large class of systems, including finite graphene flakes, and obtain analytic solutions for how the gate wave function controls the transistor.

Modeling channel interference in an orbital angular momentum-multiplexed laser link

NASA Astrophysics Data System (ADS)

Anguita, Jaime A.; Neifeld, Mark A.; Vasic, Bane V.

2009-08-01

We study the effects of optical turbulence on the energy crosstalk among constituent orbital angular momentum (OAM) states in a vortex-based multi-channel laser communication link and determine channel interference in terms of turbulence strength and OAM state separation. We characterize the channel interference as a function of C2n and transmit OAM state, and propose probability models to predict the random fluctuations in the received signals for such architecture. Simulations indicate that turbulence-induced channel interference is mutually correlated across receive channels.

Effects of additional interfering signals on adaptive array performance

NASA Technical Reports Server (NTRS)

Moses, Randolph L.

1989-01-01

The effects of additional interference signals on the performance of a fully adaptive array are considered. The case where the number of interference signals exceeds the number of array degrees of freedom is addressed. It is shown how performance is affected as a function of the number of array elements, the number of interference signals, and the directivity of the array antennas. By using directive auxiliary elements, the performance of the array can be as good as the performance when the additional interference signals are not present.

Connectivity, non-random extinction and ecosystem function in experimental metacommunities.

PubMed

Staddon, Philip; Lindo, Zoë; Crittenden, Peter D; Gilbert, Francis; Gonzalez, Andrew

2010-05-01

The spatial insurance hypothesis indicates that connectivity is an important attribute of natural ecosystems that sustains both biodiversity and ecosystem function. We tested the hypothesis by measuring the impact of manipulating connectivity in experimental metacommunties of a natural and diverse microecosystem. Isolation led to the extinction of large-bodied apex predators, subsequently followed by increases in prey species abundance. This trophic cascade was associated with significantly altered carbon and nitrogen fluxes in fragmented treatments. The ecosystem impacts were characteristic of a function debt because they persisted for several generations after the initial loss of connectivity. Local extinctions and disruption of ecosystem processes were mitigated, and even reversed, by the presence of corridors in the connected metacommunities, although these beneficial effects were unexpectedly delayed. We hypothesized that corridors maintained grazer movement between fragments, which enhanced microbial activity, and decomposition in comparison to isolated fragments. Our results indicate that knowledge of habitat connectivity and spatial processes is essential to understand the magnitude and timing of ecosystem perturbation in fragmented landscapes.

Fast metastable fragments produced by dissociative excitation of carbonyl sulfide

NASA Technical Reports Server (NTRS)

Van Brunt, R. J.; Mumma, M. J.

1975-01-01

Dissociative excitation of OCS by electron impact has been studied using the method of translational spectroscopy. Time-of-flight distributions and excitation functions of the fast metastable fragments have been measured. The results are compared with similar measurements on CO2 and show that a variety of metastable fragments including CO(a 3Pi), S(5S), O(5S) as well as long-lived high-lying atomic and molecular Rydberg fragments can contribute to dissociation.

Differential contributions of Caenorhabditis elegans histone deacetylases to huntingtin polyglutamine toxicity.

PubMed

Bates, Emily A; Victor, Martin; Jones, Adriana K; Shi, Yang; Hart, Anne C

2006-03-08

Expansion of a polyglutamine tract in the huntingtin protein causes neuronal degeneration and death in Huntington's disease patients, but the molecular mechanisms underlying polyglutamine-mediated cell death remain unclear. Previous studies suggest that expanded polyglutamine tracts alter transcription by sequestering glutamine rich transcriptional regulatory proteins, thereby perturbing their function. We tested this hypothesis in Caenorhabditis elegans neurons expressing a human huntingtin fragment with an expanded polyglutamine tract (Htn-Q150). Loss of function alleles and RNA interference (RNAi) were used to examine contributions of C. elegans cAMP response element-binding protein (CREB), CREB binding protein (CBP), and histone deacetylases (HDACs) to polyglutamine-induced neurodegeneration. Deletion of CREB (crh-1) or loss of one copy of CBP (cbp-1) enhanced polyglutamine toxicity in C. elegans neurons. Loss of function alleles and RNAi were then used to systematically reduce function of each C. elegans HDAC. Generally, knockdown of individual C. elegans HDACs enhanced Htn-Q150 toxicity, but knockdown of C. elegans hda-3 suppressed toxicity. Neuronal expression of hda-3 restored Htn-Q150 toxicity and suggested that C. elegans HDAC3 (HDA-3) acts within neurons to promote degeneration in response to Htn-Q150. Genetic epistasis experiments suggested that HDA-3 and CRH-1 (C. elegans CREB homolog) directly oppose each other in regulating transcription of genes involved in polyglutamine toxicity. hda-3 loss of function failed to suppress increased neurodegeneration in hda-1/+;Htn-Q150 animals, indicating that HDA-1 and HDA-3 have different targets with opposing effects on polyglutamine toxicity. Our results suggest that polyglutamine expansions perturb transcription of CREB/CBP targets and that specific targeting of HDACs will be useful in reducing associated neurodegeneration.

Ribonucleic acid interference (RNAi) Technology for control of Asian citrus psyllid - You Tube

USDA-ARS?s Scientific Manuscript database

RNAi, Ribonucleic acid interference, function and application are described to bring a better understanding of how this emerging technology is providing environmentally friendly, non-transgenic, insect pest control to the citrus industry....

Long-term habitual physical activity is associated with lower distractibility in a Stroop interference task in aging: Behavioral and ERP evidence.

PubMed

Gajewski, Patrick D; Falkenstein, Michael

2015-08-01

Aging is associated with compromised executive control functions. Several lines of evidence point to beneficial effects of physical activity on cognition which indicate that regular physical activity may counteract the age-related decline of some executive functions. Here, we investigate the effects of lifelong physical activity (about 50 years) on interference processing in two matched groups of 20 physically high active and 20 low active healthy older men using event-related potentials (ERPs). In a low interference block of the Stroop task, participants had to indicate the meaning of color-words, while color was either compatible or incompatible with the meaning. In the high interference block, participants were asked to respond according to the ink color of the word and to ignore its meaning. Physically active seniors showed faster reaction times, lower individual variability in reaction times, and higher accuracy compared to low active seniors, particularly in the high interference block. This result was confirmed in the classic paper-and-pencil version of the Stroop task showing higher interference score in the low active than high active individuals. ERPs revealed a shorter latency of the P2 and generally more negative amplitudes of the fronto-central N2 and N450 components in the high active group compared to the low active group. The amount of interference was negatively correlated with objectively measured fitness and self-reported physical activity. The positive effect of physical fitness on interference processing in the behavioral data was related to N2 and N450 amplitudes. Taken together, this suggests that seniors reporting long-term physical activity may exhibit generally enhanced activity in the frontal cortex which enables more efficient interference resolution in the Stroop task. Copyright © 2015 Elsevier Inc. All rights reserved.

Quantum erasure in the near-field

NASA Astrophysics Data System (ADS)

Walborn, S. P.

2018-05-01

The phenomenon of quantum erasure has shed light on the nature of wave-particle duality and quantum complementarity. A number of quantum erasers have been realized using the far-field diffraction of photons from a Young double-slit apparatus. By marking the path of a photon using an additional degree of freedom, the usual Young interference pattern is destroyed. An appropriate measurement of the system marking the photon’s path allows one to recover the interference pattern. Here quantum erasure is considered in the context of near-field diffraction. To observe interference in the near-field requires the use of two periodic wave functions, so that the usual ‘which way’ marker then becomes a ‘which-wave function’ marker. We determine the propagation distances for which quantum erasure, or more generally the observation of interference between the two periodic wave functions, can be observed. The meaning of wave and particle-like properties in this scenario is discussed. These results could lead to quantum eraser experiments with material particles, for which interference effects are more readily observed in the near-field rather than the far-field.

Inhibition of cardiac inward rectifier currents by cationic amphiphilic drugs.

PubMed

van der Heyden, M A G; Stary-Weinzinger, A; Sanchez-Chapula, J A

2013-09-01

Cardiac inward rectifier channels belong to three different classes of the KIR channel protein family. The KIR2.x proteins generate the classical inward rectifier current, IK1, while KIR3 and KIR6 members are responsible for the acetylcholine responsive and ATP sensitive inward rectifier currents IKAch and IKATP, respectively. Aberrant function of these channels has been correlated with severe cardiac arrhythmias, indicating their significant contribution to normal cardiac electrophysiology. A common feature of inward rectifier channels is their dependence on the lipid phosphatidyl-4,5-bisphospate (PIP2) interaction for functional activity. Cationic amphiphilic drugs (CADs) are one of the largest classes of pharmaceutical compounds. Several widely used CADs have been associated with inward rectifier current disturbances, and recent evidence points to interference of the channel-PIP2 interaction as the underlying mechanism of action. Here, we will review how six of these well known drugs, used for treatment in various different conditions, interfere in cardiac inward rectifier functioning. In contrast, KIR channel inhibition by the anionic anesthetic thiopental is achieved by a different mechanism of channel-PIP2 interference. We will discuss the latest basic science insights of functional inward rectifier current characteristics, recently derived KIR channel structures and specific PIP2-receptor interactions at the molecular level and provide insight in how these drugs interfere in the structure-function relationships.

Sperm DNA fragmentation: mechanisms of origin, impact on reproductive outcome, and analysis.

PubMed

Sakkas, Denny; Alvarez, Juan G

2010-03-01

To review the mechanisms responsible for DNA fragmentation in human sperm, including those occurring during spermatogenesis and transport through the reproductive tract. The mechanisms examined include: apoptosis in the seminiferous tubule epithelium, defects in chromatin remodeling during the process of spermiogenesis, oxygen radical-induced DNA damage during sperm migration from the seminiferous tubules to the epididymis, the activation of sperm caspases and endonucleases, damage induced by chemotherapy and radiotherapy, and the effect of environmental toxicants. The different tests currently used for sperm DNA fragmentation analysis and the factors that determine the predictive value of sperm DNA fragmentation testing and their implications in the diagnosis and treatment of infertility are also discussed. Finally, we also scrutinize how the presence in the embryonic genome of DNA strand breaks or modifications of DNA nucleotides inherited from the paternal genome could impact the embryo and offspring. In particular we discuss how abnormal sperm could be dealt with by the oocyte and how sperm DNA abnormalities, which have not been satisfactorily repaired by the oocyte after fertilization, may interfere with normal embryo and fetal development. Sperm DNA can be modified through various mechanisms. The integrity of the paternal genome is therefore of paramount importance in the initiation and maintenance of a viable pregnancy both in a natural conception and in assisted reproduction. The need to diagnose sperm at a nuclear level is an area that needs further understanding so that we can improve treatment of the infertile couple. Copyright 2010 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Tests of a Structural Theory of the Memory Trace.

ERIC Educational Resources Information Center

Jones, Gregory V.

1978-01-01

Jones (1976) has shown that the memory trace resulting from the viewing of a picture corresponds to a "fragment" of that picture. This research shows that the fragmentation hypothesis also correctly represents the recall of memories derived from sentences, i.e., the functional unit of memory, the mnemonic trace, is a fragment of the original item.…

The fragmentation of 510 MeV/nucleon iron-56 in polyethylene. I. Fragment fluence spectra

NASA Technical Reports Server (NTRS)

Zeitlin, C.; Miller, J.; Heilbronn, L.; Frankel, K.; Gong, W.; Schimmerling, W.

1996-01-01

The fragmentation of 510 MeV/nucleon iron ions in several thicknesses of polyethylene has been measured. Non-interacting primary beam particles and fragments have been identified and their LETs calculated by measuring ionization energy loss in a stack of silicon detectors. Fluences, normalized to the incident beam intensity and corrected for detector effects, are presented for each fragment charge and target. Histograms of fluence as a function of LET are also presented. Some implications of these data for measurements of the biological effects of heavy ions are discussed.

Discrete interference modeling via boolean algebra.

PubMed

Beckhoff, Gerhard

2011-01-01

Two types of boolean functions are considered, the locus function of n variables, and the interval function of ν = n - 1 variables. A 1-1 mapping is given that takes elements (cells) of the interval function to antidual pairs of elements in the locus function, and vice versa. A set of ν binary codewords representing the intervals are defined and used to generate the codewords of all genomic regions. Next a diallelic three-point system is reviewed in the light of boolean functions, which leads to redefining complete interference by a logic function. Together with the upper bound of noninterference already defined by a boolean function, it confines the region of interference. Extensions of these two functions to any finite number of ν are straightforward, but have been also made in terms of variables taken from the inclusion-exclusion principle (expressing "at least" and "exactly equal to" a decimal integer). Two coefficients of coincidence for systems with more than three loci are defined and discussed, one using the average of several individual coefficients and the other taking as coefficient a real number between zero and one. Finally, by way of a malfunction of the mod-2 addition, it is shown that a four-point system may produce two different functions, one of which exhibiting loss of a class of odd recombinants.

Effects of growth form and functional traits on response of woody plants to clearing and fragmentation of subtropical rainforest.

PubMed

Kooyman, R M; Zanne, A E; Gallagher, R V; Cornwell, W; Rossetto, M; O'Connor, P; Parkes, E A; Catterall, C F; Laffan, S W; Lusk, C H

2013-12-01

The conservation implications of large-scale rainforest clearing and fragmentation on the persistence of functional and taxonomic diversity remain poorly understood. If traits represent adaptive strategies of plant species to particular circumstances, the expectation is that the effect of forest clearing and fragmentation will be affected by species functional traits, particularly those related to dispersal. We used species occurrence data for woody plants in 46 rainforest patches across 75,000 ha largely cleared of forest by the early 1900s to determine the combined effects of area reduction, fragmentation, and patch size on the taxonomic structure and functional diversity of subtropical rainforest. We compiled species trait values for leaf area, seed dry mass, wood density, and maximum height and calculated species niche breadths. Taxonomic structure, trait values (means, ranges), and the functional diversity of assemblages of climbing and free-standing plants in remnant patches were quantified. Larger rainforest patches had higher species richness. Species in smaller patches were taxonomically less related than species in larger patches. Free-standing plants had a high percentage of frugivore dispersed seeds; climbers had a high proportion of small wind-dispersed seeds. Connections between the patchy spatial distribution of free-standing species, larger seed sizes, and dispersal syndrome were weak. Assemblages of free-standing plants in patches showed more taxonomic and spatial structuring than climbing plants. Smaller isolated patches retained relatively high functional diversity and similar taxonomic structure to larger tracts of forest despite lower species richness. The response of woody plants to clearing and fragmentation of subtropical rainforest differed between climbers and slow-growing mature-phase forest trees but not between climbers and pioneer trees. Quantifying taxonomic structure and functional diversity provides an improved basis for conservation planning and management by elucidating the effects of forest-area reduction and fragmentation. Efectos de la Forma de Crecimiento y Atributos Funcionales en la Respuesta de Plantas Leñosas al Desmonte y Fragmentación de Bosque Lluvioso Subtropical. © 2013 Society for Conservation Biology.

Quantifying the linear and nonlinear relations between the urban form fragmentation and the carbon emission distribution

NASA Astrophysics Data System (ADS)

Zuo, S.; Dai, S.; Ren, Y.; Yu, Z.

2017-12-01

Scientifically revealing the spatial heterogeneity and the relationship between the fragmentation of urban landscape and the direct carbon emissions are of great significance to land management and urban planning. In fact, the linear and nonlinear effects among the various factors resulted in the carbon emission spatial map. However, there is lack of the studies on the direct and indirect relations between the carbon emission and the city functional spatial form changes, which could not be reflected by the land use change. The linear strength and direction of the single factor could be calculated through the correlation and Geographically Weighted Regression (GWR) analysis, the nonlinear power of one factor and the interaction power of each two factors could be quantified by the Geodetector analysis. Therefore, we compared the landscape fragmentation metrics of the urban land cover and functional district patches to characterize the landscape form and then revealed the relations between the landscape fragmentation level and the direct the carbon emissions based on the three methods. The results showed that fragmentation decreased and the fragmented patches clustered at the coarser resolution. The direct CO2 emission density and the population density increased when the fragmentation level aggregated. The correlation analysis indicated the weak linear relation between them. The spatial variation of GWR output indicated the fragmentation indicator (MESH) had the positive influence on the carbon emission located in the relatively high emission region, and the negative effects regions accounted for the small part of the area. The Geodetector which explores the nonlinear relation identified the DIVISION and MESH as the most powerful direct factor for the land cover patches, NP and PD for the functional district patches, and the interactions between fragmentation indicator (MESH) and urban sprawl metrics (PUA and DIS) had the greatly increased explanation powers on the urban carbon emission. Overall, this study provides a framework to understand the relation between the urban landscape fragmentation and the carbon emission for the low carbon city construction planning in the other cities.

Mechanism of organic aerosol formation and aging: Role of the precursor carbon skeleton

NASA Astrophysics Data System (ADS)

Hunter, J. F.; Carrasquillo, A. J.; Daumit, K. E.; Cross, E. S.; Worsnop, D. R.; Kroll, J. H.

2012-12-01

Oxidative aging of organic aerosol consists of a complex set of reactions coupled with gas-particle partitioning processes. Functionalization reactions involve adding oxygen containing functional groups onto a molecule, leading to reduced vapor pressures and promoting aerosol formation. In fragmentation reactions carbon-carbon bonds are broken as oxygen containing functional groups are added, which generally splits the parent molecule into two smaller and more volatile products. The initial structure of an aerosol-forming precursor molecule may influence what chemistry will occur both by changing the branching between fragmentation and functionalization processes as well as changing the effects of those processes. The fate of early generation oxidation products upon further aging is dependent on this initial chemistry, leading to a persistent effect of the precursor carbon skeleton. Aging experiments have been conducted using a high NOx smog chamber based aging technique. Long residence times and modestly elevated OH concentrations lead to typical maximum OH exposure of 3e11 molecule*seconds/cc, approaching several days equivalent exposure to ambient OH concentrations. A broad set of linear, branched and cyclic aliphatic hydrocarbons has been oxidized to determine the effects of carbon skeleton on the relative importance of fragmentation and functionalization and impacts on aerosol formation chemistry. Relative degree of fragmentation and functionalization is constrained by mass spectrometry of both the gas and particle phase. Measurements of the aerosol oxygen content and mass yield are reported, and structural effects on these properties are determined. Degree of unsaturation is hypothesized to have a significant impact on the effect of fragmentation reactions and to promote additional aerosol formation, extended aging and more oxygenated aerosol.

An update on mobile phones interference with medical devices.

PubMed

Mahmoud Pashazadeh, Ali; Aghajani, Mahdi; Nabipour, Iraj; Assadi, Majid

2013-10-01

Mobile phones' electromagnetic interference with medical devices is an important issue for the medical safety of patients who are using life-supporting medical devices. This review mainly focuses on mobile phones' interference with implanted medical devices and with medical equipment located in critical areas of hospitals. A close look at the findings reveals that mobile phones may adversely affect the functioning of medical devices, and the specific effect and the degree of interference depend on the applied technology and the separation distance. According to the studies' findings and the authors' recommendations, besides mitigating interference, using mobile phones at a reasonable distance from medical devices and developing technology standards can lead to their effective use in hospital communication systems.

Ten-Year Follow-Up of a Fragment Reattachment to an Anterior Tooth: A Conservative Approach.

PubMed

Mendes, Luiz; Laxe, Laisa; Passos, Leandro

2017-01-01

This report describes the 10-year follow-up data of a patient who underwent fragment reattachment to the maxillary central incisor after coronal fracture with pulp exposure as well as the procedures followed for functional and esthetic adjustments. A 9-year-old female patient presented at the clinic of dentistry at the State University of Rio de Janeiro with a coronal fracture and pulp exposure of the right maxillary central incisor that had occurred immediately after an accident. The intact tooth fragment was recovered at the accident site and stored in milk. The treatment plan followed was to perform direct pulp capping and tooth fragment reattachment. When the patient was 14 years old, adhesion between fragment and remaining tooth was lost, and fragment reattachment was performed. Five years later, the same tooth presented clinical discoloration and absence of sensitivity during pulp vitality tests. Subsequently, a new treatment plan was formulated, which included endodontic treatment, followed by nonvital tooth bleaching and light-cured composite resin restoration. An esthetic and natural-looking restoration was achieved. Tooth fragment reattachment is not a temporary restorative technique and requires functional and esthetic adjustments over time to maintain the biomimetic characteristics of traumatized anterior teeth and predictable outcomes.

Ten-Year Follow-Up of a Fragment Reattachment to an Anterior Tooth: A Conservative Approach

PubMed Central

Mendes, Luiz; Laxe, Laisa

2017-01-01

This report describes the 10-year follow-up data of a patient who underwent fragment reattachment to the maxillary central incisor after coronal fracture with pulp exposure as well as the procedures followed for functional and esthetic adjustments. A 9-year-old female patient presented at the clinic of dentistry at the State University of Rio de Janeiro with a coronal fracture and pulp exposure of the right maxillary central incisor that had occurred immediately after an accident. The intact tooth fragment was recovered at the accident site and stored in milk. The treatment plan followed was to perform direct pulp capping and tooth fragment reattachment. When the patient was 14 years old, adhesion between fragment and remaining tooth was lost, and fragment reattachment was performed. Five years later, the same tooth presented clinical discoloration and absence of sensitivity during pulp vitality tests. Subsequently, a new treatment plan was formulated, which included endodontic treatment, followed by nonvital tooth bleaching and light-cured composite resin restoration. An esthetic and natural-looking restoration was achieved. Tooth fragment reattachment is not a temporary restorative technique and requires functional and esthetic adjustments over time to maintain the biomimetic characteristics of traumatized anterior teeth and predictable outcomes. PMID:28740741

Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals.

PubMed

Sharma, Upasna; Conine, Colin C; Shea, Jeremy M; Boskovic, Ana; Derr, Alan G; Bing, Xin Y; Belleannee, Clemence; Kucukural, Alper; Serra, Ryan W; Sun, Fengyun; Song, Lina; Carone, Benjamin R; Ricci, Emiliano P; Li, Xin Z; Fauquier, Lucas; Moore, Melissa J; Sullivan, Robert; Mello, Craig C; Garber, Manuel; Rando, Oliver J

2016-01-22

Several recent studies link parental environments to phenotypes in subsequent generations. In this work, we investigate the mechanism by which paternal diet affects offspring metabolism. Protein restriction in mice affects small RNA (sRNA) levels in mature sperm, with decreased let-7 levels and increased amounts of 5' fragments of glycine transfer RNAs (tRNAs). In testicular sperm, tRNA fragments are scarce but increase in abundance as sperm mature in the epididymis. Epididymosomes (vesicles that fuse with sperm during epididymal transit) carry RNA payloads matching those of mature sperm and can deliver RNAs to immature sperm in vitro. Functionally, tRNA-glycine-GCC fragments repress genes associated with the endogenous retroelement MERVL, in both embryonic stem cells and embryos. Our results shed light on sRNA biogenesis and its dietary regulation during posttesticular sperm maturation, and they also link tRNA fragments to regulation of endogenous retroelements active in the preimplantation embryo. Copyright © 2016, American Association for the Advancement of Science.

Albumin modification and fragmentation in renal disease.

PubMed

Donadio, Carlo; Tognotti, Danika; Donadio, Elena

2012-02-18

Albumin is the most important antioxidant substance in plasma and performs many physiological functions. Furthermore, albumin is the major carrier of endogenous molecules and exogenous ligands. This paper reviews the importance of post-translational modifications of albumin and fragments thereof in patients with renal disease. First, current views and controversies on renal handling of proteins, mainly albumin, will be discussed. Post-translational modifications, namely the fragmentation of albumin found with proteomic techniques in nephrotic patients, diabetics, and ESRD patients will be presented and discussed. It is reasonable to hypothesize that proteolytic fragmentation of serum albumin is due to a higher susceptibility to proteases, induced by oxidative stress. The clinical relevance of the fragmentation of albumin has not yet been established. These modifications could affect some physiological functions of albumin and have a patho-physiological role in uremic syndrome. Proteomic analysis of serum allows the identification of over-expressed proteins and can detect post-translational modifications of serum proteins, hitherto hidden, using standard laboratory techniques. Copyright © 2011 Elsevier B.V. All rights reserved.

Neuroimaging of response interference in twins concordant or discordant for inattention and hyperactivity symptoms

PubMed Central

van ’t Ent, D.; van Beijsterveldt, C.E.M.; Derks, E.M.; Hudziak, J.J.; Veltman, D.J.; Todd, R.D.; Boomsma, D.I.; De Geus, E.J.C.

2009-01-01

Attention deficit hyperactivity disorder (ADHD) is to a large extent influenced by genetic factors, but environmental influences are considered important as well. To distinguish between functional brain changes underlying primarily genetically and environmentally mediated ADHD, we used functional MRI to compare response interference in monozygotic twins highly concordant or discordant for attention problems (AP). AP scores were assessed longitudinally with the Child Behavior Check List attention problem scale (CBCL-AP). Response interference was measured during two executive function paradigms; a color-word Stroop and a flanker task. The neuroimaging results indicated that, across the entire sample, children with high CBCL-AP scores, relative to children with low CBCL-AP scores, showed decreased activation to response interference in dorsolateral prefrontal, parietal and temporal brain regions. Increased activation was noted in the premotor cortex and regions associated with visual selective attention processing, possibly reflecting compensatory mechanisms to maintain task performance. Specific comparisons of high and low scoring concordant twin pairs suggest that AP of genetic origin was characterized by decreased activation of the left dorsolateral prefrontal cortex during the Stroop task and right parietal lobe during the flanker task. In contrast, comparison of twins from discordant monozygotic pairs, suggest that AP of environmental origin was characterized by decreased activation in left and right temporal lobe areas, but only during Stroop interference. The finding of distinct brain activation changes to response interference in inattention/hyperactivity of ‘genetic’ versus ‘environmental’ origin, indicate that genetic and environmental risk factors for attention/hyperactivity problems affect the brain in different ways. PMID:19409224

The Conjugation-Specific Die5 Protein Is Required for Development of the Somatic Nucleus in both Paramecium and Tetrahymena▿

PubMed Central

Matsuda, Atsushi; Shieh, Annie Wan-Yi; Chalker, Douglas L.; Forney, James D.

2010-01-01

Development in ciliated protozoa involves extensive genome reorganization within differentiating macronuclei, which shapes the somatic genome of the next vegetative generation. Major events of macronuclear differentiation include excision of internal eliminated sequences (IESs), chromosome fragmentation, and genome amplification. Proteins required for these events include those with homology throughout eukaryotes as well as proteins apparently unique to ciliates. In this study, we identified the ciliate-specific Defective in IES Excision 5 (DIE5) genes of Paramecium tetraurelia (PtDIE5) and Tetrahymena thermophila (TtDIE5) as orthologs that encode nuclear proteins expressed exclusively during development. Abrogation of PtDie5 protein (PtDie5p) function by RNA interference (RNAi)-mediated silencing or TtDie5p by gene disruption resulted in the failure of developing macronuclei to differentiate into new somatic nuclei. Tetrahymena ΔDIE5 cells arrested late in development and failed to complete genome amplification, whereas RNAi-treated Paramecium cells highly amplified new macronuclear DNA before the failure in differentiation, findings that highlight clear differences in the biology of these distantly related species. Nevertheless, IES excision and chromosome fragmentation failed to occur in either ciliate, which strongly supports that Die5p is a critical player in these processes. In Tetrahymena, loss of zygotic expression during development was sufficient to block nuclear differentiation. This observation, together with the finding that knockdown of Die5p in Paramecium still allows genome amplification, indicates that this protein acts late in macronuclear development. Even though DNA rearrangements in these two ciliates look to be quite distinct, analysis of DIE5 establishes the action of a conserved mechanism within the genome reorganization pathway. PMID:20495055

The conjugation-specific Die5 protein is required for development of the somatic nucleus in both Paramecium and Tetrahymena.

PubMed

Matsuda, Atsushi; Shieh, Annie Wan-Yi; Chalker, Douglas L; Forney, James D

2010-07-01

Development in ciliated protozoa involves extensive genome reorganization within differentiating macronuclei, which shapes the somatic genome of the next vegetative generation. Major events of macronuclear differentiation include excision of internal eliminated sequences (IESs), chromosome fragmentation, and genome amplification. Proteins required for these events include those with homology throughout eukaryotes as well as proteins apparently unique to ciliates. In this study, we identified the ciliate-specific Defective in IES Excision 5 (DIE5) genes of Paramecium tetraurelia (PtDIE5) and Tetrahymena thermophila (TtDIE5) as orthologs that encode nuclear proteins expressed exclusively during development. Abrogation of PtDie5 protein (PtDie5p) function by RNA interference (RNAi)-mediated silencing or TtDie5p by gene disruption resulted in the failure of developing macronuclei to differentiate into new somatic nuclei. Tetrahymena DeltaDIE5 cells arrested late in development and failed to complete genome amplification, whereas RNAi-treated Paramecium cells highly amplified new macronuclear DNA before the failure in differentiation, findings that highlight clear differences in the biology of these distantly related species. Nevertheless, IES excision and chromosome fragmentation failed to occur in either ciliate, which strongly supports that Die5p is a critical player in these processes. In Tetrahymena, loss of zygotic expression during development was sufficient to block nuclear differentiation. This observation, together with the finding that knockdown of Die5p in Paramecium still allows genome amplification, indicates that this protein acts late in macronuclear development. Even though DNA rearrangements in these two ciliates look to be quite distinct, analysis of DIE5 establishes the action of a conserved mechanism within the genome reorganization pathway.

Evaluating Landscape Options for Corridor Restoration between Giant Panda Reserves

PubMed Central

Wang, Fang; McShea, William J.; Wang, Dajun; Li, Sheng; Zhao, Qing; Wang, Hao; Lu, Zhi

2014-01-01

The establishment of corridors can offset the negative effects of habitat fragmentation by connecting isolated habitat patches. However, the practical value of corridor planning is minimal if corridor identification is not based on reliable quantitative information about species-environment relationships. An example of this need for quantitative information is planning for giant panda conservation. Although the species has been the focus of intense conservation efforts for decades, most corridor projects remain hypothetical due to the lack of reliable quantitative researches at an appropriate spatial scale. In this paper, we evaluated a framework for giant panda forest corridor planning. We linked our field survey data with satellite imagery, and conducted species occupancy modelling to examine the habitat use of giant panda within the potential corridor area. We then conducted least-cost and circuit models to identify potential paths of dispersal across the landscape, and compared the predicted cost under current conditions and alternative conservation management options considered during corridor planning. We found that due to giant panda's association with areas of low elevation and flat terrain, human infrastructures in the same area have resulted in corridor fragmentation. We then identified areas with high potential to function as movement corridors, and our analysis of alternative conservation scenarios showed that both forest/bamboo restoration and automobile tunnel construction would significantly improve the effectiveness of corridor, while residence relocation would not significantly improve corridor effectiveness in comparison with the current condition. The framework has general value in any conservation activities that anticipate improving habitat connectivity in human modified landscapes. Specifically, our study suggested that, in this landscape, automobile tunnels are the best means to remove current barriers to giant panda movements caused by anthropogenic interferences. PMID:25133757

Evaluating landscape options for corridor restoration between giant panda reserves.

PubMed

Wang, Fang; McShea, William J; Wang, Dajun; Li, Sheng; Zhao, Qing; Wang, Hao; Lu, Zhi

2014-01-01

The establishment of corridors can offset the negative effects of habitat fragmentation by connecting isolated habitat patches. However, the practical value of corridor planning is minimal if corridor identification is not based on reliable quantitative information about species-environment relationships. An example of this need for quantitative information is planning for giant panda conservation. Although the species has been the focus of intense conservation efforts for decades, most corridor projects remain hypothetical due to the lack of reliable quantitative researches at an appropriate spatial scale. In this paper, we evaluated a framework for giant panda forest corridor planning. We linked our field survey data with satellite imagery, and conducted species occupancy modelling to examine the habitat use of giant panda within the potential corridor area. We then conducted least-cost and circuit models to identify potential paths of dispersal across the landscape, and compared the predicted cost under current conditions and alternative conservation management options considered during corridor planning. We found that due to giant panda's association with areas of low elevation and flat terrain, human infrastructures in the same area have resulted in corridor fragmentation. We then identified areas with high potential to function as movement corridors, and our analysis of alternative conservation scenarios showed that both forest/bamboo restoration and automobile tunnel construction would significantly improve the effectiveness of corridor, while residence relocation would not significantly improve corridor effectiveness in comparison with the current condition. The framework has general value in any conservation activities that anticipate improving habitat connectivity in human modified landscapes. Specifically, our study suggested that, in this landscape, automobile tunnels are the best means to remove current barriers to giant panda movements caused by anthropogenic interferences.

The use of fluorescent intrabodies to detect endogenous gankyrin in living cancer cells

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

Rinaldi, Anne-Sophie; Freund, Guillaume; Desplancq, Dominique

2013-04-01

Expression of antibody fragments in mammalian cells (intrabodies) is used to probe the target protein or interfere with its biological function. We previously described the in vitro characterisation of a single-chain Fv (scFv) antibody fragment (F5) isolated from an intrabody library that binds to the oncoprotein gankyrin (GK) in solution. Here, we have isolated several other scFvs that interact with GK in the presence of F5 and tested whether they allow, when fused to fluorescent proteins, to detect by FRET endogenous GK in living cells. The binding of pairs of scFvs to GK was analysed by gel filtration and themore » ability of each scFv to mediate nuclear import/export of GK was determined. Binding between scFv-EGFP and RFP-labelled GK in living cells was detected by fluorescence lifetime imaging microscopy (FLIM). After co-transfection of two scFvs fused to EGFP and RFP, respectively, which form a tri-molecular complex with GK in vitro, FRET signal was measured. This system allowed us to observe that GK is monomeric and distributed throughout the cytoplasm and nucleus of several cancer cell lines. Our results show that pairs of fluorescently labelled intrabodies can be monitored by FLIM–FRET microscopy and that this technique allows the detection of lowly expressed endogenous proteins in single living cells. Highlights: ► Endogenous GK in living cells was targeted with pairs of fluorescently-tagged scFvs. ► Tri-molecular complexes containing two scFvs and one molecule GK were formed. ► GK was detected using fluorescence lifetime-based FRET imaging. ► GK is monomeric and homogeneously distributed in several cancer cell lines. ► This technique may have many applications in live-cell imaging of endogenous proteins.« less

Extraction of jet properties from two particle azimuthal correlations in proton-proton and gold+gold collisions at center of mass energy = 200 GeV

NASA Astrophysics Data System (ADS)

Constantin, Paul

Two particle azimuthal correlation functions measured in pp and AuAu collisions at sNN = 200 GeV at midrapidity with the central arms of the PHENIX detector are analyzed in order to extract the properties of hadronic jets produced in QCD vacuum and highly excited QCD media, like the jet shape parameters jT and kT, the jet conditional yields (number of associated hadrons per high pT trigger hadron) and the jet fragmentation function. The analysis of pp data starts with the measurement of the vacuum fragmentation function from which the pT dependence of the mean fragmentation momentum fraction is extracted. We obtain a constant value of = 0.74 +/- 0.02 for pT above 3 GeV/c. Soft (non-perturbative) parton fragmentation becomes significant below 3 GeV/c and the slope of the fragmentation function is pT dependent in this region. Gaussian fits to jet induced azimuthal correlations are employed to measure the mean jet fragmentation transverse momentum <| jTy|> = 359 +/- 11 (stat) +/- 6 (syst) MeV/c and the mean partonic transverse momentum <|k Ty|> = 964 +/- 49 (stat) +/- 16 (syst) MeV/c. The analysis of AuAu data is based on azimuthal correlation functions between charged hadrons in the 1.5--3 GeV/c and 3--5 GeV/c pT regions in five classes of collision centrality. The mean jet fragmentation transverse momentum <|jTy|> is centrality independent and consistent with the value in pp data mentioned above. A strong broadening with the centrality of the extracted mean partonic transverse momentum <|kTy|> (multiplied by ) is observed. This is an important finding because hadronic jet quenching through energy loss is expected to be accompanied by a broadening effect. Another important finding is that the jet conditional yields in both the near (Deltaφ ˜ 0) and away (Deltaφ ˜ pi) regions exhibit a slightly raising trend with centrality. This was also expected to accompany the jet quenching found at higher pT based on simple energy conservation considerations.

In Situ X-Ray Observations of Dendritic Fragmentation During Directional Solidification of a Sn-Bi Alloy

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

Gibbs, John W.; Tourret, Damien; Gibbs, Paul J.

2015-09-25

Dendrite fragmentation is an important phenomenon in microstructural development during solidification. For instance, it plays a key role in initiating the columnar-to-equiaxed transition (CET). Here, we use x-ray radiography to study dendrite fragmentation rate in a Sn-39.5 wt.% Bi alloy during directional solidification. Experiments were performed in which solidification was parallel and anti-parallel to gravity, leading to significantly different fragmentation rates. We quantify the distribution of fragmentation rate as a function of distance from the solidification front, time in the mushy zone, and volume fraction of solid. While the observed fragmentation rate can be high, there is no evidence ofmore » a CET, illustrating that it requires more than just fragmentation to occur.« less

In Situ X-Ray Observations of Dendritic Fragmentation During Directional Solidification of a Sn-Bi Alloy

DOE PAGES

Gibbs, John W.; Tourret, Damien; Gibbs, Paul J.; ...

2015-09-25

Dendrite fragmentation is an important phenomenon in microstructural development during solidification. For instance, it plays a key role in initiating the columnar-to-equiaxed transition (CET). In this paper, we use x-ray radiography to study dendrite fragmentation rate in a Sn-39.5 wt.% Bi alloy during directional solidification. Experiments were performed in which solidification was parallel and anti-parallel to gravity, leading to significantly different fragmentation rates. We quantify the distribution of fragmentation rate as a function of distance from the solidification front, time in the mushy zone, and volume fraction of solid. Finally, while the observed fragmentation rate can be high, there ismore » no evidence of a CET, illustrating that it requires more than just fragmentation to occur.« less

Pifithrin-α provides neuroprotective effects at the level of mitochondria independently of p53 inhibition.

PubMed

Neitemeier, Sandra; Ganjam, Goutham K; Diemert, Sebastian; Culmsee, Carsten

2014-12-01

Impaired mitochondrial integrity and function are key features of intrinsic death pathways in neuronal cells. Therefore, key regulators of intrinsic death pathways acting upstream of mitochondria are potential targets for therapeutic approaches of neuroprotection. The tumor suppressor p53 is a well-established regulator of cellular responses towards different kinds of lethal stress, including oxidative stress. Recent reports suggested that p53 may affect mitochondrial integrity and function through both, transcriptional activation of mitochondria-targeted pro-death proteins and direct effects at the mitochondrial membrane. In the present study, we compared the effects of pharmacological inhibition of p53 by pifithrin-α with those of selective p53 gene silencing by RNA interference. Using MTT assay and real-time cell impedance measurements we confirmed the protective effect of both strategies against glutamate-induced oxidative stress in immortalized mouse hippocampal HT-22 neurons. Further, we observed full restoration of mitochondrial membrane potential and inhibition of glutamate-induced mitochondrial fragmentation by pifithrin-α which was, in contrast, not achieved by p53 gene silencing. Downregulation of p53 by siRNA decreased p53 transcriptional activity and reduced expression levels of p21 mRNA, while pifithrin-α did not affect these endpoints. These results suggest a neuroprotective effect of pifithrin-α which occurred at the level of mitochondria and independently of p53 inhibition.

Semi-inclusive production of two back-to-back hadron pairs in e+e- annihilation revisited

NASA Astrophysics Data System (ADS)

Matevosyan, Hrayr H.; Bacchetta, Alessandro; Boer, Daniël; Courtoy, Aurore; Kotzinian, Aram; Radici, Marco; Thomas, Anthony W.

2018-04-01

The cross section for back-to-back hadron pair production in e+e- annihilation provides access to the dihadron fragmentation functions (DiFF) needed to extract nucleon parton distribution functions from the semi-inclusive deep inelastic scattering (SIDIS) experiments with two detected final state hadrons. Particular attention is given to the so-called interference DiFF (IFF), which makes it possible to extract the transversity parton distribution of the nucleon in the collinear framework. However, previously unnoticed discrepancies were recently highlighted between the definitions of the IFFs appearing in the collinear kinematics when reconstructed from DiFFs entering the unintegrated fully differential cross sections of SIDIS and e+e- annihilation processes. In this work, to clarify this problem we re-derive the fully differential cross section for e+e- annihilation at the leading-twist approximation. We find a mistake in the definition of the kinematics in the original expression that systematically affects a subset of terms and that leads to two significant consequences. First, the discrepancy between the IFF definitions in the cross sections for SIDIS and e+e- annihilation is resolved. Second, the previously derived azimuthal asymmetry for accessing the helicity dependent DiFF G1⊥ in e+e- annihilation vanishes, which explains the nonobservation of this asymmetry in the recent experimental searches by the BELLE collaboration. We discuss the recently proposed alternative option to extract G1⊥.

A Medium-Throughput Single Cell CRISPR-Cas9 Assay to Assess Gene Essentiality.

PubMed

Grassian, A R; Scales, T M E; Knutson, S K; Kuntz, K W; McCarthy, N J; Lowe, C E; Moore, J D; Copeland, R A; Keilhack, H; Smith, J J; Wickenden, J A; Ribich, S

2015-01-01

Target selection for oncology is a crucial step in the successful development of therapeutics. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 editing of specific loci offers an alternative method to RNA interference and small molecule inhibitors for determining whether a cell line is dependent on a specific gene product for proliferation or survival. In our initial studies using CRISPR-Cas9 to verify the dependence on EZH2 activity for proliferation of a SMARCB1/SNF5/INI1 mutant malignant rhabdoid tumor (MRT) cell line, we noted that the initial reduction in proliferation was lost over time. We hypothesized that in the few cells that retain proliferative capacity, at least one allele of EZH2 remains functional. To verify this, we developed an assay to analyze 10s-100s of clonal cell populations for target gene disruption using restriction digest and fluorescent fragment length analyses. Our results clearly show that in cell lines in which EZH2 is essential for proliferation, at least one potentially functional allele of EZH2 is retained in the clones that survive. This assay clearly indicates whether or not a specific gene is essential for survival and/or proliferation in a given cell line. Such data can aid the development of more robust therapeutics by increasing confidence in target selection.

Hippocampal sharp wave-ripple: A cognitive biomarker for episodic memory and planning.

PubMed

Buzsáki, György

2015-10-01

Sharp wave ripples (SPW-Rs) represent the most synchronous population pattern in the mammalian brain. Their excitatory output affects a wide area of the cortex and several subcortical nuclei. SPW-Rs occur during "off-line" states of the brain, associated with consummatory behaviors and non-REM sleep, and are influenced by numerous neurotransmitters and neuromodulators. They arise from the excitatory recurrent system of the CA3 region and the SPW-induced excitation brings about a fast network oscillation (ripple) in CA1. The spike content of SPW-Rs is temporally and spatially coordinated by a consortium of interneurons to replay fragments of waking neuronal sequences in a compressed format. SPW-Rs assist in transferring this compressed hippocampal representation to distributed circuits to support memory consolidation; selective disruption of SPW-Rs interferes with memory. Recently acquired and pre-existing information are combined during SPW-R replay to influence decisions, plan actions and, potentially, allow for creative thoughts. In addition to the widely studied contribution to memory, SPW-Rs may also affect endocrine function via activation of hypothalamic circuits. Alteration of the physiological mechanisms supporting SPW-Rs leads to their pathological conversion, "p-ripples," which are a marker of epileptogenic tissue and can be observed in rodent models of schizophrenia and Alzheimer's Disease. Mechanisms for SPW-R genesis and function are discussed in this review. © 2015 The Authors Hippocampus Published by Wiley Periodicals, Inc.

Using a Recently Developed Self-Report Instrument to Assess Social Anxiety Life Interference in Individuals with Co-occurring Depression: A Known-Groups Analysis

PubMed Central

Garcia, Antonio F.; Acosta, Melina; Osman, Augustine

2017-01-01

Social anxiety is a common condition that often entails substantial adverse impacts on social, educational, and occupational functioning. Moreover, social anxiety often co-occurs with depression, making it difficult to distinguish the unique effects of each condition, which can pose a challenge to effective treatment planning and intervention. Until recently, clinicians have not had access to a validated psychometric instrument that measures the degree of life interference stemming from social anxiety, and that distinguishes life interference associated with social anxiety from that associated with depression. Fortunately, recent work has yielded a novel instrument that combines a measure of social anxiety life interference with a measure of depression life interference, providing a measure that can identify functional disruptions uniquely associated with social anxiety, and that may occur in the presence of comorbid depression. The present article reviews two studies describing the development and psychometric properties of the Social Anxiety and Depression Life Interference Inventory (SADLI-24) and adds to the existing literature by demonstrating the discriminative accuracy of the inventory using a “known-groups” methodology. The article concludes by providing recommendations for the practical application of the SADLI-24 and suggesting future directions for research with the instrument. PMID:28782057

Interference coupling analysis based on a hybrid method: application to a radio telescope system

NASA Astrophysics Data System (ADS)

Xu, Qing-Lin; Qiu, Yang; Tian, Jin; Liu, Qi

2018-02-01

Working in a way that passively receives electromagnetic radiation from a celestial body, a radio telescope can be easily disturbed by external radio frequency interference as well as electromagnetic interference generated by electric and electronic components operating at the telescope site. A quantitative analysis of these interferences must be taken into account carefully for further electromagnetic protection of the radio telescope. In this paper, based on electromagnetic topology theory, a hybrid method that combines the Baum-Liu-Tesche (BLT) equation and transfer function is proposed. In this method, the coupling path of the radio telescope is divided into strong coupling and weak coupling sub-paths, and the coupling intensity criterion is proposed by analyzing the conditions in which the BLT equation simplifies to a transfer function. According to the coupling intensity criterion, the topological model of a typical radio telescope system is established. The proposed method is used to solve the interference response of the radio telescope system by analyzing subsystems with different coupling modes separately and then integrating the responses of the subsystems as the response of the entire system. The validity of the proposed method is verified numerically. The results indicate that the proposed method, compared with the direct solving method, reduces the difficulty and improves the efficiency of interference prediction.

A translocated effector required for Bartonella dissemination from derma to blood safeguards migratory host cells from damage by co-translocated effectors.

PubMed

Okujava, Rusudan; Guye, Patrick; Lu, Yun-Yueh; Mistl, Claudia; Polus, Florine; Vayssier-Taussat, Muriel; Halin, Cornelia; Rolink, Antonius G; Dehio, Christoph

2014-06-01

Numerous bacterial pathogens secrete multiple effectors to modulate host cellular functions. These effectors may interfere with each other to efficiently control the infection process. Bartonellae are Gram-negative, facultative intracellular bacteria using a VirB type IV secretion system to translocate a cocktail of Bartonella effector proteins (Beps) into host cells. Based on in vitro infection models we demonstrate here that BepE protects infected migratory cells from injurious effects triggered by BepC and is required for in vivo dissemination of bacteria from the dermal site of inoculation to blood. Human endothelial cells (HUVECs) infected with a ΔbepE mutant of B. henselae (Bhe) displayed a cell fragmentation phenotype resulting from Bep-dependent disturbance of rear edge detachment during migration. A ΔbepCE mutant did not show cell fragmentation, indicating that BepC is critical for triggering this deleterious phenotype. Complementation of ΔbepE with BepEBhe or its homologues from other Bartonella species abolished cell fragmentation. This cyto-protective activity is confined to the C-terminal Bartonella intracellular delivery (BID) domain of BepEBhe (BID2.EBhe). Ectopic expression of BID2.EBhe impeded the disruption of actin stress fibers by Rho Inhibitor 1, indicating that BepE restores normal cell migration via the RhoA signaling pathway, a major regulator of rear edge retraction. An intradermal (i.d.) model for B. tribocorum (Btr) infection in the rat reservoir host mimicking the natural route of infection by blood sucking arthropods allowed demonstrating a vital role for BepE in bacterial dissemination from derma to blood. While the Btr mutant ΔbepDE was abacteremic following i.d. inoculation, complementation with BepEBtr, BepEBhe or BIDs.EBhe restored bacteremia. Given that we observed a similar protective effect of BepEBhe on infected bone marrow-derived dendritic cells migrating through a monolayer of lymphatic endothelial cells we propose that infected dermal dendritic cells may be involved in disseminating Bartonella towards the blood stream in a BepE-dependent manner.

A Translocated Effector Required for Bartonella Dissemination from Derma to Blood Safeguards Migratory Host Cells from Damage by Co-translocated Effectors

PubMed Central

Okujava, Rusudan; Guye, Patrick; Lu, Yun-Yueh; Mistl, Claudia; Polus, Florine; Vayssier-Taussat, Muriel; Halin, Cornelia; Rolink, Antonius G.; Dehio, Christoph

2014-01-01

Numerous bacterial pathogens secrete multiple effectors to modulate host cellular functions. These effectors may interfere with each other to efficiently control the infection process. Bartonellae are Gram-negative, facultative intracellular bacteria using a VirB type IV secretion system to translocate a cocktail of Bartonella effector proteins (Beps) into host cells. Based on in vitro infection models we demonstrate here that BepE protects infected migratory cells from injurious effects triggered by BepC and is required for in vivo dissemination of bacteria from the dermal site of inoculation to blood. Human endothelial cells (HUVECs) infected with a ΔbepE mutant of B. henselae (Bhe) displayed a cell fragmentation phenotype resulting from Bep-dependent disturbance of rear edge detachment during migration. A ΔbepCE mutant did not show cell fragmentation, indicating that BepC is critical for triggering this deleterious phenotype. Complementation of ΔbepE with BepEBhe or its homologues from other Bartonella species abolished cell fragmentation. This cyto-protective activity is confined to the C-terminal Bartonella intracellular delivery (BID) domain of BepEBhe (BID2.EBhe). Ectopic expression of BID2.EBhe impeded the disruption of actin stress fibers by Rho Inhibitor 1, indicating that BepE restores normal cell migration via the RhoA signaling pathway, a major regulator of rear edge retraction. An intradermal (i.d.) model for B. tribocorum (Btr) infection in the rat reservoir host mimicking the natural route of infection by blood sucking arthropods allowed demonstrating a vital role for BepE in bacterial dissemination from derma to blood. While the Btr mutant ΔbepDE was abacteremic following i.d. inoculation, complementation with BepEBtr, BepEBhe or BIDs.EBhe restored bacteremia. Given that we observed a similar protective effect of BepEBhe on infected bone marrow-derived dendritic cells migrating through a monolayer of lymphatic endothelial cells we propose that infected dermal dendritic cells may be involved in disseminating Bartonella towards the blood stream in a BepE-dependent manner. PMID:24945914

Multisegment nanowire sensors for the detection of DNA molecules.

PubMed

Wang, Xu; Ozkan, Cengiz S

2008-02-01

We describe a novel application for detecting specific single strand DNA sequences using multisegment nanowires via a straightforward surface functionalization method. Nanowires comprising CdTe-Au-CdTe segments are fabricated using electrochemical deposition, and electrical characterization indicates a p-type behavior for the multisegment nanostructures, in a back-to-back Schottky diode configuration. Such nanostructures modified with thiol-terminated probe DNA fragments could function as high fidelity sensors for biomolecules at very low concentration. The gold segment is utilized for functionalization and binding of single strand DNA (ssDNA) fragments while the CdTe segments at both ends serve to modulate the equilibrium Fermi level of the heterojunction device upon hybridization of the complementary DNA fragments (cDNA) to the ssDNA over the Au segment. Employing such multisegment nanowires could lead to the fabrication more sophisticated and high multispecificity biosensors via selective functionalization of individual segments for biowarfare sensing and medical diagnostics applications.

Heavy quarkonium production at collider energies: Factorization and evolution

NASA Astrophysics Data System (ADS)

Kang, Zhong-Bo; Ma, Yan-Qing; Qiu, Jian-Wei; Sterman, George

2014-08-01

We present a perturbative QCD factorization formalism for inclusive production of heavy quarkonia of large transverse momentum, pT at collider energies, including both leading power (LP) and next-to-leading power (NLP) behavior in pT. We demonstrate that both LP and NLP contributions can be factorized in terms of perturbatively calculable short-distance partonic coefficient functions and universal nonperturbative fragmentation functions, and derive the evolution equations that are implied by the factorization. We identify projection operators for all channels of the factorized LP and NLP infrared safe short-distance partonic hard parts, and corresponding operator definitions of fragmentation functions. For the NLP, we focus on the contributions involving the production of a heavy quark pair, a necessary condition for producing a heavy quarkonium. We evaluate the first nontrivial order of evolution kernels for all relevant fragmentation functions, and discuss the role of NLP contributions.

Herpes simplex virus interferes with amyloid precursor protein processing.

PubMed

Shipley, Suzanne J; Parkin, Edward T; Itzhaki, Ruth F; Dobson, Curtis B

2005-08-18

The early events underlying Alzheimer's disease (AD) remain uncertain, although environmental factors may be involved. Work in this laboratory has shown that the combination of herpes simplex virus type 1 (HSV1) in brain and carriage of the APOE-epsilon4 allele of the APOE gene strongly increases the risk of developing AD. The development of AD is thought to involve abnormal aggregation or deposition of a 39-43 amino acid protein--beta amyloid (Abeta)--within the brain. This is cleaved from the much larger transmembranal protein 'amyloid precursor protein' (APP). Any agent able to interfere directly with Abeta or APP metabolism may therefore have the capacity to contribute towards AD. One recent report showed that certain HSV1 glycoprotein peptides may aggregate like Abeta; a second study described a role for APP in transport of virus in squid axons. However to date the effects of acute herpesvirus infection on metabolism of APP in human neuronal-type cells have not been investigated. In order to find if HSV1 directly affects APP and its degradation, we have examined this protein from human neuroblastoma cells (normal and transfected with APP 695) infected with the virus, using Western blotting. We have found that acute HSV1 (and also HSV2) infection rapidly reduces full length APP levels--as might be expected--yet surprisingly markedly increases levels of a novel C-terminal fragment of APP of about 55 kDa. This band was not increased in cells treated with the protein synthesis inhibitor cycloheximide Herpes virus infection leads to rapid loss of full length APP from cells, yet also causes increased levels of a novel 55 kDa C-terminal APP fragment. These data suggest that infection can directly alter the processing of a transmembranal protein intimately linked to the aetiology of AD.

Effects of a Single Night of Postpartum Sleep on Childless Women’s Daytime Functioning

PubMed Central

McBean, Amanda L.; Kinsey, Steven G.; Montgomery-Downs, Hawley E.

2017-01-01

Study Objectives The maternal postpartum period is characterized by sleep fragmentation, which is associated with daytime impairment, mental health disturbances, and changes in melatonin patterns. In addition to sleep fragmentation, women undergo a complex set of physiological and environmental changes upon entering the postpartum period, confounding our understanding of effects of postpartum sleep disturbance. The primary study aim was to understand the basic impact of a single night of postpartum-like sleep fragmentation on sleep architecture, nocturnal melatonin levels, mood, daytime sleepiness, and neurobehavioral performance. Measurements and Results For one week prior to entry into the laboratory, eleven healthy nulliparous women kept a stable sleep-wake schedule (verified via actigraphy). Participants contributed three consecutive nights of laboratory overnight polysomnography: (1) a habituation/sleep disorder screening night; (2) a baseline night; and (3) a sleep fragmentation night, when participants were awakened three times for ~30 min each. Self-reported sleep quality and mood (Profile of Mood States Survey) both decreased significantly after sleep fragmentation compared to baseline measurements. Unexpectedly, daytime sleepiness (Multiple Sleep Latency Test) decreased significantly after sleep fragmentation. Experimental fragmentation had no significant effect on time spent in nocturnal sleep stages, urinary 6-sulphatoxymelatonin concentration, or psychomotor vigilance test performance. Participants continued to provide actigraphy data, and daily PVTs and self-reported sleep quality assessments at home for one week following sleep fragmentation; these assessments did not differ from baseline values. Conclusions While there were no changes in measured physiological components of a single night of postpartum-like experimental sleep fragmentation, there were decreases in self-reported measures of mood and sleep quality. Future research should examine the effects of multiple nights of modeling postpartum-like sleep fragmentation on objective measures of sleep and daytime functioning. PMID:26776447

Using a simulation model to assess risk of false negative point-of-care urinary human chorionic gonadotropin device results due to high-dose hook interference.

PubMed

Milhorn, Denise; Korpi-Steiner, Nichole

2015-02-01

It is unclear if the point-of-care (POC) Clinitest hCG device is subject to high-dose hook interference from physiological concentrations of intact human chorionic gonadotropin (hCG), β-core fragment of hCG (hCGβcf), and hCG free β-subunit (hCGβ) found in urine during pregnancy. We used a simulation model to address this question and related our findings to our institution's pregnant population in order to assess risk for potential false-negative hCG results. The expected distribution of days relative to ovulation during routine POC hCG testing was estimated from 182 patients. Clinitest-Clinitek Status hCG device susceptibility to high-dose hook interference from hCG variants and potential risk of false-negative results as it relates to this population were evaluated by testing increasing concentrations of hCG, hCGβcf, hCGβ as well as urine simulating physiological hCG, hCGβcf and hCGβ concentrations expected during early pregnancy (≤44 days post-ovulation). The Clinitest-Clinitek Status hCG device exhibited high-dose hook interference from hCGβcf alone, but not from hCG, hCGβ, or simulated physiological urinary concentrations of combined hCG, hCGβcf and hCGβ expected during early pregnancy. The majority of our patient population had urinary hCG testing conducted during early pregnancy. The Clinitest-Clinitek Status hCG device is unlikely to exhibit false-negative urinary hCG results due to high-dose hook interference for women in early healthy pregnancy, although additional studies are necessary to determine potential risk in other patient populations. Visual interpretation of POC urinary hCG device results is an important failure mode to consider in risk analyses for erroneous urinary hCG device results. Published by Elsevier Inc.

Self-polarization and directional motility of cytoplasm.

PubMed

Verkhovsky, A B; Svitkina, T M; Borisy, G G

1999-01-14

Directional cell motility implies the presence of a steering mechanism and a functional asymmetry between the front and rear of the cell. How this functional asymmetry arises and is maintained during cell locomotion is, however, unclear. Lamellar fragments of fish epidermal keratocytes, which lack nuclei, microtubules and most organelles, present a simplified, perhaps minimal, system for analyzing this problem because they consist of little other than the motile machinery enclosed by a membrane and yet can move with remarkable speed and persistence. We have produced two types of cellular fragments: discoid stationary fragments and polarized fragments undergoing locomotion. The organization and dynamics of the actin-myosin II system were isotropic in stationary fragments and anisotropic in the moving fragments. To investigate whether the creation of asymmetry could result in locomotion, a transient mechanical stimulus was applied to stationary fragments. The stimulus induced localized contraction and the formation of an actin-myosin II bundle at one edge of the fragment. Remarkably, stimulated fragments started to undergo locomotion and the locomotion and associated anisotropic organization of the actin-myosin II system were sustained after withdrawal of the stimulus. We propose a model in which lamellar cytoplasm is considered a dynamically bistable system capable of existing in a non-polarized or polarized state and interconvertible by mechanical stimulus. The model explains how the anisotropic organization of the lamellum is maintained in the process of locomotion. Polarized locomotion is sustained through a positive-feedback loop intrinsic to the actin-myosin II machinery: anisotropic organization of the machinery drives translocation, which then reinforces the asymmetry of the machinery, favoring further translocation.

Arthropods on plants in a fragmented Neotropical dry forest: a functional analysis of area loss and edge effects.

PubMed

González, Ezequiel; Salvo, Adriana; Valladares, Graciela

2015-02-01

Loss and fragmentation of natural ecosystems are widely recognized as the most important threats to biodiversity conservation, with Neotropical dry forests among the most endangered ecosystems. Area and edge effects are major factors in fragmented landscapes. Here, we examine area and edge effects and their interaction, on ensembles of arthropods associated to native vegetation in a fragmented Chaco Serrano forest. We analyzed family richness and community composition of herbivores, predators, and parasitoids on three native plant species in 12 fragments of varying size and at edge/interior positions. We also looked for indicator families by using Indicator Species Analysis. Loss of family richness with the reduction of forest fragment area was observed for the three functional groups, with similar magnitude. Herbivores were richer at the edges without interaction between edge and area effects, whereas predators were not affected by edge/interior position and parasitoid richness showed an interaction between area and position, with a steeper area slope at the edges. Family composition of herbivore, predator, and parasitoid assemblages was also affected by forest area and/or edge/interior situation. We found three indicator families for large remnants and five for edges. Our results support the key role of forest area for conservation of arthropods taxonomic and functional diversity in a highly threatened region, and emphasize the need to understand the interactions between area and edge effects on such diversity. © 2014 Institute of Zoology, Chinese Academy of Sciences.

Amino and Acetamide Functional Group Effects on the Ionization and Fragmentation of Sugar Chains in Positive-Ion Mass Spectrometry

NASA Astrophysics Data System (ADS)

Yamagaki, Tohru; Sugahara, Kohtaro; Watanabe, Takehiro

2014-01-01

To elucidate the influence of amino (-NH2) and acetamide (-NHCOCH3, -NAc) groups in sugar chains on their ionization and fragmentation, cycloamyloses (cyclodextrins, CyDs) and lacto-oligosaccharide are analyzed by MALDI TOF/TOF and ESI Q-TOF mass spectrometry. CyD derivatives substituted by amino or acetamide groups are ideal analytes to extract the function group effects, which are amino-CyD with one hexosamine (HexNH2) and acetamide-CyD with one N-acetyl hexosamine (HexNAc). Interestingly, the relative ion intensities and isotope-like patterns in their product ion spectra depend on the functional groups and ion forms of sugar chains. Consequently, the results indicate that a proton (H+) localizes on the amino group of the amino sugar, and that the proton (H+) induces their fragmentation. Sodium cation (Na+) attachment is independent from amino group and exerts no influence on their fragmentation patterns in amino group except for mono- and disaccharide fragment ions because there is the possibility of the reducing end effect. In contrast, a sodium cation localizes much more frequently on the acetamide group in acetamide-CyDs because the chemical species with HexNAc are stable. Thus, their ions with HexNAc are abundant. These results are consistent with the fragmentation of lacto-neo- N-tetraose and maltotetraose, suggesting that a sodium cation generally localizes much more frequently on the acetamide group in sugar chains.

Northeastern Regional Forest Fragmentation Assessment: Rationale, Methods, and Comparisons With Other Studies

Treesearch

Andrew Lister; Rachel Riemann; Tonya Lister; Will McWilliams

2005-01-01

Forest fragmentation is thought to impact many biotic and abiotic processes important to ecosystem function. We assessed forest fragmentation in 13 Northeastern States to gain a greater understanding of the trends in and status of this region?s forests. We reclassified and then statistically filtered and updated classified Landsat imagery from the early 1990s, and...

Complexity Reduction in Large Quantum Systems: Fragment Identification and Population Analysis via a Local Optimized Minimal Basis

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

Mohr, Stephan; Masella, Michel; Ratcliff, Laura E.

We present, within Kohn-Sham Density Functional Theory calculations, a quantitative method to identify and assess the partitioning of a large quantum mechanical system into fragments. We then introduce a simple and efficient formalism (which can be written as generalization of other well-known population analyses) to extract, from first principles, electrostatic multipoles for these fragments. The corresponding fragment multipoles can in this way be seen as reliable (pseudo-) observables. By applying our formalism within the code BigDFT, we show that the usage of a minimal set of in-situ optimized basis functions is of utmost importance for having at the same timemore » a proper fragment definition and an accurate description of the electronic structure. With this approach it becomes possible to simplify the modeling of environmental fragments by a set of multipoles, without notable loss of precision in the description of the active quantum mechanical region. Furthermore, this leads to a considerable reduction of the degrees of freedom by an effective coarsegraining approach, eventually also paving the way towards efficient QM/QM and QM/MM methods coupling together different levels of accuracy.« less

Communication: Two-step explosion processes of highly charged fullerene cations C{sub 60}{sup q+} (q = 20–60)

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

Yamazaki, Kaoru; Nakamura, Takashi; Kanno, Manabu

2014-09-28

To establish the fundamental understanding of the fragmentation dynamics of highly positive charged nano- and bio-materials, we carried out on-the-fly classical trajectory calculations on the fragmentation dynamics of C{sub 60}{sup q+} (q = 20–60). We used the UB3LYP/3-21G level of density functional theory and the self-consistent charge density-functional based tight-binding theory. For q ≥ 20, we found that a two-step explosion mechanism governs the fragmentation dynamics: C{sub 60}{sup q+} first ejects singly and multiply charged fast atomic cations C{sup z+} (z ≥ 1) via Coulomb explosions on a timescale of 10 fs to stabilize the remaining core cluster. Thermal evaporationsmore » of slow atomic and molecular fragments from the core cluster subsequently occur on a timescale of 100 fs to 1 ps. Increasing the charge q makes the fragments smaller. This two-step mechanism governs the fragmentation dynamics in the most likely case that the initial kinetic energy accumulated upon ionization to C{sub 60}{sup q+} by ion impact or X-ray free electron laser is larger than 100 eV.« less

Complexity Reduction in Large Quantum Systems: Fragment Identification and Population Analysis via a Local Optimized Minimal Basis

DOE PAGES

Mohr, Stephan; Masella, Michel; Ratcliff, Laura E.; ...

2017-07-21

We present, within Kohn-Sham Density Functional Theory calculations, a quantitative method to identify and assess the partitioning of a large quantum mechanical system into fragments. We then introduce a simple and efficient formalism (which can be written as generalization of other well-known population analyses) to extract, from first principles, electrostatic multipoles for these fragments. The corresponding fragment multipoles can in this way be seen as reliable (pseudo-) observables. By applying our formalism within the code BigDFT, we show that the usage of a minimal set of in-situ optimized basis functions is of utmost importance for having at the same timemore » a proper fragment definition and an accurate description of the electronic structure. With this approach it becomes possible to simplify the modeling of environmental fragments by a set of multipoles, without notable loss of precision in the description of the active quantum mechanical region. Furthermore, this leads to a considerable reduction of the degrees of freedom by an effective coarsegraining approach, eventually also paving the way towards efficient QM/QM and QM/MM methods coupling together different levels of accuracy.« less

14 CFR 417.303 - Command control system requirements.

Code of Federal Regulations, 2014 CFR

2014-01-01

... flight termination system used for each launch. (f) Electromagnetic interference. Each command control system component must function within the electromagnetic environment to which it is exposed. A command... must prevent electromagnetic interference. (g) Command transmitter failover. A command control system...

14 CFR 417.303 - Command control system requirements.

Code of Federal Regulations, 2010 CFR

2010-01-01

... flight termination system used for each launch. (f) Electromagnetic interference. Each command control system component must function within the electromagnetic environment to which it is exposed. A command... must prevent electromagnetic interference. (g) Command transmitter failover. A command control system...

14 CFR 417.303 - Command control system requirements.

Code of Federal Regulations, 2013 CFR

2013-01-01

... flight termination system used for each launch. (f) Electromagnetic interference. Each command control system component must function within the electromagnetic environment to which it is exposed. A command... must prevent electromagnetic interference. (g) Command transmitter failover. A command control system...

14 CFR 417.303 - Command control system requirements.

Code of Federal Regulations, 2012 CFR

2012-01-01

... flight termination system used for each launch. (f) Electromagnetic interference. Each command control system component must function within the electromagnetic environment to which it is exposed. A command... must prevent electromagnetic interference. (g) Command transmitter failover. A command control system...

14 CFR 417.303 - Command control system requirements.

Code of Federal Regulations, 2011 CFR

2011-01-01

... flight termination system used for each launch. (f) Electromagnetic interference. Each command control system component must function within the electromagnetic environment to which it is exposed. A command... must prevent electromagnetic interference. (g) Command transmitter failover. A command control system...

Quantum interference and Monte Carlo simulations of multiparticle production

NASA Astrophysics Data System (ADS)

Bialas, A.; Krzywicki, A.

1995-02-01

We show that the effects of quantum interference can be implemented in Monte Carlo generators by modelling the generalized Wigner functions. A specific prescription for an appropriate modification of the weights of events produced by standard generators is proposed.

Acoustic and semantic interference effects in words and pictures.

PubMed

Dhawan, M; Pellegrino, J W

1977-05-01

Interference effects for pictures and words were investigated using a probe-recall task. Word stimuli showed acoustic interference effects for items at the end of the list and semantic interference effects for items at the beginning of the list, similar to results of Kintsch and Buschke (1969). Picture stimuli showed large semantic interference effects at all list positions with smaller acoustic interference effects. The results were related to latency data on picture-word processing and interpreted in terms of the differential order, probability, and/or speed of access to acoustic and semantic levels of processing. A levels of processing explanation of picture-word retention differences was related to dual coding theory. Both theoretical positions converge on an explanation of picture-word retention differences as a function of the relative capacity for semantic or associative processing.

Electronic systems failures and anomalies attributed to electromagnetic interference

NASA Technical Reports Server (NTRS)

Leach, R. D. (Editor); Alexander, M. B. (Editor)

1995-01-01

The effects of electromagnetic interference can be very detrimental to electronic systems utilized in space missions. Assuring that subsystems and systems are electrically compatible is an important engineering function necessary to assure mission success. This reference publication will acquaint the reader with spacecraft electronic systems failures and anomalies caused by electromagnetic interference and will show the importance of electromagnetic compatibility activities in conjunction with space flight programs. It is also hoped that the report will illustrate that evolving electronic systems are increasingly sensitive to electromagnetic interference and that NASA personnel must continue to diligently pursue electromagnetic compatibility on space flight systems.

Multivariate fMRI and Eye Tracking Reveal Differential Effects of Visual Interference on Recognition Memory Judgments for Objects and Scenes.

PubMed

O'Neil, Edward B; Watson, Hilary C; Dhillon, Sonya; Lobaugh, Nancy J; Lee, Andy C H

2015-09-01

Recent work has demonstrated that the perirhinal cortex (PRC) supports conjunctive object representations that aid object recognition memory following visual object interference. It is unclear, however, how these representations interact with other brain regions implicated in mnemonic retrieval and how congruent and incongruent interference influences the processing of targets and foils during object recognition. To address this, multivariate partial least squares was applied to fMRI data acquired during an interference match-to-sample task, in which participants made object or scene recognition judgments after object or scene interference. This revealed a pattern of activity sensitive to object recognition following congruent (i.e., object) interference that included PRC, prefrontal, and parietal regions. Moreover, functional connectivity analysis revealed a common pattern of PRC connectivity across interference and recognition conditions. Examination of eye movements during the same task in a separate study revealed that participants gazed more at targets than foils during correct object recognition decisions, regardless of interference congruency. By contrast, participants viewed foils more than targets for incorrect object memory judgments, but only after congruent interference. Our findings suggest that congruent interference makes object foils appear familiar and that a network of regions, including PRC, is recruited to overcome the effects of interference.

Implications of discontinuous elevation gradients on fragmentation and restoration in patterned wetlands

USGS Publications Warehouse

Zweig, Christa L.; Reichert, Brian E.; Kitchens, Wiley M.

2011-01-01

Large wetlands around the world face the possibility of degradation, not only from complete conversion, but also from subtle changes in their structure and function. While fragmentation and isolation of wetlands within heterogeneous landscapes has received much attention, the disruption of spatial patterns/processes within large wetland systems and the resulting fragmentation of community components are less well documented. A greater understanding of pattern/process relationships and landscape gradients, and what occurs when they are altered, could help avoid undesirable consequences of restoration actions. The objective of this study is to determine the amount of fragmentation of sawgrass ridges due to artificial impoundment of water and how that may be differentially affected by spatial position relative to north and south levees. We also introduce groundbreaking evidence of landscape-level discontinuous elevation gradients within WCA3AS by comparing generalized linear and generalized additive models. These relatively abrupt breaks in elevation may have non-linear effects on hydrology and vegetation communities and would be crucial in restoration considerations. Modeling suggests there are abrupt breaks in elevation as a function of northing (Y-coordinate). Fragmentation indices indicate that fragmentation is a function of elevation and easting (X-coordinate), and that fragmentation has increased from 1988-2002. When landscapes change and the changes are compounded by non-linear landscape variables that are described herein, the maintenance processes change with them, creating a degraded feedback loop that alters the system's response to structuring variables and diminishes our ability to predict the effects of restoration projects or climate change. Only when these landscape variables and linkages are clearly defined can we predict the response to potential perturbations and apply the knowledge to other landscape-level wetland systems in need of future restoration.

Management of an uncomplicated crown fracture by reattaching the fractured fragment-Case report.

PubMed

Martos, Josué; Pinto, Karoline V A; Miguelis, Tiago M F; Xavier, Cristina B

2017-12-01

Coronal fractures of the anterior teeth are common sequelae of traumatic dental injuries. Reattachment of fractured tooth fragments using dental adhesive techniques offers some advantages, including restoration of the function, esthetics, shape, texture, and brightness of the surface. The present report describes a clinical case of reattachment with a 4-year clinical and radiographic follow up in a permanent maxillary central incisor with an uncomplicated crown fracture. Fragment reattachment is a conservative procedure, preserving esthetics and functionality, and it can provide an immediate positive emotional response from the patient. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Construction of Biologically Functional Bacterial Plasmids In Vitro

PubMed Central

Cohen, Stanley N.; Chang, Annie C. Y.; Boyer, Herbert W.; Helling, Robert B.

1973-01-01

The construction of new plasmid DNA species by in vitro joining of restriction endonuclease-generated fragments of separate plasmids is described. Newly constructed plasmids that are inserted into Escherichia coli by transformation are shown to be biologically functional replicons that possess genetic properties and nucleotide base sequences from both of the parent DNA molecules. Functional plasmids can be obtained by reassociation of endonuclease-generated fragments of larger replicons, as well as by joining of plasmid DNA molecules of entirely different origins. Images PMID:4594039

Advance of RNA interference technique in Hemipteran insects.

PubMed

Li, Jie; Wang, Xiaoping; Wang, Manqun; Ma, Weihua; Hua, Hongxia

2012-07-24

RNA interference (RNAi) suppressed the expression of the target genes by post transcriptional regulation and the double-stranded RNA (dsRNA) mediated gene silencing has been a conserved mechanism in many eukaryotes, which prompted RNAi to become a valuable tool for unveiling the gene function in many model insects. Recent research attested that RNAi technique can be also effective in downregulation target genes in Hemipteran insects. In this review, we collected the researches of utilizing RNAi technique in gene functional analysis in Hemipteran insects, highlighted the methods of dsRNA/siRNA uptake by insects and discussed the knock-down efficiency of these techniques. Although the RNA interference technique has drawbacks and obscure points, our primary goal of this review is try to exploit it for further discovering gene functions and pest control tactic in the Hemipteran insects. © 2012 The Societies and Blackwell Publishing Asia Pty Ltd.

Extracommunicative functions of language: verbal interference causes selective categorization impairments.

PubMed

Lupyan, Gary

2009-08-01

In addition to its communicative functions, language has been argued to have a variety of extracommunicative functions, as assessed by its causal involvement in putatively nonlinguistic tasks. In the present work, I argue that language may be critically involved in the ability of human adults to categorize objects on a specific dimension (e.g., color) while abstracting over other dimensions (e.g., size). This ability is frequently impaired in aphasic patients. The present work demonstrates that normal participants placed under conditions of verbal interference show a pattern of deficits strikingly similar to that of aphasic patients: impaired taxonomic categorization along perceptual dimensions, and preserved thematic categorization. A control experiment using a visuospatial-interference task failed to find this selective pattern of deficits. The present work has implications for understanding the online role of language in normal cognition and supports the claim that language is causally involved in nonverbal cognition.

Interpretation of scanning tunneling quasiparticle interference and impurity states in cuprates.

PubMed

Kreisel, A; Choubey, Peayush; Berlijn, T; Ku, W; Andersen, B M; Hirschfeld, P J

2015-05-29

We apply a recently developed method combining first principles based Wannier functions with solutions to the Bogoliubov-de Gennes equations to the problem of interpreting STM data in cuprate superconductors. We show that the observed images of Zn on the surface of Bi_{2}Sr_{2}CaCu_{2}O_{8} can only be understood by accounting for the tails of the Cu Wannier functions, which include significant weight on apical O sites in neighboring unit cells. This calculation thus puts earlier crude "filter" theories on a microscopic foundation and solves a long-standing puzzle. We then study quasiparticle interference phenomena induced by out-of-plane weak potential scatterers, and show how patterns long observed in cuprates can be understood in terms of the interference of Wannier functions above the surface. Our results show excellent agreement with experiment and enable a better understanding of novel phenomena in the cuprates via STM imaging.

Gas chromatography-mass spectrometric studies of O-alkyl O-2-(N,N-dialkylamino) ethyl alkylphosphonites(phosphonates) for chemical weapons convention verification.

PubMed

Saeidian, Hamid; Babri, Mehran; Ramezani, Atefeh; Ashrafi, Davood; Sarabadani, Mansour; Naseri, Mohammad Taghi

2013-01-01

The electron ionization (EI) mass spectra of a series of O-alkyl O-2-(N,N-dialkylaminolethyl alkylphosphonites(phosphonates), which are precursors of nerve agents, were studied for Chemical Weapons Convention (CWC) verification. General El fragmentation pathways were constructed and discussed. Proposed fragment structures were confirmed through analyzing fragment ions of deuterated analogs and density functional theory (DFT) calculations. The observed fragment ions are due to different fragmentation pathways such as hydrogen and McLafferty+1 rearrangements, alkene, amine and alkoxy elimination by alpha- or beta-cleavage process. Fragment ions distinctly allow unequivocal identification of the interested compounds including those of isomeric compounds. The presence and abundance of fragment ions were found to depend on the size and structure of the alkyl group attached to nitrogen, phosphorus and oxygen atoms.

Assessment of fragment projection hazard: probability distributions for the initial direction of fragments.

PubMed

Tugnoli, Alessandro; Gubinelli, Gianfilippo; Landucci, Gabriele; Cozzani, Valerio

2014-08-30

The evaluation of the initial direction and velocity of the fragments generated in the fragmentation of a vessel due to internal pressure is an important information in the assessment of damage caused by fragments, in particular within the quantitative risk assessment (QRA) of chemical and process plants. In the present study an approach is proposed to the identification and validation of probability density functions (pdfs) for the initial direction of the fragments. A detailed review of a large number of past accidents provided the background information for the validation procedure. A specific method was developed for the validation of the proposed pdfs. Validated pdfs were obtained for both the vertical and horizontal angles of projection and for the initial velocity of the fragments. Copyright © 2014 Elsevier B.V. All rights reserved.

New method to determine the total carbonyl functional group content in extractable particulate organic matter by tandem mass spectrometry.

PubMed

Dron, J; Zheng, W; Marchand, N; Wortham, H

2008-08-01

A functional group analysis method was developed to determine the quantitative content of carbonyl functional groups in atmospheric particulate organic matter (POM) using constant neutral loss scanning-tandem mass spectrometry (CNLS-MS/MS). The neutral loss method consists in monitoring the loss of a neutral fragment produced by the fragmentation of a precursor ion in a collision cell. The only ions detected are the daughter ions resulting from the loss of the neutral fragment under study. Then, scanning the loss of a neutral fragment characteristic of a functional group enables the selective detection of the compounds bearing the chemical function under study within a complex mixture. The selective detection of carbonyl functional groups was achieved after derivatization with pentafluorophenylhydrazine (PFPH) by monitoring the neutral loss of C(6)F(5)N (181 amu), which was characteristic of a large panel of derivatized carbonyl compounds. The method was tested on 25 reference mixtures of different composition, all containing 24 carbonyl compounds at randomly determined concentrations. The repeatability and calibration tests were satisfying as they resulted in a relative standard deviation below 5% and a linear range between 0.01 and 0.65 mM with a calculated detection limit of 0.0035 mM. Also, the relative deviation induced by changing the composition of the mixture while keeping the total concentration of carbonyl functional groups constant was less than 20%. These reliability experiments demonstrate the high robustness of the developed procedure for accurate carbonyl functional group measurement, which was applied to atmospheric POM samples. Copyright (c) 2008 John Wiley & Sons, Ltd.

Flow interference in a variable porosity trisonic wind tunnel.

NASA Technical Reports Server (NTRS)

Davis, J. W.; Graham, R. F.

1972-01-01

Pressure data from a 20-degree cone-cylinder in a variable porosity wind tunnel for the Mach range 0.2 to 5.0 are compared to an interference free standard in order to determine wall interference effects. Four 20-degree cone-cylinder models representing an approximate range of percent blockage from one to six were compared to curve-fits of the interference free standard at each Mach number and errors determined at each pressure tap location. The average of the absolute values of the percent error over the length of the model was determined and used as the criterion for evaluating model blockage interference effects. The results are presented in the form of the percent error as a function of model blockage and Mach number.

Stem cell system in asexual and sexual reproduction of Enchytraeus japonensis (Oligochaeta, Annelida).

PubMed

Yoshida-Noro, Chikako; Tochinai, Shin

2010-01-01

Enchytraeus japonensis is a small oligochaete species that proliferates asexually via fragmentation and regeneration. As sexual reproduction can also be induced, it is a good model system for the study of both regenerative and germline stem cells. It has been shown by histological study that putative mesodermal stem cells called neoblasts, and dedifferentiated epidermal and endodermal cells are involved in blastema formation. Recently, we isolated three region-specific marker genes expressed in the digestive tract and showed by in situ hybridization that morphallactic as well as epimorphic regulation of the body patterning occurs during regeneration. We also cloned two vasa-related genes and analyzed their expression during development and in mature worms that undergo sexual reproduction. The results arising form these studies suggest that the origin and development of germline stem cells and neoblasts may be independent. Furthermore, we carried out functional analysis using RNA interference (RNAi) and showed that a novel gene termed grimp is required for mesodermal cell proliferation at the initial stages of regeneration. These findings indicate that the stem cell system in E. japonensis is regulated by both internal and external environmental factors.

Increased localization of APP-C99 in mitochondria-associated ER membranes causes mitochondrial dysfunction in Alzheimer disease.

PubMed

Pera, Marta; Larrea, Delfina; Guardia-Laguarta, Cristina; Montesinos, Jorge; Velasco, Kevin R; Agrawal, Rishi R; Xu, Yimeng; Chan, Robin B; Di Paolo, Gilbert; Mehler, Mark F; Perumal, Geoffrey S; Macaluso, Frank P; Freyberg, Zachary Z; Acin-Perez, Rebeca; Enriquez, Jose Antonio; Schon, Eric A; Area-Gomez, Estela

2017-11-15

In the amyloidogenic pathway associated with Alzheimer disease (AD), the amyloid precursor protein (APP) is cleaved by β-secretase to generate a 99-aa C-terminal fragment (C99) that is then cleaved by γ-secretase to generate the β-amyloid (Aβ) found in senile plaques. In previous reports, we and others have shown that γ-secretase activity is enriched in mitochondria-associated endoplasmic reticulum (ER) membranes (MAM) and that ER-mitochondrial connectivity and MAM function are upregulated in AD We now show that C99, in addition to its localization in endosomes, can also be found in MAM, where it is normally processed rapidly by γ-secretase. In cell models of AD, however, the concentration of unprocessed C99 increases in MAM regions, resulting in elevated sphingolipid turnover and an altered lipid composition of both MAM and mitochondrial membranes. In turn, this change in mitochondrial membrane composition interferes with the proper assembly and activity of mitochondrial respiratory supercomplexes, thereby likely contributing to the bioenergetic defects characteristic of AD. © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

Lateral compression open cap splint with circummandibular wiring for management of pediatric mandibular fractures: a retrospective audit of 10 cases.

PubMed

Bhola, Nitin; Jadhav, Anendd; Borle, Rajiv; Khemka, Gaurav; Adwani, Nitin; Bhattad, Mayur

2014-03-01

Mandibular fractures are relatively less frequent in children when compared to adults. Pediatric patients present a unique challenge to maxillofacial surgeons in terms of their treatment planning and in their functional needs. We currently describe our experience with lateral compression open cap splint with circummandibular wiring as a treatment modality which involves fewer risks in treating pediatric symphysis/parasymphysis/body mandibular fractures. A retrospective analysis of pediatric patients with mandibular symphysis/parasymphysis/body fractures operated from January 2007 to January 2012 was performed. Clinical photographs and orthopantomogram assessment at the time of presentation, after treatment, and at 6 months postoperatively were evaluated. All the 10 patients were followed up until the period of 6 months, and none of them had any major complications. Postoperatively, there was satisfactory healing and union of fracture fragments in all the patients. Only one patient developed infection at submental region. The 6-month follow-up showed good occlusion, without interference in teeth eruption and no signs of temporomandibular joint problems. Lateral compression open cap splints for treatment of pediatric mandibular symphysis/parasymphysis/body fractures are reliable treatment modalities with regard to occlusion-guided fracture reduction.

Effects of practice on interference from an auditory task while driving : a simulation study

DOT National Transportation Integrated Search

2004-12-01

Experimental research on the effects of cellular phone conversations on driving indicates that the phone task interferes with many driving-related functions, especially with older drivers. Limitations of past research have been that (1) the dual task...

Towards the elements of successful insect Ribonucleic acid interference (RNAi)

USDA-ARS?s Scientific Manuscript database

Ribonucleic acid interference (RNAi), the sequence-specific suppression of gene expression, offers great opportunities for insect science, especially to analyze gene function, manage pest populations, and reduce disease pathogens. The accumulating body of literature on insect RNAi has revealed that ...

Ribonucleic acid interference (RNAi) technology for control of Asian citrus psyllid

USDA-ARS?s Scientific Manuscript database

Ribonucleic acid interference, RNAi, applications and function are described for the non-scientist to bring a better understanding of how this emerging technology is providing environmentally friendly, non-transgenic, insect pest control to the citrus industry. Two part Video presentation....

The Structure and Stability of Bn(+) Clusters

NASA Technical Reports Server (NTRS)

Ricca, Alessandra; Bauschlicher, Charles W., Jr.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The geometries of B+n clusters for n less than 14 have been optimized using density functional theory with the B3LYP functional. The most stable structure for each cluster is planar or quasi-planar. The B3LYP fragmentation energies are calibrated using coupled cluster theory. Overall, our corrected fragmentation energies are in reasonable agreement with experiment. Our results are compared with previous theoretical results.

The transcription factor CCAAT-binding factor CBF/NF-Y regulates the proximal promoter activity in the human alpha 1(XI) collagen gene (COL11A1).

PubMed

Matsuo, Noritaka; Yu-Hua, Wang; Sumiyoshi, Hideaki; Sakata-Takatani, Keiko; Nagato, Hitoshi; Sakai, Kumiko; Sakurai, Mami; Yoshioka, Hidekatsu

2003-08-29

We have characterized the proximal promoter region of the human COL11A1 gene. Transient transfection assays indicate that the segment from -199 to +1 is necessary for the activation of basal transcription. Electrophoretic mobility shift assays (EMSAs) demonstrated that the ATTGG sequence, within the -147 to -121 fragment, is critical to bind nuclear proteins in the proximal COL11A1 promoter. We demonstrated that the CCAAT binding factor (CBF/NF-Y) bound to this region using an interference assay with consensus oligonucleotides and a supershift assay with specific antibodies in an EMSA. In a chromatin immunoprecipitation assay and EMSA using DNA-affinity-purified proteins, CBF/NF-Y proteins directly bound this region in vitro and in vivo. We also showed that four tandem copies of the CBF/NF-Y-binding fragment produced higher transcriptional activity than one or two copies, whereas the absence of a CBF/NF-Y-binding fragment suppressed the COL11A1 promoter activity. Furthermore, overexpression of a dominant-negative CBF-B/NF-YA subunit significantly inhibited promoter activity in both transient and stable cells. These results indicate that the CBF/NF-Y proteins regulate the transcription of COL11A1 by directly binding to the ATTGG sequence in the proximal promoter region.

Importance of riparian remnants for frog species diversity in a highly fragmented rainforest.

PubMed

Rodríguez-Mendoza, Clara; Pineda, Eduardo

2010-12-23

Tropical forests undergo continuous transformation to other land uses, resulting in landscapes typified by forest fragments surrounded by anthropogenic habitats. Small forest fragments, specifically strip-shaped remnants flanking streams (referred to as riparian remnants), can be particularly important for the maintenance and conservation of biodiversity within highly fragmented forests. We compared frog species diversity between riparian remnants, other forest fragments and cattle pastures in a tropical landscape in Los Tuxtlas, Mexico. We found similar species richness in the three habitats studied and a similar assemblage structure between riparian remnants and forest fragments, although species composition differed by 50 per cent. Frog abundance was halved in riparian remnants compared with forest fragments, but was twice that found in pastures. Our results suggest that riparian remnants play an important role in maintaining a portion of frog species diversity in a highly fragmented forest, particularly during environmentally stressful (hot and dry) periods. In this regard, however, the role of riparian remnants is complementary, rather than substitutive, with respect to the function of other forest fragments within the fragmented forest.

Extraction of quark transversity distribution and Collins fragmentation functions with QCD evolution

DOE PAGES

Kang, Zhong-Bo; Prokudin, Alexei; Sun, Peng; ...

2016-01-13

In this paper, we study the transverse momentum dependent (TMD) evolution of the Collins azimuthal asymmetries in e +e - annihilations and semi-inclusive hadron production in deep inelastic scattering (SIDIS) processes. All the relevant coefficients are calculated up to the next-to-leading logarithmic (NLL) order accuracy. By applying the TMD evolution at the approximate NLL order in the Collins- Soper-Sterman (CSS) formalism, we extract transversity distributions for u and d quarks and Collins fragmentation functions from current experimental data by a global analysis of the Collins asymmetries in back-to-back di-hadron productions in e +e - annihilations measured by BELLE and BABARmore » Collaborations and SIDIS data from HERMES, COMPASS, and JLab HALL A experiments. The impact of the evolution effects and the relevant theoretical uncertainties are discussed. We further discuss the TMD interpretation for our results, and illustrate the unpolarized quark distribution, transversity distribution, unpolarized quark fragmentation and Collins fragmentation functions depending on the transverse momentum and the hard momentum scale. Finally, we give predictions and discuss impact of future experiments.« less

Extraction of quark transversity distribution and Collins fragmentation functions with QCD evolution

NASA Astrophysics Data System (ADS)

Kang, Zhong-Bo; Prokudin, Alexei; Sun, Peng; Yuan, Feng

2016-01-01

We study the transverse-momentum-dependent (TMD) evolution of the Collins azimuthal asymmetries in e+e- annihilations and semi-inclusive hadron production in deep inelastic scattering processes. All the relevant coefficients are calculated up to the next-to-leading-logarithmic-order accuracy. By applying the TMD evolution at the approximate next-to-leading-logarithmic order in the Collins-Soper-Sterman formalism, we extract transversity distributions for u and d quarks and Collins fragmentation functions from current experimental data by a global analysis of the Collins asymmetries in back-to-back dihadron productions in e+e- annihilations measured by BELLE and BABAR collaborations and semi-inclusive hadron production in deep inelastic scattering data from HERMES, COMPASS, and JLab HALL A experiments. The impact of the evolution effects and the relevant theoretical uncertainties are discussed. We further discuss the TMD interpretation for our results and illustrate the unpolarized quark distribution, transversity distribution, unpolarized quark fragmentation, and Collins fragmentation functions depending on the transverse momentum and the hard momentum scale. We make detailed predictions for future experiments and discuss their impact.

Extraction of quark transversity distribution and Collins fragmentation functions with QCD evolution

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

Kang, Zhong-Bo; Prokudin, Alexei; Sun, Peng

In this paper, we study the transverse momentum dependent (TMD) evolution of the Collins azimuthal asymmetries in e +e - annihilations and semi-inclusive hadron production in deep inelastic scattering (SIDIS) processes. All the relevant coefficients are calculated up to the next-to-leading logarithmic (NLL) order accuracy. By applying the TMD evolution at the approximate NLL order in the Collins- Soper-Sterman (CSS) formalism, we extract transversity distributions for u and d quarks and Collins fragmentation functions from current experimental data by a global analysis of the Collins asymmetries in back-to-back di-hadron productions in e +e - annihilations measured by BELLE and BABARmore » Collaborations and SIDIS data from HERMES, COMPASS, and JLab HALL A experiments. The impact of the evolution effects and the relevant theoretical uncertainties are discussed. We further discuss the TMD interpretation for our results, and illustrate the unpolarized quark distribution, transversity distribution, unpolarized quark fragmentation and Collins fragmentation functions depending on the transverse momentum and the hard momentum scale. Finally, we give predictions and discuss impact of future experiments.« less

Failure to Recover from Proactive Semantic Interference and Abnormal Limbic Connectivity in Asymptomatic, Middle-Aged Offspring of Patients with Late-Onset Alzheimer's Disease.

PubMed

Sánchez, Stella M; Abulafia, Carolina; Duarte-Abritta, Barbara; de Guevara, M Soledad Ladrón; Castro, Mariana N; Drucaroff, Lucas; Sevlever, Gustavo; Nemeroff, Charles B; Vigo, Daniel E; Loewenstein, David A; Villarreal, Mirta F; Guinjoan, Salvador M

2017-01-01

We have obtained previous evidence of limbic dysfunction in middle-aged, asymptomatic offspring of late-onset Alzheimer's disease (LOAD) patients, and failure to recover from proactive semantic interference has been shown to be a sensitive cognitive test in other groups at risk for LOAD. To assess the effects of specific proactive semantic interference deficits as they relate to functional magnetic resonance imaging (fMRI) neocortical and limbic functional connectivity in middle aged offspring of individuals with LOAD (O-LOAD) and age-equivalent controls. We examined 21 O-LOAD and 20 controls without family history of neurodegenerative disorders (CS) on traditional measures of cognitive functioning and the LASSI-L, a novel semantic interference test uniquely sensitive to the failure to recover from proactive interference (frPSI). Cognitive tests then were correlated to fMRI connectivity of seeds located in entorhinal cortex and anterodorsal thalamic nuclei among O-LOAD and CS participants. Relative to CS, O-LOAD participants evidenced lower connectivity between entorhinal cortex and orbitofrontal, anterior cingulate, and anterior temporal cortex. In the offspring of LOAD patients, LASSI-L measures of frPSI were inversely associated with connectivity between anterodorsal thalamus and contralateral posterior cingulate. Intrusions on the task related to frPSI were inversely correlated with a widespread connectivity network involving hippocampal, insular, posterior cingulate, and dorsolateral prefrontal cortices, along with precunei and anterior thalamus in this group. Different patterns of connectivity associated with frPSI were observed among controls. The present results suggest that both semantic interference deficits and connectivity abnormalities might reflect limbic circuit dysfunction as a very early clinical signature of LOAD pathology, as previously demonstrated for other limbic phenotypes, such as sleep and circadian alterations.

Fragmentation characteristics of hydroxycinnamic acids in ESI-MSn by density functional theory.

PubMed

Yin, Zhi-Hui; Sun, Chang-Hai; Fang, Hong-Zhuang

2017-07-01

This work aims to analyze the electrospray ionization multistage mass spectrometry (ESI-MS n ) fragmentation characteristics of hydroxycinnamic acids (HCAs) in negative ion mode. The geometric parameters, energies, natural bond orbitals and frontier orbitals of fragments were calculated by density functional theory (DFT) to investigate mass spectral fragmentation mechanisms. The results showed that proton transfer always occurred during fragmentation of HCAs; their quasi-molecular ions ([M - H] - ) existed in more than one form and were mainly with the lowest energy. The fragmentation characteristics included the followings: (1) according to the different substitution position of phenolic hydroxyl group, the ring contraction reaction by CO elimination from benzene was in an increasingly difficult order: m-phenolic hydroxyl > p-phenolic hydroxyl > o-phenolic hydroxyl; and (2) ortho effect always occurred in o-dihydroxycinnamic acids (o-diHCAs), i.e. one phenolic hydroxyl group offered H + , which combined with the other one to lose H 2 O. In addition, there was a nucleophilic reaction during ring contraction in diHCAs that oxygen atom attacked the carbon atom binding with the other phenolic hydroxyl to lose CO 2 . The fragmentation characteristics and mechanism of HCAs could be used for analysis and identification of such compounds quickly and effectively, and as reference for structural analogues by ESI-MS. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

The intervening removable affinity tag (iRAT) production system facilitates Fv antibody fragment‐mediated crystallography

PubMed Central

Nomura, Yayoi; Sato, Yumi; Suno, Ryoji; Horita, Shoichiro

2016-01-01

Abstract Fv antibody fragments have been used as co‐crystallization partners in structural biology, particularly in membrane protein crystallography. However, there are inherent technical issues associated with the large‐scale production of soluble, functional Fv fragments through conventional methods in various expression systems. To circumvent these problems, we developed a new method, in which a single synthetic polyprotein consisting of a variable light (VL) domain, an intervening removable affinity tag (iRAT), and a variable heavy (VH) domain is expressed by a Gram‐positive bacterial secretion system. This method ensures stoichiometric expression of VL and VH from the monocistronic construct followed by proper folding and assembly of the two variable domains. The iRAT segment can be removed by a site‐specific protease during the purification process to yield tag‐free Fv fragments suitable for crystallization trials. In vitro refolding step is not required to obtain correctly folded Fv fragments. As a proof of concept, we tested the iRAT‐based production of multiple Fv fragments, including a crystallization chaperone for a mammalian membrane protein as well as FDA‐approved therapeutic antibodies. The resulting Fv fragments were functionally active and crystallized in complex with the target proteins. The iRAT system is a reliable, rapid and broadly applicable means of producing milligram quantities of Fv fragments for structural and biochemical studies. PMID:27595817

Interference between face and non-face domains of perceptual expertise: a replication and extension

PubMed Central

Curby, Kim M.; Gauthier, Isabel

2014-01-01

As car expertise increases, so does interference between the visual processing of faces and that of cars; this suggests performance trade-offs across domains of real-world expertise. Such interference between expert domains has been previously revealed in a relatively complex design, interleaving 2-back part-judgment task with faces and cars (Gauthier et al., 2003). However, the basis of this interference is unclear. Experiment 1A replicated the finding of interference between faces and cars, as a function of car expertise. Experiments 1B and 2 investigated the mechanisms underlying this effect by (1) providing baseline measures of performance and (2) assessing the specificity of this interference effect. Our findings support the presence of expertise-dependent interference between face and non-face domains of expertise. However, surprisingly, it is in the condition where faces are processed among cars with a disrupted configuration where expertise has a greater influence on faces. This finding highlights how expertise-related processing changes also occur for transformed objects of expertise and that such changes can also drive interference across domains of expertise. PMID:25346702

Fragment Impact Toolkit (FIT)

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

Shevitz, Daniel Wolf; Key, Brian P.; Garcia, Daniel B.

2017-09-05

The Fragment Impact Toolkit (FIT) is a software package used for probabilistic consequence evaluation of fragmenting sources. The typical use case for FIT is to simulate an exploding shell and evaluate the consequence on nearby objects. FIT is written in the programming language Python and is designed as a collection of interacting software modules. Each module has a function that interacts with the other modules to produce desired results.

Simulating Global AeroMACS Airport Ground Station Antenna Power Transmission Limits to Avoid Interference With Mobile Satellite Service Feeder Uplinks

NASA Technical Reports Server (NTRS)

Wilson, Jeffrey D.

2013-01-01

The Aeronautical Mobile Airport Communications System (AeroMACS), which is based upon the IEEE 802.16e mobile wireless standard, is expected to be implemented in the 5091 to 5150 MHz frequency band. As this band is also occupied by Mobile Satellite Service feeder uplinks, AeroMACS must be designed to avoid interference with this incumbent service. The aspects of AeroMACS operation that present potential interference are under analysis in order to enable the definition of standards that assure that such interference will be avoided. In this study, the cumulative interference power distribution at low Earth orbit from transmitters at global airports was simulated with the Visualyse Professional software. The dependence of the interference power on antenna distribution, gain patterns, duty cycle, and antenna tilt was simulated. As a function of these parameters, the simulation results are presented in terms of the limitations on transmitter power from global airports required to maintain the cumulative interference power under the established threshold.

Dependence of AeroMACS Interference on Airport Radiation Pattern Characteristics

NASA Technical Reports Server (NTRS)

Wilson, Jeffrey D.

2012-01-01

AeroMACS (Aeronautical Mobile Airport Communications System), which is based upon the IEEE 802.16e mobile wireless standard, is expected to be implemented in the 5091 to 5150 MHz frequency band. As this band is also occupied by Mobile Satellite Service (MSS) feeder uplinks, AeroMACS must be designed to avoid interference with this incumbent service. The aspects of AeroMACS operation that present potential interference are under analysis in order to enable the definition of standards that assure that such interference will be avoided. In this study, the cumulative interference power distribution at low earth orbit from AeroMACS transmitters at the 497 major airports in the contiguous United States was simulated with the Visualyse Professional software. The dependence of the interference power on the number of antenna beams per airport, gain patterns, and beam direction orientations was simulated. As a function of these parameters, the simulation results are presented in terms of the limitations on transmitter power required to maintain the cumulative interference power under the established threshold.

Dependence of AeroMACS Interference on Airport Radiation Pattern Characteristics

NASA Technical Reports Server (NTRS)

Wilson, Jeffrey D.

2012-01-01

AeroMACS (Aeronautical Mobile Airport Communications System), which is based upon the IEEE 802.16e mobile wireless standard, is expected to be implemented in the 5091-5150 MHz frequency band. As this band is also occupied by Mobile Satellite Service (MSS) feeder uplinks, AeroMACS must be designed to avoid interference with this incumbent service. The aspects of AeroMACS operation that present potential interference are under analysis in order to enable the definition of standards that assure that such interference will be avoided. In this study, the cumulative interference power distribution at low earth orbit from AeroMACS transmitters at the 497 major airports in the contiguous United States was simulated with the Visualyse Professional software. The dependence of the interference power on the number of antenna beams per airport, gain patterns, and beam direction orientations was simulated. As a function of these parameters, the simulation results are presented in terms of the limitations on transmitter power required to maintain the cumulative interference power under the established threshold.

Utility of a patient-reported outcome in measuring functional impairment during autologous stem cell transplant in patients with multiple myeloma.

PubMed

Shah, Nina; Shi, Qiuling; Giralt, Sergio; Williams, Loretta; Bashir, Qaiser; Qazilbash, Muzaffar; Champlin, Richard E; Cleeland, Charles S; Wang, Xin Shelley

2018-04-01

We aimed to determine the utility of a patient-reported outcome (PRO) as it relates to patient performed testing (PPT) for measuring functional status in multiple myeloma patients after autologous hematopoietic stem cell transplantation (auto-HCT). Symptom interference on walking (a PRO) was measured by the MD Anderson Symptom Inventory (MDASI). PPT was assessed via 6-min walk test (6MWT). Mixed effects modeling was used to examine (1) the longitudinal relationship between the MDASI score and 6MWT distance and (2) the MDASI scores between patients who did or did not complete the 6WMT. Receiver operating characteristic (ROC) curve analysis was performed to quantify the construct validity of the PRO by differentiating performance status. Seventy-nine patients were included. Mean 6MWT distance significantly correlated with MDASI-walking interference score (PRO) over the first month of auto-HCT (est = 6.09, p = 0.006). There was a significantly higher completion rate for MDASI versus 6MWT at each time point (p < 0.01). Patients who completed the 6MWT reported less interference on walking during the study period (est = 1.61, p < 0.0001). Finally, the PRO demonstrated significant construct validity for measuring functioning status with MDASI-walking against ECOG-PS as the anchor (AUC = 0.77, 95% CI 0.60-0.94, p = 0.003). The PRO of MDASI-walking interference is a valid physical functioning measure, correlating with an objective functional measure (6MWT) in MM patients undergoing auto-HCT. As patients with poorer functional status during therapy are less likely to complete PPT, this PRO may offer a more practical quantitative measure of functioning in patients.

Satellite disintegration dynamics

NASA Technical Reports Server (NTRS)

Dasenbrock, R. R.; Kaufman, B.; Heard, W. B.

1975-01-01

The subject of satellite disintegration is examined in detail. Elements of the orbits of individual fragments, determined by DOD space surveillance systems, are used to accurately predict the time and place of fragmentation. Dual time independent and time dependent analyses are performed for simulated and real breakups. Methods of statistical mechanics are used to study the evolution of the fragment clouds. The fragments are treated as an ensemble of non-interacting particles. A solution of Liouville's equation is obtained which enables the spatial density to be calculated as a function of position, time and initial velocity distribution.

Xenoliths in maars and diatremes with inferences for the moon, Mars, and Venus.

NASA Technical Reports Server (NTRS)

Mcgetchin, T. R.; Ullrich, G. W.

1973-01-01

Some field observations of the occurrence of deep-seated rock fragments in three terrestrial volcanic features that may have counterparts on the moon or Mars are reviewed, and results of numerical hydrodynamic calculations of the eruption of these types of volcanoes are presented. In particular, the transport of entrained fragmental debris is investigated for the surface (muzzle) velocity of fragments that it yields as a function of fragment size and various values of surface gravity. The implications of these observations and inferences for possible future space missions are examined.

Patterns of bird functional diversity on land-bridge island fragments.

PubMed

Ding, Zhifeng; Feeley, Kenneth J; Wang, Yanping; Pakeman, Robin J; Ding, Ping

2013-07-01

The loss of species diversity due to habitat fragmentation has been extensively studied. In contrast, the impacts of habitat fragmentation on functional diversity remains relatively poorly understood. We conducted bird functional diversity studies on a set of 41 recently isolated land-bridge islands in the Thousand Island Lake, China. We analysed differences in bird species richness and a recently developed suite of complementary functional diversity indices (FRic, volume of functional space occupied; FEve, evenness of abundance distribution in the functional trait space; FDiv, divergence in the distribution of abundance in the trait volume) across different gradients (island area and isolation). We found no correlations between FRic and FEve or FEve and FDiv, but negative correlations between FRic and FDiv. As predicted, island area accounted for most of the variation in bird species richness, whereas isolation explained most of the variation in species evenness (decreasing species evenness with increasing isolation). Functional diversity appears to be more strongly influenced by habitat filtering as opposed to limiting similarity. More specifically, across all islands, both FRic and FEve were significantly lower than expected for randomly assembled communities, but FDiv showed no clear patterns. FRic increased with island area, FEve decreased with island area and FDiv showed no clear patterns. Our finding that FEve decreases with island area at TIL may indicate low functional stability on such islands, and as such large islands and habitat patches may deserve extra attention and/or protection. These results help to demonstrate the importance of considering the effects of fragmentation on functional diversity in habitat management and reserve design plans. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

Identification of peptides in functional Scamorza ovine milk cheese.

PubMed

Albenzio, M; Santillo, A; Marino, R; Della Malva, A; Caroprese, M; Sevi, A

2015-12-01

Ovine bulk milk was used to produce Scamorza cheese with probiotics: either a mix of Bifidobacterium longum and Bifidobacterium lactis or Lactobacillus acidophilus as the probiotic strains. Peptides obtained from reverse phase-HPLC water-soluble extract of Scamorza cheeses were analyzed using a quadrupole time-of-flight liquid chromatography-mass spectrometry system. Identified fragments were derived from casein hydrolysis or probiotic bacterial enzymes; some of the fragments showed encrypted peptide sequences that shared structural homology with previously described bioactive peptides in ovine milk and dairy products. Bifidobacterium longum and B. lactis showed greater proteolytic potential both in terms of level of pH 4.6 water-soluble nitrogen extract and ability to generate peptides with potential biofunctionality. Fragments deriving from microbial enzymes may be regarded as tracing fragments useful for monitoring probiotic activity in functional Scamorza cheese. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Urban habitat fragmentation and genetic population structure of bobcats in coastal southern California

USGS Publications Warehouse

Ruell, E.W.; Riley, S.P.D.; Douglas, M.R.; Antolin, M.F.; Pollinger, J.R.; Tracey, J.A.; Lyren, L.M.; Boydston, E.E.; Fisher, R.N.; Crooks, K.R.

2012-01-01

Although habitat fragmentation is recognized as a primary threat to biodiversity, the effects of urban development on genetic population structure vary among species and landscapes and are not yet well understood. Here we use non-invasive genetic sampling to compare the effects of fragmentation by major roads and urban development on levels of dispersal, genetic diversity, and relatedness between paired bobcat populations in replicate landscapes in coastal southern California. We hypothesized that bobcat populations in sites surrounded by urbanization would experience reduced functional connectivity relative to less isolated nearby populations. Our results show that bobcat genetic population structure is affected by roads and development but not always as predicted by the degree that these landscape features surround fragments. Instead, we suggest that urban development may affect functional connectivity between bobcat populations more by limiting the number and genetic diversity of source populations of migrants than by creating impermeable barriers to dispersal.

Exploring Fusarium head blight disease control by RNA interference

USDA-ARS?s Scientific Manuscript database

RNA interference (RNAi) technology provides a novel tool to study gene function and plant protection strategies. Fusarium graminearum is the causal agent of Fusarium head blight (FHB), which reduces crop yield and quality by producing trichothecene mycotoxins including 3-acetyl deoxynivalenol (3-ADO...

Aerodynamic interference effects on tilting proprotor aircraft. [using the Green function method

NASA Technical Reports Server (NTRS)

Soohoo, P.; Morino, L.; Noll, R. B.; Ham, N. D.

1977-01-01

The Green's function method was used to study tilting proprotor aircraft aerodynamics with particular application to the problem of the mutual interference of the wing-fuselage-tail-rotor wake configuration. While the formulation is valid for fully unsteady rotor aerodynamics, attention was directed to steady state aerodynamics, which was achieved by replacing the rotor with the actuator disk approximation. The use of an actuator disk analysis introduced a mathematical singularity into the formulation; this problem was studied and resolved. The pressure distribution, lift, and pitching moment were obtained for an XV-15 wing-fuselage-tail rotor configuration at various flight conditions. For the flight configurations explored, the effects of the rotor wake interference on the XV-15 tilt rotor aircraft yielded a reduction in the total lift and an increase in the nose-down pitching moment. This method provides an analytical capability that is simple to apply and can be used to investigate fuselage-tail rotor wake interference as well as to explore other rotor design problem areas.

Tuning the thermal conductance of molecular junctions with interference effects

NASA Astrophysics Data System (ADS)

Klöckner, J. C.; Cuevas, J. C.; Pauly, F.

2017-12-01

We present an ab initio study of the role of interference effects in the thermal conductance of single-molecule junctions. To be precise, using a first-principles transport method based on density functional theory, we analyze the coherent phonon transport in single-molecule junctions made of several benzene and oligo(phenylene ethynylene) derivatives. We show that the thermal conductance of these junctions can be tuned via the inclusion of substituents, which induces destructive interference effects and results in a decrease of the thermal conductance with respect to the unmodified molecules. In particular, we demonstrate that these interference effects manifest as antiresonances in the phonon transmission, whose energy positions can be tuned by varying the mass of the substituents. Our work provides clear strategies for the heat management in molecular junctions and, more generally, in nanostructured metal-organic hybrid systems, which are important to determine how these systems can function as efficient energy-conversion devices such as thermoelectric generators and refrigerators.

GNSS Space-Time Interference Mitigation and Attitude Determination in the Presence of Interference Signals

PubMed Central

Daneshmand, Saeed; Jahromi, Ali Jafarnia; Broumandan, Ali; Lachapelle, Gérard

2015-01-01

The use of Space-Time Processing (STP) in Global Navigation Satellite System (GNSS) applications is gaining significant attention due to its effectiveness for both narrowband and wideband interference suppression. However, the resulting distortion and bias on the cross correlation functions due to space-time filtering is a major limitation of this technique. Employing the steering vector of the GNSS signals in the filter structure can significantly reduce the distortion on cross correlation functions and lead to more accurate pseudorange measurements. This paper proposes a two-stage interference mitigation approach in which the first stage estimates an interference-free subspace before the acquisition and tracking phases and projects all received signals into this subspace. The next stage estimates array attitude parameters based on detecting and employing GNSS signals that are less distorted due to the projection process. Attitude parameters enable the receiver to estimate the steering vector of each satellite signal and use it in the novel distortionless STP filter to significantly reduce distortion and maximize Signal-to-Noise Ratio (SNR). GPS signals were collected using a six-element antenna array under open sky conditions to first calibrate the antenna array. Simulated interfering signals were then added to the digitized samples in software to verify the applicability of the proposed receiver structure and assess its performance for several interference scenarios. PMID:26016909

GNSS space-time interference mitigation and attitude determination in the presence of interference signals.

PubMed

Daneshmand, Saeed; Jahromi, Ali Jafarnia; Broumandan, Ali; Lachapelle, Gérard

2015-05-26

The use of Space-Time Processing (STP) in Global Navigation Satellite System (GNSS) applications is gaining significant attention due to its effectiveness for both narrowband and wideband interference suppression. However, the resulting distortion and bias on the cross correlation functions due to space-time filtering is a major limitation of this technique. Employing the steering vector of the GNSS signals in the filter structure can significantly reduce the distortion on cross correlation functions and lead to more accurate pseudorange measurements. This paper proposes a two-stage interference mitigation approach in which the first stage estimates an interference-free subspace before the acquisition and tracking phases and projects all received signals into this subspace. The next stage estimates array attitude parameters based on detecting and employing GNSS signals that are less distorted due to the projection process. Attitude parameters enable the receiver to estimate the steering vector of each satellite signal and use it in the novel distortionless STP filter to significantly reduce distortion and maximize Signal-to-Noise Ratio (SNR). GPS signals were collected using a six-element antenna array under open sky conditions to first calibrate the antenna array. Simulated interfering signals were then added to the digitized samples in software to verify the applicability of the proposed receiver structure and assess its performance for several interference scenarios.

Adeno-associated virus type 2 rep gene-mediated inhibition of basal gene expression of human immunodeficiency virus type 1 involves its negative regulatory functions.

PubMed Central

Oelze, I; Rittner, K; Sczakiel, G

1994-01-01

Adeno-associated virus type 2 (AAV-2), a human parvovirus which is apathogenic in adults, inhibits replication and gene expression of human immunodeficiency virus type 1 (HIV-1) in human cells. The rep gene of AAV-2, which was shown earlier to be sufficient for this negative interference, also down-regulated the expression of heterologous sequences driven by the long terminal repeat (LTR) of HIV-1. This effect was observed in the absence of the HIV-1 transactivator Tat, i.e., at basal levels of LTR-driven transcription. In this work, we studied the involvement of functional subsequences of the HIV-1 LTR in rep-mediated inhibition in the absence of Tat. Mutated LTRs driving an indicator gene (cat) were cointroduced into human SW480 cells together with rep alone or with double-stranded DNA fragments or RNA containing sequences of the HIV-1 LTR. The results indicate that rep strongly enhances the function of negative regulatory elements of the LTR. In addition, the experiments revealed a transcribed sequence element located within the TAR-coding sequence termed AHHH (AAV-HIV homology element derived from HIV-1) which is involved in rep-mediated inhibition. The AHHH element is also involved in down-regulation of basal expression levels in the absence of rep, suggesting that AHHH also contributes to negative regulatory functions of the LTR of HIV-1. In contrast, positive regulatory elements of the HIV-1 LTR such as the NF kappa B and SP1 binding sites have no significant influence on the rep-mediated inhibition. Images PMID:8289357

Atypical mitochondrial fission upon bacterial infection

PubMed Central

Stavru, Fabrizia; Palmer, Amy E.; Wang, Chunxin; Youle, Richard J.; Cossart, Pascale

2013-01-01

We recently showed that infection by Listeria monocytogenes causes mitochondrial network fragmentation through the secreted pore-forming toxin listeriolysin O (LLO). Here, we examine factors involved in canonical fusion and fission. Strikingly, LLO-induced mitochondrial fragmentation does not require the traditional fission machinery, as Drp1 oligomers are absent from fragmented mitochondria following Listeria infection or LLO treatment, as the dynamin-like protein 1 (Drp1) receptor Mff is rapidly degraded, and as fragmentation proceeds efficiently in cells with impaired Drp1 function. LLO does not cause processing of the fusion protein optic atrophy protein 1 (Opa1), despite inducing a decrease in the mitochondrial membrane potential, suggesting a unique Drp1- and Opa1-independent fission mechanism distinct from that triggered by uncouplers or the apoptosis inducer staurosporine. We show that the ER marks LLO-induced mitochondrial fragmentation sites even in the absence of functional Drp1, demonstrating that the ER activity in regulating mitochondrial fission can be induced by exogenous agents and that the ER appears to regulate fission by a mechanism independent of the canonical mitochondrial fission machinery. PMID:24043775

Functionalized nanoparticles for measurement of biomarkers using a SERS nanochannel platform

NASA Astrophysics Data System (ADS)

Benford, Melodie; Wang, Miao; Kameoka, Jun; Good, Theresa; Cote, Gerard

2010-02-01

The overall goal of this research is to develop a new point-of-care system for early detection and characterization of cardiac markers to aid in diagnosis of acute coronary syndrome. The envisioned final technology platform incorporates functionalized gold colloidal nanoparticles trapped at the entrance to a nanofluidic device providing a robust means for analyte detection at trace levels using surface enhanced Raman spectroscopy (SERS). To discriminate a specific biomarker, we designed an assay format analogous to a competitive ELISA. Notably, the biomarker would be captured by an antibody and in turn displace a peptide fragment, containing the binding epitope of the antibody labeled with a Raman reporter molecule that would not interfere with blood serum proteins. To demonstrate the feasibility of this approach, we used C-reactive protein (CRP) as a surrogate biomarker. We functionalized agarose beads with anti-CRP that were placed outside the nanochannel, then added either Rhodamine-6-G (R6G) labeled-CRP and gold (as a surrogate of a sample without analyte present), or R6G labeled CRP, gold, and unlabeled CRP (as a surrogate of a sample with analyte present). Analyzing the spectra we see an increase in peak intensity in the presence of analyte at characteristic peaks for R6G specifically, 1284 and1567 cm- 1. Further, our results illustrate the reproducibility of the Raman spectra collected for R6G-labeled CRP in the nanochannel. Overall, we believe that this method will provide the advantage of sensitivity and narrow line widths characteristic of SERS as well as the specificity toward the biomarker of interest.

Antigen detection at atomolar concentration using optical tweezers

NASA Astrophysics Data System (ADS)

Laliberté, Mathieu; Bordeleau, François; Marceau, Normand; Sheng, Yunlong

2009-06-01

Methods that avoid intermediate amplification steps to detect protein markers of pathological disturbances would be of wide interest in the clinical environment. This is particularly the case in cancer diagnosis, where protein fragments are released into the blood by the emerging cancer cells. These fragments generate an antigen-antibody reaction, and the concentration of the antigen is known to modulate this interaction. Here we report on the development of a novel optical tweezers-based procedure to measure minute amount of antigen in a biological fluid. The force was applied on a 3μm polystyrene bead coated with Bovine Serum Albumin (BSA) attached on a 1.5 μm diameter borosilicate rod tip coated with anti-BSA antibody. First, we verified that the binding strength was dependent on the protein concentration on the bead. We then assessed the sensitivity range by finding the minimal BSA concentration in solution that can still interfere with the bead-rod linkage. On the whole, the results demonstrated that proteinous antigen present in a biological fluid could possibly be detectable at atomolar concentration through the use of an optical tweezers.

MOCCA: A 4k-Pixel Molecule Camera for the Position- and Energy-Resolving Detection of Neutral Molecule Fragments at CSR

NASA Astrophysics Data System (ADS)

Gamer, L.; Schulz, D.; Enss, C.; Fleischmann, A.; Gastaldo, L.; Kempf, S.; Krantz, C.; Novotný, O.; Schwalm, D.; Wolf, A.

2016-08-01

We present the design of MOCCA, a large-area particle detector that is developed for the position- and energy-resolving detection of neutral molecule fragments produced in electron-ion interactions at the Cryogenic Storage Ring at the Max Planck Institute for Nuclear Physics in Heidelberg. The detector is based on metallic magnetic calorimeters and consists of 4096 particle absorbers covering a total detection area of 44.8 mathrm {mm} × 44.8 mathrm {mm}. Groups of four absorbers are thermally coupled to a common paramagnetic temperature sensor where the strength of the thermal link is different for each absorber. This allows attributing a detector event within this group to the corresponding absorber by discriminating the signal rise times. A novel readout scheme further allows reading out all 1024 temperature sensors that are arranged in a 32 × 32 square array using only 16+16 current-sensing superconducting quantum interference devices. Numerical calculations taking into account a simplified detector model predict an energy resolution of Δ E_mathrm {FWHM} le 80 mathrm {eV} for all pixels of this detector.

A ribonuclease coordinates siRNA amplification and mRNA cleavage during RNAi.

PubMed

Tsai, Hsin-Yue; Chen, Chun-Chieh G; Conte, Darryl; Moresco, James J; Chaves, Daniel A; Mitani, Shohei; Yates, John R; Tsai, Ming-Daw; Mello, Craig C

2015-01-29

Effective silencing by RNA-interference (RNAi) depends on mechanisms that amplify and propagate the silencing signal. In some organisms, small-interfering RNAs (siRNAs) are amplified from target mRNAs by RNA-dependent RNA polymerase (RdRP). Both RdRP recruitment and mRNA silencing require Argonaute proteins, which are generally thought to degrade RNAi targets by directly cleaving them. However, in C. elegans, the enzymatic activity of the primary Argonaute, RDE-1, is not required for silencing activity. We show that RDE-1 can instead recruit an endoribonuclease, RDE-8, to target RNA. RDE-8 can cleave RNA in vitro and is needed for the production of 3' uridylated fragments of target mRNA in vivo. We also find that RDE-8 promotes RdRP activity, thereby ensuring amplification of siRNAs. Together, our findings suggest a model in which RDE-8 cleaves target mRNAs to mediate silencing, while generating 3' uridylated mRNA fragments to serve as templates for the RdRP-directed amplification of the silencing signal. Copyright © 2015 Elsevier Inc. All rights reserved.

A ribonuclease coordinates siRNA amplification and mRNA cleavage during RNAi

PubMed Central

Tsai, Hsin-Yue; Chen, Chun-Chieh G.; Conte, Darryl; Moresco, James J.; Chaves, Daniel A.; Mitani, Shohei; Yates, John R.; Tsai, Ming-Daw; Mello, Craig C.

2015-01-01

SUMMARY Effective silencing by RNA-interference (RNAi) depends on mechanisms that amplify and propagate the silencing signal. In some organisms, small-interfering (si) RNAs are amplified from target mRNAs by RNA-dependent RNA polymerase (RdRP). Both RdRP recruitment and mRNA silencing require Argonaute proteins, which are generally thought to degrade RNAi targets by directly cleaving them. However in C. elegans, the enzymatic activity of the primary Argonaute, RDE-1, is not required for silencing activity. We show that RDE-1 can instead recruit an endoribonuclease, RDE-8, to target RNA. RDE-8 can cleave RNA in vitro and is needed for the production of 3′ uridylated fragments of target mRNA in vivo. We also find that RDE-8 promotes RdRP activity, thereby ensuring amplification of siRNAs. Together, our findings suggest a model in which RDE-8 cleaves target mRNAs to mediate silencing, while generating 3’ uridylated mRNA fragments to serve as templates for the RdRP-directed amplification of the silencing signal. PMID:25635455

Engineered Recombinant Single-Chain Fragment Variable Antibody for Immunosensors

PubMed Central

Shen, Zhihong; Mernaugh, Raymond L.; Yan, Heping; Yu, Lei; Zhang, Ying; Zeng, Xiangqun

2008-01-01

A recombinant single-chain fragment variable (scFv) antibody (designated A10B) was engineered to contain two histidines within the linker peptide used to join the scFv heavy and light chains. A piezoimmunosensor using the scFv was successfully developed. A10B scFv bound to the gold piezoimmunosensor surface were correctly oriented, retained antigen-binding activity, and coupled at high surface concentration. These results, and results obtained from an earlier study using an scFv containing a linker cysteine, suggest that the location on the linker sequence in which the amino acids were incorporated was well tolerated by the scFv and did not interfere with scFv antigen-binding activity. The scFv-modified QCM sensor was thoroughly characterized and used to specifically detect antigen in crude serum sample and had a sensitivity of 2.3 ± 0.15 nM (n = 4) with a linear range over 2.3 × 10−9–3.3 × 10−8 M. The piezoimmunosensor was also used to study the kinetics and thermodynamics of antigen/scFv antibody binding. PMID:16255580

Population ecology of free-roaming cats and interference competition by coyotes in urban parks.

PubMed

Gehrt, Stanley D; Wilson, Evan C; Brown, Justin L; Anchor, Chris

2013-01-01

Free-roaming cats are a common element of urban landscapes worldwide, often causing controversy regarding their impacts on ecological systems and public health. We monitored cats within natural habitat fragments in the Chicago metropolitan area to characterize population demographics, disease prevalence, movement patterns and habitat selection, in addition to assessing the possible influence of coyotes on cats. The population was dominated by adults of both sexes, and 24% of adults were in reproductive condition. Annual survival rate was relatively high (S=0.70, SE=0.10), with vehicles and predation the primary causes of death. Size of annual home range varied by sex, but not reproductive status or body weight. We observed partitioning of the landscape by cats and coyotes, with little interspecific overlap between core areas of activity. Coyotes selected for natural habitats whereas cats selected for developed areas such as residences. Free-roaming cats were in better condition than we predicted, but their use of natural habitat fragments, and presumably their ecological impact, appeared to be limited by coyotes through intraguild competition.

Quantum control of molecular fragmentation in strong laser fields

NASA Astrophysics Data System (ADS)

Zohrabi, Mohammad

Present advances in laser technology allow the production of ultrashort (<˜5 fs, approaching single cycle at 800 nm), intense tabletop laser pulses. At these high intensities laser-matter interactions cannot be described with perturbation theory since multiphoton processes are involved. This is in contrast to photodissociation by the absorption of a single photon, which is well described by perturbation theory. For example, at high intensities (<˜5x1013 W/cm2) the fragmentation of molecular hydrogen ions has been observed via the absorption of three or more photons. In another example, an intriguing dissociation mechanism has been observed where molecular hydrogen ions seem to fragment by apparently absorbing no photons. This is actually a two photon process, photoabsorption followed by stimulated emission, resulting in low energy fragments. We are interested in exploring these kinds of multiphoton processes. Our research group has studied the dynamics and control of fragmentation induced by strong laser fields in a variety of molecular targets. The main goal is to provide a basic understanding of fragmentation mechanisms and possible control schemes of benchmark systems such as H2+. This knowledge is further extended to more complex systems like the benchmark H3+ polyatomic and other molecules. In this dissertation, we report research based on two types of experiments. In the first part, we describe laser-induced fragmentation of molecular ion-beam targets. In the latter part, we discuss the formation of highly-excited neutral fragments from hydrogen molecules using ultrashort laser pulses. In carrying out these experiments, we have also extended experimental techniques beyond their previous capabilities. We have performed a few experiments to advance our understanding of laser-induced fragmentation of molecular-ion beams. For instance, we explored vibrationally resolved spectra of O2+ dissociation using various wavelengths. We observed a vibrational suppression effect in the dissociation spectra due to the small magnitude of the dipole transition moment, which depends on the photon energy --- a phenomenon known as Cooper minima. By changing the laser wavelength, the Cooper minima shift, a fact that was used to identify the dissociation pathways. In another project, we studied the carrier-envelope phase (CEP) dependences of highly-excited fragments from hydrogen molecules. General CEP theory predicts a CEP dependence in the total dissociation yield due to the interference of dissociation pathways differing by an even net number of photons, and our measurements are consistent with this prediction. Moreover, we were able to extract the difference in the net number of photons involved in the interfering pathways by using a Fourier analysis. In terms of our experimental method, we have implemented a pump-probe style technique on a thin molecular ion-beam target and explored the feasibility of such experiments. The results presented in this work should lead to a better understanding of the dynamics and control in molecular fragmentation induced by intense laser fields.

Markedly Divergent Tree Assemblage Responses to Tropical Forest Loss and Fragmentation across a Strong Seasonality Gradient.

PubMed

Orihuela, Rodrigo L L; Peres, Carlos A; Mendes, Gabriel; Jarenkow, João A; Tabarelli, Marcelo

2015-01-01

We examine the effects of forest fragmentation on the structure and composition of tree assemblages within three seasonal and aseasonal forest types of southern Brazil, including evergreen, Araucaria, and deciduous forests. We sampled three southernmost Atlantic Forest landscapes, including the largest continuous forest protected areas within each forest type. Tree assemblages in each forest type were sampled within 10 plots of 0.1 ha in both continuous forests and 10 adjacent forest fragments. All trees within each plot were assigned to trait categories describing their regeneration strategy, vertical stratification, seed-dispersal mode, seed size, and wood density. We detected differences among both forest types and landscape contexts in terms of overall tree species richness, and the density and species richness of different functional groups in terms of regeneration strategy, seed dispersal mode and woody density. Overall, evergreen forest fragments exhibited the largest deviations from continuous forest plots in assemblage structure. Evergreen, Araucaria and deciduous forests diverge in the functional composition of tree floras, particularly in relation to regeneration strategy and stress tolerance. By supporting a more diversified light-demanding and stress-tolerant flora with reduced richness and abundance of shade-tolerant, old-growth species, both deciduous and Araucaria forest tree assemblages are more intrinsically resilient to contemporary human-disturbances, including fragmentation-induced edge effects, in terms of species erosion and functional shifts. We suggest that these intrinsic differences in the direction and magnitude of responses to changes in landscape structure between forest types should guide a wide range of conservation strategies in restoring fragmented tropical forest landscapes worldwide.

Markedly Divergent Tree Assemblage Responses to Tropical Forest Loss and Fragmentation across a Strong Seasonality Gradient

PubMed Central

Orihuela, Rodrigo L. L.; Peres, Carlos A.; Mendes, Gabriel; Jarenkow, João A.; Tabarelli, Marcelo

2015-01-01

We examine the effects of forest fragmentation on the structure and composition of tree assemblages within three seasonal and aseasonal forest types of southern Brazil, including evergreen, Araucaria, and deciduous forests. We sampled three southernmost Atlantic Forest landscapes, including the largest continuous forest protected areas within each forest type. Tree assemblages in each forest type were sampled within 10 plots of 0.1 ha in both continuous forests and 10 adjacent forest fragments. All trees within each plot were assigned to trait categories describing their regeneration strategy, vertical stratification, seed-dispersal mode, seed size, and wood density. We detected differences among both forest types and landscape contexts in terms of overall tree species richness, and the density and species richness of different functional groups in terms of regeneration strategy, seed dispersal mode and woody density. Overall, evergreen forest fragments exhibited the largest deviations from continuous forest plots in assemblage structure. Evergreen, Araucaria and deciduous forests diverge in the functional composition of tree floras, particularly in relation to regeneration strategy and stress tolerance. By supporting a more diversified light-demanding and stress-tolerant flora with reduced richness and abundance of shade-tolerant, old-growth species, both deciduous and Araucaria forest tree assemblages are more intrinsically resilient to contemporary human-disturbances, including fragmentation-induced edge effects, in terms of species erosion and functional shifts. We suggest that these intrinsic differences in the direction and magnitude of responses to changes in landscape structure between forest types should guide a wide range of conservation strategies in restoring fragmented tropical forest landscapes worldwide. PMID:26309252

Simultaneous detections of genetic fragment and single nucleotide mutation with a three-tiered output for tuberculosis diagnosis.

PubMed

Huang, Shih-Ying; Chang, Jia-Ru; Liao, Yu-Chieh; Dou, Horng-Yunn; Chuang, Min-Chieh

2018-05-12

Tuberculosis (TB) remains one of the major infectious diseases worldwide. The pathogenic bacterium, Mycobacterium tuberculosis (M.tb), continuously evolves strains carrying drug-resistance genes, thus posing a growing challenge to TB prevention and treatment. We report a diagnostic system that uses a molecular beacon probe and an assistant strand as the core to simultaneously interact with an M.tb-specific fragment (in IS6110) and a single nucleotide substitution (SNS)-encoded segment (in rpoB) associated with drug resistance. A single fluorescent output in three-tiered levels was produced for combinatorial interpretations based on formation of a four-way DNA junction (4WJ). The SNS caused the 4WJ to partially dissociate, thus resulting in medium-level fluorescence. By contrast, high- and low-level fluorescence, represented the complete complementary complex and absence of either targeted fragments, respectively. Manipulating the length of the analyte-binding arm realized the medium output. The thermodynamics and kinetics of 4WJ construction were investigated to maximize the tiered-output performance. Biocatalytic amplification driven by the Klenow Fragment and Nt.AlwI was incorporated into the method to enhance the signal 64-fold and ensure long-term stability of the three-tiered output. The detection accuracy of the sensing system was verified using unpurified amplicons with templates of extracted DNA and boiled bacterial solutions. The tiered-output mechanism was usable at bacterial loads ranging from 4 × 10 0 to 4 × 10 3  CFU per reaction. The interference caused by nontuberculous mycobacteria was minimal. The results demonstrated the integrity of the sensing method as an alternative strategy for rapid screening of M.tb and detecting rifampin-resistance. Copyright © 2017 Elsevier B.V. All rights reserved.

Identification of some ectomycorrhizal basidiomycetes by PCR amplification of their gpd (glyceraldehyde-3-phosphate dehydrogenase) genes.

PubMed Central

Kreuzinger, N; Podeu, R; Gruber, F; Göbl, F; Kubicek, C P

1996-01-01

Degenerated oligonucleotide primers designed to flank an approximately 1.2-kb fragment of the gene encoding glyceraldehyde-3-phosphate dehydrogenase (gpd) from ascomycetes and basidiomycetes were used to amplify the corresponding gpd fragments from several species of the ectomycorrhizal fungal taxa Boletus, Amanita, and Lactarius. Those from B. edulis, A. muscaria, and L. deterrimus were cloned and sequenced. The respective nucleotide sequences of these gene fragments showed a moderate degree of similarity (72 to 76%) in the protein-encoding regions and only a low degree of similarity in the introns (56 to 66%). Introns, where present, occurred at conserved positions, but the respective positions and numbers of introns in a given taxon varied. The amplified fragment from a given taxon could be distinguished from that of others by both restriction nuclease cleavage analysis and Southern hybridization. A procedure for labeling DNA probes with fluorescein-12-dUTP by PCR was developed. These probes were used in a nonradioactive hybridization assay, with which the gene could be detected in 2 ng of chromosomal DNA of L. deterrimus on slot blots. Taxon-specific amplification was achieved by the design of specific oligonucleotide primers. The application of the gpd gene for the identification of mycorrhizal fungi under field conditions was demonstrated, with Picea abies (spruce) mycorrhizal roots harvested from a northern alpine forest area as well as from a plant-breeding nursery. The interference by inhibitory substances, which sometimes occurred in the DNA extracted from the root-fungus mixture, could be overcome by using very diluted concentrations of template DNA for a first round of PCR amplification followed by a second round with nested oligonucleotide primers. We conclude that gpd can be used to detect ectomycorrhizal fungi during symbiotic interaction. PMID:8795234

Habitat fragmentation and its lasting impact on Earth’s ecosystems

PubMed Central

Haddad, Nick M.; Brudvig, Lars A.; Clobert, Jean; Davies, Kendi F.; Gonzalez, Andrew; Holt, Robert D.; Lovejoy, Thomas E.; Sexton, Joseph O.; Austin, Mike P.; Collins, Cathy D.; Cook, William M.; Damschen, Ellen I.; Ewers, Robert M.; Foster, Bryan L.; Jenkins, Clinton N.; King, Andrew J.; Laurance, William F.; Levey, Douglas J.; Margules, Chris R.; Melbourne, Brett A.; Nicholls, A. O.; Orrock, John L.; Song, Dan-Xia; Townshend, John R.

2015-01-01

We conducted an analysis of global forest cover to reveal that 70% of remaining forest is within 1 km of the forest’s edge, subject to the degrading effects of fragmentation. A synthesis of fragmentation experiments spanning multiple biomes and scales, five continents, and 35 years demonstrates that habitat fragmentation reduces biodiversity by 13 to 75% and impairs key ecosystem functions by decreasing biomass and altering nutrient cycles. Effects are greatest in the smallest and most isolated fragments, and they magnify with the passage of time. These findings indicate an urgent need for conservation and restoration measures to improve landscape connectivity, which will reduce extinction rates and help maintain ecosystem services. PMID:26601154

Angular distribution of scission neutrons studied with time-dependent Schrödinger equation

NASA Astrophysics Data System (ADS)

Wada, Takahiro; Asano, Tomomasa; Carjan, Nicolae

2018-03-01

We investigate the angular distribution of scission neutrons taking account of the effects of fission fragments. The time evolution of the wave function of the scission neutron is obtained by integrating the time-dependent Schrodinger equation numerically. The effects of the fission fragments are taken into account by means of the optical potentials. The angular distribution is strongly modified by the presence of the fragments. In the case of asymmetric fission, it is found that the heavy fragment has stronger effects. Dependence on the initial distribution and on the properties of fission fragments is discussed. We also discuss on the treatment of the boundary to avoid artificial reflections

Analytic second derivative of the energy for density-functional tight-binding combined with the fragment molecular orbital method

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

Nakata, Hiroya, E-mail: hiroya.nakata.gt@kyocera.jp; Nishimoto, Yoshio; Fedorov, Dmitri G.

2016-07-28

The analytic second derivative of the energy is developed for the fragment molecular orbital (FMO) method combined with density-functional tight-binding (DFTB), enabling simulations of infrared and Raman spectra of large molecular systems. The accuracy of the method is established in comparison to full DFTB without fragmentation for a set of representative systems. The performance of the FMO-DFTB Hessian is discussed for molecular systems containing up to 10 041 atoms. The method is applied to the study of the binding of α-cyclodextrin to polyethylene glycol, and the calculated IR spectrum of an epoxy amine oligomer reproduces experiment reasonably well.

Shock whilst gardening--implantable defibrillators & lawn mowers.

PubMed

Von Olshausen, G; Lennerz, C; Grebmer, C; Pavaci, H; Kolb, C

2014-02-01

Electromagnetic interference with implantable cardioverter defibrillators (ICDs) can cause inappropriate shock delivery or temporary inhibition of ICD functions. We present a case of electromagnetic interference between a lawn mower and an ICD resulting in an inappropriate discharge of the device due to erroneous detection of ventricular fibrillation.

The Coronal Tooth Fractures: Preliminary Evaluation of a Three-Year Follow-Up of the Anterior Teeth Direct Fragment Reattachment Technique Without Additional Preparation.

PubMed

Giudice G, Lo; A, Alibrandi; F, Lipari; A, Lizio; F, Lauritano; G, Cervino; M, Cicciù

2017-01-01

The aim of this research is to describe and to analyse the long-term results and the clinical steps of direct fragment reattachment technique with no additional tooth preparation, used to treat crown fracture. This technique achieves the clinical success, combining satisfactory aesthetic and functional results with a minimally invasive approach. The 3 years follow-up included 9 patients (5 males, 4 females) with coronal fracture. In all the cases the fragment was available and intact. The authors illustrate the adhesive procedure used. Under local anaesthesia and after positioning the rubber dam, both the tooth and the fragment surface were etched, rinsed and applied by the adhesive system in order to obtain the retention of the fractured part to the tooth without additional tooth preparation or resin cement. The statistical analysis shows the good performances of direct fragment reattachment technique. After 36 months, in 22.2% of the cases, the detachment was observed of the bonded fragment and in 11.1% of patients, complications were recorded. Our clinical experience shows how the ultra-conservative procedure used is fast, easy and offers a long term predictability; it also allows good functional and aesthetic outcomes.

Sleep fragmentation alters brain energy metabolism without modifying hippocampal electrophysiological response to novelty exposure.

PubMed

Baud, Maxime O; Parafita, Julia; Nguyen, Audrey; Magistretti, Pierre J; Petit, Jean-Marie

2016-10-01

Sleep is viewed as a fundamental restorative function of the brain, but its specific role in neural energy budget remains poorly understood. Sleep deprivation dampens brain energy metabolism and impairs cognitive functions. Intriguingly, sleep fragmentation, despite normal total sleep duration, has a similar cognitive impact, and in this paper we ask the question of whether it may also impair brain energy metabolism. To this end, we used a recently developed mouse model of 2 weeks of sleep fragmentation and measured 2-deoxy-glucose uptake and glycogen, glucose and lactate concentration in different brain regions. In order to homogenize mice behaviour during metabolic measurements, we exposed them to a novel environment for 1 h. Using an intra-hippocampal electrode, we first showed that hippocampal electroencephalograph (EEG) response to exploration was unaltered by 1 or 14 days of sleep fragmentation. However, after 14 days, sleep fragmented mice exhibited a lower uptake of 2-deoxy-glucose in cortex and hippocampus and lower cortical lactate levels than control mice. Our results suggest that long-term sleep fragmentation impaired brain metabolism to a similar extent as total sleep deprivation without affecting the neuronal responsiveness of hippocampus to a novel environment. © 2016 European Sleep Research Society.

A method to calculate fission-fragment yields Y(Z,N) versus proton and neutron number in the Brownian shape-motion model

DOE PAGES

Moller, Peter; Ichikawa, Takatoshi

2015-12-23

In this study, we propose a method to calculate the two-dimensional (2D) fission-fragment yield Y(Z,N) versus both proton and neutron number, with inclusion of odd-even staggering effects in both variables. The approach is to use the Brownian shape-motion on a macroscopic-microscopic potential-energy surface which, for a particular compound system is calculated versus four shape variables: elongation (quadrupole moment Q 2), neck d, left nascent fragment spheroidal deformation ϵ f1, right nascent fragment deformation ϵ f2 and two asymmetry variables, namely proton and neutron numbers in each of the two fragments. The extension of previous models 1) introduces a method tomore » calculate this generalized potential-energy function and 2) allows the correlated transfer of nucleon pairs in one step, in addition to sequential transfer. In the previous version the potential energy was calculated as a function of Z and N of the compound system and its shape, including the asymmetry of the shape. We outline here how to generalize the model from the “compound-system” model to a model where the emerging fragment proton and neutron numbers also enter, over and above the compound system composition.« less

Measurements of charge distributions of the fragments in the low energy fission reaction

NASA Astrophysics Data System (ADS)

Wang, Taofeng; Han, Hongyin; Meng, Qinghua; Wang, Liming; Zhu, Liping; Xia, Haihong

2013-01-01

The measurement for charge distributions of fragments in spontaneous fission 252Cf has been performed by using a unique style of detector setup consisting of a typical grid ionization chamber and a ΔΕ-Ε particle telescope, in which a thin grid ionization chamber served as the ΔΕ-section and the E-section was an Au-Si surface barrier detector. The typical physical quantities of fragments, such as mass number and kinetic energies as well as the deposition in the gas ΔΕ detector and E detector were derived from the coincident measurement data. The charge distributions of the light fragments for the fixed mass number A2* and total kinetic energy (TKE) were obtained by the least-squares fits for the response functions of the ΔΕ detector with multi-Gaussian functions representing the different elements. The results of the charge distributions for some typical fragments are shown in this article which indicates that this detection setup has the charge distribution capability of Ζ:ΔΖ>40:1. The experimental method developed in this work for determining the charge distributions of fragments is expected to be employed in the neutron induced fissions of 232Th and 238U or other low energy fission reactions.

Mesophilic and hyperthermophilic adenylate kinases differ in their tolerance to random fragmentation.

PubMed

Segall-Shapiro, Thomas H; Nguyen, Peter Q; Dos Santos, Edgardo D; Subedi, Saurav; Judd, Justin; Suh, Junghae; Silberg, Jonathan J

2011-02-11

The extent to which thermostability influences the location of protein fragmentation sites that allow retention of function is not known. To evaluate this, we used a novel transposase-based approach to create libraries of vectors that express structurally-related fragments of Bacillus subtilis adenylate kinase (BsAK) and Thermotoga neapolitana adenylate kinase (TnAK) with identical modifications at their termini, and we selected for variants in each library that complement the growth of Escherichia coli with a temperature-sensitive adenylate kinase (AK). Mutants created using the hyperthermophilic TnAK were found to support growth with a higher frequency (44%) than those generated from the mesophilic BsAK (6%), and selected TnAK mutants complemented E. coli growth more strongly than homologous BsAK variants. Sequencing of functional clones from each library also identified a greater dispersion of fragmentation sites within TnAK. Nondisruptive fission sites were observed within the AMP binding and core domains of both AK homologs. However, only TnAK contained sites within the lid domain, which undergoes dynamic fluctuations that are critical for catalysis. These findings implicate the flexible lid domain as having an increased sensitivity to fission events at physiological temperatures. In addition, they provide evidence that comparisons of nondisruptive fission sites in homologous proteins could be useful for finding dynamic regions whose conformational fluctuations are important for function, and they show that the discovery of protein fragments that cooperatively function in mesophiles can be aided by the use of thermophilic enzymes as starting points for protein design. Copyright © 2010 Elsevier Ltd. All rights reserved.

Experimental modelling of fragmentation applied to volcanic explosions

NASA Astrophysics Data System (ADS)

Haug, Øystein Thordén; Galland, Olivier; Gisler, Galen R.

2013-12-01

Explosions during volcanic eruptions cause fragmentation of magma and host rock, resulting in fragments with sizes ranging from boulders to fine ash. The products can be described by fragment size distributions (FSD), which commonly follow power laws with exponent D. The processes that lead to power-law distributions and the physical parameters that control D remain unknown. We developed a quantitative experimental procedure to study the physics of the fragmentation process through time. The apparatus consists of a Hele-Shaw cell containing a layer of cohesive silica flour that is fragmented by a rapid injection of pressurized air. The evolving fragmentation of the flour is monitored with a high-speed camera, and the images are analysed to obtain the evolution of the number of fragments (N), their average size (A), and the FSD. Using the results from our image-analysis procedure, we find transient empirical laws for N, A and the exponent D of the power-law FSD as functions of the initial air pressure. We show that our experimental procedure is a promising tool for unravelling the complex physics of fragmentation during phreatomagmatic and phreatic eruptions.

Active Fragments from Pro- and Antiapoptotic BCL-2 Proteins Have Distinct Membrane Behavior Reflecting Their Functional Divergence

PubMed Central

Guillemin, Yannis; Lopez, Jonathan; Gimenez, Diana; Fuertes, Gustavo; Valero, Juan Garcia; Blum, Loïc; Gonzalo, Philippe; Salgado, Jesùs; Girard-Egrot, Agnès; Aouacheria, Abdel

2010-01-01

Background The BCL-2 family of proteins includes pro- and antiapoptotic members acting by controlling the permeabilization of mitochondria. Although the association of these proteins with the outer mitochondrial membrane is crucial for their function, little is known about the characteristics of this interaction. Methodology/Principal Findings Here, we followed a reductionist approach to clarify to what extent membrane-active regions of homologous BCL-2 family proteins contribute to their functional divergence. Using isolated mitochondria as well as model lipid Langmuir monolayers coupled with Brewster Angle Microscopy, we explored systematically and comparatively the membrane activity and membrane-peptide interactions of fragments derived from the central helical hairpin of BAX, BCL-xL and BID. The results show a connection between the differing abilities of the assayed peptide fragments to contact, insert, destabilize and porate membranes and the activity of their cognate proteins in programmed cell death. Conclusion/Significance BCL-2 family-derived pore-forming helices thus represent structurally analogous, but functionally dissimilar membrane domains. PMID:20140092

Lead generation and examples opinion regarding how to follow up hits.

PubMed

Orita, Masaya; Ohno, Kazuki; Warizaya, Masaichi; Amano, Yasushi; Niimi, Tatsuya

2011-01-01

In fragment-based drug discovery (FBDD), not only identifying the starting fragment hit to be developed but also generating a drug lead from that starting fragment hit is important. Converting fragment hits to leads is generally similar to a high-throughput screening (HTS) hits-to-leads approach in that properties associated with activity for a target protein, such as selectivity against other targets and absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox), and physicochemical properties should be taken into account. However, enhancing the potency of the fragment hit is a key requirement in FBDD, unlike HTS, because initial fragment hits are generally weak. This enhancement is presently achieved by adding additional chemical groups which bind to additional parts of the target protein or by joining or combining two or more hit fragments; however, strategies for effecting greater improvements in effective activity are needed. X-ray analysis is a key technology attractive for converting fragments to drug leads. This method makes it clear whether a fragment hit can act as an anchor and provides insight regarding introduction of functional groups to improve fragment activity. Data on follow-up chemical synthesis of fragment hits has allowed for the differentiation of four different strategies: fragment optimization, fragment linking, fragment self-assembly, and fragment evolution. Here, we discuss our opinion regarding how to follow up on fragment hits, with a focus on the importance of fragment hits as an anchor moiety to so-called hot spots in the target protein using crystallographic data. Copyright © 2011 Elsevier Inc. All rights reserved.

Finite-element computer program for axisymmetric loading situations where components may have a relative interference fit

NASA Technical Reports Server (NTRS)

Taylor, C. M.

1977-01-01

A finite element computer program which enables the analysis of distortions and stresses occurring in compounds having a relative interference is presented. The program is limited to situations in which the loading is axisymmetric. Loads arising from the interference fit(s) and external, inertial, and thermal loadings are accommodated. The components comprise several different homogeneous isotropic materials whose properties may be a function of temperature. An example illustrating the data input and program output is given.

Experimental Evidence for Quantum Interference and Vibrationally Induced Decoherence in Single-Molecule Junctions

NASA Astrophysics Data System (ADS)

Ballmann, Stefan; Härtle, Rainer; Coto, Pedro B.; Elbing, Mark; Mayor, Marcel; Bryce, Martin R.; Thoss, Michael; Weber, Heiko B.

2012-08-01

We analyze quantum interference and decoherence effects in single-molecule junctions both experimentally and theoretically by means of the mechanically controlled break junction technique and density-functional theory. We consider the case where interference is provided by overlapping quasidegenerate states. Decoherence mechanisms arising from electronic-vibrational coupling strongly affect the electrical current flowing through a single-molecule contact and can be controlled by temperature variation. Our findings underline the universal relevance of vibrations for understanding charge transport through molecular junctions.

Experimental evidence for quantum interference and vibrationally induced decoherence in single-molecule junctions.

PubMed

Ballmann, Stefan; Härtle, Rainer; Coto, Pedro B; Elbing, Mark; Mayor, Marcel; Bryce, Martin R; Thoss, Michael; Weber, Heiko B

2012-08-03

We analyze quantum interference and decoherence effects in single-molecule junctions both experimentally and theoretically by means of the mechanically controlled break junction technique and density-functional theory. We consider the case where interference is provided by overlapping quasidegenerate states. Decoherence mechanisms arising from electronic-vibrational coupling strongly affect the electrical current flowing through a single-molecule contact and can be controlled by temperature variation. Our findings underline the universal relevance of vibrations for understanding charge transport through molecular junctions.

Quasiparticle interference in multiband superconductors with strong coupling

NASA Astrophysics Data System (ADS)

Dutt, A.; Golubov, A. A.; Dolgov, O. V.; Efremov, D. V.

2017-08-01

We develop a theory of the quasiparticle interference (QPI) in multiband superconductors based on the strong-coupling Eliashberg approach within the Born approximation. In the framework of this theory, we study dependencies of the QPI response function in the multiband superconductors with the nodeless s -wave superconductive order parameter. We pay special attention to the difference in the quasiparticle scattering between the bands having the same and opposite signs of the order parameter. We show that at the momentum values close to the momentum transfer between two bands, the energy dependence of the quasiparticle interference response function has three singularities. Two of these correspond to the values of the gap functions and the third one depends on both the gaps and the transfer momentum. We argue that only the singularity near the smallest band gap may be used as a universal tool to distinguish between the s++ and s± order parameters. The robustness of the sign of the response function peak near the smaller gap value, irrespective of the change in parameters, in both the symmetry cases is a promising feature that can be harnessed experimentally.

Route to three-dimensional fragments using diversity-oriented synthesis

PubMed Central

Hung, Alvin W.; Ramek, Alex; Wang, Yikai; Kaya, Taner; Wilson, J. Anthony; Clemons, Paul A.; Young, Damian W.

2011-01-01

Fragment-based drug discovery (FBDD) has proven to be an effective means of producing high-quality chemical ligands as starting points for drug-discovery pursuits. The increasing number of clinical candidate drugs developed using FBDD approaches is a testament of the efficacy of this approach. The success of fragment-based methods is highly dependent on the identity of the fragment library used for screening. The vast majority of FBDD has centered on the use of sp2-rich aromatic compounds. An expanded set of fragments that possess more 3D character would provide access to a larger chemical space of fragments than those currently used. Diversity-oriented synthesis (DOS) aims to efficiently generate a set of molecules diverse in skeletal and stereochemical properties. Molecules derived from DOS have also displayed significant success in the modulation of function of various “difficult” targets. Herein, we describe the application of DOS toward the construction of a unique set of fragments containing highly sp3-rich skeletons for fragment-based screening. Using cheminformatic analysis, we quantified the shapes and physical properties of the new 3D fragments and compared them with a database containing known fragment-like molecules. PMID:21482811

Route to three-dimensional fragments using diversity-oriented synthesis.

PubMed

Hung, Alvin W; Ramek, Alex; Wang, Yikai; Kaya, Taner; Wilson, J Anthony; Clemons, Paul A; Young, Damian W

2011-04-26

Fragment-based drug discovery (FBDD) has proven to be an effective means of producing high-quality chemical ligands as starting points for drug-discovery pursuits. The increasing number of clinical candidate drugs developed using FBDD approaches is a testament of the efficacy of this approach. The success of fragment-based methods is highly dependent on the identity of the fragment library used for screening. The vast majority of FBDD has centered on the use of sp(2)-rich aromatic compounds. An expanded set of fragments that possess more 3D character would provide access to a larger chemical space of fragments than those currently used. Diversity-oriented synthesis (DOS) aims to efficiently generate a set of molecules diverse in skeletal and stereochemical properties. Molecules derived from DOS have also displayed significant success in the modulation of function of various "difficult" targets. Herein, we describe the application of DOS toward the construction of a unique set of fragments containing highly sp(3)-rich skeletons for fragment-based screening. Using cheminformatic analysis, we quantified the shapes and physical properties of the new 3D fragments and compared them with a database containing known fragment-like molecules.

[Fragment-based drug discovery: concept and aim].

PubMed

Tanaka, Daisuke

2010-03-01

Fragment-Based Drug Discovery (FBDD) has been recognized as a newly emerging lead discovery methodology that involves biophysical fragment screening and chemistry-driven fragment-to-lead stages. Although fragments, defined as structurally simple and small compounds (typically <300 Da), have not been employed in conventional high-throughput screening (HTS), the recent significant progress in the biophysical screening methods enables fragment screening at a practical level. The intention of FBDD primarily turns our attention to weakly but specifically binding fragments (hit fragments) as the starting point of medicinal chemistry. Hit fragments are then promoted to more potent lead compounds through linking or merging with another hit fragment and/or attaching functional groups. Another positive aspect of FBDD is ligand efficiency. Ligand efficiency is a useful guide in screening hit selection and hit-to-lead phases to achieve lead-likeness. Owing to these features, a number of successful applications of FBDD to "undruggable targets" (where HTS and other lead identification methods failed to identify useful lead compounds) have been reported. As a result, FBDD is now expected to complement more conventional methodologies. This review, as an introduction of the following articles, will summarize the fundamental concepts of FBDD and will discuss its advantages over other conventional drug discovery approaches.

Top-Down Hydrogen-Deuterium Exchange Analysis of Protein Structures Using Ultraviolet Photodissociation.

PubMed

Brodie, Nicholas I; Huguet, Romain; Zhang, Terry; Viner, Rosa; Zabrouskov, Vlad; Pan, Jingxi; Petrotchenko, Evgeniy V; Borchers, Christoph H

2018-03-06

Top-down hydrogen-deuterium exchange (HDX) analysis using electron capture or transfer dissociation Fourier transform mass spectrometry (FTMS) is a powerful method for the analysis of secondary structure of proteins in solution. The resolution of the method is a function of the degree of fragmentation of backbone bonds in the proteins. While fragmentation is usually extensive near the N- and C-termini, electron capture (ECD) or electron transfer dissociation (ETD) fragmentation methods sometimes lack good coverage of certain regions of the protein, most often in the middle of the sequence. Ultraviolet photodissociation (UVPD) is a recently developed fast-fragmentation technique, which provides extensive backbone fragmentation that can be complementary in sequence coverage to the aforementioned electron-based fragmentation techniques. Here, we explore the application of electrospray ionization (ESI)-UVPD FTMS on an Orbitrap Fusion Lumos Tribrid mass spectrometer to top-down HDX analysis of proteins. We have incorporated UVPD-specific fragment-ion types and fragment-ion mixtures into our isotopic envelope fitting software (HDX Match) for the top-down HDX analysis. We have shown that UVPD data is complementary to ETD, thus improving the overall resolution when used as a combined approach.

Participant and spectator scaling of spectator fragments in Au + Au and Cu + Cu collisions at s N N = 19.6 and 22.4 GeV

DOE PAGES

Alver, B.; Back, B. B.; Baker, M. D.; ...

2016-08-02

Specmore » tator fragments resulting from relativistic heavy ion collisions, consisting of single protons and neutrons along with groups of stable nuclear fragments up to nitrogen (Z = 7), are measured in PHOBOS. These fragments are observed in Au+Au ( s N N = 19.6 GeV) and Cu+Cu (22.4 GeV) collisions at high pseudorapidity (η). The dominant multiply-charged fragment is the tightly bound helium (α), with lithium, beryllium, and boron all clearly seen as a function of collision centrality and pseudorapidity. In this paper, we observe that in Cu+Cu collisions, it becomes much more favorable for the α fragments to be released than lithium. The yields of fragments approximately scale with the number of spectator nucleons, independent of the colliding ion. The shapes of the pseudorapidity distributions of fragments indicate that the average deflection of the fragments away from the beam direction increases for more central collisions. Finally, a detailed comparison of the shapes for α and lithium fragments indicates that the centrality dependence of the deflections favors a scaling with the number of participants in the collision.« less

Participant and spectator scaling of spectator fragments in Au + Au and Cu + Cu collisions at √{sN N}=19.6 and 22.4 GeV

NASA Astrophysics Data System (ADS)

Alver, B.; Back, B. B.; Baker, M. D.; Ballintijn, M.; Barton, D. S.; Betts, R. R.; Bickley, A. A.; Bindel, R.; Budzanowski, A.; Busza, W.; Carroll, A.; Chai, Z.; Chetluru, V.; Decowski, M. P.; García, E.; Gburek, T.; George, N.; Gulbrandsen, K.; Gushue, S.; Halliwell, C.; Hamblen, J.; Harnarine, I.; Heintzelman, G. A.; Henderson, C.; Hofman, D. J.; Hollis, R. S.; Hołyński, R.; Holzman, B.; Iordanova, A.; Johnson, E.; Kane, J. L.; Katzy, J.; Khan, N.; Kucewicz, W.; Kulinich, P.; Kuo, C. M.; Li, W.; Lin, W. T.; Loizides, C.; Manly, S.; McLeod, D.; Mignerey, A. C.; Nouicer, R.; Olszewski, A.; Pak, R.; Park, I. C.; Pernegger, H.; Reed, C.; Remsberg, L. P.; Reuter, M.; Richardson, E.; Roland, C.; Roland, G.; Rosenberg, L.; Sagerer, J.; Sarin, P.; Sawicki, P.; Sedykh, I.; Skulski, W.; Smith, C. E.; Stankiewicz, M. A.; Steinberg, P.; Stephans, G. S. F.; Sukhanov, A.; Szostak, A.; Tang, J.-L.; Tonjes, M. B.; Trzupek, A.; Vale, C.; van Nieuwenhuizen, G. J.; Vaurynovich, S. S.; Verdier, R.; Veres, G. I.; Walters, P.; Wenger, E.; Willhelm, D.; Wolfs, F. L. H.; Wosiek, B.; Woźniak, K.; Wuosmaa, A. H.; Wyngaardt, S.; Wysłouch, B.; Phobos Collaboration

2016-08-01

Spectator fragments resulting from relativistic heavy ion collisions, consisting of single protons and neutrons along with groups of stable nuclear fragments up to nitrogen (Z =7 ), are measured in PHOBOS. These fragments are observed in Au+Au (√{sNN}=19.6 GeV ) and Cu+Cu (22.4 GeV) collisions at high pseudorapidity (η ). The dominant multiply-charged fragment is the tightly bound helium (α ), with lithium, beryllium, and boron all clearly seen as a function of collision centrality and pseudorapidity. We observe that in Cu+Cu collisions, it becomes much more favorable for the α fragments to be released than lithium. The yields of fragments approximately scale with the number of spectator nucleons, independent of the colliding ion. The shapes of the pseudorapidity distributions of fragments indicate that the average deflection of the fragments away from the beam direction increases for more central collisions. A detailed comparison of the shapes for α and lithium fragments indicates that the centrality dependence of the deflections favors a scaling with the number of participants in the collision.

Coulomb Interactions in Hanbury Brown-Twiss Experiments with Electrons

ERIC Educational Resources Information Center

Shen, Kan

2009-01-01

This dissertation examines the effect of Coulomb interactions in Hanbury Brown-Twiss (HBT) type experiments with electrons. HBT experiments deal with intensity interference, which is related to the second-order correlation function of the particle field. This is an extension of the usual amplitude interference experiment, such as Young's…

Effect of gender, facial dimensions, body mass index and type of functional occlusion on bite force.

PubMed

Koç, Duygu; Doğan, Arife; Bek, Bülent

2011-01-01

Some factors such as gender, age, craniofacial morphology, body structure, occlusal contact patterns may affect the maximum bite force. Thus, the purposes of this study were to determine the mean maximum bite force in individuals with normal occlusion, and to examine the effect of gender, facial dimensions, body mass index (BMI), type of functional occlusion (canine guidance and group function occlusion) and balancing side interferences on it. Thirty-four individuals aged 19-20 years-old were selected for this study. Maximum bite force was measured with strain-gauge transducers at first molar region. Facial dimensions were defined by standardized frontal photographs as follows: anterior total facial height (ATFH), bizygomathic facial width (BFW) and intergonial width (IGW). BMI was calculated using the equation weight/height². The type of functional occlusion and the balancing side interferences of the subjects were identified by clinical examination. Bite force was found to be significantly higher in men than women (p<0.05). While there was a negative correlation between the bite force and ATFH/BFW, ATFH/IGW ratios in men (p<0.05), women did not show any statistically significant correlation (p>0.05). BMI and bite force correlation was not statistically significant (p>0.05). The average bite force did not differ in subjects with canine guidance or group function occlusion and in the presence of balancing side interferences (p>0.05). Data suggest that bite force is affected by gender. However, BMI, type of functional occlusion and the presence of balancing side interferences did not exert a meaningful influence on bite force. In addition, transverse facial dimensions showed correlation with bite force in only men.

Apolipoprotein E4 (1-272) fragment is associated with mitochondrial proteins and affects mitochondrial function in neuronal cells.

PubMed

Nakamura, Toshiyuki; Watanabe, Atsushi; Fujino, Takahiro; Hosono, Takashi; Michikawa, Makoto

2009-08-20

Apolipoprotein E allele epsilon4 (apoE4) is a strong risk factor for developing Alzheimer's disease (AD). Secreted apoE has a critical function in redistributing lipids among central nervous system cells to maintain normal lipid homeostasis. In addition, previous reports have shown that apoE4 is cleaved by a protease in neurons to generate apoE4(1-272) fragment, which is associated with neurofibrillary tanglelike structures and mitochondria, causing mitochondrial dysfunction. However, it still remains unclear how the apoE fragment associates with mitochondria and induces mitochondrial dysfunction. To clarify the molecular mechanism, we carried out experiments to identify intracellular apoE-binding molecules and their functions in modulating mitochondria function. Here, we found that apoE4 binds to ubiquinol cytochrome c reductase core protein 2 (UQCRC2) and cytochrome C1, both of which are components of mitochondrial respiratory complex III, and cytochrome c oxidase subunit 4 isoform 1 (COX IV 1), which is a component of complex IV, in Neuro-2a cells. Interestingly, these proteins associated with apoE4(1-272) more strongly than intact apoE4(1-299). Further analysis showed that in Neuro-2a cells expressing apoE4(1-272), the enzymatic activities of mitochondrial respiratory complexes III and IV were significantly lower than those in Neuro-2a cells expressing apoE4(1-299). ApoE4(1-272) fragment expressed in Neuro2a cells is associated with mitochondrial proteins, UQCRC2 and cytochrome C1, which are component of respiratory complex III, and with COX IV 1, which is a member of complex IV. Overexpression of apoE4(1-272) fragment impairs activities of complex III and IV. These results suggest that the C-terminal-truncated fragment of apoE4 binds to mitochondrial complexes and affects their activities, and thereby leading to neurodegeneration.

From a remarkable manifestation of polar effects in a radical fragmentation to the convergent synthesis of highly functionalized ketones.

PubMed

Debien, Laurent; Zard, Samir Z

2013-03-13

A new radical addition/C-C bond fragmentation process is reported. Vinyl carbinols derived from 2-methyl-2-phenylpropanal react with radicals generated from xanthates to give the corresponding ketones. The radical cleavage reaction proceeds under mild conditions, in good to high yield, and in the presence of the unprotected carbinol. Highly functionalized 1,5-diketones and pyridines are readily available using this approach.

Critical analysis of fragment-orbital DFT schemes for the calculation of electronic coupling values

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

Schober, Christoph; Reuter, Karsten; Oberhofer, Harald, E-mail: harald.oberhofer@ch.tum.de

2016-02-07

We present a critical analysis of the popular fragment-orbital density-functional theory (FO-DFT) scheme for the calculation of electronic coupling values. We discuss the characteristics of different possible formulations or “flavors” of the scheme which differ by the number of electrons in the calculation of the fragments and the construction of the Hamiltonian. In addition to two previously described variants based on neutral fragments, we present a third version taking a different route to the approximate diabatic state by explicitly considering charged fragments. In applying these FO-DFT flavors to the two molecular test sets HAB7 (electron transfer) and HAB11 (hole transfer),more » we find that our new scheme gives improved electronic couplings for HAB7 (−6.2% decrease in mean relative signed error) and greatly improved electronic couplings for HAB11 (−15.3% decrease in mean relative signed error). A systematic investigation of the influence of exact exchange on the electronic coupling values shows that the use of hybrid functionals in FO-DFT calculations improves the electronic couplings, giving values close to or even better than more sophisticated constrained DFT calculations. Comparing the accuracy and computational cost of each variant, we devise simple rules to choose the best possible flavor depending on the task. For accuracy, our new scheme with charged-fragment calculations performs best, while numerically more efficient at reasonable accuracy is the variant with neutral fragments.« less

Self-aggregation and coaggregation of the p53 core fragment with its aggregation gatekeeper variant.

PubMed

Lei, Jiangtao; Qi, Ruxi; Wei, Guanghong; Nussinov, Ruth; Ma, Buyong

2016-03-21

Recent studies suggested that p53 aggregation can lead to loss-of-function (LoF), dominant-negative (DN) and gain-of-function (GoF) effects, with adverse cancer consequences. The p53 aggregation-nucleating (251)ILTIITL(257) fragment is a key segment in wild-type p53 aggregation; however, an I254R mutation can prevent it. It was suggested that self-assembly of wild-type p53 and its cross-interaction with mutants differ from the classical amyloid nucleation-growth mechanism. Here, using replica exchange molecular dynamics (REMD) simulations, we studied the cross-interactions of this p53 core fragment and its aggregation rescue I254R mutant. We found that the core fragment displays strong aggregation propensity, whereas the gatekeeper I254R mutant tends to be disordered, consistent with experiments. Our cross-interaction results reveal that the wild-type p53 fragment promotes β-sheet formation of the I254R mutant by shifting the disordered mutant peptides into aggregating states. As a result, the system has similar oligomeric structures, inter-peptide interactions and free energy landscape as the wild type fragment does, revealing a prion-like process. We also found that in the cross-interaction system, the wild-type species has higher tendency to interact with the mutant than with itself. This phenomenon illustrates synergistic effects between the p53 (251)ILTIITL(257) fragment and the mutant resembling prion cross-species propagation, cautioning against exploiting it in drug discovery.

Semi-empirical fragmentation model of meteoroid motion and radiation during atmospheric penetration

NASA Astrophysics Data System (ADS)

Revelle, D. O.; Ceplecha, Z.

2002-11-01

A semi-empirical fragmentation model (FM) of meteoroid motion, ablation, and radiation including two types of fragmentation is outlined. The FM was applied to observational data (height as function of time and the light curve) of Lost City, Innisfree and Benešov bolides. For the Lost City bolide we were able to fit the FM to the observed height as function of time with ±13 m and to the observed light curve with ±0.17 magnitude. Corresponding numbers for Innisfree are ±25 m and ±0.14 magnitude, and for Benešov ±46 m and ±0.19 magnitude. We also define apparent and intrinsic values of σ, K, and τ. Using older results and our fit of FM to the Lost City bolide we derived corrections to intrinsic luminous efficiencies expressed as functions of velocity, mass, and normalized air density.

Brain levels of high-energy phosphate metabolites and executive function in geriatric depression.

PubMed

Harper, David G; Joe, Elizabeth B; Jensen, J Eric; Ravichandran, Caitlin; Forester, Brent P

2016-11-01

Depression in late life has been associated with difficulties in cognitive processing, particularly in the domains of executive function, processing speed and memory, and increases the risk of developing dementia suggesting a neurodegenerative phenotype. Mitochondrial dysfunction is frequently an early event in neurodegenerative illnesses and may be operative in patients with late life depression. Phosphorus magnetic resonance spectroscopy (31P MRS) allows for the quantification of bioenergetic molecules produced by mitochondria. Ten patients with late life depression and eight normal elderly controls were studied with Stroop color and interference tests, which are widely used measures of processing speed and executive function, respectively, followed by (31P) MRS 3-dimensional chemical-shift imaging measuring levels of adenosine triphosphate, phosphocreatine, inorganic phosphate, and pH over the whole brain. In all subjects, gray matter phosphocreatine was positively associated with Stroop interference. Levels of white matter adenosine triphosphate were associated with Stroop interference in subjects with late life depression but not normal elderly. There was also a complementary association between white matter inorganic phosphate and Stroop interference in late life depression patients. These findings suggest two independent sources of executive function dependence on bioenergetic state in the aging brain. The dependence of executive function performance in subjects with late life depression on ATP in white matter may be associated with mitochondrial impairment and is consistent with predictions of the vascular depression hypothesis. Further research with wider neuropsychological testing targeting bioenergetic markers could help clarify the scope of these effects. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Dimensional crossover in fragmentation

NASA Astrophysics Data System (ADS)

Sotolongo-Costa, Oscar; Rodriguez, Arezky H.; Rodgers, G. J.

2000-11-01

Experiments in which thick clay plates and glass rods are fractured have revealed different behavior of fragment mass distribution function in the small and large fragment regions. In this paper we explain this behavior using non-extensive Tsallis statistics and show how the crossover between the two regions is caused by the change in the fragments’ dimensionality during the fracture process. We obtain a physical criterion for the position of this crossover and an expression for the change in the power-law exponent between the small and large fragment regions. These predictions are in good agreement with the experiments on thick clay plates.

Final excitation energy of fission fragments

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

Schmidt, Karl-Heinz; Jurado, Beatriz

We study how the excitation energy of the fully accelerated fission fragments is built up. It is stressed that only the intrinsic excitation energy available before scission can be exchanged between the fission fragments to achieve thermal equilibrium. This is in contradiction with most models used to calculate prompt neutron emission, where it is assumed that the total excitation energy of the final fragments is shared between the fragments by the condition of equal temperatures. We also study the intrinsic excitation-energy partition in statistical equilibrium for different level-density descriptions as a function of the total intrinsic excitation energy of themore » fissioning system. Excitation energies are found to be strongly enhanced in the heavy fragment, if the level density follows a constant-temperature behavior at low energies, e.g., in the composed Gilbert-Cameron description.« less

The association between aerobic fitness and cognitive function in older men mediated by frontal lateralization.

PubMed

Hyodo, Kazuki; Dan, Ippeita; Kyutoku, Yasushi; Suwabe, Kazuya; Byun, Kyeongho; Ochi, Genta; Kato, Morimasa; Soya, Hideaki

2016-01-15

Previous studies have shown that higher aerobic fitness is related to higher cognitive function and higher task-related prefrontal activation in older adults. However, a holistic picture of these factors has yet to be presented. As a typical age-related change of brain activation, less lateralized activity in the prefrontal cortex during cognitive tasks has been observed in various neuroimaging studies. Thus, this study aimed to reveal the relationship between aerobic fitness, cognitive function, and frontal lateralization. Sixty male older adults each performed a submaximal incremental exercise test to determine their oxygen intake (V·O2) at ventilatory threshold (VT) in order to index their aerobic fitness. They performed a color-word Stroop task while prefrontal activation was monitored using functional near infrared spectroscopy. As an index of cognitive function, Stroop interference time was analyzed. Partial correlation analyses revealed significant correlations among higher VT, shorter Stroop interference time and greater left-lateralized dorsolateral prefrontal cortex (DLPFC) activation when adjusting for education. Moreover, mediation analyses showed that left-lateralized DLPFC activation significantly mediated the association between VT and Stroop interference time. These results suggest that higher aerobic fitness is associated with cognitive function via lateralized frontal activation in older adults. Copyright © 2015 Elsevier Inc. All rights reserved.

Effects of Mixtures on Liquid and Solid Fragment Size Distributions

DTIC Science & Technology

2016-05-01

bins, too few size bins, fixed bin widths, or inadequately- varying bin widths. Overpopulated bins – which typically occur for smaller fragments...2010 C. V. B. Cunningham, The Kuz-Ram Fragmentation Model – 20 Years On, In R. Holmberg et. al., Editors, Proceedings of the 3 rd World ...1992 P. K. Sahoo and T. Riedel, Mean Value Theorems and Functional Equations, World Scientific, 1998 K. A. Sallam, C. Aalburg, G.M. Faeth

Effect of a High-Intensity, Intermittent-Exercise Protocol on Neurocognitive Function in Healthy Adults: Implications for Return-to-Play Management After Sport-Related Concussion.

PubMed

Whyte, Enda F; Gibbons, Nicola; Kerr, Grainne; Moran, Kieran A

2015-12-03

Determination of return to play (RTP) after sport-related concussion (SRC) is critical given the potential consequences of premature RTP. Current RTP guidelines may not identify persistent exercise-induced neurocognitive deficits in asymptomatic athletes after SRC. Therefore, postexercise neurocognitive testing has been recommended to further inform RTP determination. To implement this recommendation, the effect of exercise on neurocognitive function in healthy athletes should be understood. To examine the acute effects of a high-intensity intermittent-exercise protocol (HIIP) on neurocognitive function assessed by the Symbol Digits Modality Test (SDMT) and Stroop Interference Test. Cohort study. University laboratory. 40 healthy male athletes (age 21.25 ± 1.29 y, education 16.95 ± 1.37 y). Each participant completed the SDMT and Stroop Interference Test at baseline and after random allocation to a condition (HIIP vs control). A mixed between-within-subjects ANOVA assessed time- (pre- vs postcondition) -by-condition interaction effects. SDMT and Stroop Interference Test scores. There was a significant time-by-condition interaction effect (P < .001, η2 = .364) for the Stroop Interference Test scores, indicating that the HIIP group scored significantly lower (56.05 ± 9.34) postcondition than the control group (66.39 ± 19.6). There was no significant time-by-condition effect (P = .997, η2 < .001) for the SDMT, indicating that there was no difference between SDMT scores for the HIIP and control groups (59.95 ± 10.7 vs 58.56 ± 14.02). In healthy athletes, the HIIP results in a reduction in neurocognitive function as assessed by the Stroop Interference Test, with no effect on function as assessed by the SDMT. Testing should also be considered after high-intensity exercise in determining RTP decisions for athletes after SRC in conjunction with the existing recommended RTP protocol. These results may provide an initial reference point for future research investigating the effects of an HIIP on the neurocognitive function of athletes recovering from SRC.

Observation of medium induced modifications of jet fragmentation in PbPb collisions using isolated-photon-tagged jets

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

Sirunyan, Albert M; et al.

Measurements of fragmentation functions for jets associated with an isolated photon are presented for the first time in pp and PbPb collisions. The analysis uses data collected with the CMS detector at the CERN LHC at a nucleon-nucleon center-of-mass energy of 5.02 TeV. Fragmentation functions are obtained for jets with pmore » $$_\\mathrm{T}^\\text{jet} >$$ 30 GeV in events containing an isolated photon with p$$_\\mathrm{T}^\\gamma>$$ 60 GeV, using charged tracks with transverse momentum p$$_\\mathrm{T}^\\text{trk} >$$ 1 GeV in a cone around the jet axis. The association with an isolated photon constrains the initial p$$_\\mathrm{T}$$ and azimuthal angle of the parton whose shower produced the jet. For central PbPb collisions, modifications of the jet fragmentation functions are observed when compared to those measured in pp collisions, while no significant differences are found in the 50% most peripheral collisions. Jets in central PbPb events show an excess (depletion) of low (high) p$$_\\mathrm{T}$$ particles, with a transition around 3 GeV.« less

Interpretation of scanning tunneling quasiparticle interference and impurity states in cuprates

DOE PAGES

Kreisel, Andreas; Choubey, Peayush; Berlijn, Tom; ...

2015-05-27

We apply a recently developed method combining first principles based Wannier functions with solutions to the Bogoliubov–de Gennes equations to the problem of interpreting STM data in cuprate superconductors. We show that the observed images of Zn on the surface of Bi 2Sr 2CaCu 2O 8 can only be understood by accounting for the tails of the Cu Wannier functions, which include significant weight on apical O sites in neighboring unit cells. This calculation thus puts earlier crude “filter” theories on a microscopic foundation and solves a long-standing puzzle. We then study quasiparticle interference phenomena induced by out-of-plane weak potentialmore » scatterers, and show how patterns long observed in cuprates can be understood in terms of the interference of Wannier functions above the surface. Furthermore, our results show excellent agreement with experiment and enable a better understanding of novel phenomena in the cuprates via STM imaging.« less

Age-related changes in overcoming proactive interference in associative memory: The role of PFC-mediated executive control processes at retrieval.

PubMed

Dulas, Michael R; Duarte, Audrey

2016-05-15

Behavioral evidence has shown age-related impairments in overcoming proactive interference in memory, but it is unclear what underlies this deficit. Imaging studies in the young suggest overcoming interference may require several executive control processes supported by the ventrolateral prefrontal cortex (VLPFC) and dorsolateral PFC (DLPFC). The present functional magnetic resonance imaging (fMRI) study investigated whether age-related changes in dissociable executive control processes underlie deficits in overcoming proactive interference in associative memory during retrieval. Participants were tasked with remembering which associate (face or scene) objects were paired with most recently during study, under conditions of high or low proactive interference. Behavioral results demonstrated that, as interference increased, memory performance decreased similarly across groups, with slight associative memory deficits in older adults. Imaging results demonstrated that, across groups, left mid-VLPFC showed increasing activity with increasing interference, though activity did not distinguish correct from incorrect associative memory responses, suggesting this region may not directly serve in successful resolution of proactive interference, per se. Under conditions of high interference, older adults showed reduced associative memory accuracy effects in the DLPFC and anterior PFC. These results suggest that age-related PFC dysfunction may not be ubiquitous. Executive processes supported by ventral regions that detect mnemonic interference may be less affected than processes supported by dorsal and anterior regions that directly resolve interference. Copyright © 2016 Elsevier Inc. All rights reserved.

Light Vector Meson Photoproduction off of 1H at Jefferson Lab and p-w Interference in the Leptonic Decay Channel

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

Djalali, Chaden; Paolone, Michael; Weygand, Dennis

2014-09-01

Although the phenomena of r – w interference has been studied at great length in pionic decay channel over the past 50 years, a study of the interference in a purely electromagnetic production and decay channel has never been performed on an elementary proton target until now. The only published photo-production data of the r - w leptonic decay channel was obtained in the early seventies on C and Be. An investigation of the r - w interference on a Hydrogen was recently completed at Jefferson Lab with the CLAS detector. The di-lepton spectra was fit with two inter- feringmore » relativistic Breit-Wigner functions, and the interference phase was extracted. Preliminary results will be compared to the previous experimental studies in nuclei.« less

Recovering Intrinsic Fragmental Vibrations Using the Generalized Subsystem Vibrational Analysis.

PubMed

Tao, Yunwen; Tian, Chuan; Verma, Niraj; Zou, Wenli; Wang, Chao; Cremer, Dieter; Kraka, Elfi

2018-05-08

Normal vibrational modes are generally delocalized over the molecular system, which makes it difficult to assign certain vibrations to specific fragments or functional groups. We introduce a new approach, the Generalized Subsystem Vibrational Analysis (GSVA), to extract the intrinsic fragmental vibrations of any fragment/subsystem from the whole system via the evaluation of the corresponding effective Hessian matrix. The retention of the curvature information with regard to the potential energy surface for the effective Hessian matrix endows our approach with a concrete physical basis and enables the normal vibrational modes of different molecular systems to be legitimately comparable. Furthermore, the intrinsic fragmental vibrations act as a new link between the Konkoli-Cremer local vibrational modes and the normal vibrational modes.

Vacuum ultraviolet photofragmentation of octadecane: photoionization mass spectrometric and theoretical investigation.

PubMed

Xu, Jing; Sang, Pengpeng; Zhao, Lianming; Guo, Wenyue; Qi, Fei; Xing, Wei; Yan, Zifeng

The photoionization and fragmentation of octadecane were investigated with infrared laser desorption/tunable synchrotron vacuum ultraviolet (VUV) photoionization mass spectrometry (IRLD/VUV PIMS) and theoretical calculations. Mass spectra of octadecane were measured at various photon energies. The fragment ions were gradually detected with the increase of photon energy. The main fragment ions were assigned to radical ions (C n H 2 n +1 + , n  = 4-11) and alkene ions (C n H 2 n + , n  = 5-10). The ionization energy of the precursor and appearance energy of ionic fragments were obtained by measuring the photoionization efficiency spectrum. Possible formation pathways of the fragment ions were discussed with the help of density functional theory calculations.

Model tool to describe chemical structures in XML format utilizing structural fragments and chemical ontology.

PubMed

Sankar, Punnaivanam; Alain, Krief; Aghila, Gnanasekaran

2010-05-24

We have developed a model structure-editing tool, ChemEd, programmed in JAVA, which allows drawing chemical structures on a graphical user interface (GUI) by selecting appropriate structural fragments defined in a fragment library. The terms representing the structural fragments are organized in fragment ontology to provide a conceptual support. ChemEd describes the chemical structure in an XML document (ChemFul) with rich semantics explicitly encoding the details of the chemical bonding, the hybridization status, and the electron environment around each atom. The document can be further processed through suitable algorithms and with the support of external chemical ontologies to generate understandable reports about the functional groups present in the structure and their specific environment.

Topoisomerase II Mediates Meiotic Crossover Interference

PubMed Central

Zhang, Liangran; Wang, Shunxin; Yin, Shen; Hong, Soogil; Kim, Keun P.; Kleckner, Nancy

2014-01-01

Summary Spatial patterning is a ubiquitous feature of biological systems. Meiotic crossovers provide an interesting example, defined by the classical phenomenon of crossover interference. Here, analysis of crossover patterns in budding yeast identifies a molecular pathway for interference. Topoisomerase II (Topo II) plays a central role, thus identifying a new function for this critical molecule. SUMOylation [of TopoII and axis component Red1] and ubiquitin-mediated removal of SUMOylated proteins are also required. These and other findings support the hypothesis that crossover interference involves accumulation, relief and redistribution of mechanical stress along the protein/DNA meshwork of meiotic chromosome axes, with TopoII required to adjust spatial relationships among DNA segments. PMID:25043020

Predator interference and stability of predator-prey dynamics.

PubMed

Přibylová, Lenka; Berec, Luděk

2015-08-01

Predator interference, that is, a decline in the per predator consumption rate as predator density increases, is generally thought to promote predator-prey stability. Indeed, this has been demonstrated in many theoretical studies on predator-prey dynamics. In virtually all of these studies, the stabilization role is demonstrated as a weakening of the paradox of enrichment. With predator interference, stable limit cycles that appear as a result of environmental enrichment occur for higher values of the environmental carrying capacity of prey, and even a complete absence of the limit cycles can happen. Here we study predator-prey dynamics using the Rosenzweig-MacArthur-like model in which the Holling type II functional response has been replaced by a predator-dependent family which generalizes many of the commonly used descriptions of predator interference. By means of a bifurcation analysis we show that sufficiently strong predator interference may bring about another stabilizing mechanism. In particular, hysteresis combined with (dis)appearance of stable limit cycles imply abrupt increases in both the prey and predator densities and enhanced persistence and resilience of the predator-prey system. We encourage refitting the previously collected data on predator consumption rates as well as for conducting further predation experiments to see what functional response from the explored family is the most appropriate.

Influence of fragment size and postoperative joint congruency on long-term outcome of posterior malleolar fractures.

PubMed

Drijfhout van Hooff, Cornelis Christiaan; Verhage, Samuel Marinus; Hoogendoorn, Jochem Maarten

2015-06-01

One of the factors contributing to long-term outcome of posterior malleolar fractures is the development of osteoarthritis. Based on biomechanical, cadaveric, and small population studies, fixation of posterior malleolar fracture fragments (PMFFs) is usually performed when fragment size exceeds 25-33%. However, the influence of fragment size on long-term clinical and radiological outcome size remains unclear. A retrospective cohort study of 131 patients treated for an isolated ankle fracture with involvement of the posterior malleolus was performed. Mean follow-up was 6.9 (range, 2.5-15.9) years. Patients were divided into groups depending on size of the fragment, small (<5%, n = 20), medium (5-25%, n = 86), or large (>25%, n = 25), and presence of step-off after operative treatment. We have compared functional outcome measures (AOFAS, AAOS), pain (VAS), and dorsiflexion restriction compared to the contralateral ankle and the incidence of osteoarthritis on X-ray. There were no nonunions, 56% of patients had no radiographic osteoarthritis, VAS was 10 of 100, and median clinical score was 90 of 100. More osteoarthritis occurred in ankle fractures with medium and large PMFFs compared to small fragments (small 16%, medium 48%, large 54%; P = .006). Also when comparing small with medium-sized fragments (P = .02), larger fragment size did not lead to a significantly decreased function (median AOFAS 95 vs 88, P = .16). If the PMFF size was >5%, osteoarthritis occurred more frequently when there was a postoperative step-off ≥1 mm in the tibiotalar joint surface (41% vs 61%, P = .02) (whether the posterior fragment had been fixed or not). In this group, fixing the PMFF did not influence development of osteoarthritis. However, in 42% of the cases with fixation of the fragment a postoperative step-off remained (vs 45% in the group without fixation). Osteoarthritis is 1 component of long-term outcome of malleolar fractures, and the results of this study demonstrate that there was more radiographic osteoarthritis in patients with medium and large posterior fragments than in those with small fragments. Radiographic osteoarthritis also occurred more frequently when postoperative step-off was 1 mm or more, whether the posterior fragment was fixed or not. However, clinical scores were not different for these groups. Level IV, retrospective case series. © The Author(s) 2015.

CRISPR-Cas Adaptive Immune Systems of the Sulfolobales: Unravelling Their Complexity and Diversity

PubMed Central

Garrett, Roger A.; Shah, Shiraz A.; Erdmann, Susanne; Liu, Guannan; Mousaei, Marzieh; León-Sobrino, Carlos; Peng, Wenfang; Gudbergsdottir, Soley; Deng, Ling; Vestergaard, Gisle; Peng, Xu; She, Qunxin

2015-01-01

The Sulfolobales have provided good model organisms for studying CRISPR-Cas systems of the crenarchaeal kingdom of the archaea. These organisms are infected by a wide range of exceptional archaea-specific viruses and conjugative plasmids, and their CRISPR-Cas systems generally exhibit extensive structural and functional diversity. They carry large and multiple CRISPR loci and often multiple copies of diverse Type I and Type III interference modules as well as more homogeneous adaptation modules. These acidothermophilic organisms have recently provided seminal insights into both the adaptation process, the diverse modes of interference, and their modes of regulation. The functions of the adaptation and interference modules tend to be loosely coupled and the stringency of the crRNA-DNA sequence matching during DNA interference is relatively low, in contrast to some more streamlined CRISPR-Cas systems of bacteria. Despite this, there is evidence for a complex and differential regulation of expression of the diverse functional modules in response to viral infection. Recent work also supports critical roles for non-core Cas proteins, especially during Type III-directed interference, and this is consistent with these proteins tending to coevolve with core Cas proteins. Various novel aspects of CRISPR-Cas systems of the Sulfolobales are considered including an alternative spacer acquisition mechanism, reversible spacer acquisition, the formation and significance of antisense CRISPR RNAs, and a novel mechanism for avoidance of CRISPR-Cas defense. Finally, questions regarding the basis for the complexity, diversity, and apparent redundancy, of the intracellular CRISPR-Cas systems are discussed. PMID:25764276

The necessity of feedback physics in setting the peak of the initial mass function

NASA Astrophysics Data System (ADS)

Guszejnov, Dávid; Krumholz, Mark R.; Hopkins, Philip F.

2016-05-01

A popular theory of star formation is gravito-turbulent fragmentation, in which self-gravitating structures are created by turbulence-driven density fluctuations. Simple theories of isothermal fragmentation successfully reproduce the core mass function (CMF) which has a very similar shape to the initial mass function (IMF) of stars. However, numerical simulations of isothermal turbulent fragmentation thus far have not succeeded in identifying a fragment mass scale that is independent of the simulation resolution. Moreover, the fluid equations for magnetized, self-gravitating, isothermal turbulence are scale-free, and do not predict any characteristic mass. In this paper we show that, although an isothermal self-gravitating flow does produce a CMF with a mass scale imposed by the initial conditions, this scale changes as the parent cloud evolves. In addition, the cores that form undergo further fragmentation and after sufficient time forget about their initial conditions, yielding a scale-free pure power-law distribution dN/dM ∝ M-2 for the stellar IMF. We show that this problem can be alleviated by introducing additional physics that provides a termination scale for the cascade. Our candidate for such physics is a simple model for stellar radiation feedback. Radiative heating, powered by accretion on to forming stars, arrests the fragmentation cascade and imposes a characteristic mass scale that is nearly independent of the time-evolution or initial conditions in the star-forming cloud, and that agrees well with the peak of the observed IMF. In contrast, models that introduce a stiff equation of state for denser clouds but that do not explicitly include the effects of feedback do not yield an invariant IMF.

Jet axes and universal transverse-momentum-dependent fragmentation

NASA Astrophysics Data System (ADS)

Neill, Duff; Scimemi, Ignazio; Waalewijn, Wouter J.

2017-04-01

We study the transverse momentum spectrum of hadrons in jets. By measuring the transverse momentum with respect to a judiciously chosen axis, we find that this observable is insensitive to (the recoil of) soft radiation. Furthermore, for small transverse momenta we show that the effects of the jet boundary factorize, leading to a new transverse-momentum-dependent (TMD) fragmentation function. In contrast to the usual TMD fragmentation functions, it does not involve rapidity divergences and is universal in the sense that it is independent of the type of process and number of jets. These results directly apply to sub-jets instead of hadrons. We discuss potential applications, which include studying nuclear modification effects in heavy-ion collisions and identifying boosted heavy resonances.

Imaging and control of interfering wave packets in a dissociating molecule.

PubMed

Skovsen, Esben; Machholm, Mette; Ejdrup, Tine; Thøgersen, Jan; Stapelfeldt, Henrik

2002-09-23

Using two identical 110 femtosecond (fs) optical pulses separated by 310 fs, we launch two dissociative wave packets in I2. We measure the square of the wave function as a function of both the internuclear separation, /Psi(R)/(2), and of the internuclear velocity, /Psi(v(R))/(2), by ionizing the dissociating molecule with an intense 20 fs probe pulse. Strong interference is observed in both /Psi(R)/(2) and in /Psi(v(R))/(2). The interference, and therefore the shape of the wave function, is controlled through the phase difference between the two dissociation pulses in good agreement with calculations.

RNA interference: learning gene knock-down from cell physiology

PubMed Central

Mocellin, Simone; Provenzano, Maurizio

2004-01-01

Over the past decade RNA interference (RNAi) has emerged as a natural mechanism for silencing gene expression. This ancient cellular antiviral response can be exploited to allow specific inhibition of the function of any chosen target gene. RNAi is proving to be an invaluable research tool, allowing much more rapid characterization of the function of known genes. More importantly, RNAi technology considerably bolsters functional genomics to aid in the identification of novel genes involved in disease processes. This review briefly describes the molecular principles underlying the biology of RNAi phenomenon and discuss the main technical issues regarding optimization of RNAi experimental design. PMID:15555080

Hippocampal sharp wave‐ripple: A cognitive biomarker for episodic memory and planning

PubMed Central

2015-01-01

ABSTRACT Sharp wave ripples (SPW‐Rs) represent the most synchronous population pattern in the mammalian brain. Their excitatory output affects a wide area of the cortex and several subcortical nuclei. SPW‐Rs occur during “off‐line” states of the brain, associated with consummatory behaviors and non‐REM sleep, and are influenced by numerous neurotransmitters and neuromodulators. They arise from the excitatory recurrent system of the CA3 region and the SPW‐induced excitation brings about a fast network oscillation (ripple) in CA1. The spike content of SPW‐Rs is temporally and spatially coordinated by a consortium of interneurons to replay fragments of waking neuronal sequences in a compressed format. SPW‐Rs assist in transferring this compressed hippocampal representation to distributed circuits to support memory consolidation; selective disruption of SPW‐Rs interferes with memory. Recently acquired and pre‐existing information are combined during SPW‐R replay to influence decisions, plan actions and, potentially, allow for creative thoughts. In addition to the widely studied contribution to memory, SPW‐Rs may also affect endocrine function via activation of hypothalamic circuits. Alteration of the physiological mechanisms supporting SPW‐Rs leads to their pathological conversion, “p‐ripples,” which are a marker of epileptogenic tissue and can be observed in rodent models of schizophrenia and Alzheimer's Disease. Mechanisms for SPW‐R genesis and function are discussed in this review. © 2015 The Authors Hippocampus Published by Wiley Periodicals, Inc. PMID:26135716

GingisKHAN™ protease cleavage allows a high-throughput antibody to Fab conversion enabling direct functional assessment during lead identification of human monoclonal and bispecific IgG1 antibodies

PubMed Central

Moelleken, Jörg; Gassner, Christian; Lingke, Sabine; Tomaschek, Simone; Tyshchuk, Oksana; Lorenz, Stefan; Mølhøj, Michael

2017-01-01

ABSTRACT The determination of the binding strength of immunoglobulins (IgGs) to targets can be influenced by avidity when the targets are soluble di- or multimeric proteins, or associated to cell surfaces, including surfaces introduced from heterogeneous assays. However, for the understanding of the contribution of a second drug-to-target binding site in molecular design, or for ranking of monovalent binders during lead identification, affinity-based assessment of the binding strength is required. Typically, monovalent binders like antigen-binding fragments (Fabs) are generated by proteolytic cleavage with papain, which often results in a combination of under- and over-digestion, and requires specific optimization and chromatographic purification of the desired Fabs. Alternatively, the Fabs are produced by recombinant approaches. Here, we report a lean approach for the functional assessment of human IgG1s during lead identification based on an in-solution digestion with the GingisKHAN™ protease, generating a homogenous pool of intact Fabs and Fcs and enabling direct assaying of the Fab in the digestion mixture. The digest with GingisKHAN™ is highly specific and quantitative, does not require much optimization, and the protease does not interfere with methods typically applied for lead identification, such as surface plasmon resonance or cell-based assays. GingisKHAN™ is highly suited to differentiate between affinity and avidity driven binding of human IgG1 monoclonal and bispecific antibodies during lead identification. PMID:28805498

Age-associated reduction of cellular spreading/mechanical force up-regulates matrix metalloproteinase-1 expression and collagen fibril fragmentation via c-Jun/AP-1 in human dermal fibroblasts.

PubMed

Qin, Zhaoping; Voorhees, John J; Fisher, Gary J; Quan, Taihao

2014-12-01

The dermal compartment of human skin is largely composed of dense collagen-rich fibrils, which provide structural and mechanical support. Skin dermal fibroblasts, the major collagen-producing cells, are interact with collagen fibrils to maintain cell spreading and mechanical force for function. A characteristic feature of aged human skin is fragmentation of collagen fibrils, which is initiated by matrix metalloproteinase 1 (MMP-1). Fragmentation impairs fibroblast attachment and thereby reduces spreading. Here, we investigated the relationship among fibroblast spreading, mechanical force, MMP-1 expression, and collagen fibril fragmentation. Reduced fibroblast spreading due to cytoskeletal disruption was associated with reduced cellular mechanical force, as determined by atomic force microscopy. These reductions substantially induced MMP-1 expression, which led to collagen fibril fragmentation and disorganization in three-dimensional collagen lattices. Constraining fibroblast size by culturing on slides coated with collagen micropatterns also significantly induced MMP-1 expression. Reduced spreading/mechanical force induced transcription factor c-Jun and its binding to a canonical AP-1 binding site in the MMP-1 proximal promoter. Blocking c-Jun function with dominant negative mutant c-Jun significantly reduced induction of MMP-1 expression in response to reduced spreading/mechanical force. Furthermore, restoration of fibroblast spreading/mechanical force led to decline of c-Jun and MMP-1 levels and eliminated collagen fibril fragmentation and disorganization. These data reveal a novel mechanism by which alteration of fibroblast shape/mechanical force regulates c-Jun/AP-1-dependent expression of MMP-1 and consequent collagen fibril fragmentation. This mechanism provides a foundation for understanding the cellular and molecular basis of age-related collagen fragmentation in human skin. © 2014 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.

Protection against β-amyloid neurotoxicity by a non-toxic endogenous N-terminal β-amyloid fragment and its active hexapeptide core sequence.

PubMed

Forest, Kelly H; Alfulaij, Naghum; Arora, Komal; Taketa, Ruth; Sherrin, Tessi; Todorovic, Cedomir; Lawrence, James L M; Yoshikawa, Gene T; Ng, Ho-Leung; Hruby, Victor J; Nichols, Robert A

2018-01-01

High levels (μM) of beta amyloid (Aβ) oligomers are known to trigger neurotoxic effects, leading to synaptic impairment, behavioral deficits, and apoptotic cell death. The hydrophobic C-terminal domain of Aβ, together with sequences critical for oligomer formation, is essential for this neurotoxicity. However, Aβ at low levels (pM-nM) has been shown to function as a positive neuromodulator and this activity resides in the hydrophilic N-terminal domain of Aβ. An N-terminal Aβ fragment (1-15/16), found in cerebrospinal fluid, was also shown to be a highly active neuromodulator and to reverse Aβ-induced impairments of long-term potentiation. Here, we show the impact of this N-terminal Aβ fragment and a shorter hexapeptide core sequence in the Aβ fragment (Aβcore: 10-15) to protect or reverse Aβ-induced neuronal toxicity, fear memory deficits and apoptotic death. The neuroprotective effects of the N-terminal Aβ fragment and Aβcore on Aβ-induced changes in mitochondrial function, oxidative stress, and apoptotic neuronal death were demonstrated via mitochondrial membrane potential, live reactive oxygen species, DNA fragmentation and cell survival assays using a model neuroblastoma cell line (differentiated NG108-15) and mouse hippocampal neuron cultures. The protective action of the N-terminal Aβ fragment and Aβcore against spatial memory processing deficits in amyloid precursor protein/PSEN1 (5XFAD) mice was demonstrated in contextual fear conditioning. Stabilized derivatives of the N-terminal Aβcore were also shown to be fully protective against Aβ-triggered oxidative stress. Together, these findings indicate an endogenous neuroprotective role for the N-terminal Aβ fragment, while active stabilized N-terminal Aβcore derivatives offer the potential for therapeutic application. © 2017 International Society for Neurochemistry.

Benchmark fragment-based 1H, 13C, 15N and 17O chemical shift predictions in molecular crystals†

PubMed Central

Hartman, Joshua D.; Kudla, Ryan A.; Day, Graeme M.; Mueller, Leonard J.; Beran, Gregory J. O.

2016-01-01

The performance of fragment-based ab initio 1H, 13C, 15N and 17O chemical shift predictions is assessed against experimental NMR chemical shift data in four benchmark sets of molecular crystals. Employing a variety of commonly used density functionals (PBE0, B3LYP, TPSSh, OPBE, PBE, TPSS), we explore the relative performance of cluster, two-body fragment, and combined cluster/fragment models. The hybrid density functionals (PBE0, B3LYP and TPSSh) generally out-perform their generalized gradient approximation (GGA)-based counterparts. 1H, 13C, 15N, and 17O isotropic chemical shifts can be predicted with root-mean-square errors of 0.3, 1.5, 4.2, and 9.8 ppm, respectively, using a computationally inexpensive electrostatically embedded two-body PBE0 fragment model. Oxygen chemical shieldings prove particularly sensitive to local many-body effects, and using a combined cluster/fragment model instead of the simple two-body fragment model decreases the root-mean-square errors to 7.6 ppm. These fragment-based model errors compare favorably with GIPAW PBE ones of 0.4, 2.2, 5.4, and 7.2 ppm for the same 1H, 13C, 15N, and 17O test sets. Using these benchmark calculations, a set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided and their robustness assessed using statistical cross-validation. We demonstrate the utility of these approaches and the reported scaling parameters on applications to 9-tertbutyl anthracene, several histidine co-crystals, benzoic acid and the C-nitrosoarene SnCl2(CH3)2(NODMA)2. PMID:27431490

Benchmark fragment-based (1)H, (13)C, (15)N and (17)O chemical shift predictions in molecular crystals.

PubMed

Hartman, Joshua D; Kudla, Ryan A; Day, Graeme M; Mueller, Leonard J; Beran, Gregory J O

2016-08-21

The performance of fragment-based ab initio(1)H, (13)C, (15)N and (17)O chemical shift predictions is assessed against experimental NMR chemical shift data in four benchmark sets of molecular crystals. Employing a variety of commonly used density functionals (PBE0, B3LYP, TPSSh, OPBE, PBE, TPSS), we explore the relative performance of cluster, two-body fragment, and combined cluster/fragment models. The hybrid density functionals (PBE0, B3LYP and TPSSh) generally out-perform their generalized gradient approximation (GGA)-based counterparts. (1)H, (13)C, (15)N, and (17)O isotropic chemical shifts can be predicted with root-mean-square errors of 0.3, 1.5, 4.2, and 9.8 ppm, respectively, using a computationally inexpensive electrostatically embedded two-body PBE0 fragment model. Oxygen chemical shieldings prove particularly sensitive to local many-body effects, and using a combined cluster/fragment model instead of the simple two-body fragment model decreases the root-mean-square errors to 7.6 ppm. These fragment-based model errors compare favorably with GIPAW PBE ones of 0.4, 2.2, 5.4, and 7.2 ppm for the same (1)H, (13)C, (15)N, and (17)O test sets. Using these benchmark calculations, a set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided and their robustness assessed using statistical cross-validation. We demonstrate the utility of these approaches and the reported scaling parameters on applications to 9-tert-butyl anthracene, several histidine co-crystals, benzoic acid and the C-nitrosoarene SnCl2(CH3)2(NODMA)2.

Cytosolic expression of functional Fab fragments in Escherichia coli using a novel combination of dual SUMO expression cassette and EnBase® cultivation mode.

PubMed

Rezaie, F; Davami, F; Mansouri, K; Agha Amiri, S; Fazel, R; Mahdian, R; Davoudi, N; Enayati, S; Azizi, M; Khalaj, V

2017-05-08

The Escherichia coli expression system is highly effective in producing recombinant proteins. However, there are some limitations in this system, especially in obtaining correctly folded forms of some complex proteins such as Fab fragments. To improve the solubility and folding quality of Fab fragments, we have examined the effect of simultaneous application of a SUMO fusion tag, EnBase ® cultivation mode and a redox mutant strain in the E. coli expression system. A bicistronic gene construct was designed to express an antivascular endothelial growth factor (VEGF) Fab fragment as a model system. The construct contained a dual SUMO fusion gene fragment to encode SUMO-tagged heavy and light chains. While the expression of the construct in batch cultures of BL21 or SHuffle ® transformants produced insoluble and unfolded products, the induction of the transformants in EnBase ® medium resulted in soluble and correctly folded Fab fragment, reaching as high as 19% of the total protein in shuffle strain. The functional assays indicated that the biological activity of the target Fab is similar to the commercial anti-VEGF, Lucentis ® . This study demonstrated that the combination of SUMO fusion technology, EnBase ® cultivation system and recruiting a redox mutant of E. coli can efficiently enhance the solubility and productivity of recombinant Fab fragments. The presented strategy provides not only a novel method to produce soluble and active form of an anti-VEGF Fab but also may use in the efficient production of other antibody fragments. © 2017 The Society for Applied Microbiology.

An Improved Time-Frequency Analysis Method in Interference Detection for GNSS Receivers

PubMed Central

Sun, Kewen; Jin, Tian; Yang, Dongkai

2015-01-01

In this paper, an improved joint time-frequency (TF) analysis method based on a reassigned smoothed pseudo Wigner–Ville distribution (RSPWVD) has been proposed in interference detection for Global Navigation Satellite System (GNSS) receivers. In the RSPWVD, the two-dimensional low-pass filtering smoothing function is introduced to eliminate the cross-terms present in the quadratic TF distribution, and at the same time, the reassignment method is adopted to improve the TF concentration properties of the auto-terms of the signal components. This proposed interference detection method is evaluated by experiments on GPS L1 signals in the disturbing scenarios compared to the state-of-the-art interference detection approaches. The analysis results show that the proposed interference detection technique effectively overcomes the cross-terms problem and also preserves good TF localization properties, which has been proven to be effective and valid to enhance the interference detection performance of the GNSS receivers, particularly in the jamming environments. PMID:25905704

Mapping interference resolution across task domains: A shared control process in left inferior frontal gyrus

PubMed Central

Nelson, James K.; Reuter-Lorenz, Patricia A.; Persson, Jonas; Sylvester, Ching-Yune C.; Jonides, John

2009-01-01

Work in functional neuroimaging has mapped interference resolution processing onto left inferior frontal regions for both verbal working memory and a variety of semantic processing tasks. The proximity of the identified regions from these different tasks suggests the existence of a common, domain-general interference resolution mechanism. The current research specifically tests this idea in a within-subject design using fMRI to assess the activation associated with variable selection requirements in a semantic retrieval task (verb generation) and a verbal working memory task with a trial-specific proactive interference manipulation (recent-probes). High interference trials on both tasks were associated with activity in the midventrolateral region of the left inferior frontal gyrus, and the regions activated in each task strongly overlapped. The results indicate that an elemental component of executive control associated with interference resolution during retrieval from working memory and from semantic memory can be mapped to a common portion of the left inferior frontal gyrus. PMID:19111526

Stroop interference associated with efficient reading fluency and prelexical orthographic processing.

PubMed

Mano, Quintino R; Williamson, Brady J; Pae, Hye K; Osmon, David C

2016-01-01

The Stroop Color-Word Test involves a dynamic interplay between reading and executive functioning that elicits intuitions of word reading automaticity. One such intuition is that strong reading skills (i.e., more automatized word reading) play a disruptive role within the test, contributing to Stroop interference. However, evidence has accumulated that challenges this intuition. The present study examined associations among Stroop interference, reading skills (i.e., isolated word identification, grapheme-to-phoneme mapping, phonemic awareness, reading fluency) measured on standardized tests, and orthographic skills measured on experimental computerized tasks. Among university students (N = 152), correlational analyses showed greater Stroop interference to be associated with (a) relatively low scores on all standardized reading tests, and (b) longer response latencies on orthographic tasks. Hierarchical regression demonstrated that reading fluency and prelexical orthographic processing predicted unique and significant variance in Stroop interference beyond baseline rapid naming. Results suggest that strong reading skills, including orthographic processing, play a supportive role in resolving Stroop interference.

Formation and distribution of fragments in the spontaneous fission of 240Pu

NASA Astrophysics Data System (ADS)

Sadhukhan, Jhilam; Zhang, Chunli; Nazarewicz, Witold; Schunck, Nicolas

2017-12-01

Background: Fission is a fundamental decay mode of heavy atomic nuclei. The prevalent theoretical approach is based on mean-field theory and its extensions where fission is modeled as a large amplitude motion of a nucleus in a multidimensional collective space. One of the important observables characterizing fission is the charge and mass distribution of fission fragments. Purpose: The goal of this Rapid Communication is to better understand the structure of fission fragment distributions by investigating the competition between the static structure of the collective manifold and the stochastic dynamics. In particular, we study the characteristics of the tails of yield distributions, which correspond to very asymmetric fission into a very heavy and a very light fragment. Methods: We use the stochastic Langevin framework to simulate the nuclear evolution after the system tunnels through the multidimensional potential barrier. For a representative sample of different initial configurations along the outer turning-point line, we define effective fission paths by computing a large number of Langevin trajectories. We extract the relative contribution of each such path to the fragment distribution. We then use nucleon localization functions along effective fission pathways to analyze the characteristics of prefragments at prescission configurations. Results: We find that non-Newtonian Langevin trajectories, strongly impacted by the random force, produce the tails of the fission fragment distribution of 240Pu. The prefragments deduced from nucleon localizations are formed early and change little as the nucleus evolves towards scission. On the other hand, the system contains many nucleons that are not localized in the prefragments even near the scission point. Such nucleons are distributed rapidly at scission to form the final fragments. Fission prefragments extracted from direct integration of the density and from the localization functions typically differ by more than 30 nucleons even near scission. Conclusions: Our Rapid Communication shows that only theoretical models of fission that account for some form of stochastic dynamics can give an accurate description of the structure of fragment distributions. In particular, it should be nearly impossible to predict the tails of these distributions within the standard formulation of time-dependent density-functional theory. At the same time, the large number of nonlocalized nucleons during fission suggests that adiabatic approaches where the interplay between intrinsic excitations and collective dynamics is neglected are ill suited to describe fission fragment properties, in particular, their excitation energy.

Global Forest Area Trends Underestimate Threats from Forest Fragmentation

EPA Science Inventory

Forest loss and fragmentation of the remainder threaten the ecological attributes and functions which depend upon forests1. Forest interior area is particularly valued because it is relatively remote from human influence2, 3, 4, 5. Recent global assessments report declines in t...

The Auditory Verbal Learning Test (Rey AVLT): An Arabic Version

ERIC Educational Resources Information Center

Sharoni, Varda; Natur, Nazeh

2014-01-01

The goals of this study were to adapt the Rey Auditory Verbal Learning Test (AVLT) into Arabic, to compare recall functioning among age groups (6:0 to 17:11), and to compare gender differences on various memory dimensions (immediate and delayed recall, learning rate, recognition, proactive interferences, and retroactive interferences). This…

Locus of Semantic Interference in Picture Naming: Evidence from Dual-Task Performance

ERIC Educational Resources Information Center

Piai, Vitória; Roelofs, Ardi; Schriefers, Herbert

2014-01-01

Disagreement exists regarding the functional locus of semantic interference of distractor words in picture naming. This effect is a cornerstone of modern psycholinguistic models of word production, which assume that it arises in lexical response-selection. However, recent evidence from studies of dual-task performance suggests a locus in…

RNA interference in Lepidoptera: an overview of successful and unsuccessful studies and implications for experimental design

USDA-ARS?s Scientific Manuscript database

Gene silencing through RNA interference (RNAi) has revolutionized the study of gene function, particularly in non-model insects. However, in Lepidoptera (moths and butterflies) RNAi has many times proven to be difficult to achieve. Most of the negative results have been anecdotal and the positive ex...

77 FR 12302 - Information Collection Being Reviewed by the Federal Communications Commission

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-29

... necessary for the proper performance of the functions of the Commission, including whether the information...). This transmitter must not cause harmful interference to stations authorized to operate on a primary... device: ``This device may not interfere with stations authorized to operate on a primary basis in the 413...

RISC-interacting clearing 3'- 5' exoribonucleases (RICEs) degrade uridylated cleavage fragments to maintain functional RISC in Arabidopsis thaliana.

PubMed

Zhang, Zhonghui; Hu, Fuqu; Sung, Min Woo; Shu, Chang; Castillo-González, Claudia; Koiwa, Hisashi; Tang, Guiliang; Dickman, Martin; Li, Pingwei; Zhang, Xiuren

2017-05-02

RNA-induced silencing complex (RISC) is composed of miRNAs and AGO proteins. AGOs use miRNAs as guides to slice target mRNAs to produce truncated 5' and 3' RNA fragments. The 5' cleaved RNA fragments are marked with uridylation for degradation. Here, we identified novel cofactors of Arabidopsis AGOs, named RICE1 and RICE2. RICE proteins specifically degraded single-strand (ss) RNAs in vitro; but neither miRNAs nor miRNA*s in vivo. RICE1 exhibited a DnaQ-like exonuclease fold and formed a homohexamer with the active sites located at the interfaces between RICE1 subunits. Notably, ectopic expression of catalytically-inactive RICE1 not only significantly reduced miRNA levels; but also increased 5' cleavage RISC fragments with extended uridine tails. We conclude that RICEs act to degrade uridylated 5' products of AGO cleavage to maintain functional RISC. Our study also suggests a possible link between decay of cleaved target mRNAs and miRNA stability in RISC.

Mechanisms and neuronal networks involved in reactive and proactive cognitive control of interference in working memory.

PubMed

Irlbacher, Kerstin; Kraft, Antje; Kehrer, Stefanie; Brandt, Stephan A

2014-10-01

Cognitive control can be reactive or proactive in nature. Reactive control mechanisms, which support the resolution of interference, start after its onset. Conversely, proactive control involves the anticipation and prevention of interference prior to its occurrence. The interrelation of both types of cognitive control is currently under debate: Are they mediated by different neuronal networks? Or are there neuronal structures that have the potential to act in a proactive as well as in a reactive manner? This review illustrates the way in which integrating knowledge gathered from behavioral studies, functional imaging, and human electroencephalography proves useful in answering these questions. We focus on studies that investigate interference resolution at the level of working memory representations. In summary, different mechanisms are instrumental in supporting reactive and proactive control. Distinct neuronal networks are involved, though some brain regions, especially pre-SMA, possess functions that are relevant to both control modes. Therefore, activation of these brain areas could be observed in reactive, as well as proactive control, but at different times during information processing. Copyright © 2014 Elsevier Ltd. All rights reserved.

Response Inhibition and Interference Control in Obsessive–Compulsive Spectrum Disorders

PubMed Central

van Velzen, Laura S.; Vriend, Chris; de Wit, Stella J.; van den Heuvel, Odile A.

2014-01-01

Over the past 20 years, motor response inhibition and interference control have received considerable scientific effort and attention, due to their important role in behavior and the development of neuropsychiatric disorders. Results of neuroimaging studies indicate that motor response inhibition and interference control are dependent on cortical–striatal–thalamic–cortical (CSTC) circuits. Structural and functional abnormalities within the CSTC circuits have been reported for many neuropsychiatric disorders, including obsessive–compulsive disorder (OCD) and related disorders, such as attention-deficit hyperactivity disorder, Tourette’s syndrome, and trichotillomania. These disorders also share impairments in motor response inhibition and interference control, which may underlie some of their behavioral and cognitive symptoms. Results of task-related neuroimaging studies on inhibitory functions in these disorders show that impaired task performance is related to altered recruitment of the CSTC circuits. Previous research has shown that inhibitory performance is dependent upon dopamine, noradrenaline, and serotonin signaling, neurotransmitters that have been implicated in the pathophysiology of these disorders. In this narrative review, we discuss the common and disorder-specific pathophysiological mechanisms of inhibition-related dysfunction in OCD and related disorders. PMID:24966828

Differential item functioning of the patient-reported outcomes information system (PROMIS®) pain interference item bank by language (Spanish versus English).

PubMed

Paz, Sylvia H; Spritzer, Karen L; Reise, Steven P; Hays, Ron D

2017-06-01

About 70% of Latinos, 5 years old or older, in the United States speak Spanish at home. Measurement equivalence of the PROMIS ® pain interference (PI) item bank by language of administration (English versus Spanish) has not been evaluated. A sample of 527 adult Spanish-speaking Latinos completed the Spanish version of the 41-item PROMIS ® pain interference item bank. We evaluate dimensionality, monotonicity and local independence of the Spanish-language items. Then we evaluate differential item functioning (DIF) using ordinal logistic regression with item response theory scores estimated from DIF-free "anchor" items. One of the 41 items in the Spanish version of the PROMIS ® PI item bank was identified as having significant uniform DIF. English- and Spanish-speaking subjects with the same level of pain interference responded differently to 1 of the 41 items in the PROMIS ® PI item bank. This item was not retained due to proprietary issues. The original English language item parameters can be used when estimating PROMIS ® PI scores.

The NH2-terminal and COOH-terminal fragments of dentin matrix protein 1 (DMP1) localize differently in the compartments of dentin and growth plate of bone.

PubMed

Maciejewska, Izabela; Cowan, Cameron; Svoboda, Kathy; Butler, William T; D'Souza, Rena; Qin, Chunlin

2009-02-01

Multiple studies have shown that dentin matrix protein 1 (DMP1) is essential for bone and dentin mineralization. After post-translational proteolytic cleavage, DMP1 exists within the extracellular matrix of bone and dentin as an NH2-terminal fragment, a COOH-terminal fragment, and the proteoglycan form of the NH2-terminal fragment (DMP1-PG). To begin to assess the biological function of each fragment, we evaluated the distribution of both fragments in the rat tooth and bone using antibodies specific to the NH2-terminal and COOH-terminal regions of DMP1 and confocal microscopy. In rat first molar organs, the NH2-terminal fragment localized to predentin, whereas the COOH-terminal fragment was mainly restricted to mineralized dentin. In the growth plate of bone, the NH2-terminal fragment appeared in the proliferation and hypertrophic zones, whereas the COOH-terminal fragment occupied the ossification zone. Forster resonance energy transfer analysis showed colocalization of both fragments of DMP1 in odontoblasts and predentin, as well as hypertrophic chondrocytes within the growth plates of bone. The biochemical analysis of bovine teeth showed that predentin is rich in DMP1-PG, whereas mineralized dentin primarily contains the COOH-terminal fragment. We conclude that the differential patterns of expression of NH2-terminal and COOH-terminal fragments of DMP1 reflect their potentially distinct roles in the biomineralization of dentin and bone matrices.

Keystone Species, Forest and Landscape: A Model to Select Protected Areas

NASA Astrophysics Data System (ADS)

Lins, Daniela Barbosa da Silva; Gardon, Fernando Ravanini; Meyer, João Frederico da Costa Azevedo; Santos, Rozely Ferreira dos

2017-06-01

The selection of forest fragments for conservation is usually based on spatial parameters as forest size and canopy integrity. This strategy assumes that chosen fragments present high conservation status, ensuring biodiversity and ecological functions. We argue that a well-preserved forest fragment that remains connected by the landscape structure, does not necessarily hold attributes that ensure the presence of keystone species. We also discuss that the presence of keystone species does not always mean that it has the best conditions for its occurrence and maintenance. We developed a model to select areas in forest landscapes to be prioritized for protection based on suitability curves that unify and compare spatial indicators of three categories: forest fragment quality, landscape quality, and environmental conditions for the occurrence of a keystone species. We use a case study to compare different suitability degrees for Euterpe edulis presence, considered an important functional element in Atlantic Forest (São Paulo, Brazil) landscapes and a forest resource for local people. The results show that the identification of medium or advanced stage fragments as singular indicator of forest quality does not guarantee the existence or maintenance of this keystone species. Even in some well-preserved forest fragments, connected to others and with palm presence, the reverse J-shaped distribution of the population size structure is not sustained and these forests continue to be threatened due to human disturbances.

On moments of the multiplicity events of slow target fragments in relativistic Sulfur-ion collisions

NASA Astrophysics Data System (ADS)

Abdelsalam, A.; Kamel, S.; Rashed, N.; Sabry, N.

2014-07-01

A detailed study on the multiplicity characteristics of the slow target fragments emitted in relativistic heavy-ion collisions has been carried out at ELab = 3.7A and 200A GeV using 32S projectile. The beam energy dependence of the black particles produced in the full phase space of 32S-emulsion (32S-Em) interactions on the target size in terms of their moments (mean, variance, skewness and kurtosis) is investigated. The various order moments of target fragments emitted in the interactions of 32S beams with the heavy (AgBr) target nuclei are estimated in the forward (FHS) and backward (BHS) hemispheres. The investigated values of ratio of variance to mean at both energies show that the multiplicity distributions (MDs) are not Poissonian and the strongly correlated emission of target fragments are in the forward directions. The degree of anisotropic fragment emission and nature of correlation among the emitted fragments are investigated. The energy dependence of entropy is examined in both hemispheres. The entropy values normalized to average multiplicity are found to be energy independent. Scaling of MD of black particles produced in these interactions has been studied to verify the validity of scaling hypothesis via two scaling (Koba-Nielsen-Olesen (KNO)-scaling and Hegyi-scaling) functions. A simplified universal function has been used in each scaling to display the experimental data.

Trophic disruption: a meta-analysis of how habitat fragmentation affects resource consumption in terrestrial arthropod systems.

PubMed

Martinson, Holly M; Fagan, William F

2014-09-01

Habitat fragmentation is a complex process that affects ecological systems in diverse ways, altering everything from population persistence to ecosystem function. Despite widespread recognition that habitat fragmentation can influence food web interactions, consensus on the factors underlying variation in the impacts of fragmentation across systems remains elusive. In this study, we conduct a systematic review and meta-analysis to quantify the effects of habitat fragmentation and spatial habitat structure on resource consumption in terrestrial arthropod food webs. Across 419 studies, we found a negative overall effect of fragmentation on resource consumption. Variation in effect size was extensive but predictable. Specifically, resource consumption was reduced on small, isolated habitat fragments, higher at patch edges, and neutral with respect to landscape-scale spatial variables. In general, resource consumption increased in fragmented settings for habitat generalist consumers but decreased for specialist consumers. Our study demonstrates widespread disruption of trophic interactions in fragmented habitats and describes variation among studies that is largely predictable based on the ecological traits of the interacting species. We highlight future prospects for understanding how changes in spatial habitat structure may influence trophic modules and food webs. © 2014 John Wiley & Sons Ltd/CNRS.

[Isolation of ABA-regulated genes in Oryza sativa through fluorescent differential display PCR (FDD-PCR)].

PubMed

Xu, Shou Ling; Shen, Si Shi; Xu, Zhi Hong; Xue, Hong Wei

2002-12-01

Abscisic acid (ABA) was critical in plant seed development and response to environmental factors such as stress situations. To study the possible ABA related signaling transduction pathways, we tried to isolate the ABA-regulated genes through fluorescent differential display PCR (FDD-PCR) technology using rice seedling as materials (treated with ABA for 2, 4, 8 and 12h). In the 17 fragments isolated, 14 and 3 clones were up-and down-regulated respectively. Sequence analyses revealed that the encoded proteins were involved in photosynthesis (7 fragments), signal transduction (1 fragments), transcription (2 fragments), metabolism and resistance (6 fragments), and unknown protein (1 fragments). 3 clones, encoding putative alpha/beta hydrolase fold, putative vacuolar H+ -ATPase B subunit, putative tyrosine phosphatase, were confirmed to be regulated under ABA treatment by RT-PCR and northern blot analysis. FDD-PCR and possible functional mechanisms of ABA were discussed.

Long-Tailed Distributions in Biological Systems:. Revisit to Lognormals

NASA Astrophysics Data System (ADS)

Kobayashi, N.; Kohyama, K.; Moriyama, O.; Sasaki, Y.; Matsushita, M.; Matsushita, S.

2007-07-01

Long-tailed distributions in biological systems have been studied. First, we found that lognormal distributions show excellent fit with various data for the duration distribution of disability in aged people, irrespective of their severity and gender. The robust lognormal distribution of disability implies that the incidence of diseases can be completed by many independent subprocesses in succession. Next, we studied food fragmentation by human mastication. A lognormal distribution well fits to the entire region for masticated food fragments for a small number of chewing strokes. Furthermore, the tail of the fragment-size distribution changes from the lognormal distribution to a power-law one as the chewing stroke number increases. The good data fitting by the lognormal and power-law distribution implies that two functions of mastication, a sequential fragmentation with cascade and randomness and a lower threshold for fragment size, may affect the size distribution of masticated food fragments.

Novel approach using DNA-RNA hybrids in RNA nanotechnology | Center for Cancer Research

Cancer.gov

Developing simple approaches to detect interactions, modifications, and cellular locations of macromolecules is essential for understanding biochemical processes. The use of protein fragment complementation assays, also called split-protein systems, is a highly sensitive approach for studying protein interactions in biological systems. In this approach, functional proteins are split into non-functional fragments, and when attached to possible interacting partners, can reassemble and become functional again. Use of split-protein assays can establish differences between a healthy and a diseased state in the cell as well as determine the outcome of a therapeutic intervention.

Comparison of Commercial Electromagnetic Interface Test Techniques to NASA Electromagnetic Interference Test Techniques

NASA Astrophysics Data System (ADS)

Smith, V.

2000-11-01

This report documents the development of analytical techniques required for interpreting and comparing space systems electromagnetic interference test data with commercial electromagnetic interference test data using NASA Specification SSP 30237A "Space Systems Electromagnetic Emission and Susceptibility Requirements for Electromagnetic Compatibility." The PSpice computer simulation results and the laboratory measurements for the test setups under study compare well. The study results, however, indicate that the transfer function required to translate test results of one setup to another is highly dependent on cables and their actual layout in the test setup. Since cables are equipment specific and are not specified in the test standards, developing a transfer function that would cover all cable types (random, twisted, or coaxial), sizes (gauge number and length), and layouts (distance from the ground plane) is not practical.

Comparison of Commercial Electromagnetic Interface Test Techniques to NASA Electromagnetic Interference Test Techniques

NASA Technical Reports Server (NTRS)

Smith, V.; Minor, J. L. (Technical Monitor)

2000-01-01

This report documents the development of analytical techniques required for interpreting and comparing space systems electromagnetic interference test data with commercial electromagnetic interference test data using NASA Specification SSP 30237A "Space Systems Electromagnetic Emission and Susceptibility Requirements for Electromagnetic Compatibility." The PSpice computer simulation results and the laboratory measurements for the test setups under study compare well. The study results, however, indicate that the transfer function required to translate test results of one setup to another is highly dependent on cables and their actual layout in the test setup. Since cables are equipment specific and are not specified in the test standards, developing a transfer function that would cover all cable types (random, twisted, or coaxial), sizes (gauge number and length), and layouts (distance from the ground plane) is not practical.

Unravelling the structural and mechanistic basis of CRISPR-Cas systems.

PubMed

van der Oost, John; Westra, Edze R; Jackson, Ryan N; Wiedenheft, Blake

2014-07-01

Bacteria and archaea have evolved sophisticated adaptive immune systems, known as CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) systems, which target and inactivate invading viruses and plasmids. Immunity is acquired by integrating short fragments of foreign DNA into CRISPR loci, and following transcription and processing of these loci, the CRISPR RNAs (crRNAs) guide the Cas proteins to complementary invading nucleic acid, which results in target interference. In this Review, we summarize the recent structural and biochemical insights that have been gained for the three major types of CRISPR-Cas systems, which together provide a detailed molecular understanding of the unique and conserved mechanisms of RNA-guided adaptive immunity in bacteria and archaea.

Gyroscopic effects in interference of matter waves

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

Tolstikhin, Oleg I.; Morishita, Toru; Watanabe, Shinichi

2005-11-15

A new gyroscopic interference effect stemming from the Galilean translational factor in the matter wave function is pointed out. In contrast to the well-known Sagnac effect that stems from the geometric phase and leads to a shift of interference fringes, this effect causes slanting of the fringes. We illustrate it by calculations for two split cigar-shaped Bose-Einstein condensates under the conditions of a recent experiment, see Y. Shin et al., Phys. Rev. Lett. 92, 050405 (2004). Importantly, the measurement of slanting obviates the need of a third reference cloud.

Oral lead bullet fragment exposure in northern bobwhite (Colinus virginianus).

PubMed

Kerr, Richard; Holladay, Jeremy; Holladay, Steven; Tannenbaum, Lawrence; Selcer, Barbara; Meldrum, Blair; Williams, Susan; Jarrett, Timothy; Gogal, Robert

2011-11-01

Lead (Pb) is a worldwide environmental contaminant known to adversely affect multiple organ systems in both mammalian and avian species. In birds, a common route of exposure is via oral ingestion of lead particles. Data are currently lacking for the retention and clearance of Pb bullet fragments in gastrointestinal (GI) tract of birds while linking toxicity with blood Pb levels. In the present study, northern bobwhite quail fed a seed-based diet were orally gavaged with Pb bullet fragments (zero, one or five fragments/bird) and evaluated for rate of fragment clearance, and changes in peripheral blood, renal, immune, and gastrointestinal parameters. Based on radiographs, the majority of the birds cleared or absorbed the fragments by seven days, with the exception of one five-fragment bird which took between 7 and 14 days. Blood Pb levels were higher in males than females, which may be related to egg production in females. In males but not females, feed consumption, body weight gain, packed cell volume (PCV), plasma protein concentration, and δ-aminolevulinic acid dehydratase (δ-ALAD) activity were all adversely affected by five Pb fragments. Birds of both sexes that received a single Pb fragment displayed depressed δ-ALAD, suggesting altered hematologic function, while all birds dosed with five bullet fragments exhibited greater morbidity.

Generating and Purifying Fab Fragments from Human and Mouse IgG Using the Bacterial Enzymes IdeS, SpeB and Kgp.

PubMed

Sjögren, Jonathan; Andersson, Linda; Mejàre, Malin; Olsson, Fredrik

2017-01-01

Fab fragments are valuable research tools in various areas of science including applications in imaging, binding studies, removal of Fc-mediated effector functions, mass spectrometry, infection biology, and many others. The enzymatic tools for the generation of Fab fragments have been discovered through basic research within the field of molecular bacterial pathogenesis. Today, these enzymes are widely applied as research tools and in this chapter, we describe methodologies based on bacterial enzymes to generate Fab fragments from both human and mouse IgG. For all human IgG subclasses, the IdeS enzyme from Streptococcus pyogenes has been applied to generate F(ab')2 fragments that subsequently can be reduced under mild conditions to generate a homogenous pool of Fab' fragments. The enzyme Kgp from Porphyromonas gingivalis has been applied to generate intact Fab fragments from human IgG1 and the Fab fragments can be purified using a CH1-specific affinity resin. The SpeB protease, also from S. pyogenes, is able to digest mouse IgGs and has been applied to digest antibodies and Fab fragments can be purified on light chain affinity resins. In this chapter, we describe methodologies that can be used to obtain Fab fragments from human and mouse IgG using bacterial proteases.

Fragmentation of amino acids induced by collisions with low-energy highly charged ions

NASA Astrophysics Data System (ADS)

Piekarski, D. G.; Maclot, S.; Domaracka, A.; Adoui, L.; Alcamí, M.; Rousseau, P.; Díaz-Tendero, S.; Huber, B. A.; Martín, F.

2014-04-01

Fragmentation of amino acids NH2-(CH2)n-COOH (n=1 glycine; n=2 β-alanine and n=3 γ-aminobutyric acid GABA) following collisions with slow highly charged ions has been studied in the gas phase by a combined experimental and theoretical approach. In the experiments, a multi-coincidence detection method was used to deduce the charge state of the molecules before fragmentation. Quantum chemistry calculations have been carried out in the basis of the density functional theory and ab initio molecular dynamics. The combination of both methodologies is essential to unambiguously unravel the different fragmentation pathways.

Extension of moment projection method to the fragmentation process

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

Wu, Shaohua; Yapp, Edward K.Y.; Akroyd, Jethro

2017-04-15

The method of moments is a simple but efficient method of solving the population balance equation which describes particle dynamics. Recently, the moment projection method (MPM) was proposed and validated for particle inception, coagulation, growth and, more importantly, shrinkage; here the method is extended to include the fragmentation process. The performance of MPM is tested for 13 different test cases for different fragmentation kernels, fragment distribution functions and initial conditions. Comparisons are made with the quadrature method of moments (QMOM), hybrid method of moments (HMOM) and a high-precision stochastic solution calculated using the established direct simulation algorithm (DSA) and advantagesmore » of MPM are drawn.« less

Cloning, bacterial expression and crystallization of Fv antibody fragments

NASA Astrophysics Data System (ADS)

E´, Jean-Luc; Boulot, Ginette; Chitarra, V´ronique; Riottot, Marie-Madeleine; Souchon, H´le`ne; Houdusse, Anne; Bentley, Graham A.; Narayana Bhat, T.; Spinelli, Silvia; Poljak, Roberto J.

1992-08-01

The variable Fv fragments of antibodies, cloned in recombinant plasmids, can be expressed in bacteria as functional proteins having immunochemical properties which are very similar or identical with those of the corresponding parts of the parent eukaryotic antibodies. They offer new possibilities for the study of antibody-antigen interactions since the crystals of Fv fragments and of their complexes with antigen reported here diffract X-rays to a higher resolution that those obtained with the cognate Fab fragments. The Fv approach should facilitate the structural study of the combining site of antibodies and the further characterization of antigen-antibody interactions by site-directed mutagenesis experiments.

Functional analysis of a frame-shift mutant of the dihydropyridine receptor pore subunit (α1S) expressing two complementary protein fragments

PubMed Central

Ahern, Chris A; Vallejo, Paola; Mortenson, Lindsay; Coronado, Roberto

2001-01-01

Background The L-type Ca2+ channel formed by the dihydropyridine receptor (DHPR) of skeletal muscle senses the membrane voltage and opens the ryanodine receptor (RyR1). This channel-to-channel coupling is essential for Ca2+ signaling but poorly understood. We characterized a single-base frame-shift mutant of α1S, the pore subunit of the DHPR, that has the unusual ability to function voltage sensor for excitation-contraction (EC) coupling by virtue of expressing two complementary hemi-Ca2+ channel fragments. Results Functional analysis of cDNA transfected dysgenic myotubes lacking α1S were carried out using voltage-clamp, confocal Ca2+ indicator fluoresence, epitope immunofluorescence and immunoblots of expressed proteins. The frame-shift mutant (fs-α1S) expressed the N-terminal half of α1S (M1 to L670) and the C-terminal half starting at M701 separately. The C-terminal fragment was generated by an unexpected restart of translation of the fs-α1S message at M701 and was eliminated by a M701I mutation. Protein-protein complementation between the two fragments produced recovery of skeletal-type EC coupling but not L-type Ca2+ current. Discussion A premature stop codon in the II-III loop may not necessarily cause a loss of DHPR function due to a restart of translation within the II-III loop, presumably by a mechanism involving leaky ribosomal scanning. In these cases, function is recovered by expression of complementary protein fragments from the same cDNA. DHPR-RyR1 interactions can be achieved via protein-protein complementation between hemi-Ca2+ channel proteins, hence an intact II-III loop is not essential for coupling the DHPR voltage sensor to the opening of RyR1 channel. PMID:11806762

Expression of the NH2-Terminal Fragment of RasGAP in Pancreatic β-Cells Increases Their Resistance to Stresses and Protects Mice From Diabetes

PubMed Central

Yang, Jiang-Yan; Walicki, Jöel; Jaccard, Evrim; Dubuis, Gilles; Bulat, Natasa; Hornung, Jean-Pierre; Thorens, Bernard; Widmann, Christian

2009-01-01

OBJECTIVE Our laboratory has previously established in vitro that a caspase-generated RasGAP NH2-terminal moiety, called fragment N, potently protects cells, including insulinomas, from apoptotic stress. We aimed to determine whether fragment N can increase the resistance of pancreatic β-cells in a physiological setting. RESEARCH DESIGN AND METHODS A mouse line, called rat insulin promoter (RIP)-N, was generated that bears a transgene containing the rat insulin promoter followed by the cDNA-encoding fragment N. The histology, functionality, and resistance to stress of RIP-N islets were then assessed. RESULTS Pancreatic β-cells of RIP-N mice express fragment N, activate Akt, and block nuclear factor κB activity without affecting islet cell proliferation or the morphology and cellular composition of islets. Intraperitoneal glucose tolerance tests revealed that RIP-N mice control their glycemia similarly as wild-type mice throughout their lifespan. Moreover, islets isolated from RIP-N mice showed normal glucose-induced insulin secretory capacities. They, however, displayed increased resistance to apoptosis induced by a series of stresses including inflammatory cytokines, fatty acids, and hyperglycemia. RIP-N mice were also protected from multiple low-dose streptozotocin-induced diabetes, and this was associated with reduced in vivo β-cell apoptosis. CONCLUSIONS Fragment N efficiently increases the overall resistance of β-cells to noxious stimuli without interfering with the physiological functions of the cells. Fragment N and the pathway it regulates represent, therefore, a potential target for the development of antidiabetes tools. PMID:19696184

Urbanization-induced habitat fragmentation erodes multiple components of temporal diversity in a Southern California native bee assemblage

PubMed Central

Ascher, John S.; Holway, David A.

2017-01-01

Despite a large number of ecological studies that document diversity loss resulting from anthropogenic disturbance, surprisingly few consider how disturbance affects temporal patterns of diversity that result from seasonal turnover of species. Temporal dynamics can play an important role in the structure and function of biological assemblages. Here, we investigate the temporal diversity patterns of bee faunas in Southern California coastal sage scrub ecosystems that have been extensively fragmented by urbanization. Using a two-year dataset of 235 bee species (n = 12,036 specimens), we compared 1-ha plots in scrub fragments and scrub reserves with respect to three components of temporal diversity: overall plot-level diversity pooled over time (temporal gamma diversity), diversity at discrete points in time (temporal alpha diversity), and seasonal turnover in assemblage composition (temporal beta diversity). Compared to reserves, fragments harbored bee assemblages with lower species richness and assemblage evenness both when summed across temporal samples (i.e., lower temporal gamma diversity) and at single points in time (i.e., lower temporal alpha diversity). Bee assemblages in fragments also exhibited reduced seasonal turnover (i.e., lower temporal beta diversity). While fragments and reserves did not differ in overall bee abundance, bee abundance in fragments peaked later in the season compared to that in reserves. Our results argue for an increased awareness of temporal diversity patterns, as information about the distinct components of temporal diversity is essential both for characterizing the assemblage dynamics of seasonal organisms and for identifying potential impacts of anthropogenic disturbance on ecosystem function through its effects on assemblage dynamics. PMID:28854229

Interference between light and heavy neutrinos for 0 νββ decay in the left–right symmetric model

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

Ahmed, Fahim; Neacsu, Andrei; Horoi, Mihai

Neutrinoless double-beta decay is proposed as an important low energy phenomenon that could test beyond the Standard Model physics. There are several potentially competing beyond the Standard Model mechanisms that can induce the process. It thus becomes important to disentangle the different processes. In the present study we consider the interference effect between the light left-handed and heavy right-handed Majorana neutrino exchange mechanisms. The decay rate, and consequently, the phase-space factors for the interference term are derived, based on the left–right symmetric model. The numerical values for the interference phase-space factors for several nuclides are calculated, taking into consideration themore » relativistic Coulomb distortion of the electron wave function and finite-size of the nucleus. As a result, the variation of the interference effect with the Q-value of the process is studied.« less

Interference between light and heavy neutrinos for 0 νββ decay in the left–right symmetric model

DOE PAGES

Ahmed, Fahim; Neacsu, Andrei; Horoi, Mihai

2017-03-31

Neutrinoless double-beta decay is proposed as an important low energy phenomenon that could test beyond the Standard Model physics. There are several potentially competing beyond the Standard Model mechanisms that can induce the process. It thus becomes important to disentangle the different processes. In the present study we consider the interference effect between the light left-handed and heavy right-handed Majorana neutrino exchange mechanisms. The decay rate, and consequently, the phase-space factors for the interference term are derived, based on the left–right symmetric model. The numerical values for the interference phase-space factors for several nuclides are calculated, taking into consideration themore » relativistic Coulomb distortion of the electron wave function and finite-size of the nucleus. As a result, the variation of the interference effect with the Q-value of the process is studied.« less

Highly Stretchable and Transparent Electromagnetic Interference Shielding Film Based on Silver Nanowire Percolation Network for Wearable Electronics Applications.

PubMed

Jung, Jinwook; Lee, Habeom; Ha, Inho; Cho, Hyunmin; Kim, Kyun Kyu; Kwon, Jinhyeong; Won, Phillip; Hong, Sukjoon; Ko, Seung Hwan

2017-12-27

Future electronics are expected to develop into wearable forms, and an adequate stretchability is required for the forthcoming wearable electronics considering various motions occurring in human body. Along with stretchability, transparency can increase both the functionality and esthetic features in future wearable electronics. In this study, we demonstrate, for the first time, a highly stretchable and transparent electromagnetic interference shielding layer for wearable electronic applications with silver nanowire percolation network on elastic poly(dimethylsiloxane) substrate. The proposed stretchable and transparent electromagnetic interference shielding layer shows a high electromagnetic wave shielding effectiveness even under a high tensile strain condition. It is expected for the silver nanowire percolation network-based electromagnetic interference shielding layer to be beyond the conventional electromagnetic interference shielding materials and to broaden its application range to various fields that require optical transparency or nonplanar surface environment, such as biological system, human skin, and wearable electronics.

Single-task fMRI overlap predicts concurrent multitasking interference.

PubMed

Nijboer, Menno; Borst, Jelmer; van Rijn, Hedderik; Taatgen, Niels

2014-10-15

There is no consensus regarding the origin of behavioral interference that occurs during concurrent multitasking. Some evidence points toward a multitasking locus in the brain, while other results imply that interference is the consequence of task interactions in several brain regions. To investigate this issue, we conducted a functional MRI (fMRI) study consisting of three component tasks, which were performed both separately and in combination. The results indicated that no specific multitasking area exists. Instead, different patterns of activation across conditions could be explained by assuming that the interference is a result of task interactions. Additionally, similarity in single-task activation patterns correlated with a decrease in accuracy during dual-task conditions. Taken together, these results support the view that multitasking interference is not due to a bottleneck in a single "multitasking" brain region, but is a result of interactions between concurrently running processes. Copyright © 2014 Elsevier Inc. All rights reserved.

Assembly and analysis of fragmentation data for liquid propellant vessels

NASA Technical Reports Server (NTRS)

Baker, W. E.; Parr, V. B.; Bessey, R. L.; Cox, P. A.

1974-01-01

Fragmentation data was assembled and analyzed for exploding liquid propellant vessels. These data were to be retrieved from reports of tests and accidents, including measurements or estimates of blast yield, etc. A significant amount of data was retrieved from a series of tests conducted for measurement of blast and fireball effects of liquid propellant explosions (Project PYRO), a few well-documented accident reports, and a series of tests to determine auto-ignition properties of mixing liquid propellants. The data were reduced and fitted to various statistical functions. Comparisons were made with methods of prediction for blast yield, initial fragment velocities, and fragment range. Reasonably good correlation was achieved. Methods presented in the report allow prediction of fragment patterns, given type and quantity of propellant, type of accident, and time of propellant mixing.

Cognitive declines in healthy aging: evidence from multiple aspects of interference resolution.

PubMed

Pettigrew, Corinne; Martin, Randi C

2014-06-01

The present study tested the hypothesis that older adults show age-related deficits in interference resolution, also referred to as inhibitory control. Although oftentimes considered as a unitary aspect of executive function, various lines of work support the notion that interference resolution may be better understood as multiple constructs, including resistance to proactive interference (PI) and response-distractor inhibition (e.g., Friedman & Miyake, 2004). Using this dichotomy, the present study assessed whether older adults (relative to younger adults) show impaired performance across both, 1, or neither of these interference resolution constructs. To do so, we used multiple tasks to tap each construct and examined age effects at both the single task and latent variable levels. Older adults consistently demonstrated exaggerated interference effects across resistance to PI tasks. Although the results for the response-distractor inhibition tasks were less consistent at the individual task level analyses, age effects were evident on multiple tasks, as well as at the latent variable level. However, results of the latent variable modeling suggested declines in interference resolution are best explained by variance that is common to the 2 interference resolution constructs measured herein. Furthermore, the effect of age on interference resolution was found to be both distinct from declines in working memory, and independent of processing speed. These findings suggest multiple cognitive domains are independently sensitive to age, but that declines in the interference resolution constructs measured herein may originate from a common cause. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Hyaluronan – A Functional and Structural Sweet Spot in the Tissue Microenvironment

PubMed Central

Monslow, James; Govindaraju, Priya; Puré, Ellen

2015-01-01

Transition from homeostatic to reactive matrix remodeling is a fundamental adaptive tissue response to injury, inflammatory disease, fibrosis, and cancer. Alterations in architecture, physical properties, and matrix composition result in changes in biomechanical and biochemical cellular signaling. The dynamics of pericellular and extracellular matrices, including matrix protein, proteoglycan, and glycosaminoglycan modification are continually emerging as essential regulatory mechanisms underlying cellular and tissue function. Nevertheless, the impact of matrix organization on inflammation and immunity in particular and the consequent effects on tissue healing and disease outcome are arguably under-studied aspects of adaptive stress responses. Herein, we review how the predominant glycosaminoglycan hyaluronan (HA) contributes to the structure and function of the tissue microenvironment. Specifically, we examine the evidence of HA degradation and the generation of biologically active smaller HA fragments in pathological settings in vivo. We discuss how HA fragments versus nascent HA via alternate receptor-mediated signaling influence inflammatory cell recruitment and differentiation, resident cell activation, as well as tumor growth, survival, and metastasis. Finally, we discuss how HA fragmentation impacts restoration of normal tissue function and pathological outcomes in disease. PMID:26029216

Neural Systems Underlying Emotional and Non-emotional Interference Processing: An ALE Meta-Analysis of Functional Neuroimaging Studies

PubMed Central

Xu, Min; Xu, Guiping; Yang, Yang

2016-01-01

Understanding how the nature of interference might influence the recruitments of the neural systems is considered as the key to understanding cognitive control. Although, interference processing in the emotional domain has recently attracted great interest, the question of whether there are separable neural patterns for emotional and non-emotional interference processing remains open. Here, we performed an activation likelihood estimation meta-analysis of 78 neuroimaging experiments, and examined common and distinct neural systems for emotional and non-emotional interference processing. We examined brain activation in three domains of interference processing: emotional verbal interference in the face-word conflict task, non-emotional verbal interference in the color-word Stroop task, and non-emotional spatial interference in the Simon, SRC and Flanker tasks. Our results show that the dorsal anterior cingulate cortex (ACC) was recruited for both emotional and non-emotional interference. In addition, the right anterior insula, presupplementary motor area (pre-SMA), and right inferior frontal gyrus (IFG) were activated by interference processing across both emotional and non-emotional domains. In light of these results, we propose that the anterior insular cortex may serve to integrate information from different dimensions and work together with the dorsal ACC to detect and monitor conflicts, whereas pre-SMA and right IFG may be recruited to inhibit inappropriate responses. In contrast, the dorsolateral prefrontal cortex (DLPFC) and posterior parietal cortex (PPC) showed different degrees of activation and distinct lateralization patterns for different processing domains, which suggests that these regions may implement cognitive control based on the specific task requirements. PMID:27895564

Enhanced NMR Discrimination of Pharmaceutically Relevant Molecular Crystal Forms through Fragment-Based Ab Initio Chemical Shift Predictions.

PubMed

Hartman, Joshua D; Day, Graeme M; Beran, Gregory J O

2016-11-02

Chemical shift prediction plays an important role in the determination or validation of crystal structures with solid-state nuclear magnetic resonance (NMR) spectroscopy. One of the fundamental theoretical challenges lies in discriminating variations in chemical shifts resulting from different crystallographic environments. Fragment-based electronic structure methods provide an alternative to the widely used plane wave gauge-including projector augmented wave (GIPAW) density functional technique for chemical shift prediction. Fragment methods allow hybrid density functionals to be employed routinely in chemical shift prediction, and we have recently demonstrated appreciable improvements in the accuracy of the predicted shifts when using the hybrid PBE0 functional instead of generalized gradient approximation (GGA) functionals like PBE. Here, we investigate the solid-state 13 C and 15 N NMR spectra for multiple crystal forms of acetaminophen, phenobarbital, and testosterone. We demonstrate that the use of the hybrid density functional instead of a GGA provides both higher accuracy in the chemical shifts and increased discrimination among the different crystallographic environments. Finally, these results also provide compelling evidence for the transferability of the linear regression parameters mapping predicted chemical shieldings to chemical shifts that were derived in an earlier study.

Enhanced NMR Discrimination of Pharmaceutically Relevant Molecular Crystal Forms through Fragment-Based Ab Initio Chemical Shift Predictions

PubMed Central

2016-01-01

Chemical shift prediction plays an important role in the determination or validation of crystal structures with solid-state nuclear magnetic resonance (NMR) spectroscopy. One of the fundamental theoretical challenges lies in discriminating variations in chemical shifts resulting from different crystallographic environments. Fragment-based electronic structure methods provide an alternative to the widely used plane wave gauge-including projector augmented wave (GIPAW) density functional technique for chemical shift prediction. Fragment methods allow hybrid density functionals to be employed routinely in chemical shift prediction, and we have recently demonstrated appreciable improvements in the accuracy of the predicted shifts when using the hybrid PBE0 functional instead of generalized gradient approximation (GGA) functionals like PBE. Here, we investigate the solid-state 13C and 15N NMR spectra for multiple crystal forms of acetaminophen, phenobarbital, and testosterone. We demonstrate that the use of the hybrid density functional instead of a GGA provides both higher accuracy in the chemical shifts and increased discrimination among the different crystallographic environments. Finally, these results also provide compelling evidence for the transferability of the linear regression parameters mapping predicted chemical shieldings to chemical shifts that were derived in an earlier study. PMID:27829821

A Developmental Window into Trade-offs in Executive Function: The Case of Task Switching versus Response Inhibition in 6-year-olds

PubMed Central

Chatham, Christopher H.; Wiseheart, Melody; Munakata, Yuko

2014-01-01

Good executive function has been linked to many positive outcomes in academic performance, health, and social competence. However, some aspects of executive function may interfere with other cognitive processes. Childhood provides a unique test case for investigating such cognitive trade-offs, given the dramatic failures and developments observed during this period. For example, most children categorically switch or perseverate when asked to switch between rules on a card-sorting task. To test potential trade-offs with the development of task switching abilities, we compared 6-year-olds who switched versus perseverated in a card-sorting task on two aspects of inhibitory control: response inhibition (via a stop signal task) and interference control (via a Simon task). Across two studies, switchers showed worse response inhibition than perseverators, consistent with the idea of cognitive trade-offs; however, switchers showed better interference control than perseverators, consistent with prior work documenting benefits associated with the development of executive function. This pattern of positive and negative associations may reflect aspects of working memory (active maintenance of current goals, and clearing of prior goals) that help children focused on a single task-goal but hurt in situations with conflicting goals. Implications for understanding components of executive function and their relationships across development are discussed. PMID:24791710

Degree centrality and fractional amplitude of low-frequency oscillations associated with Stroop interference.

PubMed

Takeuchi, Hikaru; Taki, Yasuyuki; Nouchi, Rui; Sekiguchi, Atsushi; Hashizume, Hiroshi; Sassa, Yuko; Kotozaki, Yuka; Miyauchi, Carlos Makoto; Yokoyama, Ryoichi; Iizuka, Kunio; Nakagawa, Seishu; Nagase, Tomomi; Kunitoki, Keiko; Kawashima, Ryuta

2015-10-01

Stroop paradigms are commonly used as an index of attention deficits and a tool for investigating functions of the frontal lobes and other associated structures. Here we investigated the correlation between resting-state functional magnetic imaging (fMRI) measures [degree centrality (DC)/fractional amplitude of low frequency fluctuations (fALFFs)] and Stroop interference. We examined this relationship in the brains of 958 healthy young adults. DC reflects the number of instantaneous functional connections between a region and the rest of the brain within the entire connectivity matrix of the brain (connectome), and thus how much of the node influences the entire brain areas, while fALFF is an indicator of the intensity of regional brain spontaneous activity. Reduced Stroop interference was associated with larger DC in the left lateral prefrontal cortex, left IFJ, and left inferior parietal lobule as well as larger fALFF in the areas of the dorsal attention network and the precuneus. These findings suggest that Stroop performance is reflected in resting state functional properties of these areas and the network. In addition, default brain activity of the dorsal attention network and precuneus as well as higher cognitive processes represented there, and default stronger global influence of the areas critical in executive functioning underlie better Stroop performance. Copyright © 2015 Elsevier Inc. All rights reserved.

The Buccaneer software for automated model building. 1. Tracing protein chains.

PubMed

Cowtan, Kevin

2006-09-01

A new technique for the automated tracing of protein chains in experimental electron-density maps is described. The technique relies on the repeated application of an oriented electron-density likelihood target function to identify likely C(alpha) positions. This function is applied both in the location of a few promising ;seed' positions in the map and to grow those initial C(alpha) positions into extended chain fragments. Techniques for assembling the chain fragments into an initial chain trace are discussed.

Fragmentation and Unpredictability of Early-Life Experience in Mental Disorders

PubMed Central

Baram, Tallie Z.; Solodkin, Ana; Davis, Elysia P.; Stern, Hal; Obenaus, Andre; Sandman, Curt A.; Small, Steven L.

2012-01-01

Maternal sensory signals in early life play a crucial role in programming the structure and function of the developing brain, promoting vulnerability or resilience to emotional and cognitive disorders. In rodent models of early-life stress, fragmentation and unpredictability of maternally derived sensory signals provoke persistent cognitive and emotional dysfunction in offspring. Similar variability and inconsistency of maternal signals during both gestation and early postnatal human life may influence development of emotional and cognitive functions, including those that underlie later depression and anxiety. PMID:22885631

Fragmentation functions at next-to-next-to-leading order accuracy

DOE PAGES

Anderle, Daniele P.; Stratmann, Marco; Ringer, Felix

2015-12-01

We present a first analysis of parton-to-pion fragmentation functions at next-to-next-to-leading order accuracy in QCD based on single-inclusive pion production in electron-positron annihilation. Special emphasis is put on the technical details necessary to perform the QCD scale evolution and cross section calculation in Mellin moment space. Lastly, we demonstrate how the description of the data and the theoretical uncertainties are improved when next-to-next-to-leading order QCD corrections are included.

Current facts on pacemaker electromagnetic interference and their application to clinical care

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

Sager, D.P.

1987-03-01

The development of the sensing demand cardiac pacemaker brought with it the problem of interference as a result of extraneous electric current and electromagnetic fields. This problem still deserves consideration, not only because harmful disruption of pacemaker function, while infrequent, can occur but also because myths and misunderstandings have flourished on the subject. Misinformation has often led to needless patient anxiety and unnecessary restrictions in activities of daily living. Similarly, when health care practitioners are misinformed about pacemaker interference, potentially hazardous situations can occur in the clinical environment. This article is a review of current information on the sources andmore » effects of electromagnetic interference (EMI) on pacemakers and includes a discussion of their application to patient care.« less

Agricultural matrices affect ground ant assemblage composition inside forest fragments

PubMed Central

Dos Santos, Iracenir Andrade; Ramos, Flavio Nunes; Majer, Jonathan David; Vilela, Evaldo Ferreira

2018-01-01

The establishment of agricultural matrices generally involves deforestation, which leads to fragmentation of the remaining forest. This fragmentation can affect forest dynamics both positively and negatively. Since most animal species are affected, certain groups can be used to measure the impact of such fragmentation. This study aimed to measure the impacts of agricultural crops (matrices) on ant communities of adjacent lower montane Atlantic rainforest fragments. We sampled nine forest fragments at locations surrounded by different agricultural matrices, namely: coffee (3 replicates); sugarcane (3); and pasture (3). At each site we installed pitfall traps along a 500 m transect from the interior of the matrix to the interior of the fragment (20 pitfall traps ~25 m apart). Each transect was partitioned into four categories: interior of the matrix; edge of the matrix; edge of the fragment; and interior of the fragment. For each sample site, we measured ant species richness and ant community composition within each transect category. Ant richness and composition differed between fragments and matrices. Each sample location had a specific composition of ants, probably because of the influence of the nature and management of the agricultural matrices. Species composition in the coffee matrix had the highest similarity to its corresponding fragment. The variability in species composition within forest fragments surrounded by pasture was greatest when compared with forest fragments surrounded by sugarcane or, to a lesser extent, coffee. Functional guild composition differed between locations, but the most representative guild was ‘generalist’ both in the agricultural matrices and forest fragments. Our results are important for understanding how agricultural matrices act on ant communities, and also, how these isolated forest fragments could act as an island of biodiversity in an ‘ocean of crops’. PMID:29791493

An accurate algorithm for the detection of DNA fragments from dilution pool sequencing experiments.

PubMed

Bansal, Vikas

2018-01-01

The short read lengths of current high-throughput sequencing technologies limit the ability to recover long-range haplotype information. Dilution pool methods for preparing DNA sequencing libraries from high molecular weight DNA fragments enable the recovery of long DNA fragments from short sequence reads. These approaches require computational methods for identifying the DNA fragments using aligned sequence reads and assembling the fragments into long haplotypes. Although a number of computational methods have been developed for haplotype assembly, the problem of identifying DNA fragments from dilution pool sequence data has not received much attention. We formulate the problem of detecting DNA fragments from dilution pool sequencing experiments as a genome segmentation problem and develop an algorithm that uses dynamic programming to optimize a likelihood function derived from a generative model for the sequence reads. This algorithm uses an iterative approach to automatically infer the mean background read depth and the number of fragments in each pool. Using simulated data, we demonstrate that our method, FragmentCut, has 25-30% greater sensitivity compared with an HMM based method for fragment detection and can also detect overlapping fragments. On a whole-genome human fosmid pool dataset, the haplotypes assembled using the fragments identified by FragmentCut had greater N50 length, 16.2% lower switch error rate and 35.8% lower mismatch error rate compared with two existing methods. We further demonstrate the greater accuracy of our method using two additional dilution pool datasets. FragmentCut is available from https://bansal-lab.github.io/software/FragmentCut. vibansal@ucsd.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Agricultural matrices affect ground ant assemblage composition inside forest fragments.

PubMed

Assis, Diego Santana; Dos Santos, Iracenir Andrade; Ramos, Flavio Nunes; Barrios-Rojas, Katty Elena; Majer, Jonathan David; Vilela, Evaldo Ferreira

2018-01-01

The establishment of agricultural matrices generally involves deforestation, which leads to fragmentation of the remaining forest. This fragmentation can affect forest dynamics both positively and negatively. Since most animal species are affected, certain groups can be used to measure the impact of such fragmentation. This study aimed to measure the impacts of agricultural crops (matrices) on ant communities of adjacent lower montane Atlantic rainforest fragments. We sampled nine forest fragments at locations surrounded by different agricultural matrices, namely: coffee (3 replicates); sugarcane (3); and pasture (3). At each site we installed pitfall traps along a 500 m transect from the interior of the matrix to the interior of the fragment (20 pitfall traps ~25 m apart). Each transect was partitioned into four categories: interior of the matrix; edge of the matrix; edge of the fragment; and interior of the fragment. For each sample site, we measured ant species richness and ant community composition within each transect category. Ant richness and composition differed between fragments and matrices. Each sample location had a specific composition of ants, probably because of the influence of the nature and management of the agricultural matrices. Species composition in the coffee matrix had the highest similarity to its corresponding fragment. The variability in species composition within forest fragments surrounded by pasture was greatest when compared with forest fragments surrounded by sugarcane or, to a lesser extent, coffee. Functional guild composition differed between locations, but the most representative guild was 'generalist' both in the agricultural matrices and forest fragments. Our results are important for understanding how agricultural matrices act on ant communities, and also, how these isolated forest fragments could act as an island of biodiversity in an 'ocean of crops'.

Interference Resolution in Emotional Working Memory as a Function of Alexithymia.

PubMed

Colligan, Sean M; Koven, Nancy S

2015-01-01

Although alexithymia is recognized as a set of traitlike deficits in emotion processing, research suggests there are concomitant cognitive issues as well, including what appears to be an unusual pattern of enhanced working memory (WM) despite broader executive dysfunction. It is unknown whether this enhancement includes the executive elements of WM and whether executive control of WM in alexithymia differs for emotional and neutral stimuli. This study examined how alexithymia moderates patterns of interference resolution in WM with valenced and nonvalenced stimuli. Participants (N = 93) completed the Toronto Alexithymia Scale and a recency probes WM task containing positive, negative, and neutral stimuli, with some trials containing proactive interference from previous trials. The reaction time difference between interference and noninterference trials indexed degree of interference resolution. Toronto Alexithymia Scale score moderated a within-subject effect such that, when valenced probes were used, there was less proactive interference in the positive relative to negative valence condition; this valence-based interference discrepancy was significant for a subset of highly alexithymic participants. Alexithymia did not moderate proactive interference to negative or neutral stimuli or accuracy of responses. These results suggest that, although alexithymia does not influence executive control in WM for nonemotional items, alexithymic people demonstrate an idiosyncratic response to positive stimuli that might indicate blunted reactivity.

Photon statistics as an interference phenomenon.

PubMed

Mehringer, Thomas; Mährlein, Simon; von Zanthier, Joachim; Agarwal, Girish S

2018-05-15

Interference of light fields, first postulated by Young, is one of the fundamental pillars of physics. Dirac extended this observation to the quantum world by stating that each photon interferes only with itself. A precondition for interference to occur is that no welcher-weg information labels the paths the photon takes; otherwise, the interference vanishes. This remains true, even if two-photon interference is considered, e.g., in the Hong-Ou-Mandel-experiment. Here, the two photons interfere only if they are indistinguishable, e.g., in frequency, momentum, polarization, and time. Less known is the fact that two-photon interference and photon indistinguishability also determine the photon statistics in the overlapping light fields of two independent sources. As a consequence, measuring the photon statistics in the far field of two independent sources reveals the degree of indistinguishability of the emitted photons. In this Letter, we prove this statement in theory using a quantum mechanical treatment. We also demonstrate the outcome experimentally with a simple setup consisting of two statistically independent thermal light sources with adjustable polarizations. We find that the photon statistics vary indeed as a function of the polarization settings, the latter determining the degree of welcher-weg information of the photons emanating from the two sources.

Interference tables: a useful model for interference analysis in asynchronous multicarrier transmission

NASA Astrophysics Data System (ADS)

Medjahdi, Yahia; Terré, Michel; Ruyet, Didier Le; Roviras, Daniel

2014-12-01

In this paper, we investigate the impact of timing asynchronism on the performance of multicarrier techniques in a spectrum coexistence context. Two multicarrier schemes are considered: cyclic prefix-based orthogonal frequency division multiplexing (CP-OFDM) with a rectangular pulse shape and filter bank-based multicarrier (FBMC) with physical layer for dynamic spectrum access and cognitive radio (PHYDYAS) and isotropic orthogonal transform algorithm (IOTA) waveforms. First, we present the general concept of the so-called power spectral density (PSD)-based interference tables which are commonly used for multicarrier interference characterization in spectrum sharing context. After highlighting the limits of this approach, we propose a new family of interference tables called `instantaneous interference tables'. The proposed tables give the interference power caused by a given interfering subcarrier on a victim one, not only as a function of the spectral distance separating both subcarriers but also with respect to the timing misalignment between the subcarrier holders. In contrast to the PSD-based interference tables, the accuracy of the proposed tables has been validated through different simulation results. Furthermore, due to the better frequency localization of both PHYDYAS and IOTA waveforms, FBMC technique is demonstrated to be more robust to timing asynchronism compared to OFDM one. Such a result makes FBMC a potential candidate for the physical layer of future cognitive radio systems.

A Rasch analysis of the Brief Pain Inventory Interference subscale reveals three dimensions and an age bias.

PubMed

Walton, David M; Beattie, Tyler; Putos, Joseph; MacDermid, Joy C

2016-06-01

The Brief Pain Inventory is composed of two quantifiable scales: pain severity and pain interference. The reported factor structure of the interference subscale is not consistent in the extant literature, with no clear choice between a single- or two-factor structure. Here, we report on the results of Rasch-based analysis of the interference subscale using a large population-based ambulatory patient database (the Quebec Pain Registry). Observational cohort. A total of 1,000 responses were randomly drawn from a total database of 5,654 for this analysis. Both the original 7-item and an expanded 10-item version (Tyler 2002) of the interference subscale were evaluated. Rasch analysis revealed significant misfit of both versions of the scale, with the original 7-item version outperforming the expanded 10-item version. Analysis of dimensionality revealed that both versions showed improved model fit when considered two subscales (affective and physical interference) with the item on sleep interference removed or considered separately. Additionally, significant uniform differential item functioning was identified for 6 of the 7 original items when the sample was stratified by age above or below 55 years. The interference subscale achieved adequate model fit when considered as two separate subscales with age as a mediator of response, while interpreting the sleep interference item separately. A transformation matrix revealed that in all cases, ordinal-level change at the extreme ends of the scale appears to be more meaningful than does a similar change at the midpoints. The Interference subscale of the BPI should be interpreted as two separate subscales (Affective Interference, Physical Interference) with the sleep item removed or interpreted separately for optimal fit to the Rasch model. Implications for research and clinical use are discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

The evolution of urban sprawl: evidence of spatial heterogeneity and increasing land fragmentation.

PubMed

Irwin, Elena G; Bockstael, Nancy E

2007-12-26

We investigate the dynamics and spatial distribution of land use fragmentation in a rapidly urbanizing region of the United States to test key propositions regarding the evolution of sprawl. Using selected pattern metrics and data from 1973 and 2000 for the state of Maryland, we find significant increases in developed and undeveloped land fragmentation but substantial spatial heterogeneity as well. Estimated fragmentation gradients that describe mean fragmentation as a function of distance from urban centers confirm the hypotheses that fragmentation rises and falls with distance and that the point of maximum fragmentation shifted outward over time. However, rather than outward increases in sprawl balanced by development infill, we find substantial and significant increases in mean fragmentation values along the entire urban-rural gradient. These findings are in contrast to the results of Burchfield et al. [Burchfield M, Overman HG, Puga D, Turner MA (2006) Q J Econ 121:587-633], who conclude that the extent of sprawl remained roughly unchanged in the Unites States between 1976 and 1992. As demonstrated here, both the data and pattern measure used in their study are systematically biased against recording low-density residential development, the very land use that we find is most strongly associated with fragmentation. Other results demonstrate the association between exurban growth and increasing fragmentation and the systematic variation of fragmentation with nonurban factors. In particular, proximity to the Chesapeake Bay is negatively associated with fragmentation, suggesting that an attraction effect associated with this natural amenity has concentrated development.

RNA Interference Based Approach to Down Regulate Osmoregulators of Whitefly (Bemisia tabaci): Potential Technology for the Control of Whitefly

USDA-ARS?s Scientific Manuscript database

Over the past decade RNA interference (RNAi) technology has emerged as a successful tool not only for functional genomics, but in planta expression of short interfering RNAs (siRNAs) could offer potential for insect pest management. Insects feeding exclusively on plant sap depend on osmotic pressure...

Counting statistics of many-particle quantum walks

NASA Astrophysics Data System (ADS)

Mayer, Klaus; Tichy, Malte C.; Mintert, Florian; Konrad, Thomas; Buchleitner, Andreas

2011-06-01

We study quantum walks of many noninteracting particles on a beam splitter array as a paradigmatic testing ground for the competition of single- and many-particle interference in a multimode system. We derive a general expression for multimode particle-number correlation functions, valid for bosons and fermions, and infer pronounced signatures of many-particle interferences in the counting statistics.