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Sample records for face ao novo

  1. De novo mutations in NALCN cause a syndrome characterized by congenital contractures of the limbs and face, hypotonia, and developmental delay.

    PubMed

    Chong, Jessica X; McMillin, Margaret J; Shively, Kathryn M; Beck, Anita E; Marvin, Colby T; Armenteros, Jose R; Buckingham, Kati J; Nkinsi, Naomi T; Boyle, Evan A; Berry, Margaret N; Bocian, Maureen; Foulds, Nicola; Uzielli, Maria Luisa Giovannucci; Haldeman-Englert, Chad; Hennekam, Raoul C M; Kaplan, Paige; Kline, Antonie D; Mercer, Catherine L; Nowaczyk, Malgorzata J M; Klein Wassink-Ruiter, Jolien S; McPherson, Elizabeth W; Moreno, Regina A; Scheuerle, Angela E; Shashi, Vandana; Stevens, Cathy A; Carey, John C; Monteil, Arnaud; Lory, Philippe; Tabor, Holly K; Smith, Joshua D; Shendure, Jay; Nickerson, Deborah A; Bamshad, Michael J

    2015-03-01

    Freeman-Sheldon syndrome, or distal arthrogryposis type 2A (DA2A), is an autosomal-dominant condition caused by mutations in MYH3 and characterized by multiple congenital contractures of the face and limbs and normal cognitive development. We identified a subset of five individuals who had been putatively diagnosed with "DA2A with severe neurological abnormalities" and for whom congenital contractures of the limbs and face, hypotonia, and global developmental delay had resulted in early death in three cases; this is a unique condition that we now refer to as CLIFAHDD syndrome. Exome sequencing identified missense mutations in the sodium leak channel, non-selective (NALCN) in four families affected by CLIFAHDD syndrome. We used molecular-inversion probes to screen for NALCN in a cohort of 202 distal arthrogryposis (DA)-affected individuals as well as concurrent exome sequencing of six other DA-affected individuals, thus revealing NALCN mutations in ten additional families with "atypical" forms of DA. All 14 mutations were missense variants predicted to alter amino acid residues in or near the S5 and S6 pore-forming segments of NALCN, highlighting the functional importance of these segments. In vitro functional studies demonstrated that NALCN alterations nearly abolished the expression of wild-type NALCN, suggesting that alterations that cause CLIFAHDD syndrome have a dominant-negative effect. In contrast, homozygosity for mutations in other regions of NALCN has been reported in three families affected by an autosomal-recessive condition characterized mainly by hypotonia and severe intellectual disability. Accordingly, mutations in NALCN can cause either a recessive or dominant condition characterized by varied though overlapping phenotypic features, perhaps based on the type of mutation and affected protein domain(s). PMID:25683120

  2. De Novo Mutations in NALCN Cause a Syndrome Characterized by Congenital Contractures of the Limbs and Face, Hypotonia, and Developmental Delay

    PubMed Central

    Chong, Jessica X.; McMillin, Margaret J.; Shively, Kathryn M.; Beck, Anita E.; Marvin, Colby T.; Armenteros, Jose R.; Buckingham, Kati J.; Nkinsi, Naomi T.; Boyle, Evan A.; Berry, Margaret N.; Bocian, Maureen; Foulds, Nicola; Uzielli, Maria Luisa Giovannucci; Haldeman-Englert, Chad; Hennekam, Raoul C.M.; Kaplan, Paige; Kline, Antonie D.; Mercer, Catherine L.; Nowaczyk, Malgorzata J.M.; Klein Wassink-Ruiter, Jolien S.; McPherson, Elizabeth W.; Moreno, Regina A.; Scheuerle, Angela E.; Shashi, Vandana; Stevens, Cathy A.; Carey, John C.; Monteil, Arnaud; Lory, Philippe; Tabor, Holly K.; Smith, Joshua D.; Shendure, Jay; Nickerson, Deborah A.; Bamshad, Michael J.; Shendure, Jay; Nickerson, Deborah A.; Abecasis, Gonçalo R.; Anderson, Peter; Blue, Elizabeth Marchani; Annable, Marcus; Browning, Brian L.; Buckingham, Kati J.; Chen, Christina; Chin, Jennifer; Chong, Jessica X.; Cooper, Gregory M.; Davis, Colleen P.; Frazar, Christopher; Harrell, Tanya M.; He, Zongxiao; Jain, Preti; Jarvik, Gail P.; Jimenez, Guillaume; Johanson, Eric; Jun, Goo; Kircher, Martin; Kolar, Tom; Krauter, Stephanie A.; Krumm, Niklas; Leal, Suzanne M.; Luksic, Daniel; Marvin, Colby T.; McMillin, Margaret J.; McGee, Sean; O’Reilly, Patrick; Paeper, Bryan; Patterson, Karynne; Perez, Marcos; Phillips, Sam W.; Pijoan, Jessica; Poel, Christa; Reinier, Frederic; Robertson, Peggy D.; Santos-Cortez, Regie; Shaffer, Tristan; Shephard, Cindy; Shively, Kathryn M.; Siegel, Deborah L.; Smith, Joshua D.; Staples, Jeffrey C.; Tabor, Holly K.; Tackett, Monica; Underwood, Jason G.; Wegener, Marc; Wang, Gao; Wheeler, Marsha M.; Yi, Qian; Bamshad, Michael J.

    2015-01-01

    Freeman-Sheldon syndrome, or distal arthrogryposis type 2A (DA2A), is an autosomal-dominant condition caused by mutations in MYH3 and characterized by multiple congenital contractures of the face and limbs and normal cognitive development. We identified a subset of five individuals who had been putatively diagnosed with “DA2A with severe neurological abnormalities” and for whom congenital contractures of the limbs and face, hypotonia, and global developmental delay had resulted in early death in three cases; this is a unique condition that we now refer to as CLIFAHDD syndrome. Exome sequencing identified missense mutations in the sodium leak channel, non-selective (NALCN) in four families affected by CLIFAHDD syndrome. We used molecular-inversion probes to screen for NALCN in a cohort of 202 distal arthrogryposis (DA)-affected individuals as well as concurrent exome sequencing of six other DA-affected individuals, thus revealing NALCN mutations in ten additional families with “atypical” forms of DA. All 14 mutations were missense variants predicted to alter amino acid residues in or near the S5 and S6 pore-forming segments of NALCN, highlighting the functional importance of these segments. In vitro functional studies demonstrated that NALCN alterations nearly abolished the expression of wild-type NALCN, suggesting that alterations that cause CLIFAHDD syndrome have a dominant-negative effect. In contrast, homozygosity for mutations in other regions of NALCN has been reported in three families affected by an autosomal-recessive condition characterized mainly by hypotonia and severe intellectual disability. Accordingly, mutations in NALCN can cause either a recessive or dominant condition characterized by varied though overlapping phenotypic features, perhaps based on the type of mutation and affected protein domain(s). PMID:25683120

  3. De novo mutations in NALCN cause a syndrome characterized by congenital contractures of the limbs and face, hypotonia, and developmental delay.

    PubMed

    Chong, Jessica X; McMillin, Margaret J; Shively, Kathryn M; Beck, Anita E; Marvin, Colby T; Armenteros, Jose R; Buckingham, Kati J; Nkinsi, Naomi T; Boyle, Evan A; Berry, Margaret N; Bocian, Maureen; Foulds, Nicola; Uzielli, Maria Luisa Giovannucci; Haldeman-Englert, Chad; Hennekam, Raoul C M; Kaplan, Paige; Kline, Antonie D; Mercer, Catherine L; Nowaczyk, Malgorzata J M; Klein Wassink-Ruiter, Jolien S; McPherson, Elizabeth W; Moreno, Regina A; Scheuerle, Angela E; Shashi, Vandana; Stevens, Cathy A; Carey, John C; Monteil, Arnaud; Lory, Philippe; Tabor, Holly K; Smith, Joshua D; Shendure, Jay; Nickerson, Deborah A; Bamshad, Michael J

    2015-03-01

    Freeman-Sheldon syndrome, or distal arthrogryposis type 2A (DA2A), is an autosomal-dominant condition caused by mutations in MYH3 and characterized by multiple congenital contractures of the face and limbs and normal cognitive development. We identified a subset of five individuals who had been putatively diagnosed with "DA2A with severe neurological abnormalities" and for whom congenital contractures of the limbs and face, hypotonia, and global developmental delay had resulted in early death in three cases; this is a unique condition that we now refer to as CLIFAHDD syndrome. Exome sequencing identified missense mutations in the sodium leak channel, non-selective (NALCN) in four families affected by CLIFAHDD syndrome. We used molecular-inversion probes to screen for NALCN in a cohort of 202 distal arthrogryposis (DA)-affected individuals as well as concurrent exome sequencing of six other DA-affected individuals, thus revealing NALCN mutations in ten additional families with "atypical" forms of DA. All 14 mutations were missense variants predicted to alter amino acid residues in or near the S5 and S6 pore-forming segments of NALCN, highlighting the functional importance of these segments. In vitro functional studies demonstrated that NALCN alterations nearly abolished the expression of wild-type NALCN, suggesting that alterations that cause CLIFAHDD syndrome have a dominant-negative effect. In contrast, homozygosity for mutations in other regions of NALCN has been reported in three families affected by an autosomal-recessive condition characterized mainly by hypotonia and severe intellectual disability. Accordingly, mutations in NALCN can cause either a recessive or dominant condition characterized by varied though overlapping phenotypic features, perhaps based on the type of mutation and affected protein domain(s).

  4. AO operations at Gemini South

    NASA Astrophysics Data System (ADS)

    Marin, Eduardo; Cardwell, Andrew; Pessev, Peter

    2014-08-01

    The 8m Gemini South telescope is entering an exciting new era of AO operations, which put it at the forefront of astronomical AO in terms of both wide field AO, and extreme-AO systems. Major milestones achieved were the successful commissioning of GeMS, in 2012, and GPI, in late 2013 and early 2014. Currently we are operating two of the worlds most advanced astronomical AO systems. Gemini, running primarily in queue, must balance the promise of AO with the demands of the community to use non-AO instruments. We discuss the current state of the two AO systems, and their operational models. The preparations that go into planning each AO run, the difficulties in scheduling around non-AO instruments, and the differences between scheduling LGS AO and non-LGS AO are discussed.

  5. Prospects for de novo phasing with de novo protein models

    SciTech Connect

    Das, Rhiju Baker, David

    2009-02-01

    In a first systematic exploration of phasing with Rosetta de novo models, it is shown that all-atom refinement of coarse-grained models significantly improves both the model quality and performance in molecular replacement with the Phaser software. The prospect of phasing diffraction data sets ‘de novo’ for proteins with previously unseen folds is appealing but largely untested. In a first systematic exploration of phasing with Rosetta de novo models, it is shown that all-atom refinement of coarse-grained models significantly improves both the model quality and performance in molecular replacement with the Phaser software. 15 new cases of diffraction data sets that are unambiguously phased with de novo models are presented. These diffraction data sets represent nine space groups and span a large range of solvent contents (33–79%) and asymmetric unit copy numbers (1–4). No correlation is observed between the ease of phasing and the solvent content or asymmetric unit copy number. Instead, a weak correlation is found with the length of the modeled protein: larger proteins required somewhat less accurate models to give successful molecular replacement. Overall, the results of this survey suggest that de novo models can phase diffraction data for approximately one sixth of proteins with sizes of 100 residues or less. However, for many of these cases, ‘de novo phasing with de novo models’ requires significant investment of computational power, much greater than 10{sup 3} CPU days per target. Improvements in conformational search methods will be necessary if molecular replacement with de novo models is to become a practical tool for targets without homology to previously solved protein structures.

  6. Simulations of Solar AO Systems

    NASA Astrophysics Data System (ADS)

    Sridharan, R.; Bayanna, A. Raja; Venkatakrishnan, P.

    In this paper, first we compare the two kinds of algorithms that are being used in solar AO systems to sense a distorted wave-front through simulations. Then, we comment on the various issues related to solar AO systems and describe solar features that can be studied using AO as a tool. Then we briefly describe the laboratory model of AO that is being built at the Udaipur Solar Observatory (USO), India.

  7. AO Group Annual Report

    SciTech Connect

    Olivier, S

    2005-10-04

    The Adaptive Optics (AO) Group in I Division develops and tests a broad range of advanced wavefront control technologies. Current applications focus on: Remote sensing, High power lasers, Astronomy, and Human vision. In the area of remote sensing, the AO Group leads a collaborative effort with LLNL's Nonproliferation, Arms Control & International Security (NAI) Directorate on Enhanced Surveillance Imaging. The ability to detect and identify individual people or vehicles from long-range is an important requirement for proliferation detection and homeland security. High-resolution imaging along horizontal paths through the atmosphere is limited by turbulence, which blurs and distorts the image. For ranges over {approx}one km, visible image resolution can be reduced by over an order of magnitude. We have developed an approach based on speckle imaging that can correct the turbulence-induced blurring and provide high resolution imagery. The system records a series of short exposure images which freeze the atmospheric effects. We can then estimate the image magnitude and phase using a bispectral estimation algorithm which cancels the atmospheric effects while maintaining object information at the diffraction limit of the imaging system.

  8. Recognizing faces.

    PubMed

    Ellis, H D

    1975-11-01

    Following a review of the stimulus and subject factors which have been found to affect recognition faces, the question of whether this process can be considered a special one is dealt with. Evidence from studies involving the development of face recognition, the recognition of inverted faces, and the clinical condition prosopagnosia is considered, and in each case found to be inadequate for the unequivocal conclusion that the processes underlying face recognition are qualitatively different from those employed in recognizing other pictorial material.

  9. Game Face

    ERIC Educational Resources Information Center

    Weiner, Jill

    2005-01-01

    In this article, the author discusses "Game Face: Life Lessons Across the Curriculum", a teaching kit that challenges assumptions and builds confidence. Game Face, which is derived from a book and art exhibition, "Game Face: What Does a Female Athlete Look Like?", uses layered and powerful images of women and girls participating in sports to teach…

  10. Face Painting.

    ERIC Educational Resources Information Center

    Brooks, Diana

    1995-01-01

    Discusses the use of face painting as a technique for making the endangered species issue tangible for children while addressing the complexity of the issue. Children are "given" an animal of their own and are educated about the animal while having their faces painted to resemble the animal. (LZ)

  11. Identification of a De Novo Heterozygous Missense FLNB Mutation in Lethal Atelosteogenesis Type I by Exome Sequencing

    PubMed Central

    Jeon, Ga Won; Lee, Mi-Na; Jung, Ji Mi; Hong, Seong Yeon; Kim, Young Nam; Sin, Jong Beom

    2014-01-01

    Background Atelosteogenesis type I (AO-I) is a rare lethal skeletal dysplastic disorder characterized by severe short-limbed dwarfism and dislocated hips, knees, and elbows. AO-I is caused by mutations in the filamin B (FLNB) gene; however, several other genes can cause AO-like lethal skeletal dysplasias. Methods In order to screen all possible genes associated with AO-like lethal skeletal dysplasias simultaneously, we performed whole-exome sequencing in a female newborn having clinical features of AO-I. Results Exome sequencing identified a novel missense variant (c.517G>A; p.Ala173Thr) in exon 2 of the FLNB gene in the patient. Sanger sequencing validated this variant, and genetic analysis of the patient's parents suggested a de novo occurrence of the variant. Conclusions This study shows that exome sequencing can be a useful tool for the identification of causative mutations in lethal skeletal dysplasia patients. PMID:24624349

  12. Face pain

    MedlinePlus

    ... gets worse when you bend forward) Tic douloureux Temporomandibular joint dysfunction syndrome Sometimes the reason for the face pain ... is persistent, unexplained, or accompanied by other unexplained symptoms. Call your primary provider. What to Expect at ...

  13. De Novo Glomerular Diseases after Renal Transplantation

    PubMed Central

    Moroni, Gabriella; Glassock, Richard J.

    2014-01-01

    Glomerular diseases developing in the kidney allograft are more often recurrences of the original disease affecting the native kidneys. However, in an undefined number of cases de novo, glomerular diseases unrelated to the original disease in the native kidneys can develop in the transplanted kidney. The clinical presentation and histologic features of de novo diseases are often similar to those features observed in patients with primary or secondary GN in the native kidneys. However, in transplanted kidneys, the glomerular, vascular, and tubulointerstitial changes are often intertwined with structural abnormalities already present at the time of transplant or caused by antibody- or cell-mediated allograft rejection, immunosuppressive drugs, or superimposed infection (most often of a viral nature). The pathophysiology of de novo glomerular diseases is quite variable. In rare cases of de novo minimal change disease, circulating factors increasing the glomerular permeability likely participate. Maladaptive hemodynamic changes and tissue fibrosis caused by calcineurin inhibitors or other factors may be involved in the pathogenesis of de novo FSGS. The exposure of cryptic podocyte antigens may favor the development of de novo membranous nephropathy. Many cases of de novo membranoproliferative GN are related to hepatitis C virus infection. Patients with Alport syndrome lacking antigenic epitopes in their glomerular basement membrane may develop antibodies against these glomerular basement membrane antigens expressed in the transplanted kidney. Infection may cause acute GN to have a heterogeneous clinical presentation and outcome. De novo pauci-immune GN in renal transplant is rare. Preexisting or acquired intolerance to glucose may, in the long term, cause diabetic nephropathy. The prognosis of de novo diseases depends on the type of GN, the severity of lesions caused by the alloimmune response, or the efficacy of immunosuppressive therapy. In most cases, the management

  14. Funny Faces.

    ERIC Educational Resources Information Center

    Greene, Yvonne

    2000-01-01

    Presents a torn-paper and gadget-print activity for younger students, specifically pre-kindergarten to first grade, that can be done any time over the school year or at Halloween. Discusses how the students create their funny faces and lists the materials needed. (CMK)

  15. De novo mutations in epileptic encephalopathies.

    PubMed

    Allen, Andrew S; Berkovic, Samuel F; Cossette, Patrick; Delanty, Norman; Dlugos, Dennis; Eichler, Evan E; Epstein, Michael P; Glauser, Tracy; Goldstein, David B; Han, Yujun; Heinzen, Erin L; Hitomi, Yuki; Howell, Katherine B; Johnson, Michael R; Kuzniecky, Ruben; Lowenstein, Daniel H; Lu, Yi-Fan; Madou, Maura R Z; Marson, Anthony G; Mefford, Heather C; Esmaeeli Nieh, Sahar; O'Brien, Terence J; Ottman, Ruth; Petrovski, Slavé; Poduri, Annapurna; Ruzzo, Elizabeth K; Scheffer, Ingrid E; Sherr, Elliott H; Yuskaitis, Christopher J; Abou-Khalil, Bassel; Alldredge, Brian K; Bautista, Jocelyn F; Berkovic, Samuel F; Boro, Alex; Cascino, Gregory D; Consalvo, Damian; Crumrine, Patricia; Devinsky, Orrin; Dlugos, Dennis; Epstein, Michael P; Fiol, Miguel; Fountain, Nathan B; French, Jacqueline; Friedman, Daniel; Geller, Eric B; Glauser, Tracy; Glynn, Simon; Haut, Sheryl R; Hayward, Jean; Helmers, Sandra L; Joshi, Sucheta; Kanner, Andres; Kirsch, Heidi E; Knowlton, Robert C; Kossoff, Eric H; Kuperman, Rachel; Kuzniecky, Ruben; Lowenstein, Daniel H; McGuire, Shannon M; Motika, Paul V; Novotny, Edward J; Ottman, Ruth; Paolicchi, Juliann M; Parent, Jack M; Park, Kristen; Poduri, Annapurna; Scheffer, Ingrid E; Shellhaas, Renée A; Sherr, Elliott H; Shih, Jerry J; Singh, Rani; Sirven, Joseph; Smith, Michael C; Sullivan, Joseph; Lin Thio, Liu; Venkat, Anu; Vining, Eileen P G; Von Allmen, Gretchen K; Weisenberg, Judith L; Widdess-Walsh, Peter; Winawer, Melodie R

    2013-09-12

    Epileptic encephalopathies are a devastating group of severe childhood epilepsy disorders for which the cause is often unknown. Here we report a screen for de novo mutations in patients with two classical epileptic encephalopathies: infantile spasms (n = 149) and Lennox-Gastaut syndrome (n = 115). We sequenced the exomes of 264 probands, and their parents, and confirmed 329 de novo mutations. A likelihood analysis showed a significant excess of de novo mutations in the ∼4,000 genes that are the most intolerant to functional genetic variation in the human population (P = 2.9 × 10(-3)). Among these are GABRB3, with de novo mutations in four patients, and ALG13, with the same de novo mutation in two patients; both genes show clear statistical evidence of association with epileptic encephalopathy. Given the relevant site-specific mutation rates, the probabilities of these outcomes occurring by chance are P = 4.1 × 10(-10) and P = 7.8 × 10(-12), respectively. Other genes with de novo mutations in this cohort include CACNA1A, CHD2, FLNA, GABRA1, GRIN1, GRIN2B, HNRNPU, IQSEC2, MTOR and NEDD4L. Finally, we show that the de novo mutations observed are enriched in specific gene sets including genes regulated by the fragile X protein (P < 10(-8)), as has been reported previously for autism spectrum disorders.

  16. [De novo autoimmune hepatitis after liver transplantation].

    PubMed

    Luo, Bifen; Wei, Lai

    2016-02-01

    Patients who transplanted for non-autoimmune indication may developed de novo autoimmune hepatitis after liver transplantation. It happens about 1.7%-6.6% in liver transplanted population. Most patients with de novo AIH had transplanted for HCV infection, biliary atresia and Cholestatic liver disease. The interval between transplantation and de novo AIH onset is from 3 month to 16 years, mostly more than 1 year. The disease can be seen at any age. More female patients are present in children, while there is no significant difference between male and female in adults. Clinical manifestations of de novo AIH are similar to those of AIH, namely characterized by elevated transaminase with or without bilirubin, as well as elevated serum gammaglobulin (IgG) and positive autoantibodies, while the histological features of an infiltrate rich in plasma cells with interface hepatitis and necro-inflammation and fibrosis. Treatment with corticosteroids and Azathioprine brings good outcomes, but it tends to fluctuate.

  17. MEMS AO for Planet Finding

    NASA Technical Reports Server (NTRS)

    Rao, Shanti; Wallace, J. Kent; Shao, Mike; Schmidtlin, Edouard; Levine, B. Martin; Samuele, Rocco; Lane, Benjamin; Chakrabarti, Supriya; Cook, Timothy; Hicks, Brian; Jung, Paul

    2008-01-01

    This slide presentation reviews a method for planet finding using microelectromechanical systems (MEMS) Adaptive Optics (AO). The use of a deformable mirror (DM) is described as a part of the instrument that was designed with a nulling interferometer. The strategy that is used is described in detail.

  18. DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra.

    PubMed

    Muth, Thilo; Weilnböck, Lisa; Rapp, Erdmann; Huber, Christian G; Martens, Lennart; Vaudel, Marc; Barsnes, Harald

    2014-02-01

    De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, their adoption threshold remains quite high. We here present a user-friendly and lightweight graphical user interface called DeNovoGUI for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics. Our platform-independent software is freely available under the permissible Apache2 open source license. Source code, binaries, and additional documentation are available at http://denovogui.googlecode.com .

  19. De novo mutation in the dopamine transporter gene associates dopamine dysfunction with autism spectrum disorder

    PubMed Central

    Hamilton, Peter J.; Campbell, Nicholas G.; Sharma, Shruti; Erreger, Kevin; Hansen, Freja Herborg; Saunders, Christine; Belovich, Andrea N.; Sahai, Michelle A.; Cook, Edwin H.; Gether, Ulrik; Mchaourab, Hassane S.; Matthies, Heinrich J.G.; Sutcliffe, James S.; Galli, Aurelio

    2014-01-01

    De novo genetic variation is an important class of risk factors for autism spectrum disorder (ASD). Recently, whole exome sequencing of ASD families has identified a novel de novo missense mutation in the human dopamine (DA) transporter (hDAT) gene, which results in a Thr to Met substitution at site 356 (hDAT T356M). The dopamine transporter (DAT) is a presynaptic membrane protein that regulates dopaminergic tone in the central nervous system by mediating the high-affinity re-uptake of synaptically released DA, making it a crucial regulator of DA homeostasis. Here, we report the first functional, structural, and behavioral characterization of an ASD-associated de novo mutation in the hDAT. We demonstrate that the hDAT T356M displays anomalous function, characterized as a persistent reverse transport of DA (substrate efflux). Importantly, in the bacterial homolog leucine transporter, substitution of A289 (the homologous site to T356) with a Met promotes an outward-facing conformation upon substrate binding. In the substrate-bound state, an outward-facing transporter conformation is a required for substrate efflux. In Drosophila melanogaster, expression of hDAT T356M in DA neurons lacking Drosophila DAT leads to hyperlocomotion, a trait associated with DA dysfunction and ASD. Taken together, our findings demonstrate that alterations in DA homeostasis, mediated by aberrant DAT function, may confer risk for ASD and related neuropsychiatric conditions. PMID:23979605

  20. Aerosol Observing System (AOS) Handbook

    SciTech Connect

    Jefferson, A

    2011-01-17

    The Aerosol Observing System (AOS) is a suite of in situ surface measurements of aerosol optical and cloud-forming properties. The instruments measure aerosol properties that influence the earth’s radiative balance. The primary optical measurements are those of the aerosol scattering and absorption coefficients as a function of particle size and radiation wavelength and cloud condensation nuclei (CCN) measurements as a function of percent supersaturation. Additional measurements include those of the particle number concentration and scattering hygroscopic growth. Aerosol optical measurements are useful for calculating parameters used in radiative forcing calculations such as the aerosol single-scattering albedo, asymmetry parameter, mass scattering efficiency, and hygroscopic growth. CCN measurements are important in cloud microphysical models to predict droplet formation.

  1. Evolution of Viral Proteins Originated De Novo by Overprinting

    PubMed Central

    Sabath, Niv; Wagner, Andreas; Karlin, David

    2012-01-01

    New protein-coding genes can originate either through modification of existing genes or de novo. Recently, the importance of de novo origination has been recognized in eukaryotes, although eukaryotic genes originated de novo are relatively rare and difficult to identify. In contrast, viruses contain many de novo genes, namely those in which an existing gene has been “overprinted” by a new open reading frame, a process that generates a new protein-coding gene overlapping the ancestral gene. We analyzed the evolution of 12 experimentally validated viral genes that originated de novo and estimated their relative ages. We found that young de novo genes have a different codon usage from the rest of the genome. They evolve rapidly and are under positive or weak purifying selection. Thus, young de novo genes might have strain-specific functions, or no function, and would be difficult to detect using current genome annotation methods that rely on the sequence signature of purifying selection. In contrast to young de novo genes, older de novo genes have a codon usage that is similar to the rest of the genome. They evolve slowly and are under stronger purifying selection. Some of the oldest de novo genes evolve under stronger selection pressure than the ancestral gene they overlap, suggesting an evolutionary tug of war between the ancestral and the de novo gene. PMID:22821011

  2. A Face Inversion Effect without a Face

    ERIC Educational Resources Information Center

    Brandman, Talia; Yovel, Galit

    2012-01-01

    Numerous studies have attributed the face inversion effect (FIE) to configural processing of internal facial features in upright but not inverted faces. Recent findings suggest that face mechanisms can be activated by faceless stimuli presented in the context of a body. Here we asked whether faceless stimuli with or without body context may induce…

  3. Learning Faces from Photographs

    ERIC Educational Resources Information Center

    Longmore, Christopher A.; Liu, Chang Hong; Young, Andrew W.

    2008-01-01

    Previous studies examining face learning have mostly used only a single exposure to 1 image of each of the faces to be learned. However, in daily life, faces are usually learned from multiple encounters. These 6 experiments examined the effects on face learning of repeated exposures to single or multiple images of a face. All experiments…

  4. De novo mutations in human genetic disease.

    PubMed

    Veltman, Joris A; Brunner, Han G

    2012-08-01

    New mutations have long been known to cause genetic disease, but their true contribution to the disease burden can only now be determined using family-based whole-genome or whole-exome sequencing approaches. In this Review we discuss recent findings suggesting that de novo mutations play a prominent part in rare and common forms of neurodevelopmental diseases, including intellectual disability, autism and schizophrenia. De novo mutations provide a mechanism by which early-onset reproductively lethal diseases remain frequent in the population. These mutations, although individually rare, may capture a significant part of the heritability for complex genetic diseases that is not detectable by genome-wide association studies. PMID:22805709

  5. Nanomedicine: de novo design of nanodrugs

    NASA Astrophysics Data System (ADS)

    Yang, Zaixing; Kang, Seung-Gu; Zhou, Ruhong

    2013-12-01

    Phenomenal advances in nanotechnology and nanoscience have been accompanied by exciting progress in de novo design of nanomedicines. Nanoparticles with their large space of structural amenability and excellent mechanical and electrical properties have become ideal candidates for high efficacy nanomedicines in both diagnostics and therapeutics. The therapeutic nanomedicines can be further categorized into nanocarriers for conventional drugs and nanodrugs with direct curing of target diseases. Here we review some of the recent advances in de novo design of nanodrugs, with an emphasis on the molecular level understanding of their interactions with biological systems including key proteins and cell membranes. We also include some of the latest advances in the development of nanocarriers with both passive and active targeting for completeness. These studies may shed light on a better understanding of the molecular mechanisms behind these nanodrugs, and also provide new insights and direction for the future design of nanomedicines.

  6. Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios

    PubMed Central

    Besenbacher, Søren; Liu, Siyang; Izarzugaza, José M. G.; Grove, Jakob; Belling, Kirstine; Bork-Jensen, Jette; Huang, Shujia; Als, Thomas D.; Li, Shengting; Yadav, Rachita; Rubio-García, Arcadio; Lescai, Francesco; Demontis, Ditte; Rao, Junhua; Ye, Weijian; Mailund, Thomas; Friborg, Rune M.; Pedersen, Christian N. S.; Xu, Ruiqi; Sun, Jihua; Liu, Hao; Wang, Ou; Cheng, Xiaofang; Flores, David; Rydza, Emil; Rapacki, Kristoffer; Damm Sørensen, John; Chmura, Piotr; Westergaard, David; Dworzynski, Piotr; Sørensen, Thorkild I. A.; Lund, Ole; Hansen, Torben; Xu, Xun; Li, Ning; Bolund, Lars; Pedersen, Oluf; Eiberg, Hans; Krogh, Anders; Børglum, Anders D.; Brunak, Søren; Kristiansen, Karsten; Schierup, Mikkel H.; Wang, Jun; Gupta, Ramneek; Villesen, Palle; Rasmussen, Simon

    2015-01-01

    Building a population-specific catalogue of single nucleotide variants (SNVs), indels and structural variants (SVs) with frequencies, termed a national pan-genome, is critical for further advancing clinical and public health genetics in large cohorts. Here we report a Danish pan-genome obtained from sequencing 10 trios to high depth (50 × ). We report 536k novel SNVs and 283k novel short indels from mapping approaches and develop a population-wide de novo assembly approach to identify 132k novel indels larger than 10 nucleotides with low false discovery rates. We identify a higher proportion of indels and SVs than previous efforts showing the merits of high coverage and de novo assembly approaches. In addition, we use trio information to identify de novo mutations and use a probabilistic method to provide direct estimates of 1.27e−8 and 1.5e−9 per nucleotide per generation for SNVs and indels, respectively. PMID:25597990

  7. Mechanisms of identity and gender decisions to faces: who rocked in 1986?

    PubMed

    Richards, Rachel M; Ellis, Andrew W

    2008-01-01

    Two experiments are reported in which participants made familiarity decisions (Is this face familiar or not?) or gender decisions (Is this face male or female?) to the same sets of faces presented as whole faces or as internal features only. The experimental items on which the analysis was performed were famous and unfamiliar male faces that differed on rated masculinity. The famous faces also differed on age of acquisition (AoA). The experimental male faces were combined with an equal number of famous and unfamiliar female faces for presentation to participants. In experiment 1 we found faster and more accurate familiarity decisions to whole male faces than to internal features; also an interaction between AoA and masculinity such that familiarity decisions were both faster and more accurate to high- than to low-masculinity faces when those faces were late-acquired, but not when they were early-acquired. In experiment 2 we found the same benefit for whole faces over internal features and the same interaction between AoA and masculinity in gender decisions. The similarity between the effects of AoA and masculinity in familiarity and gender decisions is more readily accounted for by models of face processing which posit a close relationship between gender and identity processing than by models which maintain that those aspects of face perception are dealt with by quite separate processing streams. We propose that gender decisions, like familiarity decisions, are semantic judgments (rather than judgments based on the analysis of the surface features of faces), and that the shared basis of the two forms of decision explains why they show similar influences of AoA and masculinity. PMID:19189733

  8. Attention Capture by Faces

    ERIC Educational Resources Information Center

    Langton, Stephen R. H.; Law, Anna S.; Burton, A. Mike; Schweinberger, Stefan R.

    2008-01-01

    We report three experiments that investigate whether faces are capable of capturing attention when in competition with other non-face objects. In Experiment 1a participants took longer to decide that an array of objects contained a butterfly target when a face appeared as one of the distracting items than when the face did not appear in the array.…

  9. Evolution and function of de novo originated genes.

    PubMed

    Wu, Dong-Dong; Zhang, Ya-Ping

    2013-05-01

    De novo origination has recently been appreciated to be an important mechanism contributing to the origin of genes. Evidence indicates that de novo originated genes can evolve important and even essential functions rapidly. We present an "adaptation following neutrality" process to explain the evolution of essential function of new genes. How new de novo originated genes become involved in pathways and interact with other old genes, and the exact functions of these new genes, however, remains largely undocumented. Examinations of the function of de novo origin and the function of noncoding RNA genes should become more frequent and appreciated in the future studies.

  10. De novo autoimmune hepatitis after liver transplantation.

    PubMed

    Lohse, Ansgar W; Weiler-Norman, Christina; Burdelski, Martin

    2007-10-01

    The Kings College group was the first to describe a clinical syndrome similar to autoimmune hepatitis in children and young adults transplanted for non-immune mediated liver diseases. They coined the term "de novo autoimmune hepatitis". Several other liver transplant centres confirmed this observation. Even though the condition is uncommon, patients with de novo AIH are now seen in most of the major transplant centres. The disease is usually characterized by features of acute hepatitis in otherwise stable transplant recipients. The most characteristic laboratory hallmark is a marked hypergammaglobulinaemia. Autoantibodies are common, mostly ANA. We described also a case of LKM1-positivity in a patients transplanted for Wilson's disease, however this patients did not develop clinical or histological features of AIH. Development of SLA/LP-autoantibodies is also not described. Therefore, serologically de novo AIH appears to correspond to type 1 AIH. Like classical AIH patients respond promptly to treatment with increased doses of prednisolone and azathioprine, while the calcineurin inhibitors cyclosporine or tacrolimus areof very limited value - which is not surprising, as almost all patients develop de novo AIH while receiving these drugs. Despite the good response to treatment, most patients remain a clinical challenge as complete stable remissions are uncommon and flares, relapses and chronic disease activity can often occur. Pathogenetically this syndrome is intriguing. It is not clear, if the immune response is directed against allo-antigens, neo-antigens in the liver, or self-antigens, possibly shared by donor and host cells. It is very likely that the inflammatory milieu due to alloreactive cells in the transplanted organ contribute to the disease process. Either leading to aberrant antigen presentation, or providing co-stimulatory signals leading to the breaking of self-tolerance. The development of this disease in the presence of treatment with calcineurin

  11. De Novo Lipogenesis Products and Endogenous Lipokines.

    PubMed

    Yilmaz, Mustafa; Claiborn, Kathryn C; Hotamisligil, Gökhan S

    2016-07-01

    Recent studies have shown that in addition to their traditionally recognized functions as building blocks, energy stores, or hazardous intermediates, lipids also have the ability to act as signaling molecules with potent effects on systemic metabolism and metabolic diseases. This Perspective highlights this somewhat less apparent biology of lipids, especially focusing on de novo lipogenesis as a process that gives rise to key messenger molecules mediating interorgan communication. Elucidating the mechanisms of lipid-dependent coordination of metabolism promises invaluable insights into the understanding of metabolic diseases and may contribute to the development of a new generation of preventative and therapeutic approaches. PMID:27288005

  12. Familiar face + novel face = familiar face? Representational bias in the perception of morphed faces in chimpanzees

    PubMed Central

    Myowa-Yamakoshi, Masako

    2016-01-01

    Highly social animals possess a well-developed ability to distinguish the faces of familiar from novel conspecifics to induce distinct behaviors for maintaining society. However, the behaviors of animals when they encounter ambiguous faces of familiar yet novel conspecifics, e.g., strangers with faces resembling known individuals, have not been well characterised. Using a morphing technique and preferential-looking paradigm, we address this question via the chimpanzee’s facial–recognition abilities. We presented eight subjects with three types of stimuli: (1) familiar faces, (2) novel faces and (3) intermediate morphed faces that were 50% familiar and 50% novel faces of conspecifics. We found that chimpanzees spent more time looking at novel faces and scanned novel faces more extensively than familiar or intermediate faces. Interestingly, chimpanzees looked at intermediate faces in a manner similar to familiar faces with regards to the fixation duration, fixation count, and saccade length for facial scanning, even though the participant was encountering the intermediate faces for the first time. We excluded the possibility that subjects merely detected and avoided traces of morphing in the intermediate faces. These findings suggest a bias for a feeling-of-familiarity that chimpanzees perceive familiarity with an intermediate face by detecting traces of a known individual, as 50% alternation is sufficient to perceive familiarity. PMID:27602275

  13. Familiar face + novel face = familiar face? Representational bias in the perception of morphed faces in chimpanzees.

    PubMed

    Matsuda, Yoshi-Taka; Myowa-Yamakoshi, Masako; Hirata, Satoshi

    2016-01-01

    Highly social animals possess a well-developed ability to distinguish the faces of familiar from novel conspecifics to induce distinct behaviors for maintaining society. However, the behaviors of animals when they encounter ambiguous faces of familiar yet novel conspecifics, e.g., strangers with faces resembling known individuals, have not been well characterised. Using a morphing technique and preferential-looking paradigm, we address this question via the chimpanzee's facial-recognition abilities. We presented eight subjects with three types of stimuli: (1) familiar faces, (2) novel faces and (3) intermediate morphed faces that were 50% familiar and 50% novel faces of conspecifics. We found that chimpanzees spent more time looking at novel faces and scanned novel faces more extensively than familiar or intermediate faces. Interestingly, chimpanzees looked at intermediate faces in a manner similar to familiar faces with regards to the fixation duration, fixation count, and saccade length for facial scanning, even though the participant was encountering the intermediate faces for the first time. We excluded the possibility that subjects merely detected and avoided traces of morphing in the intermediate faces. These findings suggest a bias for a feeling-of-familiarity that chimpanzees perceive familiarity with an intermediate face by detecting traces of a known individual, as 50% alternation is sufficient to perceive familiarity. PMID:27602275

  14. Familiar face + novel face = familiar face? Representational bias in the perception of morphed faces in chimpanzees

    PubMed Central

    Myowa-Yamakoshi, Masako

    2016-01-01

    Highly social animals possess a well-developed ability to distinguish the faces of familiar from novel conspecifics to induce distinct behaviors for maintaining society. However, the behaviors of animals when they encounter ambiguous faces of familiar yet novel conspecifics, e.g., strangers with faces resembling known individuals, have not been well characterised. Using a morphing technique and preferential-looking paradigm, we address this question via the chimpanzee’s facial–recognition abilities. We presented eight subjects with three types of stimuli: (1) familiar faces, (2) novel faces and (3) intermediate morphed faces that were 50% familiar and 50% novel faces of conspecifics. We found that chimpanzees spent more time looking at novel faces and scanned novel faces more extensively than familiar or intermediate faces. Interestingly, chimpanzees looked at intermediate faces in a manner similar to familiar faces with regards to the fixation duration, fixation count, and saccade length for facial scanning, even though the participant was encountering the intermediate faces for the first time. We excluded the possibility that subjects merely detected and avoided traces of morphing in the intermediate faces. These findings suggest a bias for a feeling-of-familiarity that chimpanzees perceive familiarity with an intermediate face by detecting traces of a known individual, as 50% alternation is sufficient to perceive familiarity.

  15. Digital 'faces' of synthetic biology.

    PubMed

    Friedrich, Kathrin

    2013-06-01

    In silicio design plays a fundamental role in the endeavour to synthesise biological systems. In particular, computer-aided design software enables users to manage the complexity of biological entities that is connected to their construction and reconfiguration. The software's graphical user interface bridges the gap between the machine-readable data on the algorithmic subface of the computer and its human-amenable surface represented by standardised diagrammatic elements. Notations like the Systems Biology Graphical Notation (SBGN), together with interactive operations such as drag & drop, allow the user to visually design and simulate synthetic systems as 'bio-algorithmic signs'. Finally, the digital programming process should be extended to the wet lab to manufacture the designed synthetic biological systems. By exploring the different 'faces' of synthetic biology, I argue that in particular computer-aided design (CAD) is pushing the idea to automatically produce de novo objects. Multifaceted software processes serve mutually aesthetic, epistemic and performative purposes by simultaneously black-boxing and bridging different data sources, experimental operations and community-wide standards. So far, synthetic biology is mainly a product of digital media technologies that structurally mimic the epistemological challenge to take both qualitative as well as quantitative aspects of biological systems into account in order to understand and produce new and functional entities.

  16. Programmed versus Face-to-Face Counseling

    ERIC Educational Resources Information Center

    Gilbert, William M.; Ewing, Thomas N.

    1971-01-01

    A comparison was made of the effectiveness of a programmed Self-Counseling Manual and a normal precollege counseling interview by experienced counselors. Findings supported the use of programmed counseling as an adjunct to or substitute for face-to-face counseling. (Author)

  17. De Novo Construction of Redox Active Proteins.

    PubMed

    Moser, C C; Sheehan, M M; Ennist, N M; Kodali, G; Bialas, C; Englander, M T; Discher, B M; Dutton, P L

    2016-01-01

    Relatively simple principles can be used to plan and construct de novo proteins that bind redox cofactors and participate in a range of electron-transfer reactions analogous to those seen in natural oxidoreductase proteins. These designed redox proteins are called maquettes. Hydrophobic/hydrophilic binary patterning of heptad repeats of amino acids linked together in a single-chain self-assemble into 4-alpha-helix bundles. These bundles form a robust and adaptable frame for uncovering the default properties of protein embedded cofactors independent of the complexities introduced by generations of natural selection and allow us to better understand what factors can be exploited by man or nature to manipulate the physical chemical properties of these cofactors. Anchoring of redox cofactors such as hemes, light active tetrapyrroles, FeS clusters, and flavins by His and Cys residues allow cofactors to be placed at positions in which electron-tunneling rates between cofactors within or between proteins can be predicted in advance. The modularity of heptad repeat designs facilitates the construction of electron-transfer chains and novel combinations of redox cofactors and new redox cofactor assisted functions. Developing de novo designs that can support cofactor incorporation upon expression in a cell is needed to support a synthetic biology advance that integrates with natural bioenergetic pathways. PMID:27586341

  18. Comparative analysis of de novo transcriptome assembly.

    PubMed

    Clarke, Kaitlin; Yang, Yi; Marsh, Ronald; Xie, Linglin; Zhang, Ke K

    2013-02-01

    The fast development of next-generation sequencing technology presents a major computational challenge for data processing and analysis. A fast algorithm, de Bruijn graph has been successfully used for genome DNA de novo assembly; nevertheless, its performance for transcriptome assembly is unclear. In this study, we used both simulated and real RNA-Seq data, from either artificial RNA templates or human transcripts, to evaluate five de novo assemblers, ABySS, Mira, Trinity, Velvet and Oases. Of these assemblers, ABySS, Trinity, Velvet and Oases are all based on de Bruijn graph, and Mira uses an overlap graph algorithm. Various numbers of RNA short reads were selected from the External RNA Control Consortium (ERCC) data and human chromosome 22. A number of statistics were then calculated for the resulting contigs from each assembler. Each experiment was repeated multiple times to obtain the mean statistics and standard error estimate. Trinity had relative good performance for both ERCC and human data, but it may not consistently generate full length transcripts. ABySS was the fastest method but its assembly quality was low. Mira gave a good rate for mapping its contigs onto human chromosome 22, but its computational speed is not satisfactory. Our results suggest that transcript assembly remains a challenge problem for bioinformatics society. Therefore, a novel assembler is in need for assembling transcriptome data generated by next generation sequencing technique.

  19. Comparative analysis of de novo transcriptome assembly.

    PubMed

    Clarke, Kaitlin; Yang, Yi; Marsh, Ronald; Xie, Linglin; Zhang, Ke K

    2013-02-01

    The fast development of next-generation sequencing technology presents a major computational challenge for data processing and analysis. A fast algorithm, de Bruijn graph has been successfully used for genome DNA de novo assembly; nevertheless, its performance for transcriptome assembly is unclear. In this study, we used both simulated and real RNA-Seq data, from either artificial RNA templates or human transcripts, to evaluate five de novo assemblers, ABySS, Mira, Trinity, Velvet and Oases. Of these assemblers, ABySS, Trinity, Velvet and Oases are all based on de Bruijn graph, and Mira uses an overlap graph algorithm. Various numbers of RNA short reads were selected from the External RNA Control Consortium (ERCC) data and human chromosome 22. A number of statistics were then calculated for the resulting contigs from each assembler. Each experiment was repeated multiple times to obtain the mean statistics and standard error estimate. Trinity had relative good performance for both ERCC and human data, but it may not consistently generate full length transcripts. ABySS was the fastest method but its assembly quality was low. Mira gave a good rate for mapping its contigs onto human chromosome 22, but its computational speed is not satisfactory. Our results suggest that transcript assembly remains a challenge problem for bioinformatics society. Therefore, a novel assembler is in need for assembling transcriptome data generated by next generation sequencing technique. PMID:23393031

  20. De novo proteins from designed combinatorial libraries

    PubMed Central

    Hecht, Michael H.; Das, Aditi; Go, Abigail; Bradley, Luke H.; Wei, Yinan

    2004-01-01

    Combinatorial libraries of de novo amino acid sequences can provide a rich source of diversity for the discovery of novel proteins with interesting and important activities. Randomly generated sequences, however, rarely fold into well-ordered proteinlike structures. To enhance the quality of a library, features of rational design must be used to focus sequence diversity into those regions of sequence space that are most likely to yield folded structures. This review describes how focused libraries can be constructed by designing the binary pattern of polar and nonpolar amino acids to favor proteins that contain abundant secondary structure, while simultaneously burying hydrophobic side chains and exposing hydrophilic side chains to solvent. The “binary code” for protein design was used to construct several libraries of de novo proteins, including both α-helical and β-sheet structures. The recently determined solution structure of a binary patterned four-helix bundle is well ordered, thereby demonstrating that sequences that have neither been selected by evolution (in vivo or in vitro) nor designed by computer can form nativelike proteins. Examples are presented demonstrating how binary patterned libraries have successfully produced well-ordered structures, cofactor binding, catalytic activity, self-assembled monolayers, amyloid-like nanofibrils, and protein-based biomaterials. PMID:15215517

  1. Insulated face brick

    SciTech Connect

    Cromrich, J.; Cromrich, L.B.

    1990-10-16

    This patent describes a method for forming insulated brick intended solely for use in building walls and having superior insulation qualities and lighter weight consonant with the load bearing capabilities of building bricks and the appearance of facing brick. It comprises dry mixing two parts of vermiculite and one part of brick clay, thereby forming a dry mixture having a vermiculite to clay ratio of approximately two-to-one by volume; adding water to the dry mixture and mixing, so that a substantially dry admixture having expanded vermiculite and brick clay is formed; forming a facing layer solely from brick clay; molding and compressing the substantially dry admixture, so as to form a generally rectangular main body layer having parallel top and bottom faces, a pair of parallel side faces and a pair of parallel end faces, respectively, the top and bottom faces being substantially larger in area than the respective side faces, and the side faces being substantially larger in area than the respective end faces, the body layer further having at least one bore formed therein, the bore running from the top face to the bottom face perpendicularly thereto and substantially parallel to the side surfaces thereof, the bore being substantially centrally disposed and wherein the facing layer is disposed on one of the side surfaces of the body portion; curing the molded admixture having the facing layer disposed thereon; whereby a cured brick is formed; and firing the cured brick and the facing layer disposed thereon, whereby an integral brick is formed having top and bottom faces of the brick which are entirely devoid of facing layers, wherein the brick has the desired load bearing capability substantially between its top and bottom faces, whereby the outer facing layer only provides the desired appearance and weather resistance, and further whereby the weight of the brick is substantially reduced.

  2. Face Validity Revisited.

    ERIC Educational Resources Information Center

    Nevo, Baruch

    1985-01-01

    A literature review and a proposed means of measuring face validity, a test's appearance of being valid, are presented. Empirical evidence from examinees' perceptions of a college entrance examination support the reliability of measuring face validity. (GDC)

  3. Face to Face Communications in Space

    NASA Technical Reports Server (NTRS)

    Cohen, Malcolm M.; Davon, Bonnie P. (Technical Monitor)

    1999-01-01

    It has been reported that human face-to-face communications in space are compromised by facial edema, variations in the orientations of speakers and listeners, and background noises that are encountered in the shuttle and in space stations. To date, nearly all reports have been anecdotal or subjective, in the form of post-flight interviews or questionnaires; objective and quantitative data are generally lacking. Although it is acknowledged that efficient face-to-face communications are essential for astronauts to work safely and effectively, specific ways in which the space environment interferes with non-linguistic communication cues are poorly documented. Because we have only a partial understanding of how non-linguistic communication cues may change with mission duration, it is critically important to obtain objective data, and to evaluate these cues under well-controlled experimental conditions.

  4. Frequency and Complexity of De Novo Structural Mutation in Autism

    PubMed Central

    Brandler, William M.; Antaki, Danny; Gujral, Madhusudan; Noor, Amina; Rosanio, Gabriel; Chapman, Timothy R.; Barrera, Daniel J.; Lin, Guan Ning; Malhotra, Dheeraj; Watts, Amanda C.; Wong, Lawrence C.; Estabillo, Jasper A.; Gadomski, Therese E.; Hong, Oanh; Fajardo, Karin V. Fuentes; Bhandari, Abhishek; Owen, Renius; Baughn, Michael; Yuan, Jeffrey; Solomon, Terry; Moyzis, Alexandra G.; Maile, Michelle S.; Sanders, Stephan J.; Reiner, Gail E.; Vaux, Keith K.; Strom, Charles M.; Zhang, Kang; Muotri, Alysson R.; Akshoomoff, Natacha; Leal, Suzanne M.; Pierce, Karen; Courchesne, Eric; Iakoucheva, Lilia M.; Corsello, Christina; Sebat, Jonathan

    2016-01-01

    Genetic studies of autism spectrum disorder (ASD) have established that de novo duplications and deletions contribute to risk. However, ascertainment of structural variants (SVs) has been restricted by the coarse resolution of current approaches. By applying a custom pipeline for SV discovery, genotyping, and de novo assembly to genome sequencing of 235 subjects (71 affected individuals, 26 healthy siblings, and their parents), we compiled an atlas of 29,719 SV loci (5,213/genome), comprising 11 different classes. We found a high diversity of de novo mutations, the majority of which were undetectable by previous methods. In addition, we observed complex mutation clusters where combinations of de novo SVs, nucleotide substitutions, and indels occurred as a single event. We estimate a high rate of structural mutation in humans (20%) and propose that genetic risk for ASD is attributable to an elevated frequency of gene-disrupting de novo SVs, but not an elevated rate of genome rearrangement. PMID:27018473

  5. De Novo Enzyme Design Using Rosetta3

    PubMed Central

    Richter, Florian; Leaver-Fay, Andrew; Khare, Sagar D.; Bjelic, Sinisa; Baker, David

    2011-01-01

    The Rosetta de novo enzyme design protocol has been used to design enzyme catalysts for a variety of chemical reactions, and in principle can be applied to any arbitrary chemical reaction of interest, The process has four stages: 1) choice of a catalytic mechanism and corresponding minimal model active site, 2) identification of sites in a set of scaffold proteins where this minimal active site can be realized, 3) optimization of the identities of the surrounding residues for stabilizing interactions with the transition state and primary catalytic residues, and 4) evaluation and ranking the resulting designed sequences. Stages two through four of this process can be carried out with the Rosetta package, while stage one needs to be done externally. Here, we demonstrate how to carry out the Rosetta enzyme design protocol from start to end in detail using for illustration the triosephosphate isomerase reaction. PMID:21603656

  6. Structural insights into de novo actin polymerization

    PubMed Central

    Dominguez, Roberto

    2010-01-01

    Summary Many cellular functions depend on rapid and localized actin polymerization/depolymerization. Yet, the de novo polymerization of actin in cells is kinetically unfavorable because of the instability of polymerization intermediates (small actin oligomers) and the actions of actin monomer binding proteins. Cells use filament nucleation and elongation factors to initiate and sustain polymerization. Structural biology is beginning to shed light on the diverse mechanisms by which these unrelated proteins initiate polymerization, undergo regulation, and mediate the transition of monomeric actin onto actin filaments. A prominent role is played by the W domain, which in some of these proteins occurs in tandem repeats that recruit multiple actin subunits. Pro-rich regions are also abundant and mediate the binding of profilin-actin complexes, which are the main source of polymerization competent actin in cells. Filament nucleation and elongation factors frequently interact with Rho family GTPases, which relay signals from membrane receptors to regulate actin cytoskeleton remodeling. PMID:20096561

  7. Energy efficient face seal

    NASA Technical Reports Server (NTRS)

    Sehnal, J.; Sedy, J.; Etsion, I.; Zobens, A.

    1982-01-01

    Torque, face temperature, leakage, and wear of a flat face seal were compared with three coned face seals at pressures up to 2758 kPa and speeds up to 8000 rpm. Axial movement of the mating seal parts was recorded by a digital data acquisition system. The coning of the tungsten carbide primary ring ranged from .51 micro-m to 5.6 micro-m. The torque of the coned face seal balanced to 76.3% was an average 42% lower, the leakage eleven times higher, than that of the standard flat face seal. The reduction of the balance of the coned face seal to 51.3% resulted by decreasing the torque by an additional 44% and increasing leakage 12 to 230 times, depending on the seal shaft speed. No measurable wear was observed on the face of the coned seals.

  8. The Representation and Processing of Familiar Faces in Dyslexia: Differences in Age of Acquisition Effects

    ERIC Educational Resources Information Center

    Smith-Spark, James H.; Moore, Viv

    2009-01-01

    Two under-explored areas of developmental dyslexia research, face naming and age of acquisition (AoA), were investigated. Eighteen dyslexic and 18 non-dyslexic university students named the faces of 50 well-known celebrities, matched for facial distinctiveness and familiarity. Twenty-five of the famous people were learned early in life, while the…

  9. Characterization of an AO-OCT system

    SciTech Connect

    Evans, J W; Zawadzki, R J; Jones, S; Olivier, S; Werner, J S

    2007-07-26

    Adaptive optics (AO) and optical coherence tomography (OCT) are powerful imaging modalities that, when combined, can provide high-volumetric-resolution, images of the retina. The AO-OCT system at UC Davis has been under development for 2 years and has demonstrated the utility of this technology for microscopic, volumetric, in vivo retinal imaging [1]. The current system uses an AOptix bimorph deformable mirror (DM) for low-order, high-stroke correction [2] and a 140-actuator Boston Micromachines DM for high-order correction [3]. We are beginning to investigate the potential for increasing the image contrast in this system using higher-order wavefront correction. The first step in this analysis is to quantify the residual wavefront error (WFE) in the current system. Developing an error budget is a common tool for improved performance and system design in astronomical AO systems [4, 5]. The process for vision science systems is also discussed in several texts e.g. [6], but results from this type of analysis have rarely been included in journal articles on AO for vision science. Careful characterization of the AO system will lead to improved performance and inform the design of a future high-contrast system. In general, an AO system error budget must include an analysis of three categories of residual WFE: errors in measuring the phase, errors caused by limitations of the DM(s), and errors introduced by temporal variation. Understanding the mechanisms and relative size of these errors is critical to improving system performance. In this paper we discuss the techniques for characterizing these error sources in the AO-OCT system. It is useful to first calculate an error budget for the simpler case using a model eye, and then add the additional errors introduced for the case of a human subject. Measurement error includes calibration error, wavefront sensor (WFS) CCD noise, and sampling errors. Calibration errors must be measured by an external system. Typically this

  10. Current challenges in de novo plant genome sequencing and assembly

    PubMed Central

    2012-01-01

    Genome sequencing is now affordable, but assembling plant genomes de novo remains challenging. We assess the state of the art of assembly and review the best practices for the community. PMID:22546054

  11. De novo peroxisome biogenesis: Evolving concepts and conundrums.

    PubMed

    Agrawal, Gaurav; Subramani, Suresh

    2016-05-01

    Peroxisomes proliferate by growth and division of pre-existing peroxisomes or could arise de novo. Though the de novo pathway of peroxisome biogenesis is a more recent discovery, several studies have highlighted key mechanistic details of the pathway. The endoplasmic reticulum (ER) is the primary source of lipids and proteins for the newly-formed peroxisomes. More recently, an intricate sorting process functioning at the ER has been proposed, that segregates specific PMPs first to peroxisome-specific ER domains (pER) and then assembles PMPs selectively into distinct pre-peroxisomal vesicles (ppVs) that later fuse to form import-competent peroxisomes. In addition, plausible roles of the three key peroxins Pex3, Pex16 and Pex19, which are also central to the growth and division pathway, have been suggested in the de novo process. In this review, we discuss key developments and highlight the unexplored avenues in de novo peroxisome biogenesis.

  12. The Subaru Coronagraphic Extreme AO Project

    NASA Astrophysics Data System (ADS)

    Martinache, Frantz; Guyon, O.; Lozi, J.; Tamura, M.; Hodapp, K.; Suzuki, R.; Hayano, Y.; McElwain, M. W.

    2009-01-01

    While the existence of large numbers of extrasolar planets around solar type stars has been unambiguously demonstrated by radial velocity, transit and microlensing surveys, attempts at direct imaging with AO-equipped large telescopes remain unsuccessful. Because they supposedly offer more favorable contrast ratios, young systems consitute prime targets for imaging. Such observations will provide key insights on the formation and early evolution of planets and disks. Current surveys are limited by modest AO performance which limits inner working angle to 0.2", and only reach maximum sensitivity outside 1". This translates into orbital distances greater than 10 AU even on most nearby systems, while only 5 % of the known exoplanets have a semimajor axis greater than 10 AU. This calls for a major change of approach in the techniques used for direct imaging of the direct vicinity of stars. A sensible way to do the job is to combine coronagraphy and Extreme AO. Only accurate and fast control of the wavefront will permit the detection of high contrast planetary companions within 10 AU. The SCExAO system, currently under assembly, is an upgrade of the HiCIAO coronagraphic differential imaging camera, mounted behind the 188-actuator curvature AO system on Subaru Telescope. This platform includes a 1000-actuator MEMS deformable mirror for high accuracy wavefront correction and a PIAA coronagraph which delivers high contrast at 0.05" from the star (5 AU at 100 pc). Key technologies have been validated in the laboratory: high performance wavefront sensing schemes, spider vanes and central obstruction removal, and lossless beam apodization. The project is designed to be highly flexible to continuously integrate new technologies with high scientific payoff. Planned upgrades include an integral field unit for spectral characterization of planets/disks and a non-redundant aperture mask to push the performance of the system toward separations less than lambda/D.

  13. Generalization of affective learning about faces to perceptually similar faces.

    PubMed

    Verosky, Sara C; Todorov, Alexander

    2010-06-01

    Different individuals have different (and different-looking) significant others, friends, and foes. The objective of this study was to investigate whether these social face environments can shape individual face preferences. First, participants learned to associate faces with positive, neutral, or negative behaviors. Then, they evaluated morphs combining novel faces with the learned faces. The morphs (65% and 80% novel faces) were within the categorical boundary of the novel faces: They were perceived as those faces in a preliminary study. Moreover, a second preliminary study showed that following the learning, the morphs' categorization as similar to the learned faces was indistinguishable from the categorization of actual novel faces. Nevertheless, in the main experiment, participants evaluated morphs of "positive" faces more positively than morphs of "negative" faces. This learning generalization effect increased as a function of the similarity of the novel faces to the learned faces. The findings suggest that general learning mechanisms based on similarity can account for idiosyncratic face preferences.

  14. Generalization of affective learning about faces to perceptually similar faces.

    PubMed

    Verosky, Sara C; Todorov, Alexander

    2010-06-01

    Different individuals have different (and different-looking) significant others, friends, and foes. The objective of this study was to investigate whether these social face environments can shape individual face preferences. First, participants learned to associate faces with positive, neutral, or negative behaviors. Then, they evaluated morphs combining novel faces with the learned faces. The morphs (65% and 80% novel faces) were within the categorical boundary of the novel faces: They were perceived as those faces in a preliminary study. Moreover, a second preliminary study showed that following the learning, the morphs' categorization as similar to the learned faces was indistinguishable from the categorization of actual novel faces. Nevertheless, in the main experiment, participants evaluated morphs of "positive" faces more positively than morphs of "negative" faces. This learning generalization effect increased as a function of the similarity of the novel faces to the learned faces. The findings suggest that general learning mechanisms based on similarity can account for idiosyncratic face preferences. PMID:20483821

  15. Genovo: De Novo Assembly for Metagenomes

    NASA Astrophysics Data System (ADS)

    Laserson, Jonathan; Jojic, Vladimir; Koller, Daphne

    Next-generation sequencing technologies produce a large number of noisy reads from the DNA in a sample. Metagenomics and population sequencing aim to recover the genomic sequences of the species in the sample, which could be of high diversity. Methods geared towards single sequence reconstruction are not sensitive enough when applied in this setting. We introduce a generative probabilistic model of read generation from environmental samples and present Genovo, a novel de novo sequence assembler that discovers likely sequence reconstructions under the model. A Chinese restaurant process prior accounts for the unknown number of genomes in the sample. Inference is made by applying a series of hill-climbing steps iteratively until convergence. We compare the performance of Genovo to three other short read assembly programs across one synthetic dataset and eight metagenomic datasets created using the 454 platform, the largest of which has 311k reads. Genovo's reconstructions cover more bases and recover more genes than the other methods, and yield a higher assembly score.

  16. Social judgments from faces.

    PubMed

    Todorov, Alexander; Mende-Siedlecki, Peter; Dotsch, Ron

    2013-06-01

    People make rapid and consequential social judgments from minimal (non-emotional) facial cues. There has been rapid progress in identifying the perceptual basis of these judgments using data-driven, computational models. In contrast, our understanding of the neural underpinnings of these judgments is rather limited. Meta-analyses of neuroimaging studies find a wide range of seemingly inconsistent responses in the amygdala that co-vary with social judgments from faces. Guided by computational models of social judgments, these responses can be accounted by positing that the amygdala (and posterior face selective regions) tracks face typicality. Atypical faces, whether positively or negatively evaluated, elicit stronger responses in the amygdala. We conclude with the promise of data-driven methods for modeling neural responses to social judgments from faces.

  17. Stable face representations

    PubMed Central

    Jenkins, Rob; Burton, A. Mike

    2011-01-01

    Photographs are often used to establish the identity of an individual or to verify that they are who they claim to be. Yet, recent research shows that it is surprisingly difficult to match a photo to a face. Neither humans nor machines can perform this task reliably. Although human perceivers are good at matching familiar faces, performance with unfamiliar faces is strikingly poor. The situation is no better for automatic face recognition systems. In practical settings, automatic systems have been consistently disappointing. In this review, we suggest that failure to distinguish between familiar and unfamiliar face processing has led to unrealistic expectations about face identification in applied settings. We also argue that a photograph is not necessarily a reliable indicator of facial appearance, and develop our proposal that summary statistics can provide more stable face representations. In particular, we show that image averaging stabilizes facial appearance by diluting aspects of the image that vary between snapshots of the same person. We review evidence that the resulting images can outperform photographs in both behavioural experiments and computer simulations, and outline promising directions for future research. PMID:21536553

  18. Dynamic Face Seal Arrangement

    NASA Technical Reports Server (NTRS)

    Dellacorte, Christopher (Inventor)

    1999-01-01

    A radial face seal arrangement is disclosed comprising a stationary seal ring that is spring loaded against a seal seat affixed to a rotating shaft. The radial face seal arrangement further comprises an arrangement that not only allows for preloading of the stationary seal ring relative to the seal seat, but also provides for dampening yielding a dynamic seating response for the radial face seal arrangement. The overall seal system, especially regarding the selection of the material for the stationary seal ring, is designed to operate over a wide temperature range from below ambient up to 900 C.

  19. Gaze cueing by pareidolia faces

    PubMed Central

    Takahashi, Kohske; Watanabe, Katsumi

    2013-01-01

    Visual images that are not faces are sometimes perceived as faces (the pareidolia phenomenon). While the pareidolia phenomenon provides people with a strong impression that a face is present, it is unclear how deeply pareidolia faces are processed as faces. In the present study, we examined whether a shift in spatial attention would be produced by gaze cueing of face-like objects. A robust cueing effect was observed when the face-like objects were perceived as faces. The magnitude of the cueing effect was comparable between the face-like objects and a cartoon face. However, the cueing effect was eliminated when the observer did not perceive the objects as faces. These results demonstrated that pareidolia faces do more than give the impression of the presence of faces; indeed, they trigger an additional face-specific attentional process. PMID:25165505

  20. Gaze cueing by pareidolia faces.

    PubMed

    Takahashi, Kohske; Watanabe, Katsumi

    2013-01-01

    Visual images that are not faces are sometimes perceived as faces (the pareidolia phenomenon). While the pareidolia phenomenon provides people with a strong impression that a face is present, it is unclear how deeply pareidolia faces are processed as faces. In the present study, we examined whether a shift in spatial attention would be produced by gaze cueing of face-like objects. A robust cueing effect was observed when the face-like objects were perceived as faces. The magnitude of the cueing effect was comparable between the face-like objects and a cartoon face. However, the cueing effect was eliminated when the observer did not perceive the objects as faces. These results demonstrated that pareidolia faces do more than give the impression of the presence of faces; indeed, they trigger an additional face-specific attentional process.

  1. MEMS DM development at Iris AO, Inc.

    NASA Astrophysics Data System (ADS)

    Helmbrecht, Michael A.; He, Min; Kempf, Carl J.; Besse, Marc

    2011-03-01

    Iris AO is actively developing piston-tip-tilt (PTT) segmented MEMS deformable mirrors (DM) and adaptive optics (AO) controllers for these DMs. This paper discusses ongoing research at Iris AO that has advanced the state-of-the-art of these devices and systems over the past year. Improvements made to open-loop operation and mirror fabrication enables mirrors to open-loop flatten to 4 nm rms. Additional testing of an anti snap-in technology was conducted and demonstrates that the technology can withstand 100 million snap-in events without failure. Deformable mirrors with dielectric coatings are shown that are capable of handling 630 W/cm2 of incident laser power. Over a localized region on the segment, the dielectric coatings can withstand 100kW/cm2 incident laser power for 30 minutes. Results from the first-ever batch of PTT489 DMs that were shipped to pilot customers are reported. Optimizations made to the open-loop PTT controller are shown to have latencies of 157.5 μs and synchronous array update rates of nearly 6.5 kHz. Finally, plans for the design and fabrication of the next-generation PTT939 DM are presented.

  2. Protective Face Mask

    NASA Technical Reports Server (NTRS)

    1981-01-01

    Mask to protect the physically impaired from injuries to the face and head has been developed by Langley Research Center. It is made of composite materials, usually graphite or boron fibers woven into a matrix. Weighs less than three ounces.

  3. Mechanization of face ends

    SciTech Connect

    Singhal, R.K.

    1984-10-01

    The author reviews developments in face-end machinery in the UK, West Germany and US. Automatic control systems such as MIDAS and MINOS are considered, as well as water-jet assisted cutting and machine health monitoring.

  4. Toward hyperspectral face recognition

    NASA Astrophysics Data System (ADS)

    Robila, Stefan A.

    2008-02-01

    Face recognition continues to meet significant challenges in reaching accurate results and still remains one of the activities where humans outperform technology. An attractive approach in improving face identification is provided by the fusion of multiple imaging sources such as visible and infrared images. Hyperspectral data, i.e. images collected over hundreds of narrow contiguous light spectrum intervals constitute a natural choice for expanding face recognition image fusion, especially since it may provide information beyond the normal visible range, thus exceeding the normal human sensing. In this paper we investigate the efficiency of hyperspectral face recognition through an in house experiment that collected data in over 120 bands within the visible and near infrared range. The imagery was produced using an off the shelf sensor in both indoors and outdoors with the subjects being photographed from various angles. Further processing included spectra collection and feature extraction. Human matching performance based on spectral properties is discussed.

  5. Into the Blue: AO Science in the Visible with MagAO

    NASA Astrophysics Data System (ADS)

    Close, Laird; Males, Jared; Morzinski, Katie; Kopon, Derek; Follette, Kate; Rodigas, Timothy; Hinz, Philip; Wu, Ya-Lin; Puglisi, Alfio; Esposito, Simone; Riccardi, Armando; Pinna, Enrico; Xompero, Marco; Briguglio, Runa; Uomoto, Alan; Hare, Tison

    2013-12-01

    The Magellan Clay telescope is a 6.5m Gregorian telescope located in Chile at Las Campanas Observatory. We have fabricated an 85 cm diameter aspheric adaptive secondary with our subcontractors and partners, MagAO passed acceptance tests in spring 2012, and the entire System was commissioned from Nov 17 to Dec 7, 2012. This secondary has 585 actuators with < 1 msec response times (0.7 ms typically). We fabricated a high order (585 mode) pyramid wavefront sensor (similar to that of LBT's FLAO). The relatively high actuator count allows moderate Strehls to be obtained in the visible (0.63-1.05 microns). We have built an CCD science camera called "jVisAO". On-sky long exposures (60s) achieve 30% Strehls at 0.62 microns (r') with the VisAO camera in 0.5" seeing with bright R < 8 mag stars. These relatively high optical wavelength Strehls are made possible by our powerful combination of a next generation ASM and a Pyramid WFS with 200-400 controlled modes and 1000 Hz loop frequencies. To minimize non-common path errors and enable visible AO the VisAO science camera is fed by an advanced triplet ADC and is piggy-backed on the WFS optical board itself. Despite the ability to make 25 mas images we still have ~4 mas of resolution loss to residual vibrations. We will discuss what the most difficult aspects are for visible AO on ELTs scaling from our experience with MagAO.

  6. Novor: Real-Time Peptide de Novo Sequencing Software

    NASA Astrophysics Data System (ADS)

    Ma, Bin

    2015-11-01

    De novo sequencing software has been widely used in proteomics to sequence new peptides from tandem mass spectrometry data. This study presents a new software tool, Novor, to greatly improve both the speed and accuracy of today's peptide de novo sequencing analyses. To improve the accuracy, Novor's scoring functions are based on two large decision trees built from a peptide spectral library with more than 300,000 spectra with machine learning. Important knowledge about peptide fragmentation is extracted automatically from the library and incorporated into the scoring functions. The decision tree model also enables efficient score calculation and contributes to the speed improvement. To further improve the speed, a two-stage algorithmic approach, namely dynamic programming and refinement, is used. The software program was also carefully optimized. On the testing datasets, Novor sequenced 7%-37% more correct residues than the state-of-the-art de novo sequencing tool, PEAKS, while being an order of magnitude faster. Novor can de novo sequence more than 300 MS/MS spectra per second on a laptop computer. The speed surpasses the acquisition speed of today's mass spectrometer and, therefore, opens a new possibility to de novo sequence in real time while the spectrometer is acquiring the spectral data.

  7. Novor: real-time peptide de novo sequencing software.

    PubMed

    Ma, Bin

    2015-11-01

    De novo sequencing software has been widely used in proteomics to sequence new peptides from tandem mass spectrometry data. This study presents a new software tool, Novor, to greatly improve both the speed and accuracy of today's peptide de novo sequencing analyses. To improve the accuracy, Novor's scoring functions are based on two large decision trees built from a peptide spectral library with more than 300,000 spectra with machine learning. Important knowledge about peptide fragmentation is extracted automatically from the library and incorporated into the scoring functions. The decision tree model also enables efficient score calculation and contributes to the speed improvement. To further improve the speed, a two-stage algorithmic approach, namely dynamic programming and refinement, is used. The software program was also carefully optimized. On the testing datasets, Novor sequenced 7%-37% more correct residues than the state-of-the-art de novo sequencing tool, PEAKS, while being an order of magnitude faster. Novor can de novo sequence more than 300 MS/MS spectra per second on a laptop computer. The speed surpasses the acquisition speed of today's mass spectrometer and, therefore, opens a new possibility to de novo sequence in real time while the spectrometer is acquiring the spectral data. Graphical Abstract ᅟ.

  8. De novo variants in sporadic cases of childhood onset schizophrenia

    PubMed Central

    Ambalavanan, Amirthagowri; Girard, Simon L; Ahn, Kwangmi; Zhou, Sirui; Dionne-Laporte, Alexandre; Spiegelman, Dan; Bourassa, Cynthia V; Gauthier, Julie; Hamdan, Fadi F; Xiong, Lan; Dion, Patrick A; Joober, Ridha; Rapoport, Judith; Rouleau, Guy A

    2016-01-01

    Childhood-onset schizophrenia (COS), defined by the onset of illness before age 13 years, is a rare severe neurodevelopmental disorder of unknown etiology. Recently, sequencing studies have identified rare, potentially causative de novo variants in sporadic cases of adult-onset schizophrenia and autism. In this study, we performed exome sequencing of 17 COS trios in order to test whether de novo variants could contribute to this disease. We identified 20 de novo variants in 17 COS probands, which is consistent with the de novo mutation rate reported in the adult form of the disease. Interestingly, the missense de novo variants in COS have a high likelihood for pathogenicity and were enriched for genes that are less tolerant to variants. Among the genes found disrupted in our study, SEZ6, RYR2, GPR153, GTF2IRD1, TTBK1 and ITGA6 have been previously linked to neuronal function or to psychiatric disorders, and thus may be considered as COS candidate genes. PMID:26508570

  9. De novo variants in sporadic cases of childhood onset schizophrenia.

    PubMed

    Ambalavanan, Amirthagowri; Girard, Simon L; Ahn, Kwangmi; Zhou, Sirui; Dionne-Laporte, Alexandre; Spiegelman, Dan; Bourassa, Cynthia V; Gauthier, Julie; Hamdan, Fadi F; Xiong, Lan; Dion, Patrick A; Joober, Ridha; Rapoport, Judith; Rouleau, Guy A

    2016-06-01

    Childhood-onset schizophrenia (COS), defined by the onset of illness before age 13 years, is a rare severe neurodevelopmental disorder of unknown etiology. Recently, sequencing studies have identified rare, potentially causative de novo variants in sporadic cases of adult-onset schizophrenia and autism. In this study, we performed exome sequencing of 17 COS trios in order to test whether de novo variants could contribute to this disease. We identified 20 de novo variants in 17 COS probands, which is consistent with the de novo mutation rate reported in the adult form of the disease. Interestingly, the missense de novo variants in COS have a high likelihood for pathogenicity and were enriched for genes that are less tolerant to variants. Among the genes found disrupted in our study, SEZ6, RYR2, GPR153, GTF2IRD1, TTBK1 and ITGA6 have been previously linked to neuronal function or to psychiatric disorders, and thus may be considered as COS candidate genes. PMID:26508570

  10. Is Face Distinctiveness Gender Based?

    ERIC Educational Resources Information Center

    Baudouin, Jean-Yves; Gallay, Mathieu

    2006-01-01

    Two experiments were carried out to study the role of gender category in evaluations of face distinctiveness. In Experiment 1, participants had to evaluate the distinctiveness and the femininity-masculinity of real or artificial composite faces. The composite faces were created by blending either faces of the same gender (sexed composite faces,…

  11. Complete De Novo Assembly of Monoclonal Antibody Sequences

    PubMed Central

    Tran, Ngoc Hieu; Rahman, M. Ziaur; He, Lin; Xin, Lei; Shan, Baozhen; Li, Ming

    2016-01-01

    De novo protein sequencing is one of the key problems in mass spectrometry-based proteomics, especially for novel proteins such as monoclonal antibodies for which genome information is often limited or not available. However, due to limitations in peptides fragmentation and coverage, as well as ambiguities in spectra interpretation, complete de novo assembly of unknown protein sequences still remains challenging. To address this problem, we propose an integrated system, ALPS, which for the first time can automatically assemble full-length monoclonal antibody sequences. Our system integrates de novo sequencing peptides, their quality scores and error-correction information from databases into a weighted de Bruijn graph to assemble protein sequences. We evaluated ALPS performance on two antibody data sets, each including a heavy chain and a light chain. The results show that ALPS was able to assemble three complete monoclonal antibody sequences of length 216–441 AA, at 100% coverage, and 96.64–100% accuracy. PMID:27562653

  12. Installing hydrolytic activity into a completely de novo protein framework

    NASA Astrophysics Data System (ADS)

    Burton, Antony J.; Thomson, Andrew R.; Dawson, William M.; Brady, R. Leo; Woolfson, Derek N.

    2016-09-01

    The design of enzyme-like catalysts tests our understanding of sequence-to-structure/function relationships in proteins. Here we install hydrolytic activity predictably into a completely de novo and thermostable α-helical barrel, which comprises seven helices arranged around an accessible channel. We show that the lumen of the barrel accepts 21 mutations to functional polar residues. The resulting variant, which has cysteine-histidine-glutamic acid triads on each helix, hydrolyses p-nitrophenyl acetate with catalytic efficiencies that match the most-efficient redesigned hydrolases based on natural protein scaffolds. This is the first report of a functional catalytic triad engineered into a de novo protein framework. The flexibility of our system also allows the facile incorporation of unnatural side chains to improve activity and probe the catalytic mechanism. Such a predictable and robust construction of truly de novo biocatalysts holds promise for applications in chemical and biochemical synthesis.

  13. Installing hydrolytic activity into a completely de novo protein framework

    NASA Astrophysics Data System (ADS)

    Burton, Antony J.; Thomson, Andrew R.; Dawson, William M.; Brady, R. Leo; Woolfson, Derek N.

    2016-09-01

    The design of enzyme-like catalysts tests our understanding of sequence-to-structure/function relationships in proteins. Here we install hydrolytic activity predictably into a completely de novo and thermostable α-helical barrel, which comprises seven helices arranged around an accessible channel. We show that the lumen of the barrel accepts 21 mutations to functional polar residues. The resulting variant, which has cysteine–histidine–glutamic acid triads on each helix, hydrolyses p-nitrophenyl acetate with catalytic efficiencies that match the most-efficient redesigned hydrolases based on natural protein scaffolds. This is the first report of a functional catalytic triad engineered into a de novo protein framework. The flexibility of our system also allows the facile incorporation of unnatural side chains to improve activity and probe the catalytic mechanism. Such a predictable and robust construction of truly de novo biocatalysts holds promise for applications in chemical and biochemical synthesis.

  14. Genetic variation and the de novo assembly of human genomes

    PubMed Central

    Chaisson, Mark J. P.; Wilson, Richard K.; Eichler, Evan E.

    2016-01-01

    The discovery of genetic variation and the assembly of genome sequences are both inextricably linked to advances in DNA-sequencing technology. Short-read massively parallel sequencing has revolutionized our ability to discover genetic variation but is insufficient to generate high-quality genome assemblies or resolve most structural variation. Full resolution of variation is only guaranteed by complete de novo assembly of a genome. Here, we review approaches to genome assembly, the nature of gaps or missing sequences, and biases in the assembly process. We describe the challenges of generating a complete de novo genome assembly using current technologies and the impact that being able to perfectly sequence the genome would have on understanding human disease and evolution. Finally, we summarize recent technological advances that improve both contiguity and accuracy and emphasize the importance of complete de novo assembly as opposed to read mapping as the primary means to understanding the full range of human genetic variation. PMID:26442640

  15. De Novo Sequencing and Homology Searching‡‡*

    PubMed Central

    Ma, Bin; Johnson, Richard

    2012-01-01

    In proteomics, de novo sequencing is the process of deriving peptide sequences from tandem mass spectra without the assistance of a sequence database. Such analyses have traditionally been performed manually by human experts, and more recently by computer programs that have been developed because of the need for higher throughput. Although powerful, de novo sequencing often can only determine partially correct sequence tags because of imperfect tandem mass spectra. However, these sequence tags can then be searched in a sequence database to identify the exact or a homologous peptide. Homology searches are particularly useful for the study of organisms whose genomes have not been sequenced. This tutorial will present background important to understanding de novo sequencing, suggestions on how to do this manually, plus descriptions of computer algorithms used to automate this process and to subsequently carryout homology-based database searches. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 1). PMID:22090170

  16. Installing hydrolytic activity into a completely de novo protein framework.

    PubMed

    Burton, Antony J; Thomson, Andrew R; Dawson, William M; Brady, R Leo; Woolfson, Derek N

    2016-09-01

    The design of enzyme-like catalysts tests our understanding of sequence-to-structure/function relationships in proteins. Here we install hydrolytic activity predictably into a completely de novo and thermostable α-helical barrel, which comprises seven helices arranged around an accessible channel. We show that the lumen of the barrel accepts 21 mutations to functional polar residues. The resulting variant, which has cysteine-histidine-glutamic acid triads on each helix, hydrolyses p-nitrophenyl acetate with catalytic efficiencies that match the most-efficient redesigned hydrolases based on natural protein scaffolds. This is the first report of a functional catalytic triad engineered into a de novo protein framework. The flexibility of our system also allows the facile incorporation of unnatural side chains to improve activity and probe the catalytic mechanism. Such a predictable and robust construction of truly de novo biocatalysts holds promise for applications in chemical and biochemical synthesis. PMID:27554410

  17. Complete De Novo Assembly of Monoclonal Antibody Sequences.

    PubMed

    Tran, Ngoc Hieu; Rahman, M Ziaur; He, Lin; Xin, Lei; Shan, Baozhen; Li, Ming

    2016-01-01

    De novo protein sequencing is one of the key problems in mass spectrometry-based proteomics, especially for novel proteins such as monoclonal antibodies for which genome information is often limited or not available. However, due to limitations in peptides fragmentation and coverage, as well as ambiguities in spectra interpretation, complete de novo assembly of unknown protein sequences still remains challenging. To address this problem, we propose an integrated system, ALPS, which for the first time can automatically assemble full-length monoclonal antibody sequences. Our system integrates de novo sequencing peptides, their quality scores and error-correction information from databases into a weighted de Bruijn graph to assemble protein sequences. We evaluated ALPS performance on two antibody data sets, each including a heavy chain and a light chain. The results show that ALPS was able to assemble three complete monoclonal antibody sequences of length 216-441 AA, at 100% coverage, and 96.64-100% accuracy. PMID:27562653

  18. How Well Do Computer-Generated Faces Tap Face Expertise?

    PubMed Central

    Crookes, Kate; Ewing, Louise; Gildenhuys, Ju-dith; Kloth, Nadine; Hayward, William G.; Oxner, Matt; Pond, Stephen; Rhodes, Gillian

    2015-01-01

    The use of computer-generated (CG) stimuli in face processing research is proliferating due to the ease with which faces can be generated, standardised and manipulated. However there has been surprisingly little research into whether CG faces are processed in the same way as photographs of real faces. The present study assessed how well CG faces tap face identity expertise by investigating whether two indicators of face expertise are reduced for CG faces when compared to face photographs. These indicators were accuracy for identification of own-race faces and the other-race effect (ORE)–the well-established finding that own-race faces are recognised more accurately than other-race faces. In Experiment 1 Caucasian and Asian participants completed a recognition memory task for own- and other-race real and CG faces. Overall accuracy for own-race faces was dramatically reduced for CG compared to real faces and the ORE was significantly and substantially attenuated for CG faces. Experiment 2 investigated perceptual discrimination for own- and other-race real and CG faces with Caucasian and Asian participants. Here again, accuracy for own-race faces was significantly reduced for CG compared to real faces. However the ORE was not affected by format. Together these results signal that CG faces of the type tested here do not fully tap face expertise. Technological advancement may, in the future, produce CG faces that are equivalent to real photographs. Until then caution is advised when interpreting results obtained using CG faces. PMID:26535910

  19. Face distortion aftereffects in personally familiar, famous, and unfamiliar faces.

    PubMed

    Walton, Billy Ronald Peter; Hills, Peter James

    2012-01-01

    The internal face prototype is thought to be a construction of the average of every previously viewed face (Schwaninger et al., 2003). However, the influence of the most frequently encountered faces (i.e., personally familiar faces) has been generally understated. The current research explored the face distortion aftereffect in unfamiliar, famous, and personally familiar (each subject's parent) faces. Forty-eight adult participants reported whether faces were distorted or not (distorted by shifting the eyes in the vertical axis) of a series of images that included unfamiliar, famous, and personally familiar faces. The number of faces perceived to be "odd" was measured pre- and post-adaptation to the most extreme distortion. Participants were adapted to either an unfamiliar, famous, or personally familiar face. The results indicate that adaptation transferred from unfamiliar faces to personally familiar faces more so than the converse and aftereffects did not transfer from famous faces to unfamiliar faces. These results are indicative of representation differences between unfamiliar, famous, and personally familiar faces, whereby personally familiar faces share representations of both unfamiliar and famous faces.

  20. Stimulus factors affecting the categorisation of faces and scrambled faces.

    PubMed

    Donnelly, N; Humphreys, G W; Sawyer, J

    1994-05-01

    Three experiments are reported which investigate the categorisation of faces and scrambled faces in a face/scrambled face decision task. Three kinds of stimuli were presented in upright and inverted orientations; faces, highly scrambled faces (all features out of position) and moderately scrambled faces (two features out of position). Experiment 1 demonstrated that faces and highly scrambled faces are categorised equally quickly and both types of stimulus were categorised faster than moderately scrambled faces. These results held for both upright and inverted presentations. It is argued that for both upright and inverted presentations, faces are categorised by being matched in parallel to a stored mental representation of a face. In contrast scrambled faces are categorised following a serial search of facial features which is probably self-terminating. Experiment 2 demonstrates that the results of Experiment 1 hold when facial features are replaced by other objects which retain the same global shape as facial features and suggest that faces are categorised using a coarsely coded visual description. Experiment 3 demonstrates the importance of stimulus outline on the categorisation of both moderately and highly scrambled faces but not real faces. The results are discussed in terms of the stimulus information used, and the effect of inversion, on face categorisation.

  1. LDEF (Prelaunch), AO038 : Interstellar Gas Experiment, Tray F06

    NASA Technical Reports Server (NTRS)

    1984-01-01

    LDEF (Prelaunch), AO038 : Interstellar Gas Experiment, Tray F06 The prelaunch photograph provides a view of the Interstellar Gas Experiment (IGE) hardware and shows a single experiment canister housing mounted in a twelve (12) inch deep peripheral tray. The experiment utilizes seven (7) canisters containing high-purity beryllium copper collecting foils, three (3) located in peripheral trays and four (4) located in trays on the space end of the LDEF, to meet experiment objectives. The active portion of the experiment consist of canister electronic timing devices and pyrotechnic cutters that control the exposure time of each collector foil. An electronic voltage multiplier system provides a bias voltage to the grid network located above the beryllium copper collecting foils.The batteries and the electronics are housed beneath the experiment baseplate facing the LDEF interior. The white painted surface area within the LDEF tray provides the optical properties required to maintain the experiment components within temperature limits. The rectangular opening in the upper right corner of the experiment baseplate provide the mounting for the ground support equipment test connector. The white grid voltage connector box, mounted on the side of the canister housing, provides the termination point for the cables running from the grid voltage box beneath the baseplate. The canister housing is a welded aluminum structure with aluminum mounting flanges. The experiment components are assembled using non-magnetic stainless steel fasteners. The aluminum housing cover, removed prior to flight, protects experiment components from damage and large particle contamination during ground handling.

  2. Ruled and holographic experiment (AO 138-5)

    NASA Astrophysics Data System (ADS)

    Bonnemason, Francis

    1993-04-01

    The AO 138-5 experiment was designed, via the FRECOPA (FRench COoperative PAyload) experiment with the aim to study the optical behavior of different diffraction gratings submitted to space vacuum long exposure and solar irradiation. Samples were ruled and holographic gratings, masters or replica, and some additional control mirrors with various coatings. The experiment was located on the B3, trailing edge of the LDEF and was protected against Atomic Oxygen flux. The experienced thermal cycling was evaluated from -23 C to 66 C during the flight, 34,000 orbits. The samples (two batches of four pieces) were located on a dedicated plate, by a pair of equivalent gratings or mirrors; optical faces were located on the external side. The plate was inside a canister, which had been opened in space for ten months. When the satellite returned to Kennedy Space Center, the remaining vacuum in the canister was still correct. The analysis focused on the triple point characterization including light efficiency, wavefront flatness quality and stray light level. Tests were conducted on control mirrors and gratings (rules and holographic master or replica) loaded but not exposed to cosmic dust or direct solar irradiations. They did not show any significant variations. Solar exposure had damaged the coating (aluminum and platinum) reflectivity in the Ultra-Violet region; the degradation is higher with the gratings, in terms of efficiency. However, wavefront flatness quality and stray light level tests revealed no additional changes.

  3. Convergent De Novo Synthesis of Vineomycinone B2 Methyl Ester

    PubMed Central

    Chen, Qian; Zhong, Yashan; O’Doherty, George A.

    2013-01-01

    An efficient de novo synthesis of vineomycinone B2 methyl ester has been achieved. The longest linear route required only 14 steps from achiral commercially available starting materials (4.0% overall yield). The key transformations included the de novo asymmetric synthesis of two key fragments, which were joined by a convergent late stage Suzuki’s glycosylation for the construction of the aryl β-C-glycoside. A subsequent BBr3 one-pot debenzylation, demethylation and air oxidation provided vineomycinone B2 methyl ester. PMID:23778961

  4. De Novo Fragment Design for Drug Discovery and Chemical Biology.

    PubMed

    Rodrigues, Tiago; Reker, Daniel; Welin, Martin; Caldera, Michael; Brunner, Cyrill; Gabernet, Gisela; Schneider, Petra; Walse, Björn; Schneider, Gisbert

    2015-12-01

    Automated molecular de novo design led to the discovery of an innovative inhibitor of death-associated protein kinase 3 (DAPK3). An unprecedented crystal structure of the inactive DAPK3 homodimer shows the fragment-like hit bound to the ATP pocket. Target prediction software based on machine learning models correctly identified additional macromolecular targets of the computationally designed compound and the structurally related marketed drug azosemide. The study validates computational de novo design as a prime method for generating chemical probes and starting points for drug discovery.

  5. Airline Maintenance Manpower Optimization from the De Novo Perspective

    NASA Astrophysics Data System (ADS)

    Liou, James J. H.; Tzeng, Gwo-Hshiung

    Human resource management (HRM) is an important issue for today’s competitive airline marketing. In this paper, we discuss a multi-objective model designed from the De Novo perspective to help airlines optimize their maintenance manpower portfolio. The effectiveness of the model and solution algorithm is demonstrated in an empirical study of the optimization of the human resources needed for airline line maintenance. Both De Novo and traditional multiple objective programming (MOP) methods are analyzed. A comparison of the results with those of traditional MOP indicates that the proposed model and solution algorithm does provide better performance and an improved human resource portfolio.

  6. Double face sealing device

    NASA Technical Reports Server (NTRS)

    Weddendorf, Bruce C. (Inventor)

    1991-01-01

    A double face sealing device for mounting between two surfaces to provide an airtight and fluid-tight seal between a closure member bearing one of the surfaces and a structure or housing bearing the other surface which extends around the opening or hatchway to be closed. The double face sealing device includes a plurality of sections or segments mounted to one of the surfaces, each having a main body portion, a pair of outwardly extending and diverging, cantilever, spring arms, and a pair of inwardly extending and diverging, cantilever, spring arms, an elastomeric cover on the distal, free, ends of the outwardly extending and diverging spring arms, and an elastomeric cover on the distal, free, ends of the inwardly extending and diverging spring arms. The double face sealing device has application or use in all environments requiring a seal, but is particularly useful to seal openings or hatchways between compartments of spacecraft or aircraft.

  7. An equine pain face

    PubMed Central

    Gleerup, Karina B; Forkman, Björn; Lindegaard, Casper; Andersen, Pia H

    2015-01-01

    Objective The objective of this study was to investigate the existence of an equine pain face and to describe this in detail. Study design Semi-randomized, controlled, crossover trial. Animals Six adult horses. Methods Pain was induced with two noxious stimuli, a tourniquet on the antebrachium and topical application of capsaicin. All horses participated in two control trials and received both noxious stimuli twice, once with and once without an observer present. During all sessions their pain state was scored. The horses were filmed and the close-up video recordings of the faces were analysed for alterations in behaviour and facial expressions. Still images from the trials were evaluated for the presence of each of the specific pain face features identified from the video analysis. Results Both noxious challenges were effective in producing a pain response resulting in significantly increased pain scores. Alterations in facial expressions were observed in all horses during all noxious stimulations. The number of pain face features present on the still images from the noxious challenges were significantly higher than for the control trial (p = 0.0001). Facial expressions representative for control and pain trials were condensed into explanatory illustrations. During pain sessions with an observer present, the horses increased their contact-seeking behavior. Conclusions and clinical relevance An equine pain face comprising ‘low’ and/or ‘asymmetrical’ ears, an angled appearance of the eyes, a withdrawn and/or tense stare, mediolaterally dilated nostrils and tension of the lips, chin and certain facial muscles can be recognized in horses during induced acute pain. This description of an equine pain face may be useful for improving tools for pain recognition in horses with mild to moderate pain. PMID:25082060

  8. AO Observations of Three Powerful Radio Galaxies

    SciTech Connect

    de Vries, W; van Bruegel, W; Quirrenbach, A

    2002-08-01

    The host galaxies of powerful radio sources are ideal laboratories to study active galactic nuclei (AGN). The galaxies themselves are among the most massive systems in the universe, and are believed to harbor supermassive black holes (SMBH). If large galaxies are formed in a hierarchical way by multiple merger events, radio galaxies at low redshift represent the end-products of this process. However, it is not clear why some of these massive ellipticals have associated radio emission, while others do not. Both are thought to contain SMBHs, with masses proportional to the total luminous mass in the bulge. It either implies every SMBH has recurrent radio-loud phases, and the radio-quiet galaxies happen to be in the ''low'' state, or that the radio galaxy nuclei are physically different from radio-quiet ones, i.e. by having a more massive SMBH for a given bulge mass. Here we present the first results from our adaptive optics imaging and spectroscopy pilot program on three nearby powerful radio galaxies. Initiating a larger, more systematic AO survey of radio galaxies (preferentially with Laser Guide Star equipped AO systems) has the potential of furthering our understanding of the physical properties of radio sources, their triggering, and their subsequent evolution.

  9. Photon counting arrays for AO wavefront sensors

    NASA Astrophysics Data System (ADS)

    Vallerga, John; Tremsin, Anton; McPhate, Jason; Mikulec, Bettina; Clark, Allan; Siegmund, Oswald

    2005-08-01

    Future wavefront sensors for AO on large telescopes will require a large number of pixels and must operate at high frame rates. Unfortunately for CCDs, there is a readout noise penalty for operating faster, and this noise can add up rather quickly when considering the number of pixels required for the extended shape of a sodium laser guide star observed with a large telescope. Imaging photon counting detectors have zero readout noise and many pixels, but have suffered in the past with low QE at the longer wavelengths (> 500 nm). Recent developments in GaAs photocathode technology, CMOS ASIC readouts and FPGA processing electronics have resulted in noiseless WFS detector designs that are competitive with silicon array detectors, though at ~ 40% the QE of CCDs. We review noiseless array detectors and compare their centroiding performance with CCDs using the best available characteristics of each. We show that for sub-aperture binning of 6x6 and greater that noiseless detectors have a smaller centroid error at fluences of 60 photons or less, though the specific number is dependent on seeing conditions and the centroid algorithm used. We then present the status of a 256x256 noiseless MCP/Medipix2 hybrid detector being developed for AO.

  10. Bayesian Face Recognition and Perceptual Narrowing in Face-Space

    ERIC Educational Resources Information Center

    Balas, Benjamin

    2012-01-01

    During the first year of life, infants' face recognition abilities are subject to "perceptual narrowing", the end result of which is that observers lose the ability to distinguish previously discriminable faces (e.g. other-race faces) from one another. Perceptual narrowing has been reported for faces of different species and different races, in…

  11. Holistic processing of faces: learning effects with Mooney faces.

    PubMed

    Latinus, Marianne; Taylor, Margot J

    2005-08-01

    The specialness of faces is seen in the face inversion effect, which disrupts the configural, but not the analytic, processing of faces. Mooney faces, which are processed holistically, allowed us to determine the contribution of holistic processing to the face inversion effect. As inverted Mooney faces are difficult to recognize as faces, we also included an intermediary training period for Mooney face recognition for half of the subjects. Early face-sensitive ERPs (N170 and P1) and P2 were measured. Behavioral data showed an increase in correct responses to inverted and upright Mooney faces after the learning phase for the experimental group. No effects were seen on P1. N170 latency did not vary with stimulus type before the intermediary phase, however, N170 amplitude was consistently larger for upright than inverted Mooney faces. After the intermediary exercise, N170 was delayed for inverted compared to upright Mooney faces. In contrast, for both groups of subjects P2 amplitude was larger for nonface stimuli, and P2 amplitude decreased after the intermediate task only for the subjects trained to recognize Mooney faces. As the usual inversion effect seen with photographic faces (delayed and larger N170) was not seen with Mooney faces, these data suggest that this effect on N170 is due to the recruitment of analytic processing. P2 reflected learning and a deeper processing of the stimuli that were not identifiable as faces.

  12. 76 FR 61103 - Draft Guidance for Industry and Food and Drug Administration Staff; De Novo Classification...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-03

    ..., including what information to submit, when seeking a path to market for a novel device via the de novo... what information to submit, when seeking a path to market via the de novo process. This...

  13. Face recognition system and method using face pattern words and face pattern bytes

    SciTech Connect

    Zheng, Yufeng

    2014-12-23

    The present invention provides a novel system and method for identifying individuals and for face recognition utilizing facial features for face identification. The system and method of the invention comprise creating facial features or face patterns called face pattern words and face pattern bytes for face identification. The invention also provides for pattern recognitions for identification other than face recognition. The invention further provides a means for identifying individuals based on visible and/or thermal images of those individuals by utilizing computer software implemented by instructions on a computer or computer system and a computer readable medium containing instructions on a computer system for face recognition and identification.

  14. Two Faces of Japan.

    ERIC Educational Resources Information Center

    Beasley, Conger, Jr.

    1992-01-01

    Discusses the inconsistency between Japanese exploitation of world natural resources and gestures to provide leadership in ecologically innovative technology. Explores Japanese culture, power structure, population trends, environmental ethics, industrialism, and international business practices as they relate to the philosophical face of…

  15. Problems Facing Rural Schools.

    ERIC Educational Resources Information Center

    Stewart, C. E.; And Others

    Problems facing rural Scottish schools range from short term consideration of daily operation to long term consideration of organizational alternatives. Addressed specifically, such problems include consideration of: (1) liaison between a secondary school and its feeder primary schools; (2) preservice teacher training for work in small, isolated…

  16. Lightweight Face Mask

    NASA Technical Reports Server (NTRS)

    Cason, W. E. I.; Baucom, R. M.; Evans, R. C.

    1982-01-01

    Lightweight face mask originally developed to protect epileptic patients during seizures could have many other medical and nonmedical applications such as muscular distrophy patients, football linesmen and riot-control police. Masks are extremely lightweight, the lightest of the configurations weighing only 136 grams.

  17. Challenges Facing Special Education.

    ERIC Educational Resources Information Center

    Meyen, Edward L., Ed.; And Others

    This book presents 17 selected papers from recent issues of the journal, "Focus on Exceptional Children," concerning current and emerging challenges facing the field of special education. The book is organized in two parts. Part 1, "Contemporary Challenges," includes the following articles: "Transitions in Early Childhood Special Education: Issues…

  18. Facing the Not Knowing

    ERIC Educational Resources Information Center

    Tennant, Roy

    2007-01-01

    In this article, the author talks about how to face the not knowing and offers a strategy to fill the gap of not knowing. In coping with constant change, he describes a strategy for library staff that might help in the absence of certainty. This includes: (a) guarding the data with one's life; (b) build not for longevity, but obsolescence; (c)…

  19. A Wall of Faces

    ERIC Educational Resources Information Center

    Stevens, Lori

    2008-01-01

    Visitors to the campus of Orland High School (OHS) will never question that they have stepped into a world of the masses: kids, activity, personalities, busyness, and playfulness--a veritable cloud of mild bedlam. The wall of ceramic faces that greets a visitor in the school office is another reminder of the organized chaos that the teachers…

  20. Diferentes Metodologias Aplicadas ao Ensino de Astronomia

    NASA Astrophysics Data System (ADS)

    Albrecht, E.; Voelzke, M. R.

    2007-08-01

    Espera-se que o educando ao final da educação básica, adquira uma compreensão atualizada das hipóteses, modelos e formas de investigação sobre a origem e evolução do Universo em que vive. O presente trabalho tem como principal objetivo compreender dentre três práticas pedagógicas adotadas no Ensino de Astronomia, na terceira série do Ensino Médio, da Escola Estadual Colônia dos Pescadores, qual melhor cumpre o papel de formação e aprendizagem para vida. A pesquisa preliminar foi através de um questionário onde o intuito foi diagnosticar o conhecimento já existente acerca do tema em questão. O questionário é composto de vinte questões dissertativas e objetivas, onde os educandos das três turmas envolvidas o responderam. Este trabalho utiliza as seguintes metodologias: a tradicional, onde o professor é um repassador de informações, fazendo uso exclusivo de lousa e giz; a segunda também de forma tradicional, porém com auxílio de multimídia para desenvolvimento das aulas e aterceira sob forma de seminários, elaborados e apresentados pelos educandos, no qual o educador faz apenas as intervenções necessárias. Ao final do trabalho os alunos responderão novamente o questionário inicial para diagnosticar dentre as três metodologias utilizadas qual apresentou melhor resultado. Os resultados preliminares obtidos, já podem ser observados e, dos 119 alunos entrevistados, as respostas obtidas são as mais diversas e evidenciam que a grande maioria nunca teve em sua vida escolar o tema Astronomia. Ao serem questionados se já haviam estudado Astronomia as respostas foram: turma A: sim 43%; turma B: sim: 21%; turma C: sim: 24%. Porém quando questionados a respeito do significado de Astronomia observou-se que: turma A: 100% de acertos; turma B: 64% acertos; turma C: 84% de acertos, demonstrando claramente a aprendizagem em diferentes esferas, não dependendo unicamente da escola. Até o presente momento, verificou-se que há interesse em

  1. Direct visualization of de novo lipogenesis in single living cells.

    PubMed

    Li, Junjie; Cheng, Ji-Xin

    2014-01-01

    Increased de novo lipogenesis is being increasingly recognized as a hallmark of cancer. Despite recent advances in fluorescence microscopy, autoradiography and mass spectrometry, direct observation of de novo lipogenesis in living systems remains to be challenging. Here, by coupling stimulated Raman scattering (SRS) microscopy with isotope labeled glucose, we were able to trace the dynamic metabolism of glucose in single living cells with high spatial-temporal resolution. As the first direct visualization, we observed that glucose was largely utilized for lipid synthesis in pancreatic cancer cells, which occurs at a much lower rate in immortalized normal pancreatic epithelial cells. By inhibition of glycolysis and fatty acid synthase (FAS), the key enzyme for fatty acid synthesis, we confirmed the deuterium labeled lipids in cancer cells were from de novo lipid synthesis. Interestingly, we also found that prostate cancer cells exhibit relatively lower level of de novo lipogenesis, but higher fatty acid uptake compared to pancreatic cancer cells. Together, our results demonstrate a valuable tool to study dynamic lipid metabolism in cancer and other disorders. PMID:25351207

  2. Exome sequencing supports a de novo mutational paradigm for schizophrenia.

    PubMed

    Xu, Bin; Roos, J Louw; Dexheimer, Phillip; Boone, Braden; Plummer, Brooks; Levy, Shawn; Gogos, Joseph A; Karayiorgou, Maria

    2011-09-01

    Despite its high heritability, a large fraction of individuals with schizophrenia do not have a family history of the disease (sporadic cases). Here we examined the possibility that rare de novo protein-altering mutations contribute to the genetic component of schizophrenia by sequencing the exomes of 53 sporadic cases, 22 unaffected controls and their parents. We identified 40 de novo mutations in 27 cases affecting 40 genes, including a potentially disruptive mutation in DGCR2, a gene located in the schizophrenia-predisposing 22q11.2 microdeletion region. A comparison to rare inherited variants indicated that the identified de novo mutations show a large excess of non-synonymous changes in schizophrenia cases, as well as a greater potential to affect protein structure and function. Our analyses suggest a major role for de novo mutations in schizophrenia as well as a large mutational target, which together provide a plausible explanation for the high global incidence and persistence of the disease. PMID:21822266

  3. Direct Visualization of De novo Lipogenesis in Single Living Cells

    NASA Astrophysics Data System (ADS)

    Li, Junjie; Cheng, Ji-Xin

    2014-10-01

    Increased de novo lipogenesis is being increasingly recognized as a hallmark of cancer. Despite recent advances in fluorescence microscopy, autoradiography and mass spectrometry, direct observation of de novo lipogenesis in living systems remains to be challenging. Here, by coupling stimulated Raman scattering (SRS) microscopy with isotope labeled glucose, we were able to trace the dynamic metabolism of glucose in single living cells with high spatial-temporal resolution. As the first direct visualization, we observed that glucose was largely utilized for lipid synthesis in pancreatic cancer cells, which occurs at a much lower rate in immortalized normal pancreatic epithelial cells. By inhibition of glycolysis and fatty acid synthase (FAS), the key enzyme for fatty acid synthesis, we confirmed the deuterium labeled lipids in cancer cells were from de novo lipid synthesis. Interestingly, we also found that prostate cancer cells exhibit relatively lower level of de novo lipogenesis, but higher fatty acid uptake compared to pancreatic cancer cells. Together, our results demonstrate a valuable tool to study dynamic lipid metabolism in cancer and other disorders.

  4. De novo synthesis of milk triglycerides in humans

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mammary gland (MG) de novo lipogenesis contributes significantly to milk fat in animals but little is known in humans. Objective: To test the hypothesis that the incorporation of 13C carbons from [U-13C]glucose into fatty acids (FA) and glycerol in triglycerides (TG) will be greater: 1) in milk tha...

  5. Measurement of de novo lipogenesis in humans during lactation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Milk fat is composed of 98% triglycerides (TG) and provides infants with approximately 50% of their calories. Mammary gland de novo lipogenesis contributes significantly to milk fat in animals. However, there are no data regarding this process in humans. Incorporation of 13C carbons from [U-13C]gluc...

  6. Face aftereffects predict individual differences in face recognition ability.

    PubMed

    Dennett, Hugh W; McKone, Elinor; Edwards, Mark; Susilo, Tirta

    2012-01-01

    Face aftereffects are widely studied on the assumption that they provide a useful tool for investigating face-space coding of identity. However, a long-standing issue concerns the extent to which face aftereffects originate in face-level processes as opposed to earlier stages of visual processing. For example, some recent studies failed to find atypical face aftereffects in individuals with clinically poor face recognition. We show that in individuals within the normal range of face recognition abilities, there is an association between face memory ability and a figural face aftereffect that is argued to reflect the steepness of broadband-opponent neural response functions in underlying face-space. We further show that this correlation arises from face-level processing, by reporting results of tests of nonface memory and nonface aftereffects. We conclude that face aftereffects can tap high-level face-space, and that face-space coding differs in quality between individuals and contributes to face recognition ability.

  7. The Caledonian face test: A new test of face discrimination.

    PubMed

    Logan, Andrew J; Wilkinson, Frances; Wilson, Hugh R; Gordon, Gael E; Loffler, Gunter

    2016-02-01

    This study aimed to develop a clinical test of face perception which is applicable to a wide range of patients and can capture normal variability. The Caledonian face test utilises synthetic faces which combine simplicity with sufficient realism to permit individual identification. Face discrimination thresholds (i.e. minimum difference between faces required for accurate discrimination) were determined in an "odd-one-out" task. The difference between faces was controlled by an adaptive QUEST procedure. A broad range of face discrimination sensitivity was determined from a group (N=52) of young adults (mean 5.75%; SD 1.18; range 3.33-8.84%). The test is fast (3-4 min), repeatable (test-re-test r(2)=0.795) and demonstrates a significant inversion effect. The potential to identify impairments of face discrimination was evaluated by testing LM who reported a lifelong difficulty with face perception. While LM's impairment for two established face tests was close to the criterion for significance (Z-scores of -2.20 and -2.27) for the Caledonian face test, her Z-score was -7.26, implying a more than threefold higher sensitivity. The new face test provides a quantifiable and repeatable assessment of face discrimination ability. The enhanced sensitivity suggests that the Caledonian face test may be capable of detecting more subtle impairments of face perception than available tests.

  8. Finding Faces Among Faces: Human Faces are Located More Quickly and Accurately than Other Primate and Mammal Faces

    PubMed Central

    Simpson, Elizabeth A.; Buchin, Zachary; Werner, Katie; Worrell, Rey; Jakobsen, Krisztina V.

    2014-01-01

    We tested the specificity of human face search efficiency by examining whether there is a broad window of detection for various face-like stimuli—human and animal faces—or whether own-species faces receive greater attentional allocation. We assessed the strength of the own-species face detection bias by testing whether human faces are located more efficiently than other animal faces, when presented among various other species’ faces, in heterogeneous 16-, 36-, and 64-item arrays. Across all array sizes, we found that, controlling for distractor type, human faces were located faster and more accurately than primate and mammal faces, and that, controlling for target type, searches were faster when distractors were human faces compared to animal faces, revealing more efficient processing of human faces regardless of their role as targets or distractors (Experiment 1). Critically, these effects remained when searches were for specific species’ faces (human, chimpanzee, otter), ruling out a category-level explanation (Experiment 2). Together, these results suggest that human faces may be processed more efficiently than animal faces, both when task-relevant (targets), and when task-irrelevant (distractors), even when in direct competition with other faces. These results suggest that there is not a broad window of detection for all face-like patterns, but that human adults process own-species’ faces more efficiently than other species’ faces. Such own-species search efficiencies may arise through experience with own-species faces throughout development, or may be privileged early in development, due to the evolutionary importance of conspecifics’ faces. PMID:25113852

  9. Human Faces Are Slower than Chimpanzee Faces

    PubMed Central

    Burrows, Anne M.; Parr, Lisa A.; Durham, Emily L.; Matthews, Lea C.; Smith, Timothy D.

    2014-01-01

    Background While humans (like other primates) communicate with facial expressions, the evolution of speech added a new function to the facial muscles (facial expression muscles). The evolution of speech required the development of a coordinated action between visual (movement of the lips) and auditory signals in a rhythmic fashion to produce “visemes” (visual movements of the lips that correspond to specific sounds). Visemes depend upon facial muscles to regulate shape of the lips, which themselves act as speech articulators. This movement necessitates a more controlled, sustained muscle contraction than that produced during spontaneous facial expressions which occur rapidly and last only a short period of time. Recently, it was found that human tongue musculature contains a higher proportion of slow-twitch myosin fibers than in rhesus macaques, which is related to the slower, more controlled movements of the human tongue in the production of speech. Are there similar unique, evolutionary physiologic biases found in human facial musculature related to the evolution of speech? Methodology/Prinicipal Findings Using myosin immunohistochemistry, we tested the hypothesis that human facial musculature has a higher percentage of slow-twitch myosin fibers relative to chimpanzees (Pan troglodytes) and rhesus macaques (Macaca mulatta). We sampled the orbicularis oris and zygomaticus major muscles from three cadavers of each species and compared proportions of fiber-types. Results confirmed our hypothesis: humans had the highest proportion of slow-twitch myosin fibers while chimpanzees had the highest proportion of fast-twitch fibers. Conclusions/significance These findings demonstrate that the human face is slower than that of rhesus macaques and our closest living relative, the chimpanzee. They also support the assertion that human facial musculature and speech co-evolved. Further, these results suggest a unique set of evolutionary selective pressures on human facial

  10. 43 CFR 30.207 - What happens if nobody files for de novo review?

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false What happens if nobody files for de novo... PROBATE HEARINGS PROCEDURES Summary Probate Proceedings § 30.207 What happens if nobody files for de novo review? If no interested party requests de novo review within 30 days of the date of the written...

  11. 43 CFR 30.206 - What happens after I file a request for de novo review?

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false What happens after I file a request for de... request for de novo review? (a) Within 10 days of receiving a request for de novo review, OHA will notify... the de novo review, and assign the case to a judge. (b) The judge will review the merits of the...

  12. Nursing student experiences with face-to-face learning.

    PubMed

    Gruendemann, Barbara J

    2011-12-01

    Face-to-face learning has been the mainstay of nursing student learning. Despite moves to online learning, face-to-face learning persists. This study focuses on how nursing students experience face-to-face learning and why it not only survives, but thrives. This study was anchored in a hermeneutic phenomenological approach, with Gadamerian concepts and van Manen's lifeworlds as frameworks to understand students' experiences of face-to-face learning. Patterns and themes were extracted from audiore-corded face-to-face interviews. Participants confirmed that face-to-face learning continues to be valued as a strong methodology in nursing education. Their experiences focused on humanism, the importance of "presence," physical proximity, classroom as "the real thing," immediacy of feedback, and learning and knowing by human connections and interaction. The study findings were a rich source for understanding how nursing students process learning experiences. Increased understanding of the meaning and essence of face-to-face learning is essential as we decide how nursing content will be taught. PMID:21956259

  13. Multiview face recognition: from TensorFace to V-TensorFace and K-TensorFace.

    PubMed

    Tian, Chunna; Fan, Guoliang; Gao, Xinbo; Tian, Qi

    2012-04-01

    Face images under uncontrolled environments suffer from the changes of multiple factors such as camera view, illumination, expression, etc. Tensor analysis provides a way of analyzing the influence of different factors on facial variation. However, the TensorFace model creates a difficulty in representing the nonlinearity of view subspace. In this paper, to break this limitation, we present a view-manifold-based TensorFace (V-TensorFace), in which the latent view manifold preserves the local distances in the multiview face space. Moreover, a kernelized TensorFace (K-TensorFace) for multiview face recognition is proposed to preserve the structure of the latent manifold in the image space. Both methods provide a generative model that involves a continuous view manifold for unseen view representation. Most importantly, we propose a unified framework to generalize TensorFace, V-TensorFace, and K-TensorFace. Finally, an expectation-maximization like algorithm is developed to estimate the identity and view parameters iteratively for a face image of an unknown/unseen view. The experiment on the PIE database shows the effectiveness of the manifold construction method. Extensive comparison experiments on Weizmann and Oriental Face databases for multiview face recognition demonstrate the superiority of the proposed V- and K-TensorFace methods over the view-based principal component analysis and other state-of-the-art approaches for such purpose. PMID:22318490

  14. CRYSTAL/FACE

    NASA Technical Reports Server (NTRS)

    Baumgardner, Darrel; Kok, Greg; Anderson, Bruce

    2004-01-01

    Droplet Measurement Technologies (DMT), under funding from NASA, participated in the CRYSTAL/FACE field campaign in July, 2002 with measurements of cirrus cloud hydrometeors in the size range from 0.5 to 1600 microns. The measurements were made with the DMT Cloud, Aerosol and Precipitation Spectrometer (CAPS) that was flown on NASA's WB57F. With the exception of the first research flight when the data system failed two hours into the mission, the measurement system performed almost flawlessly during the thirteen flights. The measurements from the CAPS have been essential for interpretation of cirrus cloud properties and their impact on climate. The CAPS data set has been used extensively by the CRYSTAL/FACE investigators and as of the date of this report, have been included in five published research articles, 10 conference presentations and six other journal articles currently in preparation.

  15. Producing desired ice faces

    PubMed Central

    Shultz, Mary Jane; Brumberg, Alexandra; Bisson, Patrick J.; Shultz, Ryan

    2015-01-01

    The ability to prepare single-crystal faces has become central to developing and testing models for chemistry at interfaces, spectacularly demonstrated by heterogeneous catalysis and nanoscience. This ability has been hampered for hexagonal ice, Ih––a fundamental hydrogen-bonded surface––due to two characteristics of ice: ice does not readily cleave along a crystal lattice plane and properties of ice grown on a substrate can differ significantly from those of neat ice. This work describes laboratory-based methods both to determine the Ih crystal lattice orientation relative to a surface and to use that orientation to prepare any desired face. The work builds on previous results attaining nearly 100% yield of high-quality, single-crystal boules. With these methods, researchers can prepare authentic, single-crystal ice surfaces for numerous studies including uptake measurements, surface reactivity, and catalytic activity of this ubiquitous, fundamental solid. PMID:26512102

  16. Producing desired ice faces.

    PubMed

    Shultz, Mary Jane; Brumberg, Alexandra; Bisson, Patrick J; Shultz, Ryan

    2015-11-10

    The ability to prepare single-crystal faces has become central to developing and testing models for chemistry at interfaces, spectacularly demonstrated by heterogeneous catalysis and nanoscience. This ability has been hampered for hexagonal ice, Ih--a fundamental hydrogen-bonded surface--due to two characteristics of ice: ice does not readily cleave along a crystal lattice plane and properties of ice grown on a substrate can differ significantly from those of neat ice. This work describes laboratory-based methods both to determine the Ih crystal lattice orientation relative to a surface and to use that orientation to prepare any desired face. The work builds on previous results attaining nearly 100% yield of high-quality, single-crystal boules. With these methods, researchers can prepare authentic, single-crystal ice surfaces for numerous studies including uptake measurements, surface reactivity, and catalytic activity of this ubiquitous, fundamental solid.

  17. Double face sealing device

    NASA Technical Reports Server (NTRS)

    Weddendorf, Bruce (Inventor)

    1991-01-01

    A double face sealing device is disclosed for mounting between two surfaces to provide an air-tight and fluid-tight seal between a closure member bearing one of the surfaces and a structure or housing bearing the other surface which extends around the opening or hatchway to be closed. The double face sealing device includes a plurality of sections or segments mounted to one of the surfaces, each having a main body portion, a pair of outwardly extending and diverging, cantilever, spring arms, and a pair of inwardly extending and diverging, cantilever, spring arms, an elastomeric cover on the distal, free ends of the outwardly extending and diverging spring arms, and an elastomeric cover on the distal, free, ends of the outwardly extending and diverging spring arms, and an elastomeric cover on the distal, free ends of the inwardly extending and diverging spring arms. The double face sealing device has application or use in all environments requiring a seal, but is particularly useful to seal openings or hatchways between compartments of spacecraft or aircraft.

  18. Beyond Faces and Expertise

    PubMed Central

    Zhao, Mintao; Bülthoff, Heinrich H.; Bülthoff, Isabelle

    2016-01-01

    Holistic processing—the tendency to perceive objects as indecomposable wholes—has long been viewed as a process specific to faces or objects of expertise. Although current theories differ in what causes holistic processing, they share a fundamental constraint for its generalization: Nonface objects cannot elicit facelike holistic processing in the absence of expertise. Contrary to this prevailing view, here we show that line patterns with salient Gestalt information (i.e., connectedness, closure, and continuity between parts) can be processed as holistically as faces without any training. Moreover, weakening the saliency of Gestalt information in these patterns reduced holistic processing of them, which indicates that Gestalt information plays a crucial role in holistic processing. Therefore, holistic processing can be achieved not only via a top-down route based on expertise, but also via a bottom-up route relying merely on object-based information. The finding that facelike holistic processing can extend beyond the domains of faces and objects of expertise poses a challenge to current dominant theories. PMID:26674129

  19. Foil Face Seal Testing

    NASA Technical Reports Server (NTRS)

    Munson, John

    2009-01-01

    In the seal literature you can find many attempts by various researchers to adapt film riding seals to the gas turbine engine. None have been successful, potential distortion of the sealing faces is the primary reason. There is a film riding device that does accommodate distortion and is in service in aircraft applications, namely the foil bearing. More specifically a foil thrust bearing. These are not intended to be seals, and they do not accommodate large axial movement between shaft & static structure. By combining the 2 a unique type of face seal has been created. It functions like a normal face seal. The foil thrust bearing replaces the normal primary sealing surface. The compliance of the foil bearing allows the foils to track distortion of the mating seal ring. The foil seal has several perceived advantages over existing hydrodynamic designs, enumerated in the chart. Materials and design methodology needed for this application already exist. Also the load capacity requirements for the foil bearing are low since it only needs to support itself and overcome friction forces at the antirotation keys.

  20. Hyperfamiliarity for faces

    PubMed Central

    Devinsky, O.; Davachi, L.; Santchi, C.; Quinn, B. T.; Staresina, B. P.; Thesen, T.

    2010-01-01

    Objective: To report 4 cases of hyperfamiliarity for faces (HFF) and review 5 previously reported cases. Methods: We identified cases of HFF from PubMed search and references in prior reports. Results: Three of our 4 cases had pathologic findings that were most extensive in the left temporal lobe. HFF occurred after a tonic-clonic seizure (cases 1 and 3), during simple partial seizures (case 2), and in the setting of an increase in simple partial seizure frequency but not during seizures (case 4). All 9 cases were adults with 1 or more seizures; symptoms first occurred after seizures in 5 cases and during seizures in 1 case. Ictal symptoms lasted from seconds to minutes and from 2 days to more than 7 years in the other 6 cases. The duration of HFF was not associated with the presence or extent of a structural lesion. While in several cases HFF appears to result from a postictal Todd paralysis, the mechanism underlying persistent cases is uncertain. Conclusions: This modality (visual)–specific and stimulus (face)–specific syndrome is associated with diverse structural, functional imaging, and neurophysiologic findings. Lesions are more often left-sided and involve the temporal lobe. Epilepsy and seizures were present in all 9 cases, suggesting a pathophysiologic relationship, which likely varies among cases. Although only reported in 9 patients, HFF is probably much more common than it is diagnosed. GLOSSARY HFF = hyperfamiliarity for faces. PMID:20308681

  1. Synthesis and characterization of "face-to-face" porphyrins.

    PubMed Central

    Collman, J P; Elliott, C M; Halbert, T R; Tovrog, B S

    1977-01-01

    The syntheses of four binary porphyrins, two of which are constrained to a "face-to-face" conformation, and their Co2+ and Cu2+ derivatives are described. Electron spin resonance indicates that the intermetallic separation in the binuclear "face-to-face" porphyrins is about 6.5-6.8 A. Electronic spectra and proton magnetic resonance spectra support the postulated "face-to-face" conformations. A hypothesis that related compounds may serve as multielectron redox catalysts for O2 and N2 is presented. PMID:189304

  2. Visual Search of Mooney Faces.

    PubMed

    Goold, Jessica E; Meng, Ming

    2016-01-01

    Faces spontaneously capture attention. However, which special attributes of a face underlie this effect is unclear. To address this question, we investigate how gist information, specific visual properties and differing amounts of experience with faces affect the time required to detect a face. Three visual search experiments were conducted investigating the rapidness of human observers to detect Mooney face images. Mooney images are two-toned, ambiguous images. They were used in order to have stimuli that maintain gist information but limit low-level image properties. Results from the experiments show: (1) Although upright Mooney faces were searched inefficiently, they were detected more rapidly than inverted Mooney face targets, demonstrating the important role of gist information in guiding attention toward a face. (2) Several specific Mooney face identities were searched efficiently while others were not, suggesting the involvement of specific visual properties in face detection. (3) By providing participants with unambiguous gray-scale versions of the Mooney face targets prior to the visual search task, the targets were detected significantly more efficiently, suggesting that prior experience with Mooney faces improves the ability to extract gist information for rapid face detection. However, a week of training with Mooney face categorization did not lead to even more efficient visual search of Mooney face targets. In summary, these results reveal that specific local image properties cannot account for how faces capture attention. On the other hand, gist information alone cannot account for how faces capture attention either. Prior experience facilitates the effect of gist on visual search of faces; making faces a special object category for guiding attention.

  3. Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus).

    PubMed

    Thanh, Nguyen Minh; Jung, Hyungtaek; Lyons, Russell E; Njaci, Isaac; Yoon, Byoung-Ha; Chand, Vincent; Tuan, Nguyen Viet; Thu, Vo Thi Minh; Mather, Peter

    2015-10-01

    Striped catfish (Pangasianodon hypophthalmus) is a commercially important freshwater fish used in inland aquaculture in the Mekong Delta, Vietnam. The culture industry is facing a significant challenge however from saltwater intrusion into many low topographical coastal provinces across the Mekong Delta as a result of predicted climate change impacts. Developing genomic resources for this species can facilitate the production of improved culture lines that can withstand raised salinity conditions, and so we have applied high-throughput Ion Torrent sequencing of transcriptome libraries from six target osmoregulatory organs from striped catfish as a genomic resource for use in future selection strategies. We obtained 12,177,770 reads after trimming and processing with an average length of 97bp. De novo assemblies were generated using CLC Genomic Workbench, Trinity and Velvet/Oases with the best overall contig performance resulting from the CLC assembly. De novo assembly using CLC yielded 66,451 contigs with an average length of 478bp and N50 length of 506bp. A total of 37,969 contigs (57%) possessed significant similarity with proteins in the non-redundant database. Comparative analyses revealed that a significant number of contigs matched sequences reported in other teleost fishes, ranging in similarity from 45.2% with Atlantic cod to 52% with zebrafish. In addition, 28,879 simple sequence repeats (SSRs) and 55,721 single nucleotide polymorphisms (SNPs) were detected in the striped catfish transcriptome. The sequence collection generated in the current study represents the most comprehensive genomic resource for P. hypophthalmus available to date. Our results illustrate the utility of next-generation sequencing as an efficient tool for constructing a large genomic database for marker development in non-model species. PMID:25979246

  4. Genes from scratch--the evolutionary fate of de novo genes.

    PubMed

    Schlötterer, Christian

    2015-04-01

    Although considered an extremely unlikely event, many genes emerge from previously noncoding genomic regions. This review covers the entire life cycle of such de novo genes. Two competing hypotheses about the process of de novo gene birth are discussed as well as the high death rate of de novo genes. Despite the high death rate, some de novo genes are retained and remain functional, even in distantly related species, through their integration into gene networks. Further studies combining gene expression with ribosome profiling in multiple populations across different species will be instrumental for an improved understanding of the evolutionary processes operating on de novo genes.

  5. Face-space: A unifying concept in face recognition research.

    PubMed

    Valentine, Tim; Lewis, Michael B; Hills, Peter J

    2016-10-01

    The concept of a multidimensional psychological space, in which faces can be represented according to their perceived properties, is fundamental to the modern theorist in face processing. Yet the idea was not clearly expressed until 1991. The background that led to the development of face-space is explained, and its continuing influence on theories of face processing is discussed. Research that has explored the properties of the face-space and sought to understand caricature, including facial adaptation paradigms, is reviewed. Face-space as a theoretical framework for understanding the effect of ethnicity and the development of face recognition is evaluated. Finally, two applications of face-space in the forensic setting are discussed. From initially being presented as a model to explain distinctiveness, inversion, and the effect of ethnicity, face-space has become a central pillar in many aspects of face processing. It is currently being developed to help us understand adaptation effects with faces. While being in principle a simple concept, face-space has shaped, and continues to shape, our understanding of face perception.

  6. LGS-AO Imaging of Every Kepler Planet Candidate: the Robo-AO KOI Survey

    NASA Astrophysics Data System (ADS)

    Baranec, Christoph; Law, Nicholas; Morton, Timothy; Ziegler, Carl; Nofi, Larissa; Atkinson, Dani; Riddle, Reed

    2015-12-01

    The Robo-AO Kepler Planetary Candidate Survey is observing every Kepler planet candidate host star with laser adaptive optics imaging, to search for blended nearby stars which may be physically associated companions and/or responsible for transit false positives. We will present the results from searching for companions around over 3,000 Kepler planet hosts in 2012-2015. We will describe our first data release covering 715 planet candidate hosts, and give a preview of ongoing results including improved statistics on the likelihood of false positive planet detections in the Kepler dataset, many new planets in multiple star systems, and new exotic multiple star systems containing Kepler planets. We will also describe the automated Robo-AO survey data reduction methods, including a method of using the large ensemble of target observations as mutual point-spread-function references, along with a new automated companion-detection algorithm designed for extremely large adaptive optics surveys. Our first data release covered 715 objects, searching for companions from 0.15” to 2.5” separation with contrast up to 6 magnitudes. We measured the overall nearby-star-probability for Kepler planet candidates to be 7.4+/-1.0%, and we will detail the variations in this number with stellar host parameters. We will also discuss plans to extend the survey to other transiting planet missions such as K2 and TESS as Robo-AO is in the process of being re-deployed to the 2.1-m telescope at Kitt Peak for 3 years and a higher-contrast Robo-AO system is being developed for the 2.2-m UH telescope on Maunakea.

  7. Age-Dependent Face Detection and Face Categorization Performance

    PubMed Central

    Carbon, Claus-Christian; Grüter, Martina; Grüter, Thomas

    2013-01-01

    Empirical studies on the development of face processing skills with age show inconsistent patterns concerning qualitative vs. quantitative changes over time or the age range for peak cognitive performance. In the present study, we tested the proficiency in face detection and face categorization with a large sample of participants (N = 312; age range: 2-88 yrs). As test objects, we used so-called Mooney faces, two-tone (black and white) images of faces lacking critical information of a local, featural and relational nature, reflecting difficult real world face processing conditions. We found that performance in the assessment of gender and age from Mooney faces increases up to about age 15, and decreases from 65 years on. The implications of these findings are discussed in the light of classic and recent findings from face development literature. PMID:24116236

  8. LDEF (Prelaunch), AO038 : Interstellar Gas Experiment, Tray H06

    NASA Technical Reports Server (NTRS)

    1984-01-01

    LDEF (Prelaunch), AO038 : Interstellar Gas Experiment, Tray H06 The prelaunch photograph was taken in SAEF II at KSC prior to installation of the Interstellar Gas Experiment on the LDEF. The prelaunch photograph provides a view of the Interstellar Gas Experiment (IGE) hardware and shows the orientation of two (2) experiment canister housings mounted in a twelve (12) inch deep end tray. The experiment utilizes seven (7) canisters containing high-purity beryllium copper collecting foils, three (3) located in peripheral trays and four (4) located in trays on the space end of the LDEF, to meet experiment objectives. The active portion of the experiment consist of canister electronic timing devices and pyrotechnic cutters that control the exposure time of each collector foil. An electronic voltage multiplier system provides a bias voltage to a wire mesh grid located above the beryllium copper collecting foils.The batteries and the electronics are housed beneath the experiment baseplate facing the LDEF interior. The white painted surface area within the LDEF tray provides the optical properties required to maintain the experiment components within temperature limits. The two (2) rectangular openings in opposite corners of the experiment baseplate provide the mountings for the grid voltage box and for the ground support equipment test connectors. A white grid voltage box, mounted on the side of each canister housing, provides the termination point for the cables running from the power supply located beneath the baseplate. The canister housing is a welded aluminum structure with aluminum mounting flanges. The experiment components are assembled using non-magnetic stainless steel fasteners. The aluminum housing cover, removed prior to flight, protects experiment components from damage and large particle contamination during ground handling.

  9. LDEF (Prelaunch), AO038 : Interstellar Gas Experiment, Tray E12

    NASA Technical Reports Server (NTRS)

    1984-01-01

    LDEF (Prelaunch), AO038 : Interstellar Gas Experiment, Tray E12 The prelaunch photograph provides a view of the Interstellar Gas Experiment (IGE) hardware and shows the orientation of two (2) experiment canister housings mounted in a twelve (12) inch deep peripheral tray. The experiment utilizes seven (7) canisters containing high-purity beryllium copper collecting foils, three (3) located in peripheral trays and four (4) located in trays on the space end of the LDEF, to meet experiment objectives. The active portion of the experiment consist of canister electronic timing devices and pyrotechnic cutters that control the exposure time of each collector foil. An electronic voltage multiplier system provides a bias voltage to the grid network located above the beryllium copper collecting foils.The batteries and the electronics are housed beneath the experiment baseplate facing the LDEF interior. The white painted surface area within the LDEF tray provides the optical properties required to maintain the experiment components within temperature limits. The two (2) rectangular openings in opposite corners of the experiment baseplate provide the mountings for the ground support equipment test connectors. A white grid voltage connector box, mounted on the side of each canister housing, provides the termination point for the cables running from the grid voltage box beneath the baseplate. The canister housing is a welded aluminum structure with aluminum mounting flanges. The experiment components are assembled using non-magnetic stainless steel fasteners. The aluminum housing cover, removed prior to flight, protects experiment components from damage and large particle contamination during ground handling.

  10. LDEF (Prelaunch), AO038 : Interstellar Gas Experiment, Tray H09

    NASA Technical Reports Server (NTRS)

    1984-01-01

    LDEF (Prelaunch), AO038 : Interstellar Gas Experiment, Tray H09 The prelaunch photograph was taken in SAEF II at KSC prior to installation of the Interstellar Gas Experiment on the LDEF. The prelaunch photograph provides a view of the Interstellar Gas Experiment (IGE) hardware and shows the orientation of two (2) experiment canister housings mounted in a twelve (12) inch deep end tray. The experiment utilizes seven (7) canisters containing high-purity beryllium copper collecting foils, three (3) located in peripheral trays and four (4) located in trays on the space end of the LDEF, to meet experiment objectives. The active portion of the experiment consist of canister electronic timing devices and pyrotechnic cutters that control the exposure time of each collector foil. An electronic voltage multiplier system provides a bias voltage to the grid network located above the beryllium copper collecting foils.The batteries and the electronics are housed beneath the experiment baseplate facing the LDEF interior. The white painted surface area within the LDEF tray provides the optical properties required to maintain the experiment components within temperature limits. The two (2) rectangular openings in opposite corners of the experiment baseplate provide the mountings for the grid voltage box and for the ground support equipment test connectors. A white grid voltage box, mounted on the side of each canister housing, provides the termination point for the cables running from the power supply located beneath the baseplate. The canister housing is a welded aluminum structure with aluminum mounting flanges. The experiment components are assembled using non-magnetic stainless steel fasteners. The aluminum housing cover, removed prior to flight, protects experiment components from damage and large particle contamination during ground handling.

  11. Bayesian face recognition and perceptual narrowing in face-space.

    PubMed

    Balas, Benjamin

    2012-07-01

    During the first year of life, infants' face recognition abilities are subject to 'perceptual narrowing', the end result of which is that observers lose the ability to distinguish previously discriminable faces (e.g. other-race faces) from one another. Perceptual narrowing has been reported for faces of different species and different races, in developing humans and primates. Though the phenomenon is highly robust and replicable, there have been few efforts to model the emergence of perceptual narrowing as a function of the accumulation of experience with faces during infancy. The goal of the current study is to examine how perceptual narrowing might manifest as statistical estimation in 'face-space', a geometric framework for describing face recognition that has been successfully applied to adult face perception. Here, I use a computer vision algorithm for Bayesian face recognition to study how the acquisition of experience in face-space and the presence of race categories affect performance for own and other-race faces. Perceptual narrowing follows from the establishment of distinct race categories, suggesting that the acquisition of category boundaries for race is a key computational mechanism in developing face expertise.

  12. Development of Face Processing: The Effect of Face Inversion.

    ERIC Educational Resources Information Center

    Schwarzer, Gudrun

    2000-01-01

    Examined degree to which analytic and holistic modes of processing play a role in children's and adults' categorization of faces. Found a developmental trend from analytic to holistic processing and an effect of face inversion with increasing age. Seven-year-olds processed faces comparably to nonfacial visual stimuli, whereas a growing proportion…

  13. Face-to-Face Interference in Typical and Atypical Development

    ERIC Educational Resources Information Center

    Riby, Deborah M.; Doherty-Sneddon, Gwyneth; Whittle, Lisa

    2012-01-01

    Visual communication cues facilitate interpersonal communication. It is important that we look at faces to retrieve and subsequently process such cues. It is also important that we sometimes look away from faces as they increase cognitive load that may interfere with online processing. Indeed, when typically developing individuals hold face gaze…

  14. Electromagnetic DM technology meets future AO demands

    NASA Astrophysics Data System (ADS)

    Hamelinck, Roger; Rosielle, Nick; Steinbuch, Maarten; Doelman, Niek

    New deformable mirror technology is developed by the Technische Universiteit Eindhoven, Delft University of Technology and TNO Science and Industry. Several prototype adaptive deformable mirrors are realized mirrors, up to 427 actuators and ∅150mm diameter, with characteristics suitable for future AO systems. The prototypes consist of a 100µm thick, continuous facesheet on which low voltage, electromagnetic, push-pull actuators impose out-of-plane displacements. The variable reluctance actuators with ±10µm stroke and nanometer resolution are located in a standard actuator module. Each module with 61 actuators connects to a single PCB with dedicated, 16 bit, PWM based, drivers. A LVDS multi-drop cable connects up to 32 actuator modules. With the actuator module, accompanying PCB and multi-drop system the deformable mirror technology is made modular in its mechanics and electronics. An Ethernet-LVDS bridge enables any commercial PC to control the mirror using the UDP standard. Latest results of the deformable mirror technology development are presented.

  15. Alkaline Bohr effect of human hemoglobin Ao.

    PubMed

    Di Cera, E; Doyle, M L; Gill, S J

    1988-04-01

    Differential oxygen binding measurements obtained over the pH range 6.95 to 9.10 at 25 degrees C have allowed a detailed description of the alkaline Bohr effect of human hemoglobin Ao. Phenomenological analysis of the data in terms of the Adair equation shows that: (1) the oxygen binding curves are asymmetrical with the population of the triply oxygenated species being negligible throughout the pH range studied: (2) the shape of the oxygen binding curve is affected by pH, especially at low saturation; and (3) the maximum O2-proton linkage is -0.52 mole of proton per mole of oxygen at pH 7.4. A possible molecular mechanism of the Bohr effect is proposed within the framework of an allosteric model which accounts for the low population of triply oxygenated hemoglobin species. At least three Bohr groups are necessary for a quantitative description of the alkaline Bohr effect. Two of these groups titrate in the range of the His146 beta and Vall alpha residues, which have long been identified as the main alkaline Bohr groups, and altogether contribute 84% of the alkaline Bohr effect at physiological pH. A third ionizable group, linked to oxygenation presumably at the beta chains, is implicated and is titrated in a pH range characteristic of a surface histidyl residue.

  16. Challenges facing production grids

    SciTech Connect

    Pordes, Ruth; /Fermilab

    2007-06-01

    Today's global communities of users expect quality of service from distributed Grid systems equivalent to that their local data centers. This must be coupled to ubiquitous access to the ensemble of processing and storage resources across multiple Grid infrastructures. We are still facing significant challenges in meeting these expectations, especially in the underlying security, a sustainable and successful economic model, and smoothing the boundaries between administrative and technical domains. Using the Open Science Grid as an example, I examine the status and challenges of Grids operating in production today.

  17. Evolution of new functions de novo and from preexisting genes.

    PubMed

    Andersson, Dan I; Jerlström-Hultqvist, Jon; Näsvall, Joakim

    2015-06-01

    How the enormous structural and functional diversity of new genes and proteins was generated (estimated to be 10(10)-10(12) different proteins in all organisms on earth [Choi I-G, Kim S-H. 2006. Evolution of protein structural classes and protein sequence families. Proc Natl Acad Sci 103: 14056-14061] is a central biological question that has a long and rich history. Extensive work during the last 80 years have shown that new genes that play important roles in lineage-specific phenotypes and adaptation can originate through a multitude of different mechanisms, including duplication, lateral gene transfer, gene fusion/fission, and de novo origination. In this review, we focus on two main processes as generators of new functions: evolution of new genes by duplication and divergence of pre-existing genes and de novo gene origination in which a whole protein-coding gene evolves from a noncoding sequence. PMID:26032716

  18. De novo membranous nephropathy associated with donor-specific alloantibody.

    PubMed

    El Kossi, M; Harmer, A; Goodwin, J; Wagner, B; Shortland, J; Angel, C; McKane, W

    2008-01-01

    Recent evidence suggests that alloantibody may play an aetiological role in the pathogenesis of membranous glomerulopathy in native kidneys. There is an increased awareness of the significance of alloantibody on renal transplant outcome, particularly with the development of more sensitive assays. We describe a kidney transplant patient who developed de novo membranous glomerulopathy (DNMG) with heavy proteinuria in the context of a donor-specific alloantibody (DSA) directed against HLA DQ7. Proteinuria resolved and kidney function stabilized following treatment with mycophenolate mofetil and an angiotensin receptor blocker. The titre of the DSA fell in parallel with resolution of the proteinuria. This is the first reported case of DNMG after kidney transplantation clearly associated with a DSA. We hypothesize that de novo membranous glomerulopathy may be an atypical manifestation of acute antibody-mediated damage. Cases of DNMG should be screened for alloantibody and the presence of alloantibody may influence the choice of therapy. PMID:18217914

  19. From de novo mutations to personalized therapeutic interventions in autism.

    PubMed

    Brandler, William M; Sebat, Jonathan

    2015-01-01

    The high heritability, early age at onset, and reproductive disadvantages of autism spectrum disorders (ASDs) are consistent with an etiology composed of dominant-acting de novo (spontaneous) mutations. Mutation detection by microarray analysis and DNA sequencing has confirmed that de novo copy-number variants or point mutations in protein-coding regions of genes contribute to risk, and some of the underlying causal variants and genes have been identified. As our understanding of autism genes develops, the spectrum of autism is breaking up into quanta of many different genetic disorders. Given the diversity of etiologies and underlying biochemical pathways, personalized therapy for ASDs is logical, and clinical genetic testing is a prerequisite.

  20. De Novo Gene Disruptions in Children on the Autistic Spectrum

    PubMed Central

    Iossifov, Ivan; Ronemus, Michael; Levy, Dan; Wang, Zihua; Hakker, Inessa; Rosenbaum, Julie; Yamrom, Boris; Lee, Yoon-ha; Narzisi, Giuseppe; Leotta, Anthony; Kendall, Jude; Grabowska, Ewa; Ma, Beicong; Marks, Steven; Rodgers, Linda; Stepansky, Asya; Troge, Jennifer; Andrews, Peter; Bekritsky, Mitchell; Pradhan, Kith; Ghiban, Elena; Kramer, Melissa; Parla, Jennifer; Demeter, Ryan; Fulton, Lucinda L.; Fulton, Robert S.; Magrini, Vincent J.; Ye, Kenny; Darnell, Jennifer C.; Darnell, Robert B.; Mardis, Elaine R.; Wilson, Richard K.; Schatz, Michael C.; McCombie, W. Richard; Wigler, Michael

    2012-01-01

    SUMMARY Exome sequencing of 343 families, each with a single child on the autism spectrum and at least one unaffected sibling, reveal de novo small indels and point substitutions, which come mostly from the paternal line in an age-dependent manner. We do not see significantly greater numbers of de novo missense mutations in affected versus unaffected children, but gene-disrupting mutations (nonsense, splice site, and frame shifts) are twice as frequent, 59 to 28. Based on this differential and the number of recurrent and total targets of gene disruption found in our and similar studies, we estimate between 350 and 400 autism susceptibility genes. Many of the disrupted genes in these studies are associated with the fragile X protein, FMRP, reinforcing links between autism and synaptic plasticity. We find FMRP-associated genes are under greater purifying selection than the remainder of genes and suggest they are especially dosage-sensitive targets of cognitive disorders. PMID:22542183

  1. De novo mutations in schizophrenia implicate synaptic networks.

    PubMed

    Fromer, Menachem; Pocklington, Andrew J; Kavanagh, David H; Williams, Hywel J; Dwyer, Sarah; Gormley, Padhraig; Georgieva, Lyudmila; Rees, Elliott; Palta, Priit; Ruderfer, Douglas M; Carrera, Noa; Humphreys, Isla; Johnson, Jessica S; Roussos, Panos; Barker, Douglas D; Banks, Eric; Milanova, Vihra; Grant, Seth G; Hannon, Eilis; Rose, Samuel A; Chambert, Kimberly; Mahajan, Milind; Scolnick, Edward M; Moran, Jennifer L; Kirov, George; Palotie, Aarno; McCarroll, Steven A; Holmans, Peter; Sklar, Pamela; Owen, Michael J; Purcell, Shaun M; O'Donovan, Michael C

    2014-02-13

    Inherited alleles account for most of the genetic risk for schizophrenia. However, new (de novo) mutations, in the form of large chromosomal copy number changes, occur in a small fraction of cases and disproportionally disrupt genes encoding postsynaptic proteins. Here we show that small de novo mutations, affecting one or a few nucleotides, are overrepresented among glutamatergic postsynaptic proteins comprising activity-regulated cytoskeleton-associated protein (ARC) and N-methyl-d-aspartate receptor (NMDAR) complexes. Mutations are additionally enriched in proteins that interact with these complexes to modulate synaptic strength, namely proteins regulating actin filament dynamics and those whose messenger RNAs are targets of fragile X mental retardation protein (FMRP). Genes affected by mutations in schizophrenia overlap those mutated in autism and intellectual disability, as do mutation-enriched synaptic pathways. Aligning our findings with a parallel case-control study, we demonstrate reproducible insights into aetiological mechanisms for schizophrenia and reveal pathophysiology shared with other neurodevelopmental disorders. PMID:24463507

  2. Face the Fats Quiz 2

    MedlinePlus

    Face the Fats Quiz II Do you know your fats by heart? Ready to make informed choices about the foods you ... to fried chicken, test your knowledge about the fats in some familiar foods. Welcome to Face the ...

  3. Arginine de novo and nitric oxide production in disease states.

    PubMed

    Luiking, Yvette C; Ten Have, Gabriella A M; Wolfe, Robert R; Deutz, Nicolaas E P

    2012-11-15

    Arginine is derived from dietary protein intake, body protein breakdown, or endogenous de novo arginine production. The latter may be linked to the availability of citrulline, which is the immediate precursor of arginine and limiting factor for de novo arginine production. Arginine metabolism is highly compartmentalized due to the expression of the enzymes involved in arginine metabolism in various organs. A small fraction of arginine enters the NO synthase (NOS) pathway. Tetrahydrobiopterin (BH4) is an essential and rate-limiting cofactor for the production of NO. Depletion of BH4 in oxidative-stressed endothelial cells can result in so-called NOS3 "uncoupling," resulting in production of superoxide instead of NO. Moreover, distribution of arginine between intracellular transporters and arginine-converting enzymes, as well as between the arginine-converting and arginine-synthesizing enzymes, determines the metabolic fate of arginine. Alternatively, NO can be derived from conversion of nitrite. Reduced arginine availability stemming from reduced de novo production and elevated arginase activity have been reported in various conditions of acute and chronic stress, which are often characterized by increased NOS2 and reduced NOS3 activity. Cardiovascular and pulmonary disorders such as atherosclerosis, diabetes, hypercholesterolemia, ischemic heart disease, and hypertension are characterized by NOS3 uncoupling. Therapeutic applications to influence (de novo) arginine and NO metabolism aim at increasing substrate availability or at influencing the metabolic fate of specific pathways related to NO bioavailability and prevention of NOS3 uncoupling. These include supplementation of arginine or citrulline, provision of NO donors including inhaled NO and nitrite (sources), NOS3 modulating agents, or the targeting of endogenous NOS inhibitors like asymmetric dimethylarginine.

  4. Effective de novo assembly of fish genome using haploid larvae.

    PubMed

    Iwasaki, Yuki; Nishiki, Issei; Nakamura, Yoji; Yasuike, Motoshige; Kai, Wataru; Nomura, Kazuharu; Yoshida, Kazunori; Nomura, Yousuke; Fujiwara, Atushi; Kobayashi, Takanori; Ototake, Mitsuru

    2016-02-01

    Recent improvements in next-generation sequencing technology have made it possible to do whole genome sequencing, on even non-model eukaryote species with no available reference genomes. However, de novo assembly of diploid genomes is still a big challenge because of allelic variation. The aim of this study was to determine the feasibility of utilizing the genome of haploid fish larvae for de novo assembly of whole-genome sequences. We compared the efficiency of assembly using the haploid genome of yellowtail (Seriola quinqueradiata) with that using the diploid genome obtained from the dam. De novo assembly from the haploid and the diploid sequence reads (100 million reads per each datasets) generated by the Ion Proton sequencer (200 bp) was done under two different assembly algorithms, namely overlap-layout-consensus (OLC) and de Bruijn graph (DBG). This revealed that the assembly of the haploid genome significantly reduced (approximately 22% for OLC, 9% for DBG) the total number of contigs (with longer average and N50 contig lengths) when compared to the diploid genome assembly. The haploid assembly also improved the quality of the scaffolds by reducing the number of regions with unassigned nucleotides (Ns) (total length of Ns; 45,331,916 bp for haploids and 67,724,360 bp for diploids) in OLC-based assemblies. It appears clear that the haploid genome assembly is better because the allelic variation in the diploid genome disrupts the extension of contigs during the assembly process. Our results indicate that utilizing the genome of haploid larvae leads to a significant improvement in the de novo assembly process, thus providing a novel strategy for the construction of reference genomes from non-model diploid organisms such as fish. PMID:26478467

  5. Effective de novo assembly of fish genome using haploid larvae.

    PubMed

    Iwasaki, Yuki; Nishiki, Issei; Nakamura, Yoji; Yasuike, Motoshige; Kai, Wataru; Nomura, Kazuharu; Yoshida, Kazunori; Nomura, Yousuke; Fujiwara, Atushi; Kobayashi, Takanori; Ototake, Mitsuru

    2016-02-01

    Recent improvements in next-generation sequencing technology have made it possible to do whole genome sequencing, on even non-model eukaryote species with no available reference genomes. However, de novo assembly of diploid genomes is still a big challenge because of allelic variation. The aim of this study was to determine the feasibility of utilizing the genome of haploid fish larvae for de novo assembly of whole-genome sequences. We compared the efficiency of assembly using the haploid genome of yellowtail (Seriola quinqueradiata) with that using the diploid genome obtained from the dam. De novo assembly from the haploid and the diploid sequence reads (100 million reads per each datasets) generated by the Ion Proton sequencer (200 bp) was done under two different assembly algorithms, namely overlap-layout-consensus (OLC) and de Bruijn graph (DBG). This revealed that the assembly of the haploid genome significantly reduced (approximately 22% for OLC, 9% for DBG) the total number of contigs (with longer average and N50 contig lengths) when compared to the diploid genome assembly. The haploid assembly also improved the quality of the scaffolds by reducing the number of regions with unassigned nucleotides (Ns) (total length of Ns; 45,331,916 bp for haploids and 67,724,360 bp for diploids) in OLC-based assemblies. It appears clear that the haploid genome assembly is better because the allelic variation in the diploid genome disrupts the extension of contigs during the assembly process. Our results indicate that utilizing the genome of haploid larvae leads to a significant improvement in the de novo assembly process, thus providing a novel strategy for the construction of reference genomes from non-model diploid organisms such as fish.

  6. Glucose-dependent de Novo Lipogenesis in B Lymphocytes

    PubMed Central

    Dufort, Fay J.; Gumina, Maria R.; Ta, Nathan L.; Tao, Yongzhen; Heyse, Shannon A.; Scott, David A.; Richardson, Adam D.; Seyfried, Thomas N.; Chiles, Thomas C.

    2014-01-01

    Bacterially derived lipopolysaccharide (LPS) stimulates naive B lymphocytes to differentiate into immunoglobulin (Ig)-secreting plasma cells. Differentiation of B lymphocytes is characterized by a proliferative phase followed by expansion of the intracellular membrane secretory network to support Ig production. A key question in lymphocyte biology is how naive B cells reprogram metabolism to support de novo lipogenesis necessary for proliferation and expansion of the endomembrane network in response to LPS. We report that extracellularly acquired glucose is metabolized, in part, to support de novo lipogenesis in response to LPS stimulation of splenic B lymphocytes. LPS stimulation leads to increased levels of endogenous ATP-citrate lyase (ACLY), and this is accompanied by increased ACLY enzymatic activity. ACLY produces cytosolic acetyl-CoA from mitochondrially derived citrate. Inhibition of ACLY activity in LPS-stimulated B cells with the selective inhibitor 2-hydroxy-N-arylbenzenesulfonamide (compound-9; C-9) blocks glucose incorporation into de novo lipid biosynthesis, including cholesterol, free fatty acids, and neutral and acidic phospholipids. Moreover, inhibition of ACLY activity in splenic B cells results in inhibition of proliferation and defective endomembrane expansion and reduced expression of CD138 and Blimp-1, markers for plasma-like B cell differentiation. ACLY activity is also required for LPS-induced IgM production in CH12 B lymphoma cells. These data demonstrate that ACLY mediates glucose-dependent de novo lipogenesis in response to LPS signaling and identify a role for ACLY in several phenotypic changes that define plasma cell differentiation. PMID:24469453

  7. Distorted color discrimination in 'de novo' parkinsonian patients.

    PubMed

    Büttner, T; Kuhn, W; Müller, T; Patzold, T; Heidbrink, K; Przuntek, H

    1995-02-01

    We performed the Farnsworth-Munsell 100-hue test in 16 "de novo" patients with Parkinson's disease and 16 age-matched controls to determine their color discrimination ability. The mean total error score in patients was significantly elevated as compared with controls (64.6 in patients versus 16.0 in controls). We conclude that the impairment of color discrimination may be an early sign in Parkinson's disease.

  8. IntraFace

    PubMed Central

    De la Torre, Fernando; Chu, Wen-Sheng; Xiong, Xuehan; Vicente, Francisco; Ding, Xiaoyu; Cohn, Jeffrey

    2016-01-01

    Within the last 20 years, there has been an increasing interest in the computer vision community in automated facial image analysis algorithms. This has been driven by applications in animation, market research, autonomous-driving, surveillance, and facial editing among others. To date, there exist several commercial packages for specific facial image analysis tasks such as facial expression recognition, facial attribute analysis or face tracking. However, free and easy-to-use software that incorporates all these functionalities is unavailable. This paper presents IntraFace (IF), a publicly-available software package for automated facial feature tracking, head pose estimation, facial attribute recognition, and facial expression analysis from video. In addition, IFincludes a newly develop technique for unsupervised synchrony detection to discover correlated facial behavior between two or more persons, a relatively unexplored problem in facial image analysis. In tests, IF achieved state-of-the-art results for emotion expression and action unit detection in three databases, FERA, CK+ and RU-FACS; measured audience reaction to a talk given by one of the authors; and discovered synchrony for smiling in videos of parent-infant interaction. IF is free of charge for academic use at http://www.humansensing.cs.cmu.edu/intraface/. PMID:27346987

  9. The Recent De Novo Origin of Protein C-Termini

    PubMed Central

    Andreatta, Matthew E.; Levine, Joshua A.; Foy, Scott G.; Guzman, Lynette D.; Kosinski, Luke J.; Cordes, Matthew H.J.; Masel, Joanna

    2015-01-01

    Protein-coding sequences can arise either from duplication and divergence of existing sequences, or de novo from noncoding DNA. Unfortunately, recently evolved de novo genes can be hard to distinguish from false positives, making their study difficult. Here, we study a more tractable version of the process of conversion of noncoding sequence into coding: the co-option of short segments of noncoding sequence into the C-termini of existing proteins via the loss of a stop codon. Because we study recent additions to potentially old genes, we are able to apply a variety of stringent quality filters to our annotations of what is a true protein-coding gene, discarding the putative proteins of unknown function that are typical of recent fully de novo genes. We identify 54 examples of C-terminal extensions in Saccharomyces and 28 in Drosophila, all of them recent enough to still be polymorphic. We find one putative gene fusion that turns out, on close inspection, to be the product of replicated assembly errors, further highlighting the issue of false positives in the study of rare events. Four of the Saccharomyces C-terminal extensions (to ADH1, ARP8, TPM2, and PIS1) that survived our quality filters are predicted to lead to significant modification of a protein domain structure. PMID:26002864

  10. Infant Mortality in Novo Hamburgo: Associated Factors and Cardiovascular Causes

    PubMed Central

    Brum, Camila de Andrade; Stein, Airton Tetelbom; Pellanda, Lucia Campos

    2015-01-01

    Background Infant mortality has decreased in Brazil, but remains high as compared to that of other developing countries. In 2010, the Rio Grande do Sul state had the lowest infant mortality rate in Brazil. However, the municipality of Novo Hamburgo had the highest infant mortality rate in the Porto Alegre metropolitan region. Objective To describe the causes of infant mortality in the municipality of Novo Hamburgo from 2007 to 2010, identifying which causes were related to heart diseases and if they were diagnosed in the prenatal period, and to assess the access to healthcare services. Methods This study assessed infants of the municipality of Novo Hamburgo, who died, and whose data were collected from the infant death investigation records. Results Of the 157 deaths in that period, 35.3% were reducible through diagnosis and early treatment, 25% were reducible through partnership with other sectors, 19.2% were non-preventable, 11.5% were reducible by means of appropriate pregnancy monitoring, 5.1% were reducible through appropriate delivery care, and 3.8% were ill defined. The major cause of death related to heart disease (13.4%), which was significantly associated with the variables ‘age at death’, ‘gestational age’ and ‘birth weight’. Regarding access to healthcare services, 60.9% of the pregnant women had a maximum of six prenatal visits. Conclusion It is mandatory to enhance prenatal care and newborn care at hospitals and basic healthcare units to prevent infant mortality. PMID:25993588

  11. FaceID: A face detection and recognition system

    SciTech Connect

    Shah, M.B.; Rao, N.S.V.; Olman, V.; Uberbacher, E.C.; Mann, R.C.

    1996-12-31

    A face detection system that automatically locates faces in gray-level images is described. Also described is a system which matches a given face image with faces in a database. Face detection in an Image is performed by template matching using templates derived from a selected set of normalized faces. Instead of using original gray level images, vertical gradient images were calculated and used to make the system more robust against variations in lighting conditions and skin color. Faces of different sizes are detected by processing the image at several scales. Further, a coarse-to-fine strategy is used to speed up the processing, and a combination of whole face and face component templates are used to ensure low false detection rates. The input to the face recognition system is a normalized vertical gradient image of a face, which is compared against a database using a set of pretrained feedforward neural networks with a winner-take-all fuser. The training is performed by using an adaptation of the backpropagation algorithm. This system has been developed and tested using images from the FERET database and a set of images obtained from Rowley, et al and Sung and Poggio.

  12. A novel thermal face recognition approach using face pattern words

    NASA Astrophysics Data System (ADS)

    Zheng, Yufeng

    2010-04-01

    A reliable thermal face recognition system can enhance the national security applications such as prevention against terrorism, surveillance, monitoring and tracking, especially at nighttime. The system can be applied at airports, customs or high-alert facilities (e.g., nuclear power plant) for 24 hours a day. In this paper, we propose a novel face recognition approach utilizing thermal (long wave infrared) face images that can automatically identify a subject at both daytime and nighttime. With a properly acquired thermal image (as a query image) in monitoring zone, the following processes will be employed: normalization and denoising, face detection, face alignment, face masking, Gabor wavelet transform, face pattern words (FPWs) creation, face identification by similarity measure (Hamming distance). If eyeglasses are present on a subject's face, an eyeglasses mask will be automatically extracted from the querying face image, and then masked with all comparing FPWs (no more transforms). A high identification rate (97.44% with Top-1 match) has been achieved upon our preliminary face dataset (of 39 subjects) from the proposed approach regardless operating time and glasses-wearing condition.e

  13. Disrupting perceptual grouping of face parts impairs holistic face processing.

    PubMed

    Curby, Kim M; Goldstein, Rebecca R; Blacker, Kara

    2013-01-01

    Face perception is widely believed to involve integration of facial features into a holistic perceptual unit, but the mechanisms underlying this integration are relatively unknown. We examined whether perceptual grouping cues influence a classic marker of holistic face perception, the "composite-face effect." Participants made same-different judgments about a cued part of sequentially presented chimeric faces, and holistic processing was indexed as the degree to which the task-irrelevant face halves impacted performance. Grouping was encouraged or discouraged by adjusting the backgrounds behind the face halves: Although the face halves were always aligned, their respective backgrounds could be misaligned and of different colors. Holistic processing of face, but not of nonface, stimuli was significantly reduced when the backgrounds were misaligned and of different colors, cues that discouraged grouping of the face halves into a cohesive unit (Exp. 1). This effect was sensitive to stimulus orientation at short (200 ms) but not at long (2,500 ms) encoding durations, consistent with the previously documented temporal properties of the holistic processing of upright and inverted faces (Exps. 2 and 3). These results suggest that grouping mechanisms, typically involved in the perception of objecthood more generally, might contribute in important ways to the holistic perception of faces.

  14. Robo-AO: Performance and Characterization at Palomar Observatory

    NASA Astrophysics Data System (ADS)

    Tendulkar, Shriharsh P.; Baranec, C.; Riddle, R. L.; Ramaprakash, A. N.; Law, N. M.; Kulkarni, S. R.; Dekany, R.; Bui, K.; Davis, J.; Burse, M.; Das, H.; Punnadi, S.; Chordia, P.

    2013-01-01

    Hosted at the Palomar 60-inch telescope, Robo-AO is the world's first completely autonomous, laser-beacon supported adaptive optics (AO) system, delivering diffraction-limited images in the visible and IR wavelengths. With simultaneous turbulence monitoring using a MASS-DIMM instrument, we have characterized the performance of Robo-AO as a function of local seeing, turbulence profile, laser return power and the brightness of the tip-tilt star. We shall present the various AO metrics: The full-width at half maxima of the point spread function, the Strehl ratio, the isoplanatic angle and their variations with the atmospheric and operating conditions. Strategies for optimizing robotic AO observations based on varying conditions will be discussed.

  15. Identification and Functional Relevance of de novo DNA Methylation in Cancerous B-Cell Populations

    PubMed Central

    Wang, Xiao-Ming; Greiner, Timothy C.; Bibikova, Marina; Pike, Brian L.; Siegmund, Kimberly D.; Sinha, Uttam K.; Müschen, Markus; Jaeger, Erich B.; Weisenburger, Dennis J.; Chan, Wing C.; Shibata, Darryl; Fan, Jian-Bing; Hacia, Joseph G.

    2011-01-01

    Epigenetic remodeling is a hallmark of cancer, with the frequent acquisition of de novo DNA methylation in CpG islands. However, the functional relevance of de novo DNA methylation in cancer is less well-defined. To begin to address this issue in B-cells, we used BeadArray assays to survey the methylation status of 1,500 cancer-related CpG loci in two molecular subtypes of diffuse large B-cell lymphoma (ABC-DLBCL and GCB-DLBCL) and cognate normal B-cell populations. We identified 81 loci that showed frequent de novo DNA methylation in GCB-DLBCL and 67 loci that showed frequent de novo DNA methylation in ABC-DLBCL. These de novo methylated CpG loci included reported targets of polycomb repressive complexes (PRC) in stem cells. All candidate loci in GCB-DLBCL are proximal to genes that are poorly expressed or silent in purified normal germinal center (GC) B-cells. This is consistent with the hypothesis that de novo DNA methylation in cancer is more frequently involved in the maintenance rather than the initiation of gene silencing (de novo repression). This suggests that epigenetic switching occurs during tumorigenesis with de novo DNA methylation locking in gene silencing normally mediated by transcriptional repressors. Furthermore, we propose that similar to de novo genetic mutations, the majority of de novo DNA methylation events observed in tumors are passengers not causally involved in tumorigenesis. PMID:20069569

  16. Face Processing: Models For Recognition

    NASA Astrophysics Data System (ADS)

    Turk, Matthew A.; Pentland, Alexander P.

    1990-03-01

    The human ability to process faces is remarkable. We can identify perhaps thousands of faces learned throughout our lifetime and read facial expression to understand such subtle qualities as emotion. These skills are quite robust, despite sometimes large changes in the visual stimulus due to expression, aging, and distractions such as glasses or changes in hairstyle or facial hair. Computers which model and recognize faces will be useful in a variety of applications, including criminal identification, human-computer interface, and animation. We discuss models for representing faces and their applicability to the task of recognition, and present techniques for identifying faces and detecting eye blinks.

  17. Face lift postoperative recovery.

    PubMed

    Mottura, A Aldo

    2002-01-01

    The purpose of this paper is to describe what I have studied and experienced, mainly regarding the control and prediction of the postoperative edema; how to achieve an agreeable recovery and give positive support to the patient, who in turn will receive pleasant sensations that neutralize the negative consequences of the surgery.After the skin is lifted, the drainage flow to the flaps is reversed abruptly toward the medial part of the face, where the flap bases are located. The thickness and extension of the flap determines the magnitude of the post-op edema, which is also augmented by medial surgeries (blepharo, rhino) whose trauma obstruct their natural drainage, increasing the congestion and edema. To study the lymphatic drainage, the day before an extended face lift (FL) a woman was infiltrated in the cheek skin with lynfofast (solution of tecmesio) and the absorption was observed by gamma camera. Seven days after the FL she underwent the same study; we observed no absorption by the lymphatic, concluding that a week after surgery, the lymphatic network was still damaged. To study the venous return during surgery, a fine catheter was introduced into the external jugular vein up to the mandibular border to measure the peripheral pressure. Following platysma plication the pressure rose, and again after a simple bandage, but with an elastic bandage it increased even further, diminishing considerably when it was released. Hence, platysma plication and the elastic bandage on the neck augment the venous congestion of the face. There are diseases that produce and can prolong the surgical edema: cardiac, hepatic, and renal insufficiencies, hypothyroidism, malnutrition, etc. According to these factors, the post-op edema can be predicted, the surgeon can choose between a wide dissection or a medial surgery, depending on the social or employment compromises the patient has, or the patient must accept a prolonged recovery if a complex surgery is necessary. Operative

  18. Energy conservation using face detection

    NASA Astrophysics Data System (ADS)

    Deotale, Nilesh T.; Kalbande, Dhananjay R.; Mishra, Akassh A.

    2011-10-01

    Computerized Face Detection, is concerned with the difficult task of converting a video signal of a person to written text. It has several applications like face recognition, simultaneous multiple face processing, biometrics, security, video surveillance, human computer interface, image database management, digital cameras use face detection for autofocus, selecting regions of interest in photo slideshows that use a pan-and-scale and The Present Paper deals with energy conservation using face detection. Automating the process to a computer requires the use of various image processing techniques. There are various methods that can be used for Face Detection such as Contour tracking methods, Template matching, Controlled background, Model based, Motion based and color based. Basically, the video of the subject are converted into images are further selected manually for processing. However, several factors like poor illumination, movement of face, viewpoint-dependent Physical appearance, Acquisition geometry, Imaging conditions, Compression artifacts makes Face detection difficult. This paper reports an algorithm for conservation of energy using face detection for various devices. The present paper suggests Energy Conservation can be done by Detecting the Face and reducing the brightness of complete image and then adjusting the brightness of the particular area of an image where the face is located using histogram equalization.

  19. First closed-loop visible AO test results for the advanced adaptive secondary AO system for the Magellan Telescope: MagAO's performance and status

    NASA Astrophysics Data System (ADS)

    Close, Laird M.; Males, Jared R.; Kopon, Derek A.; Gasho, Victor; Follette, Katherine B.; Hinz, Phil; Morzinski, Katie; Uomoto, Alan; Hare, Tyson; Riccardi, Armando; Esposito, Simone; Puglisi, Alfio; Pinna, Enrico; Busoni, Lorenzo; Arcidiacono, Carmelo; Xompero, Marco; Briguglio, Runa; Quiros-Pacheco, Fernando; Argomedo, Javier

    2012-07-01

    The heart of the 6.5 Magellan AO system (MagAO) is a 585 actuator adaptive secondary mirror (ASM) with <1 msec response times (0.7 ms typically). This adaptive secondary will allow low emissivity and high-contrast AO science. We fabricated a high order (561 mode) pyramid wavefront sensor (similar to that now successfully used at the Large Binocular Telescope). The relatively high actuator count (and small projected ~23 cm pitch) allows moderate Strehls to be obtained by MagAO in the “visible” (0.63-1.05 μm). To take advantage of this we have fabricated an AO CCD science camera called "VisAO". Complete “end-to-end” closed-loop lab tests of MagAO achieve a solid, broad-band, 37% Strehl (122 nm rms) at 0.76 μm (i’) with the VisAO camera in 0.8” simulated seeing (13 cm ro at V) with fast 33 mph winds and a 40 m Lo locked on R=8 mag artificial star. These relatively high visible wavelength Strehls are enabled by our powerful combination of a next generation ASM and a Pyramid WFS with 400 controlled modes and 1000 Hz sample speeds (similar to that used successfully on-sky at the LBT). Currently only the VisAO science camera is used for lab testing of MagAO, but this high level of measured performance (122 nm rms) promises even higher Strehls with our IR science cameras. On bright (R=8 mag) stars we should achieve very high Strehls (>70% at H) in the IR with the existing MagAO Clio2 (λ=1-5.3 μm) science camera/coronagraph or even higher (~98% Strehl) the Mid-IR (8-26 microns) with the existing BLINC/MIRAC4 science camera in the future. To eliminate non-common path vibrations, dispersions, and optical errors the VisAO science camera is fed by a common path advanced triplet ADC and is piggy-backed on the Pyramid WFS optical board itself. Also a high-speed shutter can be used to block periods of poor correction. The entire system passed CDR in June 2009, and we finished the closed-loop system level testing phase in December 2011. Final system acceptance (

  20. Face recognition performance with superresolution.

    PubMed

    Hu, Shuowen; Maschal, Robert; Young, S Susan; Hong, Tsai Hong; Phillips, P Jonathon

    2012-06-20

    With the prevalence of surveillance systems, face recognition is crucial to aiding the law enforcement community and homeland security in identifying suspects and suspicious individuals on watch lists. However, face recognition performance is severely affected by the low face resolution of individuals in typical surveillance footage, oftentimes due to the distance of individuals from the cameras as well as the small pixel count of low-cost surveillance systems. Superresolution image reconstruction has the potential to improve face recognition performance by using a sequence of low-resolution images of an individual's face in the same pose to reconstruct a more detailed high-resolution facial image. This work conducts an extensive performance evaluation of superresolution for a face recognition algorithm using a methodology and experimental setup consistent with real world settings at multiple subject-to-camera distances. Results show that superresolution image reconstruction improves face recognition performance considerably at the examined midrange and close range. PMID:22722306

  1. Face recognition based tensor structure

    NASA Astrophysics Data System (ADS)

    Yang, De-qiang; Ye, Zhi-xia; Zhao, Yang; Liu, Li-mei

    2012-01-01

    Face recognition has broad applications, and it is a difficult problem since face image can change with photographic conditions, such as different illumination conditions, pose changes and camera angles. How to obtain some invariable features for a face image is the key issue for a face recognition algorithm. In this paper, a novel tensor structure of face image is proposed to represent image features with eight directions for a pixel value. The invariable feature of the face image is then obtained from gradient decomposition to make up the tensor structure. Then the singular value decomposition (SVD) and principal component analysis (PCA) of this tensor structure are used for face recognition. The experimental results from this study show that many difficultly recognized samples can correctly be recognized, and the recognition rate is increased by 9%-11% in comparison with same type of algorithms.

  2. Face recognition performance with superresolution.

    PubMed

    Hu, Shuowen; Maschal, Robert; Young, S Susan; Hong, Tsai Hong; Phillips, P Jonathon

    2012-06-20

    With the prevalence of surveillance systems, face recognition is crucial to aiding the law enforcement community and homeland security in identifying suspects and suspicious individuals on watch lists. However, face recognition performance is severely affected by the low face resolution of individuals in typical surveillance footage, oftentimes due to the distance of individuals from the cameras as well as the small pixel count of low-cost surveillance systems. Superresolution image reconstruction has the potential to improve face recognition performance by using a sequence of low-resolution images of an individual's face in the same pose to reconstruct a more detailed high-resolution facial image. This work conducts an extensive performance evaluation of superresolution for a face recognition algorithm using a methodology and experimental setup consistent with real world settings at multiple subject-to-camera distances. Results show that superresolution image reconstruction improves face recognition performance considerably at the examined midrange and close range.

  3. [Comparative studies of face recognition].

    PubMed

    Kawai, Nobuyuki

    2012-07-01

    Every human being is proficient in face recognition. However, the reason for and the manner in which humans have attained such an ability remain unknown. These questions can be best answered-through comparative studies of face recognition in non-human animals. Studies in both primates and non-primates show that not only primates, but also non-primates possess the ability to extract information from their conspecifics and from human experimenters. Neural specialization for face recognition is shared with mammals in distant taxa, suggesting that face recognition evolved earlier than the emergence of mammals. A recent study indicated that a social insect, the golden paper wasp, can distinguish their conspecific faces, whereas a closely related species, which has a less complex social lifestyle with just one queen ruling a nest of underlings, did not show strong face recognition for their conspecifics. Social complexity and the need to differentiate between one another likely led humans to evolve their face recognition abilities.

  4. AO 0235+164 and Surrounding Field: Surprising HST Results

    NASA Technical Reports Server (NTRS)

    Burbidge, E. M.; Beaver, E. A.; Cohen, Ross D.; Junkkarinen, V. T.; Lyons, R. W.

    1996-01-01

    Results obtained with the Hubble Space Telescope on the highly variable radio, x-ray, and gamma-ray emitting QSO (or BL Lac object) AO 0235 + 164 are presented and analyzed. WFPC2 images were obtained in 1994 June, when AO 0235 + 164 was bright (m approx. 17), and the results are described in Sec. 3. After subtraction of the PSF of the QSO, hereafter called AO following the nomenclature of Yanny et al. (1989), the companion object named A, 2 sec south of AO, is discovered not to be an elliptical galaxy as hypothesized earlier, but to be an AGN object, with a central UV-bright point-source nucleus and faint surrounding nebulosity extending to AO. The second companion object 1.3 sec east of AO discovered by Yanny et al. (1989) and named object Al, appears more like a normal spiral galaxy. We have measured the positions, luminosities, and colors of some 30 faint objects in the field around AO 0235 + 16; most are extended and may be star-forming galaxies in a loose group or cluster. Our most surprising result of the HST observations comes from FOS spectra obtained in 1995 July, discussed in Sec. 4. Because of a positioning error of the telescope and AO's faintness at that time (m approx. 20), object A was observed instead of the intended target AO. Serendipitously, we discovered A to have broad deep BALQSO-type absorptions of C IV, Si IV, N V shortward of broad emissions. A is thus ejecting high velocity, highly ionized gas into the surrounding IGM. We discuss in Sec. 5 the relationship of the objects in the central 10 sec X 1O sec region around AO, where redshifts z(sub e) = 0.94, z(sub a) = 0.524, 0.851 in AO, (sub e) = 0.524 and Z(sub BAL)=0.511 in A, are found. We hypothesize that some of the 30 faint objects in the 77 sec. x 77 sec. field may be part of a large star-forming region at z approx. 0.5, as suggested for a few objects by Yanny et al. (1989). The proximity of two highly active extragalactic objects, AO 0235+164 and its AGN companion A, is remarkable and

  5. The Subaru Coronagraphic Extreme AO Project: Progress and Upgrades

    NASA Astrophysics Data System (ADS)

    Jovanovic, Nemanja; Martinache, F.; Guyon, O.; Clergeon, C.; Garrel, V.

    2013-01-01

    The Subaru Coronagraphic Extreme AO (SCExAO) instrument consists of a high performance Phase Induced Amplitude Apodisation (PIAA) coronagraph combined with an extreme Adaptive Optics (AO) system operating in the near-infrared (H band). The extreme AO system driven by the 2000 element deformable mirror will allow for Strehl ratios>90% to be achieved in the H-band when it goes closed loop. This makes the SCExAO instrument a powerful platform for high contrast imaging down to angular separations of the order of 1 λ/D. In this paper we report on the recent progress in regards to the development of the instrument, which includes the addition of a visible bench that makes use of the light at shorter wavelengths not currently utilized by SCExAO and closing the loop on the tip/tilt wavefront sensor. We will also discuss two exciting guest instruments which will expand the capabilities of SCExAO over the next few years; namely CHARIS which is a integral field spectrograph as well as VAMPIRES, a visible aperture masking experiment based on polarimetric analysis of circumstellar disks.

  6. [A review of face illusions].

    PubMed

    Kitaoka, Akiyoshi

    2012-07-01

    A variety of "face illusions," including the gaze illusion, face inversion effects, geometrical illusions, reversible figures, and other interesting phenomena related to face perception, are reviewed in the present report, with many sample images. The "gaze illusion" or the illusion of eye direction includes the Wollaston illusion, the luminance-induced gaze shift, the Bogart illusion, the eye-shadow-dependent gaze illusion, the Mona Lisa effect, etc. "Face inversion effects" refer to the Thatcher illusion, the fat face-thin illusion, underestimation of the upright face, the nose-shortening illusion of the inverted face, etc. "Geometrical illusions" include the Lee-Freire illusion, Yang's iris illusion, overestimation of the farther eye, the eye-shadow-dependent eye-size illusion, etc. "Reversible figures" contain the whole-part reversible figure, Rubin's vase-face illusion, or hybrid images. "Other interesting phenomena" include the flashed face distortion effect, the presidential illusion, predominance of the mouth or eyebrows over eye expression, the eye direction aftereffect, etc. It is suggested that some of these phenomena are highly specific to face perception.

  7. Holistic crowding of Mooney faces.

    PubMed

    Farzin, Faraz; Rivera, Susan M; Whitney, David

    2009-06-29

    An object or feature is generally more difficult to identify when other objects are presented nearby, an effect referred to as crowding. Here, we used Mooney faces to examine whether crowding can also occur within and between holistic face representations (C. M. Mooney, 1957). Mooney faces are ideal stimuli for this test because no cues exist to distinguish facial features in a Mooney face; to find any facial feature, such as an eye or a nose, one must first holistically perceive the image as a face. Through a series of six experiments we tested the effect of crowding on Mooney face recognition. Our results demonstrate crowding between and within Mooney faces and fulfill the diagnostic criteria for crowding, including eccentricity dependence and lack of crowding in the fovea, critical flanker spacing consistent with less than half the eccentricity of the target, and inner-outer flanker asymmetry. Further, our results show that recognition of an upright Mooney face is more strongly impaired by upright Mooney face flankers than inverted ones. Taken together, these results suggest crowding can occur selectively between high-level representations of faces and that crowding must occur at multiple levels in the visual system.

  8. Face-n-Food: Gender Differences in Tuning to Faces

    PubMed Central

    Pavlova, Marina A.; Scheffler, Klaus; Sokolov, Alexander N.

    2015-01-01

    Faces represent valuable signals for social cognition and non-verbal communication. A wealth of research indicates that women tend to excel in recognition of facial expressions. However, it remains unclear whether females are better tuned to faces. We presented healthy adult females and males with a set of newly created food-plate images resembling faces (slightly bordering on the Giuseppe Arcimboldo style). In a spontaneous recognition task, participants were shown a set of images in a predetermined order from the least to most resembling a face. Females not only more readily recognized the images as a face (they reported resembling a face on images, on which males still did not), but gave on overall more face responses. The findings are discussed in the light of gender differences in deficient face perception. As most neuropsychiatric, neurodevelopmental and psychosomatic disorders characterized by social brain abnormalities are sex specific, the task may serve as a valuable tool for uncovering impairments in visual face processing. PMID:26154177

  9. About-face on face recognition ability and holistic processing.

    PubMed

    Richler, Jennifer J; Floyd, R Jackie; Gauthier, Isabel

    2015-01-01

    Previous work found a small but significant relationship between holistic processing measured with the composite task and face recognition ability measured by the Cambridge Face Memory Test (CFMT; Duchaine & Nakayama, 2006). Surprisingly, recent work using a different measure of holistic processing (Vanderbilt Holistic Face Processing Test [VHPT-F]; Richler, Floyd, & Gauthier, 2014) and a larger sample found no evidence for such a relationship. In Experiment 1 we replicate this unexpected result, finding no relationship between holistic processing (VHPT-F) and face recognition ability (CFMT). A key difference between the VHPT-F and other holistic processing measures is that unique face parts are used on each trial in the VHPT-F, unlike in other tasks where a small set of face parts repeat across the experiment. In Experiment 2, we test the hypothesis that correlations between the CFMT and holistic processing tasks are driven by stimulus repetition that allows for learning during the composite task. Consistent with our predictions, CFMT performance was correlated with holistic processing in the composite task when a small set of face parts repeated over trials, but not when face parts did not repeat. A meta-analysis confirms that relationships between the CFMT and holistic processing depend on stimulus repetition. These results raise important questions about what is being measured by the CFMT, and challenge current assumptions about why faces are processed holistically.

  10. SCExAO: First Results and On-Sky Performance

    NASA Astrophysics Data System (ADS)

    Currie, Thayne; Guyon, Olivier; Martinache, Frantz; Clergeon, Christophe; McElwain, Michael; Thalmann, Christian; Jovanovic, Nemanja; Singh, Garima; Kudo, Tomoyuki

    2014-01-01

    We present new on-sky results for the Subaru Coronagraphic Extreme Adaptive Optics imager (SCExAO) verifying and quantifying the contrast gain enabled by key components: the closed-loop coronagraphic low-order wavefront sensor (CLOWFS) and focal plane wavefront control (``speckle nulling''). SCExAO will soon be coupled with a high-order, Pyramid wavefront sensor which will yield > 90% Strehl ratio and enable 106-107 contrast at small angular separations allowing us to image gas giant planets at solar system scales. Upcoming instruments like VAMPIRES, FIRST, and CHARIS will expand SCExAO's science capabilities.

  11. SCExAO: First Results and On-Sky Performance

    NASA Technical Reports Server (NTRS)

    Currie, Thayne; Guyon, Olivier; Martinache, Frantz; Clergeon, Christophe; McElwain, Michael; Thalmann, Christian; Jovanovic, Nemanja; Singh, Garima; Kudo, Tomoyuki

    2013-01-01

    We present new on-sky results for the Subaru Coronagraphic Extreme Adaptive Optics imager (SCExAO) verifying and quantifying the contrast gain enabled by key components: the closed-loop coronagraphic low-order wavefront sensor (CLOWFS) and focal plane wavefront control ("speckle nulling"). SCExAO will soon be coupled with a high-order, Pyramid wavefront sensor which will yield greater than 90% Strehl ratio and enable 10(exp 6) -10(exp 7) contrast at small angular separations allowing us to image gas giant planets at solar system scales. Upcoming instruments like VAMPIRES, FIRST, and CHARIS will expand SCExAO's science capabilities.

  12. Informed kmer selection for de novo transcriptome assembly

    PubMed Central

    Durai, Dilip A.; Schulz, Marcel H.

    2016-01-01

    Motivation: De novo transcriptome assembly is an integral part for many RNA-seq workflows. Common applications include sequencing of non-model organisms, cancer or meta transcriptomes. Most de novo transcriptome assemblers use the de Bruijn graph (DBG) as the underlying data structure. The quality of the assemblies produced by such assemblers is highly influenced by the exact word length k. As such no single kmer value leads to optimal results. Instead, DBGs over different kmer values are built and the assemblies are merged to improve sensitivity. However, no studies have investigated thoroughly the problem of automatically learning at which kmer value to stop the assembly. Instead a suboptimal selection of kmer values is often used in practice. Results: Here we investigate the contribution of a single kmer value in a multi-kmer based assembly approach. We find that a comparative clustering of related assemblies can be used to estimate the importance of an additional kmer assembly. Using a model fit based algorithm we predict the kmer value at which no further assemblies are necessary. Our approach is tested with different de novo assemblers for datasets with different coverage values and read lengths. Further, we suggest a simple post processing step that significantly improves the quality of multi-kmer assemblies. Conclusion: We provide an automatic method for limiting the number of kmer values without a significant loss in assembly quality but with savings in assembly time. This is a step forward to making multi-kmer methods more reliable and easier to use. Availability and Implementation:A general implementation of our approach can be found under: https://github.com/SchulzLab/KREATION. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: mschulz@mmci.uni-saarland.de PMID:27153653

  13. Open questions in the study of de novo genes: what, how and why.

    PubMed

    McLysaght, Aoife; Hurst, Laurence D

    2016-09-01

    The study of de novo protein-coding genes is maturing from the ad hoc reporting of individual cases to the systematic analysis of extensive genomic data from several species. We identify three key challenges for this emerging field: understanding how best to identify de novo genes, how they arise and why they spread. We highlight the intellectual challenges of understanding how a de novo gene becomes integrated into pre-existing functions and becomes essential. We suggest that, as with protein sequence evolution, antagonistic co-evolution may be key to de novo gene evolution, particularly for new essential genes and new cancer-associated genes. PMID:27452112

  14. De novo sequencing of unique sequence tags for discovery of post-translational modifications of proteins

    SciTech Connect

    Shen, Yufeng; Tolic, Nikola; Hixson, Kim K.; Purvine, Samuel O.; Anderson, Gordon A.; Smith, Richard D.

    2008-10-15

    De novo sequencing has a promise to discover the protein post-translation modifications; however, such approach is still in their infancy and not widely applied for proteomics practices due to its limited reliability. In this work, we describe a de novo sequencing approach for discovery of protein modifications through identification of the UStags (Anal. Chem. 2008, 80, 1871-1882). The de novo information was obtained from Fourier-transform tandem mass spectrometry for peptides and polypeptides in a yeast lysate, and the de novo sequences obtained were filtered to define a more limited set of UStags. The DNA-predicted database protein sequences were then compared to the UStags, and the differences observed across or in the UStags (i.e., the UStags’ prefix and suffix sequences and the UStags themselves) were used to infer the possible sequence modifications. With this de novo-UStag approach, we uncovered some unexpected variances of yeast protein sequences due to amino acid mutations and/or multiple modifications to the predicted protein sequences. Random matching of the de novo sequences to the predicted sequences were examined with use of two random (false) databases, and ~3% false discovery rates were estimated for the de novo-UStag approach. The factors affecting the reliability (e.g., existence of de novo sequencing noise residues and redundant sequences) and the sensitivity are described. The de novo-UStag complements the UStag method previously reported by enabling discovery of new protein modifications.

  15. Interpreting de novo variation in human disease using denovolyzeR

    PubMed Central

    Samocha, Kaitlin E.; Homsy, Jason; Daly, Mark J.

    2015-01-01

    Spontaneously arising (de novo) genetic variants are important in human disease, yet every individual carries many such variants, with a median of 1 de novo variant affecting the protein-coding portion of the genome. A recently described mutational model (Samocha et al., 2014) provides a powerful framework for the robust statistical evaluation of such coding variants, enabling the interpretation of de novo variation in human disease. Here we describe a new open-source software package, denovolyzeR, that implements this model and provides tools for the analysis of de novo coding sequence variants. PMID:26439716

  16. Holistic face training enhances face processing in developmental prosopagnosia

    PubMed Central

    Cohan, Sarah; Nakayama, Ken

    2014-01-01

    Prosopagnosia has largely been regarded as an untreatable disorder. However, recent case studies using cognitive training have shown that it is possible to enhance face recognition abilities in individuals with developmental prosopagnosia. Our goal was to determine if this approach could be effective in a larger population of developmental prosopagnosics. We trained 24 developmental prosopagnosics using a 3-week online face-training program targeting holistic face processing. Twelve subjects with developmental prosopagnosia were assessed before and after training, and the other 12 were assessed before and after a waiting period, they then performed the training, and were then assessed again. The assessments included measures of front-view face discrimination, face discrimination with view-point changes, measures of holistic face processing, and a 5-day diary to quantify potential real-world improvements. Compared with the waiting period, developmental prosopagnosics showed moderate but significant overall training-related improvements on measures of front-view face discrimination. Those who reached the more difficult levels of training (‘better’ trainees) showed the strongest improvements in front-view face discrimination and showed significantly increased holistic face processing to the point of being similar to that of unimpaired control subjects. Despite challenges in characterizing developmental prosopagnosics’ everyday face recognition and potential biases in self-report, results also showed modest but consistent self-reported diary improvements. In summary, we demonstrate that by using cognitive training that targets holistic processing, it is possible to enhance face perception across a group of developmental prosopagnosics and further suggest that those who improved the most on the training task received the greatest benefits. PMID:24691394

  17. Holistic face training enhances face processing in developmental prosopagnosia.

    PubMed

    DeGutis, Joseph; Cohan, Sarah; Nakayama, Ken

    2014-06-01

    Prosopagnosia has largely been regarded as an untreatable disorder. However, recent case studies using cognitive training have shown that it is possible to enhance face recognition abilities in individuals with developmental prosopagnosia. Our goal was to determine if this approach could be effective in a larger population of developmental prosopagnosics. We trained 24 developmental prosopagnosics using a 3-week online face-training program targeting holistic face processing. Twelve subjects with developmental prosopagnosia were assessed before and after training, and the other 12 were assessed before and after a waiting period, they then performed the training, and were then assessed again. The assessments included measures of front-view face discrimination, face discrimination with view-point changes, measures of holistic face processing, and a 5-day diary to quantify potential real-world improvements. Compared with the waiting period, developmental prosopagnosics showed moderate but significant overall training-related improvements on measures of front-view face discrimination. Those who reached the more difficult levels of training ('better' trainees) showed the strongest improvements in front-view face discrimination and showed significantly increased holistic face processing to the point of being similar to that of unimpaired control subjects. Despite challenges in characterizing developmental prosopagnosics' everyday face recognition and potential biases in self-report, results also showed modest but consistent self-reported diary improvements. In summary, we demonstrate that by using cognitive training that targets holistic processing, it is possible to enhance face perception across a group of developmental prosopagnosics and further suggest that those who improved the most on the training task received the greatest benefits.

  18. De Novo Designed Imaging Agents Based on Lanthanide Peptides Complexes.

    PubMed

    Peacock, A F A

    2016-01-01

    Herein are discussed a selection of lanthanide peptide/protein complexes in view of their potential applications as imaging agents, both in terms of luminescence detection and magnetic resonance imaging. Though this chapter covers a range of different peptides and protein, if focuses specifically on the opportunities afforded by the de novo design of coiled coils, miniature protein scaffolds, and the development on lanthanide-binding sites into these architectures. The requirements for lanthanide coordination and the challenges that need to be addressed when preparing lanthanide peptides with a view to their potential adoption as clinical imaging applications, will be highlighted. PMID:27586349

  19. The coming of age of de novo protein design.

    PubMed

    Huang, Po-Ssu; Boyken, Scott E; Baker, David

    2016-01-01

    There are 20(200) possible amino-acid sequences for a 200-residue protein, of which the natural evolutionary process has sampled only an infinitesimal subset. De novo protein design explores the full sequence space, guided by the physical principles that underlie protein folding. Computational methodology has advanced to the point that a wide range of structures can be designed from scratch with atomic-level accuracy. Almost all protein engineering so far has involved the modification of naturally occurring proteins; it should now be possible to design new functional proteins from the ground up to tackle current challenges in biomedicine and nanotechnology. PMID:27629638

  20. De novo periaortic fibrosis after endovascular aortic repair.

    PubMed

    Alomran, Faris; de Blic, Romain; Mallios, Alexandros; Costanzo, Alessandro; Boura, Benoit; Combes, Myriam

    2014-02-01

    We report a case of a 63-year-old man presenting with abdominal pain and hydronephrosis secondary to periaortic fibrosis (PAF) 8 months after an endovascular aortic repair (EVAR) using a woven polyester bifurcated graft. De novo delayed PAF after open repair is rare and even more infrequent after EVAR. All 3 previously reported cases occurred after woven polyester grafts and no reported cases after polytetrafluorethylene grafts. Management included steroidal anti-inflammatory treatment and bilateral double J tube placement. Satisfactory results were obtained. PMID:24275428

  1. The carbon isotopic composition of Novo Urei diamonds

    NASA Technical Reports Server (NTRS)

    Fisenko, A. V.; Semjenova, L. F.; Verchovsky, A. B.; Russell, S. S.; Pillinger, C. T.

    1993-01-01

    The carbon isotopic composition of diamond grains isolated from the Novo Urei meteorite are discussed. A diamond separate was obtained from 2g of whole rock using the chemical treatments described aimed at obtaining very pure diamond. X ray diffraction of the residue, which represented 5000 ppm of the parent mass, indicated only the presence of the desired mineral. The diamond crystals were 1-30 microns in diameter, and some grains had a yellow color. The chemical treatments were followed by a size separation to give a 1-10 microns and a 5-30 microns fraction, which were named DNU-1 and DNU-2, respectively.

  2. RNAbrowse: RNA-Seq de novo assembly results browser.

    PubMed

    Mariette, Jérôme; Noirot, Céline; Nabihoudine, Ibounyamine; Bardou, Philippe; Hoede, Claire; Djari, Anis; Cabau, Cédric; Klopp, Christophe

    2014-01-01

    Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quite diverse. This article presents a user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data. The software package is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/RNAbrowse. PMID:24823498

  3. RNAbrowse: RNA-Seq De Novo Assembly Results Browser

    PubMed Central

    Mariette, Jérôme; Noirot, Céline; Nabihoudine, Ibounyamine; Bardou, Philippe; Hoede, Claire; Djari, Anis; Cabau, Cédric; Klopp, Christophe

    2014-01-01

    Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quite diverse. This article presents a user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data. The software package is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/RNAbrowse. PMID:24823498

  4. The stereographic analysis of facing

    NASA Astrophysics Data System (ADS)

    Holdsworth, Robert E.

    Facing directions represent an accurate means by which tectonic structure and sedimentary way-up may be related. A simple method is presented for determining facing directions accurately, using a stereonet. Once determined, larger amounts of facing data can be quickly collated and analysed using similar techniques to those employed for other lineations. An example is given for some sheath fold structures in the Moine rocks of Sutherland, N. Scotland.

  5. A Tilted-Trough Mechanism for AO/NAO

    NASA Astrophysics Data System (ADS)

    Jin, F.; Kimoto, M.; Watanabe, M.; Pan, L.; Yasutomi, N.

    2001-12-01

    The least damped mode of the linear atmospheric dynamic system with the zonal mean flow interacting with stationary waves is shown to bear much resemblance to the observed Arctic Oscillation (AO)in terms of both zonal and associated stationary wave components. This AO-like mode results from the dynamic self-organization among the components of zonal mean flow and the associated stationary waves through a so-called tilted-trough positive feedback. Namely, the anomalous AO-like sheared zonal flow generates the associated anomaly in stationary waves in such a way that the tilts of the total stationary waves are altered to reinforce the sheared zonal-flow anomaly through the anomalous momentum flux convergence. Thus the AO-like least damped mode, which can be excited by surface or other forcing, is expected to be dominant over monthly and longer time scales.

  6. Holistic processing predicts face recognition.

    PubMed

    Richler, Jennifer J; Cheung, Olivia S; Gauthier, Isabel

    2011-04-01

    The concept of holistic processing is a cornerstone of face-recognition research. In the study reported here, we demonstrated that holistic processing predicts face-recognition abilities on the Cambridge Face Memory Test and on a perceptual face-identification task. Our findings validate a large body of work that relies on the assumption that holistic processing is related to face recognition. These findings also reconcile the study of face recognition with the perceptual-expertise work it inspired; such work links holistic processing of objects with people's ability to individuate them. Our results differ from those of a recent study showing no link between holistic processing and face recognition. This discrepancy can be attributed to the use in prior research of a popular but flawed measure of holistic processing. Our findings salvage the central role of holistic processing in face recognition and cast doubt on a subset of the face-perception literature that relies on a problematic measure of holistic processing.

  7. LGS-AO Imaging of Every Kepler Planet Candidate: the Robo-AO KOI Survey

    NASA Astrophysics Data System (ADS)

    Law, Nicholas Michael; Baranec, Christoph; Morton, Timothy; Ziegler, Carl; Atkinson, Dani; Riddle, Reed

    2015-08-01

    The Robo-AO Kepler Planetary Candidate Survey is observing every Kepler planet candidate host star with laser adaptive optics imaging, to search for blended nearby stars which may be physically associated companions and/or responsible for transit false positives. We will present the results from searching for companions around over 3,000 Kepler planet hosts in 2012-2015. We will describe our first data release covering 715 planet candidate hosts, and give a preview of ongoing results including improved statistics on the likelihood of false positive planet detections in the Kepler dataset, many new planets in multiple star systems, and new exotic multiple star systems containing Kepler planets.We will also describe the automated Robo-AO survey data reduction methods, including a method of using the large ensemble of target observations as mutual point-spread-function references, along with a new automated companion-detection algorithm designed for extremely large adaptive optics surveys.Our first data release covered 715 objects, searching for companions from 0.15” to 2.5” separation with contrast up to 6 magnitudes. We measured the overall nearby-star-probability for Kepler planet candidates to be 7.4+/-1.0%, and we will detail the variations in this number with stellar host parameters. We will also discuss several KOIs of particular interest, including KOI-191 and KOI-1151, which are both multi-planet systems with detected stellar companions whose unusual planetary system architecture might be best explained if they are ``coincident multiple'' systems, with several transiting planets shared between the two stars. Finally, we will discuss and update the 98%-confidence evidence from our survey that third bodies in star/planet systems produce an excess of close-in giant planets.

  8. Cyber- and Face-to-Face Bullying: Who Crosses Over?

    ERIC Educational Resources Information Center

    Shin, Hwayeon Helene; Braithwaite, Valerie; Ahmed, Eliza

    2016-01-01

    A total of 3956 children aged 12-13 years who completed the Longitudinal Study of Australian Children (LSAC Wave 5) were studied about their experiences of traditional face-to-face bullying and cyberbullying in the last month. In terms of prevalence, sixty percent of the sample had been involved in traditional bullying as the victim and/or the…

  9. Teaching On-Line versus Face-to-Face.

    ERIC Educational Resources Information Center

    Smith, Glenn Gordon; Ferguson, David; Caris, Mieke

    2002-01-01

    Investigates and describes the current instructor experience of teaching college courses over the Web versus in face-to-face formats in terms of teaching strategies, social issues, and media effects. Discusses communication styles, relationship between students and instructors, instructor workload, and discussion patterns, and proposes a model…

  10. Effects of aging on face identification and holistic face processing.

    PubMed

    Konar, Yaroslav; Bennett, Patrick J; Sekuler, Allison B

    2013-08-01

    Several studies have shown that face identification accuracy is lower in older than younger adults. This effect of aging might be due to age differences in holistic processing, which is thought to be an important component of human face processing. Currently, however, there is conflicting evidence as to whether holistic face processing is impaired in older adults. The current study therefore re-examined this issue by measuring response accuracy in a 1-of-4 face identification task and the composite face effect (CFE), a common index of holistic processing, in older adults. Consistent with previous reports, we found that face identification accuracy was lower in older adults than in younger adults tested in the same task. We also found a significant CFE in older adults that was similar in magnitude to the CFE measured in younger subjects with the same task. Finally, we found that there was a significant positive correlation between the CFE and face identification accuracy. This last result differs from the results obtained in a previous study that used the same tasks and which found no evidence of an association between the CFE and face identification accuracy in younger adults. Furthermore, the age difference was found with subtraction-, regression-, and ratio-based estimates of the CFE. The current findings are consistent with previous claims that older adults rely more heavily on holistic processing to identify objects in conditions of limited processing resources.

  11. Blended Outreach: Face-to-Face and Remote Programs

    ERIC Educational Resources Information Center

    Poeppelmeyer, Diana

    2011-01-01

    The Texas School for the Deaf (TSD) has two missions. One is to provide educational services to deaf and hard of hearing students and their families on the Austin campus--this is the traditional, face-to-face, center-based service model. The other is to serve as a resource center for the state, providing information, referral, programs, and…

  12. Comparative Analysis of Online vs. Face-to-Face Instruction.

    ERIC Educational Resources Information Center

    Johnson, Scott D.; Aragon, Steven R.; Shaik, Najmuddin; Palma-Rivas, Nilda

    This empirical study compared a graduate online course with an equivalent course taught in a traditional face-to-face format. Comparisons included student ratings of instructor and course quality; assessment of course interaction, structure, and support; and learning outcomes such as course grades and student self-assessment of ability to perform…

  13. View of Face A and Face B Arrays, looking northeast ...

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

    View of Face A and Face B Arrays, looking northeast - Beale Air Force Base, Perimeter Acquisition Vehicle Entry Phased-Array Warning System, Techinical Equipment Building, End of Spencer Paul Road, north of Warren Shingle Road (14th Street), Marysville, Yuba County, CA

  14. Looking northwest, Face B Array to left, Face C (rear) ...

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

    Looking northwest, Face B Array to left, Face C (rear) center, Power Plant (Building 5761), to right - Beale Air Force Base, Perimeter Acquisition Vehicle Entry Phased-Array Warning System, Techinical Equipment Building, End of Spencer Paul Road, north of Warren Shingle Road (14th Street), Marysville, Yuba County, CA

  15. Status of Subaru laser guide star AO system

    NASA Astrophysics Data System (ADS)

    Takami, Hideki; Colley, Stephen; Dinkins, Matt; Eldred, Michael; Guyon, Olivier; Golota, Taras; Hattori, Masayuki; Hayano, Yutaka; Ito, Meguru; Iye, Masanori; Oya, Shin; Saito, Yoshihiko; Watanabe, Makoto

    2006-06-01

    The laser guide star adaptive optics (AO188) system for Subaru Telescope is presented. The system will be installed at the IR Nasmyth platform of Subaru 8 m telescope, whereas the current AO system with 36 elements is operating at the Cassegrain focus. The new AO system has a 188 element wavefront curvature sensor with photon counting APD modules and 188 element bimorph mirror. The laser guide star system has a 4.5 W solid state sum-frequency laser on the Nasmyth platform. The laser launching telescope with 50 cm aperture will be installed at behind the secondary mirror. The laser beam will be transferred to the laser launching telescope using photonic crystal single mode fiber cable. The instrument with the AO system is IRCS, infrared camera and spectrograph which has been used for Cassegrain AO system and new instrument, HiCIAO, high dynamic range infrared camera for exsolar planet detection. The first light of the AO system is planned in 2006.

  16. Face to face with emotion: holistic face processing is modulated by emotional state.

    PubMed

    Curby, Kim M; Johnson, Kareem J; Tyson, Alyssa

    2012-01-01

    Negative emotions are linked with a local, rather than global, visual processing style, which may preferentially facilitate feature-based, relative to holistic, processing mechanisms. Because faces are typically processed holistically, and because social contexts are prime elicitors of emotions, we examined whether negative emotions decrease holistic processing of faces. We induced positive, negative, or neutral emotions via film clips and measured holistic processing before and after the induction: participants made judgements about cued parts of chimeric faces, and holistic processing was indexed by the interference caused by task-irrelevant face parts. Emotional state significantly modulated face-processing style, with the negative emotion induction leading to decreased holistic processing. Furthermore, self-reported change in emotional state correlated with changes in holistic processing. These results contrast with general assumptions that holistic processing of faces is automatic and immune to outside influences, and they illustrate emotion's power to modulate socially relevant aspects of visual perception.

  17. De novo transcriptome assembly of Setatria italica variety Taejin.

    PubMed

    Jo, Yeonhwa; Lian, Sen; Cho, Jin Kyong; Choi, Hoseong; Kim, Sang-Min; Kim, Sun-Lim; Lee, Bong Choon; Cho, Won Kyong

    2016-06-01

    Foxtail millet (Setaria italica) belonging to the family Poaceae is an important millet that is widely cultivated in East Asia. Of the cultivated millets, the foxtail millet has the longest history and is one of the main food crops in South India and China. Moreover, foxtail millet is a model plant system for biofuel generation utilizing the C4 photosynthetic pathway. In this study, we carried out de novo transcriptome assembly for the foxtail millet variety Taejin collected from Korea using next-generation sequencing. We obtained a total of 8.676 GB raw data by paired-end sequencing. The raw data in this study can be available in NCBI SRA database with accession number of SRR3406552. The Trinity program was used to de novo assemble 145,332 transcripts. Using the TransDecoder program, we predicted 82,925 putative proteins. BLASTP was performed against the Swiss-Prot protein sequence database to annotate the functions of identified proteins, resulting in 20,555 potentially novel proteins. Taken together, this study provides transcriptome data for the foxtail millet variety Taejin by RNA-Seq. PMID:27257606

  18. Origins of De Novo Genes in Human and Chimpanzee

    PubMed Central

    Ruiz-Orera, Jorge; Hernandez-Rodriguez, Jessica; Chiva, Cristina; Sabidó, Eduard; Kondova, Ivanela; Bontrop, Ronald; Marqués-Bonet, Tomàs; Albà, M.Mar

    2015-01-01

    The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that did not contain any genes or gene copies. Some of these newly expressed genes may acquire coding or non-coding functions and be preserved by natural selection. However, it is yet unclear which is the prevalence and underlying mechanisms of de novo gene emergence. In order to obtain a comprehensive view of this process, we have performed in-depth sequencing of the transcriptomes of four mammalian species—human, chimpanzee, macaque, and mouse—and subsequently compared the assembled transcripts and the corresponding syntenic genomic regions. This has resulted in the identification of over five thousand new multiexonic transcriptional events in human and/or chimpanzee that are not observed in the rest of species. Using comparative genomics, we show that the expression of these transcripts is associated with the gain of regulatory motifs upstream of the transcription start site (TSS) and of U1 snRNP sites downstream of the TSS. In general, these transcripts show little evidence of purifying selection, suggesting that many of them are not functional. However, we find signatures of selection in a subset of de novo genes which have evidence of protein translation. Taken together, the data support a model in which frequently-occurring new transcriptional events in the genome provide the raw material for the evolution of new proteins. PMID:26720152

  19. Origins of De Novo Genes in Human and Chimpanzee.

    PubMed

    Ruiz-Orera, Jorge; Hernandez-Rodriguez, Jessica; Chiva, Cristina; Sabidó, Eduard; Kondova, Ivanela; Bontrop, Ronald; Marqués-Bonet, Tomàs; Albà, M Mar

    2015-12-01

    The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that did not contain any genes or gene copies. Some of these newly expressed genes may acquire coding or non-coding functions and be preserved by natural selection. However, it is yet unclear which is the prevalence and underlying mechanisms of de novo gene emergence. In order to obtain a comprehensive view of this process, we have performed in-depth sequencing of the transcriptomes of four mammalian species--human, chimpanzee, macaque, and mouse--and subsequently compared the assembled transcripts and the corresponding syntenic genomic regions. This has resulted in the identification of over five thousand new multiexonic transcriptional events in human and/or chimpanzee that are not observed in the rest of species. Using comparative genomics, we show that the expression of these transcripts is associated with the gain of regulatory motifs upstream of the transcription start site (TSS) and of U1 snRNP sites downstream of the TSS. In general, these transcripts show little evidence of purifying selection, suggesting that many of them are not functional. However, we find signatures of selection in a subset of de novo genes which have evidence of protein translation. Taken together, the data support a model in which frequently-occurring new transcriptional events in the genome provide the raw material for the evolution of new proteins.

  20. De novo transcriptome assembly of two different apricot cultivars.

    PubMed

    Jo, Yeonhwa; Lian, Sen; Cho, Jin Kyong; Choi, Hoseong; Chu, Hyosub; Cho, Won Kyong

    2015-12-01

    Apricot (Prunus armeniaca) belonging to the Prunus species is a popular kind of stone fruit tree. Apricot is native to Armenia and is currently cultivated in many countries with climates adaptable for apricot growth. In general, fresh fruits as well as dried apricot are produced. However, the information associated with genes and genetic markers for apricot is very limited. In this study, we carried out de novo transcriptome assembly for two selected apricot cultivars referred to as Harcot and Ungarische Beste, which are commercially important apricot cultivars in the world, using next generation sequencing. We obtained a total of 9.31 GB and 8.88 GB raw data from Harcot and Ungarische Beste (NCBI accession numbers: SRX1186946 and SRX1186893), respectively. De novo transcriptome assembly using Trinity identified 147,501 and 152,235 transcripts for Harcot and Ungarische Beste, respectively. Next, we identified 113,565 and 126,444 proteins from Harcot and Ungarische Beste using the TransDecoder program. We performed BLASTP against an NCBI non-redundant (nr) dataset to annotate identified proteins. Taken together, we provide transcriptomes of two different apricot cultivars by RNA-Seq.

  1. De novo Amyloid Proteins from Designed Combinatorial Libraries

    NASA Astrophysics Data System (ADS)

    West, Michael W.; Wang, Weixun; Patterson, Jennifer; Mancias, Joseph D.; Beasley, James R.; Hecht, Michael H.

    1999-09-01

    Amyloid deposits are associated with several neurodegenerative diseases, including Alzheimer's disease and the prion diseases. The amyloid fibrils isolated from these different diseases share similar structural features. However, the protein sequences that assemble into these fibrils differ substantially from one disease to another. To probe the relationship between amino acid sequence and the propensity to form amyloid, we studied a combinatorial library of sequences designed de novo. All sequences in the library were designed to share an identical pattern of alternating polar and nonpolar residues, but the precise identities of these side chains were not constrained and were varied combinatorially. The resulting proteins self-assemble into large oligomers visible by electron microscopy as amyloid-like fibrils. Like natural amyloid, the de novo fibrils are composed of β -sheet secondary structure and bind the diagnostic dye, Congo red. Thus, binary patterning of polar and nonpolar residues arranged in alternating periodicity can direct protein sequences to form fibrils resembling amyloid. The model amyloid fibrils assemble and disassemble reversibly, providing a tractable system for both basic studies into the mechanisms of fibril assembly and the development of molecular therapies that interfere with this assembly.

  2. De novo malignant solitary fibrous tumor of the kidney.

    PubMed

    Hsieh, Tsan-Yu; ChangChien, Yi-Che; Chen, Wen-Hsiang; Chen, Siu-Chung; Chang, Liang-Che; Hwang, Cheng-Cheng; Chein, Hui-Ping; Chen, Jim-Ray

    2011-01-01

    The kidney is a relatively infrequent site for solitary fibrous tumor (SFT). Among the previously reported cases, only two cases of malignant renal SFT developing via dedifferentiation from a pre-existing benign SFT have been reported. Here we reported a case of de novo malignant renal SFT clinically diagnosed as renal cell carcinoma in a 50-year-old woman. The tumor was circumscribed but unencapsulated and showed obvious hemorrhagic necrosis. Microscopically, the tumor was composed of patternless sheets of alternating hypercellular and hypocellular areas of spindle cells displaying mild to moderate nuclear atypia, frequent mitoses up to 8 per 10 high power fields, and a 20% Ki-67 proliferative index. Immunohistochemical studies revealed reactivity for CD34, CD99 and vimentin, with no staining for all other markers, confirming the diagnosis of SFT. No areas of dedifferentiation were seen after extensive sampling. Based on the pathologic and immunohistochemical features, a diagnosis of de novo malignant renal SFT was warranted. Our report expands the spectrum of malignant progression in renal SFTs. Even though this patient has been disease-free for 30 months, long-term follow-up is still mandatory.

  3. DOGS: reaction-driven de novo design of bioactive compounds.

    PubMed

    Hartenfeller, Markus; Zettl, Heiko; Walter, Miriam; Rupp, Matthias; Reisen, Felix; Proschak, Ewgenij; Weggen, Sascha; Stark, Holger; Schneider, Gisbert

    2012-01-01

    We present a computational method for the reaction-based de novo design of drug-like molecules. The software DOGS (Design of Genuine Structures) features a ligand-based strategy for automated 'in silico' assembly of potentially novel bioactive compounds. The quality of the designed compounds is assessed by a graph kernel method measuring their similarity to known bioactive reference ligands in terms of structural and pharmacophoric features. We implemented a deterministic compound construction procedure that explicitly considers compound synthesizability, based on a compilation of 25'144 readily available synthetic building blocks and 58 established reaction principles. This enables the software to suggest a synthesis route for each designed compound. Two prospective case studies are presented together with details on the algorithm and its implementation. De novo designed ligand candidates for the human histamine H₄ receptor and γ-secretase were synthesized as suggested by the software. The computational approach proved to be suitable for scaffold-hopping from known ligands to novel chemotypes, and for generating bioactive molecules with drug-like properties.

  4. Assembly, Assessment, and Availability of De novo Generated Eukaryotic Transcriptomes

    PubMed Central

    Moreton, Joanna; Izquierdo, Abril; Emes, Richard D.

    2016-01-01

    De novo assembly of a complete transcriptome without the need for a guiding reference genome is attractive, particularly where the cost and complexity of generating a eukaryote genome is prohibitive. The transcriptome should not however be seen as just a quick and cheap alternative to building a complete genome. Transcriptomics allows the understanding and comparison of spatial and temporal samples within an organism, and allows surveying of multiple individuals or closely related species. De novo assembly in theory allows the building of a complete transcriptome without any prior knowledge of the genome. It also allows the discovery of alternate splice forms of coding RNAs and also non-coding RNAs, which are often missed by proteomic approaches, or are incompletely annotated in genome studies. The limitations of the method are that the generation of a truly complete assembly is unlikely, and so we require some methods for the assessment of the quality and appropriateness of a generated transcriptome. Whilst no single consensus pipeline or tool is agreed as optimal, various algorithms, and easy to use software do exist making transcriptome generation a more common approach. With this expansion of data, questions still exist relating to how do we make these datasets fully discoverable, comparable and most useful to understand complex biological systems? PMID:26793234

  5. A simple method suitable to study de novo root organogenesis.

    PubMed

    Chen, Xiaodong; Qu, Yuliang; Sheng, Lihong; Liu, Jingchun; Huang, Hai; Xu, Lin

    2014-01-01

    De novo root organogenesis is the process in which adventitious roots regenerate from detached or wounded plant tissues or organs. In tissue culture, appropriate types and concentrations of plant hormones in the medium are critical for inducing adventitious roots. However, in natural conditions, regeneration from detached organs is likely to rely on endogenous hormones. To investigate the actions of endogenous hormones and the molecular mechanisms guiding de novo root organogenesis, we developed a simple method to imitate natural conditions for adventitious root formation by culturing Arabidopsis thaliana leaf explants on B5 medium without additive hormones. Here we show that the ability of the leaf explants to regenerate roots depends on the age of the leaf and on certain nutrients in the medium. Based on these observations, we provide examples of how this method can be used in different situations, and how it can be optimized. This simple method could be used to investigate the effects of various physiological and molecular changes on the regeneration of adventitious roots. It is also useful for tracing cell lineage during the regeneration process by differential interference contrast observation of β-glucuronidase staining, and by live imaging of proteins labeled with fluorescent tags. PMID:24860589

  6. Molecular characterization of de novo secondary trisomy 13

    SciTech Connect

    Shaffer, L.G.; McCaskill, C.; Han, Jin-Yeong; Choo, K.H.A.; Cutillo, D.M.; Donnenfeld, A.E.; Weiss, L.; Van Dyke, D.L.

    1994-11-01

    Unbalanced Robertsonian translocations are a significant cause of mental retardation and fetal wastage. The majority of homologous rearrangements of chromosome 21 in Down syndrome have been shown to be isochromosomes. Aside from chromosome 21, very little is known about other acrocentric homologous rearrangements. In this study, four cases of de novo secondary trisomy 13 are presented. FISH using alpha-satellite sequences, rDNA, and a pTRI-6 satellite I sequence specific to the short arm of chromosome 13 showed all four rearrangements to be dicentric an apparently devoid of ribosomal genes. Three of four rearrangements retained the pTRI-6 satellite I sequence. Case 1 was the exception, showing a deletion of this sequence in the rearrangement, although both parental chromosomes 13 had strong positive hybridization signals. Eleven microsatellite markers from chromosome 13 were also used to characterize the rearrangements. Of the four possible outcomes, one maternal Robertsonian translocation, two paternal isochromosomes, and one maternal isochromosomes were observed. A double recombination was observed in the maternally derived rob(13q13q). No recombination events were detected in any isochromosome. The parental origins and molecular chromosomal structure of these cases are compared with previous studies of de novo acrocentric rearrangements. 20 refs., 3 figs., 2 tabs.

  7. Hydroxyurea induces de novo copy number variants in human cells.

    PubMed

    Arlt, Martin F; Ozdemir, Alev Cagla; Birkeland, Shanda R; Wilson, Thomas E; Glover, Thomas W

    2011-10-18

    Copy number variants (CNVs) are widely distributed throughout the human genome, where they contribute to genetic variation and phenotypic diversity. Spontaneous CNVs are also a major cause of genetic and developmental disorders and arise frequently in cancer cells. As with all mutation classes, genetic and environmental factors almost certainly increase the risk for new and deleterious CNVs. However, despite the importance of CNVs, there is limited understanding of these precipitating risk factors and the mechanisms responsible for a large percentage of CNVs. Here we report that low doses of hydroxyurea, an inhibitor of ribonucleotide reductase and an important drug in the treatment of sickle cell disease and other diseases induces a high frequency of de novo CNVs in cultured human cells that resemble pathogenic and aphidicolin-induced CNVs in size and breakpoint structure. These CNVs are distributed throughout the genome, with some hotspots of de novo CNV formation. Sequencing revealed that CNV breakpoint junctions are characterized by short microhomologies, blunt ends, and short insertions. These data provide direct experimental support for models of replication-error origins of CNVs and suggest that any agent or condition that leads to replication stress has the potential to induce deleterious CNVs. In addition, they point to a need for further study of the genomic consequences of the therapeutic use of hydroxyurea.

  8. Heavy-metal complexation by de novo peptide design.

    PubMed

    Farrer, Brian T; Pecoraro, Vincent L

    2002-11-01

    From poisoning caused by lead-based paint on domestic buildings to groundwater contamination by naturally occurring arsenic deposits in India, heavy-metal toxicity is a global health problem. Contaminated ground water and acute cases of heavy-metal poisoning are treated with chelators to remove the heavy metals from the contaminated site or person. This review discusses the effort to generate heavy-metal chelators through peptide de novo design. De novo design entails the design of a primary sequence that will precisely fold into a predetermined secondary and tertiary protein structure. The first-generation peptide chelator used to initiate this investigation is the three-stranded coild coil containing Cys. Cys provides a potential trigonal binding site with soft thiolate ligands, which has been proposed to provide specific interactions with heavy metals. This hypothesis derives from the observation that similar sites on natural proteins show selectivity for heavy metals over other essential metals, such as Zn or Mg. A description of two systems, the TRI series and the IZ-AC peptide, is given, highlighting the interaction of these peptides with Hg, Cd, As and Pb. Arguments are also presented for the potential use of three-helix bundles as a second-generation design.

  9. Histone deacetylase inhibitor romidepsin inhibits de novo HIV-1 infections.

    PubMed

    Jønsson, Kasper L; Tolstrup, Martin; Vad-Nielsen, Johan; Kjær, Kathrine; Laustsen, Anders; Andersen, Morten N; Rasmussen, Thomas A; Søgaard, Ole S; Østergaard, Lars; Denton, Paul W; Jakobsen, Martin R

    2015-07-01

    Adjunct therapy with the histone deacetylase inhibitor (HDACi) romidepsin increases plasma viremia in HIV patients on combination antiretroviral therapy (cART). However, a potential concern is that reversing HIV latency with an HDACi may reactivate the virus in anatomical compartments with suboptimal cART concentrations, leading to de novo infection of susceptible cells in these sites. We tested physiologically relevant romidepsin concentrations known to reactivate latent HIV in order to definitively address this concern. We found that romidepsin significantly inhibited HIV infection in peripheral blood mononuclear cells and CD4(+) T cells but not in monocyte-derived macrophages. In addition, romidepsin impaired HIV spreading in CD4(+) T cell cultures. When we evaluated the impact of romidepsin on quantitative viral outgrowth assays with primary resting CD4(+) T cells, we found that resting CD4(+) T cells exposed to romidepsin exhibited reduced proliferation and viability. This significantly lowered assay sensitivity when measuring the efficacy of romidepsin as an HIV latency reversal agent. Altogether, our data indicate that romidepsin-based HIV eradication strategies are unlikely to reseed a latent T cell reservoir, even under suboptimal cART conditions, because romidepsin profoundly restricts de novo HIV infections.

  10. De novo Evolution of a Small Choroidal Melanoma

    PubMed Central

    Aleksidze, Nino; Medina, Carlos A.; Singh, Arun D.

    2015-01-01

    Aim To report the evolution of a de novo choroidal melanoma. Method This is a case report of a 22-year-old white male patient who has been undergoing periodic examination for a choroidal ‘freckle’ since 10 years of age. Results In 2007, a fundus photograph of the left eye showed a nondescript area of choroidal hyperpigmentation temporal to the fovea. Progressive growth was observed and, by 2012, the lesion had become well circumscribed and raised. One year later, a 4.5 × 4.5 × 1.5 mm, dome-shaped, pigmented, choroidal mass with subretinal fluid and orange pigmentation was evident. The lesion was classified as a small choroidal melanoma. Six months after plaque radiotherapy, tumor regression with total resolution of the subretinal fluid was documented. Conclusion The distinction between small choroidal melanoma and choroidal nevus is not absolute; therefore, some choroidal melanomas may initially be mislabeled as choroidal nevi because of their small size until continued growth identifies them to be small choroidal melanomas. In our case, the documented growth of the choroidal lesion on each consecutive visit and its high-risk features strongly suggest that it had been a melanoma from the beginning. To our knowledge, this is only the second documented case of a de novo evolution of a small choroidal melanoma. PMID:27231689

  11. De novo transcriptome assembly of two different apricot cultivars.

    PubMed

    Jo, Yeonhwa; Lian, Sen; Cho, Jin Kyong; Choi, Hoseong; Chu, Hyosub; Cho, Won Kyong

    2015-12-01

    Apricot (Prunus armeniaca) belonging to the Prunus species is a popular kind of stone fruit tree. Apricot is native to Armenia and is currently cultivated in many countries with climates adaptable for apricot growth. In general, fresh fruits as well as dried apricot are produced. However, the information associated with genes and genetic markers for apricot is very limited. In this study, we carried out de novo transcriptome assembly for two selected apricot cultivars referred to as Harcot and Ungarische Beste, which are commercially important apricot cultivars in the world, using next generation sequencing. We obtained a total of 9.31 GB and 8.88 GB raw data from Harcot and Ungarische Beste (NCBI accession numbers: SRX1186946 and SRX1186893), respectively. De novo transcriptome assembly using Trinity identified 147,501 and 152,235 transcripts for Harcot and Ungarische Beste, respectively. Next, we identified 113,565 and 126,444 proteins from Harcot and Ungarische Beste using the TransDecoder program. We performed BLASTP against an NCBI non-redundant (nr) dataset to annotate identified proteins. Taken together, we provide transcriptomes of two different apricot cultivars by RNA-Seq. PMID:26697397

  12. Ethanol enhances de novo synthesis of high density lipoprotein cholesterol

    SciTech Connect

    Cluette, J.E.; Mulligan, J.J.; Noring, R.; Doyle, K.; Hojnacki, J.

    1984-05-01

    Male squirrel monkeys fed ethanol at variable doses were used to assess whether alcohol enhances de novo synthesis of high density lipoprotein (HDL) cholesterol in vivo. Monkeys were divided into three groups: 1) controls fed isocaloric liquid diet; 2) low ethanol monkeys fed liquid diet with vodka substituted isocalorically for carbohydrate at 12% of calories; and 3) High Ethanol animals fed diet plus vodka at 24% of calories. High Ethanol primates had significantly higher levels of HDL nonesterified cholesterol than Control and Low Ethanol animals while serum glutamate oxaloacetate transaminase was similar for the three treatments. There were no significant differences between the groups in HDL cholesteryl ester mass or specific activity following intravenous injection of labeled mevalonolactone. By contrast, High Ethanol monkeys had significantly greater HDL nonesterified cholesterol specific activity with approximately 60% of the radioactivity distributed in the HDL/sub 3/ subfraction. This report provides the first experimental evidence that ethanol at 24% of calories induces elevations in HDL cholesterol in primates through enhanced de novo synthesis without adverse effects on liver function.

  13. Extensive Natural Epigenetic Variation at a De Novo Originated Gene

    PubMed Central

    Silveira, Amanda Bortolini; Trontin, Charlotte; Cortijo, Sandra; Barau, Joan; Del Bem, Luiz Eduardo Vieira; Loudet, Olivier; Colot, Vincent; Vincentz, Michel

    2013-01-01

    Epigenetic variation, such as heritable changes of DNA methylation, can affect gene expression and thus phenotypes, but examples of natural epimutations are few and little is known about their stability and frequency in nature. Here, we report that the gene Qua-Quine Starch (QQS) of Arabidopsis thaliana, which is involved in starch metabolism and that originated de novo recently, is subject to frequent epigenetic variation in nature. Specifically, we show that expression of this gene varies considerably among natural accessions as well as within populations directly sampled from the wild, and we demonstrate that this variation correlates negatively with the DNA methylation level of repeated sequences located within the 5′end of the gene. Furthermore, we provide extensive evidence that DNA methylation and expression variants can be inherited for several generations and are not linked to DNA sequence changes. Taken together, these observations provide a first indication that de novo originated genes might be particularly prone to epigenetic variation in their initial stages of formation. PMID:23593031

  14. Configural Processing and Face Viewpoint

    ERIC Educational Resources Information Center

    McKone, Elinor

    2008-01-01

    Configural/holistic processing, a key property of face recognition, has previously been examined only for front views of faces. Here, 6 experiments tested front (0 degree), three-quarter (45 degree), and profile views (90 degree), using composite and peripheral inversion tasks. Results showed an overall disadvantage in identifying profiles. This…

  15. Newborns' Mooney-Face Perception

    ERIC Educational Resources Information Center

    Leo, Irene; Simion, Francesca

    2009-01-01

    The aim of this study is to investigate whether newborns detect a face on the basis of a Gestalt representation based on first-order relational information (i.e., the basic arrangement of face features) by using Mooney stimuli. The incomplete 2-tone Mooney stimuli were used because they preclude focusing both on the local features (i.e., the fine…

  16. Inversion and Configuration of Faces.

    ERIC Educational Resources Information Center

    Bartlett, James C.; Searcy, Jean

    1993-01-01

    The Thatcher illusion, in which the inverted mouth and eyes of a face appear grotesque when upright, but not when the whole configuration is inverted, was studied in 3 experiments involving 89 undergraduates. Results suggest that the illusion represents a disruption of encoding of holistic information when faces are inverted. (SLD)

  17. Parallel Processing in Face Perception

    ERIC Educational Resources Information Center

    Martens, Ulla; Leuthold, Hartmut; Schweinberger, Stefan R.

    2010-01-01

    The authors examined face perception models with regard to the functional and temporal organization of facial identity and expression analysis. Participants performed a manual 2-choice go/no-go task to classify faces, where response hand depended on facial familiarity (famous vs. unfamiliar) and response execution depended on facial expression…

  18. Priming with threatening faces modulates the self-face advantage by enhancing the other-face processing rather than suppressing the self-face processing.

    PubMed

    Guan, Lili; Qi, Mingming; Li, Haijiang; Hitchman, Glenn; Yang, Juan; Liu, Yijun

    2015-05-22

    Social emotional information influences self-processing in everyday activities, but few researchers have investigated this process. The current ERP study adopted a prime paradigm to investigate how socially threatening faces impact on the self-face processing advantage. After being primed with emotional faces (happy, angry or neutral), participants judged whether the target face (self, friend, and stranger) was familiar or unfamiliar. Results showed an interaction effect between the prime face and the target face at posterior P3, suggesting that after priming with happy and neutral faces, self-faces elicited larger P3 amplitudes than friend-faces and stranger-faces; however, after priming with angry faces, the P3 amplitudes were not significantly different between self-face and friend-face. Moreover, the P3 amplitudes of self-faces did not differ between priming with angry and neutral faces; however, the P3 amplitude of both friend-faces and stranger-faces showed enhanced responses after priming with angry faces compared to priming with neutral faces. We suggest that the self-face processing advantage (self vs. friend) could be weakened by priming with threatening faces, through enhancement of the other-faces processing rather than suppression of self-faces processing in angry vs. neutral face prime. PMID:25765156

  19. Priming with threatening faces modulates the self-face advantage by enhancing the other-face processing rather than suppressing the self-face processing.

    PubMed

    Guan, Lili; Qi, Mingming; Li, Haijiang; Hitchman, Glenn; Yang, Juan; Liu, Yijun

    2015-05-22

    Social emotional information influences self-processing in everyday activities, but few researchers have investigated this process. The current ERP study adopted a prime paradigm to investigate how socially threatening faces impact on the self-face processing advantage. After being primed with emotional faces (happy, angry or neutral), participants judged whether the target face (self, friend, and stranger) was familiar or unfamiliar. Results showed an interaction effect between the prime face and the target face at posterior P3, suggesting that after priming with happy and neutral faces, self-faces elicited larger P3 amplitudes than friend-faces and stranger-faces; however, after priming with angry faces, the P3 amplitudes were not significantly different between self-face and friend-face. Moreover, the P3 amplitudes of self-faces did not differ between priming with angry and neutral faces; however, the P3 amplitude of both friend-faces and stranger-faces showed enhanced responses after priming with angry faces compared to priming with neutral faces. We suggest that the self-face processing advantage (self vs. friend) could be weakened by priming with threatening faces, through enhancement of the other-faces processing rather than suppression of self-faces processing in angry vs. neutral face prime.

  20. Genetic specificity of face recognition.

    PubMed

    Shakeshaft, Nicholas G; Plomin, Robert

    2015-10-13

    Specific cognitive abilities in diverse domains are typically found to be highly heritable and substantially correlated with general cognitive ability (g), both phenotypically and genetically. Recent twin studies have found the ability to memorize and recognize faces to be an exception, being similarly heritable but phenotypically substantially uncorrelated both with g and with general object recognition. However, the genetic relationships between face recognition and other abilities (the extent to which they share a common genetic etiology) cannot be determined from phenotypic associations. In this, to our knowledge, first study of the genetic associations between face recognition and other domains, 2,000 18- and 19-year-old United Kingdom twins completed tests assessing their face recognition, object recognition, and general cognitive abilities. Results confirmed the substantial heritability of face recognition (61%), and multivariate genetic analyses found that most of this genetic influence is unique and not shared with other cognitive abilities.

  1. Lateralized processes in face recognition.

    PubMed

    Rhodes, G

    1985-05-01

    In this paper a model is presented in which face recognition is analysed into several stages, each of which may be independently lateralized. Evidence is reviewed which suggests that lateralization is important at all stages of processing a face. Early visuospatial processing, and the creation and comparison of facial representations, appear to be carried out more efficiently by the right hemisphere. Comparisons based on discrete, namable features of faces may yield a left hemisphere advantage. It is also proposed that faces may activate semantic information, including names, more efficiently in the left hemisphere. The model is useful in resolving inconsistencies in the degree and direction of asymmetries found in face-recognition tasks. Suggestions are also made for future research.

  2. Emotion-independent face recognition

    NASA Astrophysics Data System (ADS)

    De Silva, Liyanage C.; Esther, Kho G. P.

    2000-12-01

    Current face recognition techniques tend to work well when recognizing faces under small variations in lighting, facial expression and pose, but deteriorate under more extreme conditions. In this paper, a face recognition system to recognize faces of known individuals, despite variations in facial expression due to different emotions, is developed. The eigenface approach is used for feature extraction. Classification methods include Euclidean distance, back propagation neural network and generalized regression neural network. These methods yield 100% recognition accuracy when the training database is representative, containing one image representing the peak expression for each emotion of each person apart from the neutral expression. The feature vectors used for comparison in the Euclidean distance method and for training the neural network must be all the feature vectors of the training set. These results are obtained for a face database consisting of only four persons.

  3. Face features and face configurations both contribute to visual crowding.

    PubMed

    Sun, Hsin-Mei; Balas, Benjamin

    2015-02-01

    Crowding refers to the inability to recognize an object in peripheral vision when other objects are presented nearby (Whitney & Levi Trends in Cognitive Sciences, 15, 160-168, 2011). A popular explanation of crowding is that features of the target and flankers are combined inappropriately when they are located within an integration field, thus impairing target recognition (Pelli, Palomares, & Majaj Journal of Vision, 4(12), 12:1136-1169, 2004). However, it remains unclear which features of the target and flankers are combined inappropriately to cause crowding (Levi Vision Research, 48, 635-654, 2008). For example, in a complex stimulus (e.g., a face), to what extent does crowding result from the integration of features at a part-based level or at the level of global processing of the configural appearance? In this study, we used a face categorization task and different types of flankers to examine how much the magnitude of visual crowding depends on the similarity of face parts or of global configurations. We created flankers with face-like features (e.g., the eyes, nose, and mouth) in typical and scrambled configurations to examine the impacts of part appearance and global configuration on the visual crowding of faces. Additionally, we used "electrical socket" flankers that mimicked first-order face configuration but had only schematic features, to examine the extent to which global face geometry impacted crowding. Our results indicated that both face parts and configurations contribute to visual crowding, suggesting that face similarity as realized under crowded conditions includes both aspects of facial appearance.

  4. De Novo Meningitis Caused by Propionibacterium acnes in a Patient with Metastatic Melanoma

    PubMed Central

    Burnham, Jason P.; Trevino, Sergio E.; McElvania TeKippe, Erin; Burnham, Carey-Ann D.; Kuhlmann, F. Matthew

    2014-01-01

    Propionibacterium acnes is a known cause of postneurosurgical meningitis; however, it is rarely implicated in de novo meningitis. Herein we report a case of a 49-year-old male with de novo meningitis caused by P. acnes with metastatic melanoma as the only identified risk factor for his infection. PMID:24478417

  5. Beyond the Blur: Construction and Characterization of the First Autonomous AO System, and, An AO Survey of Magnetar Proper Motions

    NASA Astrophysics Data System (ADS)

    Tendulkar, Shriharsh Prakash

    Adaptive optics (AO) corrects distortions created by atmospheric turbulence and delivers diffraction-limited images on ground-based telescopes. The vastly improved spatial resolution and sensitivity has been utilized for studying everything from the magnetic fields of sunspots upto the internal dynamics of high-redshift galaxies. This thesis about AO science from small and large telescopes is divided into two parts: Robo-AO and magnetar kinematics. In the first part, I discuss the construction and performance of the world's first fully autonomous visible light AO system, Robo-AO, at the Palomar 60-inch telescope. Robo-AO operates extremely efficiently with an overhead < 50s, typically observing about 22 targets every hour. We have performed large AO programs observing a total of over 7,500 targets since May 2012. In the visible band, the images have a Strehl ratio of about 10% and achieve a contrast of upto 6 magnitudes at a separation of 1‧‧. The full-width at half maximum achieved is 110-130 milli-arcsecond. I describe how Robo-AO is used to constrain the evolutionary models of low-mass pre-main-sequence stars by measuring resolved spectral energy distributions of stellar multiples in the visible band, more than doubling the current sample. I conclude this part with a discussion of possible future improvements to the Robo-AO system. In the second part, I describe a study of magnetar kinematics using high-resolution near-infrared (NIR) AO imaging from the 10-meter Keck II telescope. Measuring the proper motions of five magnetars with a precision of upto 0.7 milli-arcsecond/yr -1, we have more than tripled the previously known sample of magnetar proper motions and proved that magnetar kinematics are equivalent to those of radio pulsars. We conclusively showed that SGR 1900+14 and SGR 1806-20 were ejected from the stellar clusters with which they were traditionally associated. The inferred kinematic ages of these two magnetars are 6 +/- 1.8 kyr and 650 +/-3 00

  6. Interpreting the role of de novo protein-coding mutations in neuropsychiatric disease.

    PubMed

    Gratten, Jacob; Visscher, Peter M; Mowry, Bryan J; Wray, Naomi R

    2013-03-01

    Pedigree, linkage and association studies are consistent with heritable variation for complex disease due to the segregation of genetic factors in families and in the population. In contrast, de novo mutations make only minor contributions to heritability estimates for complex traits. Nonetheless, some de novo variants are known to be important in disease etiology. The identification of risk-conferring de novo variants will contribute to the discovery of etiologically relevant genes and pathways and may help in genetic counseling. There is considerable interest in the role of such mutations in complex neuropsychiatric disease, largely driven by new genotyping and sequencing technologies. An important role for large de novo copy number variations has been established. Recently, whole-exome sequencing has been used to extend the investigation of de novo variation to point mutations in protein-coding regions. Here, we consider several challenges for the interpretation of such mutations in the context of their role in neuropsychiatric disease. PMID:23438595

  7. De novo gene mutations highlight patterns of genetic and neural complexity in schizophrenia.

    PubMed

    Xu, Bin; Ionita-Laza, Iuliana; Roos, J Louw; Boone, Braden; Woodrick, Scarlet; Sun, Yan; Levy, Shawn; Gogos, Joseph A; Karayiorgou, Maria

    2012-12-01

    To evaluate evidence for de novo etiologies in schizophrenia, we sequenced at high coverage the exomes of families recruited from two populations with distinct demographic structures and history. We sequenced a total of 795 exomes from 231 parent-proband trios enriched for sporadic schizophrenia cases, as well as 34 unaffected trios. We observed in cases an excess of de novo nonsynonymous single-nucleotide variants as well as a higher prevalence of gene-disruptive de novo mutations relative to controls. We found four genes (LAMA2, DPYD, TRRAP and VPS39) affected by recurrent de novo events within or across the two populations, which is unlikely to have occurred by chance. We show that de novo mutations affect genes with diverse functions and developmental profiles, but we also find a substantial contribution of mutations in genes with higher expression in early fetal life. Our results help define the genomic and neural architecture of schizophrenia. PMID:23042115

  8. De Novo Synonymous Mutations in Regulatory Elements Contribute to the Genetic Etiology of Autism and Schizophrenia.

    PubMed

    Takata, Atsushi; Ionita-Laza, Iuliana; Gogos, Joseph A; Xu, Bin; Karayiorgou, Maria

    2016-03-01

    We analyze de novo synonymous mutations identified in autism spectrum disorders (ASDs) and schizophrenia (SCZ) with potential impact on regulatory elements using data from whole-exome sequencing (WESs) studies. Focusing on five types of genetic regulatory functions, we found that de novo near-splice site synonymous mutations changing exonic splicing regulators and those within frontal cortex-derived DNase I hypersensitivity sites are significantly enriched in ASD and SCZ, respectively. These results remained significant, albeit less so, after incorporating two additional ASD datasets. Among the genes identified, several are hit by multiple functional de novo mutations, with RAB2A and SETD1A showing the highest statistical significance in ASD and SCZ, respectively. The estimated contribution of these synonymous mutations to disease liability is comparable to de novo protein-truncating mutations. These findings expand the repertoire of functional de novo mutations to include "functional" synonymous ones and strengthen the role of rare variants in neuropsychiatric disease risk. PMID:26938441

  9. De Novo duplication in Charcot-Marie-Tooth Type 1A

    SciTech Connect

    Mandich, P.; Bellone, E.; Ajmar, F.

    1996-09-01

    We read with interest the paper on {open_quotes}Prevalence and Origin of De Novo Duplications in Charcot-Marie-Tooth Disease Type 1A: First Report of a De Novo Duplication with a Maternal Origin,{close_quotes}. They reported their experience with 10 sporadic cases of Charcot-Marie-Tooth type 1A (CMT1A) in which it was demonstrated that the disease had arisen as the result of a de novo duplication. They analyzed the de novo-duplication families by using microsatellite markers and identified the parental origin of the duplication in eight cases. In one family the duplication was of maternal origin, whereas in the remaining seven cases it was of paternal origin. The authors concluded that their report was the first evidence of a de novo duplication of maternal origin, suggesting that this is not a phenomenon associated solely with male meiosis. 7 refs.

  10. Application of de Novo Sequencing to Large-Scale Complex Proteomics Data Sets.

    PubMed

    Devabhaktuni, Arun; Elias, Joshua E

    2016-03-01

    Dependent on concise, predefined protein sequence databases, traditional search algorithms perform poorly when analyzing mass spectra derived from wholly uncharacterized protein products. Conversely, de novo peptide sequencing algorithms can interpret mass spectra without relying on reference databases. However, such algorithms have been difficult to apply to complex protein mixtures, in part due to a lack of methods for automatically validating de novo sequencing results. Here, we present novel metrics for benchmarking de novo sequencing algorithm performance on large-scale proteomics data sets and present a method for accurately calibrating false discovery rates on de novo results. We also present a novel algorithm (LADS) that leverages experimentally disambiguated fragmentation spectra to boost sequencing accuracy and sensitivity. LADS improves sequencing accuracy on longer peptides relative to that of other algorithms and improves discriminability of correct and incorrect sequences. Using these advancements, we demonstrate accurate de novo identification of peptide sequences not identifiable using database search-based approaches. PMID:26743026

  11. Modeling Human Dynamics of Face-to-Face Interaction Networks

    NASA Astrophysics Data System (ADS)

    Starnini, Michele; Baronchelli, Andrea; Pastor-Satorras, Romualdo

    2013-04-01

    Face-to-face interaction networks describe social interactions in human gatherings, and are the substrate for processes such as epidemic spreading and gossip propagation. The bursty nature of human behavior characterizes many aspects of empirical data, such as the distribution of conversation lengths, of conversations per person, or of interconversation times. Despite several recent attempts, a general theoretical understanding of the global picture emerging from data is still lacking. Here we present a simple model that reproduces quantitatively most of the relevant features of empirical face-to-face interaction networks. The model describes agents that perform a random walk in a two-dimensional space and are characterized by an attractiveness whose effect is to slow down the motion of people around them. The proposed framework sheds light on the dynamics of human interactions and can improve the modeling of dynamical processes taking place on the ensuing dynamical social networks.

  12. The face, beauty, and symmetry: perceiving asymmetry in beautiful faces.

    PubMed

    Zaidel, D W; Cohen, J A

    2005-08-01

    The relationship between bilateral facial symmetry and beauty remains to be clarified. Here, straight head-on photographs of "beautiful" faces from the collections of professional modeling agencies were selected. First, beauty ratings were obtained for these faces. Then, the authors created symmetrical left-left and right-right composites of the beautiful faces and asked a new group of subjects to choose the most attractive pair member. "Same" responses were allowed. No difference between the left-left and right-right composites was revealed but significant differences were obtained between "same" and the left-left or right-right. These results show that subjects detected asymmetry in beauty and suggest that very beautiful faces can be functionally asymmetrical.

  13. Accuracy enhanced thermal face recognition

    NASA Astrophysics Data System (ADS)

    Lin, Chun-Fu; Lin, Sheng-Fuu

    2013-11-01

    Human face recognition has been generally researched for the last three decades. Face recognition with thermal image has begun to attract significant attention gradually since illumination of environment would not affect the recognition performance. However, the recognition performance of traditional thermal face recognizer is still insufficient in practical application. This study presents a novel thermal face recognizer employing not only thermal features but also critical facial geometric features which would not be influenced by hair style to improve the recognition performance. A three-layer back-propagation feed-forward neural network is applied as the classifier. Traditional thermal face recognizers only use the indirect information of the topography of blood vessels like thermogram as features. To overcome this limitation, the proposed thermal face recognizer can use not only the indirect information but also the direct information of the topography of blood vessels which is unique for every human. Moreover, the recognition performance of the proposed thermal features would not decrease even if the hair of frontal bone varies, the eye blinks or the nose breathes. Experimental results show that the proposed features are significantly more effective than traditional thermal features and the recognition performance of thermal face recognizer is improved.

  14. SNL3dFace

    2007-07-20

    This software distribution contains MATLAB and C++ code to enable identity verification using 3D images that may or may not contain a texture component. The code is organized to support system performance testing and system capability demonstration through the proper configuration of the available user interface. Using specific algorithm parameters the face recognition system has been demonstrated to achieve a 96.6% verification rate (Pd) at 0.001 false alarm rate. The system computes robust facial featuresmore » of a 3D normalized face using Principal Component Analysis (PCA) and Fisher Linear Discriminant Analysis (FLDA). A 3D normalized face is obtained by alighning each face, represented by a set of XYZ coordinated, to a scaled reference face using the Iterative Closest Point (ICP) algorithm. The scaled reference face is then deformed to the input face using an iterative framework with parameters that control the deformed surface regulation an rate of deformation. A variety of options are available to control the information that is encoded by the PCA. Such options include the XYZ coordinates, the difference of each XYZ coordinates from the reference, the Z coordinate, the intensity/texture values, etc. In addition to PCA/FLDA feature projection this software supports feature matching to obtain similarity matrices for performance analysis. In addition, this software supports visualization of the STL, MRD, 2D normalized, and PCA synthetic representations in a 3D environment.« less

  15. SNL3dFace

    SciTech Connect

    Russ, Trina; Koch, Mark; Koudelka, Melissa; Peters, Ralph; Little, Charles; Boehnen, Chris; Peters, Tanya

    2007-07-20

    This software distribution contains MATLAB and C++ code to enable identity verification using 3D images that may or may not contain a texture component. The code is organized to support system performance testing and system capability demonstration through the proper configuration of the available user interface. Using specific algorithm parameters the face recognition system has been demonstrated to achieve a 96.6% verification rate (Pd) at 0.001 false alarm rate. The system computes robust facial features of a 3D normalized face using Principal Component Analysis (PCA) and Fisher Linear Discriminant Analysis (FLDA). A 3D normalized face is obtained by alighning each face, represented by a set of XYZ coordinated, to a scaled reference face using the Iterative Closest Point (ICP) algorithm. The scaled reference face is then deformed to the input face using an iterative framework with parameters that control the deformed surface regulation an rate of deformation. A variety of options are available to control the information that is encoded by the PCA. Such options include the XYZ coordinates, the difference of each XYZ coordinates from the reference, the Z coordinate, the intensity/texture values, etc. In addition to PCA/FLDA feature projection this software supports feature matching to obtain similarity matrices for performance analysis. In addition, this software supports visualization of the STL, MRD, 2D normalized, and PCA synthetic representations in a 3D environment.

  16. Can Faces Prime a Language?

    PubMed

    Woumans, Evy; Martin, Clara D; Vanden Bulcke, Charlotte; Van Assche, Eva; Costa, Albert; Hartsuiker, Robert J; Duyck, Wouter

    2015-09-01

    Bilinguals have two languages that are activated in parallel. During speech production, one of these languages must be selected on the basis of some cue. The present study investigated whether the face of an interlocutor can serve as such a cue. Spanish-Catalan and Dutch-French bilinguals were first familiarized with certain faces, each of which was associated with only one language, during simulated Skype conversations. Afterward, these participants performed a language production task in which they generated words associated with the words produced by familiar and unfamiliar faces displayed on-screen. When responding to familiar faces, participants produced words faster if the faces were speaking the same language as in the previous Skype simulation than if the same faces were speaking a different language. Furthermore, this language priming effect disappeared when it became clear that the interlocutors were actually bilingual. These findings suggest that faces can prime a language, but their cuing effect disappears when it turns out that they are unreliable as language cues. PMID:26209531

  17. Visual adaptation and face perception

    PubMed Central

    Webster, Michael A.; MacLeod, Donald I. A.

    2011-01-01

    The appearance of faces can be strongly affected by the characteristics of faces viewed previously. These perceptual after-effects reflect processes of sensory adaptation that are found throughout the visual system, but which have been considered only relatively recently in the context of higher level perceptual judgements. In this review, we explore the consequences of adaptation for human face perception, and the implications of adaptation for understanding the neural-coding schemes underlying the visual representation of faces. The properties of face after-effects suggest that they, in part, reflect response changes at high and possibly face-specific levels of visual processing. Yet, the form of the after-effects and the norm-based codes that they point to show many parallels with the adaptations and functional organization that are thought to underlie the encoding of perceptual attributes like colour. The nature and basis for human colour vision have been studied extensively, and we draw on ideas and principles that have been developed to account for norms and normalization in colour vision to consider potential similarities and differences in the representation and adaptation of faces. PMID:21536555

  18. Sm-Nd Isotopic Studies of Ureilite Novo Urei

    NASA Technical Reports Server (NTRS)

    Shih, C.-Y.; Nyquist, L. E.; Reese, Y.; Goodrich, C. A.

    2011-01-01

    Ureilites are ultramafic (harzburgitic) achondrites composed predominantly of olivine and pyroxenes, abundant carbon (graphites and shock-produced diamonds), some metal and sulfides. These rocks probably represent ultramafic mantles of differentiated parent asteroidal bodies. Age determinations of these rocks by Rb-Sr and Sm-Nd methods have been difficult because of their extremely low abundances of these parent-daughter elements. Nevertheless, Sm-Nd isochron ages were reported for Kenna, Goalpara, MET 78008 and PCA 82506 yielding ages of 3.74+/-0.02 Ga, approx.3.7 Ga, 4.09+/-0.08 Ga, 4.23+/-0.06 Ga, respectively [1-4]. These "young" Sm-Nd ages may represent secondary metasomatism events [1] related to impacts [5], as indicated by the similarly young Ar-39-Ar-40 degassing ages of 3.3-4.1 Ga for ureilites Kenna, Novo Urei and Havero [6]. Alternatively, it has been suggested that these rocks may have been contaminated with terrestrial crustal materials and the isochrons do not have any age significance [2,7]. Indications of old approx.4.56 Ga ages for ureilites were reported from the U-Pb and Sm-Nd model ages for MET 78008 [8]. More reliable evidences for old formation ages of ureilites were reported recently using the short-lived chronometers Hf-182-W-182, Al-26-Mg-26 and Mn-53-Cr-53. The deficits of 182W in ureilites suggest the metal-silicate segregation occurred very early, approx.1-2 Ma after CAI [9]. The Al-26-Mg-26 and Mn-53-Cr-53 studies for a feldspathic lithology [10] and the Mn-53-Cr-53 for olivine- and pyroxene-dominant lithologies [11] in ureilites revealed that they crystallized approx.5.4 Ma after CAI, i.e., at 4563.8+/-0.5 Ma relative to D.Orbigny. In this report, we present Sm-Nd isotopic data for a relatively fresh ureilite, Novo Urei, a rare ureilite fall (1886). We compare these data to Sm-Nd data for other ureilites, and discuss Novo Urei's petrogenesis

  19. SPACE: Vision and Reality: Face to Face. Proceedings Report

    NASA Technical Reports Server (NTRS)

    1995-01-01

    The proceedings of the 11th National Space Symposium entitled 'Vision and Reality: Face to Face' is presented. Technological areas discussed include the following sections: Vision for the future; Positioning for the future; Remote sensing, the emerging era; space opportunities, Competitive vision with acquisition reality; National security requirements in space; The world is into space; and The outlook for space. An appendice is also attached.

  20. Laser guide star AO project at the Subaru Telescope

    NASA Astrophysics Data System (ADS)

    Takami, Hideki; Watanabe, Makoto; Takato, Naruhisa; Colley, Stephen; Eldred, Michael; Kane, Thomas; Guyon, Olivier; Hattori, Masayuki; Goto, Miwa; Iye, Masanori; Hayano, Yutaka; Kamata, Yukiko; Arimoto, Nobou; Kobayashi, Naoto; Minowa, Yosuke

    2004-10-01

    The laser guide star adaptive optics (AO) system for Subaru Telescope is presented. The system will be installed at the IR Nasmyth platform, whereas the current AO system with 36 elements is operating at the Cassegrain focus. The new AO system has a 188 element wavefront curvature sensor with photon counting APD modules which is the largest control element curvature sensor system ever. The system will have 4-10 W solid state sum-frequency laser to generate a laser guide star. The laser launching telescope with 50 cm aperture will be installed at behind the secondary mirror. The laser unit will be installed on the third floor of the dome and the laser beam will be transferred to the laser launching telescope using single mode photonic crystal fiber cable. The field of view of the optics is 2.7 arcmin to maximize the probability to find tilt guide stars for laser guide star operation. The expected Strehl ratio as raw AO performance is 0.46 at H-band under 0.60" seeing with 12 th mag guide star, and 0.71 for 8 th mag stars. New wavefront modulation technique, dual stroke membrane mirror control, is developed to reduce the tilt error which is more dominant for curvature sensor AO system. The superb contrast imaging capability will be expected as natural guide star system. The first light as the natural guide star system is planned in March 2006, the laser first light will be expected in March 2007.

  1. Faces in the mist: illusory face and letter detection

    PubMed Central

    Rieth, Cory A.; Lee, Kang; Lui, Jiangang; Tian, Jie; Huber, David E.

    2011-01-01

    We report three behavioral experiments on the spatial characteristics evoking illusory face and letter detection. False detections made to pure noise images were analyzed using a modified reverse correlation method in which hundreds of observers rated a modest number of noise images (480) during a single session. This method was originally developed for brain imaging research, and has been used in a number of fMRI publications, but this is the first report of the behavioral classification images. In Experiment 1 illusory face detection occurred in response to scattered dark patches throughout the images, with a bias to the left visual field. This occurred despite the use of a fixation cross and expectations that faces would be centered. In contrast, illusory letter detection (Experiment 2) occurred in response to centrally positioned dark patches. Experiment 3 included an oval in all displays to spatially constrain illusory face detection. With the addition of this oval the classification image revealed an eyes/nose/mouth pattern. These results suggest that face detection is triggered by a minimal face-like pattern even when these features are not centered in visual focus. PMID:23145238

  2. Adaptation improves discrimination of face identity.

    PubMed

    Oruç, Ipek; Barton, Jason J S

    2011-09-01

    Whether face adaptation confers any advantages to perceptual processing remains an open question. We investigated whether face adaptation can enhance the ability to make fine discriminations in the vicinity of the adapted face. We compared face discrimination thresholds in three adapting conditions: (i) same-face: where adapting and test faces were the same, (ii) different-face: where adapting and test faces differed, and (iii) baseline: where the adapting stimulus was a blank. Discrimination thresholds for morphed identity changes involving the adapted face (same-face) improved compared with those from both the baseline (no-adaptation) and different-face conditions. Since adapting to a face did not alter discrimination performance for other faces, this effect is selective for the facial identity that is adapted. These results indicate a form of gain control to heighten perceptual sensitivity in the vicinity of a currently viewed face, analogous to forms of adaptive gain control at lower levels of the visual system.

  3. Non-Complement-Binding De Novo Donor-Specific Anti-HLA Antibodies and Kidney Allograft Survival.

    PubMed

    Guidicelli, Gwendaline; Guerville, Florent; Lepreux, Sébastien; Wiebe, Chris; Thaunat, Olivier; Dubois, Valérie; Visentin, Jonathan; Bachelet, Thomas; Morelon, Emmanuel; Nickerson, Peter; Merville, Pierre; Taupin, Jean-Luc; Couzi, Lionel

    2016-02-01

    C1q-binding ability may indicate the clinical relevance of de novo donor-specific anti-HLA antibodies (DSA). This study investigated the incidence and risk factors for the appearance of C1q-binding de novo DSA and their long-term impact. Using Luminex Single Antigen Flow Bead assays, 346 pretransplant nonsensitized kidney recipients were screened at 2 and 5 years after transplantation for de novo DSA, which was followed when positive by a C1q Luminex assay. At 2 and 5 years, 12 (3.5%) and eight (2.5%) patients, respectively, had C1q-binding de novo DSA. De novo DSA mean fluorescence intensity >6237 and >10,000 at 2 and 5 years, respectively, predicted C1q binding. HLA mismatches and cyclosporine A were independently associated with increased risk of C1q-binding de novo DSA. When de novo DSA were analyzed at 2 years, the 5-year death-censored graft survival was similar between patients with C1q-nonbinding de novo DSA and those without de novo DSA, but was lower for patients with C1q-binding de novo DSA (P=0.003). When de novo DSA were analyzed at 2 and 5 years, the 10-year death-censored graft survival was lower for patients with C1q-nonbinding de novo DSA detected at both 2 and 5 years (P<0.001) and for patients with C1q-binding de novo DSA (P=0.002) than for patients without de novo DSA. These results were partially confirmed in two validation cohorts. In conclusion, C1q-binding de novo DSA are associated with graft loss occurring quickly after their appearance. However, the long-term persistence of C1q-nonbinding de novo DSA could lead to lower graft survival. PMID:26047793

  4. Non-Complement-Binding De Novo Donor-Specific Anti-HLA Antibodies and Kidney Allograft Survival.

    PubMed

    Guidicelli, Gwendaline; Guerville, Florent; Lepreux, Sébastien; Wiebe, Chris; Thaunat, Olivier; Dubois, Valérie; Visentin, Jonathan; Bachelet, Thomas; Morelon, Emmanuel; Nickerson, Peter; Merville, Pierre; Taupin, Jean-Luc; Couzi, Lionel

    2016-02-01

    C1q-binding ability may indicate the clinical relevance of de novo donor-specific anti-HLA antibodies (DSA). This study investigated the incidence and risk factors for the appearance of C1q-binding de novo DSA and their long-term impact. Using Luminex Single Antigen Flow Bead assays, 346 pretransplant nonsensitized kidney recipients were screened at 2 and 5 years after transplantation for de novo DSA, which was followed when positive by a C1q Luminex assay. At 2 and 5 years, 12 (3.5%) and eight (2.5%) patients, respectively, had C1q-binding de novo DSA. De novo DSA mean fluorescence intensity >6237 and >10,000 at 2 and 5 years, respectively, predicted C1q binding. HLA mismatches and cyclosporine A were independently associated with increased risk of C1q-binding de novo DSA. When de novo DSA were analyzed at 2 years, the 5-year death-censored graft survival was similar between patients with C1q-nonbinding de novo DSA and those without de novo DSA, but was lower for patients with C1q-binding de novo DSA (P=0.003). When de novo DSA were analyzed at 2 and 5 years, the 10-year death-censored graft survival was lower for patients with C1q-nonbinding de novo DSA detected at both 2 and 5 years (P<0.001) and for patients with C1q-binding de novo DSA (P=0.002) than for patients without de novo DSA. These results were partially confirmed in two validation cohorts. In conclusion, C1q-binding de novo DSA are associated with graft loss occurring quickly after their appearance. However, the long-term persistence of C1q-nonbinding de novo DSA could lead to lower graft survival.

  5. Toehold Switches: De-Novo-Designed Regulators of Gene Expression

    PubMed Central

    Green, Alexander A.; Silver, Pamela A.; Collins, James J.; Yin, Peng

    2014-01-01

    SUMMARY Efforts to construct synthetic networks in living cells have been hindered by the limited number of regulatory components that provide wide dynamic range and low crosstalk. Here, we report a new class of de-novo-designed prokaryotic riboregulators called toehold switches that activate gene expression in response to cognate RNAs with arbitrary sequences. Toehold switches provide a high level of orthogonality and can be forward-engineered to provide average dynamic range above 400. We show that switches can be integrated into the genome to regulate endogenous genes and use them as sensors that respond to endogenous RNAs. We exploit the orthogonality of toehold switches to regulate 12 genes independently and to construct a genetic circuit that evaluates 4-input AND logic. Toehold switches, with their wide dynamic range, orthogonality, and programmability, represent a versatile and powerful platform for regulation of translation, offering diverse applications in molecular biology, synthetic biology, and biotechnology. PMID:25417166

  6. De novo synthesis of a sunscreen compound in vertebrates.

    PubMed

    Osborn, Andrew R; Almabruk, Khaled H; Holzwarth, Garrett; Asamizu, Shumpei; LaDu, Jane; Kean, Kelsey M; Karplus, P Andrew; Tanguay, Robert L; Bakalinsky, Alan T; Mahmud, Taifo

    2015-01-01

    Ultraviolet-protective compounds, such as mycosporine-like amino acids (MAAs) and related gadusols produced by some bacteria, fungi, algae, and marine invertebrates, are critical for the survival of reef-building corals and other marine organisms exposed to high-solar irradiance. These compounds have also been found in marine fish, where their accumulation is thought to be of dietary or symbiont origin. In this study, we report the unexpected discovery that fish can synthesize gadusol de novo and that the analogous pathways are also present in amphibians, reptiles, and birds. Furthermore, we demonstrate that engineered yeast containing the fish genes can produce and secrete gadusol. The discovery of the gadusol pathway in vertebrates provides a platform for understanding its role in these animals, and the possibility of engineering yeast to efficiently produce a natural sunscreen and antioxidant presents an avenue for its large-scale production for possible use in pharmaceuticals and cosmetics. PMID:25965179

  7. De novo development of artistic creativity in Alzheimer's disease

    PubMed Central

    Chakravarty, Ambar

    2011-01-01

    The case of an 82-year-old female with probable Alzheimer's disease (AD), who developed unusual artistic creativity after development of her disease, is described. The possible pathogenetic mechanism is discussed. The patient showed no inclination toward visual arts during her premorbid years. However, 4 years after development of AD suggestive symptoms she started painting beautiful pictures rather impulsively. Some such paintings have been appreciated even by a qualified art expert. Such de novo development of artistic creativity had been described earlier in subjects with the semantic form of fronto-temporal dementia (FTD), but not in AD. The prevailing concept of lateralized compromise and paradoxical functional facilitation, proposed in connection with FTD subjects, may not be applicable in AD subjects where the affection is more diffuse and more posterior in the brain. Hence, the likely pathogenetic mechanism involved in the case described may remain uncertain. Possibilities are discussed. PMID:22346020

  8. De novo assembly of a haplotype-resolved human genome.

    PubMed

    Cao, Hongzhi; Wu, Honglong; Luo, Ruibang; Huang, Shujia; Sun, Yuhui; Tong, Xin; Xie, Yinlong; Liu, Binghang; Yang, Hailong; Zheng, Hancheng; Li, Jian; Li, Bo; Wang, Yu; Yang, Fang; Sun, Peng; Liu, Siyang; Gao, Peng; Huang, Haodong; Sun, Jing; Chen, Dan; He, Guangzhu; Huang, Weihua; Huang, Zheng; Li, Yue; Tellier, Laurent C A M; Liu, Xiao; Feng, Qiang; Xu, Xun; Zhang, Xiuqing; Bolund, Lars; Krogh, Anders; Kristiansen, Karsten; Drmanac, Radoje; Drmanac, Snezana; Nielsen, Rasmus; Li, Songgang; Wang, Jian; Yang, Huanming; Li, Yingrui; Wong, Gane Ka-Shu; Wang, Jun

    2015-06-01

    The human genome is diploid, and knowledge of the variants on each chromosome is important for the interpretation of genomic information. Here we report the assembly of a haplotype-resolved diploid genome without using a reference genome. Our pipeline relies on fosmid pooling together with whole-genome shotgun strategies, based solely on next-generation sequencing and hierarchical assembly methods. We applied our sequencing method to the genome of an Asian individual and generated a 5.15-Gb assembled genome with a haplotype N50 of 484 kb. Our analysis identified previously undetected indels and 7.49 Mb of novel coding sequences that could not be aligned to the human reference genome, which include at least six predicted genes. This haplotype-resolved genome represents the most complete de novo human genome assembly to date. Application of our approach to identify individual haplotype differences should aid in translating genotypes to phenotypes for the development of personalized medicine. PMID:26006006

  9. Neoplastic disease after liver transplantation: Focus on de novo neoplasms

    PubMed Central

    Burra, Patrizia; Rodriguez-Castro, Kryssia I

    2015-01-01

    De novo neoplasms account for almost 30% of deaths 10 years after liver transplantation and are the most common cause of mortality in patients surviving at least 1 year after transplant. The risk of malignancy is two to four times higher in transplant recipients than in an age- and sex-matched population, and cancer is expected to surpass cardiovascular complications as the primary cause of death in transplanted patients within the next 2 decades. Since exposure to immunosuppression is associated with an increased frequency of developing neoplasm, long-term immunosuppression should be therefore minimized. Promising results in the prevention of hepatocellular carcinoma (HCC) recurrence have been reported with the use of mTOR inhibitors including everolimus and sirolimus and the ongoing open-label prospective randomized controlled SILVER. Study will provide more information on whether sirolimus-containing vs mTOR-inhibitor-free immunosuppression is more efficacious in reducing HCC recurrence. PMID:26269665

  10. Herpes simplex virus 1 induces de novo phospholipid synthesis

    SciTech Connect

    Sutter, Esther; Oliveira, Anna Paula de; Tobler, Kurt; Schraner, Elisabeth M.; Sonda, Sabrina; Kaech, Andres; Lucas, Miriam S.; Ackermann, Mathias; Wild, Peter

    2012-08-01

    Herpes simplex virus type 1 capsids bud at nuclear membranes and Golgi membranes acquiring an envelope composed of phospholipids. Hence, we measured incorporation of phospholipid precursors into these membranes, and quantified changes in size of cellular compartments by morphometric analysis. Incorporation of [{sup 3}H]-choline into both nuclear and cytoplasmic membranes was significantly enhanced upon infection. [{sup 3}H]-choline was also part of isolated virions even grown in the presence of brefeldin A. Nuclei expanded early in infection. The Golgi complex and vacuoles increased substantially whereas the endoplasmic reticulum enlarged only temporarily. The data suggest that HSV-1 stimulates phospholipid synthesis, and that de novo synthesized phospholipids are inserted into nuclear and cytoplasmic membranes to i) maintain membrane integrity in the course of nuclear and cellular expansion, ii) to supply membrane constituents for envelopment of capsids by budding at nuclear membranes and Golgi membranes, and iii) to provide membranes for formation of transport vacuoles.

  11. De-Novo Design of Antimicrobial Peptides for Plant Protection

    PubMed Central

    Zeitler, Benjamin; Herrera Diaz, Areli; Dangel, Alexandra; Thellmann, Martha; Meyer, Helge; Sattler, Michael; Lindermayr, Christian

    2013-01-01

    This work describes the de-novo design of peptides that inhibit a broad range of plant pathogens. Four structurally different groups of peptides were developed that differ in size and position of their charged and hydrophobic clusters and were assayed for their ability to inhibit bacterial growth and fungal spore germination. Several peptides are highly active at concentrations between 0,1 and 1 µg/ml against plant pathogenic bacteria, such as Pseudomonas syringae, Pectobacterium carotovorum, and Xanthomonas vesicatoria. Importantly, no hemolytic activity could be detected for these peptides at concentrations up to 200 µg/ml. Moreover, the peptides are also active after spraying on the plant surface demonstrating a possible way of application. In sum, our designed peptides represent new antimicrobial agents and with the increasing demand for antimicrobial compounds for production of “healthy” food, these peptides might serve as templates for novel antibacterial and antifungal agents. PMID:23951222

  12. De novo assembly of a haplotype-resolved human genome.

    PubMed

    Cao, Hongzhi; Wu, Honglong; Luo, Ruibang; Huang, Shujia; Sun, Yuhui; Tong, Xin; Xie, Yinlong; Liu, Binghang; Yang, Hailong; Zheng, Hancheng; Li, Jian; Li, Bo; Wang, Yu; Yang, Fang; Sun, Peng; Liu, Siyang; Gao, Peng; Huang, Haodong; Sun, Jing; Chen, Dan; He, Guangzhu; Huang, Weihua; Huang, Zheng; Li, Yue; Tellier, Laurent C A M; Liu, Xiao; Feng, Qiang; Xu, Xun; Zhang, Xiuqing; Bolund, Lars; Krogh, Anders; Kristiansen, Karsten; Drmanac, Radoje; Drmanac, Snezana; Nielsen, Rasmus; Li, Songgang; Wang, Jian; Yang, Huanming; Li, Yingrui; Wong, Gane Ka-Shu; Wang, Jun

    2015-06-01

    The human genome is diploid, and knowledge of the variants on each chromosome is important for the interpretation of genomic information. Here we report the assembly of a haplotype-resolved diploid genome without using a reference genome. Our pipeline relies on fosmid pooling together with whole-genome shotgun strategies, based solely on next-generation sequencing and hierarchical assembly methods. We applied our sequencing method to the genome of an Asian individual and generated a 5.15-Gb assembled genome with a haplotype N50 of 484 kb. Our analysis identified previously undetected indels and 7.49 Mb of novel coding sequences that could not be aligned to the human reference genome, which include at least six predicted genes. This haplotype-resolved genome represents the most complete de novo human genome assembly to date. Application of our approach to identify individual haplotype differences should aid in translating genotypes to phenotypes for the development of personalized medicine.

  13. De novo design of the hydrophobic cores of proteins.

    PubMed Central

    Desjarlais, J. R.; Handel, T. M.

    1995-01-01

    We have developed and experimentally tested a novel computational approach for the de novo design of hydrophobic cores. A pair of computer programs has been written, the first of which creates a "custom" rotamer library for potential hydrophobic residues, based on the backbone structure of the protein of interest. The second program uses a genetic algorithm to globally optimize for a low energy core sequence and structure, using the custom rotamer library as input. Success of the programs in predicting the sequences of native proteins indicates that they should be effective tools for protein design. Using these programs, we have designed and engineered several variants of the phage 434 cro protein, containing five, seven, or eight sequence changes in the hydrophobic core. As controls, we have produced a variant consisting of a randomly generated core with six sequence changes but equal volume relative to the native core and a variant with a "minimalist" core containing predominantly leucine residues. Two of the designs, including one with eight core sequence changes, have thermal stabilities comparable to the native protein, whereas the third design and the minimalist protein are significantly destabilized. The randomly designed control is completely unfolded under equivalent conditions. These results suggest that rational de novo design of hydrophobic cores is feasible, and stress the importance of specific packing interactions for the stability of proteins. A surprising aspect of the results is that all of the variants display highly cooperative thermal denaturation curves and reasonably dispersed NMR spectra. This suggests that the non-core residues of a protein play a significant role in determining the uniqueness of the folded structure. PMID:8535237

  14. Genome-wide characteristics of de novo mutations in autism

    PubMed Central

    Yuen, Ryan K C; Merico, Daniele; Cao, Hongzhi; Pellecchia, Giovanna; Alipanahi, Babak; Thiruvahindrapuram, Bhooma; Tong, Xin; Sun, Yuhui; Cao, Dandan; Zhang, Tao; Wu, Xueli; Jin, Xin; Zhou, Ze; Liu, Xiaomin; Nalpathamkalam, Thomas; Walker, Susan; Howe, Jennifer L.; Wang, Zhuozhi; MacDonald, Jeffrey R.; Chan, Ada; D’Abate, Lia; Deneault, Eric; Siu, Michelle T.; Tammimies, Kristiina; Uddin, Mohammed; Zarrei, Mehdi; Wang, Mingbang; Li, Yingrui; Wang, Jun; Wang, Jian; Yang, Huanming; Bookman, Matt; Bingham, Jonathan; Gross, Samuel S.; Loy, Dion; Pletcher, Mathew; Marshall, Christian R.; Anagnostou, Evdokia; Zwaigenbaum, Lonnie; Weksberg, Rosanna; Fernandez, Bridget A; Roberts, Wendy; Szatmari, Peter; Glazer, David; Frey, Brendan J.; Ring, Robert H.; Xu, Xun; Scherer, Stephen W.

    2016-01-01

    De novo mutations (DNMs) are important in Autism Spectrum Disorder (ASD), but so far analyses have mainly been on the ~1.5% of the genome encoding genes. Here, we performed whole genome sequencing (WGS) of 200 ASD parent-child trios and characterized germline and somatic DNMs. We confirmed that the majority of germline DNMs (75.6%) originated from the father, and these increased significantly with paternal age only (p=4.2×10−10). However, when clustered DNMs (those within 20kb) were found in ASD, not only did they mostly originate from the mother (p=7.7×10−13), but they could also be found adjacent to de novo copy number variations (CNVs) where the mutation rate was significantly elevated (p=2.4×10−24). By comparing DNMs detected in controls, we found a significant enrichment of predicted damaging DNMs in ASD cases (p=8.0×10−9; OR=1.84), of which 15.6% (p=4.3×10−3) and 22.5% (p=7.0×10−5) were in the non-coding or genic non-coding, respectively. The non-coding elements most enriched for DNM were untranslated regions of genes, boundaries involved in exon-skipping and DNase I hypersensitive regions. Using microarrays and a novel outlier detection test, we also found aberrant methylation profiles in 2/185 (1.1%) of ASD cases. These same individuals carried independently identified DNMs in the ASD risk- and epigenetic- genes DNMT3A and ADNP. Our data begins to characterize different genome-wide DNMs, and highlight the contribution of non-coding variants, to the etiology of ASD. PMID:27525107

  15. De novo mutations in moderate or severe intellectual disability.

    PubMed

    Hamdan, Fadi F; Srour, Myriam; Capo-Chichi, Jose-Mario; Daoud, Hussein; Nassif, Christina; Patry, Lysanne; Massicotte, Christine; Ambalavanan, Amirthagowri; Spiegelman, Dan; Diallo, Ousmane; Henrion, Edouard; Dionne-Laporte, Alexandre; Fougerat, Anne; Pshezhetsky, Alexey V; Venkateswaran, Sunita; Rouleau, Guy A; Michaud, Jacques L

    2014-10-01

    Genetics is believed to have an important role in intellectual disability (ID). Recent studies have emphasized the involvement of de novo mutations (DNMs) in ID but the extent to which they contribute to its pathogenesis and the identity of the corresponding genes remain largely unknown. Here, we report a screen for DNMs in subjects with moderate or severe ID. We sequenced the exomes of 41 probands and their parents, and confirmed 81 DNMs affecting the coding sequence or consensus splice sites (1.98 DNMs/proband). We observed a significant excess of de novo single nucleotide substitutions and loss-of-function mutations in these cases compared to control subjects, suggesting that at least a subset of these variations are pathogenic. A total of 12 likely pathogenic DNMs were identified in genes previously associated with ID (ARID1B, CHD2, FOXG1, GABRB3, GATAD2B, GRIN2B, MBD5, MED13L, SETBP1, TBR1, TCF4, WDR45), resulting in a diagnostic yield of ∼29%. We also identified 12 possibly pathogenic DNMs in genes (HNRNPU, WAC, RYR2, SET, EGR1, MYH10, EIF2C1, COL4A3BP, CHMP2A, PPP1CB, VPS4A, PPP2R2B) that have not previously been causally linked to ID. Interestingly, no case was explained by inherited mutations. Protein network analysis indicated that the products of many of these known and candidate genes interact with each other or with products of other ID-associated genes further supporting their involvement in ID. We conclude that DNMs represent a major cause of moderate or severe ID. PMID:25356899

  16. Congenital cataracts: de novo gene conversion event in CRYBB2

    PubMed Central

    Garnai, Sarah J.; Huyghe, Jeroen R.; Reed, David M.; Scott, Kathleen M.; Liebmann, Jeffrey M.; Boehnke, Michael; Ritch, Robert; Pawar, Hemant

    2014-01-01

    Purpose To identify the cause of congenital cataracts in a consanguineous family of Ashkenazi Jewish ancestry. Methods We performed genome-wide linkage analysis and whole-exome sequencing for the initial discovery of variants, and we confirmed the variants using gene-specific primers and Sanger sequencing. Results We found significant evidence of linkage to chromosome 22, under an autosomal dominant inheritance model, with a maximum logarithm of the odds (LOD) score of 3.91 (16.918 to 25.641 Mb). Exome sequencing identified three nonsynonymous changes in the CRYBB2 exon 5 coding sequence that are consistent with the sequence of the corresponding region of the pseudogene CRYBB2P1. The identification of these changes was complicated by possible mismapping of some mutated CRYBB2 sequences to CRYBB2P1. Sequencing with gene-specific primers confirmed that the changes—rs2330991, c.433 C>T (p.R145W); rs2330992, c.440A>G (p.Q147R); and rs4049504, c.449C>T (p.T150M)—present in all ten affected family members are located in CRYBB2 and are not artifacts of cross-reaction with CRYBB2P1. We did not find these changes in six unaffected family members, including the unaffected grandfather who contributed the affected haplotype, nor did we find them in the 100 Ashkenazi Jewish controls. Conclusions Our data are consistent with a de novo gene conversion event, transferring 270 base pairs at most from CRYBB2P1 to exon 5 of CRYBB2. This study highlights how linkage mapping can be complicated by de novo mutation events, as well as how sequence-analysis pipeline mapping of short reads from next-generation sequencing can be complicated by the existence of pseudogenes or other highly homologous sequences. PMID:25489230

  17. De Novo Mutations in Moderate or Severe Intellectual Disability

    PubMed Central

    Hamdan, Fadi F.; Srour, Myriam; Capo-Chichi, Jose-Mario; Daoud, Hussein; Nassif, Christina; Patry, Lysanne; Massicotte, Christine; Ambalavanan, Amirthagowri; Spiegelman, Dan; Diallo, Ousmane; Henrion, Edouard; Dionne-Laporte, Alexandre; Fougerat, Anne; Pshezhetsky, Alexey V.; Venkateswaran, Sunita; Rouleau, Guy A.; Michaud, Jacques L.

    2014-01-01

    Genetics is believed to have an important role in intellectual disability (ID). Recent studies have emphasized the involvement of de novo mutations (DNMs) in ID but the extent to which they contribute to its pathogenesis and the identity of the corresponding genes remain largely unknown. Here, we report a screen for DNMs in subjects with moderate or severe ID. We sequenced the exomes of 41 probands and their parents, and confirmed 81 DNMs affecting the coding sequence or consensus splice sites (1.98 DNMs/proband). We observed a significant excess of de novo single nucleotide substitutions and loss-of-function mutations in these cases compared to control subjects, suggesting that at least a subset of these variations are pathogenic. A total of 12 likely pathogenic DNMs were identified in genes previously associated with ID (ARID1B, CHD2, FOXG1, GABRB3, GATAD2B, GRIN2B, MBD5, MED13L, SETBP1, TBR1, TCF4, WDR45), resulting in a diagnostic yield of ∼29%. We also identified 12 possibly pathogenic DNMs in genes (HNRNPU, WAC, RYR2, SET, EGR1, MYH10, EIF2C1, COL4A3BP, CHMP2A, PPP1CB, VPS4A, PPP2R2B) that have not previously been causally linked to ID. Interestingly, no case was explained by inherited mutations. Protein network analysis indicated that the products of many of these known and candidate genes interact with each other or with products of other ID-associated genes further supporting their involvement in ID. We conclude that DNMs represent a major cause of moderate or severe ID. PMID:25356899

  18. Second generation Robo-AO instruments and systems

    NASA Astrophysics Data System (ADS)

    Baranec, Christoph; Riddle, Reed; Law, Nicholas M.; Chun, Mark R.; Lu, Jessica R.; Connelley, Michael S.; Hall, Donald; Atkinson, Dani; Jacobson, Shane

    2014-07-01

    The prototype Robo-AO system at the Palomar Observatory 1.5-m telescope is the world's first fully automated laser adaptive optics instrument. Scientific operations commenced in June 2012 and more than 12,000 observations have since been performed at the ~0.12" visible-light diffraction limit. Two new infrared cameras providing high-speed tip-tilt sensing and a 2' field-of-view will be integrated in 2014. In addition to a Robo-AO clone for the 2-m IGO and the natural guide star variant KAPAO at the 1-m Table Mountain telescope, a second generation of facility-class Robo-AO systems are in development for the 2.2-m University of Hawai'i and 3-m IRTF telescopes which will provide higher Strehl ratios, sharper imaging, ~0.07", and correction to λ = 400 nm.

  19. Matching Faces Against the Clock

    PubMed Central

    Fysh, Matthew; Cross, Katie; Watts, Rebecca

    2016-01-01

    This study examined the effect of time pressure on face-matching accuracy. Across two experiments, observers decided whether pairs of faces depict one person or different people. Time pressure was exerted via two additional displays, which were constantly updated to inform observers on whether they were on track to meet or miss a time target. In this paradigm, faces were matched under increasing or decreasing (Experiment 1) and constant time pressure (Experiment 2), which varied from 10 to 2 seconds. In both experiments, time pressure reduced accuracy, but the point at which this declined varied from 8 to 2 seconds. A separate match response bias was found, which developed over the course of the experiments. These results indicate that both time pressure and the repetitive nature of face matching are detrimental to performance. PMID:27757219

  20. Erysipelas on the face (image)

    MedlinePlus

    Erysipelas produces a rash that is red, slightly swollen, very defined (well demarcated), warm, and tender to ... face, however, bilateral (both side) involvement is infrequent. Erysipelas may produce symptoms that affect the entire body ( ...

  1. Aging changes in the face

    MedlinePlus

    ... spots on the face increase as well. These pigment changes are largely due to sun exposure. Missing ... The colored portion of the eye (iris) loses pigment, making most very elderly people appear to have ...

  2. Carbon-Type Analysis and Comparison of Original and Reblended FACE Diesel Fuels (FACE 2, FACE 4, and FACE 7)

    SciTech Connect

    Bays, J. Timothy; King, David L.; O'Hagan, Molly J.

    2012-10-01

    This report summarizes the carbon-type analysis from 1H and 13C{1H} nuclear magnetic resonance spectroscopy (NMR) of Fuels for Advanced Combustion Engines (FACE) diesel blends, FD-2B, FD 4B, and FD-7B, and makes comparison of the new blends with the original FACE diesel blends, FD 2A, FD 4A, and FD-7A, respectively. Generally, FD-2A and FD-2B are more similar than the A and B blends of FD-4 and FD-7. The aromatic carbon content is roughly equivalent, although the new FACE blends have decreased monoaromatic content and increased di- and tri-cycloaromatic content, as well as a higher overall aromatic content, than the original FACE blends. The aromatic components of the new FACE blends generally have a higher alkyl substitution with longer alkyl substituents. The naphthenic and paraffinic contents remained relatively consistent. Based on aliphatic methyl and methylene carbon ratios, cetane numbers for FD-2A and -2B, and FD-7A and -7B are predicted to be consistent, while the cetane number for FD-4B is predicted to be higher than FD-4A. Overall, the new FACE fuel blends are fairly consistent with the original FACE fuel blends, but there are observable differences. In addition to providing important comparative compositional information on reformulated FACE diesel blends, this report also provides important information about the capabilities of the team at Pacific Northwest National Laboratory in the use of NMR spectroscopy for the detailed characterization and comparison of fuels and fuel blends.

  3. Face verification with balanced thresholds.

    PubMed

    Yan, Shuicheng; Xu, Dong; Tang, Xiaoou

    2007-01-01

    The process of face verification is guided by a pre-learned global threshold, which, however, is often inconsistent with class-specific optimal thresholds. It is, hence, beneficial to pursue a balance of the class-specific thresholds in the model-learning stage. In this paper, we present a new dimensionality reduction algorithm tailored to the verification task that ensures threshold balance. This is achieved by the following aspects. First, feasibility is guaranteed by employing an affine transformation matrix, instead of the conventional projection matrix, for dimensionality reduction, and, hence, we call the proposed algorithm threshold balanced transformation (TBT). Then, the affine transformation matrix, constrained as the product of an orthogonal matrix and a diagonal matrix, is optimized to improve the threshold balance and classification capability in an iterative manner. Unlike most algorithms for face verification which are directly transplanted from face identification literature, TBT is specifically designed for face verification and clarifies the intrinsic distinction between these two tasks. Experiments on three benchmark face databases demonstrate that TBT significantly outperforms the state-of-the-art subspace techniques for face verification.

  4. [Faces affect recognition in schizophrenia].

    PubMed

    Prochwicz, Katarzyna; Rózycka, Jagoda

    2012-01-01

    Clinical observations and the results of many experimental researches indicate that individuals suffering from schizophrenia reveal difficulties in the recognition of emotional states experienced by other people; however the causes and the range of these problems have not been clearly described. Despite early research results confirming that difficulties in emotion recognition are related only to negative emotions, the results of the researches conducted over the lat 30 years indicate that emotion recognition problems are a manifestation of a general cognitive deficit, and they do not concern specific emotions. The article contains a review of the research on face affect recognition in schizophrenia. It discusses the causes of these difficulties, the differences in the accuracy of the recognition of specific emotions, the relationship between the symptoms of schizophrenia and the severity of problems with face perception, and the types of cognitive processes which influence the disturbances in face affect recognition. Particular attention was paid to the methodology of the research on face affect recognition, including the methods used in control tasks relying on the identification of neutral faces designed to assess the range of deficit underlying the face affect recognition problems. The analysis of methods used in particular researches revealed some weaknesses. The article also deals with the question of the possibilities of improving the ability to recognise the emotions, and briefly discusses the efficiency of emotion recognition training programs designed for patients suffering from schizophrenia.

  5. Real-time face tracking

    NASA Astrophysics Data System (ADS)

    Liang, Yufeng; Wilder, Joseph

    1998-10-01

    A real-time face tracker is presented in this paper. The system has achieved 15 frames/second tracking using a Pentium 200 PC with a Datacube MaxPCI image processing board and a Panasonic RGB color camera. It tracks human faces in the camera's field of view while people move freely. A stochastic model to characterize the skin color distribution of human skin is used to segment the face and other skin areas from the background. Median filtering is then used to clean up the background noise. Geometric constraints are applied to the segmented image to extract the face from the background. To reduce computation and achieve real-time tracking, 1D projections (horizontal and vertical) of the image are analyzed instead of the 2D image. Run-length- encoding and frequency domain analysis algorithms are used to separate faces from other skin-like blobs. The system is robust to illumination intensity variations and different skin colors. It can be applied to many human-computer interaction applications such as sound locating, lip- reading, gaze tracking and face recognition.

  6. High-Performance CCSDS AOS Protocol Implementation in FPGA

    NASA Technical Reports Server (NTRS)

    Clare, Loren P.; Torgerson, Jordan L.; Pang, Jackson

    2010-01-01

    The Consultative Committee for Space Data Systems (CCSDS) Advanced Orbiting Systems (AOS) space data link protocol provides a framing layer between channel coding such as LDPC (low-density parity-check) and higher-layer link multiplexing protocols such as CCSDS Encapsulation Service, which is described in the following article. Recent advancement in RF modem technology has allowed multi-megabit transmission over space links. With this increase in data rate, the CCSDS AOS protocol implementation needs to be optimized to both reduce energy consumption and operate at a high rate.

  7. Initial Performance of the Keck AO Wavefront Controller System

    SciTech Connect

    Johansson, E M; Acton, D S; An, J R; Avicola, K; Beeman, B V; Brase, J M; Carrano, C J; Gathright, J; Gavel, D T; Hurd, R L; Lai, O; Lupton, W; Macintosh, B A; Max, C E; Olivier, S S; Shelton, J C; Stomski, P J; Tsubota, K; Waltjen, K E; Watson, J A; Wizinowich, P L

    2001-03-01

    The wavefront controller for the Keck Observatory AO system consists of two separate real-time control loops: a tip-tilt control loop to remove tilt from the incoming wavefront, and a deformable mirror control loop to remove higher-order aberrations. In this paper, we describe these control loops and analyze their performance using diagnostic data acquired during the integration and testing of the AO system on the telescope. Disturbance rejection curves for the controllers are calculated from the experimental data and compared to theory. The residual wavefront errors due to control loop bandwidth are also calculated from the data, and possible improvements to the controller performance are discussed.

  8. Photoreceptor counting and montaging of en-face retinal images from an adaptive optics fundus camera.

    PubMed

    Xue, Bai; Choi, Stacey S; Doble, Nathan; Werner, John S

    2007-05-01

    A fast and efficient method for quantifying photoreceptor density in images obtained with an en-face flood-illuminated adaptive optics (AO) imaging system is described. To improve accuracy of cone counting, en-face images are analyzed over extended areas. This is achieved with two separate semiautomated algorithms: (1) a montaging algorithm that joins retinal images with overlapping common features without edge effects and (2) a cone density measurement algorithm that counts the individual cones in the montaged image. The accuracy of the cone density measurement algorithm is high, with >97% agreement for a simulated retinal image (of known density, with low contrast) and for AO images from normal eyes when compared with previously reported histological data. Our algorithms do not require spatial regularity in cone packing and are, therefore, useful for counting cones in diseased retinas, as demonstrated for eyes with Stargardt's macular dystrophy and retinitis pigmentosa. PMID:17429482

  9. A Prediction of the Damping Properties of Hindered Phenol AO-60/polyacrylate Rubber (AO-60/ACM) Composites through Molecular Dynamics Simulation

    NASA Astrophysics Data System (ADS)

    Yang, Da-Wei; Zhao, Xiu-Ying; Zhang, Geng; Li, Qiang-Guo; Wu, Si-Zhu

    2016-05-01

    Molecule dynamics (MD) simulation, a molecular-level method, was applied to predict the damping properties of AO-60/polyacrylate rubber (AO-60/ACM) composites before experimental measures were performed. MD simulation results revealed that two types of hydrogen bond, namely, type A (AO-60) -OH•••O=C- (ACM), type B (AO-60) - OH•••O=C- (AO-60) were formed. Then, the AO-60/ACM composites were fabricated and tested to verify the accuracy of the MD simulation through dynamic mechanical thermal analysis (DMTA). DMTA results showed that the introduction of AO-60 could remarkably improve the damping properties of the composites, including the increase of glass transition temperature (Tg) alongside with the loss factor (tan δ), also indicating the AO-60/ACM(98/100) had the best damping performance amongst the composites which verified by the experimental.

  10. Semantic Learning Modifies Perceptual Face Processing

    ERIC Educational Resources Information Center

    Heisz, Jennifer J.; Shedden, Judith M.

    2009-01-01

    Face processing changes when a face is learned with personally relevant information. In a five-day learning paradigm, faces were presented with rich semantic stories that conveyed personal information about the faces. Event-related potentials were recorded before and after learning during a passive viewing task. When faces were novel, we observed…

  11. Post-zygotic Point Mutations Are an Underrecognized Source of De Novo Genomic Variation

    PubMed Central

    Acuna-Hidalgo, Rocio; Bo, Tan; Kwint, Michael P.; van de Vorst, Maartje; Pinelli, Michele; Veltman, Joris A.; Hoischen, Alexander; Vissers, Lisenka E.L.M.; Gilissen, Christian

    2015-01-01

    De novo mutations are recognized both as an important source of genetic variation and as a prominent cause of sporadic disease in humans. Mutations identified as de novo are generally assumed to have occurred during gametogenesis and, consequently, to be present as germline events in an individual. Because Sanger sequencing does not provide the sensitivity to reliably distinguish somatic from germline mutations, the proportion of de novo mutations that occur somatically rather than in the germline remains largely unknown. To determine the contribution of post-zygotic events to de novo mutations, we analyzed a set of 107 de novo mutations in 50 parent-offspring trios. Using four different sequencing techniques, we found that 7 (6.5%) of these presumed germline de novo mutations were in fact present as mosaic mutations in the blood of the offspring and were therefore likely to have occurred post-zygotically. Furthermore, genome-wide analysis of “de novo” variants in the proband led to the identification of 4/4,081 variants that were also detectable in the blood of one of the parents, implying parental mosaicism as the origin of these variants. Thus, our results show that an important fraction of de novo mutations presumed to be germline in fact occurred either post-zygotically in the offspring or were inherited as a consequence of low-level mosaicism in one of the parents. PMID:26054435

  12. On the Origin of De Novo Genes in Arabidopsis thaliana Populations.

    PubMed

    Li, Zi-Wen; Chen, Xi; Wu, Qiong; Hagmann, Jörg; Han, Ting-Shen; Zou, Yu-Pan; Ge, Song; Guo, Ya-Long

    2016-08-03

    De novo genes, which originate from ancestral nongenic sequences, are one of the most important sources of protein-coding genes. This origination process is crucial for the adaptation of organisms. However, how de novo genes arise and become fixed in a population or species remains largely unknown. Here, we identified 782 de novo genes from the model plant Arabidopsis thaliana and divided them into three types based on the availability of translational evidence, transcriptional evidence, and neither transcriptional nor translational evidence for their origin. Importantly, by integrating multiple types of omics data, including data from genomes, epigenomes, transcriptomes, and translatomes, we found that epigenetic modifications (DNA methylation and histone modification) play an important role in the origination process of de novo genes. Intriguingly, using the transcriptomes and methylomes from the same population of 84 accessions, we found that de novo genes that are transcribed in approximately half of the total accessions within the population are highly methylated, with lower levels of transcription than those transcribed at other frequencies within the population. We hypothesized that, during the origin of de novo gene alleles, those neutralized to low expression states via DNA methylation have relatively high probabilities of spreading and becoming fixed in a population. Our results highlight the process underlying the origin of de novo genes at the population level, as well as the importance of DNA methylation in this process.

  13. On the Origin of De Novo Genes in Arabidopsis thaliana Populations.

    PubMed

    Li, Zi-Wen; Chen, Xi; Wu, Qiong; Hagmann, Jörg; Han, Ting-Shen; Zou, Yu-Pan; Ge, Song; Guo, Ya-Long

    2016-01-01

    De novo genes, which originate from ancestral nongenic sequences, are one of the most important sources of protein-coding genes. This origination process is crucial for the adaptation of organisms. However, how de novo genes arise and become fixed in a population or species remains largely unknown. Here, we identified 782 de novo genes from the model plant Arabidopsis thaliana and divided them into three types based on the availability of translational evidence, transcriptional evidence, and neither transcriptional nor translational evidence for their origin. Importantly, by integrating multiple types of omics data, including data from genomes, epigenomes, transcriptomes, and translatomes, we found that epigenetic modifications (DNA methylation and histone modification) play an important role in the origination process of de novo genes. Intriguingly, using the transcriptomes and methylomes from the same population of 84 accessions, we found that de novo genes that are transcribed in approximately half of the total accessions within the population are highly methylated, with lower levels of transcription than those transcribed at other frequencies within the population. We hypothesized that, during the origin of de novo gene alleles, those neutralized to low expression states via DNA methylation have relatively high probabilities of spreading and becoming fixed in a population. Our results highlight the process underlying the origin of de novo genes at the population level, as well as the importance of DNA methylation in this process. PMID:27401176

  14. On the Origin of De Novo Genes in Arabidopsis thaliana Populations

    PubMed Central

    Li, Zi-Wen; Chen, Xi; Wu, Qiong; Hagmann, Jörg; Han, Ting-Shen; Zou, Yu-Pan; Ge, Song; Guo, Ya-Long

    2016-01-01

    De novo genes, which originate from ancestral nongenic sequences, are one of the most important sources of protein-coding genes. This origination process is crucial for the adaptation of organisms. However, how de novo genes arise and become fixed in a population or species remains largely unknown. Here, we identified 782 de novo genes from the model plant Arabidopsis thaliana and divided them into three types based on the availability of translational evidence, transcriptional evidence, and neither transcriptional nor translational evidence for their origin. Importantly, by integrating multiple types of omics data, including data from genomes, epigenomes, transcriptomes, and translatomes, we found that epigenetic modifications (DNA methylation and histone modification) play an important role in the origination process of de novo genes. Intriguingly, using the transcriptomes and methylomes from the same population of 84 accessions, we found that de novo genes that are transcribed in approximately half of the total accessions within the population are highly methylated, with lower levels of transcription than those transcribed at other frequencies within the population. We hypothesized that, during the origin of de novo gene alleles, those neutralized to low expression states via DNA methylation have relatively high probabilities of spreading and becoming fixed in a population. Our results highlight the process underlying the origin of de novo genes at the population level, as well as the importance of DNA methylation in this process. PMID:27401176

  15. Apple fruit copper amine oxidase isoforms: peroxisomal MdAO1 prefers diamines as substrates, whereas extracellular MdAO2 exclusively utilizes monoamines.

    PubMed

    Zarei, Adel; Trobacher, Christopher P; Cooke, Alison R; Meyers, Ashley J; Hall, J Christopher; Shelp, Barry J

    2015-01-01

    4-Aminobutyrate (GABA) accumulates in apple fruit during controlled atmosphere storage. A potential source of GABA is the polyamine putrescine, which can be oxidized via copper-containing amine oxidase (CuAO), resulting in the production 4-aminobutanal/Δ(1)-pyrroline, with the consumption of O2 and release of H2O2 and ammonia. Five putative CuAO genes (MdAO genes) were cloned from apple (Malus domestica Borkh. cv. Empire) fruit, and the deduced amino acid sequences found to contain the active sites typically conserved in CuAOs. Genes encoding two of these enzymes, MdAO1 and MdAO2, were highly expressed in apple fruit and selected for further analysis. Amino acid sequence analysis predicted the presence of a C-terminal peroxisomal targeting signal 1 tripeptide in MdAO1 and an N-terminal signal peptide and N-glycosylation site in MdAO2. Transient expression of green fluorescent fusion proteins in Arabidopsis protoplasts or onion epidermal cells revealed a peroxisomal localization for MdAO1 and an extracellular localization for MdAO2. The enzymatic activities of purified recombinant MdAO1 and MdAO2 were measured continuously as H2O2 production using a coupled reaction. MdAO1 did not use monoamines or polyamines and displayed high catalytic efficiency for 1,3-diaminopropane, putrescine and cadaverine, whereas MdAO2 exclusively utilized aliphatic and aromatic monoamines, including 2-phenylethylamine and tyramine. Together, these results indicate that MdAO1 may contribute to GABA production via putrescine oxidation in the peroxisome of apple fruit under controlled atmosphere conditions. MdAO2 seems to be involved in deamination of 2-phenylethylamine, which is a step in the biosynthesis of 2-phenylethanol, a contributor to fruit flavor and flower fragrance.

  16. Apple fruit copper amine oxidase isoforms: peroxisomal MdAO1 prefers diamines as substrates, whereas extracellular MdAO2 exclusively utilizes monoamines.

    PubMed

    Zarei, Adel; Trobacher, Christopher P; Cooke, Alison R; Meyers, Ashley J; Hall, J Christopher; Shelp, Barry J

    2015-01-01

    4-Aminobutyrate (GABA) accumulates in apple fruit during controlled atmosphere storage. A potential source of GABA is the polyamine putrescine, which can be oxidized via copper-containing amine oxidase (CuAO), resulting in the production 4-aminobutanal/Δ(1)-pyrroline, with the consumption of O2 and release of H2O2 and ammonia. Five putative CuAO genes (MdAO genes) were cloned from apple (Malus domestica Borkh. cv. Empire) fruit, and the deduced amino acid sequences found to contain the active sites typically conserved in CuAOs. Genes encoding two of these enzymes, MdAO1 and MdAO2, were highly expressed in apple fruit and selected for further analysis. Amino acid sequence analysis predicted the presence of a C-terminal peroxisomal targeting signal 1 tripeptide in MdAO1 and an N-terminal signal peptide and N-glycosylation site in MdAO2. Transient expression of green fluorescent fusion proteins in Arabidopsis protoplasts or onion epidermal cells revealed a peroxisomal localization for MdAO1 and an extracellular localization for MdAO2. The enzymatic activities of purified recombinant MdAO1 and MdAO2 were measured continuously as H2O2 production using a coupled reaction. MdAO1 did not use monoamines or polyamines and displayed high catalytic efficiency for 1,3-diaminopropane, putrescine and cadaverine, whereas MdAO2 exclusively utilized aliphatic and aromatic monoamines, including 2-phenylethylamine and tyramine. Together, these results indicate that MdAO1 may contribute to GABA production via putrescine oxidation in the peroxisome of apple fruit under controlled atmosphere conditions. MdAO2 seems to be involved in deamination of 2-phenylethylamine, which is a step in the biosynthesis of 2-phenylethanol, a contributor to fruit flavor and flower fragrance. PMID:25378687

  17. De novo inference of protein function from coarse-grained dynamics.

    PubMed

    Bhadra, Pratiti; Pal, Debnath

    2014-10-01

    Inference of molecular function of proteins is the fundamental task in the quest for understanding cellular processes. The task is getting increasingly difficult with thousands of new proteins discovered each day. The difficulty arises primarily due to lack of high-throughput experimental technique for assessing protein molecular function, a lacunae that computational approaches are trying hard to fill. The latter too faces a major bottleneck in absence of clear evidence based on evolutionary information. Here we propose a de novo approach to annotate protein molecular function through structural dynamics match for a pair of segments from two dissimilar proteins, which may share even <10% sequence identity. To screen these matches, corresponding 1 µs coarse-grained (CG) molecular dynamics trajectories were used to compute normalized root-mean-square-fluctuation graphs and select mobile segments, which were, thereafter, matched for all pairs using unweighted three-dimensional autocorrelation vectors. Our in-house custom-built forcefield (FF), extensively validated against dynamics information obtained from experimental nuclear magnetic resonance data, was specifically used to generate the CG dynamics trajectories. The test for correspondence of dynamics-signature of protein segments and function revealed 87% true positive rate and 93.5% true negative rate, on a dataset of 60 experimentally validated proteins, including moonlighting proteins and those with novel functional motifs. A random test against 315 unique fold/function proteins for a negative test gave >99% true recall. A blind prediction on a novel protein appears consistent with additional evidences retrieved therein. This is the first proof-of-principle of generalized use of structural dynamics for inferring protein molecular function leveraging our custom-made CG FF, useful to all.

  18. Eye tracking unconscious face-to-face confrontations: dominance motives prolong gaze to masked angry faces.

    PubMed

    Terburg, David; Hooiveld, Nicole; Aarts, Henk; Kenemans, J Leon; van Honk, Jack

    2011-03-01

    In primates, dominance/submission relationships are generally automatically and nonaggressively established in face-to-face confrontations. Researchers have argued that this process involves an explicit psychological stress-manipulation mechanism: Striding with a threatening expression, while keeping direct eye contact, outstresses rivals so that they submissively avert their gaze. In contrast, researchers have proposed a reflexive and implicit modulation of face-to-face confrontation in humans, on the basis of evidence that dominant and submissive individuals exhibit vigilant and avoidant responses, respectively, to facial anger in masked emotional Stroop tasks. However, these tasks do not provide an ecologically valid index of gaze behavior. Therefore, we directly measured gaze responses to masked angry, happy, and neutral facial expressions with a saccade-latency paradigm and found that increased dominance traits predict a more prolonged gaze to (or reluctance to avert gaze from) masked anger. Furthermore, greater non-dominance-related reward sensitivity predicts more persistent gaze to masked happiness. These results strongly suggest that implicit and reflexive mechanisms underlie dominant and submissive gaze behavior in face-to-face confrontations. PMID:21303993

  19. Course Material Model in A&O Learning Environment.

    ERIC Educational Resources Information Center

    Levasma, Jarkko; Nykanen, Ossi

    One of the problematic issues in the content development for learning environments is the process of importing various types of course material into the environment. This paper describes a method for importing material into the A&O open learning environment by introducing a material model for metadata recognized by the environment. The first…

  20. Atypical face gaze in autism.

    PubMed

    Trepagnier, Cheryl; Sebrechts, Marc M; Peterson, Rebecca

    2002-06-01

    An eye-tracking study of face and object recognition was conducted to clarify the character of face gaze in autistic spectrum disorders. Experimental participants were a group of individuals diagnosed with Asperger's disorder or high-functioning autistic disorder according to their medical records and confirmed by the Autism Diagnostic Interview-Revised (ADI-R). Controls were selected on the basis of age, gender, and educational level to be comparable to the experimental group. In order to maintain attentional focus, stereoscopic images were presented in a virtual reality (VR) headset in which the eye-tracking system was installed. Preliminary analyses show impairment in face recognition, in contrast with equivalent and even superior performance in object recognition among participants with autism-related diagnoses, relative to controls. Experimental participants displayed less fixation on the central face than did control-group participants. The findings, within the limitations of the small number of subjects and technical difficulties encountered in utilizing the helmet-mounted display, suggest an impairment in face processing on the part of the individuals in the experimental group. This is consistent with the hypothesis of disruption in the first months of life, a period that may be critical to typical social and cognitive development, and has important implications for selection of appropriate targets of intervention.

  1. Atypical face gaze in autism.

    PubMed

    Trepagnier, Cheryl; Sebrechts, Marc M; Peterson, Rebecca

    2002-06-01

    An eye-tracking study of face and object recognition was conducted to clarify the character of face gaze in autistic spectrum disorders. Experimental participants were a group of individuals diagnosed with Asperger's disorder or high-functioning autistic disorder according to their medical records and confirmed by the Autism Diagnostic Interview-Revised (ADI-R). Controls were selected on the basis of age, gender, and educational level to be comparable to the experimental group. In order to maintain attentional focus, stereoscopic images were presented in a virtual reality (VR) headset in which the eye-tracking system was installed. Preliminary analyses show impairment in face recognition, in contrast with equivalent and even superior performance in object recognition among participants with autism-related diagnoses, relative to controls. Experimental participants displayed less fixation on the central face than did control-group participants. The findings, within the limitations of the small number of subjects and technical difficulties encountered in utilizing the helmet-mounted display, suggest an impairment in face processing on the part of the individuals in the experimental group. This is consistent with the hypothesis of disruption in the first months of life, a period that may be critical to typical social and cognitive development, and has important implications for selection of appropriate targets of intervention. PMID:12123243

  2. Face recognition for uncontrolled environments

    NASA Astrophysics Data System (ADS)

    Podilchuk, Christine; Hulbert, William; Flachsbart, Ralph; Barinov, Lev

    2010-04-01

    A new face recognition algorithm has been proposed which is robust to variations in pose, expression, illumination and occlusions such as sunglasses. The algorithm is motivated by the Edit Distance used to determine the similarity between strings of one dimensional data such as DNA and text. The key to this approach is how to extend the concept of an Edit Distance on one-dimensional data to two-dimensional image data. The algorithm is based on mapping one image into another and using the characteristics of the mapping to determine a two-dimensional Pictorial-Edit Distance or P-Edit Distance. We show how the properties of the mapping are similar to insertion, deletion and substitution errors defined in an Edit Distance. This algorithm is particularly well suited for face recognition in uncontrolled environments such as stand-off and other surveillance applications. We will describe an entire system designed for face recognition at a distance including face detection, pose estimation, multi-sample fusion of video frames and identification. Here we describe how the algorithm is used for face recognition at a distance, present some initial results and describe future research directions.(

  3. Empirical temporal networks of face-to-face human interactions

    NASA Astrophysics Data System (ADS)

    Barrat, A.; Cattuto, C.; Colizza, V.; Gesualdo, F.; Isella, L.; Pandolfi, E.; Pinton, J.-F.; Ravà, L.; Rizzo, C.; Romano, M.; Stehlé, J.; Tozzi, A. E.; Van den Broeck, W.

    2013-09-01

    The ever increasing adoption of mobile technologies and ubiquitous services allows to sense human behavior at unprecedented level of details and scale. Wearable sensors, in particular, open up a new window on human mobility and proximity in a variety of indoor environments. Here we review stylized facts on the structural and dynamical properties of empirical networks of human face-to-face proximity, measured in three different real-world contexts: an academic conference, a hospital ward, and a museum exhibition. First, we discuss the structure of the aggregated contact networks, that project out the detailed ordering of contact events while preserving temporal heterogeneities in their weights. We show that the structural properties of aggregated networks highlight important differences and unexpected similarities across contexts, and discuss the additional complexity that arises from attributes that are typically associated with nodes in real-world interaction networks, such as role classes in hospitals. We then consider the empirical data at the finest level of detail, i.e., we consider time-dependent networks of face-to-face proximity between individuals. To gain insights on the effects that causal constraints have on spreading processes, we simulate the dynamics of a simple susceptible-infected model over the empirical time-resolved contact data. We show that the spreading pathways for the epidemic process are strongly affected by the temporal structure of the network data, and that the mere knowledge of static aggregated networks leads to erroneous conclusions about the transmission paths on the corresponding dynamical networks.

  4. Incorporating Online Discussion in Face to Face Classroom Learning: A New Blended Learning Approach

    ERIC Educational Resources Information Center

    Chen, Wenli; Looi, Chee-Kit

    2007-01-01

    This paper discusses an innovative blended learning strategy which incorporates online discussion in both in-class face to face, and off-classroom settings. Online discussion in a face to face class is compared with its two counterparts, off-class online discussion as well as in-class, face to face oral discussion, to examine the advantages and…

  5. A Comparison of Online and Face-to-Face Approaches to Teaching Introduction to American Government

    ERIC Educational Resources Information Center

    Bolsen, Toby; Evans, Michael; Fleming, Anna McCaghren

    2016-01-01

    This article reports results from a large study comparing four different approaches to teaching Introduction to American Government: (1) traditional, a paper textbook with 100% face-to-face lecture-style teaching; (2) breakout, a paper textbook with 50% face-to-face lecture-style teaching and 50% face-to-face small-group breakout discussion…

  6. De novo arteriovenous malformation in a patient with hereditary hemorrhagic telangiectasia.

    PubMed

    Shimoda, Yusuke; Osanai, Toshiya; Nakayama, Naoki; Ushikoshi, Satoshi; Hokari, Masaaki; Shichinohe, Hideo; Abumiya, Takeo; Kazumata, Ken; Houkin, Kiyohiro

    2016-03-01

    Hereditary hemorrhagic telangiectasia (HHT) is an autosomal dominant systemic disorder characterized by the enlargement of capillaries, recurrent nosebleeds, and multiple arteriovenous malformations (AVMs). Although cerebral AVMs are traditionally considered to be congenital lesions, some reports have described de novo AVMs, which suggests that the authors believed them to be dynamic conditions. In this article, the authors describe the case of a 5-year-old boy with HHT in whom a de novo cerebral AVM was detected after a negative MRI result at 5 months. To the authors' knowledge, this is the first report of a de novo AVM in a patient with HHT. In patients with a family history of HHT, de novo AVMs are possible, even when no lesions are detected at the first screening. Therefore, regular screenings need to be performed, and the family should be informed that AVMs could still develop despite normal MRI results. PMID:26613274

  7. Rapid centriole assembly in Naegleria reveals conserved roles for both de novo and mentored assembly.

    PubMed

    Fritz-Laylin, Lillian K; Levy, Yaron Y; Levitan, Edward; Chen, Sean; Cande, W Zacheus; Lai, Elaine Y; Fulton, Chandler

    2016-03-01

    Centrioles are eukaryotic organelles whose number and position are critical for cilia formation and mitosis. Many cell types assemble new centrioles next to existing ones ("templated" or mentored assembly). Under certain conditions, centrioles also form without pre-existing centrioles (de novo). The synchronous differentiation of Naegleria amoebae to flagellates represents a unique opportunity to study centriole assembly, as nearly 100% of the population transitions from having no centrioles to having two within minutes. Here, we find that Naegleria forms its first centriole de novo, immediately followed by mentored assembly of the second. We also find both de novo and mentored assembly distributed among all major eukaryote lineages. We therefore propose that both modes are ancestral and have been conserved because they serve complementary roles, with de novo assembly as the default when no pre-existing centriole is available, and mentored assembly allowing precise regulation of number, timing, and location of centriole assembly.

  8. Ameliorated de novo transcriptome assembly using Illumina paired end sequence data with Trinity Assembler

    PubMed Central

    Bankar, Kiran Gopinath; Todur, Vivek Nagaraj; Shukla, Rohit Nandan; Vasudevan, Madavan

    2015-01-01

    Advent of Next Generation Sequencing has led to possibilities of de novo transcriptome assembly of organisms without availability of complete genome sequence. Among various sequencing platforms available, Illumina is the most widely used platform based on data quality, quantity and cost. Various de novo transcriptome assemblers are also available today for construction of de novo transcriptome. In this study, we aimed at obtaining an ameliorated de novo transcriptome assembly with sequence reads obtained from Illumina platform and assembled using Trinity Assembler. We found that, primary transcriptome assembly obtained as a result of Trinity can be ameliorated on the basis of transcript length, coverage, and depth and protein homology. Our approach to ameliorate is reproducible and could enhance the sensitivity and specificity of the assembled transcriptome which could be critical for validation of the assembled transcripts and for planning various downstream biological assays. PMID:26484285

  9. Biological Sex Determines Whether Faces Look Real

    PubMed Central

    Balas, Benjamin

    2013-01-01

    Judging whether a face is real or artificial can be done relatively rapidly and accurately, even when visual information is substantially impoverished. The perception of animacy in the face also has several interesting properties that may reflect both the underlying “tuning” of face space to preferentially represent real face appearance and the diagnosticity of individual features for categorizing faces as animate or inanimate. In the current study, we examined how sex categories interact with animacy perception by separately characterizing animacy judgments as a function of stimulus sex. We find that stimulus sex affects subjective ratings of animacy and sex categorization of real and artificial faces. Specifically, female faces look more artificial and artificial faces look more female. We discuss our results in terms of the ecology of real and artificial faces and the possible role of visual experience with artificial female faces, and the objectification of female faces. PMID:24244103

  10. LESSONS IN DE NOVO PEPTIDE SEQUENCING BY TANDEM MASS SPECTROMETRY

    PubMed Central

    Medzihradszky, Katalin F.; Chalkley, Robert J.

    2015-01-01

    Mass spectrometry has become the method of choice for the qualitative and quantitative characterization of protein mixtures isolated from all kinds of living organisms. The raw data in these studies are MS/MS spectra, usually of peptides produced by proteolytic digestion of a protein. These spectra are “translated” into peptide sequences, normally with the help of various search engines. Data acquisition and interpretation have both been automated, and most researchers look only at the summary of the identifications without ever viewing the underlying raw data used for assignments. Automated analysis of data is essential due to the volume produced. However, being familiar with the finer intricacies of peptide fragmentation processes, and experiencing the difficulties of manual data interpretation allow a researcher to be able to more critically evaluate key results, particularly because there are many known rules of peptide fragmentation that are not incorporated into search engine scoring. Since the most commonly used MS/MS activation method is collision-induced dissociation (CID), in this article we present a brief review of the history of peptide CID analysis. Next, we provide a detailed tutorial on how to determine peptide sequences from CID data. Although the focus of the tutorial is de novo sequencing, the lessons learned and resources supplied are useful for data interpretation in general. PMID:25667941

  11. De novo transcriptome assembly of Sorghum bicolor variety Taejin.

    PubMed

    Jo, Yeonhwa; Lian, Sen; Cho, Jin Kyong; Choi, Hoseong; Kim, Sang-Min; Kim, Sun-Lim; Lee, Bong Choon; Cho, Won Kyong

    2016-06-01

    Sorghum (Sorghum bicolor), also known as great millet, is one of the most popular cultivated grass species in the world. Sorghum is frequently consumed as food for humans and animals as well as used for ethanol production. In this study, we conducted de novo transcriptome assembly for sorghum variety Taejin by next-generation sequencing, obtaining 8.748 GB of raw data. The raw data in this study can be available in NCBI SRA database with accession number of SRX1715644. Using the Trinity program, we identified 222,161 transcripts from sorghum variety Taejin. We further predicted coding regions within the assembled transcripts by the TransDecoder program, resulting in a total of 148,531 proteins. We carried out BLASTP against the Swiss-Prot protein sequence database to annotate the functions of the identified proteins. To our knowledge, this is the first transcriptome data for a sorghum variety derived from Korea, and it can be usefully applied to the generation of genetic markers. PMID:27257604

  12. 8-oxoguanine causes spontaneous de novo germline mutations in mice

    PubMed Central

    Ohno, Mizuki; Sakumi, Kunihiko; Fukumura, Ryutaro; Furuichi, Masato; Iwasaki, Yuki; Hokama, Masaaki; Ikemura, Toshimichi; Tsuzuki, Teruhisa; Gondo, Yoichi; Nakabeppu, Yusaku

    2014-01-01

    Spontaneous germline mutations generate genetic diversity in populations of sexually reproductive organisms, and are thus regarded as a driving force of evolution. However, the cause and mechanism remain unclear. 8-oxoguanine (8-oxoG) is a candidate molecule that causes germline mutations, because it makes DNA more prone to mutation and is constantly generated by reactive oxygen species in vivo. We show here that endogenous 8-oxoG caused de novo spontaneous and heritable G to T mutations in mice, which occurred at different stages in the germ cell lineage and were distributed throughout the chromosomes. Using exome analyses covering 40.9 Mb of mouse transcribed regions, we found increased frequencies of G to T mutations at a rate of 2 × 10−7 mutations/base/generation in offspring of Mth1/Ogg1/Mutyh triple knockout (TOY-KO) mice, which accumulate 8-oxoG in the nuclear DNA of gonadal cells. The roles of MTH1, OGG1, and MUTYH are specific for the prevention of 8-oxoG-induced mutation, and 99% of the mutations observed in TOY-KO mice were G to T transversions caused by 8-oxoG; therefore, we concluded that 8-oxoG is a causative molecule for spontaneous and inheritable mutations of the germ lineage cells. PMID:24732879

  13. De novo transcriptome assembly of Sorghum bicolor variety Taejin.

    PubMed

    Jo, Yeonhwa; Lian, Sen; Cho, Jin Kyong; Choi, Hoseong; Kim, Sang-Min; Kim, Sun-Lim; Lee, Bong Choon; Cho, Won Kyong

    2016-06-01

    Sorghum (Sorghum bicolor), also known as great millet, is one of the most popular cultivated grass species in the world. Sorghum is frequently consumed as food for humans and animals as well as used for ethanol production. In this study, we conducted de novo transcriptome assembly for sorghum variety Taejin by next-generation sequencing, obtaining 8.748 GB of raw data. The raw data in this study can be available in NCBI SRA database with accession number of SRX1715644. Using the Trinity program, we identified 222,161 transcripts from sorghum variety Taejin. We further predicted coding regions within the assembled transcripts by the TransDecoder program, resulting in a total of 148,531 proteins. We carried out BLASTP against the Swiss-Prot protein sequence database to annotate the functions of the identified proteins. To our knowledge, this is the first transcriptome data for a sorghum variety derived from Korea, and it can be usefully applied to the generation of genetic markers.

  14. Parental Origin and Timing of De Novo Robertsonian Translocation Formation

    PubMed Central

    Bandyopadhyay, Ruma; Heller, Anita; Knox-DuBois, Cami; McCaskill, Christopher; Berend, Sue Ann; Page, Scott L.; Shaffer, Lisa G.

    2002-01-01

    Robertsonian translocations (ROBs) are the most common chromosomal rearrangements in humans. ROBs are whole-arm rearrangements between the acrocentric chromosomes 13–15, 21, and 22. ROBs can be classified into two groups depending on their frequency of occurrence, common (rob(13q14q) and rob(14q21q)), and rare (all remaining possible nonhomologous combinations). Herein, we have studied 29 case subjects of common and rare de novo ROBs to determine their parental origins and timing of formation. We compared these case subjects to 35 published case subjects of common ROBs and found that most common ROBs apparently have the same breakpoints and arise mainly during oogenesis (50/54). These probably form through a common mechanism and have been termed “class 1.” Collectively, rare ROBs also occur mostly during oogenesis (7/10) but probably arise through a more “random” mechanism or a variety of mechanisms and have been termed “class 2.” Thus, we demonstrate that although both classes of ROBs occur predominantly during meiosis, the common, class 1 ROBs occur primarily during oogenesis and likely form through a mechanism distinct from that forming class 2 ROBs. PMID:12424707

  15. Ultrafast de novo docking combining pharmacophores and combinatorics.

    PubMed

    Gastreich, Marcus; Lilienthal, Markus; Briem, Hans; Claussen, Holger

    2006-12-01

    We report on a successful de novo design approach which relies on the combination of multi-million compound combinatorial docking under receptor-based pharmacophore constraints. Inspired by a rationale by A.R. Leach et al., we document on the unification of two steps into one for ligand assembly. In the original work, fragments known to bind in protein active sites were connected forming novel ligand compounds by means of generic skeleton linkers and following a combinatorial approach. In our approach, the knowledge of fragments binding to the protein has been expressed in terms of a receptor-based pharmacophore definition. The combinatorial linking step is performed in situ during docking, starting from combinatorial libraries. Three sample scenarios growing in size and complexity (combinatorial libraries of 1 million, 1.3 million, and 22.4 million compounds) have been created to illustrate the method. Docking could be accomplished between minutes and several hours depending on the outset; the results were throughout promising. Technically, a module compatibility between FlexX(C) and FlexX-Pharm has been established. The background is explained, and the crucial points from an information scientist's perspective are highlighted.

  16. De novo transcriptome assembly of a sour cherry cultivar, Schattenmorelle.

    PubMed

    Jo, Yeonhwa; Chu, Hyosub; Cho, Jin Kyong; Choi, Hoseong; Lian, Sen; Cho, Won Kyong

    2015-12-01

    Sour cherry (Prunus cerasus) in the genus Prunus in the family Rosaceae is one of the most popular stone fruit trees worldwide. Of known sour cherry cultivars, the Schattenmorelle is a famous old sour cherry with a high amount of fruit production. The Schattenmorelle was selected before 1650 and described in the 1800s. This cultivar was named after gardens of the Chateau de Moreille in which the cultivar was initially found. In order to identify new genes and to develop genetic markers for sour cherry, we performed a transcriptome analysis of a sour cherry. We selected the cultivar Schattenmorelle, which is among commercially important cultivars in Europe and North America. We obtained 2.05 GB raw data from the Schattenmorelle (NCBI accession number: SRX1187170). De novo transcriptome assembly using Trinity identified 61,053 transcripts in which N50 was 611 bp. Next, we identified 25,585 protein coding sequences using TransDecoder. The identified proteins were blasted against NCBI's non-redundant database for annotation. Based on blast search, we taxonomically classified the obtained sequences. As a result, we provide the transcriptome of sour cherry cultivar Schattenmorelle using next generation sequencing. PMID:26697395

  17. De novo transcriptome assembly of a sour cherry cultivar, Schattenmorelle

    PubMed Central

    Jo, Yeonhwa; Chu, Hyosub; Cho, Jin Kyong; Choi, Hoseong; Lian, Sen; Cho, Won Kyong

    2015-01-01

    Sour cherry (Prunus cerasus) in the genus Prunus in the family Rosaceae is one of the most popular stone fruit trees worldwide. Of known sour cherry cultivars, the Schattenmorelle is a famous old sour cherry with a high amount of fruit production. The Schattenmorelle was selected before 1650 and described in the 1800s. This cultivar was named after gardens of the Chateau de Moreille in which the cultivar was initially found. In order to identify new genes and to develop genetic markers for sour cherry, we performed a transcriptome analysis of a sour cherry. We selected the cultivar Schattenmorelle, which is among commercially important cultivars in Europe and North America. We obtained 2.05 GB raw data from the Schattenmorelle (NCBI accession number: SRX1187170). De novo transcriptome assembly using Trinity identified 61,053 transcripts in which N50 was 611 bp. Next, we identified 25,585 protein coding sequences using TransDecoder. The identified proteins were blasted against NCBI's non-redundant database for annotation. Based on blast search, we taxonomically classified the obtained sequences. As a result, we provide the transcriptome of sour cherry cultivar Schattenmorelle using next generation sequencing. PMID:26697395

  18. Programming peptidomimetic syntheses by translating genetic codes designed de novo.

    PubMed

    Forster, Anthony C; Tan, Zhongping; Nalam, Madhavi N L; Lin, Hening; Qu, Hui; Cornish, Virginia W; Blacklow, Stephen C

    2003-05-27

    Although the universal genetic code exhibits only minor variations in nature, Francis Crick proposed in 1955 that "the adaptor hypothesis allows one to construct, in theory, codes of bewildering variety." The existing code has been expanded to enable incorporation of a variety of unnatural amino acids at one or two nonadjacent sites within a protein by using nonsense or frameshift suppressor aminoacyl-tRNAs (aa-tRNAs) as adaptors. However, the suppressor strategy is inherently limited by compatibility with only a small subset of codons, by the ways such codons can be combined, and by variation in the efficiency of incorporation. Here, by preventing competing reactions with aa-tRNA synthetases, aa-tRNAs, and release factors during translation and by using nonsuppressor aa-tRNA substrates, we realize a potentially generalizable approach for template-encoded polymer synthesis that unmasks the substantially broader versatility of the core translation apparatus as a catalyst. We show that several adjacent, arbitrarily chosen sense codons can be completely reassigned to various unnatural amino acids according to de novo genetic codes by translating mRNAs into specific peptide analog polymers (peptidomimetics). Unnatural aa-tRNA substrates do not uniformly function as well as natural substrates, revealing important recognition elements for the translation apparatus. Genetic programming of peptidomimetic synthesis should facilitate mechanistic studies of translation and may ultimately enable the directed evolution of small molecules with desirable catalytic or pharmacological properties.

  19. De novo synthesis of a sunscreen compound in vertebrates

    PubMed Central

    Osborn, Andrew R; Almabruk, Khaled H; Holzwarth, Garrett; Asamizu, Shumpei; LaDu, Jane; Kean, Kelsey M; Karplus, P Andrew; Tanguay, Robert L; Bakalinsky, Alan T; Mahmud, Taifo

    2015-01-01

    Ultraviolet-protective compounds, such as mycosporine-like amino acids (MAAs) and related gadusols produced by some bacteria, fungi, algae, and marine invertebrates, are critical for the survival of reef-building corals and other marine organisms exposed to high-solar irradiance. These compounds have also been found in marine fish, where their accumulation is thought to be of dietary or symbiont origin. In this study, we report the unexpected discovery that fish can synthesize gadusol de novo and that the analogous pathways are also present in amphibians, reptiles, and birds. Furthermore, we demonstrate that engineered yeast containing the fish genes can produce and secrete gadusol. The discovery of the gadusol pathway in vertebrates provides a platform for understanding its role in these animals, and the possibility of engineering yeast to efficiently produce a natural sunscreen and antioxidant presents an avenue for its large-scale production for possible use in pharmaceuticals and cosmetics. DOI: http://dx.doi.org/10.7554/eLife.05919.001 PMID:25965179

  20. Considering Transposable Element Diversification in De Novo Annotation Approaches

    PubMed Central

    Flutre, Timothée; Duprat, Elodie; Feuillet, Catherine; Quesneville, Hadi

    2011-01-01

    Transposable elements (TEs) are mobile, repetitive DNA sequences that are almost ubiquitous in prokaryotic and eukaryotic genomes. They have a large impact on genome structure, function and evolution. With the recent development of high-throughput sequencing methods, many genome sequences have become available, making possible comparative studies of TE dynamics at an unprecedented scale. Several methods have been proposed for the de novo identification of TEs in sequenced genomes. Most begin with the detection of genomic repeats, but the subsequent steps for defining TE families differ. High-quality TE annotations are available for the Drosophila melanogaster and Arabidopsis thaliana genome sequences, providing a solid basis for the benchmarking of such methods. We compared the performance of specific algorithms for the clustering of interspersed repeats and found that only a particular combination of algorithms detected TE families with good recovery of the reference sequences. We then applied a new procedure for reconciling the different clustering results and classifying TE sequences. The whole approach was implemented in a pipeline using the REPET package. Finally, we show that our combined approach highlights the dynamics of well defined TE families by making it possible to identify structural variations among their copies. This approach makes it possible to annotate TE families and to study their diversification in a single analysis, improving our understanding of TE dynamics at the whole-genome scale and for diverse species. PMID:21304975

  1. De novo assembly and analysis of crow lungs transcriptome.

    PubMed

    Vijayakumar, Periyasamy; Raut, Ashwin Ashok; Kumar, Pushpendra; Sharma, Deepak; Mishra, Anamika

    2014-09-01

    The jungle crow (Corvus macrorhynchos) belongs to the order Passeriformes of bird species and is important for avian ecological and evolutionary genetics studies. However, there is limited information on the transcriptome data of this species. In the present study, we report the characterization of the lung transcriptome of the jungle crow using GS FLX Titanium XLR70. Altogether, 1,510,303 high-quality sequence reads with 581,198,230 bases was de novo assembled into 22,169 isotigs (isotig represents an individual transcript) and 784,009 singletons. Using these isotigs and 581,681 length-filtered (greater than 300 bp) singletons, 20,010 unique protein-coding genes were identified by BLASTx comparison against a nonredundant (nr) protein sequence database. Comparative analysis revealed that 46,604 (70.29%) and 51,642 (72.48%) of the assembled transcripts have significant similarity to zebra finch and chicken RefSeq proteins, respectively. As determined by GO annotation and KEGG pathway mapping, functional annotation of the unigenes recovered diverse biological functions and processes. Transcripts putatively involved in the immune response were identified. Furthermore, 20,599 single nucleotide polymorphisms (SNPs) and 7525 simple sequence repeats (SSRs) were retrieved from the assembled transcript database. This resource should lay an important base for future ecological, evolutionary, and conservation genetic studies on this species and in other related species.

  2. MITOS: improved de novo metazoan mitochondrial genome annotation.

    PubMed

    Bernt, Matthias; Donath, Alexander; Jühling, Frank; Externbrink, Fabian; Florentz, Catherine; Fritzsch, Guido; Pütz, Joern; Middendorf, Martin; Stadler, Peter F

    2013-11-01

    About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. This annotation information, which has accumulated over two decades, has been obtained with a diverse set of computational tools and annotation strategies. Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations in particular for the RNA genes. Taken together, this causes substantial problems for fully automatic pipelines that aim to use these data comprehensively for studies of animal phylogenetics and the molecular evolution of mitogenomes. The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences. We show that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality. At the same time we avoid biases, inconsistencies of nomenclature, and typos originating from manual curation strategies. The MITOS pipeline is accessible online at http://mitos.bioinf.uni-leipzig.de.

  3. De novo C3 glomerulonephritis in a renal allograft.

    PubMed

    Nahm, Ji Hae; Song, Seung Hwan; Kim, Yu Seun; Cheong, Hae-Il; Lim, Beom Jin; Kim, Beom Seok; Jeong, Hyeon Joo

    2016-01-01

    C3 glomerulonephritis (C3GN) is a recently described, rare glomerular disease characterized by predominant or sole glomerular C3 deposits. Morphologic features of C3GN are similar to those of dense deposit disease (DDD); however, ribbon-like intramembranous electron-dense deposits are absent in the former. We report a case of de novo C3GN in a renal allograft with morphologic transformation to DDD. A 6-year-old boy presented with congenital left renal agenesis and right ureteropelvic junction obstruction. The patient underwent pyeloplasty but experienced recurrent urinary tract infections. At the age of 22 years, he received a renal allograft from a living related donor. C3GN was diagnosed after 1 year of transplantation; initial histology showed minimal mesangiopathy and this progressed to mesangial proliferation and membranoproliferative features over the next 7 years. Serum creatinine levels were stabilized with anti-rejection treatments for combating repeated episodes of acute rejection; however, glomerular and tubular band-like electron-dense deposits became evident.

  4. De novo transcriptome assembly of mangosteen (Garcinia mangostana L.) fruit.

    PubMed

    Matra, Deden Derajat; Kozaki, Toshinori; Ishii, Kazuo; Poerwanto, Roedhy; Inoue, Eiichi

    2016-12-01

    Garcinia mangostana L. (Mangosteen), of the family Clusiaceae, is one of the economically important tropical fruits in Indonesia. In the present study, we performed de novo transcriptomic analysis of Garcinia mangostana L. through RNA-Seq technology. We obtained the raw data from 12 libraries through Ion Proton System. Clean reads of 191,735,809 were obtained from 307,634,890 raw reads. The raw data obtained in this study can be accessible in DDBJ database with accession number of DRA005014 with bioproject accession number of PRJDB5091. We obtained 268,851 transcripts as well as 155,850 unigenes, having N50 value of 555 and 433 bp, respectively. Transcript/unigene length ranged from 201 to 5916 bp. The unigenes were annotated with two main databases from NCBI and UniProtKB, respectively having annotated-sequences of 73,287 and 73,107, respectively. These transcriptomic data will be beneficial for studying transcriptome of Garcinia mangostana L.

  5. Spaced Seed Data Structures for De Novo Assembly

    PubMed Central

    Birol, Inanç; Chu, Justin; Mohamadi, Hamid; Jackman, Shaun D.; Raghavan, Karthika; Vandervalk, Benjamin P.; Raymond, Anthony; Warren, René L.

    2015-01-01

    De novo assembly of the genome of a species is essential in the absence of a reference genome sequence. Many scalable assembly algorithms use the de Bruijn graph (DBG) paradigm to reconstruct genomes, where a table of subsequences of a certain length is derived from the reads, and their overlaps are analyzed to assemble sequences. Despite longer subsequences unlocking longer genomic features for assembly, associated increase in compute resources limits the practicability of DBG over other assembly archetypes already designed for longer reads. Here, we revisit the DBG paradigm to adapt it to the changing sequencing technology landscape and introduce three data structure designs for spaced seeds in the form of paired subsequences. These data structures address memory and run time constraints imposed by longer reads. We observe that when a fixed distance separates seed pairs, it provides increased sequence specificity with increased gap length. Further, we note that Bloom filters would be suitable to implicitly store spaced seeds and be tolerant to sequencing errors. Building on this concept, we describe a data structure for tracking the frequencies of observed spaced seeds. These data structure designs will have applications in genome, transcriptome and metagenome assemblies, and read error correction. PMID:26539459

  6. A de novo convergence of autism genetics and molecular neuroscience.

    PubMed

    Krumm, Niklas; O'Roak, Brian J; Shendure, Jay; Eichler, Evan E

    2014-02-01

    Autism spectrum disorder (ASD) and intellectual disability (ID) are neurodevelopmental disorders with large genetic components, but identification of pathogenic genes has proceeded slowly because hundreds of loci are involved. New exome sequencing technology has identified novel rare variants and has found that sporadic cases of ASD/ID are enriched for disruptive de novo mutations. Targeted large-scale resequencing studies have confirmed the significance of specific loci, including chromodomain helicase DNA binding protein 8 (CHD8), sodium channel, voltage-gated, type II, alpha subunit (SCN2A), dual specificity tyrosine-phosphorylation-regulated kinase 1A (DYRK1A), and catenin (cadherin-associated protein), beta 1, 88 kDa (CTNNB1, beta-catenin). We review recent studies and suggest that they have led to a convergence on three functional pathways: (i) chromatin remodeling; (ii) wnt signaling during development; and (iii) synaptic function. These pathways and genes significantly expand the neurobiological targets for study, and suggest a path for future genetic and functional studies. PMID:24387789

  7. Pathway Engineered Enzymatic de novo Purine Nucleotide Synthesis

    PubMed Central

    Schultheisz, Heather L.; Szymczyna, Blair R.; Scott, Lincoln G.; Williamson, James R.

    2009-01-01

    A general method for isotopic labeling of the purine base moiety of nucleotides and RNA has been developed through biochemical pathway engineering in vitro. A synthetic scheme was designed and implemented utilizing recombinant enzymes from the pentose phosphate and de novo purine synthesis pathways, with regeneration of folate, aspartate, glutamine, ATP, and NADPH cofactors, in a single-pot reaction. Syntheses proceeded quickly and efficiently in comparison to chemical methods with isolated yields up to 66% for 13C, 15N enriched ATP and GTP. The scheme is robust and flexible, requiring only serine, NH4+, glucose and CO2 as stoichiometric precursors in labeled form. Using this approach, U-13C- GTP, U-13C,15N- GTP, 13C2,8- ATP and U-15N- GTP were synthesized on a millimole scale, and the utility of the isotope labeling is illustrated in NMR spectra of HIV-2 transactivation region (TAR) RNA containing 13C 2,8-adenosine and 15N-1,3,7,9,2-guanosine. Pathway engineering in vitro permits complex synthetic cascades to be effected expanding the applicability of enzymatic synthesis. PMID:18707057

  8. De Novo Transcriptome Analysis of Cucumis melo L. var. makuwa

    PubMed Central

    Kim, Hyun A; Shin, Ah-Young; Lee, Min-Seon; Lee, Hee-Jeong; Lee, Heung-Ryul; Ahn, Jongmoon; Nahm, Seokhyeon; Jo, Sung-Hwan; Park, Jeong Mee; Kwon, Suk-Yoon

    2016-01-01

    Oriental melon (Cucumis melo L. var. makuwa) is one of six subspecies of melon and is cultivated widely in East Asia, including China, Japan, and Korea. Although oriental melon is economically valuable in Asia and is genetically distinct from other subspecies, few reports of genome-scale research on oriental melon have been published. We generated 30.5 and 36.8 Gb of raw RNA sequence data from the female and male flowers, leaves, roots, and fruit of two oriental melon varieties, Korean landrace (KM) and Breeding line of NongWoo Bio Co. (NW), respectively. From the raw reads, 64,998 transcripts from KM and 100,234 transcripts from NW were de novo assembled. The assembled transcripts were used to identify molecular markers (e.g., single-nucleotide polymorphisms and simple sequence repeats), detect tissue-specific expressed genes, and construct a genetic linkage map. In total, 234 single-nucleotide polymorphisms and 25 simple sequence repeats were screened from 7,871 and 8,052 candidates, respectively, between the KM and NW varieties and used for construction of a genetic map with 94 F2 population specimens. The genetic linkage map consisted of 12 linkage groups, and 248 markers were assigned. These transcriptome and molecular marker data provide information useful for molecular breeding of oriental melon and further comparative studies of the Cucurbitaceae family. PMID:26743902

  9. De novo transcriptome assembly of mangosteen (Garcinia mangostana L.) fruit.

    PubMed

    Matra, Deden Derajat; Kozaki, Toshinori; Ishii, Kazuo; Poerwanto, Roedhy; Inoue, Eiichi

    2016-12-01

    Garcinia mangostana L. (Mangosteen), of the family Clusiaceae, is one of the economically important tropical fruits in Indonesia. In the present study, we performed de novo transcriptomic analysis of Garcinia mangostana L. through RNA-Seq technology. We obtained the raw data from 12 libraries through Ion Proton System. Clean reads of 191,735,809 were obtained from 307,634,890 raw reads. The raw data obtained in this study can be accessible in DDBJ database with accession number of DRA005014 with bioproject accession number of PRJDB5091. We obtained 268,851 transcripts as well as 155,850 unigenes, having N50 value of 555 and 433 bp, respectively. Transcript/unigene length ranged from 201 to 5916 bp. The unigenes were annotated with two main databases from NCBI and UniProtKB, respectively having annotated-sequences of 73,287 and 73,107, respectively. These transcriptomic data will be beneficial for studying transcriptome of Garcinia mangostana L. PMID:27668185

  10. De Novo Transcriptome Analysis of Cucumis melo L. var. makuwa.

    PubMed

    Kim, Hyun A; Shin, Ah-Young; Lee, Min-Seon; Lee, Hee-Jeong; Lee, Heung-Ryul; Ahn, Jongmoon; Nahm, Seokhyeon; Jo, Sung-Hwan; Park, Jeong Mee; Kwon, Suk-Yoon

    2016-02-01

    Oriental melon (Cucumis melo L. var. makuwa) is one of six subspecies of melon and is cultivated widely in East Asia, including China, Japan, and Korea. Although oriental melon is economically valuable in Asia and is genetically distinct from other subspecies, few reports of genome-scale research on oriental melon have been published. We generated 30.5 and 36.8 Gb of raw RNA sequence data from the female and male flowers, leaves, roots, and fruit of two oriental melon varieties, Korean landrace (KM) and Breeding line of NongWoo Bio Co. (NW), respectively. From the raw reads, 64,998 transcripts from KM and 100,234 transcripts from NW were de novo assembled. The assembled transcripts were used to identify molecular markers (e.g., single-nucleotide polymorphisms and simple sequence repeats), detect tissue-specific expressed genes, and construct a genetic linkage map. In total, 234 single-nucleotide polymorphisms and 25 simple sequence repeats were screened from 7,871 and 8,052 candidates, respectively, between the KM and NW varieties and used for construction of a genetic map with 94 F2 population specimens. The genetic linkage map consisted of 12 linkage groups, and 248 markers were assigned. These transcriptome and molecular marker data provide information useful for molecular breeding of oriental melon and further comparative studies of the Cucurbitaceae family. PMID:26743902

  11. De novo design of protein mimics of B-DNA.

    PubMed

    Yüksel, Deniz; Bianco, Piero R; Kumar, Krishna

    2016-01-01

    Structural mimicry of DNA is utilized in nature as a strategy to evade molecular defences mounted by host organisms. One such example is the protein Ocr - the first translation product to be expressed as the bacteriophage T7 infects E. coli. The structure of Ocr reveals an intricate and deliberate arrangement of negative charges that endows it with the ability to mimic ∼24 base pair stretches of B-DNA. This uncanny resemblance to DNA enables Ocr to compete in binding the type I restriction modification (R/M) system, and neutralizes the threat of hydrolytic cleavage of viral genomic material. Here, we report the de novo design and biophysical characterization of DNA mimicking peptides, and describe the inhibitory action of the designed helical bundles on a type I R/M enzyme, EcoR124I. This work validates the use of charge patterning as a design principle for creation of protein mimics of DNA, and serves as a starting point for development of therapeutic peptide inhibitors against human pathogens that employ molecular camouflage as part of their invasion stratagem. PMID:26568416

  12. Dynamic actin controls polarity induction de novo in protoplasts.

    PubMed

    Zaban, Beatrix; Maisch, Jan; Nick, Peter

    2013-02-01

    Cell polarity and axes are central for plant morphogenesis. To study how polarity and axes are induced de novo, we investigated protoplasts of tobacco Nicotiana tabacum cv. BY-2 expressing fluorescently-tagged cytoskeletal markers. We standardized the system to such a degree that we were able to generate quantitative data on the temporal patterns of regeneration stages. The synthesis of a new cell wall marks the transition to the first stage of regeneration, and proceeds after a long preparatory phase within a few minutes. During this preparatory phase, the nucleus migrates actively, and cytoplasmic strands remodel vigorously. We probed this system for the effect of anti-cytoskeletal compounds, inducible bundling of actin, RGD-peptides, and temperature. Suppression of actin dynamics at an early stage leads to aberrant tripolar cells, whereas suppression of microtubule dynamics produces aberrant sausage-like cells with asymmetric cell walls. We integrated these data into a model, where the microtubular cytoskeleton conveys positional information between the nucleus and the membrane controlling the release or activation of components required for cell wall synthesis. Cell wall formation is followed by the induction of a new cell pole requiring dynamic actin filaments, and the new cell axis is manifested as elongation growth perpendicular to the orientation of the aligned cortical microtubules.

  13. Enzyme-like replication de novo in a microcontroller environment.

    PubMed

    Tangen, Uwe

    2010-01-01

    The desire to start evolution from scratch inside a computer memory is as old as computing. Here we demonstrate how viable computer programs can be established de novo in a Precambrian environment without supplying any specific instantiation, just starting with random bit sequences. These programs are not self-replicators, but act much more like catalysts. The microcontrollers used in the end are the result of a long series of simplifications. The objective of this simplification process was to produce universal machines with a human-readable interface, allowing software and/or hardware evolution to be studied. The power of the instruction set can be modified by introducing a secondary structure-folding mechanism, which is a state machine, allowing nontrivial replication to emerge with an instruction width of only a few bits. This state-machine approach not only attenuates the problems of brittleness and encoding functionality (too few bits available for coding, and too many instructions needed); it also enables the study of hardware evolution as such. Furthermore, the instruction set is sufficiently powerful to permit external signals to be processed. This information-theoretic approach forms one vertex of a triangle alongside artificial cell research and experimental research on the creation of life. Hopefully this work helps develop an understanding of how information—in a similar sense to the account of functional information described by Hazen et al.—is created by evolution and how this information interacts with or is embedded in its physico-chemical environment. PMID:20712511

  14. De novo design of protein mimics of B-DNA.

    PubMed

    Yüksel, Deniz; Bianco, Piero R; Kumar, Krishna

    2016-01-01

    Structural mimicry of DNA is utilized in nature as a strategy to evade molecular defences mounted by host organisms. One such example is the protein Ocr - the first translation product to be expressed as the bacteriophage T7 infects E. coli. The structure of Ocr reveals an intricate and deliberate arrangement of negative charges that endows it with the ability to mimic ∼24 base pair stretches of B-DNA. This uncanny resemblance to DNA enables Ocr to compete in binding the type I restriction modification (R/M) system, and neutralizes the threat of hydrolytic cleavage of viral genomic material. Here, we report the de novo design and biophysical characterization of DNA mimicking peptides, and describe the inhibitory action of the designed helical bundles on a type I R/M enzyme, EcoR124I. This work validates the use of charge patterning as a design principle for creation of protein mimics of DNA, and serves as a starting point for development of therapeutic peptide inhibitors against human pathogens that employ molecular camouflage as part of their invasion stratagem.

  15. A de novo convergence of autism genetics and molecular neuroscience

    PubMed Central

    Krumm, Niklas; O’Roak, Brian J.; Shendure, Jay; Eichler, Evan E.

    2014-01-01

    Autism spectrum disorder (ASD) and intellectual disability (ID) are neurodevelopmental disorders with large genetic components, but identification of pathogenic genes has proceeded slowly because hundreds of loci are involved. New exome sequencing technology has identified novel rare variants and has found that sporadic cases of ASD/ID are enriched for disruptive de novo mutations. Targeted large-scale resequencing studies have confirmed the significance of specific loci, including chromodomain helicase DNA binding protein 8 (CHD8), sodium channel, voltage-gated, type II, alpha subunit (SCN2A), dual specificity tyrosine-phosphorylation-regulated kinase 1A (DYRK1A), and catenin (cadherin-associated protein), beta 1, 88 kDa (CTNNB1, beta-catenin). We review recent studies and suggest that they have led to a convergence on three functional pathways: (i) chromatin remodeling; (ii) wnt signaling during development; and (iii) synaptic function. These pathways and genes significantly expand the neurobiological targets for study, and suggest a path for future genetic and functional studies. PMID:24387789

  16. Growth Hormone Inhibits Hepatic De Novo Lipogenesis in Adult Mice.

    PubMed

    Cordoba-Chacon, Jose; Majumdar, Neena; List, Edward O; Diaz-Ruiz, Alberto; Frank, Stuart J; Manzano, Anna; Bartrons, Ramon; Puchowicz, Michelle; Kopchick, John J; Kineman, Rhonda D

    2015-09-01

    Patients with nonalcoholic fatty liver disease (NAFLD) are reported to have low growth hormone (GH) production and/or hepatic GH resistance. GH replacement can resolve the fatty liver condition in diet-induced obese rodents and in GH-deficient patients. However, it remains to be determined whether this inhibitory action of GH is due to direct regulation of hepatic lipid metabolism. Therefore, an adult-onset, hepatocyte-specific, GH receptor (GHR) knockdown (aLivGHRkd) mouse was developed to model hepatic GH resistance in humans that may occur after sexual maturation. Just 7 days after aLivGHRkd, hepatic de novo lipogenesis (DNL) was increased in male and female chow-fed mice, compared with GHR-intact littermate controls. However, hepatosteatosis developed only in male and ovariectomized female aLivGHRkd mice. The increase in DNL observed in aLivGHRkd mice was not associated with hyperactivation of the pathway by which insulin is classically considered to regulate DNL. However, glucokinase mRNA and protein levels as well as fructose-2,6-bisphosphate levels were increased in aLivGHRkd mice, suggesting that enhanced glycolysis drives DNL in the GH-resistant liver. These results demonstrate that hepatic GH actions normally serve to inhibit DNL, where loss of this inhibitory signal may explain, in part, the inappropriate increase in hepatic DNL observed in NAFLD patients. PMID:26015548

  17. Spaced Seed Data Structures for De Novo Assembly.

    PubMed

    Birol, Inanç; Chu, Justin; Mohamadi, Hamid; Jackman, Shaun D; Raghavan, Karthika; Vandervalk, Benjamin P; Raymond, Anthony; Warren, René L

    2015-01-01

    De novo assembly of the genome of a species is essential in the absence of a reference genome sequence. Many scalable assembly algorithms use the de Bruijn graph (DBG) paradigm to reconstruct genomes, where a table of subsequences of a certain length is derived from the reads, and their overlaps are analyzed to assemble sequences. Despite longer subsequences unlocking longer genomic features for assembly, associated increase in compute resources limits the practicability of DBG over other assembly archetypes already designed for longer reads. Here, we revisit the DBG paradigm to adapt it to the changing sequencing technology landscape and introduce three data structure designs for spaced seeds in the form of paired subsequences. These data structures address memory and run time constraints imposed by longer reads. We observe that when a fixed distance separates seed pairs, it provides increased sequence specificity with increased gap length. Further, we note that Bloom filters would be suitable to implicitly store spaced seeds and be tolerant to sequencing errors. Building on this concept, we describe a data structure for tracking the frequencies of observed spaced seeds. These data structure designs will have applications in genome, transcriptome and metagenome assemblies, and read error correction. PMID:26539459

  18. Spaced Seed Data Structures for De Novo Assembly.

    PubMed

    Birol, Inanç; Chu, Justin; Mohamadi, Hamid; Jackman, Shaun D; Raghavan, Karthika; Vandervalk, Benjamin P; Raymond, Anthony; Warren, René L

    2015-01-01

    De novo assembly of the genome of a species is essential in the absence of a reference genome sequence. Many scalable assembly algorithms use the de Bruijn graph (DBG) paradigm to reconstruct genomes, where a table of subsequences of a certain length is derived from the reads, and their overlaps are analyzed to assemble sequences. Despite longer subsequences unlocking longer genomic features for assembly, associated increase in compute resources limits the practicability of DBG over other assembly archetypes already designed for longer reads. Here, we revisit the DBG paradigm to adapt it to the changing sequencing technology landscape and introduce three data structure designs for spaced seeds in the form of paired subsequences. These data structures address memory and run time constraints imposed by longer reads. We observe that when a fixed distance separates seed pairs, it provides increased sequence specificity with increased gap length. Further, we note that Bloom filters would be suitable to implicitly store spaced seeds and be tolerant to sequencing errors. Building on this concept, we describe a data structure for tracking the frequencies of observed spaced seeds. These data structure designs will have applications in genome, transcriptome and metagenome assemblies, and read error correction.

  19. De novo C3 glomerulonephritis in a renal allograft.

    PubMed

    Nahm, Ji Hae; Song, Seung Hwan; Kim, Yu Seun; Cheong, Hae-Il; Lim, Beom Jin; Kim, Beom Seok; Jeong, Hyeon Joo

    2016-01-01

    C3 glomerulonephritis (C3GN) is a recently described, rare glomerular disease characterized by predominant or sole glomerular C3 deposits. Morphologic features of C3GN are similar to those of dense deposit disease (DDD); however, ribbon-like intramembranous electron-dense deposits are absent in the former. We report a case of de novo C3GN in a renal allograft with morphologic transformation to DDD. A 6-year-old boy presented with congenital left renal agenesis and right ureteropelvic junction obstruction. The patient underwent pyeloplasty but experienced recurrent urinary tract infections. At the age of 22 years, he received a renal allograft from a living related donor. C3GN was diagnosed after 1 year of transplantation; initial histology showed minimal mesangiopathy and this progressed to mesangial proliferation and membranoproliferative features over the next 7 years. Serum creatinine levels were stabilized with anti-rejection treatments for combating repeated episodes of acute rejection; however, glomerular and tubular band-like electron-dense deposits became evident. PMID:26986539

  20. Artificial faces are harder to remember

    PubMed Central

    Balas, Benjamin; Pacella, Jonathan

    2015-01-01

    Observers interact with artificial faces in a range of different settings and in many cases must remember and identify computer-generated faces. In general, however, most adults have heavily biased experience favoring real faces over synthetic faces. It is well known that face recognition abilities are affected by experience such that faces belonging to “out-groups” defined by race or age are more poorly remembered and harder to discriminate from one another than faces belonging to the “in-group.” Here, we examine the extent to which artificial faces form an “out-group” in this sense when other perceptual categories are matched. We rendered synthetic faces using photographs of real human faces and compared performance in a memory task and a discrimination task across real and artificial versions of the same faces. We found that real faces were easier to remember, but only slightly more discriminable than artificial faces. Artificial faces were also equally susceptible to the well-known face inversion effect, suggesting that while these patterns are still processed by the human visual system in a face-like manner, artificial appearance does compromise the efficiency of face processing. PMID:26195852

  1. Increased burden of de novo predicted deleterious variants in complex congenital diaphragmatic hernia

    PubMed Central

    Yu, Lan; Sawle, Ashley D.; Wynn, Julia; Aspelund, Gudrun; Stolar, Charles J.; Arkovitz, Marc S.; Potoka, Douglas; Azarow, Kenneth S.; Mychaliska, George B.; Shen, Yufeng; Chung, Wendy K.

    2015-01-01

    Congenital diaphragmatic hernia (CDH) is a serious birth defect that accounts for 8% of all major birth anomalies. Approximately 40% of cases occur in association with other anomalies. As sporadic complex CDH likely has a significant impact on reproductive fitness, we hypothesized that de novo variants would account for the etiology in a significant fraction of cases. We performed exome sequencing in 39 CDH trios and compared the frequency of de novo variants with 787 unaffected controls from the Simons Simplex Collection. We found no significant difference in overall frequency of de novo variants between cases and controls. However, among genes that are highly expressed during diaphragm development, there was a significant burden of likely gene disrupting (LGD) and predicted deleterious missense variants in cases (fold enrichment = 3.2, P-value = 0.003), and these genes are more likely to be haploinsufficient (P-value = 0.01) than the ones with benign missense or synonymous de novo variants in cases. After accounting for the frequency of de novo variants in the control population, we estimate that 15% of sporadic complex CDH patients are attributable to de novo LGD or deleterious missense variants. We identified several genes with predicted deleterious de novo variants that fall into common categories of genes related to transcription factors and cell migration that we believe are related to the pathogenesis of CDH. These data provide supportive evidence for novel genes in the pathogenesis of CDH associated with other anomalies and suggest that de novo variants play a significant role in complex CDH cases. PMID:26034137

  2. De novo sequencing of unique sequence tags for discovery of post-translational modifications of proteins.

    PubMed

    Shen, Yufeng; Tolić, Nikola; Hixson, Kim K; Purvine, Samuel O; Anderson, Gordon A; Smith, Richard D

    2008-10-15

    De novo sequencing is a spectrum analysis approach for mass spectrometry data to discover post-translational modifications in proteins; however, such an approach is still in its infancy and is still not widely applied to proteomic practices due to its limited reliability. In this work, we describe a de novo sequencing approach for the discovery of protein modifications based on identification of the proteome UStags (Shen, Y.; Tolić, N.; Hixson, K. K.; Purvine, S. O.; Pasa-Tolić, L.; Qian, W. J.; Adkins, J. N.; Moore, R. J.; Smith, R. D. Anal. Chem. 2008, 80, 1871-1882). The de novo information was obtained from Fourier-transform tandem mass spectrometry data for peptides and polypeptides from a yeast lysate, and the de novo sequences obtained were selected based on filter levels designed to provide a limited yet high quality subset of UStags. The DNA-predicted database protein sequences were then compared to the UStags, and the differences observed across or in the UStags (i.e., the UStags' prefix and suffix sequences and the UStags themselves) were used to infer possible sequence modifications. With this de novo-UStag approach, we uncovered some unexpected variances within several yeast protein sequences due to amino acid mutations and/or multiple modifications to the predicted protein sequences. To determine false discovery rates, two random (false) databases were independently used for sequence matching, and ~3% false discovery rates were estimated for the de novo-UStag approach. The factors affecting the reliability (e.g., existence of de novo sequencing noise residues and redundant sequences) and the sensitivity of the approach were investigated and described. The combined de novo-UStag approach complements the UStag method previously reported by enabling the discovery of new protein modifications. PMID:18783246

  3. De Novo Histoid Leprosy: A Case Report from a Post-Elimination Area

    PubMed Central

    Bhat, Yasmeen J; Hassan, Iffat; Yaseen, Atiya; Wani, Rohi

    2015-01-01

    Histoid leprosy is an uncommon variant of lepromatous leprosy that usually follows treatment failure. Occasionally it occurs de novo without any history of previous inadequate or irregular treatment. We, hereby, report a case of de novo histoid leprosy in a 25-year-old man from the post-elimination area of Kashmir, where the prevalence rate of the disease was reported to be 0.17/10000 in March, 2013 (NLEP). PMID:25814742

  4. The Ontogeny of Face Identity

    ERIC Educational Resources Information Center

    Blass, Elliott M.; Camp, Carole Ann

    2004-01-01

    A paradigm was designed to study how infants identify live faces. Eight- to 21-week-old infants were seated comfortably and were presented an adult female, dressed in a white laboratory coat and a white turtle neck sweater, until habituation ensued. The adult then left the room. One minute later either she or an identically garbed confederate…

  5. The Two Faces of Micropolitics.

    ERIC Educational Resources Information Center

    Hoyle, Eric

    1999-01-01

    Demystifies the two "faces" of micropolitics. "Policy micropolitics" distinguishes between micropolitics and management and focuses on the relationship between school micropolitics and the wider macropolitical context. "Management micropolitics" makes no clear micropolitics/management distinction and focuses on educators' strategies to pursue…

  6. Families Facing the Nuclear Taboo.

    ERIC Educational Resources Information Center

    Jacobs, Judith Bula

    1988-01-01

    Discusses attitudes of 12 families participating in group which was formed to focus on issues related to the possibility of a nuclear disaster. Why and how these families are facing the nuclear taboo plus various outcomes of doing so are discussed as well as the role of the professional in encouraging such openness about these difficult issues.…

  7. Putting a Face to Faith

    ERIC Educational Resources Information Center

    Haynes, Charles C.

    2011-01-01

    U.S. schools are becoming increasingly religiously diverse, but students rarely learn about different religious beliefs and how those beliefs--or nonbelief--might shape people's responses to important issues. Face to Faith is a free program that uses videoconferencing to connect students with peers from around the world to discuss issues related…

  8. Mechanical Coal-Face Fracturer

    NASA Technical Reports Server (NTRS)

    Collins, E. R., Jr.

    1984-01-01

    Radial points on proposed drill bit take advantage of natural fracture planes of coal. Radial fracture points retracted during drilling and impacted by piston to fracture coal once drilling halts. Group of bits attached to array of pneumatic drivers to fracture large areas of coal face.

  9. Face liveness detection using defocus.

    PubMed

    Kim, Sooyeon; Ban, Yuseok; Lee, Sangyoun

    2015-01-01

    In order to develop security systems for identity authentication, face recognition (FR) technology has been applied. One of the main problems of applying FR technology is that the systems are especially vulnerable to attacks with spoofing faces (e.g., 2D pictures). To defend from these attacks and to enhance the reliability of FR systems, many anti-spoofing approaches have been recently developed. In this paper, we propose a method for face liveness detection using the effect of defocus. From two images sequentially taken at different focuses, three features, focus, power histogram and gradient location and orientation histogram (GLOH), are extracted. Afterwards, we detect forged faces through the feature-level fusion approach. For reliable performance verification, we develop two databases with a handheld digital camera and a webcam. The proposed method achieves a 3.29% half total error rate (HTER) at a given depth of field (DoF) and can be extended to camera-equipped devices, like smartphones. PMID:25594594

  10. Face Liveness Detection Using Defocus

    PubMed Central

    Kim, Sooyeon; Ban, Yuseok; Lee, Sangyoun

    2015-01-01

    In order to develop security systems for identity authentication, face recognition (FR) technology has been applied. One of the main problems of applying FR technology is that the systems are especially vulnerable to attacks with spoofing faces (e.g., 2D pictures). To defend from these attacks and to enhance the reliability of FR systems, many anti-spoofing approaches have been recently developed. In this paper, we propose a method for face liveness detection using the effect of defocus. From two images sequentially taken at different focuses, three features, focus, power histogram and gradient location and orientation histogram (GLOH), are extracted. Afterwards, we detect forged faces through the feature-level fusion approach. For reliable performance verification, we develop two databases with a handheld digital camera and a webcam. The proposed method achieves a 3.29% half total error rate (HTER) at a given depth of field (DoF) and can be extended to camera-equipped devices, like smartphones. PMID:25594594

  11. Face-Sealing Butterfly Valve

    NASA Technical Reports Server (NTRS)

    Tervo, John N.

    1992-01-01

    Valve plate made to translate as well as rotate. Valve opened and closed by turning shaft and lever. Interactions among lever, spring, valve plate, and face seal cause plate to undergo combination of translation and rotation so valve plate clears seal during parts of opening and closing motions.

  12. The Many Faces of Language.

    ERIC Educational Resources Information Center

    Werdmann, Anne M.

    In a sixth-grade unit, students learned about people's facial expressions through careful observation, recording, reporting, and generalizing. The students studied the faces of people of various ages; explored "masks" that people wear in different situations; learned about the use of ritual masks; made case studies of individuals to show facial…

  13. Put On a Happy Face.

    ERIC Educational Resources Information Center

    Bratina, Tuiren A.

    1996-01-01

    This article on mathematics in the curriculum describes how students learn the characteristics of conic section equations by entering them into graphing calculators to make happy faces in a high school or college algebra class. A sample worksheet page is included. (Author/LRW)

  14. Groundwater contamination in relation with the increasing urbanization rate in Africa. Case of Cotonou and Porto Novo (Benin).

    NASA Astrophysics Data System (ADS)

    Odeloui, Diane; Celle-Jeanton, Hélène; Huneau, Frédéric; Boukari, Moussa; Alassane, Abdelkarim; Garel, Emilie; Lavastre, Véronique; Bertrand, Guillaume

    2016-04-01

    More than one billion people in the world still have no access to sufficient resources in drinking water (United Nation, 2014). In particular, large cities in Africa have to face several problems: 1) population growth associated with the strongest urbanization rate increase (5% per year) of the world leading to a dramatic increase in good-quality water needs, 2) low levels of solid waste management and sanitation services, 3) insufficient or disconnected water supply services, 4) low knowledge of water resources availabilities. The situation in Benin is a relevant illustration of the problems that Africa has to face to. As many other coastal urban areas in Africa (Showers, 2002; Re et al., 2011), Cotonou and Porto Novo cities have seen a rapid increase of their population as these towns constitute a corridor of transit for the imports and the exports in the nearby countries. Hence, they are very attractive for job hunters, and constitute the administrative centers for the whole country. This rapid population growth amplifies the problem of water supply and may generate serious impacts on groundwater resources: depletion due to overexploitation, salinization due to seawater intrusion and pollution linked to human activities. In order to insure a safe water supply in the context of increasing urbanization and population in the coastal area of Cotonou and Porto Novo, the identification of the main sources of pollution is essential for the implementation of long-term water management procedures. Based on two field campaigns carried out in January-2012 (dry season) and August-2012 (rainy season), hydrochemical analysis have been realized on groundwater sampled from boreholes drilled in the CTA (Continental Terminal Aquifer) and wells dug in the QCA (Quaternary Coastal Aquifer) in order to investigate the origin of salinization and the present time extension of the nitrate contamination. Historical data have also been collected from previous studies in order to

  15. Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome

    PubMed Central

    Honaas, Loren A.; Wafula, Eric K.; Wickett, Norman J.; Der, Joshua P.; Zhang, Yeting; Edger, Patrick P.; Altman, Naomi S.; Pires, J. Chris; Leebens-Mack, James H.; dePamphilis, Claude W.

    2016-01-01

    Whereas de novo assemblies of RNA-Seq data are being published for a growing number of species across the tree of life, there are currently no broadly accepted methods for evaluating such assemblies. Here we present a detailed comparison of 99 transcriptome assemblies, generated with 6 de novo assemblers including CLC, Trinity, SOAP, Oases, ABySS and NextGENe. Controlled analyses of de novo assemblies for Arabidopsis thaliana and Oryza sativa transcriptomes provide new insights into the strengths and limitations of transcriptome assembly strategies. We find that the leading assemblers generate reassuringly accurate assemblies for the majority of transcripts. At the same time, we find a propensity for assemblers to fail to fully assemble highly expressed genes. Surprisingly, the instance of true chimeric assemblies is very low for all assemblers. Normalized libraries are reduced in highly abundant transcripts, but they also lack 1000s of low abundance transcripts. We conclude that the quality of de novo transcriptome assemblies is best assessed through consideration of a combination of metrics: 1) proportion of reads mapping to an assembly 2) recovery of conserved, widely expressed genes, 3) N50 length statistics, and 4) the total number of unigenes. We provide benchmark Illumina transcriptome data and introduce SCERNA, a broadly applicable modular protocol for de novo assembly improvement. Finally, our de novo assembly of the Arabidopsis leaf transcriptome revealed ~20 putative Arabidopsis genes lacking in the current annotation. PMID:26731733

  16. A Novel de novo Mutation in CEACAM16 Associated with Postlingual Hearing Impairment

    PubMed Central

    Hofrichter, Michaela A.H.; Nanda, Indrajit; Gräf, Jens; Schröder, Jörg; Shehata-Dieler, Wafaa; Vona, Barbara; Haaf, Thomas

    2015-01-01

    Mutations in CEACAM16 cause autosomal dominant nonsyndromic hearing loss (DFNA4B). So far, 2 families have been reported with segregating missense mutations, both in the immunoglobulin constant domain A of the CEACAM16 protein. In this study, we used the TruSight One panel to investigate a parent-child trio without familial history of hearing loss and one affected child. When filtering for recessive inheritance and de novo events, we discovered a de novo CEACAM16 mutation (c.1094T>G, p.Leu365Arg) as the sole likely pathogenic variant. The de novo mutation was confirmed by Sanger sequencing and STR analysis. The proband's hearing loss closely matches the described onset and severity for DFNA4B. We present the third CEACAM16 variant and the first de novo mutation in CEACAM16. This de novo mutation is robustly described as a pathogenic mutation according to in silico mutation prediction tools and affects a highly conserved amino acid in the most strongly conserved CEACAM16 N2 domain. Our strategy of screening family trios enhances de novo mutation discovery and the exclusion of other variants of potential interest through pedigree filtering. PMID:26648831

  17. Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome.

    PubMed

    Honaas, Loren A; Wafula, Eric K; Wickett, Norman J; Der, Joshua P; Zhang, Yeting; Edger, Patrick P; Altman, Naomi S; Pires, J Chris; Leebens-Mack, James H; dePamphilis, Claude W

    2016-01-01

    Whereas de novo assemblies of RNA-Seq data are being published for a growing number of species across the tree of life, there are currently no broadly accepted methods for evaluating such assemblies. Here we present a detailed comparison of 99 transcriptome assemblies, generated with 6 de novo assemblers including CLC, Trinity, SOAP, Oases, ABySS and NextGENe. Controlled analyses of de novo assemblies for Arabidopsis thaliana and Oryza sativa transcriptomes provide new insights into the strengths and limitations of transcriptome assembly strategies. We find that the leading assemblers generate reassuringly accurate assemblies for the majority of transcripts. At the same time, we find a propensity for assemblers to fail to fully assemble highly expressed genes. Surprisingly, the instance of true chimeric assemblies is very low for all assemblers. Normalized libraries are reduced in highly abundant transcripts, but they also lack 1000s of low abundance transcripts. We conclude that the quality of de novo transcriptome assemblies is best assessed through consideration of a combination of metrics: 1) proportion of reads mapping to an assembly 2) recovery of conserved, widely expressed genes, 3) N50 length statistics, and 4) the total number of unigenes. We provide benchmark Illumina transcriptome data and introduce SCERNA, a broadly applicable modular protocol for de novo assembly improvement. Finally, our de novo assembly of the Arabidopsis leaf transcriptome revealed ~20 putative Arabidopsis genes lacking in the current annotation.

  18. TransRate: reference-free quality assessment of de novo transcriptome assemblies

    PubMed Central

    Smith-Unna, Richard; Boursnell, Chris; Patro, Rob; Hibberd, Julian M.; Kelly, Steven

    2016-01-01

    TransRate is a tool for reference-free quality assessment of de novo transcriptome assemblies. Using only the sequenced reads and the assembly as input, we show that multiple common artifacts of de novo transcriptome assembly can be readily detected. These include chimeras, structural errors, incomplete assembly, and base errors. TransRate evaluates these errors to produce a diagnostic quality score for each contig, and these contig scores are integrated to evaluate whole assemblies. Thus, TransRate can be used for de novo assembly filtering and optimization as well as comparison of assemblies generated using different methods from the same input reads. Applying the method to a data set of 155 published de novo transcriptome assemblies, we deconstruct the contribution that assembly method, read length, read quantity, and read quality make to the accuracy of de novo transcriptome assemblies and reveal that variance in the quality of the input data explains 43% of the variance in the quality of published de novo transcriptome assemblies. Because TransRate is reference-free, it is suitable for assessment of assemblies of all types of RNA, including assemblies of long noncoding RNA, rRNA, mRNA, and mixed RNA samples. PMID:27252236

  19. Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome.

    PubMed

    Honaas, Loren A; Wafula, Eric K; Wickett, Norman J; Der, Joshua P; Zhang, Yeting; Edger, Patrick P; Altman, Naomi S; Pires, J Chris; Leebens-Mack, James H; dePamphilis, Claude W

    2016-01-01

    Whereas de novo assemblies of RNA-Seq data are being published for a growing number of species across the tree of life, there are currently no broadly accepted methods for evaluating such assemblies. Here we present a detailed comparison of 99 transcriptome assemblies, generated with 6 de novo assemblers including CLC, Trinity, SOAP, Oases, ABySS and NextGENe. Controlled analyses of de novo assemblies for Arabidopsis thaliana and Oryza sativa transcriptomes provide new insights into the strengths and limitations of transcriptome assembly strategies. We find that the leading assemblers generate reassuringly accurate assemblies for the majority of transcripts. At the same time, we find a propensity for assemblers to fail to fully assemble highly expressed genes. Surprisingly, the instance of true chimeric assemblies is very low for all assemblers. Normalized libraries are reduced in highly abundant transcripts, but they also lack 1000s of low abundance transcripts. We conclude that the quality of de novo transcriptome assemblies is best assessed through consideration of a combination of metrics: 1) proportion of reads mapping to an assembly 2) recovery of conserved, widely expressed genes, 3) N50 length statistics, and 4) the total number of unigenes. We provide benchmark Illumina transcriptome data and introduce SCERNA, a broadly applicable modular protocol for de novo assembly improvement. Finally, our de novo assembly of the Arabidopsis leaf transcriptome revealed ~20 putative Arabidopsis genes lacking in the current annotation. PMID:26731733

  20. Breast and ovarian cancer predisposition due to de novo BRCA1 and BRCA2 mutations.

    PubMed

    Golmard, L; Delnatte, C; Laugé, A; Moncoutier, V; Lefol, C; Abidallah, K; Tenreiro, H; Copigny, F; Giraudeau, M; Guy, C; Barbaroux, C; Amorim, G; Briaux, A; Guibert, V; Tarabeux, J; Caputo, S; Collet, A; Gesta, P; Ingster, O; Stern, M-H; Rouleau, E; de Pauw, A; Gauthier-Villars, M; Buecher, B; Bézieau, S; Stoppa-Lyonnet, D; Houdayer, C

    2016-03-10

    BRCA1 and BRCA2 are the two major genes predisposing to breast and ovarian cancer. Whereas high de novo mutation rates have been demonstrated for several genes, only 11 cases of de novo BRCA1/2 mutations have been reported to date and the BRCA1/2 de novo mutation rate remains unknown. The present study was designed to fill this gap based on a series of 12 805 consecutive unrelated patients diagnosed with breast and/or ovarian cancer who met the inclusion criteria for BRCA1/2 gene analysis according to French guidelines. BRCA1/2 mutations were detected in 1527 (12%) patients, and three BRCA1 mutations and one BRCA2 mutation were de novo. The BRCA1/2 de novo mutation rate was estimated to be 0.3% (0.1%; 0.7%). Although rare, it may be useful to take the possibility of de novo BRCA1/2 mutation into account in genetic counseling of relatives and to improve the understanding of complex family histories of breast and ovarian cancers.

  1. [Treatment outcome for forearm shaft fracture using AO plate stabilization].

    PubMed

    Kaleta, M; Małecki, P; Tokarowski, A; Kusz, D

    1995-01-01

    Results of treatment for 104 forearm shaft fractures in 70 patients have been presented. In all cases included in this study an open reduction of the fracture was followed by AO plate stabilization. Functional and radiological assessment was carried out according to the criteria of Anderson et al. Excellent and good functional results were achieved in 48 cases, fair in 10 and poor in 12 cases. The ulna united in 75%, the radius in 78% (delayed union included). Cross- union occurred in three patients, one case of destabilization at fracture site was observed, no infection has been noted. AO plate osteosynthesis proved to be still valuable mode of treatment for forearm shaft fracture. PMID:7587501

  2. Face to Face : The Perception of Automotive Designs.

    PubMed

    Windhager, Sonja; Slice, Dennis E; Schaefer, Katrin; Oberzaucher, Elisabeth; Thorstensen, Truls; Grammer, Karl

    2008-12-01

    Over evolutionary time, humans have developed a selective sensitivity to features in the human face that convey information on sex, age, emotions, and intentions. This ability might not only be applied to our conspecifics nowadays, but also to other living objects (i.e., animals) and even to artificial structures, such as cars. To investigate this possibility, we asked people to report the characteristics, emotions, personality traits, and attitudes they attribute to car fronts, and we used geometric morphometrics (GM) and multivariate statistical methods to determine and visualize the corresponding shape information. Automotive features and proportions are found to covary with trait perception in a manner similar to that found with human faces. Emerging analogies are discussed. This study should have implications for both our understanding of our prehistoric psyche and its interrelation with the modern world.

  3. Race Categorization Modulates Holistic Face Encoding

    ERIC Educational Resources Information Center

    Michel, Caroline; Corneille, Olivier; Rossion, Bruno

    2007-01-01

    Recent studies have shown that same-race (SR) faces are processed more holistically than other-race (OR) faces, a difference that may underlie the greater difficulty at recognizing OR than SR faces (the "other-race effect"). This article provides original evidence suggesting that the holistic processing of faces may be sensitive to the observers'…

  4. High-Resolution Imaging of Asteroids/Satellites with AO

    NASA Astrophysics Data System (ADS)

    Merline, William

    2012-02-01

    We propose to make high-resolution observations of asteroids using AO, to measure size, shape, and pole position (spin vectors), and/or to search for satellites. We have demonstrated that AO imaging allows determination of the pole/dimensions in 1 or 2 nights on a single target, rather than the years of observations with lightcurve inversion techniques that only yield poles and axial ratios, not true dimensions. Our new technique (KOALA) combines AO imaging with lightcurve and occultation data for optimum size/shape determinations. We request that LGS be available for faint targets, but using NGS AO, we will measure several large and intermediate asteroids that are favorably placed in spring/summer of 2012 for size/shape/pole. Accurately determining the volume from the often-irregular shape allows us to derive densities to much greater precision in cases where the mass is known, e.g., from the presence of a satellite. We will search several d! ozen asteroids for the presence of satellites, particularly in under-studied populations, particularly NEOs (we have recently achieved the first-ever optical image of an NEO binary [Merline et al. 2008b, IAUC 8977]). Satellites provide a real-life lab for testing collisional models. We will search for satellites around special objects at the request of lightcurve observers, and we will make a search for debris in the vicinity of Pluto, in support of the New Horizons mission. Our shape/size work requires observations over most of a full rotation period (typically several hours).

  5. Neandertal faces were not long; modern human faces are short

    PubMed Central

    Trinkaus, Erik

    2003-01-01

    Neandertal faces have been described as being derived with respect to their overall length or degree of anterior projection. A comparison of cranial and mandibular indicators of lower facial projection across archaic and modern Homo indicates that Neandertal facial lengths on average are similar to those of preceding archaic Homo and principally contrast with those of recent humans. Neandertal facial length is not derived. The shortness of recent human facial skeletons is the evolutionarily derived condition. PMID:12815095

  6. The Face-to-Face Light Detection Paradigm: A New Methodology for Investigating Visuospatial Attention Across Different Face Regions in Live Face-to-Face Communication Settings

    PubMed Central

    Thompson, Laura A.; Malloy, Daniel M.; Cone, John M.; Hendrickson, David L.

    2009-01-01

    We introduce a novel paradigm for studying the cognitive processes used by listeners within interactive settings. This paradigm places the talker and the listener in the same physical space, creating opportunities for investigations of attention and comprehension processes taking place during interactive discourse situations. An experiment was conducted to compare results from previous research using videotaped stimuli to those obtained within the live face-to-face task paradigm. A headworn apparatus is used to briefly display LEDs on the talker’s face in four locations as the talker communicates with the participant. In addition to the primary task of comprehending speeches, participants make a secondary task light detection response. In the present experiment, the talker gave non-emotionally-expressive speeches that were used in past research with videotaped stimuli. Signal detection analysis was employed to determine which areas of the face received the greatest focus of attention. Results replicate previous findings using videotaped methods. PMID:21113354

  7. Neural correlates of personally familiar faces: parents, partner and own faces.

    PubMed

    Taylor, Margot J; Arsalidou, Marie; Bayless, Sarah J; Morris, Drew; Evans, Jennifer W; Barbeau, Emmanuel J

    2009-07-01

    Investigations of the neural correlates of face recognition have typically used old/new paradigms where subjects learn to recognize new faces or identify famous faces. Familiar faces, however, include one's own face, partner's and parents' faces. Using event-related fMRI, we examined the neural correlates of these personally familiar faces. Ten participants were presented with photographs of own, partner, parents, famous and unfamiliar faces and responded to a distinct target. Whole brain, two regions of interest (fusiform gyrus and cingulate gyrus), and multiple linear regression analyses were conducted. Compared with baseline, all familiar faces activated the fusiform gyrus; own faces also activated occipital regions and the precuneus; partner faces activated similar areas, but in addition, the parahippocampal gyrus, middle superior temporal gyri and middle frontal gyrus. Compared with unfamiliar faces, only personally familiar faces activated the cingulate gyrus and the extent of activation varied with face category. Partner faces also activated the insula, amygdala and thalamus. Regions of interest analyses and laterality indices showed anatomical distinctions of processing the personally familiar faces within the fusiform and cingulate gyri. Famous faces were right lateralized whereas personally familiar faces, particularly partner and own faces, elicited bilateral activations. Regression analyses show experiential predictors modulated with neural activity related to own and partner faces. Thus, personally familiar faces activated the core visual areas and extended frontal regions, related to semantic and person knowledge and the extent and areas of activation varied with face type.

  8. Neural microgenesis of personally familiar face recognition

    PubMed Central

    Ramon, Meike; Vizioli, Luca; Liu-Shuang, Joan; Rossion, Bruno

    2015-01-01

    Despite a wealth of information provided by neuroimaging research, the neural basis of familiar face recognition in humans remains largely unknown. Here, we isolated the discriminative neural responses to unfamiliar and familiar faces by slowly increasing visual information (i.e., high-spatial frequencies) to progressively reveal faces of unfamiliar or personally familiar individuals. Activation in ventral occipitotemporal face-preferential regions increased with visual information, independently of long-term face familiarity. In contrast, medial temporal lobe structures (perirhinal cortex, amygdala, hippocampus) and anterior inferior temporal cortex responded abruptly when sufficient information for familiar face recognition was accumulated. These observations suggest that following detailed analysis of individual faces in core posterior areas of the face-processing network, familiar face recognition emerges categorically in medial temporal and anterior regions of the extended cortical face network. PMID:26283361

  9. Neural microgenesis of personally familiar face recognition.

    PubMed

    Ramon, Meike; Vizioli, Luca; Liu-Shuang, Joan; Rossion, Bruno

    2015-09-01

    Despite a wealth of information provided by neuroimaging research, the neural basis of familiar face recognition in humans remains largely unknown. Here, we isolated the discriminative neural responses to unfamiliar and familiar faces by slowly increasing visual information (i.e., high-spatial frequencies) to progressively reveal faces of unfamiliar or personally familiar individuals. Activation in ventral occipitotemporal face-preferential regions increased with visual information, independently of long-term face familiarity. In contrast, medial temporal lobe structures (perirhinal cortex, amygdala, hippocampus) and anterior inferior temporal cortex responded abruptly when sufficient information for familiar face recognition was accumulated. These observations suggest that following detailed analysis of individual faces in core posterior areas of the face-processing network, familiar face recognition emerges categorically in medial temporal and anterior regions of the extended cortical face network. PMID:26283361

  10. Neural microgenesis of personally familiar face recognition.

    PubMed

    Ramon, Meike; Vizioli, Luca; Liu-Shuang, Joan; Rossion, Bruno

    2015-09-01

    Despite a wealth of information provided by neuroimaging research, the neural basis of familiar face recognition in humans remains largely unknown. Here, we isolated the discriminative neural responses to unfamiliar and familiar faces by slowly increasing visual information (i.e., high-spatial frequencies) to progressively reveal faces of unfamiliar or personally familiar individuals. Activation in ventral occipitotemporal face-preferential regions increased with visual information, independently of long-term face familiarity. In contrast, medial temporal lobe structures (perirhinal cortex, amygdala, hippocampus) and anterior inferior temporal cortex responded abruptly when sufficient information for familiar face recognition was accumulated. These observations suggest that following detailed analysis of individual faces in core posterior areas of the face-processing network, familiar face recognition emerges categorically in medial temporal and anterior regions of the extended cortical face network.

  11. Lost in Translation: Adapting a Face-to-Face Course Into an Online Learning Experience.

    PubMed

    Kenzig, Melissa J

    2015-09-01

    Online education has grown dramatically over the past decade. Instructors who teach face-to-face courses are being called on to adapt their courses to the online environment. Many instructors do not have sufficient training to be able to effectively move courses to an online format. This commentary discusses the growth of online learning, common challenges faced by instructors adapting courses from face-to-face to online, and best practices for translating face-to-face courses into online learning opportunities.

  12. De novo hepatitis B infection after liver transplantation: source of disease, incidence, and impact.

    PubMed

    Fabia, R; Levy, M F; Crippin, J; Tillery, W; Netto, G J; Aguanno, J; Dysert, P; Goldstein, R M; Husberg, B S; Gonwa, T A; Klintmalm, G B

    1998-03-01

    New-onset hepatitis B (de novo B) after liver transplantation (OLTX) is an emerging concern. The goals of our study were to determine the incidence and pattern of this infection, to attempt determination of risk factors and the role of immunosuppression, and to review its morbidity/mortality. Over a 10-year period, 1078 OLTX were performed in 956 patients at our institution. Eight hundred twenty-six patients had proven negative hepatitis B surface antigen (HBsAg) before transplantation. Among these, 14 patients (1.7%), 8 women and 6 men, ages 21-59 years (median, 42 years), developed positive HBsAg after transplantation and were defined as de novo B. In 10 of 14 patients (71%), positive HBsAg was revealed during routine annual visits, whereas 4 patients had titer verification prompted by illness. Blood product use (cryoprecipitate, fresh-frozen plasma, platelets, and packed red blood cells) during the transplant hospitalization was similar between groups. Pretransplant hepatitis C infection was more prevalent among the 14 patients with de-novo B (7 of 14, 50% v 129 of 812, 16%; P < or = 05). Hepatitis B vaccine had been given to 12 patients (86%) (but not given to 2) who developed de novo B. Incidence and severity of rejection were similar in both populations, although de novo B patients had more late rejections. Our use of immunosuppressive protocols was the same in both groups. Mean follow-up of the infected patients is 24 (5-51) months. Twelve of these 14 de novo B patients were not clinically ill, with normal or near-normal transaminase levels. One of 14 has died from complications related to hepatic artery revascularization, and another is well after repeat OLTX for biliary strictures. Half of these de novo B patients remain free from viral antigens in their transplanted liver tissue. The high percentage of positive hepatitis C patients who acquire de novo B may indicate a link between these two viral infections and potential risk factor for de novo B. The

  13. Phenolic Amides Are Potent Inhibitors of De Novo Nucleotide Biosynthesis.

    PubMed

    Pisithkul, Tippapha; Jacobson, Tyler B; O'Brien, Thomas J; Stevenson, David M; Amador-Noguez, Daniel

    2015-09-01

    An outstanding challenge toward efficient production of biofuels and value-added chemicals from plant biomass is the impact that lignocellulose-derived inhibitors have on microbial fermentations. Elucidating the mechanisms that underlie their toxicity is critical for developing strategies to overcome them. Here, using Escherichia coli as a model system, we investigated the metabolic effects and toxicity mechanisms of feruloyl amide and coumaroyl amide, the predominant phenolic compounds in ammonia-pretreated biomass hydrolysates. Using metabolomics, isotope tracers, and biochemical assays, we showed that these two phenolic amides act as potent and fast-acting inhibitors of purine and pyrimidine biosynthetic pathways. Feruloyl or coumaroyl amide exposure leads to (i) a rapid buildup of 5-phosphoribosyl-1-pyrophosphate (PRPP), a key precursor in nucleotide biosynthesis, (ii) a rapid decrease in the levels of pyrimidine biosynthetic intermediates, and (iii) a long-term generalized decrease in nucleotide and deoxynucleotide levels. Tracer experiments using (13)C-labeled sugars and [(15)N]ammonia demonstrated that carbon and nitrogen fluxes into nucleotides and deoxynucleotides are inhibited by these phenolic amides. We found that these effects are mediated via direct inhibition of glutamine amidotransferases that participate in nucleotide biosynthetic pathways. In particular, feruloyl amide is a competitive inhibitor of glutamine PRPP amidotransferase (PurF), which catalyzes the first committed step in de novo purine biosynthesis. Finally, external nucleoside supplementation prevents phenolic amide-mediated growth inhibition by allowing nucleotide biosynthesis via salvage pathways. The results presented here will help in the development of strategies to overcome toxicity of phenolic compounds and facilitate engineering of more efficient microbial producers of biofuels and chemicals.

  14. Phenolic Amides Are Potent Inhibitors of De Novo Nucleotide Biosynthesis

    PubMed Central

    Pisithkul, Tippapha; Jacobson, Tyler B.; O'Brien, Thomas J.; Stevenson, David M.

    2015-01-01

    An outstanding challenge toward efficient production of biofuels and value-added chemicals from plant biomass is the impact that lignocellulose-derived inhibitors have on microbial fermentations. Elucidating the mechanisms that underlie their toxicity is critical for developing strategies to overcome them. Here, using Escherichia coli as a model system, we investigated the metabolic effects and toxicity mechanisms of feruloyl amide and coumaroyl amide, the predominant phenolic compounds in ammonia-pretreated biomass hydrolysates. Using metabolomics, isotope tracers, and biochemical assays, we showed that these two phenolic amides act as potent and fast-acting inhibitors of purine and pyrimidine biosynthetic pathways. Feruloyl or coumaroyl amide exposure leads to (i) a rapid buildup of 5-phosphoribosyl-1-pyrophosphate (PRPP), a key precursor in nucleotide biosynthesis, (ii) a rapid decrease in the levels of pyrimidine biosynthetic intermediates, and (iii) a long-term generalized decrease in nucleotide and deoxynucleotide levels. Tracer experiments using 13C-labeled sugars and [15N]ammonia demonstrated that carbon and nitrogen fluxes into nucleotides and deoxynucleotides are inhibited by these phenolic amides. We found that these effects are mediated via direct inhibition of glutamine amidotransferases that participate in nucleotide biosynthetic pathways. In particular, feruloyl amide is a competitive inhibitor of glutamine PRPP amidotransferase (PurF), which catalyzes the first committed step in de novo purine biosynthesis. Finally, external nucleoside supplementation prevents phenolic amide-mediated growth inhibition by allowing nucleotide biosynthesis via salvage pathways. The results presented here will help in the development of strategies to overcome toxicity of phenolic compounds and facilitate engineering of more efficient microbial producers of biofuels and chemicals. PMID:26070680

  15. Protein engineering and de novo designing of a biocatalyst.

    PubMed

    Kaushik, Mahima; Sinha, Prashant; Jaiswal, Pragya; Mahendru, Swati; Roy, Kapil; Kukreti, Shrikant

    2016-10-01

    Proteins as a biomolecule have been recognized as a "molecule with manifold biological functions". The functions not only include the structural, regulatory and transportation processes inside the body but also its capacity as an extremely specific catalyst for various biochemical reactions. Nature has been quite admirably using proteins as biocatalysts which are known as enzymes. Properties like higher reaction rate, good specificity, faster kinetics, production of lesser by-products and their non-hazardous nature make enzymes the most suitable targets for a process chemist to exploit. At the same time, limitations like a narrow range of substrates, requirement of coenzymes, lesser stability, smaller shelf-life, along with difficulties in procuring these enzymes, make this biocatalysis field quite challenging. For exploiting a broad range of applications related to therapeutics, biosensors, biotechnology, nanotechnology etc., de novo designing of proteins is of utmost importance. Enzymes with altered, specific and modified properties might be designed by utilizing the prior knowledge of structure and function of a protein with the help of computational modeling. Various protein engineering techniques like directed evolution, rational designing and immobilization strategies etc. have already been extensively used to address some of the issues. This review aims to update the repertoire of the advancements in the field of protein engineering, which can help in laying some guiding principles about designing, modifying and altering their usage for commercial industrial purposes. This possibility of effective and novel designing of peptides and proteins might further facilitate our understanding about the structure, function and folding patterns along with their inter-relationships. Copyright © 2016 John Wiley & Sons, Ltd.

  16. Phenolic Amides Are Potent Inhibitors of De Novo Nucleotide Biosynthesis.

    PubMed

    Pisithkul, Tippapha; Jacobson, Tyler B; O'Brien, Thomas J; Stevenson, David M; Amador-Noguez, Daniel

    2015-09-01

    An outstanding challenge toward efficient production of biofuels and value-added chemicals from plant biomass is the impact that lignocellulose-derived inhibitors have on microbial fermentations. Elucidating the mechanisms that underlie their toxicity is critical for developing strategies to overcome them. Here, using Escherichia coli as a model system, we investigated the metabolic effects and toxicity mechanisms of feruloyl amide and coumaroyl amide, the predominant phenolic compounds in ammonia-pretreated biomass hydrolysates. Using metabolomics, isotope tracers, and biochemical assays, we showed that these two phenolic amides act as potent and fast-acting inhibitors of purine and pyrimidine biosynthetic pathways. Feruloyl or coumaroyl amide exposure leads to (i) a rapid buildup of 5-phosphoribosyl-1-pyrophosphate (PRPP), a key precursor in nucleotide biosynthesis, (ii) a rapid decrease in the levels of pyrimidine biosynthetic intermediates, and (iii) a long-term generalized decrease in nucleotide and deoxynucleotide levels. Tracer experiments using (13)C-labeled sugars and [(15)N]ammonia demonstrated that carbon and nitrogen fluxes into nucleotides and deoxynucleotides are inhibited by these phenolic amides. We found that these effects are mediated via direct inhibition of glutamine amidotransferases that participate in nucleotide biosynthetic pathways. In particular, feruloyl amide is a competitive inhibitor of glutamine PRPP amidotransferase (PurF), which catalyzes the first committed step in de novo purine biosynthesis. Finally, external nucleoside supplementation prevents phenolic amide-mediated growth inhibition by allowing nucleotide biosynthesis via salvage pathways. The results presented here will help in the development of strategies to overcome toxicity of phenolic compounds and facilitate engineering of more efficient microbial producers of biofuels and chemicals. PMID:26070680

  17. SIMS chemical and isotopic analysis of impact features from LDEF experiments AO187-1 and AO187-2

    NASA Technical Reports Server (NTRS)

    Stadermann, Frank J.; Amari, Sachiko; Foote, John; Swan, Pat; Walker, Robert M.; Zinner, Ernst

    1995-01-01

    Previous secondary ion mass spectrometry (SIMS) studies of extended impact features from LDEF capture cell experiment AO187-2 showed that it is possible to distinguish natural and man-made particle impacts based on the chemical composition of projectile residues. The same measurement technique has now been applied to specially prepared gold target impacts from experiment AO187-1 in order to identify the origins of projectiles that left deposits too thin to be analyzed by conventional energy-dispersive x-ray (EDX) spectroscopy. The results indicate that SIMS may be the method of choice for the analysis of impact deposits on a variety of sample surfaces. SIMS was also used to determine the isotopic compositions of impact residues from several natural projectiles. Within the precision of the measurements all analyzed residues show isotopically normal compositions.

  18. Seeing Objects as Faces Enhances Object Detection.

    PubMed

    Takahashi, Kohske; Watanabe, Katsumi

    2015-10-01

    The face is a special visual stimulus. Both bottom-up processes for low-level facial features and top-down modulation by face expectations contribute to the advantages of face perception. However, it is hard to dissociate the top-down factors from the bottom-up processes, since facial stimuli mandatorily lead to face awareness. In the present study, using the face pareidolia phenomenon, we demonstrated that face awareness, namely seeing an object as a face, enhances object detection performance. In face pareidolia, some people see a visual stimulus, for example, three dots arranged in V shape, as a face, while others do not. This phenomenon allows us to investigate the effect of face awareness leaving the stimulus per se unchanged. Participants were asked to detect a face target or a triangle target. While target per se was identical between the two tasks, the detection sensitivity was higher when the participants recognized the target as a face. This was the case irrespective of the stimulus eccentricity or the vertical orientation of the stimulus. These results demonstrate that seeing an object as a face facilitates object detection via top-down modulation. The advantages of face perception are, therefore, at least partly, due to face awareness.

  19. Seeing Objects as Faces Enhances Object Detection

    PubMed Central

    Watanabe, Katsumi

    2015-01-01

    The face is a special visual stimulus. Both bottom-up processes for low-level facial features and top-down modulation by face expectations contribute to the advantages of face perception. However, it is hard to dissociate the top-down factors from the bottom-up processes, since facial stimuli mandatorily lead to face awareness. In the present study, using the face pareidolia phenomenon, we demonstrated that face awareness, namely seeing an object as a face, enhances object detection performance. In face pareidolia, some people see a visual stimulus, for example, three dots arranged in V shape, as a face, while others do not. This phenomenon allows us to investigate the effect of face awareness leaving the stimulus per se unchanged. Participants were asked to detect a face target or a triangle target. While target per se was identical between the two tasks, the detection sensitivity was higher when the participants recognized the target as a face. This was the case irrespective of the stimulus eccentricity or the vertical orientation of the stimulus. These results demonstrate that seeing an object as a face facilitates object detection via top-down modulation. The advantages of face perception are, therefore, at least partly, due to face awareness. PMID:27648219

  20. Social Cognition in Williams Syndrome: Face Tuning

    PubMed Central

    Pavlova, Marina A.; Heiz, Julie; Sokolov, Alexander N.; Barisnikov, Koviljka

    2016-01-01

    Many neurological, neurodevelopmental, neuropsychiatric, and psychosomatic disorders are characterized by impairments in visual social cognition, body language reading, and facial assessment of a social counterpart. Yet a wealth of research indicates that individuals with Williams syndrome exhibit remarkable concern for social stimuli and face fascination. Here individuals with Williams syndrome were presented with a set of Face-n-Food images composed of food ingredients and in different degree resembling a face (slightly bordering on the Giuseppe Arcimboldo style). The primary advantage of these images is that single components do not explicitly trigger face-specific processing, whereas in face images commonly used for investigating face perception (such as photographs or depictions), the mere occurrence of typical cues already implicates face presence. In a spontaneous recognition task, participants were shown a set of images in a predetermined order from the least to most resembling a face. Strikingly, individuals with Williams syndrome exhibited profound deficits in recognition of the Face-n-Food images as a face: they did not report seeing a face on the images, which typically developing controls effortlessly recognized as a face, and gave overall fewer face responses. This suggests atypical face tuning in Williams syndrome. The outcome is discussed in the light of a general pattern of social cognition in Williams syndrome and brain mechanisms underpinning face processing. PMID:27531986

  1. Social Cognition in Williams Syndrome: Face Tuning.

    PubMed

    Pavlova, Marina A; Heiz, Julie; Sokolov, Alexander N; Barisnikov, Koviljka

    2016-01-01

    Many neurological, neurodevelopmental, neuropsychiatric, and psychosomatic disorders are characterized by impairments in visual social cognition, body language reading, and facial assessment of a social counterpart. Yet a wealth of research indicates that individuals with Williams syndrome exhibit remarkable concern for social stimuli and face fascination. Here individuals with Williams syndrome were presented with a set of Face-n-Food images composed of food ingredients and in different degree resembling a face (slightly bordering on the Giuseppe Arcimboldo style). The primary advantage of these images is that single components do not explicitly trigger face-specific processing, whereas in face images commonly used for investigating face perception (such as photographs or depictions), the mere occurrence of typical cues already implicates face presence. In a spontaneous recognition task, participants were shown a set of images in a predetermined order from the least to most resembling a face. Strikingly, individuals with Williams syndrome exhibited profound deficits in recognition of the Face-n-Food images as a face: they did not report seeing a face on the images, which typically developing controls effortlessly recognized as a face, and gave overall fewer face responses. This suggests atypical face tuning in Williams syndrome. The outcome is discussed in the light of a general pattern of social cognition in Williams syndrome and brain mechanisms underpinning face processing.

  2. Social Cognition in Williams Syndrome: Face Tuning.

    PubMed

    Pavlova, Marina A; Heiz, Julie; Sokolov, Alexander N; Barisnikov, Koviljka

    2016-01-01

    Many neurological, neurodevelopmental, neuropsychiatric, and psychosomatic disorders are characterized by impairments in visual social cognition, body language reading, and facial assessment of a social counterpart. Yet a wealth of research indicates that individuals with Williams syndrome exhibit remarkable concern for social stimuli and face fascination. Here individuals with Williams syndrome were presented with a set of Face-n-Food images composed of food ingredients and in different degree resembling a face (slightly bordering on the Giuseppe Arcimboldo style). The primary advantage of these images is that single components do not explicitly trigger face-specific processing, whereas in face images commonly used for investigating face perception (such as photographs or depictions), the mere occurrence of typical cues already implicates face presence. In a spontaneous recognition task, participants were shown a set of images in a predetermined order from the least to most resembling a face. Strikingly, individuals with Williams syndrome exhibited profound deficits in recognition of the Face-n-Food images as a face: they did not report seeing a face on the images, which typically developing controls effortlessly recognized as a face, and gave overall fewer face responses. This suggests atypical face tuning in Williams syndrome. The outcome is discussed in the light of a general pattern of social cognition in Williams syndrome and brain mechanisms underpinning face processing. PMID:27531986

  3. Seeing Objects as Faces Enhances Object Detection

    PubMed Central

    Watanabe, Katsumi

    2015-01-01

    The face is a special visual stimulus. Both bottom-up processes for low-level facial features and top-down modulation by face expectations contribute to the advantages of face perception. However, it is hard to dissociate the top-down factors from the bottom-up processes, since facial stimuli mandatorily lead to face awareness. In the present study, using the face pareidolia phenomenon, we demonstrated that face awareness, namely seeing an object as a face, enhances object detection performance. In face pareidolia, some people see a visual stimulus, for example, three dots arranged in V shape, as a face, while others do not. This phenomenon allows us to investigate the effect of face awareness leaving the stimulus per se unchanged. Participants were asked to detect a face target or a triangle target. While target per se was identical between the two tasks, the detection sensitivity was higher when the participants recognized the target as a face. This was the case irrespective of the stimulus eccentricity or the vertical orientation of the stimulus. These results demonstrate that seeing an object as a face facilitates object detection via top-down modulation. The advantages of face perception are, therefore, at least partly, due to face awareness.

  4. Seeing Objects as Faces Enhances Object Detection.

    PubMed

    Takahashi, Kohske; Watanabe, Katsumi

    2015-10-01

    The face is a special visual stimulus. Both bottom-up processes for low-level facial features and top-down modulation by face expectations contribute to the advantages of face perception. However, it is hard to dissociate the top-down factors from the bottom-up processes, since facial stimuli mandatorily lead to face awareness. In the present study, using the face pareidolia phenomenon, we demonstrated that face awareness, namely seeing an object as a face, enhances object detection performance. In face pareidolia, some people see a visual stimulus, for example, three dots arranged in V shape, as a face, while others do not. This phenomenon allows us to investigate the effect of face awareness leaving the stimulus per se unchanged. Participants were asked to detect a face target or a triangle target. While target per se was identical between the two tasks, the detection sensitivity was higher when the participants recognized the target as a face. This was the case irrespective of the stimulus eccentricity or the vertical orientation of the stimulus. These results demonstrate that seeing an object as a face facilitates object detection via top-down modulation. The advantages of face perception are, therefore, at least partly, due to face awareness. PMID:27648219

  5. Using color for face verification

    NASA Astrophysics Data System (ADS)

    Leszczynski, Mariusz

    2009-06-01

    This paper presents research on importance of color information in face verification system. Four most popular color spaces where used: RGB, YIQ, YCbCr, luminance and compared using four types of discriminant classifiers. Experiments conducted on facial databases with complex background, different poses and light condition show that color information can improve the verification accuracy compared to the traditionally used luminance information. To achieve the best performance we recommend to use multi frames verification encoded to YIQ color space.

  6. The Philadelphia Face Perception Battery

    PubMed Central

    Thomas, Amy; Lawler, Kathy; Olson, Ingrid R; Aguirre, Geoffrey K

    2008-01-01

    The Philadelphia Face Perception Battery (PFPB) tests four aspects of face perception: discrimination of facial similarity, attractiveness, gender, and age. Calibration with 116 neurologically intact subjects yielded average performance of ~90%. Across subjects, there was a low correlation (<0.22) in performance between the tests (with the exception of the attractiveness and age discrimination tests) suggesting that the tests measure independent aspects of face perception. There were modest effects of subject demographic factors upon performance, and test-retest reliability scores (between 0.37 and 0.75) were comparable to other neuropsychological batteries. Modification of the stimuli to obscure internal facial features lowered performance on the age, gender, and attractiveness discrimination tests between 2 and 4 standard deviations. The clinical sensitivity of the battery was demonstrated by testing a patient with acquired prosopagnosia. She showed performance impairments of between 2 and 4 standard deviations on all sub-tests. The PFPB is freely available for non-commercial use. PMID:18082362

  7. From the periphery to centre stage: de novo single nucleotide variants play a key role in human genetic disease.

    PubMed

    Ku, Chee-Seng; Tan, Eng King; Cooper, David N

    2013-04-01

    Human germline mutations arise anew during meiosis in every generation. Such spontaneously occurring genetic variants are termed de novo mutations. Although the introduction of microarray based approaches led to the discovery of numerous de novo copy number variants underlying a range of human genetic conditions, de novo single nucleotide variants (SNVs) remained refractory to analysis at the whole genome level until the advent of next generation sequencing technologies such as whole genome sequencing and whole exome sequencing. These approaches have recently allowed the estimation of the mutation rate of de novo SNVs and greatly increased our understanding of their contribution to human genetic disease. Indeed, de novo SNVs have been found to underlie various common human neurodevelopmental conditions such as schizophrenia, autism and intellectual disability, as well as sporadic cases of rare Mendelian disorders. In many cases, however, confirmation of the pathogenicity of identified de novo SNVs remains a major challenge. PMID:23396985

  8. Prevalence and origin of De Novo duplications in Charcot-Marie-Tooth disease type 1A: First report of a De Novo duplication with a maternal origin

    SciTech Connect

    Blair, I.P.; Nash, J.; Gordon, M.J.; Nicholson, G.A.

    1996-03-01

    Charcot-Marie-Tooth disease (CMT) is the most common inherited peripheral neuropathy. Sporadic cases of CMT have been described since the earliest reports of the disease. The most frequent form of the disorder, CMT1A, is associated with a 1.5-Mb DNA duplication on chromosome 17p11.2, which segregates with the disease. In order to investigate the prevalence of de novo CMT1A duplications, this study examined 118 duplication-positive CMT1A families. In 10 of these families it was demonstrated that the disease had arisen as the result of a de novo mutation. By taking into account the ascertainment of families, it can be estimated that {>=}10% of autosomal dominant CMT1 families are due to de novo duplications. The CMT1A duplication is thought to be the product of unequal crossing over between parental chromosome 17 homologues during meiosis. Polymorphic markers from within the duplicated region were used to determine the parental origin of these de novo duplications in eight informative families. Seven were of paternal and one of maternal origin. This study represents the first report of a de novo duplication with a maternal origin and indicates that it is not a phenomenon associated solely with male meioses. Recombination fractions for the region duplicated in CMT1A are larger in females than in males. That suggests that oogenesis may be afforded greater protection from misalignment during synapsis, and/or that there may be lower activity of those factors or mechanisms that lead to unequal crossing over at the CMT1A locus. 41 refs., 2 figs.

  9. De novo mutations in synaptic transmission genes including DNM1 cause epileptic encephalopathies.

    PubMed

    2014-10-01

    Emerging evidence indicates that epileptic encephalopathies are genetically highly heterogeneous, underscoring the need for large cohorts of well-characterized individuals to further define the genetic landscape. Through a collaboration between two consortia (EuroEPINOMICS and Epi4K/EPGP), we analyzed exome-sequencing data of 356 trios with the "classical" epileptic encephalopathies, infantile spasms and Lennox Gastaut syndrome, including 264 trios previously analyzed by the Epi4K/EPGP consortium. In this expanded cohort, we find 429 de novo mutations, including de novo mutations in DNM1 in five individuals and de novo mutations in GABBR2, FASN, and RYR3 in two individuals each. Unlike previous studies, this cohort is sufficiently large to show a significant excess of de novo mutations in epileptic encephalopathy probands compared to the general population using a likelihood analysis (p = 8.2 × 10(-4)), supporting a prominent role for de novo mutations in epileptic encephalopathies. We bring statistical evidence that mutations in DNM1 cause epileptic encephalopathy, find suggestive evidence for a role of three additional genes, and show that at least 12% of analyzed individuals have an identifiable causal de novo mutation. Strikingly, 75% of mutations in these probands are predicted to disrupt a protein involved in regulating synaptic transmission, and there is a significant enrichment of de novo mutations in genes in this pathway in the entire cohort as well. These findings emphasize an important role for synaptic dysregulation in epileptic encephalopathies, above and beyond that caused by ion channel dysfunction.

  10. De Novo Mutations in Synaptic Transmission Genes Including DNM1 Cause Epileptic Encephalopathies

    PubMed Central

    Appenzeller, Silke; Balling, Rudi; Barisic, Nina; Baulac, Stéphanie; Caglayan, Hande; Craiu, Dana; De Jonghe, Peter; Depienne, Christel; Dimova, Petia; Djémié, Tania; Gormley, Padhraig; Guerrini, Renzo; Helbig, Ingo; Hjalgrim, Helle; Hoffman-Zacharska, Dorota; Jähn, Johanna; Klein, Karl Martin; Koeleman, Bobby; Komarek, Vladimir; Krause, Roland; Kuhlenbäumer, Gregor; Leguern, Eric; Lehesjoki, Anna-Elina; Lemke, Johannes R.; Lerche, Holger; Linnankivi, Tarja; Marini, Carla; May, Patrick; Møller, Rikke S.; Muhle, Hiltrud; Pal, Deb; Palotie, Aarno; Pendziwiat, Manuela; Robbiano, Angela; Roelens, Filip; Rosenow, Felix; Selmer, Kaja; Serratosa, Jose M.; Sisodiya, Sanjay; Stephani, Ulrich; Sterbova, Katalin; Striano, Pasquale; Suls, Arvid; Talvik, Tiina; von Spiczak, Sarah; Weber, Yvonne; Weckhuysen, Sarah; Zara, Federico; Abou-Khalil, Bassel; Alldredge, Brian K.; Andermann, Eva; Andermann, Frederick; Amron, Dina; Bautista, Jocelyn F.; Berkovic, Samuel F.; Bluvstein, Judith; Boro, Alex; Cascino, Gregory; Consalvo, Damian; Crumrine, Patricia; Devinsky, Orrin; Dlugos, Dennis; Epstein, Michael P.; Fiol, Miguel; Fountain, Nathan B.; French, Jacqueline; Friedman, Daniel; Geller, Eric B.; Glauser, Tracy; Glynn, Simon; Haas, Kevin; Haut, Sheryl R.; Hayward, Jean; Helmers, Sandra L.; Joshi, Sucheta; Kanner, Andres; Kirsch, Heidi E.; Knowlton, Robert C.; Kossoff, Eric H.; Kuperman, Rachel; Kuzniecky, Ruben; Lowenstein, Daniel H.; McGuire, Shannon M.; Motika, Paul V.; Novotny, Edward J.; Ottman, Ruth; Paolicchi, Juliann M.; Parent, Jack; Park, Kristen; Poduri, Annapurna; Sadleir, Lynette; Scheffer, Ingrid E.; Shellhaas, Renée A.; Sherr, Elliott; Shih, Jerry J.; Singh, Rani; Sirven, Joseph; Smith, Michael C.; Sullivan, Joe; Thio, Liu Lin; Venkat, Anu; Vining, Eileen P.G.; Von Allmen, Gretchen K.; Weisenberg, Judith L.; Widdess-Walsh, Peter; Winawer, Melodie R.; Allen, Andrew S.; Berkovic, Samuel F.; Cossette, Patrick; Delanty, Norman; Dlugos, Dennis; Eichler, Evan E.; Epstein, Michael P.; Glauser, Tracy; Goldstein, David B.; Han, Yujun; Heinzen, Erin L.; Johnson, Michael R.; Kuzniecky, Ruben; Lowenstein, Daniel H.; Marson, Anthony G.; Mefford, Heather C.; Nieh, Sahar Esmaeeli; O’Brien, Terence J.; Ottman, Ruth; Petrou, Stephen; Petrovski, Slavé; Poduri, Annapurna; Ruzzo, Elizabeth K.; Scheffer, Ingrid E.; Sherr, Elliott

    2014-01-01

    Emerging evidence indicates that epileptic encephalopathies are genetically highly heterogeneous, underscoring the need for large cohorts of well-characterized individuals to further define the genetic landscape. Through a collaboration between two consortia (EuroEPINOMICS and Epi4K/EPGP), we analyzed exome-sequencing data of 356 trios with the “classical” epileptic encephalopathies, infantile spasms and Lennox Gastaut syndrome, including 264 trios previously analyzed by the Epi4K/EPGP consortium. In this expanded cohort, we find 429 de novo mutations, including de novo mutations in DNM1 in five individuals and de novo mutations in GABBR2, FASN, and RYR3 in two individuals each. Unlike previous studies, this cohort is sufficiently large to show a significant excess of de novo mutations in epileptic encephalopathy probands compared to the general population using a likelihood analysis (p = 8.2 × 10−4), supporting a prominent role for de novo mutations in epileptic encephalopathies. We bring statistical evidence that mutations in DNM1 cause epileptic encephalopathy, find suggestive evidence for a role of three additional genes, and show that at least 12% of analyzed individuals have an identifiable causal de novo mutation. Strikingly, 75% of mutations in these probands are predicted to disrupt a protein involved in regulating synaptic transmission, and there is a significant enrichment of de novo mutations in genes in this pathway in the entire cohort as well. These findings emphasize an important role for synaptic dysregulation in epileptic encephalopathies, above and beyond that caused by ion channel dysfunction. PMID:25262651

  11. Crossing the “Uncanny Valley”: adaptation to cartoon faces can influence perception of human faces

    PubMed Central

    Chen, Haiwen; Russell, Richard; Nakayama, Ken; Livingstone, Margaret

    2013-01-01

    Adaptation can shift what individuals identify to be a prototypical or attractive face. Past work suggests that low-level shape adaptation can affect high-level face processing but is position dependent. Adaptation to distorted images of faces can also affect face processing but only within sub-categories of faces, such as gender, age, and race/ethnicity. This study assesses whether there is a representation of face that is specific to faces (as opposed to all shapes) but general to all kinds of faces (as opposed to subcategories) by testing whether adaptation to one type of face can affect perception of another. Participants were shown cartoon videos containing faces with abnormally large eyes. Using animated videos allowed us to simulate naturalistic exposure and avoid positional shape adaptation. Results suggest that adaptation to cartoon faces with large eyes shifts preferences for human faces toward larger eyes, supporting the existence of general face representations. PMID:20465173

  12. Online or Face to Face? A Comparison of Two Methods of Training Professionals

    ERIC Educational Resources Information Center

    Dillon, Kristin; Dworkin, Jodi; Gengler, Colleen; Olson, Kathleen

    2008-01-01

    Online courses offer benefits over face-to-face courses such as accessibility, affordability, and flexibility. Literature assessing the effectiveness of face-to-face and online courses is growing, but findings remain inconclusive. This study compared evaluations completed by professionals who had taken a research update short course either face to…

  13. Familiar Face Recognition in Children with Autism: The Differential Use of Inner and Outer Face Parts

    ERIC Educational Resources Information Center

    Wilson, Rebecca; Pascalis, Olivier; Blades, Mark

    2007-01-01

    We investigated whether children with autistic spectrum disorders (ASD) have a deficit in recognising familiar faces. Children with ASD were given a forced choice familiar face recognition task with three conditions: full faces, inner face parts and outer face parts. Control groups were children with developmental delay (DD) and typically…

  14. Face feature processor on mobile service robot

    NASA Astrophysics Data System (ADS)

    Ahn, Ho Seok; Park, Myoung Soo; Na, Jin Hee; Choi, Jin Young

    2005-12-01

    In recent years, many mobile service robots have been developed. These robots are different from industrial robots. Service robots were confronted to unexpected changes in the human environment. So many capabilities were needed to service mobile robot, for example, the capability to recognize people's face and voice, the capability to understand people's conversation, and the capability to express the robot's thinking etc. This research considered face detection, face tracking and face recognition from continuous camera image. For face detection module, it used CBCH algorithm using openCV library from Intel Corporation. For face tracking module, it used the fuzzy controller to control the pan-tilt camera movement smoothly with face detection result. A PCA-FX, which adds class information to PCA, was used for face recognition module. These three procedures were called face feature processor, which were implemented on mobile service robot OMR to verify.

  15. Maternal face processing in Mosuo preschool children.

    PubMed

    Dai, Junqiang; Zhai, Hongchang; Wu, Haiyan; Yang, Suyong; Cacioppo, John T; Cacioppo, Stephanie; Luo, Yue-jia

    2014-05-01

    Instinctively responding to maternal face is an evolutionary function of enhancing survival and development. However, because of the confounding nature of familiarity, little is known concerning the neural mechanism involved in maternal face recognition. We had a rare opportunity to examine Mosuo preschool children who were raised in a matrilineal society in which mothers and aunts represent equally familiar faces to the children. The participants were exposed to photographs of their mother's face, aunt's face, and an unfamiliar female's faces during electroencephalography (EEG) recording. The EEG results showed that the mother's face elicited a more negative N1 component, a larger left N170 component, and a larger P300 component; both the mother's and aunt's faces elicited a larger right N170 component. These results suggest that the emotional attachment between mother and child has neural ramifications across three successive face processing stages that are distinguished from the neural effects of facial familiarity. PMID:24631724

  16. Efficient human face detection in infancy.

    PubMed

    Jakobsen, Krisztina V; Umstead, Lindsey; Simpson, Elizabeth A

    2016-01-01

    Adults detect conspecific faces more efficiently than heterospecific faces; however, the development of this own-species bias (OSB) remains unexplored. We tested whether 6- and 11-month-olds exhibit OSB in their attention to human and animal faces in complex visual displays with high perceptual load (25 images competing for attention). Infants (n = 48) and adults (n = 43) passively viewed arrays containing a face among 24 non-face distractors while we measured their gaze with remote eye tracking. While OSB is typically not observed until about 9 months, we found that, already by 6 months, human faces were more likely to be detected, were detected more quickly (attention capture), and received longer looks (attention holding) than animal faces. These data suggest that 6-month-olds already exhibit OSB in face detection efficiency, consistent with perceptual attunement. This specialization may reflect the biological importance of detecting conspecific faces, a foundational ability for early social interactions.

  17. An example-based face relighting

    NASA Astrophysics Data System (ADS)

    Shim, Hyunjung; Chen, Tsuhan

    2012-03-01

    In this paper, we propose a new face relighting algorithm powered by a large database of face images captured under various known lighting conditions (a Multi-PIE database). Key insight of our algorithm is that a face can be represented by an assemble of patches from many other faces. The algorithm finds the most similar face patches in the database in terms of the lighting and the appearance. By assembling the matched patches, we can visualize the input face under various lighting conditions. Unlike existing face relighting algorithms, we neither use any kinds of face model nor make a physical assumption. Instead, our algorithm is a data-driven approach, synthesizing the appearance of the image patch using the appearance of the example patch. Using a data-driven approach, we can account for various intrinsic facial features including the non-Lambertian skin properties as well as the hair. Also, our algorithm is insensitive to the face misalignment. We demonstrate the performance of our algorithm by face relighting and face recognition experiments. Especially, the synthesized results show that the proposed algorithm can successfully handle various intrinsic features of an input face. Also, from the face recognition experiment, we show that our method is comparable to the most recent face relighting work.

  18. Familiar Face Detection in 180 ms.

    PubMed

    Visconti di Oleggio Castello, Matteo; Gobbini, M Ida

    2015-01-01

    The visual system is tuned for rapid detection of faces, with the fastest choice saccade to a face at 100 ms. Familiar faces have a more robust representation than do unfamiliar faces, and are detected faster in the absence of awareness and with reduced attentional resources. Faces of family and close friends become familiar over a protracted period involving learning the unique visual appearance, including a view-invariant representation, as well as person knowledge. We investigated the effect of personal familiarity on the earliest stages of face processing by using a saccadic-choice task to measure how fast familiar face detection can happen. Subjects made correct and reliable saccades to familiar faces when unfamiliar faces were distractors at 180 ms--very rapid saccades that are 30 to 70 ms earlier than the earliest evoked potential modulated by familiarity. By contrast, accuracy of saccades to unfamiliar faces with familiar faces as distractors did not exceed chance. Saccades to faces with object distractors were even faster (110 to 120 ms) and equivalent for familiar and unfamiliar faces, indicating that familiarity does not affect ultra-rapid saccades. We propose that detectors of diagnostic facial features for familiar faces develop in visual cortices through learning and allow rapid detection that precedes explicit recognition of identity. PMID:26305788

  19. Face recognition increases during saccade preparation.

    PubMed

    Lin, Hai; Rizak, Joshua D; Ma, Yuan-ye; Yang, Shang-chuan; Chen, Lin; Hu, Xin-tian

    2014-01-01

    Face perception is integral to human perception system as it underlies social interactions. Saccadic eye movements are frequently made to bring interesting visual information, such as faces, onto the fovea for detailed processing. Just before eye movement onset, the processing of some basic features, such as the orientation, of an object improves at the saccade landing point. Interestingly, there is also evidence that indicates faces are processed in early visual processing stages similar to basic features. However, it is not known whether this early enhancement of processing includes face recognition. In this study, three experiments were performed to map the timing of face presentation to the beginning of the eye movement in order to evaluate pre-saccadic face recognition. Faces were found to be similarly processed as simple objects immediately prior to saccadic movements. Starting ∼ 120 ms before a saccade to a target face, independent of whether or not the face was surrounded by other faces, the face recognition gradually improved and the critical spacing of the crowding decreased as saccade onset was approaching. These results suggest that an upcoming saccade prepares the visual system for new information about faces at the saccade landing site and may reduce the background in a crowd to target the intended face. This indicates an important role of pre-saccadic eye movement signals in human face recognition.

  20. Face-to-face or not-to-face: A technology preference for communication.

    PubMed

    Jaafar, Noor Ismawati; Darmawan, Bobby; Mohamed Ariffin, Mohd Yahya

    2014-11-01

    This study employed the Model of Technology Preference (MTP) to explain the relationship of the variables as the antecedents of behavioral intention to adopt a social networking site (SNS) for communication. Self-administered questionnaires were distributed to SNS account users using paper-based and web-based surveys that led to 514 valid responses. The data were analyzed using structural equation modeling (SEM). The results show that two out of three attributes of the attribute-based preference (ATRP) affect attitude-based preference (ATTP). The data support the hypotheses that perceived enjoyment and social presence are predictors of ATTP. In this study, the findings further indicated that ATTP has no relationship with the behavioral intention of using SNS, but it has a relationship with the attitude of using SNS. SNS development should provide features that ensure enjoyment and social presence for users to communicate instead of using the traditional face-to-face method of communication.

  1. Face-to-Face or Not-to-Face: A Technology Preference for Communication

    PubMed Central

    Darmawan, Bobby; Mohamed Ariffin, Mohd Yahya

    2014-01-01

    Abstract This study employed the Model of Technology Preference (MTP) to explain the relationship of the variables as the antecedents of behavioral intention to adopt a social networking site (SNS) for communication. Self-administered questionnaires were distributed to SNS account users using paper-based and web-based surveys that led to 514 valid responses. The data were analyzed using structural equation modeling (SEM). The results show that two out of three attributes of the attribute-based preference (ATRP) affect attitude-based preference (ATTP). The data support the hypotheses that perceived enjoyment and social presence are predictors of ATTP. In this study, the findings further indicated that ATTP has no relationship with the behavioral intention of using SNS, but it has a relationship with the attitude of using SNS. SNS development should provide features that ensure enjoyment and social presence for users to communicate instead of using the traditional face-to-face method of communication. PMID:25405782

  2. Synthesis and Characterization of Metal-Organic Frameworks (MOFs) That Are Difficult to Access De Novo

    NASA Astrophysics Data System (ADS)

    Karagiaridi, Olga

    Metal-organic frameworks (MOFs) are a class of intriguing hybrid materials, comprised of metal-based nodes joined by organic linkers into a crystalline, porous, three-dimensional lattice. Their signature properties (well-defined surfaces, tailorability and ultra-high porosity) render them promising candidates for many applications, including, but not limited to, gas storage, gas separation, catalysis and sensing. One of the greatest challenges associated with MOF synthesis lies in the fact that obtaining a desired MOF structure that is tailored to perform a specific application is often not trivial. Traditional synthetic pathways termed "de novo synthesis" (typically one-pot reactions between the MOF structural building blocks under solvothermal conditions) often give rise to side products that do not possess the desired structure. To circumvent this problem, we have studied in depth two powerful MOF synthetic techniques -- solvent-assisted linker exchange (SALE) and transmetalation. These are heterogeneous reactions of parent MOF crystals with concentrated solutions of organic linkers and inorganic metal salts, respectively, that lead to the replacement of the linkers or metal nodes within the parent MOFs by the desired components, while the overall framework topology is preserved. The projects described in this dissertation have aimed to apply these techniques to transform simple (unfunctionalized) and easy to synthesize representative materials from various MOF systems to structurally and functionally interesting daughter products. Examples include synthesis of MOFs that are energetically "unfavorable", extension of MOF cages by longer linker incorporation, functionalization of MOF pores and endowment of MOFs with permanent and persistent porosity. Through these projects, we have been able to formulate a set of rules that can be applied to predict the successful outcome of SALE. Since the allure of MOFs lies in their applications, expanding the range of

  3. Advanced Face Gear Surface Durability Evaluations

    NASA Technical Reports Server (NTRS)

    Lewicki, David G.; Heath, Gregory F.

    2016-01-01

    The surface durability life of helical face gears and isotropic super-finished (ISF) face gears was investigated. Experimental fatigue tests were performed at the NASA Glenn Research Center. Endurance tests were performed on 10 sets of helical face gears in mesh with tapered involute helical pinions, and 10 sets of ISF-enhanced straight face gears in mesh with tapered involute spur pinions. The results were compared to previous tests on straight face gears. The life of the ISF configuration was slightly less than that of previous tests on straight face gears. The life of the ISF configuration was slightly greater than that of the helical configuration.

  4. Stream-Field Interactions in the Magnetic Accretor AO Piscium

    NASA Astrophysics Data System (ADS)

    Hellier, Coel; van Zyl, Liza

    2005-06-01

    UV spectra of the magnetic accretor AO Psc show absorption features for half the binary orbit. The absorption is unlike the wind-formed features often seen in similar stars. Instead, we attribute it to a fraction of the stream that overflows the impact with the accretion disk. Rapid velocity variations can be explained by changes in the trajectory of the stream depending on the orientation of the white dwarf's magnetic field. Hence, we are directly observing the interaction of an accretion stream with a rotating field. We compare this behavior to that seen in other intermediate polars and in SW Sex stars.

  5. Intramedullary locking femoral nails. Experience with the AO nail.

    PubMed Central

    Fogarty, A. B.; Yeates, H. A.

    1991-01-01

    The AO interlocking nail was introduced to the Ulster Hospital, Dundonald in 1988 and since then has been used in over 50 patients with femoral shaft fractures. We have reviewed 45 patients with 46 femoral shaft fractures treated between June 1988 and April 1990. These included four compound fractures and 13 comminuted fractures. The results compare favourably with other series. The union rate was 98% and there were no instances of deep infection. The alternative treatment methods available are discussed along with a review of the relevant literature. Images Fig 3 Fig 5 PMID:1785145

  6. LDEF (Postflight), AO201 : Interplanetary Dust Experiment, Tray C03

    NASA Technical Reports Server (NTRS)

    1990-01-01

    LDEF (Postflight), AO201 : Interplanetary Dust Experiment, Tray C03 The IDE mounting plate and the detector frames are coated with a brown stain similiar to that seen on the other experiments in this and other trays located nearby. The stain seems to be slightly darker along the lower edge of the solar sensor mounting plate. The colors and designs seen on the detectors are reflections of the surrounding area. The thin brown film on the detectors metallic surface has resulted in a duller reflection of a technician, in the upper left, and other items.

  7. Partial face recognition: alignment-free approach.

    PubMed

    Liao, Shengcai; Jain, Anil K; Li, Stan Z

    2013-05-01

    Numerous methods have been developed for holistic face recognition with impressive performance. However, few studies have tackled how to recognize an arbitrary patch of a face image. Partial faces frequently appear in unconstrained scenarios, with images captured by surveillance cameras or handheld devices (e.g., mobile phones) in particular. In this paper, we propose a general partial face recognition approach that does not require face alignment by eye coordinates or any other fiducial points. We develop an alignment-free face representation method based on Multi-Keypoint Descriptors (MKD), where the descriptor size of a face is determined by the actual content of the image. In this way, any probe face image, holistic or partial, can be sparsely represented by a large dictionary of gallery descriptors. A new keypoint descriptor called Gabor Ternary Pattern (GTP) is also developed for robust and discriminative face recognition. Experimental results are reported on four public domain face databases (FRGCv2.0, AR, LFW, and PubFig) under both the open-set identification and verification scenarios. Comparisons with two leading commercial face recognition SDKs (PittPatt and FaceVACS) and two baseline algorithms (PCA+LDA and LBP) show that the proposed method, overall, is superior in recognizing both holistic and partial faces without requiring alignment.

  8. Still another confounded face in the crowd.

    PubMed

    Purcell, Dean G; Stewart, Alan L

    2010-11-01

    Experiments using schematic faces developed by Öhman (Öhman, Lundqvist, & Esteves, 2001) seem to document an anger-superiority effect, although we have come to question these experiments. Our work shows that the low-level features of these schematic faces interact with the face's surround to produce effects that have been attributed to facial affect. Using relatively neutral faces that preserved the feature and surround spatial relationships of angry and happy schematic faces, we produced reaction times (RTs) that were indistinguishable from those found with angry and happy faces. We also found that the target face's position within the crowd determined the magnitude of the advantage for angry faces as well as for relatively affect-neutral faces. Removing the facial surround reduces the advantage for angry faces, largely by improving performance on happy faces. There was an apparent small advantage for angry features without a surround. Öhman faces avoid the problems associated with modified grayscale faces only to introduce an equally troubling confound.

  9. Partial face recognition: alignment-free approach.

    PubMed

    Liao, Shengcai; Jain, Anil K; Li, Stan Z

    2013-05-01

    Numerous methods have been developed for holistic face recognition with impressive performance. However, few studies have tackled how to recognize an arbitrary patch of a face image. Partial faces frequently appear in unconstrained scenarios, with images captured by surveillance cameras or handheld devices (e.g., mobile phones) in particular. In this paper, we propose a general partial face recognition approach that does not require face alignment by eye coordinates or any other fiducial points. We develop an alignment-free face representation method based on Multi-Keypoint Descriptors (MKD), where the descriptor size of a face is determined by the actual content of the image. In this way, any probe face image, holistic or partial, can be sparsely represented by a large dictionary of gallery descriptors. A new keypoint descriptor called Gabor Ternary Pattern (GTP) is also developed for robust and discriminative face recognition. Experimental results are reported on four public domain face databases (FRGCv2.0, AR, LFW, and PubFig) under both the open-set identification and verification scenarios. Comparisons with two leading commercial face recognition SDKs (PittPatt and FaceVACS) and two baseline algorithms (PCA+LDA and LBP) show that the proposed method, overall, is superior in recognizing both holistic and partial faces without requiring alignment. PMID:23520259

  10. Faciotopy-A face-feature map with face-like topology in the human occipital face area.

    PubMed

    Henriksson, Linda; Mur, Marieke; Kriegeskorte, Nikolaus

    2015-11-01

    The occipital face area (OFA) and fusiform face area (FFA) are brain regions thought to be specialized for face perception. However, their intrinsic functional organization and status as cortical areas with well-defined boundaries remains unclear. Here we test these regions for "faciotopy", a particular hypothesis about their intrinsic functional organisation. A faciotopic area would contain a face-feature map on the cortical surface, where cortical patches represent face features and neighbouring patches represent features that are physically neighbouring in a face. The faciotopy hypothesis is motivated by the idea that face regions might develop from a retinotopic protomap and acquire their selectivity for face features through natural visual experience. Faces have a prototypical configuration of features, are usually perceived in a canonical upright orientation, and are frequently fixated in particular locations. To test the faciotopy hypothesis, we presented images of isolated face features at fixation to subjects during functional magnetic resonance imaging. The responses in V1 were best explained by low-level image properties of the stimuli. OFA, and to a lesser degree FFA, showed evidence for faciotopic organization. When a single patch of cortex was estimated for each face feature, the cortical distances between the feature patches reflected the physical distance between the features in a face. Faciotopy would be the first example, to our knowledge, of a cortical map reflecting the topology, not of a part of the organism itself (its retina in retinotopy, its body in somatotopy), but of an external object of particular perceptual significance. PMID:26235800

  11. Emotional expression and heart rate in high-risk infants during the face-to-face/still-face.

    PubMed

    Mattson, Whitney I; Ekas, Naomi V; Lambert, Brittany; Tronick, Ed; Lester, Barry M; Messinger, Daniel S

    2013-12-01

    In infants, eye constriction-the Duchenne marker-and mouth opening appear to index the intensity of both positive and negative facial expressions. We combined eye constriction and mouth opening that co-occurred with smiles and cry-faces (respectively, the prototypic expressions of infant joy and distress) to measure emotional expression intensity. Expression intensity and heart rate were measured throughout the face-to-face/still-face (FFSF) in a sample of infants with prenatal cocaine exposure who were at risk for developmental difficulties. Smiles declined and cry-faces increased in the still-face episode, but the distribution of eye constriction and mouth opening in smiles and cry-faces did not differ across episodes of the FFSF. As time elapsed in the still face episode potential indices of intensity increased, cry-faces were more likely to be accompanied by eye constriction and mouth opening. During cry-faces there were also moderately stable individual differences in the quantity of eye constriction and mouth opening. Infant heart rate was higher during cry-faces and lower during smiles, but did not vary with intensity of expression or by episode. In sum, infants express more intense negative affect as the still-face progresses, but do not show clear differences in expressive intensity between episodes of the FFSF.

  12. JAMES RIVER FACE WILDERNESS, VIRGINIA.

    USGS Publications Warehouse

    Brown, C. Ervin; Gazdik, Gertrude C.

    1984-01-01

    A mineral survey concluded that the James River Face Wilderness, Virginia, had little promise for the occurrence of metallic mineral resources. Two major rock units in the area do contain large nonmetallic mineral resources of quartzite and shale that have been mined for silica products and for brick and expanded aggregate, respectively. Because large deposits of the same material are more easily available in nearby areas, demand for the deposits within the wilderness is highly unlikely. No energy resources were identified in the course of this study.

  13. Face recognition based on fringe pattern analysis

    NASA Astrophysics Data System (ADS)

    Guo, Hong; Huang, Peisen

    2010-03-01

    Two-dimensional face-recognition techniques suffer from facial texture and illumination variations. Although 3-D techniques can overcome these limitations, the reconstruction and storage expenses of 3-D information are extremely high. We present a novel face-recognition method that directly utilizes 3-D information encoded in face fringe patterns without having to reconstruct 3-D geometry. In the proposed method, a digital video projector is employed to sequentially project three phase-shifted sinusoidal fringe patterns onto the subject's face. Meanwhile, a camera is used to capture the distorted fringe patterns from an offset angle. Afterward, the face fringe images are analyzed by the phase-shifting method and the Fourier transform method to obtain a spectral representation of the 3-D face. Finally, the eigenface algorithm is applied to the face-spectrum images to perform face recognition. Simulation and experimental results demonstrate that the proposed method achieved satisfactory recognition rates with reduced computational complexity and storage expenses.

  14. Facing Diabetes: What You Need to Know

    MedlinePlus

    ... of this page please turn Javascript on. Feature: Diabetes Facing Diabetes: What You Need to Know Past Issues / Fall ... your loved ones. Photos: AP The Faces of Diabetes Diabetes strikes millions of Americans, young and old, ...

  15. Hospital design and face-to-face interaction among clinicians: a theoretical model.

    PubMed

    Rashid, Mahbub

    2009-01-01

    A growing body of literature suggests that face-to-face interaction among clinicians in hospitals affects patient outcomes. How can face-to-face interaction among clinicians be influenced positively to improve patient outcomes in hospitals? So far, most strategies for improving face-to-face interaction in hospitals have focused on changing organizational culture. In contrast, this paper proposes a theoretical model that shows how spatial program and structure can help face-to-face interaction fulfill its purposes in hospitals by controlling the interfaces among different communities of clinicians. PMID:21165842

  16. Misaligned and Polarity-Reversed Faces Determine Face-specific Capacity Limits

    PubMed Central

    Thoma, Volker; Ward, Neil; de Fockert, Jan W.

    2016-01-01

    Previous research using flanker paradigms suggests that peripheral distracter faces are automatically processed when participants have to classify a single central familiar target face. These distracter interference effects disappear when the central task contains additional anonymous (non-target) faces that load the search for the face target, but not when the central task contains additional non-face stimuli, suggesting there are face-specific capacity limits in visual processing. Here we tested whether manipulating the format of non-target faces in the search task affected face-specific capacity limits. Experiment 1 replicated earlier findings that a distracter face is processed even in high load conditions when participants looked for a target name of a famous person among additional names (non-targets) in a central search array. Two further experiments show that when targets and non-targets were faces (instead of names), however, distracter interference was eliminated under high load—adding non-target faces to the search array exhausted processing capacity for peripheral faces. The novel finding was that replacing non-target faces with images that consisted of two horizontally misaligned face-parts reduced distracter processing. Similar results were found when the polarity of a non-target face image was reversed. These results indicate that face-specific capacity limits are not determined by the configural properties of face processing, but by face parts. PMID:27729889

  17. Face Recognition Incorporating Ancillary Information

    NASA Astrophysics Data System (ADS)

    Kim, Sang-Ki; Toh, Kar-Ann; Lee, Sangyoun

    2007-12-01

    Due to vast variations of extrinsic and intrinsic imaging conditions, face recognition remained to be a challenging computer vision problem even today. This is particularly true when the passive imaging approach is considered for robust applications. To advance existing recognition systems for face, numerous techniques and methods have been proposed to overcome the almost inevitable performance degradation due to external factors such as pose, expression, occlusion, and illumination. In particular, the recent part-based method has provided noticeable room for verification performance improvement based on the localized features which have good tolerance to variation of external conditions. The part-based method, however, does not really stretch the performance without incorporation of global information from the holistic method. In view of the need to fuse the local information and the global information in an adaptive manner for reliable recognition, in this paper we investigate whether such external factors can be explicitly estimated and be used to boost the verification performance during fusion of the holistic and part-based methods. Our empirical evaluations show noticeable performance improvement adopting the proposed method.

  18. A decade of letrozole: FACE.

    PubMed

    O'Shaughnessy, Joyce

    2007-01-01

    Third-generation nonsteroidal aromatase inhibitors (AIs), letrozole and anastrozole, are superior to tamoxifen as initial therapy for early breast cancer but have not been directly compared in a head-to-head adjuvant trial. Cumulative evidence suggests that AIs are not equivalent in terms of potency of estrogen suppression and that there may be differences in clinical efficacy. Thus, with no data from head-to-head comparisons of the AIs as adjuvant therapy yet available, the question of whether there are efficacy differences between the AIs remains. To help answer this question, the Femara versus Anastrozole Clinical Evaluation (FACE) is a phase IIIb open-label, randomized, multicenter trial designed to test whether letrozole or anastrozole has superior efficacy as adjuvant treatment of postmenopausal women with hormone receptor (HR)- and lymph node-positive breast cancer. Eligible patients (target accrual, N=4,000) are randomized to receive either letrozole 2.5 mg or anastrozole 1 mg daily for up to 5 years. The primary objective is to compare disease-free survival at 5 years. Secondary end points include safety, overall survival, time to distant metastases, and time to contralateral breast cancer. The FACE trial will determine whether or not letrozole offers a greater clinical benefit to postmenopausal women with HR+ early breast cancer at increased risk of early recurrence compared with anastrozole. PMID:17912637

  19. Development of a dichroic beam splitter for Subaru AO188

    NASA Astrophysics Data System (ADS)

    Minowa, Yosuke; Takami, Hideki; Watanabe, Makoto; Hayano, Yutaka; Miyake, Masaaki; Iye, Masanori; Oya, Shin; Hattori, Masayuki; Murakami, Naoshi; Guyon, Olivier; Saito, Yoshihiko; Itoh, Meguru; Colley, Stephen; Dinkins, Matthew; Eldred, Michael; Golota, Taras

    2008-07-01

    We have developed a dichroic beam splitter for the Subaru AO188, which reflects optical light (0.4-0.9 μm) for wavefront sensing and transmits near-infrared light (0.93-5.2 μm) for science observations. The beam splitter is made of 145mm × 200mm calcium fluoride substrate coated by fluoride and metal chalcogen compound multilayer, which should be a best way to realize high transmittance over wide wavelength range in the near infrared. However, since typical fluoride soft coating is less resistant to the moisture in the air, the fluoride coating become damaged as we use on the AO188 optical bench which is placed in the room temperature condition. We have performed several accelerated endurance tests of the beam splitter under high-humidity condition by changing the design of the coatings, and found an optimal solution with an oxide protection layer which prevents the damage of the dichroic coating and keeps high transmittance at near-infrared wavelength. In this paper, we report the results of the endurance tests and the performance of our dichroic beam splitter.

  20. SPIDER: software for protein identification from sequence tags with de novo sequencing error.

    PubMed

    Han, Yonghua; Ma, Bin; Zhang, Kaizhong

    2005-06-01

    For the identification of novel proteins using MS/MS, de novo sequencing software computes one or several possible amino acid sequences (called sequence tags) for each MS/MS spectrum. Those tags are then used to match, accounting amino acid mutations, the sequences in a protein database. If the de novo sequencing gives correct tags, the homologs of the proteins can be identified by this approach and software such as MS-BLAST is available for the matching. However, de novo sequencing very often gives only partially correct tags. The most common error is that a segment of amino acids is replaced by another segment with approximately the same masses. We developed a new efficient algorithm to match sequence tags with errors to database sequences for the purpose of protein and peptide identification. A software package, SPIDER, was developed and made available on Internet for free public use. This paper describes the algorithms and features of the SPIDER software. PMID:16108090

  1. SPIDER: software for protein identification from sequence tags with de novo sequencing error.

    PubMed

    Han, Yonghua; Ma, Bin; Zhang, Kaizhong

    2004-01-01

    For the identification of novel proteins using MS/MS, de novo sequencing software computes one or several possible amino acid sequences (called sequence tags) for each MS/MS spectrum. Those tags are then used to match, accounting amino acid mutations, the sequences in a protein database. If the de novo sequencing gives correct tags, the homologs of the proteins can be identified by this approach and software such as MS-BLAST is available for the matching. However, de novo sequencing very often gives only partially correct tags. The most common error is that a segment of amino acids is replaced by another segment with approximately the same masses. We developed a new efficient algorithm to match sequence tags with errors to database sequences for the purpose of protein and peptide identification. A software package, SPIDER, was developed and made available on Internet for free public use. This paper describes the algorithms and features of the SPIDER software. PMID:16448014

  2. Rare De Novo Germline Copy-Number Variation in Testicular Cancer

    PubMed Central

    Stadler, Zsofia K.; Esposito, Diane; Shah, Sohela; Vijai, Joseph; Yamrom, Boris; Levy, Dan; Lee, Yoon-ha; Kendall, Jude; Leotta, Anthony; Ronemus, Michael; Hansen, Nichole; Sarrel, Kara; Rau-Murthy, Rohini; Schrader, Kasmintan; Kauff, Noah; Klein, Robert J.; Lipkin, Steven M.; Murali, Rajmohan; Robson, Mark; Sheinfeld, Joel; Feldman, Darren; Bosl, George; Norton, Larry; Wigler, Michael; Offit, Kenneth

    2012-01-01

    Although heritable factors are an important determinant of risk of early-onset cancer, the majority of these malignancies appear to occur sporadically without identifiable risk factors. Germline de novo copy-number variations (CNVs) have been observed in sporadic neurocognitive and cardiovascular disorders. We explored this mechanism in 382 genomes of 116 early-onset cancer case-parent trios and unaffected siblings. Unique de novo germline CNVs were not observed in 107 breast or colon cancer trios or controls but were indeed found in 7% of 43 testicular germ cell tumor trios; this percentage exceeds background CNV rates and suggests a rare de novo genetic paradigm for susceptibility to some human malignancies. PMID:22863192

  3. De novo formation of centrosomes in vertebrate cells arrested during S phase.

    PubMed

    Khodjakov, Alexey; Rieder, Conly L; Sluder, Greenfield; Cassels, Grisel; Sibon, Ody; Wang, Chuo-Lung

    2002-09-30

    The centrosome usually replicates in a semiconservative fashion, i.e., new centrioles form in association with preexisting "maternal" centrioles. De novo formation of centrioles has been reported for a few highly specialized cell types but it has not been seen in vertebrate somatic cells. We find that when centrosomes are completely destroyed by laser microsurgery in CHO cells arrested in S phase by hydroxyurea, new centrosomes form by de novo assembly. Formation of new centrosomes occurs in two steps: approximately 5-8 h after ablation, clouds of pericentriolar material (PCM) containing gamma-tubulin and pericentrin appear in the cell. By 24 h, centrioles have formed inside of already well-developed PCM clouds. This de novo pathway leads to the formation of a random number of centrioles (2-14 per cell). Although clouds of PCM consistently form even when microtubules are completely disassembled by nocodazole, the centrioles are not assembled under these conditions.

  4. Defining the maize transcriptome de novo using deep RNA-Seq

    SciTech Connect

    Martin, Jeffrey; Gross, Stephen; Choi, Cindy; Zhang, Tao; Lindquist, Erika; Wei, Chia-Lin; Wang, Zhong

    2011-06-01

    De novo assembly of the transcriptome is crucial for functional genomics studies in bioenergy research, since many of the organisms lack high quality reference genomes. In a previous study we successfully de novo assembled simple eukaryote transcriptomes exclusively from short Illumina RNA-Seq reads [1]. However, extensive alternative splicing, present in most of the higher eukaryotes, poses a significant challenge for current short read assembly processes. Furthermore, the size of next-generation datasets, often large for plant genomes, presents an informatics challenge. To tackle these challenges we present a combined experimental and informatics strategy for de novo assembly in higher eukaryotes. Using maize as a test case, preliminary results suggest our approach can resolve transcript variants and improve gene annotations.

  5. Defining the maize transcriptome de novo using deep RNA-Seq

    SciTech Connect

    Martin, Jeffrey; Gross, Stephen; Choi, Cindy; Zhang, Tao; Lindquist, Erika; Wei, Chia-Lin; Wang, Zhong

    2011-06-02

    De novo assembly of the transcriptome is crucial for functional genomics studies in bioenergy research, since many of the organisms lack high quality reference genomes. In a previous study we successfully de novo assembled simple eukaryote transcriptomes exclusively from short Illumina RNA-Seq reads [1]. However, extensive alternative splicing, present in most of the higher eukaryotes, poses a significant challenge for current short read assembly processes. Furthermore, the size of next-generation datasets, often large for plant genomes, presents an informatics challenge. To tackle these challenges we present a combined experimental and informatics strategy for de novo assembly in higher eukaryotes. Using maize as a test case, preliminary results suggest our approach can resolve transcript variants and improve gene annotations.

  6. Slow and Bimolecular Folding of a De Novo Designed Monomeric Protein DS119

    PubMed Central

    Zhu, Cheng; Dai, Ziwei; Liang, Huanhuan; Zhang, Tao; Gai, Feng; Lai, Luhua

    2013-01-01

    De novo protein design offers a unique means to test and advance our understanding of how proteins fold. However, most current design methods are native structure eccentric and folding kinetics has rarely been considered in the design process. Here, we show that a de novo designed mini-protein DS119, which folds into a βαβ structure, exhibits unusually slow and concentration-dependent folding kinetics. For example, the folding time for 50 μM of DS119 was estimated to be ∼2 s. Stopped-flow fluorescence resonance energy transfer experiments further suggested that its folding was likely facilitated by a transient dimerization process. Taken together, these results highlight the need for consideration of the entire folding energy landscape in de novo protein design and provide evidence suggesting nonnative interactions can play a key role in protein folding. PMID:24209859

  7. [AO distribution and fluorescence spectra in myoblasts and single muscle fibres].

    PubMed

    Beliaeva, T N; Krolenko, S A; Leont'eva, E A; Mozhenok, T P; Salova, A V; Faddeeva, M D

    2009-01-01

    Using spectral scanning regime of Leica TCS SL confocal microscope, acridine orange (AO) fluorescence spectra in nuclei and cytoplasms of living myoblasts L6J1 and frog single muscle fibres have been studied. AO fluorescence spectra in salt solutions dependent on free AO concentrations and in AO complexes with DNA have also been obtained for comparison. Myoblasts nuclei fluoresced in green spectral region with maximum at approximately 530 nm (corresponding AO monomers fluorescence), nucleoli fluoresced most brightly. Nuclear chromatin fluoresced not uniformly in these cells. We saw similar to myoblasts AO emission in nucleoli and nuclei of frog single muscle fibres. The uniformed weak green fluorescence was observed for myoblast cytoplasm. As to the muscle fibres sarcoplasm, we saw also AO green fluorescence in A-discs. In myoblasts and muscle fibre cytoplasm we saw the fluorescent red, yellow and green granules which were acidic organelles. The comparison of AO fluorescence spectra in living cells with fluorescence spectra of different AO concentrations and complexes of AO with DNA in buffer solutions allows estimation of AO concentration in acidic granules which is of interest in the investigation of cellular organelles functions in the processes of intracellular transport, adaptation, apoptosis and a number of pathological conditions.

  8. Robo-AO: autonomous and replicable laser-adaptive-optics and science system

    NASA Astrophysics Data System (ADS)

    Baranec, C.; Riddle, R.; Ramaprakash, A. N.; Law, N.; Tendulkar, S.; Kulkarni, S.; Dekany, R.; Bui, K.; Davis, J.; Burse, M.; Das, H.; Hildebrandt, S.; Punnadi, S.; Smith, R.

    2012-07-01

    We have created a new autonomous laser-guide-star adaptive-optics (AO) instrument on the 60-inch (1.5-m) telescope at Palomar Observatory called Robo-AO. The instrument enables diffraction-limited resolution observing in the visible and near-infrared with the ability to observe well over one-hundred targets per night due to its fully robotic operation. Robo-AO is being used for AO surveys of targets numbering in the thousands, rapid AO imaging of transient events and long-term AO monitoring not feasible on large diameter telescope systems. We have taken advantage of cost-effective advances in deformable mirror and laser technology while engineering Robo-AO with the intention of cloning the system for other few-meter class telescopes around the world.

  9. Recognition of Unfamiliar Talking Faces at Birth

    ERIC Educational Resources Information Center

    Coulon, Marion; Guellai, Bahia; Streri, Arlette

    2011-01-01

    Sai (2005) investigated the role of speech in newborns' recognition of their mothers' faces. Her results revealed that, when presented with both their mother's face and that of a stranger, newborns preferred looking at their mother only if she had previously talked to them. The present study attempted to extend these findings to any other faces.…

  10. [Neural Mechanisms Underlying the Face Inversion Effect].

    PubMed

    Sugase-Miyamoto, Yasuko; Matsumoto, Narihisa; Kawano, Kenji

    2015-10-01

    The ability to recognize faces is reduced with a picture-plane inversion of the faces, known as the face inversion effect. It has been reported that the configuration of facial features, for example, the distance between the eyes and mouth, becomes less perceptible when the face is inverted. In macaque monkeys, designated cortical areas, i.e., face patches, where face images are processed, have been found in the temporal visual cortex along the ventral visual pathway. Neurons in the anterior face patch (anterior part of the inferior temporal cortex) are known to encode view-invariant identity information. Thus, the anterior face patch is believed to be the final processing stage in the face patch system. A recent study showed that the face-inversion decreases the amount of the information about facial identity and facial expression conveyed by neurons, though it did not affect the information about the global category of the stimulus images (monkey versus human versus shape). The anterior face patch may, therefore, serve as the neural basis underlying the face inversion effect. PMID:26450075

  11. Perception and recognition of faces in adolescence

    PubMed Central

    Fuhrmann, D.; Knoll, L. J.; Sakhardande, A. L.; Speekenbrink, M.; Kadosh, K. C.; Blakemore, S. -J.

    2016-01-01

    Most studies on the development of face cognition abilities have focussed on childhood, with early maturation accounts contending that face cognition abilities are mature by 3–5 years. Late maturation accounts, in contrast, propose that some aspects of face cognition are not mature until at least 10 years. Here, we measured face memory and face perception, two core face cognition abilities, in 661 participants (397 females) in four age groups (younger adolescents (11.27–13.38 years); mid-adolescents (13.39–15.89 years); older adolescents (15.90–18.00 years); and adults (18.01–33.15 years)) while controlling for differences in general cognitive ability. We showed that both face cognition abilities mature relatively late, at around 16 years, with a female advantage in face memory, but not in face perception, both in adolescence and adulthood. Late maturation in the face perception task was driven mainly by protracted development in identity perception, while gaze perception abilities were already comparatively mature in early adolescence. These improvements in the ability to memorize, recognize and perceive faces during adolescence may be related to increasing exploratory behaviour and exposure to novel faces during this period of life. PMID:27647477

  12. Stimulus Selectivity of Figural Aftereffects for Faces

    ERIC Educational Resources Information Center

    Yamashita, Jill A.; Hardy, Joseph L.; De Valois, Karen K.; Webster, Michael A.

    2005-01-01

    Viewing a distorted face induces large aftereffects in the appearance of an undistorted face. The authors examined the processes underlying this adaptation by comparing how selective the aftereffects are for different dimensions of the images including size, spatial frequency content, contrast, and color. Face aftereffects had weaker selectivity…

  13. Infants Experience Perceptual Narrowing for Nonprimate Faces

    ERIC Educational Resources Information Center

    Simpson, Elizabeth A.; Varga, Krisztina; Frick, Janet E.; Fragaszy, Dorothy

    2011-01-01

    Perceptual narrowing--a phenomenon in which perception is broad from birth, but narrows as a function of experience--has previously been tested with primate faces. In the first 6 months of life, infants can discriminate among individual human and monkey faces. Though the ability to discriminate monkey faces is lost after about 9 months, infants…

  14. Psychophysical Thresholds of Face Visibility during Infancy

    ERIC Educational Resources Information Center

    Gelskov, Sofie V.; Kouider, Sid

    2010-01-01

    The ability to detect and focus on faces is a fundamental prerequisite for developing social skills. But how well can infants detect faces? Here, we address this question by studying the minimum duration at which faces must appear to trigger a behavioral response in infants. We used a preferential looking method in conjunction with masking and…

  15. Perception and recognition of faces in adolescence.

    PubMed

    Fuhrmann, D; Knoll, L J; Sakhardande, A L; Speekenbrink, M; Kadosh, K C; Blakemore, S-J

    2016-01-01

    Most studies on the development of face cognition abilities have focussed on childhood, with early maturation accounts contending that face cognition abilities are mature by 3-5 years. Late maturation accounts, in contrast, propose that some aspects of face cognition are not mature until at least 10 years. Here, we measured face memory and face perception, two core face cognition abilities, in 661 participants (397 females) in four age groups (younger adolescents (11.27-13.38 years); mid-adolescents (13.39-15.89 years); older adolescents (15.90-18.00 years); and adults (18.01-33.15 years)) while controlling for differences in general cognitive ability. We showed that both face cognition abilities mature relatively late, at around 16 years, with a female advantage in face memory, but not in face perception, both in adolescence and adulthood. Late maturation in the face perception task was driven mainly by protracted development in identity perception, while gaze perception abilities were already comparatively mature in early adolescence. These improvements in the ability to memorize, recognize and perceive faces during adolescence may be related to increasing exploratory behaviour and exposure to novel faces during this period of life. PMID:27647477

  16. Visual Search for Faces with Emotional Expressions

    ERIC Educational Resources Information Center

    Frischen, Alexandra; Eastwood, John D.; Smilek, Daniel

    2008-01-01

    The goal of this review is to critically examine contradictory findings in the study of visual search for emotionally expressive faces. Several key issues are addressed: Can emotional faces be processed preattentively and guide attention? What properties of these faces influence search efficiency? Is search moderated by the emotional state of the…

  17. De novo mutations in KIF1A cause progressive encephalopathy and brain atrophy

    PubMed Central

    Esmaeeli Nieh, Sahar; Madou, Maura R Z; Sirajuddin, Minhajuddin; Fregeau, Brieana; McKnight, Dianalee; Lexa, Katrina; Strober, Jonathan; Spaeth, Christine; Hallinan, Barbara E; Smaoui, Nizar; Pappas, John G; Burrow, Thomas A; McDonald, Marie T; Latibashvili, Mariam; Leshinsky-Silver, Esther; Lev, Dorit; Blumkin, Luba; Vale, Ronald D; Barkovich, Anthony James; Sherr, Elliott H

    2015-01-01

    Objective To determine the cause and course of a novel syndrome with progressive encephalopathy and brain atrophy in children. Methods Clinical whole-exome sequencing was performed for global developmental delay and intellectual disability; some patients also had spastic paraparesis and evidence of clinical regression. Six patients were identified with de novo missense mutations in the kinesin gene KIF1A. The predicted functional disruption of these mutations was assessed in silico to compare the calculated conformational flexibility and estimated efficiency of ATP binding to kinesin motor domains of wild-type (WT) versus mutant alleles. Additionally, an in vitro microtubule gliding assay was performed to assess the effects of de novo dominant, inherited recessive, and polymorphic variants on KIF1A motor function. Results All six subjects had severe developmental delay, hypotonia, and varying degrees of hyperreflexia and spastic paraparesis. Microcephaly, cortical visual impairment, optic neuropathy, peripheral neuropathy, ataxia, epilepsy, and movement disorders were also observed. All six patients had a degenerative neurologic course with progressive cerebral and cerebellar atrophy seen on sequential magnetic resonance imaging scans. Computational modeling of mutant protein structures when compared to WT kinesin showed substantial differences in conformational flexibility and ATP-binding efficiency. The de novo KIF1A mutants were nonmotile in the microtubule gliding assay. Interpretation De novo mutations in KIF1A cause a degenerative neurologic syndrome with brain atrophy. Computational and in vitro assays differentiate the severity of dominant de novo heterozygous versus inherited recessive KIF1A mutations. The profound effect de novo mutations have on axonal transport is likely related to the cause of progressive neurologic impairment in these patients. PMID:26125038

  18. A suite of de novo c-type cytochromes for functional oxidoreductase engineering.

    PubMed

    Watkins, Daniel W; Armstrong, Craig T; Beesley, Joseph L; Marsh, Jane E; Jenkins, Jonathan M X; Sessions, Richard B; Mann, Stephen; Anderson, J L Ross

    2016-05-01

    Central to the design of an efficient de novo enzyme is a robust yet mutable protein scaffold. The maquette approach to protein design offers precisely this, employing simple four-α-helix bundle scaffolds devoid of evolutionary complexity and with proven tolerance towards iterative protein engineering. We recently described the design of C2, a de novo designed c-type cytochrome maquette that undergoes post-translational modification in E. coli to covalently graft heme onto the protein backbone in vivo. This de novo cytochrome is capable of reversible oxygen binding, an obligate step in the catalytic cycle of many oxygen-activating oxidoreductases. Here we demonstrate the flexibility of both the maquette platform and the post-translational machinery of E. coli by creating a suite of functional de novo designed c-type cytochromes. We explore the engineering tolerances of the maquette by selecting alternative binding sites for heme C attachment and creating di-heme maquettes either by appending an additional heme C binding motif to the maquette scaffold or by binding heme B through simple bis-histidine ligation to a second binding site. The new designs retain the essential properties of the parent design but with significant improvements in structural stability. Molecular dynamics simulations aid the rationalization of these functional improvements while providing insight into the rules for engineering heme C binding sites in future iterations. This versatile, functional suite of de novo c-type cytochromes shows significant promise in providing robust platforms for the future engineering of de novo oxygen-activating oxidoreductases. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electron transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.

  19. Visual search efficiency is greater for human faces compared to animal faces.

    PubMed

    Simpson, Elizabeth A; Husband, Haley L; Yee, Krysten; Fullerton, Alison; Jakobsen, Krisztina V

    2014-01-01

    The Animate Monitoring Hypothesis proposes that humans and animals were the most important categories of visual stimuli for ancestral humans to monitor, as they presented important challenges and opportunities for survival and reproduction; however, it remains unknown whether animal faces are located as efficiently as human faces. We tested this hypothesis by examining whether human, primate, and mammal faces elicit similar searches, or whether human faces are privileged. In the first three experiments, participants located a target (human, primate, or mammal face) among distractors (non-face objects). We found fixations on human faces were faster and more accurate than fixations on primate faces, even when controlling for search category specificity. A final experiment revealed that, even when task-irrelevant, human faces slowed searches for non-faces, suggesting some bottom-up processing may be responsible for the human face search efficiency advantage.

  20. From Parts to Identity: Invariance and Sensitivity of Face Representations to Different Face Halves.

    PubMed

    Anzellotti, Stefano; Caramazza, Alfonso

    2016-05-01

    Recognizing the identity of a face is computationally challenging, because it requires distinguishing between similar images depicting different people, while recognizing even very different images depicting a same person. Previous human fMRI studies investigated representations of face identity in the presence of changes in viewpoint and in expression. Despite the importance of holistic processing for face recognition, an investigation of representations of face identity across different face parts is missing. To fill this gap, we investigated representations of face identity and their invariance across different face halves. Information about face identity with invariance across changes in the face half was individuated in the right anterior temporal lobe, indicating this region as the most plausible candidate brain area for the representation of face identity. In a complementary analysis, information distinguishing between different face halves was found to decline along the posterior to anterior axis in the ventral stream. PMID:25628344

  1. Not just another face in the crowd: detecting emotional schematic faces during continuous flash suppression.

    PubMed

    Stein, Timo; Sterzer, Philipp

    2012-10-01

    To test whether threatening visual information receives prioritized processing, many studies have examined visual search for emotional schematic faces. Still, it has remained unclear whether negative or positive schematic faces are processed more efficiently. We used continuous flash suppression, a variant of binocular rivalry, to render single emotional schematic faces invisible and measured whether negative or positive faces have an advantage in accessing awareness. Across three experiments, positive faces were detected more quickly than negative faces. A fourth experiment indicated that this positive face advantage was unrelated to the valence of the face stimuli but due to the relative orientation of the mouth curvature and the face contour. These findings demonstrate the impact of configural stimulus properties on perceptual suppression during binocular rivalry and point to a perceptual confound present in emotional schematic faces that might account for some ambiguous results obtained with schematic face stimuli in previous studies.

  2. Visual Search Efficiency is Greater for Human Faces Compared to Animal Faces

    PubMed Central

    Simpson, Elizabeth A.; Mertins, Haley L.; Yee, Krysten; Fullerton, Alison; Jakobsen, Krisztina V.

    2015-01-01

    The Animate Monitoring Hypothesis proposes that humans and animals were the most important categories of visual stimuli for ancestral humans to monitor, as they presented important challenges and opportunities for survival and reproduction; however, it remains unknown whether animal faces are located as efficiently as human faces. We tested this hypothesis by examining whether human, primate, and mammal faces elicit similarly efficient searches, or whether human faces are privileged. In the first three experiments, participants located a target (human, primate, or mammal face) among distractors (non-face objects). We found fixations on human faces were faster and more accurate than primate faces, even when controlling for search category specificity. A final experiment revealed that, even when task-irrelevant, human faces slowed searches for non-faces, suggesting some bottom-up processing may be responsible for the human face search efficiency advantage. PMID:24962122

  3. From Parts to Identity: Invariance and Sensitivity of Face Representations to Different Face Halves.

    PubMed

    Anzellotti, Stefano; Caramazza, Alfonso

    2016-05-01

    Recognizing the identity of a face is computationally challenging, because it requires distinguishing between similar images depicting different people, while recognizing even very different images depicting a same person. Previous human fMRI studies investigated representations of face identity in the presence of changes in viewpoint and in expression. Despite the importance of holistic processing for face recognition, an investigation of representations of face identity across different face parts is missing. To fill this gap, we investigated representations of face identity and their invariance across different face halves. Information about face identity with invariance across changes in the face half was individuated in the right anterior temporal lobe, indicating this region as the most plausible candidate brain area for the representation of face identity. In a complementary analysis, information distinguishing between different face halves was found to decline along the posterior to anterior axis in the ventral stream.

  4. Visual search efficiency is greater for human faces compared to animal faces.

    PubMed

    Simpson, Elizabeth A; Husband, Haley L; Yee, Krysten; Fullerton, Alison; Jakobsen, Krisztina V

    2014-01-01

    The Animate Monitoring Hypothesis proposes that humans and animals were the most important categories of visual stimuli for ancestral humans to monitor, as they presented important challenges and opportunities for survival and reproduction; however, it remains unknown whether animal faces are located as efficiently as human faces. We tested this hypothesis by examining whether human, primate, and mammal faces elicit similar searches, or whether human faces are privileged. In the first three experiments, participants located a target (human, primate, or mammal face) among distractors (non-face objects). We found fixations on human faces were faster and more accurate than fixations on primate faces, even when controlling for search category specificity. A final experiment revealed that, even when task-irrelevant, human faces slowed searches for non-faces, suggesting some bottom-up processing may be responsible for the human face search efficiency advantage. PMID:24962122

  5. The shape of the face template: geometric distortions of faces and their detection in natural scenes.

    PubMed

    Pongakkasira, Kaewmart; Bindemann, Markus

    2015-04-01

    Human face detection might be driven by skin-coloured face-shaped templates. To explore this idea, this study compared the detection of faces for which the natural height-to-width ratios were preserved with distorted faces that were stretched vertically or horizontally. The impact of stretching on detection performance was not obvious when faces were equated to their unstretched counterparts in terms of their height or width dimension (Experiment 1). However, stretching impaired detection when the original and distorted faces were matched for their surface area (Experiment 2), and this was found with both vertically and horizontally stretched faces (Experiment 3). This effect was evident in accuracy, response times, and also observers' eye movements to faces. These findings demonstrate that height-to-width ratios are an important component of the cognitive template for face detection. The results also highlight important differences between face detection and face recognition.

  6. De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia.

    PubMed

    Kirov, G; Pocklington, A J; Holmans, P; Ivanov, D; Ikeda, M; Ruderfer, D; Moran, J; Chambert, K; Toncheva, D; Georgieva, L; Grozeva, D; Fjodorova, M; Wollerton, R; Rees, E; Nikolov, I; van de Lagemaat, L N; Bayés, A; Fernandez, E; Olason, P I; Böttcher, Y; Komiyama, N H; Collins, M O; Choudhary, J; Stefansson, K; Stefansson, H; Grant, S G N; Purcell, S; Sklar, P; O'Donovan, M C; Owen, M J

    2012-02-01

    A small number of rare, recurrent genomic copy number variants (CNVs) are known to substantially increase susceptibility to schizophrenia. As a consequence of the low fecundity in people with schizophrenia and other neurodevelopmental phenotypes to which these CNVs contribute, CNVs with large effects on risk are likely to be rapidly removed from the population by natural selection. Accordingly, such CNVs must frequently occur as recurrent de novo mutations. In a sample of 662 schizophrenia proband-parent trios, we found that rare de novo CNV mutations were significantly more frequent in cases (5.1% all cases, 5.5% family history negative) compared with 2.2% among 2623 controls, confirming the involvement of de novo CNVs in the pathogenesis of schizophrenia. Eight de novo CNVs occurred at four known schizophrenia loci (3q29, 15q11.2, 15q13.3 and 16p11.2). De novo CNVs of known pathogenic significance in other genomic disorders were also observed, including deletion at the TAR (thrombocytopenia absent radius) region on 1q21.1 and duplication at the WBS (Williams-Beuren syndrome) region at 7q11.23. Multiple de novos spanned genes encoding members of the DLG (discs large) family of membrane-associated guanylate kinases (MAGUKs) that are components of the postsynaptic density (PSD). Two de novos also affected EHMT1, a histone methyl transferase known to directly regulate DLG family members. Using a systems biology approach and merging novel CNV and proteomics data sets, systematic analysis of synaptic protein complexes showed that, compared with control CNVs, case de novos were significantly enriched for the PSD proteome (P=1.72 × 10⁻⁶. This was largely explained by enrichment for members of the N-methyl-D-aspartate receptor (NMDAR) (P=4.24 × 10⁻⁶) and neuronal activity-regulated cytoskeleton-associated protein (ARC) (P=3.78 × 10⁻⁸) postsynaptic signalling complexes. In an analysis of 18 492 subjects (7907 cases and 10 585 controls), case CNVs were

  7. Detection of de novo synthesized form of microsomal cytochrome P-448 by autofluorography

    SciTech Connect

    Chasonikova, O.B.; Lab. of Xenobiochemistry, Inst. of Clinical and Experimental Medicine, Siberian Branch, Academy of Medical Sciences of the USSR, Novosibirsk; Tsyrlov, I.B.

    1986-06-01

    This paper suggests a simple and informative method of detection of de novo synthesized forms of microsomal cytochrome P-450. The method is based on autofluorography of the gel after electrophoretic fractionation of liver microsomal proteins of rats previously injected with inducers of components of the monooxygenase system, followed by C 14-leucine. From the results obtained by autofluorography it is shown that during induction of the monooxygenase system of rat liver with MCh and TCDD at least two forms of cytochromes of the P-448 type with mol. wt. of 53 and 56 kd were synthesized de novo.

  8. [CYTOSKELETON ORIENTATION IN THE EPIDERMAL CELLS OF ROOTS FORMED DE NOVO ON LEAF EXPLANTS UNDER CLINOROTATION].

    PubMed

    Bulavin, I V

    2016-01-01

    Root anatomy, cytoskeleton orientation and cell wall thickness in cells of the roots formed de novo in vitro under clinorotation (simulated microgravity) were investigated. Structure of the embryonic roots and of the roots formed de novo in cambium cells of the leaf petiole explants was shown to be similar. Root cell differentiation in vitro under clinorotation did not differ from that in control. Changes of tubulin microtubules' orientation in the epidermis of the distal elongation zone were observed under clinorotation that seems to be associated with specific physiological properties of the cells. Under clinorotation, the tendency of cell wall thinning was detected in the root cells formed in vitro.

  9. A hybrid approach for de novo human genome sequence assembly and phasing.

    PubMed

    Mostovoy, Yulia; Levy-Sakin, Michal; Lam, Jessica; Lam, Ernest T; Hastie, Alex R; Marks, Patrick; Lee, Joyce; Chu, Catherine; Lin, Chin; Džakula, Željko; Cao, Han; Schlebusch, Stephen A; Giorda, Kristina; Schnall-Levin, Michael; Wall, Jeffrey D; Kwok, Pui-Yan

    2016-07-01

    Despite tremendous progress in genome sequencing, the basic goal of producing a phased (haplotype-resolved) genome sequence with end-to-end contiguity for each chromosome at reasonable cost and effort is still unrealized. In this study, we describe an approach to performing de novo genome assembly and experimental phasing by integrating the data from Illumina short-read sequencing, 10X Genomics linked-read sequencing, and BioNano Genomics genome mapping to yield a high-quality, phased, de novo assembled human genome.

  10. Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools

    PubMed Central

    Fierst, Janna L.

    2015-01-01

    Modern high-throughput DNA sequencing has made it possible to inexpensively produce genome sequences, but in practice many of these draft genomes are fragmented and incomplete. Genetic linkage maps based on recombination rates between physical markers have been used in biology for over 100 years and a linkage map, when paired with a de novo sequencing project, can resolve mis-assemblies and anchor chromosome-scale sequences. Here, I summarize the methodology behind integrating de novo assemblies and genetic linkage maps, outline the current challenges, review the available software tools, and discuss new mapping technologies. PMID:26150829

  11. What’s in a Face? How Face Gender and Current Affect Influence Perceived Emotion

    PubMed Central

    Harris, Daniel A.; Hayes-Skelton, Sarah A.; Ciaramitaro, Vivian M.

    2016-01-01

    Faces drive our social interactions. A vast literature suggests an interaction between gender and emotional face perception, with studies using different methodologies demonstrating that the gender of a face can affect how emotions are processed. However, how different is our perception of affective male and female faces? Furthermore, how does our current affective state when viewing faces influence our perceptual biases? We presented participants with a series of faces morphed along an emotional continuum from happy to angry. Participants judged each face morph as either happy or angry. We determined each participant’s unique emotional ‘neutral’ point, defined as the face morph judged to be perceived equally happy and angry, separately for male and female faces. We also assessed how current state affect influenced these perceptual neutral points. Our results indicate that, for both male and female participants, the emotional neutral point for male faces is perceptually biased to be happier than for female faces. This bias suggests that more happiness is required to perceive a male face as emotionally neutral, i.e., we are biased to perceive a male face as more negative. Interestingly, we also find that perceptual biases in perceiving female faces are correlated with current mood, such that positive state affect correlates with perceiving female faces as happier, while we find no significant correlation between negative state affect and the perception of facial emotion. Furthermore, we find reaction time biases, with slower responses for angry male faces compared to angry female faces. PMID:27733839

  12. A randomized, double-blind, cross-over, phase IV trial of oros-methylphenidate (CONCERTA®) and generic novo-methylphenidate ER-C (NOVO-generic)

    PubMed Central

    Fallu, Angelo; Dabouz, Farida; Furtado, Melissa; Anand, Leena; Katzman, Martin A.

    2016-01-01

    Objective: Attention-deficit/hyperactivity disorder (ADHD) is a common neurobehavioral disorder with onset during childhood. Multiple aspects of a child’s development are hindered, in both home and school settings, with negative impacts on social, emotional, and cognitive functioning. If left untreated, ADHD is commonly associated with poor academic achievement and low occupational status, as well as increased risk of substance abuse and delinquency. The objective of this study was to evaluate adult ADHD subject reported outcomes when switched from a stable dose of CONCERTA® to the same dose of generic Novo-methylphenidate ER-C®. Methods: Randomized, double-blind, cross-over, phase IV trial consisted of two phases in which participants with a primary diagnosis of ADHD were randomized in a 1:1 ratio to 3 weeks of treatment with CONCERTA or generic Novo-Methylphenidate ER-C. Following 3 weeks of treatment, participants were crossed-over to receive the other treatment for an additional 3 weeks. Primary efficacy was assessed through the use of the Treatment Satisfaction Questionnaire for Medication, Version II (TSQM-II). Results: Participants with ADHD treated with CONCERTA were more satisfied in terms of efficacy and side effects compared to those receiving an equivalent dose of generic Novo-Methylphenidate ER-C. All participants chose to continue with CONCERTA treatment at the conclusion of the study. Conclusion: Although CONCERTA and generic Novo-Methylphenidate ER-C have been deemed bioequivalent, however the present findings demonstrate clinically and statistically significant differences between generic and branded CONCERTA. Further investigation of these differences is warranted. PMID:27536342

  13. Symmetry, probability, and recognition in face space.

    PubMed

    Sirovich, Lawrence; Meytlis, Marsha

    2009-04-28

    The essential midline symmetry of human faces is shown to play a key role in facial coding and recognition. This also has deep and important connections with recent explorations of the organization of primate cortex, as well as human psychophysical experiments. Evidence is presented that the dimension of face recognition space for human faces is dramatically lower than previous estimates. One result of the present development is the construction of a probability distribution in face space that produces an interesting and realistic range of (synthetic) faces. Another is a recognition algorithm that by reasonable criteria is nearly 100% accurate.

  14. 78 FR 38027 - Novo BioPower LLC; Supplemental Notice That Initial Market-Based Rate Filing Includes Request for...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-25

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Novo BioPower LLC; Supplemental Notice That Initial Market-Based Rate Filing...-referenced proceeding, of Novo BioPower LLC's application for market-based rate authority, with...

  15. Very low resolution face recognition problem.

    PubMed

    Zou, Wilman W W; Yuen, Pong C

    2012-01-01

    This paper addresses the very low resolution (VLR) problem in face recognition in which the resolution of the face image to be recognized is lower than 16 × 16. With the increasing demand of surveillance camera-based applications, the VLR problem happens in many face application systems. Existing face recognition algorithms are not able to give satisfactory performance on the VLR face image. While face super-resolution (SR) methods can be employed to enhance the resolution of the images, the existing learning-based face SR methods do not perform well on such a VLR face image. To overcome this problem, this paper proposes a novel approach to learn the relationship between the high-resolution image space and the VLR image space for face SR. Based on this new approach, two constraints, namely, new data and discriminative constraints, are designed for good visuality and face recognition applications under the VLR problem, respectively. Experimental results show that the proposed SR algorithm based on relationship learning outperforms the existing algorithms in public face databases. PMID:21775262

  16. The hierarchical brain network for face recognition.

    PubMed

    Zhen, Zonglei; Fang, Huizhen; Liu, Jia

    2013-01-01

    Numerous functional magnetic resonance imaging (fMRI) studies have identified multiple cortical regions that are involved in face processing in the human brain. However, few studies have characterized the face-processing network as a functioning whole. In this study, we used fMRI to identify face-selective regions in the entire brain and then explore the hierarchical structure of the face-processing network by analyzing functional connectivity among these regions. We identified twenty-five regions mainly in the occipital, temporal and frontal cortex that showed a reliable response selective to faces (versus objects) across participants and across scan sessions. Furthermore, these regions were clustered into three relatively independent sub-networks in a face-recognition task on the basis of the strength of functional connectivity among them. The functionality of the sub-networks likely corresponds to the recognition of individual identity, retrieval of semantic knowledge and representation of emotional information. Interestingly, when the task was switched to object recognition from face recognition, the functional connectivity between the inferior occipital gyrus and the rest of the face-selective regions were significantly reduced, suggesting that this region may serve as an entry node in the face-processing network. In sum, our study provides empirical evidence for cognitive and neural models of face recognition and helps elucidate the neural mechanisms underlying face recognition at the network level.

  17. Evaluating face trustworthiness: a model based approach

    PubMed Central

    Baron, Sean G.; Oosterhof, Nikolaas N.

    2008-01-01

    Judgments of trustworthiness from faces determine basic approach/avoidance responses and approximate the valence evaluation of faces that runs across multiple person judgments. Here, based on trustworthiness judgments and using a computer model for face representation, we built a model for representing face trustworthiness (study 1). Using this model, we generated novel faces with an increased range of trustworthiness and used these faces as stimuli in a functional Magnetic Resonance Imaging study (study 2). Although participants did not engage in explicit evaluation of the faces, the amygdala response changed as a function of face trustworthiness. An area in the right amygdala showed a negative linear response—as the untrustworthiness of faces increased so did the amygdala response. Areas in the left and right putamen, the latter area extended into the anterior insula, showed a similar negative linear response. The response in the left amygdala was quadratic—strongest for faces on both extremes of the trustworthiness dimension. The medial prefrontal cortex and precuneus also showed a quadratic response, but their response was strongest to faces in the middle range of the trustworthiness dimension. PMID:19015102

  18. Evaluating face trustworthiness: a model based approach.

    PubMed

    Todorov, Alexander; Baron, Sean G; Oosterhof, Nikolaas N

    2008-06-01

    Judgments of trustworthiness from faces determine basic approach/avoidance responses and approximate the valence evaluation of faces that runs across multiple person judgments. Here, based on trustworthiness judgments and using a computer model for face representation, we built a model for representing face trustworthiness (study 1). Using this model, we generated novel faces with an increased range of trustworthiness and used these faces as stimuli in a functional Magnetic Resonance Imaging study (study 2). Although participants did not engage in explicit evaluation of the faces, the amygdala response changed as a function of face trustworthiness. An area in the right amygdala showed a negative linear response-as the untrustworthiness of faces increased so did the amygdala response. Areas in the left and right putamen, the latter area extended into the anterior insula, showed a similar negative linear response. The response in the left amygdala was quadratic--strongest for faces on both extremes of the trustworthiness dimension. The medial prefrontal cortex and precuneus also showed a quadratic response, but their response was strongest to faces in the middle range of the trustworthiness dimension. PMID:19015102

  19. Extraversion predicts individual differences in face recognition.

    PubMed

    Li, Jingguang; Tian, Moqian; Fang, Huizhen; Xu, Miao; Li, He; Liu, Jia

    2010-07-01

    In daily life, one of the most common social tasks we perform is to recognize faces. However, the relation between face recognition ability and social activities is largely unknown. Here we ask whether individuals with better social skills are also better at recognizing faces. We found that extraverts who have better social skills correctly recognized more faces than introverts. However, this advantage was absent when extraverts were asked to recognize non-social stimuli (e.g., flowers). In particular, the underlying facet that makes extraverts better face recognizers is the gregariousness facet that measures the degree of inter-personal interaction. In addition, the link between extraversion and face recognition ability was independent of general cognitive abilities. These findings provide the first evidence that links face recognition ability to our daily activity in social communication, supporting the hypothesis that extraverts are better at decoding social information than introverts.

  20. The activation of visual face memory and explicit face recognition are delayed in developmental prosopagnosia.

    PubMed

    Parketny, Joanna; Towler, John; Eimer, Martin

    2015-08-01

    Individuals with developmental prosopagnosia (DP) are strongly impaired in recognizing faces, but the causes of this deficit are not well understood. We employed event-related brain potentials (ERPs) to study the time-course of neural processes involved in the recognition of previously unfamiliar faces in DPs and in age-matched control participants with normal face recognition abilities. Faces of different individuals were presented sequentially in one of three possible views, and participants had to detect a specific Target Face ("Joe"). EEG was recorded during task performance to Target Faces, Nontarget Faces, or the participants' Own Face (which had to be ignored). The N250 component was measured as a marker of the match between a seen face and a stored representation in visual face memory. The subsequent P600f was measured as an index of attentional processes associated with the conscious awareness and recognition of a particular face. Target Faces elicited reliable N250 and P600f in the DP group, but both of these components emerged later in DPs than in control participants. This shows that the activation of visual face memory for previously unknown learned faces and the subsequent attentional processing and conscious recognition of these faces are delayed in DP. N250 and P600f components to Own Faces did not differ between the two groups, indicating that the processing of long-term familiar faces is less affected in DP. However, P600f components to Own Faces were absent in two participants with DP who failed to recognize their Own Face during the experiment. These results provide new evidence that face recognition deficits in DP may be linked to a delayed activation of visual face memory and explicit identity recognition mechanisms.

  1. The activation of visual face memory and explicit face recognition are delayed in developmental prosopagnosia.

    PubMed

    Parketny, Joanna; Towler, John; Eimer, Martin

    2015-08-01

    Individuals with developmental prosopagnosia (DP) are strongly impaired in recognizing faces, but the causes of this deficit are not well understood. We employed event-related brain potentials (ERPs) to study the time-course of neural processes involved in the recognition of previously unfamiliar faces in DPs and in age-matched control participants with normal face recognition abilities. Faces of different individuals were presented sequentially in one of three possible views, and participants had to detect a specific Target Face ("Joe"). EEG was recorded during task performance to Target Faces, Nontarget Faces, or the participants' Own Face (which had to be ignored). The N250 component was measured as a marker of the match between a seen face and a stored representation in visual face memory. The subsequent P600f was measured as an index of attentional processes associated with the conscious awareness and recognition of a particular face. Target Faces elicited reliable N250 and P600f in the DP group, but both of these components emerged later in DPs than in control participants. This shows that the activation of visual face memory for previously unknown learned faces and the subsequent attentional processing and conscious recognition of these faces are delayed in DP. N250 and P600f components to Own Faces did not differ between the two groups, indicating that the processing of long-term familiar faces is less affected in DP. However, P600f components to Own Faces were absent in two participants with DP who failed to recognize their Own Face during the experiment. These results provide new evidence that face recognition deficits in DP may be linked to a delayed activation of visual face memory and explicit identity recognition mechanisms. PMID:26169316

  2. Divided by a Common Degree Program? Profiling Online and Face-to-Face Information Science Students

    ERIC Educational Resources Information Center

    Haigh, Maria

    2007-01-01

    This study examines profiles of online and face-to-face students in a single information science school: the University of Wisconsin-Milwaukee School of Information Studies. A questionnaire was administered to 76 students enrolled in online course sections and 72 students enrolled in face-to-face course sections. The questionnaire examined student…

  3. The Impact of Face-to-Face Orientation on Online Retention: A Pilot Study

    ERIC Educational Resources Information Center

    Ali, Radwan; Leeds, Elke M.

    2009-01-01

    Student retention in online education is a concern for students, faculty and administration. Retention rates are 20% lower in online courses than in traditional face-to-face courses. As part of an integration and engagement strategy, a face-to-face orientation was added to an online undergraduate business information systems course to examine its…

  4. Faces forming traces: neurophysiological correlates of learning naturally distinctive and caricatured faces.

    PubMed

    Schulz, Claudia; Kaufmann, Jürgen M; Kurt, Alexander; Schweinberger, Stefan R

    2012-10-15

    Distinctive faces are easier to learn and recognise than typical faces. We investigated effects of natural vs. artificial distinctiveness on performance and neural correlates of face learning. Spatial caricatures of initially non-distinctive faces were created such that their rated distinctiveness matched a set of naturally distinctive faces. During learning, we presented naturally distinctive, caricatured, and non-distinctive faces for later recognition among novel faces, using different images of the same identities at learning and test. For learned faces, an advantage in performance was observed for naturally distinctive and caricatured over non-distinctive faces, with larger benefits for naturally distinctive faces. Distinctive and caricatured faces elicited more negative occipitotemporal ERPs (P200, N250) and larger centroparietal positivity (LPC) during learning. At test, earliest distinctiveness effects were again seen in the P200. In line with recent research, N250 and LPC were larger for learned than for novel faces overall. Importantly, whereas left hemispheric N250 was increased for learned naturally distinctive faces, right hemispheric N250 responded particularly to caricatured novel faces. We conclude that natural distinctiveness induces benefits to face recognition beyond those induced by exaggeration of a face's idiosyncratic shape, and that the left hemisphere in particular may mediate recognition across different images.

  5. Faces Are "Spatial"--Holistic Face Perception Is Supported by Low Spatial Frequencies

    ERIC Educational Resources Information Center

    Goffaux, Valerie; Rossion, Bruno

    2006-01-01

    Faces are perceived holistically, a phenomenon best illustrated when the processing of a face feature is affected by the other features. Here, the authors tested the hypothesis that the holistic perception of a face mainly relies on its low spatial frequencies. Holistic face perception was tested in two classical paradigms: the whole-part…

  6. Highlights from a Literature Review Prepared for the Face to Face Research Project

    ERIC Educational Resources Information Center

    National Literacy Trust, 2010

    2010-01-01

    Between March 2009 and March 2011, Talk To Your Baby has been engaged in a research project, under the title of Face to Face, to identify key messages for parents and carers in relation to communicating with babies and young children, and has examined the most effective ways to promote these messages to parents and carers. The Face to Face project…

  7. Can Face-to-Face Mobilization Boost Student Voter Turnout? Results of a Campus Field Experiment

    ERIC Educational Resources Information Center

    Hill, David; Lachelier, Paul

    2014-01-01

    American colleges and universities have an expanding role to play in nurturing political engagement as more youth attend college. Given low voter turnout among college students yet growing experimental evidence that face-to-face mobilization can boost turnout, the experiment reported in this article examined the impact of a face-to-face college…

  8. Teacher and Student Behaviors in Face-to-Face and Online Courses: Dealing with Complex Concepts

    ERIC Educational Resources Information Center

    Cragg, C. E.; Dunning, Jean; Ellis, Jaqueline

    2008-01-01

    The objective of this research was to compare the quality and quantity of teacher and student interaction in an on-line versus face-to-face learning environment. A Master's level course on nursing theories was taught by the same professor by both methods. Transcripts of the face-to-face class and on-line postings were analyzed to identify…

  9. Why Use the Online Environment with Face-to-Face Students? Insights from Early Adopters.

    ERIC Educational Resources Information Center

    Bunker, Alison; Vardi, Iris

    This study illustrates the convergence of two teaching and learning media, face-to-face and online, as reflective lecturers seek to address the limitations of a single medium. Innovative university lecturers at a large Western Australia university were interviewed about their use of online environments with face-to-face students. The interview…

  10. The complex duration perception of emotional faces: effects of face direction

    PubMed Central

    Kliegl, Katrin M.; Limbrecht-Ecklundt, Kerstin; Dürr, Lea; Traue, Harald C.; Huckauf, Anke

    2015-01-01

    The perceived duration of emotional face stimuli strongly depends on the expressed emotion. But, emotional faces also differ regarding a number of other features like gaze, face direction, or sex. Usually, these features have been controlled by only using pictures of female models with straight gaze and face direction. Doi and Shinohara (2009) reported that an overestimation of angry faces could only be found when the model’s gaze was oriented toward the observer. We aimed at replicating this effect for face direction. Moreover, we explored the effect of face direction on the duration perception sad faces. Controlling for the sex of the face model and the participant, female and male participants rated the duration of neutral, angry, and sad face stimuli of both sexes photographed from different perspectives in a bisection task. In line with current findings, we report a significant overestimation of angry compared to neutral face stimuli that was modulated by face direction. Moreover, the perceived duration of sad face stimuli did not differ from that of neutral faces and was not influenced by face direction. Furthermore, we found that faces of the opposite sex appeared to last longer than those of the same sex. This outcome is discussed with regards to stimulus parameters like the induced arousal, social relevance, and an evolutionary context. PMID:25852589

  11. The Challenges of Interfacing between Face-To-Face and Online Instruction.

    ERIC Educational Resources Information Center

    Dabbagh, Nada H.

    2000-01-01

    Discussion of the development and use of Web-based instruction in higher education focuses on issues of course content; technological assumptions; logistical and implementation challenges; interfacing between face-to-face and online learning environments; and the use of a Web-based course management tool to support face-to-face instruction. (LRW)

  12. Moodle: A Way for Blending VLE and Face-to-Face Instruction in the ELT Context?

    ERIC Educational Resources Information Center

    Ilin, Gulden

    2013-01-01

    This classroom research explores the probable consequences of a blended Teaching English to Young Learners (TEYLs) course comprised of Moodle applications and face to face instruction in the English Language Teaching (ELT) context. Contrary to previous face to face only procedure, the course was divided into two segments: traditional classroom…

  13. On the facilitative effects of face motion on face recognition and its development

    PubMed Central

    Xiao, Naiqi G.; Perrotta, Steve; Quinn, Paul C.; Wang, Zhe; Sun, Yu-Hao P.; Lee, Kang

    2014-01-01

    For the past century, researchers have extensively studied human face processing and its development. These studies have advanced our understanding of not only face processing, but also visual processing in general. However, most of what we know about face processing was investigated using static face images as stimuli. Therefore, an important question arises: to what extent does our understanding of static face processing generalize to face processing in real-life contexts in which faces are mostly moving? The present article addresses this question by examining recent studies on moving face processing to uncover the influence of facial movements on face processing and its development. First, we describe evidence on the facilitative effects of facial movements on face recognition and two related theoretical hypotheses: the supplementary information hypothesis and the representation enhancement hypothesis. We then highlight several recent studies suggesting that facial movements optimize face processing by activating specific face processing strategies that accommodate to task requirements. Lastly, we review the influence of facial movements on the development of face processing in the first year of life. We focus on infants' sensitivity to facial movements and explore the facilitative effects of facial movements on infants' face recognition performance. We conclude by outlining several future directions to investigate moving face processing and emphasize the importance of including dynamic aspects of facial information to further understand face processing in real-life contexts. PMID:25009517

  14. Web-Based vs. Face-to-Face MBA Classes: A Comparative Assessment Study

    ERIC Educational Resources Information Center

    Brownstein, Barry; Brownstein, Deborah; Gerlowski, Daniel A.

    2008-01-01

    The challenges of online learning include ensuring that the learning outcomes are at least as robust as in the face-to-face sections of the same course. At the University of Baltimore, both online sections and face-to-face sections of core MBA courses are offered. Once admitted to the MBA, students are free to enroll in any combination of…

  15. One Professor's Face-to-Face Teaching Strategies while Becoming an Online Instructor

    ERIC Educational Resources Information Center

    Sugar, William; Martindale, Trey; Crawley, Frank E.

    2007-01-01

    With the increasing number of online courses within many higher education institutions, experienced instructors are facing the possibility of teaching online. These faculty members may face the task of converting their well-established face-to-face teaching strategies into an online environment. To better understand this transition, we analyzed…

  16. Face Aftereffects Indicate Dissociable, but Not Distinct, Coding of Male and Female Faces

    ERIC Educational Resources Information Center

    Jaquet, Emma; Rhodes, Gillian

    2008-01-01

    It has been claimed that exposure to distorted faces of one sex induces perceptual aftereffects for test faces that are of the same sex, but not for test faces of the other sex (A. C. Little, L. M. DeBruine, & B. C. Jones, 2005). This result suggests that male and female faces have separate neural coding. Given the high degree of visual similarity…

  17. Comparing the Roles of Representations in Face-to-Face and Online Computer Supported Collaborative Learning

    ERIC Educational Resources Information Center

    Suthers, Daniel D.; Hundhausen, Christopher D.; Girardeau, Laura E.

    2003-01-01

    This paper reports an empirical study comparing the role of discourse and knowledge representations (graphical evidence mapping) in face-to-face versus synchronous online collaborative learning. Prior work in face-to-face collaborative learning situations has shown that the features of representational notations can influence the focus of…

  18. On the facilitative effects of face motion on face recognition and its development.

    PubMed

    Xiao, Naiqi G; Perrotta, Steve; Quinn, Paul C; Wang, Zhe; Sun, Yu-Hao P; Lee, Kang

    2014-01-01

    For the past century, researchers have extensively studied human face processing and its development. These studies have advanced our understanding of not only face processing, but also visual processing in general. However, most of what we know about face processing was investigated using static face images as stimuli. Therefore, an important question arises: to what extent does our understanding of static face processing generalize to face processing in real-life contexts in which faces are mostly moving? The present article addresses this question by examining recent studies on moving face processing to uncover the influence of facial movements on face processing and its development. First, we describe evidence on the facilitative effects of facial movements on face recognition and two related theoretical hypotheses: the supplementary information hypothesis and the representation enhancement hypothesis. We then highlight several recent studies suggesting that facial movements optimize face processing by activating specific face processing strategies that accommodate to task requirements. Lastly, we review the influence of facial movements on the development of face processing in the first year of life. We focus on infants' sensitivity to facial movements and explore the facilitative effects of facial movements on infants' face recognition performance. We conclude by outlining several future directions to investigate moving face processing and emphasize the importance of including dynamic aspects of facial information to further understand face processing in real-life contexts. PMID:25009517

  19. Trial-level information for individual faces in the fusiform face area depends on subsequent memory.

    PubMed

    Hasinski, Adam E; Sederberg, Per B

    2016-01-01

    Previous research has shown that face-sensitive brain regions, such as the fusiform face area (FFA) and anterior inferior temporal lobe (aIT), not only respond selectively to face stimuli, but also respond uniquely to individual faces. A common factor in the existing literature is that face stimuli in these experiments are highly familiar to participants, usually by design. We set out to investigate to what extent familiarity correlates with the emergence of face-specific information in face-sensitive regions by testing novel faces with only a single repetition. Our results, consistent with a familiarity hypothesis, demonstrate that the FFA and aIT show face-specific information only when participants demonstrate subsequent memory for those faces. Functionally-defined regions that are not believed to process faces holistically showed no face-specific information, regardless of subsequent memory. To our knowledge, this is the first demonstration of face-specific information in face-sensitive regions for stimuli that were not highly familiar. These results contribute to our understanding of how individuating information comes to be represented in face-sensitive regions and suggest that this process can take place even after a single repetition of a particular face.

  20. LDEF (Postflight), AO201 : Interplanetary Dust Experiment, Tray H11

    NASA Technical Reports Server (NTRS)

    1990-01-01

    LDEF (Postflight), AO201 : Interplanetary Dust Experiment, Tray H11 The Interplanetary Dust Experiment hardware has a thin brown stain on the exposed surfaces. A deeper brown stain, probably from the material underneath the small electrical cover plate of the detector frame, can be seen in the upper right corner of some of the detectors. Stain that was seen on the solar sensor base plate in the flight photograph cannot be seen because of reflected light. The colors seen in the detector's mirror like surface are reflections of the surrounding area. A dark spot seen on a detector in the third row from the top in the flight photograph, was not found in a postflight inspection. A close inspection of this photograph does reveal several impact damage locations.

  1. LDEF (Flight), AO201 : Interplanetary Dust Experiment, Tray C09

    NASA Technical Reports Server (NTRS)

    1990-01-01

    LDEF (Flight), AO201 : Interplanetary Dust Experiment, Tray C09 The flight photograph was taken during the LDEF retrieval and provides an on-orbit view of the C09 integrated tray. When comparing this photograph with the prelaunch photograph, very little difference can be seen. A brown stain is visible around some of the fasteners and on mounting plates. The stain has been attributed to outgassing and contamination from the LDEF and experiment related materials being flown. When compared to the prelaunch photograph, the C09 integrated tray seems to be in excellent condition. The Interplanetary Dust Experiment appears to have a thin brown stain around some of the fasteners and also a small rectangular stain, in the center, along the bottom edge of the detector mounting plate. The IDE seems to be in excellent condition with all hardware intact. The colors seen in the detectors is a reflection of the Orbiter's white cargo bay liner.

  2. LDEF (Postflight), AO201 : Interplanetary Dust Experiment, Tray C09

    NASA Technical Reports Server (NTRS)

    1990-01-01

    LDEF (Postflight), AO201 : Interplanetary Dust Experiment, Tray C09 The postflight photograph was taken prior to the experiment tray being removed from the LDEF. The tray corner clamp blocks are un-anodized aluminum and that alone accounts for the major difference in color between the corner clamp blocks and the center clamp blocks. The IDE mounting plate and the detector frames and detectors seem to be in excellent condition. Close inspection of the photograph reveals several locations where impacts on detector surfaces are visible. A faint gold or tan stain can be seen around several of the fasteners and in a rectangular configuration, near the center, along the bottom edge of the detector mounting plate. Stains can also be seen near the top right edge of the solar sensor, on the mounting plate, and around the extreme edges of the solar sensor baseplate. The colors and designs seen on the detectors are reflections of the surrounding area.

  3. The 1987 outburst of the BL Lacertid AO 0235 + 164

    NASA Astrophysics Data System (ADS)

    Webb, J. R.; Smith, A. G.

    1989-08-01

    The violently variable BL Lacertid AO 0235 + 164 displayed a 3.24 magnitude outburst in early 1987. This outburst was observed intensively from Rosemary Hill Observatory in three colors. Long term monitoring observations made at Rosemary Hill are examined in an effort to find any recurring timescales associated with this outburst and previous large amplitude outbursts. The energetics of the 1987 outburst are analyzed in terms of the Shields and Wheeler model of a magnetized accretion disk. The timescales identified in the power spectrum (2.8 and 1.6 yr) are input into the model as the storage timescales. Since the emitted energy calculated from the optical burst cannot be stored in a magnetized disk at an allowable radius, it is concluded that either the storage timescales are longer than those identified in the power spectrum, or relativistic beaming effects must be considered, with a Doppler factor of 1.3 to 1.6.

  4. NFIRAOS: first facility AO system for the Thirty Meter Telescope

    NASA Astrophysics Data System (ADS)

    Herriot, Glen; Andersen, David; Atwood, Jenny; Boyer, Corinne; Byrnes, Peter; Caputa, Kris; Ellerbroek, Brent; Gilles, Luc; Hill, Alexis; Ljusic, Zoran; Pazder, John; Rosensteiner, Matthias; Smith, Malcolm; Spano, Paolo; Szeto, Kei; Véran, Jean-Pierre; Wevers, Ivan; Wang, Lianqi; Wooff, Robert

    2014-07-01

    NFIRAOS, the Thirty Meter Telescope's first adaptive optics system is an order 60x60 Multi-Conjugate AO system with two deformable mirrors. Although most observing will use 6 laser guide stars, it also has an NGS-only mode. Uniquely, NFIRAOS is cooled to -30 °C to reduce thermal background. NFIRAOS delivers a 2-arcminute beam to three client instruments, and relies on up to three IR WFSs in each instrument. We present recent work including: robust automated acquisition on these IR WFSs; trade-off studies for a common-size of deformable mirror; real-time computing architectures; simplified designs for high-order NGS-mode wavefront sensing; modest upgrade concepts for high-contrast imaging.

  5. Neonatal face-to-face interactions promote later social behaviour in infant rhesus monkeys

    PubMed Central

    Dettmer, Amanda M.; Kaburu, Stefano S. K.; Simpson, Elizabeth A.; Paukner, Annika; Sclafani, Valentina; Byers, Kristen L.; Murphy, Ashley M.; Miller, Michelle; Marquez, Neal; Miller, Grace M.; Suomi, Stephen J.; Ferrari, Pier F.

    2016-01-01

    In primates, including humans, mothers engage in face-to-face interactions with their infants, with frequencies varying both within and across species. However, the impact of this variation in face-to-face interactions on infant social development is unclear. Here we report that infant monkeys (Macaca mulatta) who engaged in more neonatal face-to-face interactions with mothers have increased social interactions at 2 and 5 months. In a controlled experiment, we show that this effect is not due to physical contact alone: monkeys randomly assigned to receive additional neonatal face-to-face interactions (mutual gaze and intermittent lip-smacking) with human caregivers display increased social interest at 2 months, compared with monkeys who received only additional handling. These studies suggest that face-to-face interactions from birth promote young primate social interest and competency. PMID:27300086

  6. Facebook and MySpace: complement or substitute for face-to-face interaction?

    PubMed

    Kujath, Carlyne L

    2011-01-01

    Previous studies have claimed that social-networking sites are used as a substitute for face-to-face interaction, resulting in deteriorating relationship quality and decreased intimacy among its users. The present study hypothesized that this type of communication is not a substitute for face-to-face interaction; rather, that it is an extension of communication with face-to-face partners. A survey was administered to examine the use of Facebook and MySpace in this regard among 183 college students. The study confirmed that Facebook and MySpace do act as an extension of face-to-face interaction, but that some users do tend to rely on Facebook and MySpace for interpersonal communication more than face-to-face interaction. PMID:21329446

  7. Early (N170) activation of face-specific cortex by face-like objects

    PubMed Central

    Hadjikhani, Nouchine; Kveraga, Kestutis; Naik, Paulami; Ahlfors, Seppo P.

    2009-01-01

    The tendency to perceive faces in random patterns exhibiting configural properties of faces is an example of pareidolia. Perception of ‘real’ faces has been associated with a cortical response signal arising at about 170ms after stimulus onset; but what happens when non-face objects are perceived as faces? Using magnetoencephalography (MEG), we found that objects incidentally perceived as faces evoked an early (165ms) activation in the ventral fusiform cortex, at a time and location similar to that evoked by faces, whereas common objects did not evoke such activation. An earlier peak at 130 ms was also seen for images of real faces only. Our findings suggest that face perception evoked by face-like objects is a relatively early process, and not a late re-interpretation cognitive phenomenon. PMID:19218867

  8. De novo ring chromosome 3: a new case with a mild phenotype.

    PubMed

    McKinley, M; Colley, A; Sinclair, P; Donnai, D; Andrews, T

    1991-08-01

    We report an 18 year old female with a de novo ring chromosome 3 found after investigation for short stature. Her karyotype was interpreted as 46,XX, r(3)(p26.2q29). Her phenotype is milder than previously reported cases and illustrates the mild end of the spectrum of the ring chromosome 3 phenotype.

  9. De novo transcriptome assembly of the plant-parasitic nematode Rotylenchulus reniformis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rotylenchulus reniformis, commonly known as the reniform nematode, is a pathogen of cotton, soybean, and sweet potatoes in the Southeastern United States. An estimate of cotton production loss due to R. reniformis parasitism in the United States in 2011 was 279,000 bales. Here, we present a de novo...

  10. De novo insertions and deletions of predominantly paternal origin are associated with autism spectrum disorder

    PubMed Central

    Dong, Shan; Walker, Michael F.; Carriero, Nicholas J.; DiCola, Michael; Willsey, A. Jeremy; Ye, Adam Y.; Waqar, Zainulabedin; Gonzalez, Luis E.; Overton, John D.; Frahm, Stephanie; Keaney, John F.; Teran, Nicole A.; Dea, Jeanselle; Mandell, Jeffrey D.; Bal, Vanessa Hus; Sullivan, Catherine A.; DiLullo, Nicholas M.; Khalil, Rehab O.; Gockley, Jake; Yuksel, Zafer; Sertel, Sinem M.; Ercan-Sencicek, A. Gulhan; Gupta, Abha R.; Mane, Shrikant M.; Sheldon, Michael; Brooks, Andrew I.; Roeder, Kathryn; Devlin, Bernie; State, Matthew W.; Wei, Liping; Sanders, Stephan J.

    2014-01-01

    SUMMARY Whole-exome sequencing (WES) studies have demonstrated the contribution of de novo loss-of-function single nucleotide variants to autism spectrum disorders (ASD). However, challenges in the reliable detection of de novo insertions and deletions (indels) have limited inclusion of these variants in prior analyses. Through the application of a robust indel detection method to WES data from 787 ASD families (2,963 individuals), we demonstrate that de novo frameshift indels contribute to ASD risk (OR=1.6; 95%CI=1.0-2.7; p=0.03), are more common in female probands (p=0.02), are enriched among genes encoding FMRP targets (p=6×10−9), and arise predominantly on the paternal chromosome (p<0.001). Based on mutation rates in probands versus unaffected siblings, de novo frameshift indels contribute to risk in approximately 3.0% of individuals with ASD. Finally, through observing clustering of mutations in unrelated probands, we report two novel ASD-associated genes: KMT2E (MLL5), a chromatin regulator, and RIMS1, a regulator of synaptic vesicle release. PMID:25284784

  11. Human mutations in methylenetetrahydrofolate dehydrogenase 1 impair nuclear de novo thymidylate biosynthesis.

    PubMed

    Field, Martha S; Kamynina, Elena; Watkins, David; Rosenblatt, David S; Stover, Patrick J

    2015-01-13

    An inborn error of metabolism associated with mutations in the human methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) gene has been identified. The proband presented with SCID, megaloblastic anemia, and neurologic abnormalities, but the causal metabolic impairment is unknown. SCID has been associated with impaired purine nucleotide metabolism, whereas megaloblastic anemia has been associated with impaired de novo thymidylate (dTMP) biosynthesis. MTHFD1 functions to condense formate with tetrahydrofolate and serves as the primary entry point of single carbons into folate-dependent one-carbon metabolism in the cytosol. In this study, we examined the impact of MTHFD1 loss of function on folate-dependent purine, dTMP, and methionine biosynthesis in fibroblasts from the proband with MTHFD1 deficiency. The flux of formate incorporation into methionine and dTMP was decreased by 90% and 50%, respectively, whereas formate flux through de novo purine biosynthesis was unaffected. Patient fibroblasts exhibited enriched MTHFD1 in the nucleus, elevated uracil in DNA, lower rates of de novo dTMP synthesis, and increased salvage pathway dTMP biosynthesis relative to control fibroblasts. These results provide evidence that impaired nuclear de novo dTMP biosynthesis can lead to both megaloblastic anemia and SCID in MTHFD1 deficiency.

  12. De novo reconstruction of plant RNA and DNA virus genomes from viral siRNAs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In antiviral defense, plants produce massive quantities of 21-24 nucleotide siRNAs. Here we demonstrate that the complete genomes of DNA and RNA viruses and viroids can be reconstructed by deep sequencing and de novo assembly of viral/viroid siRNAs from experimentally- and naturally-infected plants....

  13. De Novo nonreciprocal translocation 1;8 confirmed by fluorescent in situ hybridization

    SciTech Connect

    Wiley, J.E.; Stout, C.; Palmer, S.M.

    1995-07-17

    Constitutional nonreciprocal translocations are extremely rare, and even their existence is controversial. We report on a newborn infant with a de novo nonreciprocal translocation between chromosomes 1 and 8 resulting in 1q42.3 deletion syndrome. Fluorescent in situ hybridization with whole chromosome paints confirmed the conventional cytogenetic diagnosis. 3 refs., 2 figs., 1 tab.

  14. A Likelihood-Based Framework for Variant Calling and De Novo Mutation Detection in Families

    PubMed Central

    Li, Bingshan; Chen, Wei; Zhan, Xiaowei; Busonero, Fabio; Sanna, Serena; Sidore, Carlo; Cucca, Francesco; Kang, Hyun M.; Abecasis, Gonçalo R.

    2012-01-01

    Family samples, which can be enriched for rare causal variants by focusing on families with multiple extreme individuals and which facilitate detection of de novo mutation events, provide an attractive resource for next-generation sequencing studies. Here, we describe, implement, and evaluate a likelihood-based framework for analysis of next generation sequence data in family samples. Our framework is able to identify variant sites accurately and to assign individual genotypes, and can handle de novo mutation events, increasing the sensitivity and specificity of variant calling and de novo mutation detection. Through simulations we show explicit modeling of family relationships is especially useful for analyses of low-frequency variants and that genotype accuracy increases with the number of individuals sequenced per family. Compared with the standard approach of ignoring relatedness, our methods identify and accurately genotype more variants, and have high specificity for detecting de novo mutation events. The improvement in accuracy using our methods over the standard approach is particularly pronounced for low-frequency variants. Furthermore the family-aware calling framework dramatically reduces Mendelian inconsistencies and is beneficial for family-based analysis. We hope our framework and software will facilitate continuing efforts to identify genetic factors underlying human diseases. PMID:23055937

  15. De novo autoimmune hepatitis in liver transplant: State-of-the-art review.

    PubMed

    Vukotic, Ranka; Vitale, Giovanni; D'Errico-Grigioni, Antonia; Muratori, Luigi; Andreone, Pietro

    2016-03-14

    In the two past decades, a number of communications, case-control studies, and retrospective reports have appeared in the literature with concerns about the development of a complex set of clinical, laboratory and histological characteristics of a liver graft dysfunction that is compatible with autoimmune hepatitis. The de novo prefix was added to distinguish this entity from a pre-transplant primary autoimmune hepatitis, but the globally accepted criteria for the diagnosis of autoimmune hepatitis have been adopted in the diagnostic algorithm. Indeed, de novo autoimmune hepatitis is characterized by the typical liver necro-inflammation that is rich in plasma cells, the presence of interface hepatitis and the consequent laboratory findings of elevations in liver enzymes, increases in serum gamma globulin and the appearance of non-organ specific auto-antibodies. Still, the overall features of de novo autoimmune hepatitis appear not to be attributable to a univocal patho-physiological pathway because they can develop in the patients who have undergone liver transplantation due to different etiologies. Specifically, in subjects with hepatitis C virus recurrence, an interferon-containing antiviral treatment has been indicated as a potential inception of immune system derangement. Herein, we attempt to review the currently available knowledge about de novo liver autoimmunity and its clinical management.

  16. De novo autoimmune hepatitis in liver transplant: State-of-the-art review

    PubMed Central

    Vukotic, Ranka; Vitale, Giovanni; D’Errico-Grigioni, Antonia; Muratori, Luigi; Andreone, Pietro

    2016-01-01

    In the two past decades, a number of communications, case-control studies, and retrospective reports have appeared in the literature with concerns about the development of a complex set of clinical, laboratory and histological characteristics of a liver graft dysfunction that is compatible with autoimmune hepatitis. The de novo prefix was added to distinguish this entity from a pre-transplant primary autoimmune hepatitis, but the globally accepted criteria for the diagnosis of autoimmune hepatitis have been adopted in the diagnostic algorithm. Indeed, de novo autoimmune hepatitis is characterized by the typical liver necro-inflammation that is rich in plasma cells, the presence of interface hepatitis and the consequent laboratory findings of elevations in liver enzymes, increases in serum gamma globulin and the appearance of non-organ specific auto-antibodies. Still, the overall features of de novo autoimmune hepatitis appear not to be attributable to a univocal patho-physiological pathway because they can develop in the patients who have undergone liver transplantation due to different etiologies. Specifically, in subjects with hepatitis C virus recurrence, an interferon-containing antiviral treatment has been indicated as a potential inception of immune system derangement. Herein, we attempt to review the currently available knowledge about de novo liver autoimmunity and its clinical management. PMID:26973387

  17. Taurine homeostasis requires de novo synthesis via cysteine sulfinic acid decarboxylase during zebrafish early embryogenesis.

    PubMed

    Chang, Yen-Chia; Ding, Shih-Torng; Lee, Yen-Hua; Wang, Ya-Ching; Huang, Ming-Feng; Liu, I-Hsuan

    2013-02-01

    Cysteine sulfinic acid decarboxylase (Csad) is the rate-limiting enzyme in the de novo biosynthesis of taurine. There are a number of physiological roles of taurine, such as bile salt synthesis, osmoregulation, lipid metabolism, and oxidative stress inhibition. To investigate the role of de novo synthesis of taurine during embryonic development, zebrafish csad was cloned and functionally analyzed. Semi-quantitative RT-PCR showed that csad transcripts are maternally deposited, while whole-mount in situ hybridization demonstrated that csad is expressed in yolk syncytial layer and various embryonic tissues such as notochord, brain, retina, pronephric duct, liver, and pancreas. Knockdown of csad significantly reduced the embryonic taurine level, and the affected embryos had increased early mortality and cardiac anomalies. mRNA coinjection and taurine supplementation rescued the cardiac phenotypes suggesting that taurine originating from the de novo synthesis pathway plays a role in cardiac development. Our findings indicated that the de novo synthesis pathway via Csad plays a critical role in taurine homeostasis and cardiac development in zebrafish early embryos. PMID:22907836

  18. 76 FR 68767 - Draft Guidance for Industry and Food and Drug Administration Staff; De Novo Classification...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-07

    ... HUMAN SERVICES Food and Drug Administration Draft Guidance for Industry and Food and Drug Administration Staff; De Novo Classification Process (Evaluation of Automatic Class III Designation); Availability; Extension of Comment Period AGENCY: Food and Drug Administration, HHS. ACTION: Notice; extension of...

  19. A glance at quality score: implication for de novo transcriptome reconstruction of Illumina reads.

    PubMed

    Mbandi, Stanley Kimbung; Hesse, Uljana; Rees, D Jasper G; Christoffels, Alan

    2014-01-01

    Downstream analyses of short-reads from next-generation sequencing platforms are often preceded by a pre-processing step that removes uncalled and wrongly called bases. Standard approaches rely on their associated base quality scores to retain the read or a portion of it when the score is above a predefined threshold. It is difficult to differentiate sequencing error from biological variation without a reference using quality scores. The effects of quality score based trimming have not been systematically studied in de novo transcriptome assembly. Using RNA-Seq data produced from Illumina, we teased out the effects of quality score based filtering or trimming on de novo transcriptome reconstruction. We showed that assemblies produced from reads subjected to different quality score thresholds contain truncated and missing transfrags when compared to those from untrimmed reads. Our data supports the fact that de novo assembling of untrimmed data is challenging for de Bruijn graph assemblers. However, our results indicates that comparing the assemblies from untrimmed and trimmed read subsets can suggest appropriate filtering parameters and enable selection of the optimum de novo transcriptome assembly in non-model organisms.

  20. De novo autoimmune hepatitis in liver transplant: State-of-the-art review.

    PubMed

    Vukotic, Ranka; Vitale, Giovanni; D'Errico-Grigioni, Antonia; Muratori, Luigi; Andreone, Pietro

    2016-03-14

    In the two past decades, a number of communications, case-control studies, and retrospective reports have appeared in the literature with concerns about the development of a complex set of clinical, laboratory and histological characteristics of a liver graft dysfunction that is compatible with autoimmune hepatitis. The de novo prefix was added to distinguish this entity from a pre-transplant primary autoimmune hepatitis, but the globally accepted criteria for the diagnosis of autoimmune hepatitis have been adopted in the diagnostic algorithm. Indeed, de novo autoimmune hepatitis is characterized by the typical liver necro-inflammation that is rich in plasma cells, the presence of interface hepatitis and the consequent laboratory findings of elevations in liver enzymes, increases in serum gamma globulin and the appearance of non-organ specific auto-antibodies. Still, the overall features of de novo autoimmune hepatitis appear not to be attributable to a univocal patho-physiological pathway because they can develop in the patients who have undergone liver transplantation due to different etiologies. Specifically, in subjects with hepatitis C virus recurrence, an interferon-containing antiviral treatment has been indicated as a potential inception of immune system derangement. Herein, we attempt to review the currently available knowledge about de novo liver autoimmunity and its clinical management. PMID:26973387

  1. Identification of a de novo DYNC1H1 mutation via WES according to published guidelines

    PubMed Central

    Ding, Dongxue; Chen, Zhao; Li, Kai; Long, Zhe; Ye, Wei; Tang, Zhaoli; Xia, Kun; Qiu, Rong; Tang, Beisha; Jiang, Hong

    2016-01-01

    De novo mutations that contribute to rare Mendelian diseases, including neurological disorders, have been recently identified. Whole-exome sequencing (WES) has become a powerful tool for the identification of inherited and de novo mutations in Mendelian diseases. Two important guidelines were recently published regarding the investigation of causality of sequence variant in human disease and the interpretation of novel variants identified in human genome sequences. In this study, a family with supposed movement disorders was sequenced via WES (including the proband and her unaffected parents), and a standard investigation and interpretation of the identified variants was performed according to the published guidelines. We identified a novel de novo mutation (c.2327C > T, p.P776L) in DYNC1H1 gene and confirmed that it was the causal variant. The phenotype of the affected twins included delayed motor milestones, pes cavus, lower limb weakness and atrophy, and a waddling gait. Electromyographic (EMG) recordings revealed typical signs of chronic denervation. Our study demonstrates the power of WES to discover the de novo mutations associated with a neurological disease on the whole exome scale, and guidelines to conduct WES studies and interpret of identified variants are a preferable option for the exploration of the pathogenesis of rare neurological disorders. PMID:26846447

  2. 12 CFR 1263.14 - De novo insured depository institution applicants.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 percent requirement. (4) Conditional approval deemed null and void. If the requirements of...)) and § 1263.6(b), and its conditional membership approval is deemed null and void. (5) Treatment of outstanding advances and Bank stock. If a de novo applicant's conditional membership approval is deemed...

  3. 12 CFR 1263.14 - De novo insured depository institution applicants.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 percent requirement. (4) Conditional approval deemed null and void. If the requirements of...)) and § 1263.6(b), and its conditional membership approval is deemed null and void. (5) Treatment of outstanding advances and Bank stock. If a de novo applicant's conditional membership approval is deemed...

  4. 12 CFR 925.14 - De novo insured depository institution applicants.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... deemed null and void. If the requirements of paragraph (c)(3) of this section are not satisfied, a de... deemed null and void. (5) Treatment of outstanding advances and Bank stock. If a de novo applicant's conditional membership approval is deemed null and void pursuant to paragraph (c)(4) of this section,...

  5. 12 CFR 1263.14 - De novo insured depository institution applicants.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 percent requirement. (4) Conditional approval deemed null and void. If the requirements of...)) and § 1263.6(b), and its conditional membership approval is deemed null and void. (5) Treatment of outstanding advances and Bank stock. If a de novo applicant's conditional membership approval is deemed...

  6. 12 CFR 1263.14 - De novo insured depository institution applicants.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 percent requirement. (4) Conditional approval deemed null and void. If the requirements of...)) and § 1263.6(b), and its conditional membership approval is deemed null and void. (5) Treatment of outstanding advances and Bank stock. If a de novo applicant's conditional membership approval is deemed...

  7. Glutamine supplementation, citrulline production, and de novo arginine synthesis: Is there a relation?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We would like to comment on the recent publications by Buijs et al. The authors hypothesized that a parenteral supplement of glutamine stimulates citrulline formation and enhances de novo arginine synthesis. To test this hypothesis, they conducted an experiment with stable isotopes in patients under...

  8. De novo mutations from sporadic schizophrenia cases highlight important signaling genes in an independent sample.

    PubMed

    Kranz, Thorsten M; Harroch, Sheila; Manor, Orly; Lichtenberg, Pesach; Friedlander, Yechiel; Seandel, Marco; Harkavy-Friedman, Jill; Walsh-Messinger, Julie; Dolgalev, Igor; Heguy, Adriana; Chao, Moses V; Malaspina, Dolores

    2015-08-01

    Schizophrenia is a debilitating syndrome with high heritability. Genomic studies reveal more than a hundred genetic variants, largely nonspecific and of small effect size, and not accounting for its high heritability. De novo mutations are one mechanism whereby disease related alleles may be introduced into the population, although these have not been leveraged to explore the disease in general samples. This paper describes a framework to find high impact genes for schizophrenia. This study consists of two different datasets. First, whole exome sequencing was conducted to identify disruptive de novo mutations in 14 complete parent-offspring trios with sporadic schizophrenia from Jerusalem, which identified 5 sporadic cases with de novo gene mutations in 5 different genes (PTPRG, TGM5, SLC39A13, BTK, CDKN3). Next, targeted exome capture of these genes was conducted in 48 well-characterized, unrelated, ethnically diverse schizophrenia cases, recruited and characterized by the same research team in New York (NY sample), which demonstrated extremely rare and potentially damaging variants in three of the five genes (MAF<0.01) in 12/48 cases (25%); including PTPRG (5 cases), SCL39A13 (4 cases) and TGM5 (4 cases), a higher number than usually identified by whole exome sequencing. Cases differed in cognition and illness features based on which mutation-enriched gene they carried. Functional de novo mutations in protein-interaction domains in sporadic schizophrenia can illuminate risk genes that increase the propensity to develop schizophrenia across ethnicities. PMID:26091878

  9. Rare variants in complex traits: novel identification strategies and the role of de novo mutations.

    PubMed

    Jouan, Loubna; Gauthier, Julie; Dion, Patrick A; Rouleau, Guy A

    2012-01-01

    Following the limited success of linkage and association studies aimed at identifying the genetic causes of common neurodevelopmental syndromes like autism and schizophrenia, complex traits such as these have recently been considered under the 'common disease-rare variant' hypothesis. Prior to this hypothesis, the study of candidate genes has enabled the discovery of rare variants in complex disorders, and in turn some of these variants have highlighted the genetic contribution of de novo variants. De novo variants belong to a subcategory of spontaneous rare variants that are largely associated with sporadic diseases, which include some complex psychiatric disorders where the affected individuals do not transmit the genetic defects they carry because of their reduced reproductive fitness. Interestingly, recent studies have demonstrated the rate of germline de novo mutations to be higher in individuals with complex psychiatric disorders by comparison to what is seen in unaffected control individuals; moreover, de novo mutations carried by affected individuals have generally been more deleterious than those observed in control individuals. Advanced sequencing technologies have recently enabled the undertaking of massive parallel sequencing projects that can cover the entire coding sequences (exome) or genome of several individuals at once. Such advances have thus fostered the emergence of novel genetic hypotheses and ideas to investigate disease-causative genetic variations. The genetic underpinnings of a number of sporadic complex diseases is now becoming partly explained and more major breakthroughs for complex traits genomics should be expected in the near future. PMID:23594499

  10. De novo assembly of a bell pepper endornavirus genome sequence using RNA sequencing data.

    PubMed

    Jo, Yeonhwa; Choi, Hoseng; Cho, Won Kyong

    2015-03-19

    The genus Endornavirus is a double-stranded RNA virus that infects a wide range of hosts. In this study, we report on the de novo assembly of a bell pepper endornavirus genome sequence by RNA sequencing (RNA-Seq). Our result demonstrates the successful application of RNA-Seq to obtain a complete viral genome sequence from the transcriptome data.

  11. De novo mutations from sporadic schizophrenia cases highlight important signaling genes in an independent sample

    PubMed Central

    Kranz, Thorsten M; Harroch, Sheila; Manor, Orly; Lichtenberg, Pesach; Friedlander, Yechiel; Seandel, Marco; Harkavy-Friedman, Jill; Walsh-Messinger, Julie; Dolgalev, Igor; Heguy, Adriana; Chao, Moses V; Malaspina, Dolores

    2015-01-01

    Schizophrenia is a debilitating syndrome with high heritability. Genomic studies reveal more than a hundred genetic variants, largely nonspecific and of small effect size, and not accounting for its high heritability. De novo mutations are one mechanism whereby disease related alleles may be introduced into the population, although these have not been leveraged to explore the disease in general samples. This paper describes a framework to find high impact genes for schizophrenia. This study consists of two different datasets. First, whole exome sequencing was conducted to identify disruptive de novo mutations in 14 complete parent–offspring trios with sporadic schizophrenia from Jerusalem, which identified 5 sporadic cases with de novo gene mutations in 5 different genes (PTPRG, TGM5, SLC39A13, BTK, CDKN3). Next, targeted exome capture of these genes was conducted in 48 well-characterized, unrelated, ethnically diverse schizophrenia cases, recruited and characterized by the same research team in New York (NY sample), which demonstrated extremely rare and potentially damaging variants in three of the five genes (MAF < 0.01) in 12/48 cases (25%); including PTPRG (5 cases), SCL39A13 (4 cases) and TGM5 (4 cases), a higher number than usually identified by whole exome sequencing. Cases differed in cognition and illness features based on which mutation-enriched gene they carried. Functional de novo mutations in protein-interaction domains in sporadic schizophrenia can illuminate risk genes that increase the propensity to develop schizophrenia across ethnicities. PMID:26091878

  12. Three families with 'de novo' m.3243A > G mutation.

    PubMed

    de Laat, Paul; Janssen, Mirian C H; Alston, Charlotte L; Taylor, Robert W; Rodenburg, Richard J T; Smeitink, Jan A M

    2016-12-01

    The m.3243A > G mutation is the most prevalent, disease-causing mitochondrial DNA (mtDNA) mutation. In a national cohort study of 48 families harbouring the m.3243A > G mutation, we identified three families in which the mutation appeared to occur sporadically within these families. In this report we describe these three families. Based on detailed mtDNA analysis of three different tissues using two different quantitative pyrosequencing assays with sensitivity to a level of 1% mutated mtDNA, we conclude that the m.3243A > G mutation has arisen de novo in each of these families. The symptomatic carriers presented with a variety of symptoms frequently observed in patients harbouring the m.3243A > G mutation. A more severe phenotype is seen in the de novo families compared to recent cohort studies, which might be due to reporting bias. The observation that de novo m.3243A > G mutations exist is of relevance for both diagnostic investigations and genetic counselling. Firstly, even where there is no significant (maternal) family history in patients with stroke-like episodes, diabetes and deafness or other unexplained organ dysfunction, the m.3243A > G mutation should be screened as a possible cause of the disease. Second, analysis of maternally-related family members is highly recommended to provide reliable counselling for these families, given that the m.3243A > G mutation may have arisen de novo.

  13. De novo mutations from sporadic schizophrenia cases highlight important signaling genes in an independent sample.

    PubMed

    Kranz, Thorsten M; Harroch, Sheila; Manor, Orly; Lichtenberg, Pesach; Friedlander, Yechiel; Seandel, Marco; Harkavy-Friedman, Jill; Walsh-Messinger, Julie; Dolgalev, Igor; Heguy, Adriana; Chao, Moses V; Malaspina, Dolores

    2015-08-01

    Schizophrenia is a debilitating syndrome with high heritability. Genomic studies reveal more than a hundred genetic variants, largely nonspecific and of small effect size, and not accounting for its high heritability. De novo mutations are one mechanism whereby disease related alleles may be introduced into the population, although these have not been leveraged to explore the disease in general samples. This paper describes a framework to find high impact genes for schizophrenia. This study consists of two different datasets. First, whole exome sequencing was conducted to identify disruptive de novo mutations in 14 complete parent-offspring trios with sporadic schizophrenia from Jerusalem, which identified 5 sporadic cases with de novo gene mutations in 5 different genes (PTPRG, TGM5, SLC39A13, BTK, CDKN3). Next, targeted exome capture of these genes was conducted in 48 well-characterized, unrelated, ethnically diverse schizophrenia cases, recruited and characterized by the same research team in New York (NY sample), which demonstrated extremely rare and potentially damaging variants in three of the five genes (MAF<0.01) in 12/48 cases (25%); including PTPRG (5 cases), SCL39A13 (4 cases) and TGM5 (4 cases), a higher number than usually identified by whole exome sequencing. Cases differed in cognition and illness features based on which mutation-enriched gene they carried. Functional de novo mutations in protein-interaction domains in sporadic schizophrenia can illuminate risk genes that increase the propensity to develop schizophrenia across ethnicities.

  14. A glance at quality score: implication for de novo transcriptome reconstruction of Illumina reads.

    PubMed

    Mbandi, Stanley Kimbung; Hesse, Uljana; Rees, D Jasper G; Christoffels, Alan

    2014-01-01

    Downstream analyses of short-reads from next-generation sequencing platforms are often preceded by a pre-processing step that removes uncalled and wrongly called bases. Standard approaches rely on their associated base quality scores to retain the read or a portion of it when the score is above a predefined threshold. It is difficult to differentiate sequencing error from biological variation without a reference using quality scores. The effects of quality score based trimming have not been systematically studied in de novo transcriptome assembly. Using RNA-Seq data produced from Illumina, we teased out the effects of quality score based filtering or trimming on de novo transcriptome reconstruction. We showed that assemblies produced from reads subjected to different quality score thresholds contain truncated and missing transfrags when compared to those from untrimmed reads. Our data supports the fact that de novo assembling of untrimmed data is challenging for de Bruijn graph assemblers. However, our results indicates that comparing the assemblies from untrimmed and trimmed read subsets can suggest appropriate filtering parameters and enable selection of the optimum de novo transcriptome assembly in non-model organisms. PMID:24575122

  15. Insulin rapidly increases diacylglycerol by activating de novo phosphatidic acid synthesis.

    PubMed

    Farese, R V; Konda, T S; Davis, J S; Standaert, M L; Pollet, R J; Cooper, D R

    1987-05-01

    The mechanisms whereby insulin increases diacylglycerol in BC3H-1 myocytes were examined. When [3H]arachidonate labeling of phospholipids was used as an indicator of phospholipase C activation, transient increases in [3H]diacylglycerol were observed between 0.5 and 10 minutes after the onset of insulin treatment. With [3H]glycerol labeling as an indicator of de novo phospholipid synthesis, [3H]diacylglycerol was increased maximally at 1 minute and remained elevated for 20 minutes. [3H]Glycerol-labeled diacylglycerol was largely derived directly from phosphatidic acid. Insulin increased de novo phosphatidic acid synthesis within 5 to 10 seconds; within 1 minute, this synthesis was 60 times greater than that of controls. Thus, the initial increase in diacylglycerol is due to both increased hydrolysis of phospholipids and a burst of de novo phosphatidic acid synthesis. After 5 to 10 minutes, de novo phosphatidic acid synthesis continues as a major source of diacylglycerol. Both phospholipid effects of insulin seem important for generating diacylglycerol and other phospholipid-derived intracellular signaling substances.

  16. De novo-synthesized ceramide is involved in cannabinoid-induced apoptosis.

    PubMed Central

    Gómez del Pulgar, Teresa; Velasco, Guillermo; Sánchez, Cristina; Haro, Amador; Guzmán, Manuel

    2002-01-01

    Delta(9)-Tetrahydrocannabinol (THC) and other cannabinoids have been shown to induce apoptosis of glioma cells via ceramide generation. In the present study, we investigated the metabolic origin of the ceramide responsible for this cannabinoid-induced apoptosis by using two subclones of C6 glioma cells: C6.9, which is sensitive to THC-induced apoptosis; and C6.4, which is resistant to THC-induced apoptosis. Pharmacological inhibition of ceramide synthesis de novo, but not of neutral and acid sphingomyelinases, prevented THC-induced apoptosis in C6.9 cells. The activity of serine palmitoyltransferase (SPT), which catalyses the rate-limiting step of ceramide synthesis de novo, was remarkably enhanced by THC in C6.9 cells, but not in C6.4 cells. However, no major changes in SPT mRNA and protein levels were evident. Changes in SPT activity paralleled changes in ceramide levels. Pharmacological inhibition of ceramide synthesis de novo also prevented the stimulation of extracellular-signal-regulated kinase and the inhibition of protein kinase B triggered by cannabinoids. These findings show that de novo-synthesized ceramide is involved in cannabinoid-induced apoptosis of glioma cells. PMID:11903061

  17. De Novo Synthesis of Furanose Sugars: Catalytic Asymmetric Synthesis of Apiose and Apiose-Containing Oligosaccharides.

    PubMed

    Kim, Mijin; Kang, Soyeong; Rhee, Young Ho

    2016-08-01

    A de novo synthetic method towards apiose, a structurally unusual furanose, is reported. The key feature is sequential metal catalysis consisting of the palladium-catalyzed asymmetric intermolecular hydroalkoxylation of an alkoxyallene and subsequent ring-closing metathesis (RCM). This strategy enabled the efficient synthesis of various apiose-containing disaccharides and a unique convergent synthesis of trisaccharides. PMID:27381592

  18. De novo assembly of a bell pepper endornavirus genome sequence using RNA sequencing data.

    PubMed

    Jo, Yeonhwa; Choi, Hoseng; Cho, Won Kyong

    2015-01-01

    The genus Endornavirus is a double-stranded RNA virus that infects a wide range of hosts. In this study, we report on the de novo assembly of a bell pepper endornavirus genome sequence by RNA sequencing (RNA-Seq). Our result demonstrates the successful application of RNA-Seq to obtain a complete viral genome sequence from the transcriptome data. PMID:25792042

  19. Thermogravimetric desorption and de novo tests I: method development and validation.

    PubMed

    Tsytsik, Palina; Czech, Jan; Carleer, Robert; Reggers, Guy; Buekens, Alfons

    2008-08-01

    Thermogravimetric analysis (TGA) has been combined with evolved gas analysis (EGA) with the purpose of simulating the thermal behaviour of filter dust samples under inert (desorption) and de novo test oxidising conditions. Emphasis is on studying de novo formation of dioxins, surrogates and precursors arising from filter dust derived from thermal processes, such as municipal solid waste incineration and metallurgy. A new method is tested for sampling and analysing dioxin surrogates and precursors in the TGA effluent, which are collected on sampling tubes; the adsorbed compounds are eventually desorbed and quantified by TD-GC-MS. The major sources of error and losses are considered, including potential sorbent artefacts, possible breakthrough of volatiles through sampling tubes, or eventual losses of semi-volatiles due to their incomplete desorption or re-condensation inside the TG Analyser. The method is optimised and validated for di- to hexa-chlorinated benzenes in a range of 10-1000 ppb with average recovery exceeding 85%. The results are compared with data obtained in similar studies, performed by other research groups. As a result, the method provides the means for simulating de novo synthesis of dioxins in fly-ash and facilitates reliable and easy estimation of de novo activity, comparable with results of other studies, in combination with wide flexibility of testing conditions.

  20. Designing functional materials using the hydrophobic face of a self-assembling amphiphilic beta-hairpin peptide

    NASA Astrophysics Data System (ADS)

    Micklitsch, Christopher M.

    The ability of proteins to adopt discrete structures, as well as the ability of folded proteins to undergo supramolecular assembly, is based on the display of chemical functionality of the protein. Proteins fold and assemble according to the influence of intra- and intermolecular forces that act upon it to form ordered structures. By identifying these forces and how they influence assembly, they, in turn, can be exploited to design and synthesize materials from protein-based building blocks. By fabricating materials in this manner, the bulk material properties can be tuned by engineering at the molecular level. This study explores how modulation of the hydrophobic face of a de novo designed self-assembling beta-hairpin peptide affects its ability to fold and self-assemble to form a hydrogel, as well as on the resulting hydrogel's nanoscale structure and bulk properties. Initially, sequence modifications using amino acids of varying hydrophobicity were used to modify the hydrophobic face of the amphiphilic peptide. These modifications demonstrate how important hydrophobic regions of the peptide are to its ability to fold, self-assemble and form a hydrogel. The knowledge acquired from these studies was then used in the de novo design of a zinc-triggered peptide hydrogel, employing a nonnatural metal-binding amino acid on the hydrophobic face to instill metal-sensitivity in the peptide. Finally, aromatic interactions were incorporated on the topologically smooth hydrophobic face to direct self-assembly so as to impede the formation of interfibril junctions that lead to crosslinking of the fibrils that comprise the hydrogel scaffold.