Bio-recognitive photonics of a DNA-guided organic semiconductor

NASA Astrophysics Data System (ADS)

Back, Seung Hyuk; Park, Jin Hyuk; Cui, Chunzhi; Ahn, Dong June

2016-01-01

Incorporation of duplex DNA with higher molecular weights has attracted attention for a new opportunity towards a better organic light-emitting diode (OLED) capability. However, biological recognition by OLED materials is yet to be addressed. In this study, specific oligomeric DNA-DNA recognition is successfully achieved by tri (8-hydroxyquinoline) aluminium (Alq3), an organic semiconductor. Alq3 rods crystallized with guidance from single-strand DNA molecules show, strikingly, a unique distribution of the DNA molecules with a shape of an `inverted' hourglass. The crystal's luminescent intensity is enhanced by 1.6-fold upon recognition of the perfect-matched target DNA sequence, but not in the case of a single-base mismatched one. The DNA-DNA recognition forming double-helix structure is identified to occur only in the rod's outer periphery. This study opens up new opportunities of Alq3, one of the most widely used OLED materials, enabling biological recognition.

DNA Shape Dominates Sequence Affinity in Nucleosome Formation

NASA Astrophysics Data System (ADS)

Freeman, Gordon S.; Lequieu, Joshua P.; Hinckley, Daniel M.; Whitmer, Jonathan K.; de Pablo, Juan J.

2014-10-01

Nucleosomes provide the basic unit of compaction in eukaryotic genomes, and the mechanisms that dictate their position at specific locations along a DNA sequence are of central importance to genetics. In this Letter, we employ molecular models of DNA and proteins to elucidate various aspects of nucleosome positioning. In particular, we show how DNA's histone affinity is encoded in its sequence-dependent shape, including subtle deviations from the ideal straight B-DNA form and local variations of minor groove width. By relying on high-precision simulations of the free energy of nucleosome complexes, we also demonstrate that, depending on DNA's intrinsic curvature, histone binding can be dominated by bending interactions or electrostatic interactions. More generally, the results presented here explain how sequence, manifested as the shape of the DNA molecule, dominates molecular recognition in the problem of nucleosome positioning.

Global RNA Fold and Molecular Recognition for a pfl Riboswitch Bound to ZMP, a Master Regulator of One-Carbon Metabolism

DOE PAGES

Ren, Aiming; Rajashankar, Kanagalaghatta R.; Patel, Dinshaw J.

2015-06-25

ZTP, the pyrophosphorylated analog of ZMP (5- amino-4-imidazole carboxamide ribose-5'-monophosphate), was identified as an alarmone that senses 10-formyl-tetrahydroflate deficiency in bacteria. Recently, a pfl riboswitch was identified that selectively binds ZMP and regulates genes associated with purine biosynthesis and one-carbon metabolism. Here we report on the structure of the ZMP-bound Thermosinus carboxydivorans pfl riboswitch sensing domain, thereby defining the pseudoknot-based tertiary RNA fold, the binding-pocket architecture, and principles underlying ligand recognition specificity. Molecular recognition involves shape complementarity, with the ZMP 5-amino and carboxamide groups paired with the Watson-Crick edge of an invariant uracil, and the imidazole ring sandwiched between guanines,more » while the sugar hydroxyls form intermolecular hydrogen bond contacts. The burial of the ZMP base and ribose moieties, together with unanticipated coordination of the carboxamide by Mg 2+, contrasts with exposure of the 5'-phosphate to solvent. Lastly, our studies highlight the principles underlying RNA-based recognition of ZMP, a master regulator of one-carbon metabolism.« less

Global RNA Fold and Molecular Recognition for a pfl Riboswitch Bound to ZMP, a Master Regulator of One-Carbon Metabolism

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

Ren, Aiming; Rajashankar, Kanagalaghatta R.; Patel, Dinshaw J.

ZTP, the pyrophosphorylated analog of ZMP (5- amino-4-imidazole carboxamide ribose-5'-monophosphate), was identified as an alarmone that senses 10-formyl-tetrahydroflate deficiency in bacteria. Recently, a pfl riboswitch was identified that selectively binds ZMP and regulates genes associated with purine biosynthesis and one-carbon metabolism. Here we report on the structure of the ZMP-bound Thermosinus carboxydivorans pfl riboswitch sensing domain, thereby defining the pseudoknot-based tertiary RNA fold, the binding-pocket architecture, and principles underlying ligand recognition specificity. Molecular recognition involves shape complementarity, with the ZMP 5-amino and carboxamide groups paired with the Watson-Crick edge of an invariant uracil, and the imidazole ring sandwiched between guanines,more » while the sugar hydroxyls form intermolecular hydrogen bond contacts. The burial of the ZMP base and ribose moieties, together with unanticipated coordination of the carboxamide by Mg 2+, contrasts with exposure of the 5'-phosphate to solvent. Lastly, our studies highlight the principles underlying RNA-based recognition of ZMP, a master regulator of one-carbon metabolism.« less

Rotor-stator molecular crystals of fullerenes with cubane.

PubMed

Pekker, Sándor; Kováts, Eva; Oszlányi, Gábor; Bényei, Gyula; Klupp, Gyöngyi; Bortel, Gábor; Jalsovszky, István; Jakab, Emma; Borondics, Ferenc; Kamarás, Katalin; Bokor, Mónika; Kriza, György; Tompa, Kálmán; Faigel, Gyula

2005-10-01

Cubane (C8H8) and fullerene (C60) are famous cage molecules with shapes of platonic or archimedean solids. Their remarkable chemical and solid-state properties have induced great scientific interest. Both materials form polymorphic crystals of molecules with variable orientational ordering. The idea of intercalating fullerene with cubane was raised several years ago but no attempts at preparation have been reported. Here we show that C60 and similarly C70 form high-symmetry molecular crystals with cubane owing to topological molecular recognition between the convex surface of fullerenes and the concave cubane. Static cubane occupies the octahedral voids of the face-centred-cubic structures and acts as a bearing between the rotating fullerene molecules. The smooth contact of the rotor and stator molecules decreases significantly the temperature of orientational ordering. These materials have great topochemical importance: at elevated temperatures they transform to high-stability covalent derivatives although preserving their crystalline appearance. The size-dependent molecular recognition promises selective formation of related structures with higher fullerenes and/or substituted cubanes.

C60 Recognition from Extended Tetrathiafulvalene Bis-acetylide Platinum(II) Complexes.

PubMed

Bastien, Guillaume; Dron, Paul I; Vincent, Manon; Canevet, David; Allain, Magali; Goeb, Sébastien; Sallé, Marc

2016-11-18

The favorable spatial organization imposed by the square planar 4,4'-di(tert-butyl)-2,2'-bipyridine (dbbpy) platinum(II) complex associated with the electronic and shape complementarity of π-extended tetrathiafulvalene derivatives (exTTF) toward fullerenes is usefully exploited to construct molecular tweezers, which display good affinities for C 60 .

An Effective 3D Shape Descriptor for Object Recognition with RGB-D Sensors

PubMed Central

Liu, Zhong; Zhao, Changchen; Wu, Xingming; Chen, Weihai

2017-01-01

RGB-D sensors have been widely used in various areas of computer vision and graphics. A good descriptor will effectively improve the performance of operation. This article further analyzes the recognition performance of shape features extracted from multi-modality source data using RGB-D sensors. A hybrid shape descriptor is proposed as a representation of objects for recognition. We first extracted five 2D shape features from contour-based images and five 3D shape features over point cloud data to capture the global and local shape characteristics of an object. The recognition performance was tested for category recognition and instance recognition. Experimental results show that the proposed shape descriptor outperforms several common global-to-global shape descriptors and is comparable to some partial-to-global shape descriptors that achieved the best accuracies in category and instance recognition. Contribution of partial features and computational complexity were also analyzed. The results indicate that the proposed shape features are strong cues for object recognition and can be combined with other features to boost accuracy. PMID:28245553

Preparation of monodisperse curcumin-imprinted polymer by precipitation polymerization and its application for the extraction of curcuminoids from Curcuma longa L.

PubMed

Kitabatake, Tomoko; Tabo, Hiromi; Matsunaga, Hisami; Haginaka, Jun

2013-08-01

A monodisperse molecularly imprinted polymer (MIP) for curcumin was first prepared by precipitation polymerization using methacrylamide (MAM) and 4-vinylpyridine as functional co-monomers, divinylbenzene as a crosslinker, and a mixture of acetonitrile and toluene as a porogen. The use of MAM as the co-monomer resulted in the formation of a monodisperse MIP and non-imprinted polymer (NIP). MIP and NIP, respectively, were monodispersed with a narrow particle size distribution (3.3 ± 0.09 and 3.5 ± 0.10 μm). In addition to shape recognition, hydrophobic and hydrogen-bonding interactions affected the retention and molecular-recognition of curcumin on the MIP. The MIP for curcumin could extract curcuminoids (curcumin, demethoxycurcumin, and bisdemethoxycurcumin) in Curcuma longa L.

Assembling oppositely charged lock and key responsive colloids: A mesoscale analog of adaptive chemistry

PubMed Central

Mihut, Adriana M.; Stenqvist, Björn; Lund, Mikael; Schurtenberger, Peter; Crassous, Jérôme J.

2017-01-01

We have seen a considerable effort in colloid sciences to copy Nature’s successful strategies to fabricate complex functional structures through self-assembly. This includes attempts to design colloidal building blocks and their intermolecular interactions, such as creating the colloidal analogs of directional molecular interactions, molecular recognition, host-guest systems, and specific binding. We show that we can use oppositely charged thermoresponsive particles with complementary shapes, such as spherical and bowl-shaped particles, to implement an externally controllable lock-and-key self-assembly mechanism. The use of tunable electrostatic interactions combined with the temperature-dependent size and shape and van der Waals interactions of these building blocks provides an exquisite control over the selectivity and specificity of the interactions and self-assembly process. The dynamic nature of the mechanism allows for reversibly cycling through various structures that range from weakly structured dense liquids to well-defined molecule-shaped clusters with different configurations through variations in temperature and ionic strength. We link this complex and dynamic self-assembly behavior to the relevant molecular interactions, such as screened Coulomb and van der Waals forces and the geometrical complementarity of the two building blocks, and discuss our findings in the context of the concepts of adaptive chemistry recently introduced to molecular systems. PMID:28929133

Molecularly imprinted polymer for glutathione by modified precipitation polymerization and its application to determination of glutathione in supplements.

PubMed

Nakamura, Yukari; Masumoto, Shizuka; Matsunaga, Hisami; Haginaka, Jun

2017-09-10

Molecularly imprinted polymers (MIP) particles for glutathione (GSH) with a narrow particle size distribution were prepared by modified precipitation polymerization using methacrylic acid as a functional monomer, divinylbenzene as a crosslinker and water as a co-solvent. The particle diameters of the MIP and non-imprinted polymer (NIP) prepared under the optimum conditions were 3.81±0.95 (average±standard deviation) and 3.39±1.22μm, respectively. The retention and molecular-recognition properties of the prepared MIP were evaluated using a mixture of acetonitrile and water as a mobile phase in hydrophilic interaction chromatography. With an increase of acetonitrile content, the retention factor of GSH was increased on the MIP. In addition to shape recognition, hydrophilic interactions seem to work for the recognition of GSH on the MIP. The MIP had a specific molecular-recognition ability for GSH, while glutathione disulfide, l-Glu, l-Cys, Gly-Gly and l-Cys-Gly could not be retained or recognized on the MIP. The effect of column temperature revealed that the separation of GSH on the MIP was entropically driven. Binding experiments and Scatchard analyses revealed that one binding sites were formed on both the MIP and NIP, while the MIP gave higher affinity and capacity for GSH than the NIP. Furthermore, the MIP was successfully applied for determination of GSH in the supplements. Copyright © 2016 Elsevier B.V. All rights reserved.

Quantum dot nanocrystals having guanosine imprinted nanoshell for DNA recognition.

PubMed

Diltemiz, Sibel Emir; Say, Ridvan; Büyüktiryaki, Sibel; Hür, Deniz; Denizli, Adil; Ersöz, Arzu

2008-05-30

Molecular imprinted polymers (MIPs) as a recognition element for sensors are increasingly of interest and MIP nanoparticles have started to appear in the literature. In this study, we have proposed a novel thiol ligand-capping method with polymerizable methacryloylamido-cysteine (MAC) attached to CdS quantum dots (QDs), reminiscent of a self-assembled monolayer and have reconstructed surface shell by synthetic host polymers based on molecular imprinting method for DNA recognition. In this method, methacryloylamidohistidine-platinium (MAH-Pt(II)) is used as a new metal-chelating monomer via metal coordination-chelation interactions and guanosine templates of DNA. Nanoshell sensors with guanosine templates give a cavity that is selective for guanosine and its analogues. The guanosine can simultaneously chelate to Pt(II) metal ion and fit into the shape-selective cavity. Thus, the interaction between Pt(II) ion and free coordination spheres has an effect on the binding ability of the CdS QD nanosensor. The binding affinity of the guanosine imprinted nanocrystals has investigated by using the Langmuir and Scatchard methods, and experiments have shown the shape-selective cavity formation with O6 and N7 of a guanosine nucleotide (K(a) = 4.841x10(6) mol L(-1)) and a free guanine base (K(a) = 0.894x10(6) mol L(-1)). Additionally, the guanosine template of the nanocrystals is more favored for single stranded DNA compared to double stranded DNA.

Profiling charge complementarity and selectivity for binding at the protein surface.

PubMed

Sulea, Traian; Purisima, Enrico O

2003-05-01

A novel analysis and representation of the protein surface in terms of electrostatic binding complementarity and selectivity is presented. The charge optimization methodology is applied in a probe-based approach that simulates the binding process to the target protein. The molecular surface is color coded according to calculated optimal charge or according to charge selectivity, i.e., the binding cost of deviating from the optimal charge. The optimal charge profile depends on both the protein shape and charge distribution whereas the charge selectivity profile depends only on protein shape. High selectivity is concentrated in well-shaped concave pockets, whereas solvent-exposed convex regions are not charge selective. This suggests the synergy of charge and shape selectivity hot spots toward molecular selection and recognition, as well as the asymmetry of charge selectivity at the binding interface of biomolecular systems. The charge complementarity and selectivity profiles map relevant electrostatic properties in a readily interpretable way and encode information that is quite different from that visualized in the standard electrostatic potential map of unbound proteins.

Vibrational Detection of Odorant Functional Groups by Drosophila melanogaster

PubMed Central

Maniati, Klio; Haralambous, Katherine-Joanne

2017-01-01

Abstract A remarkable feature of olfaction, and perhaps the hardest one to explain by shape-based molecular recognition, is the ability to detect the presence of functional groups in odorants, irrespective of molecular context. We previously showed that Drosophila trained to avoid deuterated odorants could respond to a molecule bearing a nitrile group, which shares the vibrational stretch frequency with the CD bond. Here, we reproduce and extend this finding by showing analogous olfactory responses of Drosophila to the chemically vastly different functional groups, thiols and boranes, that nevertheless possess a common vibration at 2600 cm−1. Furthermore, we show that Drosophila do not respond to a cyanohydrin structure that renders nitrile groups invisible to IR spectroscopy. We argue that the response of Drosophila to these odorants which parallels their perception in humans, supports the hypothesis that odor character is encoded in odorant molecular vibrations, not in the specific shape-based activation pattern of receptors. PMID:29094064

Aging and solid shape recognition: Vision and haptics.

PubMed

Norman, J Farley; Cheeseman, Jacob R; Adkins, Olivia C; Cox, Andrea G; Rogers, Connor E; Dowell, Catherine J; Baxter, Michael W; Norman, Hideko F; Reyes, Cecia M

2015-10-01

The ability of 114 younger and older adults to recognize naturally-shaped objects was evaluated in three experiments. The participants viewed or haptically explored six randomly-chosen bell peppers (Capsicum annuum) in a study session and were later required to judge whether each of twelve bell peppers was "old" (previously presented during the study session) or "new" (not presented during the study session). When recognition memory was tested immediately after study, the younger adults' (Experiment 1) performance for vision and haptics was identical when the individual study objects were presented once. Vision became superior to haptics, however, when the individual study objects were presented multiple times. When 10- and 20-min delays (Experiment 2) were inserted in between study and test sessions, no significant differences occurred between vision and haptics: recognition performance in both modalities was comparable. When the recognition performance of older adults was evaluated (Experiment 3), a negative effect of age was found for visual shape recognition (younger adults' overall recognition performance was 60% higher). There was no age effect, however, for haptic shape recognition. The results of the present experiments indicate that the visual recognition of natural object shape is different from haptic recognition in multiple ways: visual shape recognition can be superior to that of haptics and is affected by aging, while haptic shape recognition is less accurate and unaffected by aging. Copyright © 2015 Elsevier Ltd. All rights reserved.

Molecular Imprinting Applications in Forensic Science

PubMed Central

Yılmaz, Erkut; Garipcan, Bora; Patra, Hirak K.; Uzun, Lokman

2017-01-01

Producing molecular imprinting-based materials has received increasing attention due to recognition selectivity, stability, cast effectiveness, and ease of production in various forms for a wide range of applications. The molecular imprinting technique has a variety of applications in the areas of the food industry, environmental monitoring, and medicine for diverse purposes like sample pretreatment, sensing, and separation/purification. A versatile usage, stability and recognition capabilities also make them perfect candidates for use in forensic sciences. Forensic science is a demanding area and there is a growing interest in molecularly imprinted polymers (MIPs) in this field. In this review, recent molecular imprinting applications in the related areas of forensic sciences are discussed while considering the literature of last two decades. Not only direct forensic applications but also studies of possible forensic value were taken into account like illicit drugs, banned sport drugs, effective toxins and chemical warfare agents in a review of over 100 articles. The literature was classified according to targets, material shapes, production strategies, detection method, and instrumentation. We aimed to summarize the current applications of MIPs in forensic science and put forth a projection of their potential uses as promising alternatives for benchmark competitors. PMID:28350333

Molecular Imprinting Applications in Forensic Science.

PubMed

Yılmaz, Erkut; Garipcan, Bora; Patra, Hirak K; Uzun, Lokman

2017-03-28

Producing molecular imprinting-based materials has received increasing attention due to recognition selectivity, stability, cast effectiveness, and ease of production in various forms for a wide range of applications. The molecular imprinting technique has a variety of applications in the areas of the food industry, environmental monitoring, and medicine for diverse purposes like sample pretreatment, sensing, and separation/purification. A versatile usage, stability and recognition capabilities also make them perfect candidates for use in forensic sciences. Forensic science is a demanding area and there is a growing interest in molecularly imprinted polymers (MIPs) in this field. In this review, recent molecular imprinting applications in the related areas of forensic sciences are discussed while considering the literature of last two decades. Not only direct forensic applications but also studies of possible forensic value were taken into account like illicit drugs, banned sport drugs, effective toxins and chemical warfare agents in a review of over 100 articles. The literature was classified according to targets, material shapes, production strategies, detection method, and instrumentation. We aimed to summarize the current applications of MIPs in forensic science and put forth a projection of their potential uses as promising alternatives for benchmark competitors.

Developmental prosopagnosia and super-recognition: no special role for surface reflectance processing

PubMed Central

Russell, Richard; Chatterjee, Garga; Nakayama, Ken

2011-01-01

Face recognition by normal subjects depends in roughly equal proportions on shape and surface reflectance cues, while object recognition depends predominantly on shape cues. It is possible that developmental prosopagnosics are deficient not in their ability to recognize faces per se, but rather in their ability to use reflectance cues. Similarly, super-recognizers’ exceptional ability with face recognition may be a result of superior surface reflectance perception and memory. We tested this possibility by administering tests of face perception and face recognition in which only shape or reflectance cues are available to developmental prosopagnosics, super-recognizers, and control subjects. Face recognition ability and the relative use of shape and pigmentation were unrelated in all the tests. Subjects who were better at using shape or reflectance cues were also better at using the other type of cue. These results do not support the proposal that variation in surface reflectance perception ability is the underlying cause of variation in face recognition ability. Instead, these findings support the idea that face recognition ability is related to neural circuits using representations that integrate shape and pigmentation information. PMID:22192636

Profiling Charge Complementarity and Selectivity for Binding at the Protein Surface

PubMed Central

Sulea, Traian; Purisima, Enrico O.

2003-01-01

A novel analysis and representation of the protein surface in terms of electrostatic binding complementarity and selectivity is presented. The charge optimization methodology is applied in a probe-based approach that simulates the binding process to the target protein. The molecular surface is color coded according to calculated optimal charge or according to charge selectivity, i.e., the binding cost of deviating from the optimal charge. The optimal charge profile depends on both the protein shape and charge distribution whereas the charge selectivity profile depends only on protein shape. High selectivity is concentrated in well-shaped concave pockets, whereas solvent-exposed convex regions are not charge selective. This suggests the synergy of charge and shape selectivity hot spots toward molecular selection and recognition, as well as the asymmetry of charge selectivity at the binding interface of biomolecular systems. The charge complementarity and selectivity profiles map relevant electrostatic properties in a readily interpretable way and encode information that is quite different from that visualized in the standard electrostatic potential map of unbound proteins. PMID:12719221

[Synthesis and Study on Adsorption Property of Congo Red Molecularly Imprinted Polymer Nanospheres].

PubMed

Chang, Zi-qiang; Chen, Fu-bin; Zhang, Yu; Shi, Zuo-long; Yang, Chun-yan; Zhang, Zhu-jun

2015-07-01

Molecularly imprinted polymer nanospheres (MIP) were prepared with Congo red as the template, methacrylic acid (MAA) as a functional monomer, ethylene glycol dimethacrylate (EGDMA) as the cross linker, azodiisobutyronitrile (AIBN) as an initiator, and acetonitrile as the porogen by precipitation polymerization. The morphology of MIP was characterized by SEM and TEM which showed that the diameter of MIP was nanometer grade (90 nm) and the shape was homogeneous. The specific surface area and pore volumes of MIP and NIP were examined through Brunauer-Emett-Teller method of nitrogen adsorption experiments. Then, the adsorption and selective recognition ability of MIPs were evaluated using the equilibrium rebinding experiments. The results indicated that the prepared MIP showed a good selectivity recognition ability to its template. It concluded that MIP could be employed as an effective material for removing Congo red from waste water.

Gas Sensors Based on Molecular Imprinting Technology.

PubMed

Zhang, Yumin; Zhang, Jin; Liu, Qingju

2017-07-04

Molecular imprinting technology (MIT); often described as a method of designing a material to remember a target molecular structure (template); is a technique for the creation of molecularly imprinted polymers (MIPs) with custom-made binding sites complementary to the target molecules in shape; size and functional groups. MIT has been successfully applied to analyze; separate and detect macromolecular organic compounds. Furthermore; it has been increasingly applied in assays of biological macromolecules. Owing to its unique features of structure specificity; predictability; recognition and universal application; there has been exploration of the possible application of MIPs in the field of highly selective gas sensors. In this present study; we outline the recent advances in gas sensors based on MIT; classify and introduce the existing molecularly imprinted gas sensors; summarize their advantages and disadvantages; and analyze further research directions.

Equilibrium shift in solution: molecular shape recognition and precipitation of a synthetic double helix using helicene-grafted silica nanoparticles.

PubMed

Miyagawa, Masamichi; Ichinose, Wataru; Yamaguchi, Masahiko

2014-01-27

Chiral silica nanoparticles (70 nm) grafted with (P)-helicene recognized the molecular shape of double helix and random coil (P)-ethynylhelicene oligomers in solution. A mixture of the (P)-nanoparticles and double helix precipitated much faster than a mixture of the (P)-nanoparticles and random coil, and the precipitate contained only the double helix. The mixture of the (P)-nanoparticles and (P)-ethynylhelicene pentamer reversibly dispersed in trifluoromethylbenzene upon heating at 70 °C and precipitated upon cooling at 25 °C. When a 10:90 equilibrium mixture of the double helix and random coil in solution was treated with the (P)-nanoparticles, the double helix was precipitated in 53% yield and was accompanied by equilibrium shift. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Developmental prosopagnosia and super-recognition: no special role for surface reflectance processing.

PubMed

Russell, Richard; Chatterjee, Garga; Nakayama, Ken

2012-01-01

Face recognition by normal subjects depends in roughly equal proportions on shape and surface reflectance cues, while object recognition depends predominantly on shape cues. It is possible that developmental prosopagnosics are deficient not in their ability to recognize faces per se, but rather in their ability to use reflectance cues. Similarly, super-recognizers' exceptional ability with face recognition may be a result of superior surface reflectance perception and memory. We tested this possibility by administering tests of face perception and face recognition in which only shape or reflectance cues are available to developmental prosopagnosics, super-recognizers, and control subjects. Face recognition ability and the relative use of shape and pigmentation were unrelated in all the tests. Subjects who were better at using shape or reflectance cues were also better at using the other type of cue. These results do not support the proposal that variation in surface reflectance perception ability is the underlying cause of variation in face recognition ability. Instead, these findings support the idea that face recognition ability is related to neural circuits using representations that integrate shape and pigmentation information. Copyright © 2011 Elsevier Ltd. All rights reserved.

Dissociated active and passive tactile shape recognition: a case study of pure tactile apraxia.

PubMed

Valenza, N; Ptak, R; Zimine, I; Badan, M; Lazeyras, F; Schnider, A

2001-11-01

Disorders of tactile object recognition (TOR) may result from primary motor or sensory deficits or higher cognitive impairment of tactile shape representations or semantic memory. Studies with healthy participants suggest the existence of exploratory motor procedures directly linked to the extraction of specific properties of objects. A pure deficit of these procedures without concomitant gnostic disorders has never been described in a brain-damaged patient. Here, we present a patient with a right hemispheric infarction who, in spite of intact sensorimotor functions, had impaired TOR with the left hand. Recognition of 2D shapes and objects was severely deficient under the condition of spontaneous exploration. Tactile exploration of shapes was disorganized and exploratory procedures, such as the contour-following strategy, which is necessary to identify the precise shape of an object, were severely disturbed. However, recognition of 2D shapes under manually or verbally guided exploration and the recognition of shapes traced on the skin were intact, indicating a dissociation in shape recognition between active and passive touch. Functional MRI during sensory stimulation of the left hand showed preserved activation of the spared primary sensory cortex in the right hemisphere. We interpret the deficit of our patient as a pure tactile apraxia without tactile agnosia, i.e. a specific inability to use tactile feedback to generate the exploratory procedures necessary for tactile shape recognition.

Mathematical morphology-based shape feature analysis for Chinese character recognition systems

NASA Astrophysics Data System (ADS)

Pai, Tun-Wen; Shyu, Keh-Hwa; Chen, Ling-Fan; Tai, Gwo-Chin

1995-04-01

This paper proposes an efficient technique of shape feature extraction based on the application of mathematical morphology theory. A new shape complexity index for preclassification of machine printed Chinese Character Recognition (CCR) is also proposed. For characters represented in different fonts/sizes or in a low resolution environment, a more stable local feature such as shape structure is preferred for character recognition. Morphological valley extraction filters are applied to extract the protrusive strokes from four sides of an input Chinese character. The number of extracted local strokes reflects the shape complexity of each side. These shape features of characters are encoded as corresponding shape complexity indices. Based on the shape complexity index, data base is able to be classified into 16 groups prior to recognition procedures. The performance of associating with shape feature analysis reclaims several characters from misrecognized character sets and results in an average of 3.3% improvement of recognition rate from an existing recognition system. In addition to enhance the recognition performance, the extracted stroke information can be further analyzed and classified its own stroke type. Therefore, the combination of extracted strokes from each side provides a means for data base clustering based on radical or subword components. It is one of the best solutions for recognizing high complexity characters such as Chinese characters which are divided into more than 200 different categories and consist more than 13,000 characters.

A microflow chemiluminescence sensor for indirect determination of dibutyl phthalate by hydrolyzing based on biological recognition materials.

PubMed

Qiu, Huamin; Fan, Lulu; Li, Xiangjun; Li, Leilei; Sun, Min; Luo, Chuannan

2013-03-05

A microflow chemiluminescence (CL) sensor for determination of dibutyl phthalate (DBP) based on magnetic molecularly imprinted polymer (MMIP) as recognition element was fabricated. Briefly, a hydrophilic molecularly imprinted polymer layer was produced at the surface of Fe₃O₄@SiO₂ magnetic nanoparticles (MNPs) via combination of molecular imprinting and reversible stimuli responsive hydrogel. In this protocol, the initial step involved co-precipitation of Fe²⁺ and Fe³⁺ in an ammonia solution. Silica was then coated on the Fe₃O₄ nanoparticles using a sol-gel method to obtain silica shell magnetic nanoparticles. The MMIP was synthesized using methacrylic acid (MAA) as functional monomer and ethylene glycol dimethacrylate (EGDMA) as cross-linker and 2,2-azobisisobutyronitrile (AIBN) as initiator in chloroform. Then the synthesized MMIP and magnetic non-molecular imprinted polymers (MNIP) were employed as recognition by packing into lab-made straight shape tubes, connected in CL analyzer for establishing the novel sensor with a single channel syringe pump. And a mixer for hydrolyzing of DBP was followed. Based on this experiment principle, DBP was determined indirectly. And the MMIP showed satisfactory recognition capacity to DBP, resulting to the wide linear range of 3.84 × 10⁻⁸ to 2.08 × 10⁻⁵ M and the low detection limit of 2.09 × 10⁻⁹ M (3σ) for DBP. The relative standard deviation (RSD) for DBP (3.20 × 10⁻⁶ M) was 1.40% (n=11). Besides improving sensitivity and selectivity, the sensor was reusable. The proposed DBP-MMIP-CL sensor has been successfully applied to determine DBP in drink samples. Copyright © 2012 Elsevier B.V. All rights reserved.

Shape and Color Features for Object Recognition Search

NASA Technical Reports Server (NTRS)

Duong, Tuan A.; Duong, Vu A.; Stubberud, Allen R.

2012-01-01

A bio-inspired shape feature of an object of interest emulates the integration of the saccadic eye movement and horizontal layer in vertebrate retina for object recognition search where a single object can be used one at a time. The optimal computational model for shape-extraction-based principal component analysis (PCA) was also developed to reduce processing time and enable the real-time adaptive system capability. A color feature of the object is employed as color segmentation to empower the shape feature recognition to solve the object recognition in the heterogeneous environment where a single technique - shape or color - may expose its difficulties. To enable the effective system, an adaptive architecture and autonomous mechanism were developed to recognize and adapt the shape and color feature of the moving object. The bio-inspired object recognition based on bio-inspired shape and color can be effective to recognize a person of interest in the heterogeneous environment where the single technique exposed its difficulties to perform effective recognition. Moreover, this work also demonstrates the mechanism and architecture of the autonomous adaptive system to enable the realistic system for the practical use in the future.

Defining scaffold geometries for interacting with proteins: geometrical classification of secondary structure linking regions.

PubMed

Tran, Tran T; Kulis, Christina; Long, Steven M; Bryant, Darryn; Adams, Peter; Smythe, Mark L

2010-11-01

Medicinal chemists synthesize arrays of molecules by attaching functional groups to scaffolds. There is evidence suggesting that some scaffolds yield biologically active molecules more than others, these are termed privileged substructures. One role of the scaffold is to present its side-chains for molecular recognition, and biologically relevant scaffolds may present side-chains in biologically relevant geometries or shapes. Since drug discovery is primarily focused on the discovery of compounds that bind to proteinaceous targets, we have been deciphering the scaffold shapes that are used for binding proteins as they reflect biologically relevant shapes. To decipher the scaffold architecture that is important for binding protein surfaces, we have analyzed the scaffold architecture of protein loops, which are defined in this context as continuous four residue segments of a protein chain that are not part of an α-helix or β-strand secondary structure. Loops are an important molecular recognition motif of proteins. We have found that 39 clusters reflect the scaffold architecture of 89% of the 23,331 loops in the dataset, with average intra-cluster and inter-cluster RMSD of 0.47 and 1.91, respectively. These protein loop scaffolds all have distinct shapes. We have used these 39 clusters that reflect the scaffold architecture of protein loops as biological descriptors. This involved generation of a small dataset of scaffold-based peptidomimetics. We found that peptidomimetic scaffolds with reported biological activities matched loop scaffold geometries and those peptidomimetic scaffolds with no reported biologically activities did not. This preliminary evidence suggests that organic scaffolds with tight matches to the preferred loop scaffolds of proteins, implies the likelihood of the scaffold to be biologically relevant.

Defining scaffold geometries for interacting with proteins: geometrical classification of secondary structure linking regions

NASA Astrophysics Data System (ADS)

Tran, Tran T.; Kulis, Christina; Long, Steven M.; Bryant, Darryn; Adams, Peter; Smythe, Mark L.

2010-11-01

Medicinal chemists synthesize arrays of molecules by attaching functional groups to scaffolds. There is evidence suggesting that some scaffolds yield biologically active molecules more than others, these are termed privileged substructures. One role of the scaffold is to present its side-chains for molecular recognition, and biologically relevant scaffolds may present side-chains in biologically relevant geometries or shapes. Since drug discovery is primarily focused on the discovery of compounds that bind to proteinaceous targets, we have been deciphering the scaffold shapes that are used for binding proteins as they reflect biologically relevant shapes. To decipher the scaffold architecture that is important for binding protein surfaces, we have analyzed the scaffold architecture of protein loops, which are defined in this context as continuous four residue segments of a protein chain that are not part of an α-helix or β-strand secondary structure. Loops are an important molecular recognition motif of proteins. We have found that 39 clusters reflect the scaffold architecture of 89% of the 23,331 loops in the dataset, with average intra-cluster and inter-cluster RMSD of 0.47 and 1.91, respectively. These protein loop scaffolds all have distinct shapes. We have used these 39 clusters that reflect the scaffold architecture of protein loops as biological descriptors. This involved generation of a small dataset of scaffold-based peptidomimetics. We found that peptidomimetic scaffolds with reported biological activities matched loop scaffold geometries and those peptidomimetic scaffolds with no reported biologically activities did not. This preliminary evidence suggests that organic scaffolds with tight matches to the preferred loop scaffolds of proteins, implies the likelihood of the scaffold to be biologically relevant.

Preparation of molecularly imprinted polymers for strychnine by precipitation polymerization and multistep swelling and polymerization and their application for the selective extraction of strychnine from nux-vomica extract powder.

PubMed

Nakamura, Yukari; Matsunaga, Hisami; Haginaka, Jun

2016-04-01

Monodisperse molecularly imprinted polymers for strychnine were prepared by precipitation polymerization and multistep swelling and polymerization, respectively. In precipitation polymerization, methacrylic acid and divinylbenzene were used as a functional monomer and crosslinker, respectively, while in multistep swelling and polymerization, methacrylic acid and ethylene glycol dimethacrylate were used as a functional monomer and crosslinker, respectively. The retention and molecular recognition properties of the molecularly imprinted polymers prepared by both methods for strychnine were evaluated using a mixture of sodium phosphate buffer and acetonitrile as a mobile phase by liquid chromatography. In addition to shape recognition, ionic and hydrophobic interactions could affect the retention of strychnine in low acetonitrile content. Furthermore, molecularly imprinted polymers prepared by both methods could selectively recognize strychnine among solutes tested. The retention factors and imprinting factors of strychnine on the molecularly imprinted polymer prepared by precipitation polymerization were 220 and 58, respectively, using 20 mM sodium phosphate buffer (pH 6.0)/acetonitrile (50:50, v/v) as a mobile phase, and those on the molecularly imprinted polymer prepared by multistep swelling and polymerization were 73 and 4.5. These results indicate that precipitation polymerization is suitable for the preparation of a molecularly imprinted polymer for strychnine. Furthermore, the molecularly imprinted polymer could be successfully applied for selective extraction of strychnine in nux-vomica extract powder. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Shape Recognition Inputs to Figure-Ground Organization in Three-Dimensional Displays.

ERIC Educational Resources Information Center

Peterson, Mary A.; Gibson, Bradley S.

1993-01-01

Three experiments with 29 college students and 8 members of a university community demonstrate that shape recognition processes influence perceived figure-ground relationships in 3-dimensional displays when the edge between 2 potential figural regions is both a luminance contrast edge and a disparity edge. Implications for shape recognition and…

Influence of Size and Shape of Silica Supports on the Sol⁻Gel Surface Molecularly Imprinted Polymers for Selective Adsorption of Gossypol.

PubMed

Zhi, Keke; Wang, Lulu; Zhang, Yagang; Jiang, Yingfang; Zhang, Letao; Yasin, Akram

2018-05-11

The influence of various silica gel supports with different shapes and sizes on the recognition properties of surface molecular imprinted polymers (MIPs) was investigated. MIPs for selective recognition and adsorption of gossypol were synthesized via the sol⁻gel process with a surface imprinting technique on silica gel substrates. 3-aminopropyltriethoxysilane (APTES) and tetraethoxysilane (TEOS) were chosen as the functional monomer and the cross-linker. The morphology and structure of the gossypol-MIPs were characterized using Fourier transform infrared spectroscopy (FT-IR), scanning electron microscopy (SEM), and a standard Brunauer⁻Emett⁻Teller (BET) analysis. Results indicated that the surface imprinted polymer layer facilitated the removal and rebinding of the template, and thus, achieved fast binding kinetics. Compared with the MIPs prepared on irregularly shaped silica with a broad particle size distribution, the MIPs using regularly-shaped silica of uniform size showed higher imprinting factor (IF), and the MIP made with a relatively larger sized (60 μm) spherical silica, demonstrated higher adsorption capacity compared to the MIPs made with smaller sized, spherical silica. The MIP prepared with 60 μm spherically shaped silica, featured a fast adsorption kinetic of 10 min, and a saturated adsorption capacity of 204 mg·g −1 . The gossypol-MIP had higher selectivity (IF = 2.20) for gossypol over its structurally-similar analogs ellagic acid (IF = 1.13) and quercetin (IF = 1.20). The adsorption data of the MIP correlated well with the pseudo-second-order kinetic model and the Freundlich isotherm model, which implied that chemical adsorption dominated, and that multilayer adsorption occurred. Furthermore, the MIP exhibited an excellent regeneration performance, and the adsorption capacity of the MIP for gossypol only decreased by 6% after six reused cycles, indicating good application potential for selective adsorption of gossypol.

DMG-α--a computational geometry library for multimolecular systems.

PubMed

Szczelina, Robert; Murzyn, Krzysztof

2014-11-24

The DMG-α library grants researchers in the field of computational biology, chemistry, and biophysics access to an open-sourced, easy to use, and intuitive software for performing fine-grained geometric analysis of molecular systems. The library is capable of computing power diagrams (weighted Voronoi diagrams) in three dimensions with 3D periodic boundary conditions, computing approximate projective 2D Voronoi diagrams on arbitrarily defined surfaces, performing shape properties recognition using α-shape theory and can do exact Solvent Accessible Surface Area (SASA) computation. The software is written mainly as a template-based C++ library for greater performance, but a rich Python interface (pydmga) is provided as a convenient way to manipulate the DMG-α routines. To illustrate possible applications of the DMG-α library, we present results of sample analyses which allowed to determine nontrivial geometric properties of two Escherichia coli-specific lipids as emerging from molecular dynamics simulations of relevant model bilayers.

Surface molecular imprinting onto fluorescein-coated magnetic nanoparticlesvia reversible addition fragmentation chain transfer polymerization: A facile three-in-one system for recognition and separation of endocrine disrupting chemicals

NASA Astrophysics Data System (ADS)

Li, Ying; Dong, Cunku; Chu, Jia; Qi, Jingyao; Li, Xin

2011-01-01

In this study, we present a general protocol for the making of surface-imprinted magnetic fluorescence beads viareversible addition-fragmentation chain transfer polymerization. The resulting composites were characterized by X-ray diffraction analysis, transmission electron microscopy, scanning electron microscopy, fluorescence spectroscopy, Fourier transform infrared spectroscopy, and energy dispersive spectroscopy. The as-synthesized beads exhibited homogeneous polymer films (thickness of about 5.7 nm), spherical shape, high fluorescence intensity and magnetic property (Magnetization (Ms) = 3.67 emu g-1). The hybrids bind the original template 17β-estradiol with an appreciable selectivity over structurally related compounds. In addition, the resulting hybrids performed without obvious deterioration after five repeated cycles. This study therefore demonstrates the potential of molecularly imprinted polymers for the recognition and separation of endocrine disrupting chemicals.In this study, we present a general protocol for the making of surface-imprinted magnetic fluorescence beads viareversible addition-fragmentation chain transfer polymerization. The resulting composites were characterized by X-ray diffraction analysis, transmission electron microscopy, scanning electron microscopy, fluorescence spectroscopy, Fourier transform infrared spectroscopy, and energy dispersive spectroscopy. The as-synthesized beads exhibited homogeneous polymer films (thickness of about 5.7 nm), spherical shape, high fluorescence intensity and magnetic property (Magnetization (Ms) = 3.67 emu g-1). The hybrids bind the original template 17β-estradiol with an appreciable selectivity over structurally related compounds. In addition, the resulting hybrids performed without obvious deterioration after five repeated cycles. This study therefore demonstrates the potential of molecularly imprinted polymers for the recognition and separation of endocrine disrupting chemicals. Electronic supplementary information (ESI) available: Supplementary figure S1. The hysteresis loop of Fe3O4 (a), Fe3O4@SiO2 (b), and Fe3O4@SiO2-Dye-SiO2 (c). See DOI: 10.1039/c0nr00614a

Modeling the preferred shapes of polyamine transporter ligands and dihydromotuporamine-C mimics: shovel versus hoe.

PubMed

Breitbeil, Fred; Kaur, Navneet; Delcros, Jean-Guy; Martin, Bénédicte; Abboud, Khalil A; Phanstiel, Otto

2006-04-20

Preferred conformers generated from motuporamine and anthracene-polyamine derivatives provided insight into the shapes associated with polyamine transporter (PAT) recognition and potentially dihydromotuporamine C (4a) bioactivity. Molecular modeling revealed that N(1)-(anthracen-9-ylmethyl)-3,3-triamine (6a), N(1)-(anthracen-9-ylmethyl)-4,4-triamine (6b), N(1)-(anthracen-9-ylmethyl)-N(1)-ethyl-3,3-triamine (7a), N(1)-(anthracen-9-ylmethyl)-N(1)-ethyl-4,4-triamine (7b), and 4a all preferred a hoe motif. This hoe shape was defined by the all-anti polyamine shaft extending above the relatively flat, appended ring system. The hoe geometry was also inferred by the (1)H NMR spectrum of the free amine of 7a (CDCl(3)), which showed a strong shielding effect of the anthracene ring on the chemical shifts associated with the appended polyamine chain. This shielding effect was found to be independent over a broad concentration range of 7a, which also supported an intramolecular phenomenon. The degree of substitution at the N(1)-position seems to be an important determinant of both the molecular shape preferences and biological activity of anthracenylmethyl-polyamine conjugates.

Changes in Visual Object Recognition Precede the Shape Bias in Early Noun Learning

PubMed Central

Yee, Meagan; Jones, Susan S.; Smith, Linda B.

2012-01-01

Two of the most formidable skills that characterize human beings are language and our prowess in visual object recognition. They may also be developmentally intertwined. Two experiments, a large sample cross-sectional study and a smaller sample 6-month longitudinal study of 18- to 24-month-olds, tested a hypothesized developmental link between changes in visual object representation and noun learning. Previous findings in visual object recognition indicate that children’s ability to recognize common basic level categories from sparse structural shape representations of object shape emerges between the ages of 18 and 24 months, is related to noun vocabulary size, and is lacking in children with language delay. Other research shows in artificial noun learning tasks that during this same developmental period, young children systematically generalize object names by shape, that this shape bias predicts future noun learning, and is lacking in children with language delay. The two experiments examine the developmental relation between visual object recognition and the shape bias for the first time. The results show that developmental changes in visual object recognition systematically precede the emergence of the shape bias. The results suggest a developmental pathway in which early changes in visual object recognition that are themselves linked to category learning enable the discovery of higher-order regularities in category structure and thus the shape bias in novel noun learning tasks. The proposed developmental pathway has implications for understanding the role of specific experience in the development of both visual object recognition and the shape bias in early noun learning. PMID:23227015

Support vector machine-based facial-expression recognition method combining shape and appearance

NASA Astrophysics Data System (ADS)

Han, Eun Jung; Kang, Byung Jun; Park, Kang Ryoung; Lee, Sangyoun

2010-11-01

Facial expression recognition can be widely used for various applications, such as emotion-based human-machine interaction, intelligent robot interfaces, face recognition robust to expression variation, etc. Previous studies have been classified as either shape- or appearance-based recognition. The shape-based method has the disadvantage that the individual variance of facial feature points exists irrespective of similar expressions, which can cause a reduction of the recognition accuracy. The appearance-based method has a limitation in that the textural information of the face is very sensitive to variations in illumination. To overcome these problems, a new facial-expression recognition method is proposed, which combines both shape and appearance information, based on the support vector machine (SVM). This research is novel in the following three ways as compared to previous works. First, the facial feature points are automatically detected by using an active appearance model. From these, the shape-based recognition is performed by using the ratios between the facial feature points based on the facial-action coding system. Second, the SVM, which is trained to recognize the same and different expression classes, is proposed to combine two matching scores obtained from the shape- and appearance-based recognitions. Finally, a single SVM is trained to discriminate four different expressions, such as neutral, a smile, anger, and a scream. By determining the expression of the input facial image whose SVM output is at a minimum, the accuracy of the expression recognition is much enhanced. The experimental results showed that the recognition accuracy of the proposed method was better than previous researches and other fusion methods.

Structural evolution of glycan recognition by a family of potent HIV antibodies.

PubMed

Garces, Fernando; Sok, Devin; Kong, Leopold; McBride, Ryan; Kim, Helen J; Saye-Francisco, Karen F; Julien, Jean-Philippe; Hua, Yuanzi; Cupo, Albert; Moore, John P; Paulson, James C; Ward, Andrew B; Burton, Dennis R; Wilson, Ian A

2014-09-25

The HIV envelope glycoprotein (Env) is densely covered with self-glycans that should help shield it from recognition by the human immune system. Here, we examine how a particularly potent family of broadly neutralizing antibodies (Abs) has evolved common and distinct structural features to counter the glycan shield and interact with both glycan and protein components of HIV Env. The inferred germline antibody already harbors potential binding pockets for a glycan and a short protein segment. Affinity maturation then leads to divergent evolutionary branches that either focus on a single glycan and protein segment (e.g., Ab PGT124) or engage multiple glycans (e.g., Abs PGT121-123). Furthermore, other surrounding glycans are avoided by selecting an appropriate initial antibody shape that prevents steric hindrance. Such molecular recognition lessons are important for engineering proteins that can recognize or accommodate glycans. Copyright © 2014 Elsevier Inc. All rights reserved.

Contour matching for a fish recognition and migration-monitoring system

NASA Astrophysics Data System (ADS)

Lee, Dah-Jye; Schoenberger, Robert B.; Shiozawa, Dennis; Xu, Xiaoqian; Zhan, Pengcheng

2004-12-01

Fish migration is being monitored year round to provide valuable information for the study of behavioral responses of fish to environmental variations. However, currently all monitoring is done by human observers. An automatic fish recognition and migration monitoring system is more efficient and can provide more accurate data. Such a system includes automatic fish image acquisition, contour extraction, fish categorization, and data storage. Shape is a very important characteristic and shape analysis and shape matching are studied for fish recognition. Previous work focused on finding critical landmark points on fish shape using curvature function analysis. Fish recognition based on landmark points has shown satisfying results. However, the main difficulty of this approach is that landmark points sometimes cannot be located very accurately. Whole shape matching is used for fish recognition in this paper. Several shape descriptors, such as Fourier descriptors, polygon approximation and line segments, are tested. A power cepstrum technique has been developed in order to improve the categorization speed using contours represented in tangent space with normalized length. Design and integration including image acquisition, contour extraction and fish categorization are discussed in this paper. Fish categorization results based on shape analysis and shape matching are also included.

Developments in Molecular Recognition and Sensing at Interfaces

PubMed Central

Ariga, Katsuhiko; Hill, Jonathan P.; Endo, Hiroshi

2007-01-01

In biological systems, molecular recognition events occur mostly within interfacial environments such as at membrane surfaces, enzyme reaction sites, or at the interior of the DNA double helix. Investigation of molecular recognition at model interfaces provides great insights into biological phenomena. Molecular recognition at interfaces not only has relevance to biological systems but is also important for modern applications such as high sensitivity sensors. Selective binding of guest molecules in solution to host molecules located at solid surfaces is crucial for electronic or photonic detection of analyte substances. In response to these demands, molecular recognition at interfaces has been investigated extensively during the past two decades using Langmuir monolayers, self-assembled monolayers, and lipid assemblies as recognition media. In this review, advances of molecular recognition at interfaces are briefly summarized.

Method and System for Object Recognition Search

NASA Technical Reports Server (NTRS)

Duong, Tuan A. (Inventor); Duong, Vu A. (Inventor); Stubberud, Allen R. (Inventor)

2012-01-01

A method for object recognition using shape and color features of the object to be recognized. An adaptive architecture is used to recognize and adapt the shape and color features for moving objects to enable object recognition.

Development and evaluation of spherical molecularly imprinted polymer beads.

PubMed

Kempe, Henrik; Kempe, Maria

2006-06-01

The majority of studies on molecularly imprinted polymers has until now been carried out on irregularly shaped particles prepared by grinding of polymer monoliths. The preparation procedures are time- and labor-consuming and produce particles of wide size distributions. To answer the need for fast and straightforward routes to spherical molecularly imprinted polymer beads, we have developed a method comprising the formation of droplets of pre-polymerization solution directly in mineral oil by vigorous mixing followed by transformation of the droplets into solid spherical beads by photoinduced free-radical polymerization. No detergents or stabilizers were required for the droplet formation. Factors influencing the bead synthesis have been investigated and are detailed here. The beads were evaluated in parallel with corresponding irregularly shaped particles prepared from polymer monoliths. Conditions for the synthesis of propranolol-imprinted poly(methacrylic acid-co-trimethylolpropane trimethacrylate) beads in the size range of 1-100 microm in almost quantitative yield are described. The beads were applied as the recognition element in a 96-well plate format radioligand assay of propranolol in human serum.

Formation of Ordered Arrays of Proteins on Surfaces

NASA Technical Reports Server (NTRS)

Lenhoff, A. M.

1996-01-01

Van der Waals (dispersion) forces contribute to interactions of proteins with other molecules or with surfaces, but because of the structural complexity of protein molecules, the magnitude of these effects is usually estimated based on idealized models of the molecular geometry, e.g., spheres or spheroids. The calculations reported here seek to account for both the geometric irregularity of protein molecules and the material properties of the interacting media. While the latter are found to fall in the generally accepted range, the molecular shape is shown to cause the magnitudes of the interactions to differ significantly from those calculated using idealized models, with important consequences. First, the roughness of the molecular surface leads to much lower average interaction energies for both protein-protein and protein-surface cases relative to calculations in which the protein molecule is approximated as a sphere. These results indicate that a form of steric stabilization may be an important effect in protein solutions. Underlying this behavior is appreciable orientational dependence, one reflection of which is that molecules of complementary shape are found to exhibit very strong attractive dispersion interactions. Although this has been widely discussed previously in the context of molecular recognition processes, the broader implications of these phenomena may also be important at larger molecular separations, e.g., in the dynamics of aggregation, precipitation and crystal growth.

Van der Waals Interactions Involving Proteins

NASA Technical Reports Server (NTRS)

Roth, Charles M.; Neal, Brian L.; Lenhoff, Abraham M.

1996-01-01

Van der Waals (dispersion) forces contribute to interactions of proteins with other molecules or with surfaces, but because of the structural complexity of protein molecules, the magnitude of these effects is usually estimated based on idealized models of the molecular geometry, e.g., spheres or spheroids. The calculations reported here seek to account for both the geometric irregularity of protein molecules and the material properties of the interacting media. Whereas the latter are found to fall in the generally accepted range, the molecular shape is shown to cause the magnitudes of the interactions to differ significantly from those calculated using idealized models. with important consequences. First, the roughness of the molecular surface leads to much lower average interaction energies for both protein-protein and protein-surface cases relative to calculations in which the protein molecule is approximated as a sphere. These results indicate that a form of steric stabilization may be an important effect in protein solutions. Underlying this behavior is appreciable orientational dependence, one reflection of which is that molecules of complementary shape are found to exhibit very strong attractive dispersion interactions. Although this has been widely discussed previously in the context of molecular recognition processes, the broader implications of these phenomena may also be important at larger molecular separations, e.g., in the dynamics of aggregation, precipitation, and crystal growth.

Digital and optical shape representation and pattern recognition; Proceedings of the Meeting, Orlando, FL, Apr. 4-6, 1988

NASA Technical Reports Server (NTRS)

Juday, Richard D. (Editor)

1988-01-01

The present conference discusses topics in pattern-recognition correlator architectures, digital stereo systems, geometric image transformations and their applications, topics in pattern recognition, filter algorithms, object detection and classification, shape representation techniques, and model-based object recognition methods. Attention is given to edge-enhancement preprocessing using liquid crystal TVs, massively-parallel optical data base management, three-dimensional sensing with polar exponential sensor arrays, the optical processing of imaging spectrometer data, hybrid associative memories and metric data models, the representation of shape primitives in neural networks, and the Monte Carlo estimation of moment invariants for pattern recognition.

Recognition ROCS Are Curvilinear--Or Are They? On Premature Arguments against the Two-High-Threshold Model of Recognition

ERIC Educational Resources Information Center

Broder, Arndt; Schutz, Julia

2009-01-01

Recent reviews of recognition receiver operating characteristics (ROCs) claim that their curvilinear shape rules out threshold models of recognition. However, the shape of ROCs based on confidence ratings is not diagnostic to refute threshold models, whereas ROCs based on experimental bias manipulations are. Also, fitting predicted frequencies to…

Shape and texture fused recognition of flying targets

NASA Astrophysics Data System (ADS)

Kovács, Levente; Utasi, Ákos; Kovács, Andrea; Szirányi, Tamás

2011-06-01

This paper presents visual detection and recognition of flying targets (e.g. planes, missiles) based on automatically extracted shape and object texture information, for application areas like alerting, recognition and tracking. Targets are extracted based on robust background modeling and a novel contour extraction approach, and object recognition is done by comparisons to shape and texture based query results on a previously gathered real life object dataset. Application areas involve passive defense scenarios, including automatic object detection and tracking with cheap commodity hardware components (CPU, camera and GPS).

Structural insight into RNA recognition motifs: versatile molecular Lego building blocks for biological systems.

PubMed

Muto, Yutaka; Yokoyama, Shigeyuki

2012-01-01

'RNA recognition motifs (RRMs)' are common domain-folds composed of 80-90 amino-acid residues in eukaryotes, and have been identified in many cellular proteins. At first they were known as RNA binding domains. Through discoveries over the past 20 years, however, the RRMs have been shown to exhibit versatile molecular recognition activities and to behave as molecular Lego building blocks to construct biological systems. Novel RNA/protein recognition modes by RRMs are being identified, and more information about the molecular recognition by RRMs is becoming available. These RNA/protein recognition modes are strongly correlated with their biological significance. In this review, we would like to survey the recent progress on these versatile molecular recognition modules. Copyright © 2012 John Wiley & Sons, Ltd.

Extracellular matrix and cell shape: potential control points for inhibition of angiogenesis

NASA Technical Reports Server (NTRS)

Ingber, D.

1991-01-01

Capillary endothelial (CE) cells require two extracellular signals in order to switch from quiescence to growth and back to differentiation during angiogenesis: soluble angiogenic factors and insoluble extracellular matrix (ECM) molecules. Soluble endothelial mitogens, such as basic fibroblast growth factor (FGF), act over large distances to trigger capillary growth, whereas ECM molecules act locally to modulate cell responsiveness to these soluble cues. Recent studies reveal that ECM molecules regulate CE cell growth and differentiation by modulating cell shape and by activating intracellular chemical signaling pathways inside the cell. Recognition of the importance of ECM and cell shape during capillary morphogenesis has led to the identification of a series of new angiogenesis inhibitors. Elucidation of the molecular mechanism of capillary regulation may result in development of even more potent angiogenesis modulators in the future.

Integrated structural biology to unravel molecular mechanisms of protein-RNA recognition.

PubMed

Schlundt, Andreas; Tants, Jan-Niklas; Sattler, Michael

2017-04-15

Recent advances in RNA sequencing technologies have greatly expanded our knowledge of the RNA landscape in cells, often with spatiotemporal resolution. These techniques identified many new (often non-coding) RNA molecules. Large-scale studies have also discovered novel RNA binding proteins (RBPs), which exhibit single or multiple RNA binding domains (RBDs) for recognition of specific sequence or structured motifs in RNA. Starting from these large-scale approaches it is crucial to unravel the molecular principles of protein-RNA recognition in ribonucleoprotein complexes (RNPs) to understand the underlying mechanisms of gene regulation. Structural biology and biophysical studies at highest possible resolution are key to elucidate molecular mechanisms of RNA recognition by RBPs and how conformational dynamics, weak interactions and cooperative binding contribute to the formation of specific, context-dependent RNPs. While large compact RNPs can be well studied by X-ray crystallography and cryo-EM, analysis of dynamics and weak interaction necessitates the use of solution methods to capture these properties. Here, we illustrate methods to study the structure and conformational dynamics of protein-RNA complexes in solution starting from the identification of interaction partners in a given RNP. Biophysical and biochemical techniques support the characterization of a protein-RNA complex and identify regions relevant in structural analysis. Nuclear magnetic resonance (NMR) is a powerful tool to gain information on folding, stability and dynamics of RNAs and characterize RNPs in solution. It provides crucial information that is complementary to the static pictures derived from other techniques. NMR can be readily combined with other solution techniques, such as small angle X-ray and/or neutron scattering (SAXS/SANS), electron paramagnetic resonance (EPR), and Förster resonance energy transfer (FRET), which provide information about overall shapes, internal domain arrangements and dynamics. Principles of protein-RNA recognition and current approaches are reviewed and illustrated with recent studies. Copyright © 2017 Elsevier Inc. All rights reserved.

Feature extraction for face recognition via Active Shape Model (ASM) and Active Appearance Model (AAM)

NASA Astrophysics Data System (ADS)

Iqtait, M.; Mohamad, F. S.; Mamat, M.

2018-03-01

Biometric is a pattern recognition system which is used for automatic recognition of persons based on characteristics and features of an individual. Face recognition with high recognition rate is still a challenging task and usually accomplished in three phases consisting of face detection, feature extraction, and expression classification. Precise and strong location of trait point is a complicated and difficult issue in face recognition. Cootes proposed a Multi Resolution Active Shape Models (ASM) algorithm, which could extract specified shape accurately and efficiently. Furthermore, as the improvement of ASM, Active Appearance Models algorithm (AAM) is proposed to extracts both shape and texture of specified object simultaneously. In this paper we give more details about the two algorithms and give the results of experiments, testing their performance on one dataset of faces. We found that the ASM is faster and gains more accurate trait point location than the AAM, but the AAM gains a better match to the texture.

Regulation Effects by Programmed Molecules for Transcription-Based Diagnostic Automata towards Therapeutic Use

NASA Astrophysics Data System (ADS)

Hirabayashi, Miki; Ohashi, Hirotada; Kubo, Tai

We have presented experimental analysis on the controllability of our transcription-based diagnostic biomolecular automata by programmed molecules. Focusing on the noninvasive transcriptome diagnosis by salivary mRNAs, we already proposed the novel concept of diagnostic device using DNA computation. This system consists of the main computational element which has a stem shaped promoter region and a pseudo-loop shaped read-only memory region for transcription regulation through the conformation change caused by the recognition of disease-related biomarkers. We utilize the transcription of malachite green aptamer sequence triggered by the target recognition for observation of detection. This algorithm makes it possible to release RNA-aptamer drugs multiply, different from the digestion-based systems by the restriction enzyme which was proposed previously, for the in-vivo use, however, the controllability of aptamer release is not enough at the previous stage. In this paper, we verified the regulation effect on aptamer transcription by programmed molecules in basic conditions towards the developm! ent of therapeutic automata. These results would bring us one step closer to the realization of new intelligent diagnostic and therapeutic automata based on molecular circuits.

Discriminating Power of Localized Three-Dimensional Facial Morphology

PubMed Central

Hammond, Peter; Hutton, Tim J.; Allanson, Judith E.; Buxton, Bernard; Campbell, Linda E.; Clayton-Smith, Jill; Donnai, Dian; Karmiloff-Smith, Annette; Metcalfe, Kay; Murphy, Kieran C.; Patton, Michael; Pober, Barbara; Prescott, Katrina; Scambler, Pete; Shaw, Adam; Smith, Ann C. M.; Stevens, Angela F.; Temple, I. Karen; Hennekam, Raoul; Tassabehji, May

2005-01-01

Many genetic syndromes involve a facial gestalt that suggests a preliminary diagnosis to an experienced clinical geneticist even before a clinical examination and genotyping are undertaken. Previously, using visualization and pattern recognition, we showed that dense surface models (DSMs) of full face shape characterize facial dysmorphology in Noonan and in 22q11 deletion syndromes. In this much larger study of 696 individuals, we extend the use of DSMs of the full face to establish accurate discrimination between controls and individuals with Williams, Smith-Magenis, 22q11 deletion, or Noonan syndromes and between individuals with different syndromes in these groups. However, the full power of the DSM approach is demonstrated by the comparable discriminating abilities of localized facial features, such as periorbital, perinasal, and perioral patches, and the correlation of DSM-based predictions and molecular findings. This study demonstrates the potential of face shape models to assist clinical training through visualization, to support clinical diagnosis of affected individuals through pattern recognition, and to enable the objective comparison of individuals sharing other phenotypic or genotypic properties. PMID:16380911

Combining color and shape information for illumination-viewpoint invariant object recognition.

PubMed

Diplaros, Aristeidis; Gevers, Theo; Patras, Ioannis

2006-01-01

In this paper, we propose a new scheme that merges color- and shape-invariant information for object recognition. To obtain robustness against photometric changes, color-invariant derivatives are computed first. Color invariance is an important aspect of any object recognition scheme, as color changes considerably with the variation in illumination, object pose, and camera viewpoint. These color invariant derivatives are then used to obtain similarity invariant shape descriptors. Shape invariance is equally important as, under a change in camera viewpoint and object pose, the shape of a rigid object undergoes a perspective projection on the image plane. Then, the color and shape invariants are combined in a multidimensional color-shape context which is subsequently used as an index. As the indexing scheme makes use of a color-shape invariant context, it provides a high-discriminative information cue robust against varying imaging conditions. The matching function of the color-shape context allows for fast recognition, even in the presence of object occlusion and cluttering. From the experimental results, it is shown that the method recognizes rigid objects with high accuracy in 3-D complex scenes and is robust against changing illumination, camera viewpoint, object pose, and noise.

Recognition of the folded conformation of plant hormone (auxin, IAA) conjugates with glutamic and aspartic acids and their amides

NASA Astrophysics Data System (ADS)

Antolić, S.; Kveder, M.; Klaić, B.; Magnus, V.; Kojić-Prodić, B.

2001-01-01

The molecular structure of the endogenous plant hormone (auxin) conjugate, N-(indol-3-ylacetyl)-L-glutamic acid, is deduced by comparison with N2-(indol-3-ylacetyl)glutamine (IAA-Gln), N2-(indol-3-ylacetyl)asparagine (IAA-Asn) and N-(indol-3-ylacetyl)-L-aspartic acid using X-ray structure analysis, 1H-NMR spectroscopy (NOE measurements) and molecular modelling. The significance of the overall molecular shape, and of the resulting amphiphilic properties, of the compounds studied are discussed in terms of possible implications for trafficking between cell compartments. Both in the solid state and in solution, the molecules are in the hair-pin (folded) conformation in which the side chain is folded over the indole ring. While extended conformations can be detected by molecular dynamics simulations, they are so short-lived that any major influence on the biological properties of the compounds studied is unlikely.

Contributions of feature shapes and surface cues to the recognition and neural representation of facial identity.

PubMed

Andrews, Timothy J; Baseler, Heidi; Jenkins, Rob; Burton, A Mike; Young, Andrew W

2016-10-01

A full understanding of face recognition will involve identifying the visual information that is used to discriminate different identities and how this is represented in the brain. The aim of this study was to explore the importance of shape and surface properties in the recognition and neural representation of familiar faces. We used image morphing techniques to generate hybrid faces that mixed shape properties (more specifically, second order spatial configural information as defined by feature positions in the 2D-image) from one identity and surface properties from a different identity. Behavioural responses showed that recognition and matching of these hybrid faces was primarily based on their surface properties. These behavioural findings contrasted with neural responses recorded using a block design fMRI adaptation paradigm to test the sensitivity of Haxby et al.'s (2000) core face-selective regions in the human brain to the shape or surface properties of the face. The fusiform face area (FFA) and occipital face area (OFA) showed a lower response (adaptation) to repeated images of the same face (same shape, same surface) compared to different faces (different shapes, different surfaces). From the behavioural data indicating the critical contribution of surface properties to the recognition of identity, we predicted that brain regions responsible for familiar face recognition should continue to adapt to faces that vary in shape but not surface properties, but show a release from adaptation to faces that vary in surface properties but not shape. However, we found that the FFA and OFA showed an equivalent release from adaptation to changes in both shape and surface properties. The dissociation between the neural and perceptual responses suggests that, although they may play a role in the process, these core face regions are not solely responsible for the recognition of facial identity. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

PubMed Central

Nanjunda, Rupesh; Wilson, W. David

2012-01-01

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

Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator

NASA Astrophysics Data System (ADS)

Deng, Zengqin; Wang, Qing; Liu, Zhao; Zhang, Manfeng; Machado, Ana Carolina Dantas; Chiu, Tsu-Pei; Feng, Chong; Zhang, Qi; Yu, Lin; Qi, Lei; Zheng, Jiangge; Wang, Xu; Huo, Xinmei; Qi, Xiaoxuan; Li, Xiaorong; Wu, Wei; Rohs, Remo; Li, Ying; Chen, Zhongzhou

2015-07-01

Ferric uptake regulator (Fur) plays a key role in the iron homeostasis of prokaryotes, such as bacterial pathogens, but the molecular mechanisms and structural basis of Fur-DNA binding remain incompletely understood. Here, we report high-resolution structures of Magnetospirillum gryphiswaldense MSR-1 Fur in four different states: apo-Fur, holo-Fur, the Fur-feoAB1 operator complex and the Fur-Pseudomonas aeruginosa Fur box complex. Apo-Fur is a transition metal ion-independent dimer whose binding induces profound conformational changes and confers DNA-binding ability. Structural characterization, mutagenesis, biochemistry and in vivo data reveal that Fur recognizes DNA by using a combination of base readout through direct contacts in the major groove and shape readout through recognition of the minor-groove electrostatic potential by lysine. The resulting conformational plasticity enables Fur binding to diverse substrates. Our results provide insights into metal ion activation and substrate recognition by Fur that suggest pathways to engineer magnetotactic bacteria and antipathogenic drugs.

Contributions of feature shapes and surface cues to the recognition of facial expressions.

PubMed

Sormaz, Mladen; Young, Andrew W; Andrews, Timothy J

2016-10-01

Theoretical accounts of face processing often emphasise feature shapes as the primary visual cue to the recognition of facial expressions. However, changes in facial expression also affect the surface properties of the face. In this study, we investigated whether this surface information can also be used in the recognition of facial expression. First, participants identified facial expressions (fear, anger, disgust, sadness, happiness) from images that were manipulated such that they varied mainly in shape or mainly in surface properties. We found that the categorization of facial expression is possible in either type of image, but that different expressions are relatively dependent on surface or shape properties. Next, we investigated the relative contributions of shape and surface information to the categorization of facial expressions. This employed a complementary method that involved combining the surface properties of one expression with the shape properties from a different expression. Our results showed that the categorization of facial expressions in these hybrid images was equally dependent on the surface and shape properties of the image. Together, these findings provide a direct demonstration that both feature shape and surface information make significant contributions to the recognition of facial expressions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Flower-like superstructures of AIE-active tetraphenylethylene through solvophobic controlled self-assembly

NASA Astrophysics Data System (ADS)

Salimimarand, Mina; La, Duong Duc; Kobaisi, Mohammad Al; Bhosale, Sheshanath V.

2017-02-01

The development of well-organized structures with high luminescent properties in the solid and aggregated states is of both scientific and technological interest due to their applications in nanotechnology. In this paper we described the synthesis of amphiphilic and dumbbell shaped AIE-active tetraphenylethylene (TPE) derivatives and studied their self-assembly with solvophobic control. Interestingly, both TPE derivatives form a 3D flower-shape supramolecular structure from THF/water solutions at varying water fractions. SEM microscopy was used to visualise step-wise growth of flower-shape assembly. TPE derivatives also show good mechanochromic properties which can be observed in the process of grinding, fuming and heating. These TPE derivative self-assemblies are formed due to two main important properties: (i) the TPE-core along with alkyl chains, optimizing the dispersive interactions within a construct, and (ii) amide-linkage through molecular recognition. We believe such arrangements prevent crystallization and favour the directional growth of flower-shape nanostructures in a 3D fashion.

Preserved Haptic Shape Processing after Bilateral LOC Lesions.

PubMed

Snow, Jacqueline C; Goodale, Melvyn A; Culham, Jody C

2015-10-07

The visual and haptic perceptual systems are understood to share a common neural representation of object shape. A region thought to be critical for recognizing visual and haptic shape information is the lateral occipital complex (LOC). We investigated whether LOC is essential for haptic shape recognition in humans by studying behavioral responses and brain activation for haptically explored objects in a patient (M.C.) with bilateral lesions of the occipitotemporal cortex, including LOC. Despite severe deficits in recognizing objects using vision, M.C. was able to accurately recognize objects via touch. M.C.'s psychophysical response profile to haptically explored shapes was also indistinguishable from controls. Using fMRI, M.C. showed no object-selective visual or haptic responses in LOC, but her pattern of haptic activation in other brain regions was remarkably similar to healthy controls. Although LOC is routinely active during visual and haptic shape recognition tasks, it is not essential for haptic recognition of object shape. The lateral occipital complex (LOC) is a brain region regarded to be critical for recognizing object shape, both in vision and in touch. However, causal evidence linking LOC with haptic shape processing is lacking. We studied recognition performance, psychophysical sensitivity, and brain response to touched objects, in a patient (M.C.) with extensive lesions involving LOC bilaterally. Despite being severely impaired in visual shape recognition, M.C. was able to identify objects via touch and she showed normal sensitivity to a haptic shape illusion. M.C.'s brain response to touched objects in areas of undamaged cortex was also very similar to that observed in neurologically healthy controls. These results demonstrate that LOC is not necessary for recognizing objects via touch. Copyright © 2015 the authors 0270-6474/15/3513745-16$15.00/0.

Parts and Relations in Young Children's Shape-Based Object Recognition

ERIC Educational Resources Information Center

Augustine, Elaine; Smith, Linda B.; Jones, Susan S.

2011-01-01

The ability to recognize common objects from sparse information about geometric shape emerges during the same period in which children learn object names and object categories. Hummel and Biederman's (1992) theory of object recognition proposes that the geometric shapes of objects have two components--geometric volumes representing major object…

Is it the shape of the cavity, or the shape of the water in the cavity?

NASA Astrophysics Data System (ADS)

Snyder, Phillip W.; Lockett, Matthew R.; Moustakas, Demetri T.; Whitesides, George M.

2014-04-01

Historical interpretations of the thermodynamics characterizing biomolecular recognition have marginalized the role of water. An important (even, perhaps, dominant) contribution to molecular recognition in water comes from the "hydrophobic effect," in which non-polar portions of a ligand interact preferentially with non-polar regions of a protein. Water surrounds the ligand, and water fills the binding pocket of the protein: when the protein-ligand complex forms, and hydrophobic surfaces of the binding pocket and the ligand approach one another, the molecules (and hydrogen-bonded networks of molecules) of water associated with both surfaces rearrange and, in part, entirely escape into the bulk solution. It is now clear that neither of the two most commonly cited rationalizations for the hydrophobic effect-an entropy-dominated hydrophobic effect, in which ordered waters at the surface of the ligand, and water at the surface of the protein, are released to the bulk upon binding, and a "lock-and-key" model, in which the surface of a ligand interacts directly with a surface of a protein having a complementary shape-can account for water-mediated interactions between the ligand and the protein, and neither is sufficient to account for the experimental observation of both entropy- andenthalpy-dominated hydrophobic effects. What is now clear is that there is no single hydrophobic effect, with a universally applicable, common, thermodynamic description: different processes (i.e., partitioning between phases of different hydrophobicity, aggregation in water, and binding) with different thermodynamics, depend on the molecular-level details of the structures of the molecules involved, and of the aggregates that form. A "water-centric" description of the hydrophobic effect in biomolecular recognition focuses on the structures of water surrounding the ligand, and of water filling the binding pocket of the protein, both before and after binding. This view attributes the hydrophobic effect to changes in the free energy of the networks of hydrogen bonds that are formed, broken, or re-arranged when two hydrophobic surfaces approach (but do not necessarily contact) one another. The details of the molecular topography (and the polar character) of the mole- cular surfaces play an important role in determining the structure of these networks of hydrogen-bonded waters, and in the thermodynamic description of the hydrophobic effect(s). Theorists have led the formulation of this "water-centric view", although experiments are now supplying support for it. It poses complex problems for would-be "designers" of protein-ligand interactions, and for so-called "rational drug design".

Mechanistic Study of Human Glucose Transport Mediated by GLUT1.

PubMed

Fu, Xuegang; Zhang, Gang; Liu, Ran; Wei, Jing; Zhang-Negrerie, Daisy; Jian, Xiaodong; Gao, Qingzhi

2016-03-28

The glucose transporter 1 (GLUT1) belongs to the major facilitator superfamily (MFS) and is responsible for the constant uptake of glucose. However, the molecular mechanism of sugar transport remains obscure. In this study, homology modeling and molecular dynamics (MD) simulations in lipid bilayers were performed to investigate the combination of the alternate and multisite transport mechanism of glucose with GLUT1 in atomic detail. To explore the substrate recognition mechanism, the outward-open state human GLUT1 homology model was generated based on the template of xylose transporter XylE (PDB ID: 4GBZ), which shares up to 29% sequence identity and 49% similarity with GLUT1. Through the MD simulation study of glucose across lipid bilayer with both the outward-open GLUT1 and the GLUT1 inward-open crystal structure, we investigated six different conformational states and identified four key binding sites in both exofacial and endofacial loops that are essential for glucose recognition and transport. The study further revealed that four flexible gates consisting of W65/Y292/Y293-M420/TM10b-W388 might play important roles in the transport cycle. The study showed that some side chains close to the central ligand binding site underwent larger position changes. These conformational interchanges formed gated networks within an S-shaped central channel that permitted staged ligand diffusion across the transporter. This study provides new inroads for the understanding of GLUT1 ligand recognition paradigm and configurational features which are important for molecular, structural, and physiological research of the MFS members, especially for GLUT1-targeted drug design and discovery.

Thermometric MIP sensor for fructosyl valine.

PubMed

Rajkumar, Rajagopal; Katterle, Martin; Warsinke, Axel; Möhwald, Helmuth; Scheller, Frieder W

2008-02-28

Interactions of molecularly imprinted polymers containing phenyl boronic acid residues with fructosyl valine, fructose and pinacol, respectively are analysed in aqueous solution (pH 11.4) by using a flow calorimeter. The reversible formation of (two) cyclic boronic acid diesters per fructosyl molecule generates a 40-fold higher exothermic signal as compared to the control polymer. Whereas binding of pinacol to either the MIP or the control polymer generates a very small endothermic signal reflecting a negligible contribution of the esterification to the overall process. An "apparent imprinting factor" of 41 is found which exceeds the respective value of batch binding procedures by a factor of 30. Furthermore, the MIP sensor was used to characterise the crossreactivity. The influence of shape selective molecular recognition is discussed.

Personal recognition using hand shape and texture.

PubMed

Kumar, Ajay; Zhang, David

2006-08-01

This paper proposes a new bimodal biometric system using feature-level fusion of hand shape and palm texture. The proposed combination is of significance since both the palmprint and hand-shape images are proposed to be extracted from the single hand image acquired from a digital camera. Several new hand-shape features that can be used to represent the hand shape and improve the performance are investigated. The new approach for palmprint recognition using discrete cosine transform coefficients, which can be directly obtained from the camera hardware, is demonstrated. None of the prior work on hand-shape or palmprint recognition has given any attention on the critical issue of feature selection. Our experimental results demonstrate that while majority of palmprint or hand-shape features are useful in predicting the subjects identity, only a small subset of these features are necessary in practice for building an accurate model for identification. The comparison and combination of proposed features is evaluated on the diverse classification schemes; naive Bayes (normal, estimated, multinomial), decision trees (C4.5, LMT), k-NN, SVM, and FFN. Although more work remains to be done, our results to date indicate that the combination of selected hand-shape and palmprint features constitutes a promising addition to the biometrics-based personal recognition systems.

A look at plant immunity through the window of the multitasking coreceptor BAK1.

PubMed

Yasuda, Shigetaka; Okada, Kentaro; Saijo, Yusuke

2017-08-01

Recognition of microbe- and danger-associated molecular patterns (MAMPs and DAMPs, respectively) by pattern recognition receptors (PRRs) is central to innate immunity in both plants and animals. The plant PRRs described to date are all cell surface-localized receptors. According to their ligand-binding ectodomains, each PRR engages a specific coreceptor or adaptor kinase in its signaling complexes to regulate defense signaling. With a focus on the coreceptor RLK BRI1-ASSOCIATED RECEPTOR KINASE1 (BAK1) and related SOMATIC EMBRYOGENESIS RECEPTOR KINASEs (SERKs), here we review the increasing inventory of BAK1 partners and their functions in plant immunity. We also discuss the significance of autoimmunity triggered by BAK1/SERK4 disintegration in shaping the strategies for attenuation of PRR signaling by infectious microbes and host plants. Copyright © 2017 Elsevier Ltd. All rights reserved.

Caricature generalization benefits for faces learned with enhanced idiosyncratic shape or texture.

PubMed

Itz, Marlena L; Schweinberger, Stefan R; Kaufmann, Jürgen M

2017-02-01

Recent findings show benefits for learning and subsequent recognition of faces caricatured in shape or texture, but there is little evidence on whether this caricature learning advantage generalizes to recognition of veridical counterparts at test. Moreover, it has been reported that there is a relatively higher contribution of texture information, at the expense of shape information, for familiar compared to unfamiliar face recognition. The aim of this study was to examine whether veridical faces are recognized better when they were learned as caricatures compared to when they were learned as veridicals-what we call a caricature generalization benefit. Photorealistic facial stimuli derived from a 3-D camera system were caricatured selectively in either shape or texture by 50 %. Faces were learned across different images either as veridicals, shape caricatures, or texture caricatures. At test, all learned and novel faces were presented as previously unseen frontal veridicals, and participants performed an old-new task. We assessed accuracies, reaction times, and face-sensitive event-related potentials (ERPs). Faces learned as caricatures were recognized more accurately than faces learned as veridicals. At learning, N250 and LPC were largest for shape caricatures, suggesting encoding advantages of distinctive facial shape. At test, LPC was largest for faces that had been learned as texture caricatures, indicating the importance of texture for familiar face recognition. Overall, our findings demonstrate that caricature learning advantages can generalize to and, importantly, improve recognition of veridical versions of faces.

Short temporal asynchrony disrupts visual object recognition

PubMed Central

Singer, Jedediah M.; Kreiman, Gabriel

2014-01-01

Humans can recognize objects and scenes in a small fraction of a second. The cascade of signals underlying rapid recognition might be disrupted by temporally jittering different parts of complex objects. Here we investigated the time course over which shape information can be integrated to allow for recognition of complex objects. We presented fragments of object images in an asynchronous fashion and behaviorally evaluated categorization performance. We observed that visual recognition was significantly disrupted by asynchronies of approximately 30 ms, suggesting that spatiotemporal integration begins to break down with even small deviations from simultaneity. However, moderate temporal asynchrony did not completely obliterate recognition; in fact, integration of visual shape information persisted even with an asynchrony of 100 ms. We describe the data with a concise model based on the dynamic reduction of uncertainty about what image was presented. These results emphasize the importance of timing in visual processing and provide strong constraints for the development of dynamical models of visual shape recognition. PMID:24819738

Experimental mixture design as a tool for the synthesis of antimicrobial selective molecularly imprinted monodisperse microbeads.

PubMed

Benito-Peña, Elena; Navarro-Villoslada, Fernando; Carrasco, Sergio; Jockusch, Steffen; Ottaviani, M Francesca; Moreno-Bondi, Maria C

2015-05-27

The effect of the cross-linker on the shape and size of molecular imprinted polymer (MIP) beads prepared by precipitation polymerization has been evaluated using a chemometric approach. Molecularly imprinted microspheres for the selective recognition of fluoroquinolone antimicrobials were prepared in a one-step precipitation polymerization procedure using enrofloxacin (ENR) as the template molecule, methacrylic acid as functional monomer, 2-hydroxyethyl methacrylate as hydrophilic comonomer, and acetonitrile as the porogen. The type and amount of cross-linker, namely ethylene glycol dimethacrylate, divinylbenzene or trimethylolpropane trimethacrylate, to obtain monodispersed MIP spherical beads in the micrometer range was optimized using a simplex lattice design. Particle size and morphology were assessed by scanning electron microscopy, dynamic light scattering, and nitrogen adsorption measurements. Electron paramagnetic resonance spectroscopy in conjunction with a nitroxide as spin probe revealed information about the microviscosity and polarity of the binding sites in imprinted and nonimprinted polymer beads.

Structure and molecular dynamics simulation of archaeal prefoldin: the molecular mechanism for binding and recognition of nonnative substrate proteins.

PubMed

Ohtaki, Akashi; Kida, Hiroshi; Miyata, Yusuke; Ide, Naoki; Yonezawa, Akihiro; Arakawa, Takatoshi; Iizuka, Ryo; Noguchi, Keiichi; Kita, Akiko; Odaka, Masafumi; Miki, Kunio; Yohda, Masafumi

2008-02-29

Prefoldin (PFD) is a heterohexameric molecular chaperone complex in the eukaryotic cytosol and archaea with a jellyfish-like structure containing six long coiled-coil tentacles. PFDs capture protein folding intermediates or unfolded polypeptides and transfer them to group II chaperonins for facilitated folding. Although detailed studies on the mechanisms for interaction with unfolded proteins or cooperation with chaperonins of archaeal PFD have been performed, it is still unclear how PFD captures the unfolded protein. In this study, we determined the X-ray structure of Pyrococcus horikoshii OT3 PFD (PhPFD) at 3.0 A resolution and examined the molecular mechanism for binding and recognition of nonnative substrate proteins by molecular dynamics (MD) simulation and mutation analyses. PhPFD has a jellyfish-like structure with six long coiled-coil tentacles and a large central cavity. Each subunit has a hydrophobic groove at the distal region where an unfolded substrate protein is bound. During MD simulation at 330 K, each coiled coil was highly flexible, enabling it to widen its central cavity and capture various nonnative proteins. Docking MD simulation of PhPFD with unfolded insulin showed that the beta subunit is essentially involved in substrate binding and that the alpha subunit modulates the shape and width of the central cavity. Analyses of mutant PhPFDs with amino acid replacement of the hydrophobic residues of the beta subunit in the hydrophobic groove have shown that beta Ile107 has a critical role in forming the hydrophobic groove.

Size-Sensitive Perceptual Representations Underlie Visual and Haptic Object Recognition

PubMed Central

Craddock, Matt; Lawson, Rebecca

2009-01-01

A variety of similarities between visual and haptic object recognition suggests that the two modalities may share common representations. However, it is unclear whether such common representations preserve low-level perceptual features or whether transfer between vision and haptics is mediated by high-level, abstract representations. Two experiments used a sequential shape-matching task to examine the effects of size changes on unimodal and crossmodal visual and haptic object recognition. Participants felt or saw 3D plastic models of familiar objects. The two objects presented on a trial were either the same size or different sizes and were the same shape or different but similar shapes. Participants were told to ignore size changes and to match on shape alone. In Experiment 1, size changes on same-shape trials impaired performance similarly for both visual-to-visual and haptic-to-haptic shape matching. In Experiment 2, size changes impaired performance on both visual-to-haptic and haptic-to-visual shape matching and there was no interaction between the cost of size changes and direction of transfer. Together the unimodal and crossmodal matching results suggest that the same, size-specific perceptual representations underlie both visual and haptic object recognition, and indicate that crossmodal memory for objects must be at least partly based on common perceptual representations. PMID:19956685

Structural study and conformational behavior of the two different lipopolysaccharide O-antigens produced by the cystic fibrosis pathogen Burkholderia multivorans.

PubMed

Ieranò, Teresa; Silipo, Alba; Cescutti, Paola; Leone, Maria Rosaria; Rizzo, Roberto; Lanzetta, Rosa; Parrilli, Michelangelo; Molinaro, Antonio

2009-07-20

Lipopolysaccharides (LPSs) are virulence factors expressed by gram-negative bacteria; they are among those mainly responsible for bacterial virulence. In this work we define the primary structure and the conformational features of the O-chain from the LPS produced by the highly virulent clinical isolate Burkholderia multivorans strain C1576, an opportunistic human pathogen isolated in a cystic fibrosis center and causative of an outbreak with lethal outcome. We demonstrate that the LPS from this clinical isolate consists of two O-polysaccharide chains present in different amounts and made up of repeating units, both containing deoxy sugar. Additionally, conformational studies have been performed to establish and compare the spatial arrangements of the two polysaccharides and differences in their shape have been highlighted. The comprehension of the structural and conformational features of the two repeating units may help to explain their biological significance, the molecular shape of the bacterial external surface, and the comprehension at the molecular level of the recognition mechanisms of the antibodies.

Does viotin activate violin more than viocin? On the use of visual cues during visual-word recognition.

PubMed

Perea, Manuel; Panadero, Victoria

2014-01-01

The vast majority of neural and computational models of visual-word recognition assume that lexical access is achieved via the activation of abstract letter identities. Thus, a word's overall shape should play no role in this process. In the present lexical decision experiment, we compared word-like pseudowords like viotín (same shape as its base word: violín) vs. viocín (different shape) in mature (college-aged skilled readers), immature (normally reading children), and immature/impaired (young readers with developmental dyslexia) word-recognition systems. Results revealed similar response times (and error rates) to consistent-shape and inconsistent-shape pseudowords for both adult skilled readers and normally reading children - this is consistent with current models of visual-word recognition. In contrast, young readers with developmental dyslexia made significantly more errors to viotín-like pseudowords than to viocín-like pseudowords. Thus, unlike normally reading children, young readers with developmental dyslexia are sensitive to a word's visual cues, presumably because of poor letter representations.

Molecular recognition by gold, silver and copper nanoparticles

PubMed Central

Tauran, Yannick; Brioude, Arnaud; Coleman, Anthony W; Rhimi, Moez; Kim, Beonjoom

2013-01-01

The intrinsic physical properties of the noble metal nanoparticles, which are highly sensitive to the nature of their local molecular environment, make such systems ideal for the detection of molecular recognition events. The current review describes the state of the art concerning molecular recognition of Noble metal nanoparticles. In the first part the preparation of such nanoparticles is discussed along with methods of capping and stabilization. A brief discussion of the three common methods of functionalization: Electrostatic adsorption; Chemisorption; Affinity-based coordination is given. In the second section a discussion of the optical and electrical properties of nanoparticles is given to aid the reader in understanding the use of such properties in molecular recognition. In the main section the various types of capping agents for molecular recognition; nucleic acid coatings, protein coatings and molecules from the family of supramolecular chemistry are described along with their numerous applications. Emphasis for the nucleic acids is on complementary oligonucleotide and aptamer recognition. For the proteins the recognition properties of antibodies form the core of the section. With respect to the supramolecular systems the cyclodextrins, calix[n]arenes, dendrimers, crown ethers and the cucurbitales are treated in depth. Finally a short section deals with the possible toxicity of the nanoparticles, a concern in public health. PMID:23977421

Automated transformation-invariant shape recognition through wavelet multiresolution

NASA Astrophysics Data System (ADS)

Brault, Patrice; Mounier, Hugues

2001-12-01

We present here new results in Wavelet Multi-Resolution Analysis (W-MRA) applied to shape recognition in automatic vehicle driving applications. Different types of shapes have to be recognized in this framework. They pertain to most of the objects entering the sensors field of a car. These objects can be road signs, lane separation lines, moving or static obstacles, other automotive vehicles, or visual beacons. The recognition process must be invariant to global, affine or not, transformations which are : rotation, translation and scaling. It also has to be invariant to more local, elastic, deformations like the perspective (in particular with wide angle camera lenses), and also like deformations due to environmental conditions (weather : rain, mist, light reverberation) or optical and electrical signal noises. To demonstrate our method, an initial shape, with a known contour, is compared to the same contour altered by rotation, translation, scaling and perspective. The curvature computed for each contour point is used as a main criterion in the shape matching process. The original part of this work is to use wavelet descriptors, generated with a fast orthonormal W-MRA, rather than Fourier descriptors, in order to provide a multi-resolution description of the contour to be analyzed. In such way, the intrinsic spatial localization property of wavelet descriptors can be used and the recognition process can be speeded up. The most important part of this work is to demonstrate the potential performance of Wavelet-MRA in this application of shape recognition.

Designing of MIP based QCM sensor having thymine recognition sites based on biomimicking DNA approach.

PubMed

Diltemiz, S Emir; Hür, D; Ersöz, A; Denizli, A; Say, R

2009-11-15

Quartz crystal microbalance (QCM) sensors coated with molecular imprinted polymers (MIP) have been developed for the determination of thymine. In this method, methacryloylamidoadenine (MA-Ade) have used as a new monomer and thymine template for inspiration of DNA nucleobases interaction. The thymine can be simultaneously hydrogen binding to MA-Ade and fit into the shape-selective cavities. Thus, the interaction between nucleobases has an effect on the binding ability of the QCM sensors. The binding affinity of the thymine imprinted sensors has investigated by using the Langmuir isotherm. The thymine imprinted QCM electrodes have shown homogeneous binding sites for thymine (K(a): 1.0 x 10(5)M(-1)) while heterogeneous binding sites for uracil. On the other hand, recognition selectivity of the QCM sensor based on thymine imprinted polymer toward to uracil, ssDNA and ssRNA has been reported in this work.

Propagating Molecular Recognition Events through Highly Integrated Sense-Response Chemical Systems

DTIC Science & Technology

2017-08-01

Propagating Molecular Recognition Events through Highly Integrated Sense-Response Chemical Systems The views, opinions and/or findings contained in...University of California - San Diego Title: Propagating Molecular Recognition Events through Highly Integrated Sense-Response Chemical Systems Report Term...including enzymatic reactions , occurring at the aqueous interfaces of thermotropic LCs show promise as the basis of biomolecular triggers of LC

A Biological-Plausable Architecture for Shape Recognition

DTIC Science & Technology

2006-06-30

between curves. Information Processing Letters, 64, 1997. [4] Irving Biederman . Recognition-by-components: A theory of human image understanding...Psychological Review, 94(2):115–147, 1987 . 43 [5] C. Cadieu, M. Kouh, M. Riesenhuber, and T. Poggio. Shape representation in v4: Investi- gating position

Efficient local representations for three-dimensional palmprint recognition

NASA Astrophysics Data System (ADS)

Yang, Bing; Wang, Xiaohua; Yao, Jinliang; Yang, Xin; Zhu, Wenhua

2013-10-01

Palmprints have been broadly used for personal authentication because they are highly accurate and incur low cost. Most previous works have focused on two-dimensional (2-D) palmprint recognition in the past decade. Unfortunately, 2-D palmprint recognition systems lose the shape information when capturing palmprint images. Moreover, such 2-D palmprint images can be easily forged or affected by noise. Hence, three-dimensional (3-D) palmprint recognition has been regarded as a promising way to further improve the performance of palmprint recognition systems. We have developed a simple, but efficient method for 3-D palmprint recognition by using local features. We first utilize shape index representation to describe the geometry of local regions in 3-D palmprint data. Then, we extract local binary pattern and Gabor wavelet features from the shape index image. The two types of complementary features are finally fused at a score level for further improvements. The experimental results on the Hong Kong Polytechnic 3-D palmprint database, which contains 8000 samples from 400 palms, illustrate the effectiveness of the proposed method.

Optical detection of λ-cyhalothrin by core-shell fluorescent molecularly imprinted polymers in Chinese spirits.

PubMed

Wang, Jixiang; Gao, Lin; Han, Donglai; Pan, Jianming; Qiu, Hao; Li, Hongji; Wei, Xiao; Dai, Jiangdong; Yang, Jinghai; Yao, Hui; Yan, Yongsheng

2015-03-11

In this study, fluorescent molecularly imprinted polymers (FMIPs), which were for the selective recognition and fluorescence detection of λ-cyhalothrin (LC), were synthesized via fluorescein 5(6)-isothiocyanate (FITC) and 3-aminopropyltriethoxysilane (APTS)/SiO2 particles. The SiO2@FITC-APTS@MIPs were characterized by Fourier transform infrared (FT-IR), UV-vis spectrophotometer (UV-vis), fluorescence spectrophotometer, thermogravimetric analysis (TGA), confocal laser scanning microscope (CLSM), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). The as-synthesized SiO2@FITC-APTS@MIPs with an imprinted polymer film (thickness was about 100 nm) was demonstrated to be spherically shaped and had good monodispersity, high fluorescence intensity, and good selective recognition. Using fluorescence quenching as the detection tool, the largest fluorescence quenching efficiency (F0/F - 1) of SiO2@FITC-APTS@MIPs is close to 2.5 when the concentration of the LC is 1.0 μM L(-1). In addition, a linear relationship (F0/F - 1= 0.0162C + 0.0272) could be obtained covering a wide concentration range of 0-60 nM L(-1) with a correlation coefficient of 0.9968 described by the Stern-Volmer equation. Moreover, the limit of detection (LOD) of the SiO2@FITC-APTS@MIPs was 9.17 nM L(-1). The experiment results of practical detection revealed that the SiO2@FITC-APTS@MIPs as an attractive recognition element was satisfactory for the determination of LC in Chinese spirits. Therefore, this study demonstrated the potential of SiO2@FITC-APTS@MIPs for the recognition and detection of LC in food.

Branch length similarity entropy-based descriptors for shape representation

NASA Astrophysics Data System (ADS)

Kwon, Ohsung; Lee, Sang-Hee

2017-11-01

In previous studies, we showed that the branch length similarity (BLS) entropy profile could be successfully used for the shape recognition such as battle tanks, facial expressions, and butterflies. In the present study, we proposed new descriptors, roundness, symmetry, and surface roughness, for the recognition, which are more accurate and fast in the computation than the previous descriptors. The roundness represents how closely a shape resembles to a circle, the symmetry characterizes how much one shape is similar with another when the shape is moved in flip, and the surface roughness quantifies the degree of vertical deviations of a shape boundary. To evaluate the performance of the descriptors, we used the database of leaf images with 12 species. Each species consisted of 10 - 20 leaf images and the total number of images were 160. The evaluation showed that the new descriptors successfully discriminated the leaf species. We believe that the descriptors can be a useful tool in the field of pattern recognition.

Unsaturated fatty acyl recognition by Frizzled receptors mediates dimerization upon Wnt ligand binding

PubMed Central

Nile, Aaron H.; Mukund, Susmith; Stanger, Karen; Wang, Weiru; Hannoush, Rami N.

2017-01-01

Frizzled (FZD) receptors mediate Wnt signaling in diverse processes ranging from bone growth to stem cell activity. Moreover, high FZD receptor expression at the cell surface contributes to overactive Wnt signaling in subsets of pancreatic, ovarian, gastric, and colorectal tumors. Despite the progress in biochemical understanding of Wnt–FZD receptor interactions, the molecular basis for recognition of Wnt cis-unsaturated fatty acyl groups by the cysteine-rich domain (CRD) of FZD receptors remains elusive. Here, we determined a crystal structure of human FZD7 CRD unexpectedly bound to a 24-carbon fatty acid. We also report a crystal structure of human FZD5 CRD bound to C16:1 cis-Δ9 unsaturated fatty acid. Both structures reveal a dimeric arrangement of the CRD. The lipid-binding groove exhibits flexibility and spans both monomers, adopting a U-shaped geometry that accommodates the fatty acid. Re-evaluation of the published mouse FZD8 CRD structure reveals that it also shares the same architecture as FZD5 and FZD7 CRDs. Our results define a common molecular mechanism for recognition of the cis-unsaturated fatty acyl group, a necessary posttranslational modification of Wnts, by multiple FZD receptors. The fatty acid bridges two CRD monomers, implying that Wnt binding mediates FZD receptor dimerization. Our data uncover possibilities for the arrangement of Wnt–FZD CRD complexes and shed structural insights that could aide in the identification of pharmacological strategies to modulate FZD receptor function. PMID:28377511

Molecular tips for scanning tunneling microscopy: intermolecular electron tunneling for single-molecule recognition and electronics.

PubMed

Nishino, Tomoaki

2014-01-01

This paper reviews the development of molecular tips for scanning tunneling microscopy (STM). Molecular tips offer many advantages: first is their ability to perform chemically selective imaging because of chemical interactions between the sample and the molecular tip, thus improving a major drawback of conventional STM. Rational design of the molecular tip allows sophisticated chemical recognition; e.g., chiral recognition and selective visualization of atomic defects in carbon nanotubes. Another advantage is that they provide a unique method to quantify electron transfer between single molecules. Understanding such electron transfer is mandatory for the realization of molecular electronics.

Human action recognition based on point context tensor shape descriptor

NASA Astrophysics Data System (ADS)

Li, Jianjun; Mao, Xia; Chen, Lijiang; Wang, Lan

2017-07-01

Motion trajectory recognition is one of the most important means to determine the identity of a moving object. A compact and discriminative feature representation method can improve the trajectory recognition accuracy. This paper presents an efficient framework for action recognition using a three-dimensional skeleton kinematic joint model. First, we put forward a rotation-scale-translation-invariant shape descriptor based on point context (PC) and the normal vector of hypersurface to jointly characterize local motion and shape information. Meanwhile, an algorithm for extracting the key trajectory based on the confidence coefficient is proposed to reduce the randomness and computational complexity. Second, to decrease the eigenvalue decomposition time complexity, a tensor shape descriptor (TSD) based on PC that can globally capture the spatial layout and temporal order to preserve the spatial information of each frame is proposed. Then, a multilinear projection process is achieved by tensor dynamic time warping to map the TSD to a low-dimensional tensor subspace of the same size. Experimental results show that the proposed shape descriptor is effective and feasible, and the proposed approach obtains considerable performance improvement over the state-of-the-art approaches with respect to accuracy on a public action dataset.

Automatic casting surface defect recognition and classification

NASA Astrophysics Data System (ADS)

Wong, Boon K.; Elliot, M. P.; Rapley, C. W.

1995-03-01

High integrity castings require surfaces free from defects to reduce, if not eliminate, vulnerability to component failure from such as physical or thermal fatigue or corrosion attack. Previous studies have shown that defects on casting surfaces can be optically enhanced from the surrounding randomly textured surface by liquid penetrants, magnetic particle and other methods. However, very little has been reported on recognition and classification of the defects. The basic problem is one of shape recognition and classification, where the shape can vary in size and orientation as well as in actual shape generally within an envelope that classifies it as a particular defect. The initial work done towards this has focused on recognizing and classifying standard shapes such as the circle, square, rectangle and triangle. Various approaches were tried and this led eventually to a series of fuzzy logic based algorithms from which very good results were obtained. From this work fuzzy logic memberships were generated for the detection of defects found on casting surfaces. Simulated model shapes of such as the quench crack, mechanical crack and hole have been used to test the generated algorithm and the results for recognition and classification are very encouraging.

Face shape and face identity processing in behavioral variant fronto-temporal dementia: A specific deficit for familiarity and name recognition of famous faces.

PubMed

De Winter, François-Laurent; Timmers, Dorien; de Gelder, Beatrice; Van Orshoven, Marc; Vieren, Marleen; Bouckaert, Miriam; Cypers, Gert; Caekebeke, Jo; Van de Vliet, Laura; Goffin, Karolien; Van Laere, Koen; Sunaert, Stefan; Vandenberghe, Rik; Vandenbulcke, Mathieu; Van den Stock, Jan

2016-01-01

Deficits in face processing have been described in the behavioral variant of fronto-temporal dementia (bvFTD), primarily regarding the recognition of facial expressions. Less is known about face shape and face identity processing. Here we used a hierarchical strategy targeting face shape and face identity recognition in bvFTD and matched healthy controls. Participants performed 3 psychophysical experiments targeting face shape detection (Experiment 1), unfamiliar face identity matching (Experiment 2), familiarity categorization and famous face-name matching (Experiment 3). The results revealed group differences only in Experiment 3, with a deficit in the bvFTD group for both familiarity categorization and famous face-name matching. Voxel-based morphometry regression analyses in the bvFTD group revealed an association between grey matter volume of the left ventral anterior temporal lobe and familiarity recognition, while face-name matching correlated with grey matter volume of the bilateral ventral anterior temporal lobes. Subsequently, we quantified familiarity-specific and name-specific recognition deficits as the sum of the celebrities of which respectively only the name or only the familiarity was accurately recognized. Both indices were associated with grey matter volume of the bilateral anterior temporal cortices. These findings extent previous results by documenting the involvement of the left anterior temporal lobe (ATL) in familiarity detection and the right ATL in name recognition deficits in fronto-temporal lobar degeneration.

Mechanism of molecular recognition on molecular imprinted monolith by capillary electrochromatography.

PubMed

Liu, Zhao-Sheng; Xu, Yan-Li; Yan, Chao; Gao, Ru-Yu

2005-09-16

The recognition mechanism of molecularly imprinted polymer (MIP) in capillary electrochromatography (CEC) is complicated since it possesses a hybrid process, which comprises the features of chromatographic retention, electrophoretic migration and molecular imprinting. For an understanding of the molecular recognition of MIP in CEC, a monolithic MIP in a capillary with 1,1'-binaphthyl-2,2'-diamine (BNA) imprinting was prepared by in situ copolymerization of imprinted molecule, methacrylic acid and ethylene glycol dimethacrylate in porogenic solvent, a mixture of toluene-isooctane. Strong recognition ability and high column performance (theory plates was 43,000 plates/m) of BNA were achieved on this monolithic MIP in CEC mode. In addition, BNA and its structural analogue, 1,1'-bi-2, 2'-naphthol, differing in functional groups, were used as model compounds to study imprinting effect on the resultant BNA-imprinted monolithic column, a reference column without imprinting of BNA and a open capillary. The effects of organic modifier concentration, pH value of buffer, salt concentration of buffer and column temperature on the retention and recognition of two compounds were investigated. The results showed that the molecular recognition on MIP monolith in CEC mode mainly derived from imprinting cavities on BNA-imprinted polymer other than chromatographic retention and electrophoretic migration.

Deconstructing a Species-Complex: Geometric Morphometric and Molecular Analyses Define Species in the Western Rattlesnake (Crotalus viridis)

PubMed Central

Davis, Mark A.; Douglas, Marlis R.; Collyer, Michael L.; Douglas, Michael E.

2016-01-01

Morphological data are a conduit for the recognition and description of species, and their acquisition has recently been broadened by geometric morphometric (GM) approaches that co-join the collection of digital data with exploratory ‘big data’ analytics. We employed this approach to dissect the Western Rattlesnake (Crotalus viridis) species-complex in North America, currently partitioned by mitochondrial (mt)DNA analyses into eastern and western lineages (two and seven subspecies, respectively). The GM data (i.e., 33 dorsal and 50 lateral head landmarks) were gleaned from 2,824 individuals located in 10 museum collections. We also downloaded and concatenated sequences for six mtDNA genes from the NCBI GenBank database. GM analyses revealed significant head shape differences attributable to size and subspecies-designation (but not their interactions). Pairwise shape distances among subspecies were significantly greater than those derived from ancestral character states via squared-change parsimony, with the greatest differences separating those most closely related. This, in turn, suggests the potential for historic character displacement as a diversifying force in the complex. All subspecies, save one, were significantly differentiated in a Bayesian discriminant function analysis (DFA), regardless of whether our priors were uniform or informative (i.e., mtDNA data). Finally, shape differences among sister-clades were significantly greater than expected by chance alone under a Brownian model of evolution, promoting the hypothesis that selection rather than drift was the driving force in the evolution of the complex. Lastly, we combine head shape and mtDNA data so as to derived an integrative taxonomy that produced robust boundaries for six OTUs (operational taxonomic units) of the C. viridis complex. We suggest these boundaries are concomitant with species-status and subsequently provide a relevant nomenclature for its recognition and representation. PMID:26816132

Ring-through-ring molecular shuttling in a saturated [3]rotaxane

NASA Astrophysics Data System (ADS)

Zhu, Kelong; Baggi, Giorgio; Loeb, Stephen J.

2018-06-01

Mechanically interlocked molecules such as rotaxanes and catenanes comprise two or more components whose motion relative to each other can be controlled. A [2]rotaxane molecular shuttle, for example, consists of an axle bearing two recognition sites and a single macrocyclic wheel that can undergo a to-and-fro motion along the axle—shuttling between the recognition sites. The ability of mechanically interlocked molecules to undergo this type of large-amplitude change is the core mechanism behind almost every interlocked molecular switch or machine, including sophisticated mechanical systems such as a molecular elevator and a peptide synthesizer. Here, as a way to expand the scope of dynamics possible at the molecular level, we have developed a molecular shuttling mechanism involving the exchange of rings between two recognition sites in a saturated [3]rotaxane (one with no empty recognition sites). This was accomplished by passing a smaller ring through a larger one, thus achieving ring-through-ring molecular shuttling.

Recognition of Similar Shaped Handwritten Marathi Characters Using Artificial Neural Network

NASA Astrophysics Data System (ADS)

Jane, Archana P.; Pund, Mukesh A.

2012-03-01

The growing need have handwritten Marathi character recognition in Indian offices such as passport, railways etc has made it vital area of a research. Similar shape characters are more prone to misclassification. In this paper a novel method is provided to recognize handwritten Marathi characters based on their features extraction and adaptive smoothing technique. Feature selections methods avoid unnecessary patterns in an image whereas adaptive smoothing technique form smooth shape of charecters.Combination of both these approaches leads to the better results. Previous study shows that, no one technique achieves 100% accuracy in handwritten character recognition area. This approach of combining both adaptive smoothing & feature extraction gives better results (approximately 75-100) and expected outcomes.

Multiscale characterization and analysis of shapes

DOEpatents

Prasad, Lakshman; Rao, Ramana

2002-01-01

An adaptive multiscale method approximates shapes with continuous or uniformly and densely sampled contours, with the purpose of sparsely and nonuniformly discretizing the boundaries of shapes at any prescribed resolution, while at the same time retaining the salient shape features at that resolution. In another aspect, a fundamental geometric filtering scheme using the Constrained Delaunay Triangulation (CDT) of polygonized shapes creates an efficient parsing of shapes into components that have semantic significance dependent only on the shapes' structure and not on their representations per se. A shape skeletonization process generalizes to sparsely discretized shapes, with the additional benefit of prunability to filter out irrelevant and morphologically insignificant features. The skeletal representation of characters of varying thickness and the elimination of insignificant and noisy spurs and branches from the skeleton greatly increases the robustness, reliability and recognition rates of character recognition algorithms.

Recognizing familiar objects by hand and foot: Haptic shape perception generalizes to inputs from unusual locations and untrained body parts.

PubMed

Lawson, Rebecca

2014-02-01

The limits of generalization of our 3-D shape recognition system to identifying objects by touch was investigated by testing exploration at unusual locations and using untrained effectors. In Experiments 1 and 2, people found identification by hand of real objects, plastic 3-D models of objects, and raised line drawings placed in front of themselves no easier than when exploration was behind their back. Experiment 3 compared one-handed, two-handed, one-footed, and two-footed haptic object recognition of familiar objects. Recognition by foot was slower (7 vs. 13 s) and much less accurate (9 % vs. 47 % errors) than recognition by either one or both hands. Nevertheless, item difficulty was similar across hand and foot exploration, and there was a strong correlation between an individual's hand and foot performance. Furthermore, foot recognition was better with the largest 20 of the 80 items (32 % errors), suggesting that physical limitations hampered exploration by foot. Thus, object recognition by hand generalized efficiently across the spatial location of stimuli, while object recognition by foot seemed surprisingly good given that no prior training was provided. Active touch (haptics) thus efficiently extracts 3-D shape information and accesses stored representations of familiar objects from novel modes of input.

Vibrotactile feedback for conveying object shape information as perceived by artificial sensing of robotic arm.

PubMed

Khasnobish, Anwesha; Pal, Monalisa; Sardar, Dwaipayan; Tibarewala, D N; Konar, Amit

2016-08-01

This work is a preliminary study towards developing an alternative communication channel for conveying shape information to aid in recognition of items when tactile perception is hindered. Tactile data, acquired during object exploration by sensor fitted robot arm, are processed to recognize four basic geometric shapes. Patterns representing each shape, classified from tactile data, are generated using micro-controller-driven vibration motors which vibrotactually stimulate users to convey the particular shape information. These motors are attached on the subject's arm and their psychological (verbal) responses are recorded to assess the competence of the system to convey shape information to the user in form of vibrotactile stimulations. Object shapes are classified from tactile data with an average accuracy of 95.21 %. Three successive sessions of shape recognition from vibrotactile pattern depicted learning of the stimulus from subjects' psychological response which increased from 75 to 95 %. This observation substantiates the learning of vibrotactile stimulation in user over the sessions which in turn increase the system efficacy. The tactile sensing module and vibrotactile pattern generating module are integrated to complete the system whose operation is analysed in real-time. Thus, the work demonstrates a successful implementation of the complete schema of artificial tactile sensing system for object-shape recognition through vibrotactile stimulations.

Eye movements during object recognition in visual agnosia.

PubMed

Charles Leek, E; Patterson, Candy; Paul, Matthew A; Rafal, Robert; Cristino, Filipe

2012-07-01

This paper reports the first ever detailed study about eye movement patterns during single object recognition in visual agnosia. Eye movements were recorded in a patient with an integrative agnosic deficit during two recognition tasks: common object naming and novel object recognition memory. The patient showed normal directional biases in saccades and fixation dwell times in both tasks and was as likely as controls to fixate within object bounding contour regardless of recognition accuracy. In contrast, following initial saccades of similar amplitude to controls, the patient showed a bias for short saccades. In object naming, but not in recognition memory, the similarity of the spatial distributions of patient and control fixations was modulated by recognition accuracy. The study provides new evidence about how eye movements can be used to elucidate the functional impairments underlying object recognition deficits. We argue that the results reflect a breakdown in normal functional processes involved in the integration of shape information across object structure during the visual perception of shape. Copyright © 2012 Elsevier Ltd. All rights reserved.

Recognition-driven chemical labeling of endogenous proteins in multi-molecular crowding in live cells.

PubMed

Amaike, Kazuma; Tamura, Tomonori; Hamachi, Itaru

2017-11-14

Endogenous protein labeling is one of the most invaluable methods for studying the bona fide functions of proteins in live cells. However, multi-molecular crowding conditions, such as those that occur in live cells, hamper the highly selective chemical labeling of a protein of interest (POI). We herein describe how the efficient coupling of molecular recognition with a chemical reaction is crucial for selective protein labeling. Recognition-driven protein labeling is carried out by a synthetic labeling reagent containing a protein (recognition) ligand, a reporter tag, and a reactive moiety. The molecular recognition of a POI can be used to greatly enhance the reaction kinetics and protein selectivity, even under live cell conditions. In this review, we also briefly discuss how such selective chemical labeling of an endogenous protein can have a variety of applications at the interface of chemistry and biology.

Effects of Anticaricaturing vs. Caricaturing and Their Neural Correlates Elucidate a Role of Shape for Face Learning

ERIC Educational Resources Information Center

Schulz, Claudia; Kaufmann, Jurgen M.; Walther, Lydia; Schweinberger, Stefan R.

2012-01-01

To assess the role of shape information for unfamiliar face learning, we investigated effects of photorealistic spatial anticaricaturing and caricaturing on later face recognition. We assessed behavioural performance and event-related brain potential (ERP) correlates of recognition, using different images of anticaricatures, veridical faces, or…

Fully automatic segmentation of the femur from 3D-CT images using primitive shape recognition and statistical shape models.

PubMed

Ben Younes, Lassad; Nakajima, Yoshikazu; Saito, Toki

2014-03-01

Femur segmentation is well established and widely used in computer-assisted orthopedic surgery. However, most of the robust segmentation methods such as statistical shape models (SSM) require human intervention to provide an initial position for the SSM. In this paper, we propose to overcome this problem and provide a fully automatic femur segmentation method for CT images based on primitive shape recognition and SSM. Femur segmentation in CT scans was performed using primitive shape recognition based on a robust algorithm such as the Hough transform and RANdom SAmple Consensus. The proposed method is divided into 3 steps: (1) detection of the femoral head as sphere and the femoral shaft as cylinder in the SSM and the CT images, (2) rigid registration between primitives of SSM and CT image to initialize the SSM into the CT image, and (3) fitting of the SSM to the CT image edge using an affine transformation followed by a nonlinear fitting. The automated method provided good results even with a high number of outliers. The difference of segmentation error between the proposed automatic initialization method and a manual initialization method is less than 1 mm. The proposed method detects primitive shape position to initialize the SSM into the target image. Based on primitive shapes, this method overcomes the problem of inter-patient variability. Moreover, the results demonstrate that our method of primitive shape recognition can be used for 3D SSM initialization to achieve fully automatic segmentation of the femur.

The effect of colour congruency on shape discriminations of novel objects.

PubMed

Nicholson, Karen G; Humphrey, G Keith

2004-01-01

Although visual object recognition is primarily shape driven, colour assists the recognition of some objects. It is unclear, however, just how colour information is coded with respect to shape in long-term memory and how the availability of colour in the visual image facilitates object recognition. We examined the role of colour in the recognition of novel, 3-D objects by manipulating the congruency of object colour across the study and test phases, using an old/new shape-identification task. In experiment 1, we found that participants were faster at correctly identifying old objects on the basis of shape information when these objects were presented in their original colour, rather than in a different colour. In experiments 2 and 3, we found that participants were faster at correctly identifying old objects on the basis of shape information when these objects were presented with their original part-colour conjunctions, rather than in different or in reversed part-colour conjunctions. In experiment 4, we found that participants were quite poor at the verbal recall of part-colour conjunctions for correctly identified old objects, presented as grey-scale images at test. In experiment 5, we found that participants were significantly slower at correctly identifying old objects when object colour was incongruent across study and test, than when background colour was incongruent across study and test. The results of these experiments suggest that both shape and colour information are stored as part of the long-term representation of these novel objects. Results are discussed in terms of how colour might be coded with respect to shape in stored object representations.

Comparing object recognition from binary and bipolar edge images for visual prostheses.

PubMed

Jung, Jae-Hyun; Pu, Tian; Peli, Eli

2016-11-01

Visual prostheses require an effective representation method due to the limited display condition which has only 2 or 3 levels of grayscale in low resolution. Edges derived from abrupt luminance changes in images carry essential information for object recognition. Typical binary (black and white) edge images have been used to represent features to convey essential information. However, in scenes with a complex cluttered background, the recognition rate of the binary edge images by human observers is limited and additional information is required. The polarity of edges and cusps (black or white features on a gray background) carries important additional information; the polarity may provide shape from shading information missing in the binary edge image. This depth information may be restored by using bipolar edges. We compared object recognition rates from 16 binary edge images and bipolar edge images by 26 subjects to determine the possible impact of bipolar filtering in visual prostheses with 3 or more levels of grayscale. Recognition rates were higher with bipolar edge images and the improvement was significant in scenes with complex backgrounds. The results also suggest that erroneous shape from shading interpretation of bipolar edges resulting from pigment rather than boundaries of shape may confound the recognition.

Wireless sensor for detecting explosive material

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

Lamberti, Vincent E; Howell, Jr., Layton N; Mee, David K

Disclosed is a sensor for detecting explosive devices. The sensor includes a ferromagnetic metal and a molecular recognition reagent coupled to the ferromagnetic metal. The molecular recognition reagent is operable to expand upon absorption of vapor from an explosive material such that the molecular recognition reagent changes a tensile stress upon the ferromagnetic metal. The explosive device is detected based on changes in the magnetic switching characteristics of the ferromagnetic metal caused by the tensile stress.

Molecular Recognition: Detection of Colorless Compounds Based on Color Change

ERIC Educational Resources Information Center

Khalafi, Lida; Kashani, Samira; Karimi, Javad

2016-01-01

A laboratory experiment is described in which students measure the amount of cetirizine in allergy-treatment tablets based on molecular recognition. The basis of recognition is competition of cetirizine with phenolphthalein to form an inclusion complex with ß-cyclodextrin. Phenolphthalein is pinkish under basic condition, whereas it's complex form…

Is visual image segmentation a bottom-up or an interactive process?

PubMed

Vecera, S P; Farah, M J

1997-11-01

Visual image segmentation is the process by which the visual system groups features that are part of a single shape. Is image segmentation a bottom-up or an interactive process? In Experiments 1 and 2, we presented subjects with two overlapping shapes and asked them to determine whether two probed locations were on the same shape or on different shapes. The availability of top-down support was manipulated by presenting either upright or rotated letters. Subjects were fastest to respond when the shapes corresponded to familiar shapes--the upright letters. In Experiment 3, we used a variant of this segmentation task to rule out the possibility that subjects performed same/different judgments after segmentation and recognition of both letters. Finally, in Experiment 4, we ruled out the possibility that the advantage for upright letters was merely due to faster recognition of upright letters relative to rotated letters. The results suggested that the previous effects were not due to faster recognition of upright letters; stimulus familiarity influenced segmentation per se. The results are discussed in terms of an interactive model of visual image segmentation.

Binding of intrinsic and extrinsic features in working memory.

PubMed

Ecker, Ullrich K H; Maybery, Murray; Zimmer, Hubert D

2013-02-01

There is ongoing debate concerning the mechanisms of feature binding in working memory. In particular, there is controversy regarding the extent to which these binding processes are automatic. The present article demonstrates that binding mechanisms differ depending on whether the to-be-integrated features are perceived as forming a coherent object. We presented a series of experiments that investigated the binding of color and shape, whereby color was either an intrinsic feature of the shape or an extrinsic feature of the shape's background. Results show that intrinsic color affected shape recognition, even when it was incidentally studied and irrelevant for the recognition task. In contrast, extrinsic color did not affect shape recognition, even when the association of color and shape was encoded and retrievable on demand. This strongly suggests that binding of intrinsic intra-item information but not extrinsic contextual information is obligatory in visual working memory. We highlight links to perception as well as implicit and explicit long-term memory, which suggest that the intrinsic-extrinsic dimension is a principle relevant to multiple domains of human cognition. 2013 APA, all rights reserved

Molecular imprinted polymer functionalized carbon nanotube sensors for detection of saccharides

NASA Astrophysics Data System (ADS)

Badhulika, Sushmee; Mulchandani, Ashok

2015-08-01

In this work, we report the synthesis and fabrication of an enzyme-free sugar sensor based on molecularly imprinted polymer (MIP) on the surface of single walled carbon nanotubes (SWNTs). Electropolymerization of 3-aminophenylboronic acid (3-APBA) in the presence of 10 M d-fructose and fluoride at neutral pH conditions resulted in the formation of a self-doped, molecularly imprinted conducting polymer (MICP) via the formation of a stable anionic boronic ester complex between poly(aniline boronic acid) and d-fructose. Template removal generated binding sites on the polymer matrix that were complementary to d-fructose both in structure, i.e., shape, size, and positioning of functional groups, thus enabling sensing of d-fructose with enhanced affinity and specificity over non-MIP based sensors. Using carbon nanotubes along with MICPs helped to develop an efficient electrochemical sensor by enhancing analyte recognition and signal generation. These sensors could be regenerated and used multiple times unlike conventional affinity based biosensors which suffer from physical and chemical stability.

Molecular Imprinting Technology in Quartz Crystal Microbalance (QCM) Sensors.

PubMed

Emir Diltemiz, Sibel; Keçili, Rüstem; Ersöz, Arzu; Say, Rıdvan

2017-02-24

Molecularly imprinted polymers (MIPs) as artificial antibodies have received considerable scientific attention in the past years in the field of (bio)sensors since they have unique features that distinguish them from natural antibodies such as robustness, multiple binding sites, low cost, facile preparation and high stability under extreme operation conditions (higher pH and temperature values, etc.). On the other hand, the Quartz Crystal Microbalance (QCM) is an analytical tool based on the measurement of small mass changes on the sensor surface. QCM sensors are practical and convenient monitoring tools because of their specificity, sensitivity, high accuracy, stability and reproducibility. QCM devices are highly suitable for converting the recognition process achieved using MIP-based memories into a sensor signal. Therefore, the combination of a QCM and MIPs as synthetic receptors enhances the sensitivity through MIP process-based multiplexed binding sites using size, 3D-shape and chemical function having molecular memories of the prepared sensor system toward the target compound to be detected. This review aims to highlight and summarize the recent progress and studies in the field of (bio)sensor systems based on QCMs combined with molecular imprinting technology.

Corona Phase Molecular Recognition (CoPhMoRe) to Enable New Nanosensor Interfaces

NASA Astrophysics Data System (ADS)

Strano, Michael

2015-03-01

Our lab at MIT has been interested in how the 1D and 2D electronic structures of carbon nanotubes and graphene respectively can be utilized to advance new concepts in molecular detection. We introduce CoPhMoRe or corona phase molecular recognition as a method of discovering synthetic antibodies, or nanotube-templated recognition sites from a heteropolymer library. We show that certain synthetic heteropolymers, once constrained onto a single-walled carbon nanotube by chemical adsorption, also form a new corona phase that exhibits highly selective recognition for specific molecules. To prove the generality of this phenomenon, we report three examples of heteropolymers-nanotube recognition complexes for riboflavin, L-thyroxine and estradiol. The platform opens new opportunities to create synthetic recognition sites for molecular detection. We have also extended this molecular recognition technique to neurotransmitters, producing the first fluorescent sensor for dopamine. Another area of advancement in biosensor development is the use of near infrared fluorescent carbon nanotube sensors for in-vivo detection. Here, we show that PEG-ligated d(AAAT)7 DNA wrapped SWNT are selective for nitric oxide, a vasodilator of blood vessels, and can be tail vein injected into mice and localized within the viable mouse liver. We use an SJL mouse model to study liver inflammation in vivo using the spatially and spectrally resolved nIR signature of the localized SWNT sensors.

POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics

PubMed Central

2015-01-01

Analysis of macromolecular/small-molecule binding pockets can provide important insights into molecular recognition and receptor dynamics. Since its release in 2011, the POVME (POcket Volume MEasurer) algorithm has been widely adopted as a simple-to-use tool for measuring and characterizing pocket volumes and shapes. We here present POVME 2.0, which is an order of magnitude faster, has improved accuracy, includes a graphical user interface, and can produce volumetric density maps for improved pocket analysis. To demonstrate the utility of the algorithm, we use it to analyze the binding pocket of RNA editing ligase 1 from the unicellular parasite Trypanosoma brucei, the etiological agent of African sleeping sickness. The POVME analysis characterizes the full dynamics of a potentially druggable transient binding pocket and so may guide future antitrypanosomal drug-discovery efforts. We are hopeful that this new version will be a useful tool for the computational- and medicinal-chemist community. PMID:25400521

A New Representative of Star-Shaped Fungi: Astraeus sirindhorniae sp. nov. from Thailand

PubMed Central

Phosri, Cherdchai; Watling, Roy; Suwannasai, Nuttika; Wilson, Andrew; Martín, María P.

2014-01-01

Phu Khieo Wildlife Sanctuary (PKWS) is a major hotspot of biological diversity in Thailand but its fungal diversity has not been thouroughly explored. A two-year macrofungal study of this remote locality has resulted in the recognition of a new species of a star-shaped gasteroid fungus in the genus Astraeus. This fungus has been identified based on a morphological approach and the molecular study of five loci (LSU nrDNA, 5.8S nrDNA, RPB1, RPB2 and EF1-a). Multigene phylogenetic analysis of this new species places it basal relative to other Astraeus, providing additional evidence for the SE Asian orgin of the genus. The fungus is named in honour of Her Majesty Princess Sirindhorn on the occasion the 84th birthday of her father, who have both been supportive of natural heritage studies in Thailand. PMID:24806455

A new representative of star-shaped fungi: Astraeus sirindhorniae sp. nov. from Thailand.

PubMed

Phosri, Cherdchai; Watling, Roy; Suwannasai, Nuttika; Wilson, Andrew; Martín, María P

2014-01-01

Phu Khieo Wildlife Sanctuary (PKWS) is a major hotspot of biological diversity in Thailand but its fungal diversity has not been thouroughly explored. A two-year macrofungal study of this remote locality has resulted in the recognition of a new species of a star-shaped gasteroid fungus in the genus Astraeus. This fungus has been identified based on a morphological approach and the molecular study of five loci (LSU nrDNA, 5.8S nrDNA, RPB1, RPB2 and EF1-a). Multigene phylogenetic analysis of this new species places it basal relative to other Astraeus, providing additional evidence for the SE Asian origin of the genus. The fungus is named in honour of Her Majesty Princess Sirindhorn on the occasion the 84th birthday of her father, who have both been supportive of natural heritage studies in Thailand.

Learning through hand- or typewriting influences visual recognition of new graphic shapes: behavioral and functional imaging evidence.

PubMed

Longcamp, Marieke; Boucard, Céline; Gilhodes, Jean-Claude; Anton, Jean-Luc; Roth, Muriel; Nazarian, Bruno; Velay, Jean-Luc

2008-05-01

Fast and accurate visual recognition of single characters is crucial for efficient reading. We explored the possible contribution of writing memory to character recognition processes. We evaluated the ability of adults to discriminate new characters from their mirror images after being taught how to produce the characters either by traditional pen-and-paper writing or with a computer keyboard. After training, we found stronger and longer lasting (several weeks) facilitation in recognizing the orientation of characters that had been written by hand compared to those typed. Functional magnetic resonance imaging recordings indicated that the response mode during learning is associated with distinct pathways during recognition of graphic shapes. Greater activity related to handwriting learning and normal letter identification was observed in several brain regions known to be involved in the execution, imagery, and observation of actions, in particular, the left Broca's area and bilateral inferior parietal lobules. Taken together, these results provide strong arguments in favor of the view that the specific movements memorized when learning how to write participate in the visual recognition of graphic shapes and letters.

Wireless sensor

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

Lamberti, Vincent E.; Howell, JR, Layton N.; Mee, David K.

Disclosed is a sensor for detecting a target material. The sensor includes a ferromagnetic metal and a molecular recognition reagent coupled to the ferromagnetic metal. The molecular recognition reagent is operable to expand upon exposure to vapor or liquid from the target material such that the molecular recognition reagent changes a tensile stress upon the ferromagnetic metal. The target material is detected based on changes in the magnetic switching characteristics of the ferromagnetic metal caused by the changes in the tensile stress.

Learning Weight Uncertainty with Stochastic Gradient MCMC for Shape Classification

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

Li, Chunyuan; Stevens, Andrew J.; Chen, Changyou

2016-08-10

Learning the representation of shape cues in 2D & 3D objects for recognition is a fundamental task in computer vision. Deep neural networks (DNNs) have shown promising performance on this task. Due to the large variability of shapes, accurate recognition relies on good estimates of model uncertainty, ignored in traditional training of DNNs, typically learned via stochastic optimization. This paper leverages recent advances in stochastic gradient Markov Chain Monte Carlo (SG-MCMC) to learn weight uncertainty in DNNs. It yields principled Bayesian interpretations for the commonly used Dropout/DropConnect techniques and incorporates them into the SG-MCMC framework. Extensive experiments on 2D &more » 3D shape datasets and various DNN models demonstrate the superiority of the proposed approach over stochastic optimization. Our approach yields higher recognition accuracy when used in conjunction with Dropout and Batch-Normalization.« less

Hapten-antibody recognition studies in competitive immunoassay of α-zearalanol analogs by computational chemistry and Pearson Correlation analysis.

PubMed

Wang, Zhanhui; Luo, Pengjie; Cheng, Linli; Zhang, Suxia; Shen, Jianzhong

2011-01-01

The molecular recognition of hapten-antibody is a fundamental event in competitive immunoassay, which guarantees the sensitivity and specificity of immunoassay for the detection of haptens. The aim of this study is to investigate the correlation between binding ability of one monoclonal antibody, 1H9B4, recognizing and the molecular aspects of α-zearalanol analogs. The mouse-derived monoclonal antibody was produced by using α-zearalanol conjugated to bovine serum albumin as an immunogen. The antibody recognition abilities, expressed as IC(50) values, were determined by a competitive ELISA. All of the hapten molecules were optimized by Density Function Theory (DFT) at B3LYP/ 6-31G* level and the conformation and electrostatic molecular isosurface were employed to explain the molecular recognition between α-zearalanol analogs and antibody 1H9B4. Pearson Correlation analysis between molecular descriptors and IC(50) values was qualitatively undertaken and the results showed that one molecular descriptor, surface of the hapten molecule, clearly demonstrated linear relationship with antibody recognition ability, where the relationship coefficient was 0.88 and the correlation was significant at p < 0.05 level. The study shows that computational chemistry and Pearson Correlation analysis can be used as tool to help the immunochemistries better understand the processing of antibody recognition of hapten molecules in competitive immunoassay. Copyright © 2011 John Wiley & Sons, Ltd.

Intrinsic Bayesian Active Contours for Extraction of Object Boundaries in Images

PubMed Central

Srivastava, Anuj

2010-01-01

We present a framework for incorporating prior information about high-probability shapes in the process of contour extraction and object recognition in images. Here one studies shapes as elements of an infinite-dimensional, non-linear quotient space, and statistics of shapes are defined and computed intrinsically using differential geometry of this shape space. Prior models on shapes are constructed using probability distributions on tangent bundles of shape spaces. Similar to the past work on active contours, where curves are driven by vector fields based on image gradients and roughness penalties, we incorporate the prior shape knowledge in the form of vector fields on curves. Through experimental results, we demonstrate the use of prior shape models in the estimation of object boundaries, and their success in handling partial obscuration and missing data. Furthermore, we describe the use of this framework in shape-based object recognition or classification. PMID:21076692

Recognition and use of line drawings by children with severe intellectual disabilities: the effects of color and outline shape.

PubMed

Stephenson, Jennifer

2009-03-01

Communication symbols for students with severe intellectual disabilities often take the form of computer-generated line drawings. This study investigated the effects of the match between color and shape of line drawings and the objects they represented on drawing recognition and use. The match or non-match between color and shape of the objects and drawings did not have an effect on participants' ability to match drawings to objects, or to use drawings to make choices.

Global precedence effects account for individual differences in both face and object recognition performance.

PubMed

Gerlach, Christian; Starrfelt, Randi

2018-03-20

There has been an increase in studies adopting an individual difference approach to examine visual cognition and in particular in studies trying to relate face recognition performance with measures of holistic processing (the face composite effect and the part-whole effect). In the present study we examine whether global precedence effects, measured by means of non-face stimuli in Navon's paradigm, can also account for individual differences in face recognition and, if so, whether the effect is of similar magnitude for faces and objects. We find evidence that global precedence effects facilitate both face and object recognition, and to a similar extent. Our results suggest that both face and object recognition are characterized by a coarse-to-fine temporal dynamic, where global shape information is derived prior to local shape information, and that the efficiency of face and object recognition is related to the magnitude of the global precedence effect.

Mechanisms and evolution of plant resistance to aphids.

PubMed

Züst, Tobias; Agrawal, Anurag A

2016-01-06

Aphids are important herbivores of both wild and cultivated plants. Plants rely on unique mechanisms of recognition, signalling and defence to cope with the specialized mode of phloem feeding by aphids. Aspects of the molecular mechanisms underlying aphid-plant interactions are beginning to be understood. Recent advances include the identification of aphid salivary proteins involved in host plant manipulation, and plant receptors involved in aphid recognition. However, a complete picture of aphid-plant interactions requires consideration of the ecological outcome of these mechanisms in nature, and the evolutionary processes that shaped them. Here we identify general patterns of resistance, with a special focus on recognition, phytohormonal signalling, secondary metabolites and induction of plant resistance. We discuss how host specialization can enable aphids to co-opt both the phytohormonal responses and defensive compounds of plants for their own benefit at a local scale. In response, systemically induced resistance in plants is common and often involves targeted responses to specific aphid species or even genotypes. As co-evolutionary adaptation between plants and aphids is ongoing, the stealthy nature of aphid feeding makes both the mechanisms and outcomes of these interactions highly distinct from those of other herbivore-plant interactions.

Soluble Molecularly Imprinted Nanorods for Homogeneous Molecular Recognition

NASA Astrophysics Data System (ADS)

Liang, Rongning; Wang, Tiantian; Zhang, Huan; Yao, Ruiqing; Qin, Wei

2018-03-01

Nowadays, it is still difficult for molecularly imprinted polymer (MIPs) to achieve homogeneous recognition since they cannot be easily dissolved in organic or aqueous phase. To address this issue, soluble molecularly imprinted nanorods have been synthesized by using soluble polyaniline doped with a functionalized organic protonic acid as the polymer matrix. By employing 1-naphthoic acid as a model, the proposed imprinted nanorods exhibit an excellent solubility and good homogeneous recognition ability. The imprinting factor for the soluble imprinted nanoroads is 6.8. The equilibrium dissociation constant and the apparent maximum number of the proposed imprinted nanorods are 248.5 μM and 22.1 μmol/g, respectively. We believe that such imprinted nanorods may provide an appealing substitute for natural receptors in homogeneous recognition related fields.

New synthesis method for 4-MAPBA monomer and using for the recognition of IgM and mannose with MIP-based QCM sensors.

PubMed

Diltemiz, Sibel Emir; Hür, Deniz; Keçili, Rüstem; Ersöz, Arzu; Say, Rıdvan

2013-03-07

Quartz crystal microbalance (QCM) sensors coated with molecularly imprinted polymers (MIP) have been developed for the recognition of immunoglobulin M (IgM) and mannose. In this method, methacryloylamidophenylboronic acid (MAPBA) was used as a monomer and mannose was used as a template. For this purpose, initially, QCM electrodes were modified with 2-propene-1-thiol to form mannose-binding regions on the QCM sensor surface. In the second step, the methacryloylamidophenylboronic acid-mannose [MAPBA-mannose], pre-organized monomer system, was prepared using the MAPBA monomer. Then, a molecularly imprinted film was coated on to the QCM electrode surface under UV light using ethylene glycol dimethacrylate (EDMA), and azobisisobutyronitrile (AIBN) as a cross-linking agent and an initiator, respectively. The mannose can be simultaneously bound to MAPBA and fitted into the shape-selective cavities. The binding affinity of the mannose-imprinted sensors was investigated using the Langmuir isotherm. The mannose-imprinted QCM electrodes have shown homogeneous binding sites for mannose (K(a): 3.3 × 10(4) M(-1)) and heterogeneous binding sites for IgM (K(a1): 1.0 × 10(4) M(-1); K(a2): 3.3 × 10(3) M(-1)).

Analysis and Recognition of Curve Type as The Basis of Object Recognition in Image

NASA Astrophysics Data System (ADS)

Nugraha, Nurma; Madenda, Sarifuddin; Indarti, Dina; Dewi Agushinta, R.; Ernastuti

2016-06-01

An object in an image when analyzed further will show the characteristics that distinguish one object with another object in an image. Characteristics that are used in object recognition in an image can be a color, shape, pattern, texture and spatial information that can be used to represent objects in the digital image. The method has recently been developed for image feature extraction on objects that share characteristics curve analysis (simple curve) and use the search feature of chain code object. This study will develop an algorithm analysis and the recognition of the type of curve as the basis for object recognition in images, with proposing addition of complex curve characteristics with maximum four branches that will be used for the process of object recognition in images. Definition of complex curve is the curve that has a point of intersection. By using some of the image of the edge detection, the algorithm was able to do the analysis and recognition of complex curve shape well.

Automatic detection and recognition of traffic signs in stereo images based on features and probabilistic neural networks

NASA Astrophysics Data System (ADS)

Sheng, Yehua; Zhang, Ka; Ye, Chun; Liang, Cheng; Li, Jian

2008-04-01

Considering the problem of automatic traffic sign detection and recognition in stereo images captured under motion conditions, a new algorithm for traffic sign detection and recognition based on features and probabilistic neural networks (PNN) is proposed in this paper. Firstly, global statistical color features of left image are computed based on statistics theory. Then for red, yellow and blue traffic signs, left image is segmented to three binary images by self-adaptive color segmentation method. Secondly, gray-value projection and shape analysis are used to confirm traffic sign regions in left image. Then stereo image matching is used to locate the homonymy traffic signs in right image. Thirdly, self-adaptive image segmentation is used to extract binary inner core shapes of detected traffic signs. One-dimensional feature vectors of inner core shapes are computed by central projection transformation. Fourthly, these vectors are input to the trained probabilistic neural networks for traffic sign recognition. Lastly, recognition results in left image are compared with recognition results in right image. If results in stereo images are identical, these results are confirmed as final recognition results. The new algorithm is applied to 220 real images of natural scenes taken by the vehicle-borne mobile photogrammetry system in Nanjing at different time. Experimental results show a detection and recognition rate of over 92%. So the algorithm is not only simple, but also reliable and high-speed on real traffic sign detection and recognition. Furthermore, it can obtain geometrical information of traffic signs at the same time of recognizing their types.

A complex journey: transmission of microbial symbionts

PubMed Central

Bright, Monika; Bulgheresi, Silvia

2010-01-01

The perpetuation of symbioses through host generations relies on symbiont transmission. Horizontally transmitted symbionts are taken up from the environment anew by each host generation, and vertically transmitted symbionts are most often transferred through the female germ line. Mixed modes also exist. In this Review we describe the journey of symbionts from the initial contact to their final residence. We provide an overview of the molecular mechanisms that mediate symbiont attraction and accumulation, interpartner recognition and selection, as well as symbiont confrontation with the host immune system. We also discuss how the two main transmission modes shape the evolution of the symbiotic partners. PMID:20157340

Shape recognition of microbial cells by colloidal cell imprints

NASA Astrophysics Data System (ADS)

Borovička, Josef; Stoyanov, Simeon D.; Paunov, Vesselin N.

2013-08-01

We have engineered a class of colloids which can recognize the shape and size of targeted microbial cells and selectively bind to their surfaces. These imprinted colloid particles, which we called ``colloid antibodies'', were fabricated by partial fragmentation of silica shells obtained by templating the targeted microbial cells. We successfully demonstrated the shape and size recognition between such colloidal imprints and matching microbial cells. High percentage of binding events of colloidal imprints with the size matching target particles was achieved. We demonstrated selective binding of colloidal imprints to target microbial cells in a binary mixture of cells of different shapes and sizes, which also resulted in high binding selectivity. We explored the role of the electrostatic interactions between the target cells and their colloid imprints by pre-coating both of them with polyelectrolytes. Selective binding occurred predominantly in the case of opposite surface charges of the colloid cell imprint and the targeted cells. The mechanism of the recognition is based on the amplification of the surface adhesion in the case of shape and size match due to the increased contact area between the target cell and the colloidal imprint. We also tested the selective binding for colloid imprints of particles of fixed shape and varying sizes. The concept of cell recognition by colloid imprints could be used for development of colloid antibodies for shape-selective binding of microbes. Such colloid antibodies could be additionally functionalized with surface groups to enhance their binding efficiency to cells of specific shape and deliver a drug payload directly to their surface or allow them to be manipulated using external fields. They could benefit the pharmaceutical industry in developing selective antimicrobial therapies and formulations.

Effect of buffer at nanoscale molecular recognition interfaces - electrostatic binding of biological polyanions.

PubMed

Rodrigo, Ana C; Laurini, Erik; Vieira, Vânia M P; Pricl, Sabrina; Smith, David K

2017-10-19

We investigate the impact of an over-looked component on molecular recognition in water-buffer. The binding of a cationic dye to biological polyanion heparin is shown by isothermal calorimetry to depend on buffer (Tris-HCl > HEPES > PBS). The heparin binding of self-assembled multivalent (SAMul) cationic micelles is even more buffer dependent. Multivalent electrostatic molecular recognition is buffer dependent as a result of competitive interactions between the cationic binding interface and anions present in the buffer.

Piezoelectric sensors based on molecular imprinted polymers for detection of low molecular mass analytes.

PubMed

Uludağ, Yildiz; Piletsky, Sergey A; Turner, Anthony P F; Cooper, Matthew A

2007-11-01

Biomimetic recognition elements employed for the detection of analytes are commonly based on proteinaceous affibodies, immunoglobulins, single-chain and single-domain antibody fragments or aptamers. The alternative supra-molecular approach using a molecularly imprinted polymer now has proven utility in numerous applications ranging from liquid chromatography to bioassays. Despite inherent advantages compared with biochemical/biological recognition (which include robustness, storage endurance and lower costs) there are few contributions that describe quantitative analytical applications of molecularly imprinted polymers for relevant small molecular mass compounds in real-world samples. There is, however, significant literature describing the use of low-power, portable piezoelectric transducers to detect analytes in environmental monitoring and other application areas. Here we review the combination of molecularly imprinted polymers as recognition elements with piezoelectric biosensors for quantitative detection of small molecules. Analytes are classified by type and sample matrix presentation and various molecularly imprinted polymer synthetic fabrication strategies are also reviewed.

Plastic Antibodies: Molecular Recognition with Imprinted Polymers

ERIC Educational Resources Information Center

Rushton, Gregory T.; Furmanski, Brian; Shimizu, Ken D.

2005-01-01

Synthetic polymers are prepared and tested in a study for their molecular recognition properties of an adenine derivative, ethyl adenine-9-acetate (EA9A), within two laboratory periods. The procedure introduces undergraduate chemistry students to noncovalent molecular imprinting as well as the analytical techniques for assessing their recognition…

Comparing object recognition from binary and bipolar edge images for visual prostheses

PubMed Central

Jung, Jae-Hyun; Pu, Tian; Peli, Eli

2017-01-01

Visual prostheses require an effective representation method due to the limited display condition which has only 2 or 3 levels of grayscale in low resolution. Edges derived from abrupt luminance changes in images carry essential information for object recognition. Typical binary (black and white) edge images have been used to represent features to convey essential information. However, in scenes with a complex cluttered background, the recognition rate of the binary edge images by human observers is limited and additional information is required. The polarity of edges and cusps (black or white features on a gray background) carries important additional information; the polarity may provide shape from shading information missing in the binary edge image. This depth information may be restored by using bipolar edges. We compared object recognition rates from 16 binary edge images and bipolar edge images by 26 subjects to determine the possible impact of bipolar filtering in visual prostheses with 3 or more levels of grayscale. Recognition rates were higher with bipolar edge images and the improvement was significant in scenes with complex backgrounds. The results also suggest that erroneous shape from shading interpretation of bipolar edges resulting from pigment rather than boundaries of shape may confound the recognition. PMID:28458481

A Comparison of the Effects of Depth Rotation on Visual and Haptic Three-Dimensional Object Recognition

ERIC Educational Resources Information Center

Lawson, Rebecca

2009-01-01

A sequential matching task was used to compare how the difficulty of shape discrimination influences the achievement of object constancy for depth rotations across haptic and visual object recognition. Stimuli were nameable, 3-dimensional plastic models of familiar objects (e.g., bed, chair) and morphs midway between these endpoint shapes (e.g., a…

Imaging Metastasis Using an Integrin-Targeting Chain-Shaped Nanoparticle

PubMed Central

Peiris, Pubudu M.; Toy, Randall; Doolittle, Elizabeth; Pansky, Jenna; Abramowski, Aaron; Tam, Morgan; Vicente, Peter; Tran, Emily; Hayden, Elliott; Camann, Andrew; Mayer, Aaron; Erokwu, Bernadette O.; Berman, Zachary; Wilson, David; Baskaran, Harihara; Flask, Chris A.; Keri, Ruth A.; Karathanasis, Efstathios

2012-01-01

While the enhanced permeability and retention effect may promote the preferential accumulation of nanoparticles into well-vascularized primary tumors, it is ineffective in the case of metastases hidden within a large population of normal cells. Due to their small size, high dispersion to organs, and low vascularization, metastatic tumors are less accessible to targeted nanoparticles. To tackle these challenges, we designed a nanoparticle for vascular targeting based on an αvβ3 integrin-targeted nanochain particle composed of four iron oxide nanospheres chemically linked in a linear assembly. The chain-shaped nanoparticles enabled enhanced ‘sensing’ of the tumor-associated remodeling of the vascular bed offering increased likelihood of specific recognition of metastatic tumors. Compared to spherical nanoparticles, the chain-shaped nanoparticles resulted in superior targeting of αvβ3 integrin due to geometrically enhanced multivalent docking. We performed multimodal in vivo imaging (Fluorescence Molecular Tomography and Magnetic Resonance Imaging) in a non-invasive and quantitative manner, which showed that the nanoparticles targeted metastases in the liver and lungs with high specificity in a highly aggressive breast tumor model in mice. PMID:23005348

Synthetic tripodal receptors for carbohydrates. Pyrrole, a hydrogen bonding partner for saccharidic hydroxyls.

PubMed

Francesconi, Oscar; Gentili, Matteo; Roelens, Stefano

2012-09-07

The carbohydrate recognition properties of synthetic tripodal receptors relying on H-bonding interactions have highlighted the crucial role played by the functional groups matching saccharidic hydroxyls. Herein, pyrrole and pyridine, which emerged as two of the most effective H-bonding groups, were quantitatively compared through their isostructural substitution within the architecture of a shape-persistent bicyclic cage receptor. NMR and ITC binding studies gave for the pyrrolic receptor a 20-fold larger affinity toward octyl-β-d-glucopyranoside in CDCl(3), demonstrating the superior recognition properties of pyrrole under conditions in which differences would depend on the intrinsic binding ability of the two groups. The three-dimensional structures of the two glucoside complexes in solution were elucidated by combined NMR and molecular mechanics computational techniques, showing that the origin of the stability difference between the two closely similar complex structures resides in the ability of pyrrole to establish shorter/stronger H-bonds with the glucosidic ligand compared to pyridine.

Matrine- and oxymatrine-imprinted monodisperse polymers prepared by precipitation polymerization and their applications for the selective extraction of matrine-type alkaloids from Sophora flavescens Aiton.

PubMed

Funaya, Noriko; Haginaka, Jun

2012-07-27

Matrine (MT)- and oxymatrine (OMT)-imprinted monodisperse polymers have been prepared by precipitation polymerization. The prepared molecularly imprinted polymers (MIPs) for MT and OMT, MIP(MT) and MIP(OMT), were monodispersed microspheres of 3.3 and 3.9 μm in diameter, respectively. Binding experiments and Scatchard analyses revealed that two classes of binding sites were formed on MIP(MT) and MIP(OMT). In addition to shape recognition, ionic and hydrophobic interactions seemed to affect the retention and recognition of MT and OMT on MIP(MT) and MIP(OMT), respectively, in low acetonitrile content, and ionic and hydrophilic interactions affected these properties in high acetonitrile content. MIP(MT) was used to selectively extract MT and sophocarpine (13,14-dehydromatrine) from Sophora flavescens root, while MIP(OMT) was used to extract OMT and oxysophocarpine (13,14-dehydrooxymatrine). Copyright © 2012 Elsevier B.V. All rights reserved.

Molecularly imprinted polymers for the recognition of proteins: the state of the art.

PubMed

Bossi, A; Bonini, F; Turner, A P F; Piletsky, S A

2007-01-15

Molecular imprinting has proved to be an effective technique for the creation of recognition sites on a polymer scaffold. Protein imprinting has been a focus for many chemists working in the area of molecular recognition, since the creation of synthetic polymers that can specifically recognise proteins is a very challenging but potentially extremely rewarding objective. It is expected that molecularly imprinted polymers (MIPs) with specificity for proteins will find application in medicine, diagnostics, proteomics, environmental analysis, sensors and drug delivery. In this review, the authors provide an overview of the progress achieved in the decade between 1994 and 2005, with respect to the challenging area of MIPs for protein recognition. The discussion furnishes a comparative analysis of different approaches developed, underlining their relative advantages and disadvantages and highlighting trends and possible future directions.

A survey of visual preprocessing and shape representation techniques

NASA Technical Reports Server (NTRS)

Olshausen, Bruno A.

1988-01-01

Many recent theories and methods proposed for visual preprocessing and shape representation are summarized. The survey brings together research from the fields of biology, psychology, computer science, electrical engineering, and most recently, neural networks. It was motivated by the need to preprocess images for a sparse distributed memory (SDM), but the techniques presented may also prove useful for applying other associative memories to visual pattern recognition. The material of this survey is divided into three sections: an overview of biological visual processing; methods of preprocessing (extracting parts of shape, texture, motion, and depth); and shape representation and recognition (form invariance, primitives and structural descriptions, and theories of attention).

Tactile agnosia. Underlying impairment and implications for normal tactile object recognition.

PubMed

Reed, C L; Caselli, R J; Farah, M J

1996-06-01

In a series of experimental investigations of a subject with a unilateral impairment of tactile object recognition without impaired tactile sensation, several issues were addressed. First, is tactile agnosia secondary to a general impairment of spatial cognition? On tests of spatial ability, including those directed at the same spatial integration process assumed to be taxed by tactile object recognition, the subject performed well, implying a more specific impairment of high level, modality specific tactile perception. Secondly, within the realm of high level tactile perception, is there a distinction between the ability to derive shape ('what') and spatial ('where') information? Our testing showed an impairment confined to shape perception. Thirdly, what aspects of shape perception are impaired in tactile agnosia? Our results indicate that despite accurate encoding of metric length and normal manual exploration strategies, the ability tactually to perceive objects with the impaired hand, deteriorated as the complexity of shape increased. In addition, asymmetrical performance was not found for other body surfaces (e.g. her feet). Our results suggest that tactile shape perception can be disrupted independent of general spatial ability, tactile spatial ability, manual shape exploration, or even the precise perception of metric length in the tactile modality.

Wilsonosiphonia gen. nov. (Rhodomelaceae, Rhodophyta) based on molecular and morpho-anatomical characters.

PubMed

Bustamante, Danilo E; Won, Boo Yeon; Miller, Kathy Ann; Cho, Tae Oh

2017-04-01

Morphological, anatomical, and molecular sequence data were used to assess the establishment and phylogenetic position of the genus Wilsonosiphonia gen. nov. Phylogenies based on rbcL and concatenated rbcL and cox1 loci support recognition of Wilsonosiphonia gen. nov., sister to Herposiphonia. Diagnostic features for Wilsonosiphonia are rhizoids located at distal ends of pericentral cells and taproot-shaped multicellular tips of rhizoids. Wilsonosiphonia includes three species with diagnostic rbcL and cox1 sequences, Wilsonosiphonia fujiae sp. nov. (the generitype), W. howei comb. nov., and W. indica sp. nov. These three species resemble each other in external morphology, but W. fujiae is distinguished by having two tetrasporangia per segment rather than one, W. indica by having abundant and persistent trichoblasts, and W. howei by having few and deciduous trichoblasts. © 2017 Phycological Society of America.

What Types of Visual Recognition Tasks Are Mediated by the Neural Subsystem that Subserves Face Recognition?

ERIC Educational Resources Information Center

Brooks, Brian E.; Cooper, Eric E.

2006-01-01

Three divided visual field experiments tested current hypotheses about the types of visual shape representation tasks that recruit the cognitive and neural mechanisms underlying face recognition. Experiment 1 found a right hemisphere advantage for subordinate but not basic-level face recognition. Experiment 2 found a right hemisphere advantage for…

Confinement of Aggregation-Induced Emission Molecular Rotors in Ultrathin Two-Dimensional Porous Organic Nanosheets for Enhanced Molecular Recognition.

PubMed

Dong, Jinqiao; Li, Xu; Zhang, Kang; Di Yuan, Yi; Wang, Yuxiang; Zhai, Linzhi; Liu, Guoliang; Yuan, Daqiang; Jiang, Jianwen; Zhao, Dan

2018-03-21

Despite the rapid development of molecular rotors over the past decade, it still remains a huge challenge to understand their confined behavior in ultrathin two-dimensional (2D) nanomaterials for molecular recognition. Here, we report an all-carbon, 2D π-conjugated aromatic polymer, named NUS-25, containing flexible tetraphenylethylene (TPE) units as aggregation-induced emission (AIE) molecular rotors. NUS-25 bulk powder can be easily exfoliated into micrometer-sized lamellar freestanding nanosheets with a thickness of 2-5 nm. The dynamic behavior of the TPE rotors is partially restricted through noncovalent interactions in the ultrathin 2D nanosheets, which is proved by comparative experimental studies including AIE characteristics, size-selective molecular recognition, and theoretical calculations of rotary energy barrier. Because of the partially restricted TPE rotors, NUS-25 nanosheets are highly fluorescent. This property allows NUS-25 nanosheets to be used as a chemical sensor for the specific detection of acenaphthylene among a series of polycyclic aromatic hydrocarbons (PAHs) via fluorescent quenching mechanism. Further investigations show that NUS-25 nanosheets have much higher sensitivity and selectivity than their stacked bulk powder and other similar polymers containing dynamic TPE rotors. The highly efficient molecular recognition can be attributed to the photoinduced electron transfer (PET) from NUS-25 nanosheets to acenaphthylene, which is investigated by time-resolved photoluminescence measurements (TRPL), excitation and emission spectra, and density functional theory (DFT) calculations. Our findings demonstrate that confinement of AIE molecular rotors in 2D nanomaterials can enhance the molecular recognition. We anticipate that the material design strategy demonstrated in this study will inspire the development of other ultrathin 2D nanomaterials equipped with smart molecular machines for various applications.

Deep Neural Networks as a Computational Model for Human Shape Sensitivity

PubMed Central

Op de Beeck, Hans P.

2016-01-01

Theories of object recognition agree that shape is of primordial importance, but there is no consensus about how shape might be represented, and so far attempts to implement a model of shape perception that would work with realistic stimuli have largely failed. Recent studies suggest that state-of-the-art convolutional ‘deep’ neural networks (DNNs) capture important aspects of human object perception. We hypothesized that these successes might be partially related to a human-like representation of object shape. Here we demonstrate that sensitivity for shape features, characteristic to human and primate vision, emerges in DNNs when trained for generic object recognition from natural photographs. We show that these models explain human shape judgments for several benchmark behavioral and neural stimulus sets on which earlier models mostly failed. In particular, although never explicitly trained for such stimuli, DNNs develop acute sensitivity to minute variations in shape and to non-accidental properties that have long been implicated to form the basis for object recognition. Even more strikingly, when tested with a challenging stimulus set in which shape and category membership are dissociated, the most complex model architectures capture human shape sensitivity as well as some aspects of the category structure that emerges from human judgments. As a whole, these results indicate that convolutional neural networks not only learn physically correct representations of object categories but also develop perceptually accurate representational spaces of shapes. An even more complete model of human object representations might be in sight by training deep architectures for multiple tasks, which is so characteristic in human development. PMID:27124699

[Study on molecular recognition technology in active constituents extracted and isolated from Aconitum pendulum].

PubMed

Ma, Xue-Qin; Li, Guo-Shan; Fu, Xue-Yan; Ma, Jing-Zu

2011-03-01

To investigate CD molecular recognition technology applied in active constituents extracted and isolated from traditional Chinese medicine--Aconitum pendulum. The inclusion constant and form probability of the inclusion complex of Aconitum pendulum with p-CD was calculated by UV spectra method. The active constituents of Aconitum pendulum were extracted and isolated by molecular recognition technology. The inclusion complex was identified by UV. The chemical constituents of Aconitum pendulum and inclusion complex was determined by HPLC. The analgesic effects of inclusion complex was investigated by experiment of intraperitoneal injection of acetic acid in rats. The inclusion complex was identified and confirmed by UV spectra method, the chemical components of inclusion complex were simple, and the content of active constituents increased significantly, the analgesic effects of inclusion complex was well. The molecular recognition technology can be used for extracting and isolating active constituents of Aconitum pendulum, and the effects are obvious.

Molecular recognition and colorimetric detection of cholera toxin by poly(diacetylene) liposomes incorporating G{sub m1} ganglioside

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

Pan, J.J.; Charych, D.

1997-03-19

Molecular recognition sites on cell membranes serve as the main communication channels between the inside of a cell and its surroundings. Upon receptor binding, cellular messages such as ion channel opening or activation of enzymes are triggered. In this report, we demonstrate that artificial cell membranes made from conjugated lipid polymers (poly(diacetylene)) can, on a simple level, mimic membrane processes of molecular recognition and signal transduction. The ganglioside GM1 was incorporated into poly(diacetylene) liposomes. Molecular recognition of cholera toxin at the interface of the liposome resulted in a change of the membrane color due to conformational charges in the conjugatedmore » (ene-yne) polymer backbone. The `colored liposomes` might be used as simple colorimetric sensors for drug screening or as new tools to study membrane-membrane or membrane-receptor interactions. 21 refs., 3 figs.« less

Molecular recognition of organic ammonium ions in solution using synthetic receptors

PubMed Central

Späth, Andreas

2010-01-01

Summary Ammonium ions are ubiquitous in chemistry and molecular biology. Considerable efforts have been undertaken to develop synthetic receptors for their selective molecular recognition. The type of host compounds for organic ammonium ion binding span a wide range from crown ethers to calixarenes to metal complexes. Typical intermolecular interactions are hydrogen bonds, electrostatic and cation–π interactions, hydrophobic interactions or reversible covalent bond formation. In this review we discuss the different classes of synthetic receptors for organic ammonium ion recognition and illustrate the scope and limitations of each class with selected examples from the recent literature. The molecular recognition of ammonium ions in amino acids is included and the enantioselective binding of chiral ammonium ions by synthetic receptors is also covered. In our conclusion we compare the strengths and weaknesses of the different types of ammonium ion receptors which may help to select the best approach for specific applications. PMID:20502608

Interactions between Membranes and "Metaphilic" Polypeptide Architectures with Diverse Side-Chain Populations.

PubMed

Lee, Michelle W; Han, Ming; Bossa, Guilherme Volpe; Snell, Carly; Song, Ziyuan; Tang, Haoyu; Yin, Lichen; Cheng, Jianjun; May, Sylvio; Luijten, Erik; Wong, Gerard C L

2017-03-28

At physiological conditions, most proteins or peptides can fold into relatively stable structures that present on their molecular surfaces specific chemical patterns partially smeared out by thermal fluctuations. These nanoscopically defined patterns of charge, hydrogen bonding, and/or hydrophobicity, along with their elasticity and shape stability (folded proteins have Young's moduli of ∼1 × 10 8 Pa), largely determine and limit the interactions of these molecules, such as molecular recognition and allosteric regulation. In this work, we show that the membrane-permeating activity of antimicrobial peptides (AMPs) and cell-penetrating peptides (CPPs) can be significantly enhanced using prototypical peptides with "molten" surfaces: metaphilic peptides with quasi-liquid surfaces and adaptable shapes. These metaphilic peptides have a bottlebrush-like architecture consisting of a rigid helical core decorated with mobile side chains that are terminated by cationic or hydrophobic groups. Computer simulations show that these flexible side chains can undergo significant rearrangement in response to different environments, giving rise to adaptable surface chemistry of the peptide. This quality makes it possible to control their hydrophobicity over a broad range while maintaining water solubility, unlike many AMPs and CPPs. Thus, we are able to show how the activity of these peptides is amplified by hydrophobicity and cationic charge, and rationalize these results using a quantitative mean-field theory. Computer simulations show that the shape-changing properties of the peptides and the resultant adaptive presentation of chemistry play a key enabling role in their interactions with membranes.

Impairment of nonverbal recognition in Alzheimer disease: a PET O-15 study.

PubMed

Anderson, K E; Brickman, A M; Flynn, J; Scarmeas, N; Van Heertum, R; Sackeim, H; Marder, K S; Bell, K; Moeller, J R; Stern, Y

2007-07-03

To characterize deficits in nonverbal recognition memory and functional brain changes associated with these deficits in Alzheimer disease (AD). Using O-15 PET, we studied 11 patients with AD and 17 cognitively intact elders during the combined encoding and retrieval periods of a nonverbal recognition task. Both task conditions involved recognition of line drawings of abstract shapes. In both conditions, subjects were first presented a list of shapes as study items, and then a list as test items, containing items from the study list and foils. In the titrated demand condition, the shape study list size (SLS) was adjusted prior to imaging so that each subject performed at approximately 75% recognition accuracy; difficulty during PET scanning in this condition was approximately matched across subjects. A control task was used in which SLS = 1 shape. During performance of the titrated demand condition, SLS averaged 4.55 (+/-1.86) shapes for patients with AD and 7.53 (+/-4.81) for healthy elderly subjects (p = 0.031). However, both groups of subjects were closely matched on performance in the titrated demand condition during PET scanning with 72.17% (+/-7.98%) correct for patients with AD and 72.25% (+/-7.03%) for elders (p = 0.979). PET results demonstrated that patients with AD showed greater mean differences between the titrated demand condition and control in areas including the left fusiform and inferior frontal regions (Brodmann areas 19 and 45). Relative fusiform and inferior frontal differences may reflect the Alzheimer disease (AD) patients' compensatory engagement of alternate brain regions. The strategy used by patients with AD is likely to be a general mechanism of compensation, rather than task-specific.

The role of conformational selection in the molecular recognition of the wild type and mutants XPA67-80 peptides by ERCC1.

PubMed

Fadda, Elisa

2015-07-01

Molecular recognition is a fundamental step in the coordination of biomolecular pathways. Understanding how recognition and binding occur between highly flexible protein domains is a complex task. The conformational selection theory provides an elegant rationalization of the recognition mechanism, especially valid in cases when unstructured protein regions are involved. The recognition of a poorly structured peptide, namely XPA67-80 , by its target receptor ERCC1, falls in this challenging study category. The microsecond molecular dynamics (MD) simulations, discussed in this work, show that the conformational propensity of the wild type XPA67-80 peptide in solution supports conformational selection as the key mechanism driving its molecular recognition by ERCC1. Moreover, all the mutations of the XPA67-80 peptide studied here cause a significant increase of its conformational disorder, relative to the wild type. Comparison to experimental data suggests that the loss of the recognized structural motifs at the microscopic time scale can contribute to the critical decrease in binding observed for one of the mutants, further substantiating the key role of conformational selection in recognition. Ultimately, because of the high sequence identity and analogy in binding, it is conceivable that the conclusions of this study on the XPA67-80 peptide also apply to the ERCC1-binding domain of the XPA protein. © 2015 Wiley Periodicals, Inc.

Language comprehenders retain implied shape and orientation of objects.

PubMed

Pecher, Diane; van Dantzig, Saskia; Zwaan, Rolf A; Zeelenberg, René

2009-06-01

According to theories of embodied cognition, language comprehenders simulate sensorimotor experiences to represent the meaning of what they read. Previous studies have shown that picture recognition is better if the object in the picture matches the orientation or shape implied by a preceding sentence. In order to test whether strategic imagery may explain previous findings, language comprehenders first read a list of sentences in which objects were mentioned. Only once the complete list had been read was recognition memory tested with pictures. Recognition performance was better if the orientation or shape of the object matched that implied by the sentence, both immediately after reading the complete list of sentences and after a 45-min delay. These results suggest that previously found match effects were not due to strategic imagery and show that details of sensorimotor simulations are retained over longer periods.

Shape recognition contributions to figure-ground reversal: which route counts?

PubMed

Peterson, M A; Harvey, E M; Weidenbacher, H J

1991-11-01

Observers viewed upright and inverted versions of figure-ground stimuli, in which Gestalt variables specified that the center was figure. In upright versions, the surround was high in denotivity, in that most viewers agreed it depicted the same shape; in inverted versions, the surround was low in denotivity. The surround was maintained as figure longer and was more likely to be obtained as figure when the stimuli were upright rather than inverted. In four experiments, these effects reflected inputs to figure-ground computations from orientation-specific shape representations only. To account for these findings, a nonratiomorphic mechanism is proposed that enables shape recognition processes before figure-ground relationships are determined.

Developmental Differences in Shape Processing

ERIC Educational Resources Information Center

Sera, Maria D.; Gordon Millett, Katherine

2011-01-01

Considerable evidence indicates that shape similarity plays a major role in object recognition, identification and categorization. However, little is known about shape processing and its development. Across four experiments, we addressed two related questions. First, what makes objects similar in shape? Second, how does the processing of shape…

Molecular Imprinting Technology in Quartz Crystal Microbalance (QCM) Sensors

PubMed Central

Emir Diltemiz, Sibel; Keçili, Rüstem; Ersöz, Arzu; Say, Rıdvan

2017-01-01

Molecularly imprinted polymers (MIPs) as artificial antibodies have received considerable scientific attention in the past years in the field of (bio)sensors since they have unique features that distinguish them from natural antibodies such as robustness, multiple binding sites, low cost, facile preparation and high stability under extreme operation conditions (higher pH and temperature values, etc.). On the other hand, the Quartz Crystal Microbalance (QCM) is an analytical tool based on the measurement of small mass changes on the sensor surface. QCM sensors are practical and convenient monitoring tools because of their specificity, sensitivity, high accuracy, stability and reproducibility. QCM devices are highly suitable for converting the recognition process achieved using MIP-based memories into a sensor signal. Therefore, the combination of a QCM and MIPs as synthetic receptors enhances the sensitivity through MIP process-based multiplexed binding sites using size, 3D-shape and chemical function having molecular memories of the prepared sensor system toward the target compound to be detected. This review aims to highlight and summarize the recent progress and studies in the field of (bio)sensor systems based on QCMs combined with molecular imprinting technology. PMID:28245588

Static sign language recognition using 1D descriptors and neural networks

NASA Astrophysics Data System (ADS)

Solís, José F.; Toxqui, Carina; Padilla, Alfonso; Santiago, César

2012-10-01

A frame work for static sign language recognition using descriptors which represents 2D images in 1D data and artificial neural networks is presented in this work. The 1D descriptors were computed by two methods, first one consists in a correlation rotational operator.1 and second is based on contour analysis of hand shape. One of the main problems in sign language recognition is segmentation; most of papers report a special color in gloves or background for hand shape analysis. In order to avoid the use of gloves or special clothing, a thermal imaging camera was used to capture images. Static signs were picked up from 1 to 9 digits of American Sign Language, a multilayer perceptron reached 100% recognition with cross-validation.

Bioimprinted QCM sensors for virus detection-screening of plant sap.

PubMed

Dickert, Franz L; Hayden, Oliver; Bindeus, Roland; Mann, Karl-J; Blaas, Dieter; Waigmann, Elisabeth

2004-04-01

Surface imprinting techniques on polymer-coated quartz-crystal microbalances (QCM) have been used to detect tobacco mosaic viruses (TMV) in aqueous media. Molecularly imprinted polymers (MIP), tailor-made by self organisation of monomers around a template (TMV), were generated directly on the gold electrodes. Imprinted trenches on the polymer surface mimicking the shape and surface functionality of the virus serve as recognition sites for re-adsorption after washing out of the template. The sensors are applicable to TMV detection ranging from 100 ng mL(-1) to 1 mg mL(-1) within minutes. Furthermore, direct measurements without time-consuming sample preparation are possible in complex matrices such as tobacco plant sap.

Analyte-Responsive Hydrogels: Intelligent Materials for Biosensing and Drug Delivery.

PubMed

Culver, Heidi R; Clegg, John R; Peppas, Nicholas A

2017-02-21

Nature has mastered the art of molecular recognition. For example, using synergistic non-covalent interactions, proteins can distinguish between molecules and bind a partner with incredible affinity and specificity. Scientists have developed, and continue to develop, techniques to investigate and better understand molecular recognition. As a consequence, analyte-responsive hydrogels that mimic these recognitive processes have emerged as a class of intelligent materials. These materials are unique not only in the type of analyte to which they respond but also in how molecular recognition is achieved and how the hydrogel responds to the analyte. Traditional intelligent hydrogels can respond to environmental cues such as pH, temperature, and ionic strength. The functional monomers used to make these hydrogels can be varied to achieve responsive behavior. For analyte-responsive hydrogels, molecular recognition can also be achieved by incorporating biomolecules with inherent molecular recognition properties (e.g., nucleic acids, peptides, enzymes, etc.) into the polymer network. Furthermore, in addition to typical swelling/syneresis responses, these materials exhibit unique responsive behaviors, such as gel assembly or disassembly, upon interaction with the target analyte. With the diverse tools available for molecular recognition and the ability to generate unique responsive behaviors, analyte-responsive hydrogels have found great utility in a wide range of applications. In this Account, we discuss strategies for making four different classes of analyte-responsive hydrogels, specifically, non-imprinted, molecularly imprinted, biomolecule-containing, and enzymatically responsive hydrogels. Then we explore how these materials have been incorporated into sensors and drug delivery systems, highlighting examples that demonstrate the versatility of these materials. For example, in addition to the molecular recognition properties of analyte-responsive hydrogels, the physicochemical changes that are induced upon analyte binding can be exploited to generate a detectable signal for sensing applications. As research in this area has grown, a number of creative approaches for improving the selectivity and sensitivity (i.e., detection limit) of these sensors have emerged. For applications in drug delivery systems, therapeutic release can be triggered by competitive molecular interactions or physicochemical changes in the network. Additionally, including degradable units within the network can enable sustained and responsive therapeutic release. Several exciting examples exploiting the analyte-responsive behavior of hydrogels for the treatment of cancer, diabetes, and irritable bowel syndrome are discussed in detail. We expect that creative and combinatorial approaches used in the design of analyte-responsive hydrogels will continue to yield materials with great potential in the fields of sensing and drug delivery.

Bio-Mimetic Sensors Based on Molecularly Imprinted Membranes

PubMed Central

Algieri, Catia; Drioli, Enrico; Guzzo, Laura; Donato, Laura

2014-01-01

An important challenge for scientific research is the production of artificial systems able to mimic the recognition mechanisms occurring at the molecular level in living systems. A valid contribution in this direction resulted from the development of molecular imprinting. By means of this technology, selective molecular recognition sites are introduced in a polymer, thus conferring it bio-mimetic properties. The potential applications of these systems include affinity separations, medical diagnostics, drug delivery, catalysis, etc. Recently, bio-sensing systems using molecularly imprinted membranes, a special form of imprinted polymers, have received the attention of scientists in various fields. In these systems imprinted membranes are used as bio-mimetic recognition elements which are integrated with a transducer component. The direct and rapid determination of an interaction between the recognition element and the target analyte (template) was an encouraging factor for the development of such systems as alternatives to traditional bio-assay methods. Due to their high stability, sensitivity and specificity, bio-mimetic sensors-based membranes are used for environmental, food, and clinical uses. This review deals with the development of molecularly imprinted polymers and their different preparation methods. Referring to the last decades, the application of these membranes as bio-mimetic sensor devices will be also reported. PMID:25196110

Face recognition from unconstrained three-dimensional face images using multitask sparse representation

NASA Astrophysics Data System (ADS)

Bentaieb, Samia; Ouamri, Abdelaziz; Nait-Ali, Amine; Keche, Mokhtar

2018-01-01

We propose and evaluate a three-dimensional (3D) face recognition approach that applies the speeded up robust feature (SURF) algorithm to the depth representation of shape index map, under real-world conditions, using only a single gallery sample for each subject. First, the 3D scans are preprocessed, then SURF is applied on the shape index map to find interest points and their descriptors. Each 3D face scan is represented by keypoints descriptors, and a large dictionary is built from all the gallery descriptors. At the recognition step, descriptors of a probe face scan are sparsely represented by the dictionary. A multitask sparse representation classification is used to determine the identity of each probe face. The feasibility of the approach that uses the SURF algorithm on the shape index map for face identification/authentication is checked through an experimental investigation conducted on Bosphorus, University of Milano Bicocca, and CASIA 3D datasets. It achieves an overall rank one recognition rate of 97.75%, 80.85%, and 95.12%, respectively, on these datasets.

Layers: A molecular surface peeling algorithm and its applications to analyze protein structures

PubMed Central

Karampudi, Naga Bhushana Rao; Bahadur, Ranjit Prasad

2015-01-01

We present an algorithm ‘Layers’ to peel the atoms of proteins as layers. Using Layers we show an efficient way to transform protein structures into 2D pattern, named residue transition pattern (RTP), which is independent of molecular orientations. RTP explains the folding patterns of proteins and hence identification of similarity between proteins is simple and reliable using RTP than with the standard sequence or structure based methods. Moreover, Layers generates a fine-tunable coarse model for the molecular surface by using non-random sampling. The coarse model can be used for shape comparison, protein recognition and ligand design. Additionally, Layers can be used to develop biased initial configuration of molecules for protein folding simulations. We have developed a random forest classifier to predict the RTP of a given polypeptide sequence. Layers is a standalone application; however, it can be merged with other applications to reduce the computational load when working with large datasets of protein structures. Layers is available freely at http://www.csb.iitkgp.ernet.in/applications/mol_layers/main. PMID:26553411

Prospective virtual screening for novel p53-MDM2 inhibitors using ultrafast shape recognition

NASA Astrophysics Data System (ADS)

Patil, Sachin P.; Ballester, Pedro J.; Kerezsi, Cassidy R.

2014-02-01

The p53 protein, known as the guardian of genome, is mutated or deleted in approximately 50 % of human tumors. In the rest of the cancers, p53 is expressed in its wild-type form, but its function is inhibited by direct binding with the murine double minute 2 (MDM2) protein. Therefore, inhibition of the p53-MDM2 interaction, leading to the activation of tumor suppressor p53 protein presents a fundamentally novel therapeutic strategy against several types of cancers. The present study utilized ultrafast shape recognition (USR), a virtual screening technique based on ligand-receptor 3D shape complementarity, to screen DrugBank database for novel p53-MDM2 inhibitors. Specifically, using 3D shape of one of the most potent crystal ligands of MDM2, MI-63, as the query molecule, six compounds were identified as potential p53-MDM2 inhibitors. These six USR hits were then subjected to molecular modeling investigations through flexible receptor docking followed by comparative binding energy analysis. These studies suggested a potential role of the USR-selected molecules as p53-MDM2 inhibitors. This was further supported by experimental tests showing that the treatment of human colon tumor cells with the top USR hit, telmisartan, led to a dose-dependent cell growth inhibition in a p53-dependent manner. It is noteworthy that telmisartan has a long history of safe human use as an approved anti-hypertension drug and thus may present an immediate clinical potential as a cancer therapeutic. Furthermore, it could also serve as a structurally-novel lead molecule for the development of more potent, small-molecule p53-MDM2 inhibitors against variety of cancers. Importantly, the present study demonstrates that the adopted USR-based virtual screening protocol is a useful tool for hit identification in the domain of small molecule p53-MDM2 inhibitors.

Subjectively Interpreted Shape Dimensions as Privileged and Orthogonal Axes in Mental Shape Space

ERIC Educational Resources Information Center

Ons, Bart; De Baene, Wouter; Wagemans, Johan

2011-01-01

The shape of an object is fundamental in object recognition but it is still an open issue to what extent shape differences are perceived analytically (i.e., by the dimensional structure of the shapes) or holistically (i.e., by the overall similarity of the shapes). The dimensional structure of a stimulus is available in a primary stage of…

Adaptive Hybrid Picture Coding. Volume 2.

DTIC Science & Technology

1985-02-01

ooo5 V.a Measurement Vector ..eho..............57 V.b Size Variable o .entroi* Vector .......... .- 59 V * c Shape Vector .Ř 0-60o oe 6 I V~d...the Program for the Adaptive Line of Sight Method .i.. 18.. o ... .... .... 1 B Details of the Feature Vector FormationProgram .. o ...oo..-....- .122 C ...shape recognition is analogous to recognition of curves in space. Therefore, well known concepts and theorems from differential geometry can be 34 . o

ATR applications of minimax entropy models of texture and shape

NASA Astrophysics Data System (ADS)

Zhu, Song-Chun; Yuille, Alan L.; Lanterman, Aaron D.

2001-10-01

Concepts from information theory have recently found favor in both the mainstream computer vision community and the military automatic target recognition community. In the computer vision literature, the principles of minimax entropy learning theory have been used to generate rich probabilitistic models of texture and shape. In addition, the method of types and large deviation theory has permitted the difficulty of various texture and shape recognition tasks to be characterized by 'order parameters' that determine how fundamentally vexing a task is, independent of the particular algorithm used. These information-theoretic techniques have been demonstrated using traditional visual imagery in applications such as simulating cheetah skin textures and such as finding roads in aerial imagery. We discuss their application to problems in the specific application domain of automatic target recognition using infrared imagery. We also review recent theoretical and algorithmic developments which permit learning minimax entropy texture models for infrared textures in reasonable timeframes.

Shape analysis modeling for character recognition

NASA Astrophysics Data System (ADS)

Khan, Nadeem A. M.; Hegt, Hans A.

1998-10-01

Optimal shape modeling of character-classes is crucial for achieving high performance on recognition of mixed-font, hand-written or (and) poor quality text. A novel scheme is presented in this regard focusing on constructing such structural models that can be hierarchically examined. These models utilize a certain `well-thought' set of shape primitives. They are simplified enough to ignore the inter- class variations in font-type or writing style yet retaining enough details for discrimination between the samples of the similar classes. Thus the number of models per class required can be kept minimal without sacrificing the recognition accuracy. In this connection a flexible multi- stage matching scheme exploiting the proposed modeling is also described. This leads to a system which is robust against various distortions and degradation including those related to cases of touching and broken characters. Finally, we present some examples and test results as a proof-of- concept demonstrating the validity and the robustness of the approach.

Shape-Based Virtual Screening with Volumetric Aligned Molecular Shapes

PubMed Central

Koes, David Ryan; Camacho, Carlos J.

2014-01-01

Shape-based virtual screening is an established and effective method for identifying small molecules that are similar in shape and function to a reference ligand. We describe a new method of shape-based virtual screening, volumetric aligned molecular shapes (VAMS). VAMS uses efficient data structures to encode and search molecular shapes. We demonstrate that VAMS is an effective method for shape-based virtual screening and that it can be successfully used as a pre-filter to accelerate more computationally demanding search algorithms. Unique to VAMS is a novel minimum/maximum shape constraint query for precisely specifying the desired molecular shape. Shape constraint searches in VAMS are particularly efficient and millions of shapes can be searched in a fraction of a second. We compare the performance of VAMS with two other shape-based virtual screening algorithms a benchmark of 102 protein targets consisting of more than 32 million molecular shapes and find that VAMS provides a competitive trade-off between run-time performance and virtual screening performance. PMID:25049193

Reversible mechanical protection: building a 3D “suit” around a T-shaped benzimidazole axle† †Electronic supplementary information (ESI) available: Synthetic details and full characterisation of all new compounds. CCDC 1533271 and 1533272. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc00790f Click here for additional data file. Click here for additional data file.

PubMed Central

Baggi, Giorgio; Vukotic, V. Nicholas

2017-01-01

The T-shaped benzimidazolium/crown ether recognition motif was used to prepare suit[1]anes. These novel mechanically interlocked molecules (MIMs) were fully characterized by 1H and 13C NMR spectroscopy, single-crystal X-ray diffraction, UV-vis absorption and fluorescence spectroscopy. By conversion to a suit[1]ane, a simple benzimidazole was shown to be protected from deprotonation by strong base. Moreover, it was demonstrated that this unique three-dimensional encapsulation can be made reversible, thus introducing the concept of “reversible mechanical protection”; a protecting methodology that may have potential applications in synthetic organic chemistry and the design of molecular machinery. PMID:28626559

Exploring Protein-Peptide Recognition Pathways Using a Supervised Molecular Dynamics Approach.

PubMed

Salmaso, Veronica; Sturlese, Mattia; Cuzzolin, Alberto; Moro, Stefano

2017-04-04

Peptides have gained increased interest as therapeutic agents during recent years. The high specificity and relatively low toxicity of peptide drugs derive from their extremely tight binding to their targets. Indeed, understanding the molecular mechanism of protein-peptide recognition has important implications in the fields of biology, medicine, and pharmaceutical sciences. Even if crystallography and nuclear magnetic resonance are offering valuable atomic insights into the assembling of the protein-peptide complexes, the mechanism of their recognition and binding events remains largely unclear. In this work we report, for the first time, the use of a supervised molecular dynamics approach to explore the possible protein-peptide binding pathways within a timescale reduced up to three orders of magnitude compared with classical molecular dynamics. The better and faster understating of the protein-peptide recognition pathways could be very beneficial in enlarging the applicability of peptide-based drug design approaches in several biotechnological and pharmaceutical fields. Copyright © 2017 Elsevier Ltd. All rights reserved.

SAR target recognition using behaviour library of different shapes in different incidence angles and polarisations

NASA Astrophysics Data System (ADS)

Fallahpour, Mojtaba Behzad; Dehghani, Hamid; Jabbar Rashidi, Ali; Sheikhi, Abbas

2018-05-01

Target recognition is one of the most important issues in the interpretation of the synthetic aperture radar (SAR) images. Modelling, analysis, and recognition of the effects of influential parameters in the SAR can provide a better understanding of the SAR imaging systems, and therefore facilitates the interpretation of the produced images. Influential parameters in SAR images can be divided into five general categories of radar, radar platform, channel, imaging region, and processing section, each of which has different physical, structural, hardware, and software sub-parameters with clear roles in the finally formed images. In this paper, for the first time, a behaviour library that includes the effects of polarisation, incidence angle, and shape of targets, as radar and imaging region sub-parameters, in the SAR images are extracted. This library shows that the created pattern for each of cylindrical, conical, and cubic shapes is unique, and due to their unique properties these types of shapes can be recognised in the SAR images. This capability is applied to data acquired with the Canadian RADARSAT1 satellite.

Target recognition for ladar range image using slice image

NASA Astrophysics Data System (ADS)

Xia, Wenze; Han, Shaokun; Wang, Liang

2015-12-01

A shape descriptor and a complete shape-based recognition system using slice images as geometric feature descriptor for ladar range images are introduced. A slice image is a two-dimensional image generated by three-dimensional Hough transform and the corresponding mathematical transformation. The system consists of two processes, the model library construction and recognition. In the model library construction process, a series of range images are obtained after the model object is sampled at preset attitude angles. Then, all the range images are converted into slice images. The number of slice images is reduced by clustering analysis and finding a representation to reduce the size of the model library. In the recognition process, the slice image of the scene is compared with the slice image in the model library. The recognition results depend on the comparison. Simulated ladar range images are used to analyze the recognition and misjudgment rates, and comparison between the slice image representation method and moment invariants representation method is performed. The experimental results show that whether in conditions without noise or with ladar noise, the system has a high recognition rate and low misjudgment rate. The comparison experiment demonstrates that the slice image has better representation ability than moment invariants.

Target recognition of ladar range images using slice image: comparison of four improved algorithms

NASA Astrophysics Data System (ADS)

Xia, Wenze; Han, Shaokun; Cao, Jingya; Wang, Liang; Zhai, Yu; Cheng, Yang

2017-07-01

Compared with traditional 3-D shape data, ladar range images possess properties of strong noise, shape degeneracy, and sparsity, which make feature extraction and representation difficult. The slice image is an effective feature descriptor to resolve this problem. We propose four improved algorithms on target recognition of ladar range images using slice image. In order to improve resolution invariance of the slice image, mean value detection instead of maximum value detection is applied in these four improved algorithms. In order to improve rotation invariance of the slice image, three new improved feature descriptors-which are feature slice image, slice-Zernike moments, and slice-Fourier moments-are applied to the last three improved algorithms, respectively. Backpropagation neural networks are used as feature classifiers in the last two improved algorithms. The performance of these four improved recognition systems is analyzed comprehensively in the aspects of the three invariances, recognition rate, and execution time. The final experiment results show that the improvements for these four algorithms reach the desired effect, the three invariances of feature descriptors are not directly related to the final recognition performance of recognition systems, and these four improved recognition systems have different performances under different conditions.

Localization and recognition of traffic signs for automated vehicle control systems

NASA Astrophysics Data System (ADS)

Zadeh, Mahmoud M.; Kasvand, T.; Suen, Ching Y.

1998-01-01

We present a computer vision system for detection and recognition of traffic signs. Such systems are required to assist drivers and for guidance and control of autonomous vehicles on roads and city streets. For experiments we use sequences of digitized photographs and off-line analysis. The system contains four stages. First, region segmentation based on color pixel classification called SRSM. SRSM limits the search to regions of interest in the scene. Second, we use edge tracing to find parts of outer edges of signs which are circular or straight, corresponding to the geometrical shapes of traffic signs. The third step is geometrical analysis of the outer edge and preliminary recognition of each candidate region, which may be a potential traffic sign. The final step in recognition uses color combinations within each region and model matching. This system maybe used for recognition of other types of objects, provided that the geometrical shape and color content remain reasonably constant. The method is reliable, easy to implement, and fast, This differs form the road signs recognition method in the PROMETEUS. The overall structure of the approach is sketched.

Songbirds use spectral shape, not pitch, for sound pattern recognition

PubMed Central

Bregman, Micah R.; Patel, Aniruddh D.; Gentner, Timothy Q.

2016-01-01

Humans easily recognize “transposed” musical melodies shifted up or down in log frequency. Surprisingly, songbirds seem to lack this capacity, although they can learn to recognize human melodies and use complex acoustic sequences for communication. Decades of research have led to the widespread belief that songbirds, unlike humans, are strongly biased to use absolute pitch (AP) in melody recognition. This work relies almost exclusively on acoustically simple stimuli that may belie sensitivities to more complex spectral features. Here, we investigate melody recognition in a species of songbird, the European Starling (Sturnus vulgaris), using tone sequences that vary in both pitch and timbre. We find that small manipulations altering either pitch or timbre independently can drive melody recognition to chance, suggesting that both percepts are poor descriptors of the perceptual cues used by birds for this task. Instead we show that melody recognition can generalize even in the absence of pitch, as long as the spectral shapes of the constituent tones are preserved. These results challenge conventional views regarding the use of pitch cues in nonhuman auditory sequence recognition. PMID:26811447

Limited receptive area neural classifier for recognition of swallowing sounds using continuous wavelet transform.

PubMed

Makeyev, Oleksandr; Sazonov, Edward; Schuckers, Stephanie; Lopez-Meyer, Paulo; Melanson, Ed; Neuman, Michael

2007-01-01

In this paper we propose a sound recognition technique based on the limited receptive area (LIRA) neural classifier and continuous wavelet transform (CWT). LIRA neural classifier was developed as a multipurpose image recognition system. Previous tests of LIRA demonstrated good results in different image recognition tasks including: handwritten digit recognition, face recognition, metal surface texture recognition, and micro work piece shape recognition. We propose a sound recognition technique where scalograms of sound instances serve as inputs of the LIRA neural classifier. The methodology was tested in recognition of swallowing sounds. Swallowing sound recognition may be employed in systems for automated swallowing assessment and diagnosis of swallowing disorders. The experimental results suggest high efficiency and reliability of the proposed approach.

Ground target recognition using rectangle estimation.

PubMed

Grönwall, Christina; Gustafsson, Fredrik; Millnert, Mille

2006-11-01

We propose a ground target recognition method based on 3-D laser radar data. The method handles general 3-D scattered data. It is based on the fact that man-made objects of complex shape can be decomposed to a set of rectangles. The ground target recognition method consists of four steps; 3-D size and orientation estimation, target segmentation into parts of approximately rectangular shape, identification of segments that represent the target's functional/main parts, and target matching with CAD models. The core in this approach is rectangle estimation. The performance of the rectangle estimation method is evaluated statistically using Monte Carlo simulations. A case study on tank recognition is shown, where 3-D data from four fundamentally different types of laser radar systems are used. Although the approach is tested on rather few examples, we believe that the approach is promising.

Target recognition of log-polar ladar range images using moment invariants

NASA Astrophysics Data System (ADS)

Xia, Wenze; Han, Shaokun; Cao, Jie; Yu, Haoyong

2017-01-01

The ladar range image has received considerable attentions in the automatic target recognition field. However, previous research does not cover target recognition using log-polar ladar range images. Therefore, we construct a target recognition system based on log-polar ladar range images in this paper. In this system combined moment invariants and backpropagation neural network are selected as shape descriptor and shape classifier, respectively. In order to fully analyze the effect of log-polar sampling pattern on recognition result, several comparative experiments based on simulated and real range images are carried out. Eventually, several important conclusions are drawn: (i) if combined moments are computed directly by log-polar range images, translation, rotation and scaling invariant properties of combined moments will be invalid (ii) when object is located in the center of field of view, recognition rate of log-polar range images is less sensitive to the changing of field of view (iii) as object position changes from center to edge of field of view, recognition performance of log-polar range images will decline dramatically (iv) log-polar range images has a better noise robustness than Cartesian range images. Finally, we give a suggestion that it is better to divide field of view into recognition area and searching area in the real application.

Communication: Ion mobility of the radical cation dimers: (Naphthalene)2+• and naphthalene+•-benzene: Evidence for stacked sandwich and T-shape structures

NASA Astrophysics Data System (ADS)

Platt, Sean P.; Attah, Isaac K.; Aziz, Saadullah; El-Shall, M. Samy

2015-05-01

Dimer radical cations of aromatic and polycyclic aromatic molecules are good model systems for a fundamental understanding of photoconductivity and ferromagnetism in organic materials which depend on the degree of charge delocalization. The structures of the dimer radical cations are difficult to determine theoretically since the potential energy surface is often very flat with multiple shallow minima representing two major classes of isomers adopting the stacked parallel or the T-shape structure. We present experimental results, based on mass-selected ion mobility measurements, on the gas phase structures of the naphthalene+ṡ ṡ naphthalene homodimer and the naphthalene+ṡ ṡ benzene heterodimer radical cations at different temperatures. Ion mobility studies reveal a persistence of the stacked parallel structure of the naphthalene+ṡ ṡ naphthalene homodimer in the temperature range 230-300 K. On the other hand, the results reveal that the naphthalene+ṡ ṡ benzene heterodimer is able to exhibit both the stacked parallel and T-shape structural isomers depending on the experimental conditions. Exploitation of the unique structural motifs among charged homo- and heteroaromatic-aromatic interactions may lead to new opportunities for molecular design and recognition involving charged aromatic systems.

Image recognition on raw and processed potato detection: a review

NASA Astrophysics Data System (ADS)

Qi, Yan-nan; Lü, Cheng-xu; Zhang, Jun-ning; Li, Ya-shuo; Zeng, Zhen; Mao, Wen-hua; Jiang, Han-lu; Yang, Bing-nan

2018-02-01

Objective: Chinese potato staple food strategy clearly pointed out the need to improve potato processing, while the bottleneck of this strategy is technology and equipment of selection of appropriate raw and processed potato. The purpose of this paper is to summarize the advanced raw and processed potato detection methods. Method: According to consult research literatures in the field of image recognition based potato quality detection, including the shape, weight, mechanical damage, germination, greening, black heart, scab potato etc., the development and direction of this field were summarized in this paper. Result: In order to obtain whole potato surface information, the hardware was built by the synchronous of image sensor and conveyor belt to achieve multi-angle images of a single potato. Researches on image recognition of potato shape are popular and mature, including qualitative discrimination on abnormal and sound potato, and even round and oval potato, with the recognition accuracy of more than 83%. Weight is an important indicator for potato grading, and the image classification accuracy presents more than 93%. The image recognition of potato mechanical damage focuses on qualitative identification, with the main affecting factors of damage shape and damage time. The image recognition of potato germination usually uses potato surface image and edge germination point. Both of the qualitative and quantitative detection of green potato have been researched, currently scab and blackheart image recognition need to be operated using the stable detection environment or specific device. The image recognition of processed potato mainly focuses on potato chips, slices and fries, etc. Conclusion: image recognition as a food rapid detection tool have been widely researched on the area of raw and processed potato quality analyses, its technique and equipment have the potential for commercialization in short term, to meet to the strategy demand of development potato as staple food in China.

The Coding of Biological Information: From Nucleotide Sequence to Protein Recognition

NASA Astrophysics Data System (ADS)

Štambuk, Nikola

The paper reviews the classic results of Swanson, Dayhoff, Grantham, Blalock and Root-Bernstein, which link genetic code nucleotide patterns to the protein structure, evolution and molecular recognition. Symbolic representation of the binary addresses defining particular nucleotide and amino acid properties is discussed, with consideration of: structure and metric of the code, direct correspondence between amino acid and nucleotide information, and molecular recognition of the interacting protein motifs coded by the complementary DNA and RNA strands.

Effects of anticaricaturing vs. caricaturing and their neural correlates elucidate a role of shape for face learning.

PubMed

Schulz, Claudia; Kaufmann, Jürgen M; Walther, Lydia; Schweinberger, Stefan R

2012-08-01

To assess the role of shape information for unfamiliar face learning, we investigated effects of photorealistic spatial anticaricaturing and caricaturing on later face recognition. We assessed behavioural performance and event-related brain potential (ERP) correlates of recognition, using different images of anticaricatures, veridical faces, or caricatures at learning and test. Relative to veridical faces, recognition performance improved for caricatures, with performance decrements for anticaricatures in response times. During learning, an amplitude pattern with caricatures>veridicals=anticaricatures was seen for N170, left-hemispheric ERP negativity during the P200 and N250 time segments (200-380 ms), and for a late positive component (LPC, 430-830 ms), whereas P200 and N250 responses exhibited an additional difference between veridicals and anticaricatures over the right hemisphere. During recognition, larger amplitudes for caricatures again started in the N170, whereas the P200 and the right-hemispheric N250 exhibited a more graded pattern of amplitude effects (caricatures>veridicals>anticaricatures), a result which was specific to learned but not novel faces in the N250. Together, the results (i) emphasise the role of facial shape for visual encoding in the learning of previously unfamiliar faces and (ii) provide important information about the neuronal timing of the encoding advantage enjoyed by faces with distinctive shape. Copyright © 2012 Elsevier Ltd. All rights reserved.

Shape shifting: Local landmarks interfere with navigation by, and recognition of, global shape.

PubMed

Buckley, Matthew G; Smith, Alastair D; Haselgrove, Mark

2014-03-01

An influential theory of spatial navigation states that the boundary shape of an environment is preferentially encoded over and above other spatial cues, such that it is impervious to interference from alternative sources of information. We explored this claim with 3 intradimensional-extradimensional shift experiments, designed to examine the interaction of landmark and geometric features of the environment in a virtual navigation task. In Experiments 1 and 2, participants were first required to find a hidden goal using information provided by the shape of the arena or landmarks integrated into the arena boundary (Experiment 1) or within the arena itself (Experiment 2). Participants were then transferred to a different-shaped arena that contained novel landmarks and were again required to find a hidden goal. In both experiments, participants who were navigating on the basis of cues that were from the same dimension that was previously relevant (intradimensional shift) learned to find the goal significantly faster than participants who were navigating on the basis of cues that were from a dimension that was previously irrelevant (extradimensional shift). This suggests that shape information does not hold special status when learning about an environment. Experiment 3 replicated Experiment 2 and also assessed participants' recognition of the global shape of the navigated arenas. Recognition was attenuated when landmarks were relevant to navigation throughout the experiment. The results of these experiments are discussed in terms of associative and non-associative theories of spatial learning.

Biometric recognition using 3D ear shape.

PubMed

Yan, Ping; Bowyer, Kevin W

2007-08-01

Previous works have shown that the ear is a promising candidate for biometric identification. However, in prior work, the preprocessing of ear images has had manual steps and algorithms have not necessarily handled problems caused by hair and earrings. We present a complete system for ear biometrics, including automated segmentation of the ear in a profile view image and 3D shape matching for recognition. We evaluated this system with the largest experimental study to date in ear biometrics, achieving a rank-one recognition rate of 97.8 percent for an identification scenario and an equal error rate of 1.2 percent for a verification scenario on a database of 415 subjects and 1,386 total probes.

Molecular Recognition in Gels, Monolayers, and Solids

DTIC Science & Technology

1991-12-01

monolayers (SAMs) of alkyl thiolates on gold to the study of protein adsorption on organic surfaces; and the use of networkc 20. ISTIBUION AVALABLITYOF...areas of molecular recognition: affinity polymers and molecular self-assembly. We illustrute these artas by examples drawn frozr affinity gel electro...polyacmy~amides be’.ring,,sialic acid groups; the application of self-a-eseinbled monolayers (SAMs) of alkyl thiolates on gold to the study of protein

On the influence of crosslinker on template complexation in molecularly imprinted polymers: a computational study of prepolymerization mixture events with correlations to template-polymer recognition behavior and NMR spectroscopic studies.

PubMed

Shoravi, Siamak; Olsson, Gustaf D; Karlsson, Björn C G; Nicholls, Ian A

2014-06-12

Aspects of the molecular-level basis for the function of ethylene glycol dimethacrylate and trimethylolproprane trimethacrylate crosslinked methacrylic acid copolymers molecularly imprinted with (S)-propranolol have been studied using a series of all-component and all-atom molecular dynamics studies of the corresponding prepolymerization systems. The crosslinking agents were observed to contribute to template complexation, and the results were contrasted with previously reported template-recognition behavior of the corresponding polymers. Differences in the extent to which the two crosslinkers interacted with the functional monomer were identified, and correlations were made to polymer-ligand recognition behavior and the results of nuclear magnetic resonance spectroscopic studies studies. This study demonstrates the importance of considering the functional monomer-crosslinker interaction when designing molecularly imprinted polymers, and highlights the often neglected general contribution of crosslinker to determining the nature of molecularly imprinted polymer-template selectivity.

Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex.

PubMed

Jiang, F; Kumar, R A; Jones, R A; Patel, D J

1996-07-11

The catalytic properties of RNA and its well known role in gene expression and regulation are the consequence of its unique solution structures. Identification of the structural determinants of ligand recognition by RNA molecules is of fundamental importance for understanding the biological functions of RNA, as well as for the rational design of RNA Sequences with specific catalytic activities. Towards this latter end, Szostak et al. used in vitro selection techniques to isolate RNA sequences ('aptamers') containing a high-affinity binding site for ATP, the universal currency of cellular energy, and then used this motif to engineer ribozymes with polynucleotide kinase activity. Here we present the solution structure, as determined by multidimensional NMR spectroscopy and molecular dynamics calculations, of both uniformly and specifically 13C-, 15N-labelled 40-mer RNA containing the ATP-binding motif complexed with AMP. The aptamer adopts an L-shaped structure with two nearly orthogonal stems, each capped proximally by a G x G mismatch pair, binding the AMP ligand at their junction in a GNRA-like motif.

Protein Camouflage: Supramolecular Anion Recognition by Ubiquitin.

PubMed

Mallon, Madeleine; Dutt, Som; Schrader, Thomas; Crowley, Peter B

2016-04-15

Progress in the field of bio-supramolecular chemistry, the bottom-up assembly of protein-ligand systems, relies on a detailed knowledge of molecular recognition. To address this issue, we have characterised complex formation between human ubiquitin (HUb) and four supramolecular anions. The ligands were: pyrenetetrasulfonic acid (4PSA), p-sulfonato-calix[4]arene (SCLX4), bisphosphate tweezers (CLR01) and meso-tetrakis (4-sulfonatophenyl)porphyrin (TPPS), which vary in net charge, size, shape and hydrophobicity. All four ligands induced significant changes in the HSQC spectrum of HUb. Chemical shift perturbations and line-broadening effects were used to identify binding sites and to quantify affinities. Supporting data were obtained from docking simulations. It was found that these weakly interacting ligands bind to extensive surface patches on HUb. A comparison of the data suggests some general indicators for the protein-binding specificity of supramolecular anions. Differences in binding were observed between the cavity-containing and planar ligands. The former had a preference for the arginine-rich, flexible C terminus of HUb. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Vibration mode shape recognition using image processing

NASA Astrophysics Data System (ADS)

Wang, Weizhuo; Mottershead, John E.; Mares, Cristinel

2009-10-01

Currently the most widely used method for comparing mode shapes from finite elements and experimental measurements is the modal assurance criterion (MAC), which can be interpreted as the cosine of the angle between the numerical and measured eigenvectors. However, the eigenvectors only contain the displacement of discrete coordinates, so that the MAC index carries no explicit information on shape features. New techniques, based upon the well-developed philosophies of image processing (IP) and pattern recognition (PR) are considered in this paper. The Zernike moment descriptor (ZMD), Fourier descriptor (FD), and wavelet descriptor (WD) are the most popular shape descriptors due to their outstanding properties in IP and PR. These include (1) for the ZMD-rotational invariance, expression and computing efficiency, ease of reconstruction and robustness to noise; (2) for the FD—separation of the global shape and shape-details by low and high frequency components, respectively, invariance under geometric transformation; (3) for the WD—multi-scale representation and local feature detection. Once a shape descriptor has been adopted, the comparison of mode shapes is transformed to a comparison of multidimensional shape feature vectors. Deterministic and statistical methods are presented. The deterministic problem of measuring the degree of similarity between two mode shapes (possibly one from a vibration test and the other from a finite element model) may be carried out using Pearson's correlation. Similar shape feature vectors may be arranged in clusters separated by Euclidian distances in the feature space. In the statistical analysis we are typically concerned with the classification of a test mode shape according to clusters of shape feature vectors obtained from a randomised finite element model. The dimension of the statistical problem may often be reduced by principal component analysis. Then, in addition to the Euclidian distance, the Mahalanobis distance, defining the separation of the test point from the cluster in terms of its standard deviation, becomes an important measure. Bayesian decision theory may be applied to formally minimise the risk of misclassification of the test shape feature vector. In this paper the ZMD is applied to the problem of mode shape recognition for a circular plate. Results show that the ZMD has considerable advantages over the traditional MAC index when identifying the cyclically symmetric mode shapes that occur in axisymmetric structures at identical frequencies. Mode shape recognition of rectangular plates is carried out by the FD. Also, the WD is applied to the problem of recognising the mode shapes in the thin and thick regions of a plate with different thicknesses. It shows the benefit of using the WD to identify mode-shapes having both local and global components. The comparison and classification of mode shapes using IP and PR provides a 'toolkit' to complement the conventional MAC approach. The selection of a particular shape descriptor and classification method will depend upon the problem in hand and the experience of the analyst.

Learning from the Messengers: Innate Sensing of Viruses and Cytokine Regulation of Immunity—Clues for Treatments and Vaccines

PubMed Central

Melchjorsen, Jesper

2013-01-01

Virus infections are a major global public health concern, and only via substantial knowledge of virus pathogenesis and antiviral immune responses can we develop and improve medical treatments, and preventive and therapeutic vaccines. Innate immunity and the shaping of efficient early immune responses are essential for control of viral infections. In order to trigger an efficient antiviral defense, the host senses the invading microbe via pattern recognition receptors (PRRs), recognizing distinct conserved pathogen-associated molecular patterns (PAMPs). The innate sensing of the invading virus results in intracellular signal transduction and subsequent production of interferons (IFNs) and proinflammatory cytokines. Cytokines, including IFNs and chemokines, are vital molecules of antiviral defense regulating cell activation, differentiation of cells, and, not least, exerting direct antiviral effects. Cytokines shape and modulate the immune response and IFNs are principle antiviral mediators initiating antiviral response through induction of antiviral proteins. In the present review, I describe and discuss the current knowledge on early virus–host interactions, focusing on early recognition of virus infection and the resulting expression of type I and type III IFNs, proinflammatory cytokines, and intracellular antiviral mediators. In addition, the review elucidates how targeted stimulation of innate sensors, such as toll-like receptors (TLRs) and intracellular RNA and DNA sensors, may be used therapeutically. Moreover, I present and discuss data showing how current antimicrobial therapies, including antibiotics and antiviral medication, may interfere with, or improve, immune response. PMID:23435233

The Struggle for Identity in Today's Schools: Cultural Recognition in a Time of Increasing Diversity

ERIC Educational Resources Information Center

Jenlink, Patrick M., Ed; Townes, Faye Hicks, Ed

2009-01-01

The "Struggle for Identity in Today's Schools" examines cultural recognition and the struggle for identity in America's schools. In particular, the contributing authors focus on the recognition and misrecognition as antagonistic cultural forces that work to shape, and at times distort identity. What surfaces throughout the chapters are two lessons…

Global shape recognition is modulated by the spatial distance of local elements--evidence from simultanagnosia.

PubMed

Huberle, Elisabeth; Karnath, Hans-Otto

2006-01-01

Simultanagnosia is a rare deficit that impairs individuals in perceiving several objects at the same time. It is usually observed following bilateral parieto-occipital brain damage. Despite the restrictions in perceiving the global aspect of a scene, processing of individual objects remains unaffected. The mechanisms underlying simultanagnosia are not well understood. Previous findings indicated that the integration of multiple objects into a holistic representation of the environment is not impossible per se, but might depend on the spatial relationship between individual objects. The present study examined the influence of inter-element distances between individual objects on the recognition of global shapes in two patients with simultanagnosia. We presented Navon hierarchical letter stimuli with different inter-element distances between letters at the Local Scale. Improved recognition at the Global Scale was observed in both patients by reducing the inter-element distance. Global shape recognition in simultanagnosia thus seems to be modulated by the spatial distance of local elements and does not appear to be an all-or-nothing phenomenon depending on spatial continuity. The findings seem to argue against a deficit in visual working memory capacity as the primary deficit in simultanagnosia. However, further research is necessary to investigate alternative interpretations.

Automatic lip reading by using multimodal visual features

NASA Astrophysics Data System (ADS)

Takahashi, Shohei; Ohya, Jun

2013-12-01

Since long time ago, speech recognition has been researched, though it does not work well in noisy places such as in the car or in the train. In addition, people with hearing-impaired or difficulties in hearing cannot receive benefits from speech recognition. To recognize the speech automatically, visual information is also important. People understand speeches from not only audio information, but also visual information such as temporal changes in the lip shape. A vision based speech recognition method could work well in noisy places, and could be useful also for people with hearing disabilities. In this paper, we propose an automatic lip-reading method for recognizing the speech by using multimodal visual information without using any audio information such as speech recognition. First, the ASM (Active Shape Model) is used to track and detect the face and lip in a video sequence. Second, the shape, optical flow and spatial frequencies of the lip features are extracted from the lip detected by ASM. Next, the extracted multimodal features are ordered chronologically so that Support Vector Machine is performed in order to learn and classify the spoken words. Experiments for classifying several words show promising results of this proposed method.

Molecularly Imprinted Polymers: Present and Future Prospective

PubMed Central

Vasapollo, Giuseppe; Sole, Roberta Del; Mergola, Lucia; Lazzoi, Maria Rosaria; Scardino, Anna; Scorrano, Sonia; Mele, Giuseppe

2011-01-01

Molecular Imprinting Technology (MIT) is a technique to design artificial receptors with a predetermined selectivity and specificity for a given analyte, which can be used as ideal materials in various application fields. Molecularly Imprinted Polymers (MIPs), the polymeric matrices obtained using the imprinting technology, are robust molecular recognition elements able to mimic natural recognition entities, such as antibodies and biological receptors, useful to separate and analyze complicated samples such as biological fluids and environmental samples. The scope of this review is to provide a general overview on MIPs field discussing first general aspects in MIP preparation and then dealing with various application aspects. This review aims to outline the molecularly imprinted process and present a summary of principal application fields of molecularly imprinted polymers, focusing on chemical sensing, separation science, drug delivery and catalysis. Some significant aspects about preparation and application of the molecular imprinting polymers with examples taken from the recent literature will be discussed. Theoretical and experimental parameters for MIPs design in terms of the interaction between template and polymer functionalities will be considered and synthesis methods for the improvement of MIP recognition properties will also be presented. PMID:22016636

Molecular recognition in protein modification with rhodium metallopeptides

PubMed Central

Ball, Zachary T.

2015-01-01

Chemical manipulation of natural, unengineered proteins is a daunting challenge which tests the limits of reaction design. By combining transition-metal or other catalysts with molecular recognition ideas, it is possible to achieve site-selective protein reactivity without the need for engineered recognition sequences or reactive sites. Some recent examples in this area have used ruthenium photocatalysis, pyridine organocatalysis, and rhodium(II) metallocarbene catalysis, indicating that the fundamental ideas provide opportunities for using diverse reactivity on complex protein substrates and in complex cell-like environments. PMID:25588960

Production of anti-amoxicillin ScFv antibody and simulation studying its molecular recognition mechanism for penicillins.

PubMed

Liu, Jing; Zhang, Hui C; Duan, Chang F; Dong, Jun; Zhao, Guo X; Wang, Jian P; Li, Nan; Liu, Jin Z; Li, Yu W

2016-11-01

The molecular recognition mechanism of an antibody for its hapten is very interesting. The objective of this research was to study the intermolecular interactions of an anti-amoxicillin antibody with penicillin drugs. The single chain variable fragment (ScFv) antibody was generated from a hybridoma cell strain excreting the monoclonal antibody for amoxicillin. The recombinant ScFv antibody showed similar recognition ability for penicillins to its parental monoclonal antibody: simultaneous recognizing 11 penicillins with cross-reactivities of 18-107%. The three-dimensional structure of the ScFv antibody was simulated by using homology modeling, and its intermolecular interactions with 11 penicillins were studied by using molecular docking. Results showed that three CDRs are involved in antibody recognition; CDR L3 Arg 100, CDR H3 Tyr226, and CDR H3 Arg 228 were the key contact amino acid residues; hydrogen bonding was the main antibody-drug intermolecular force; and the core structure of penicillin drugs was the main antibody binding position. These results could explain the recognition mechanism of anti-amoxicillin antibody for amoxicillin and its analogs. This is the first study reporting the production of ScFv antibody for penicillins and stimulation studying its recognition mechanism.

Multifunctional receptor model for dioxin and related compound toxic action: possible thyroid hormone-responsive effector-linked site.

PubMed Central

McKinney, J D

1989-01-01

Molecular/theoretical modeling studies have revealed that thyroid hormones and toxic chlorinated aromatic hydrocarbons of environmental significance (for which dioxin or TCDD is the prototype) have similar structural properties that could be important in molecular recognition in biochemical systems. These molecular properties include a somewhat rigid, sterically accessible and polarizable aromatic ring and size-limited, hydrophobic lateral substituents, usually contained in opposite adjoining rings of a diphenyl compound. These molecular properties define the primary binding groups thought to be important in molecular recognition of both types of structures in biochemical systems. Similar molecular reactivities are supported by the demonstration of effective specific binding of thyroid hormones and chlorinated aromatic hydrocarbons with four different proteins, enzymes, or receptor preparations that are known or suspected to be involved in the expression of thyroid hormone activity. These binding interactions represent both aromatic-aromatic (stacking) and molecular cleft-type recognition processes. A multiple protein or multifunctional receptor-ligand binding mechanism model is proposed as a way of visualizing the details and possible role of both the stacking and cleft type molecular recognition factors in the expression of biological activity. The model suggests a means by which hormone-responsive effector-linked sites (possible protein-protein-DNA complexes) can maintain highly structurally specific control of hormone action. Finally, the model also provides a theoretical basis for the design and conduct of further biological experimentation on the molecular mechanism(s) of action of toxic chlorinated aromatic hydrocarbons and thyroid hormones. Images FIGURE 3. A FIGURE 3. B FIGURE 3. C FIGURE 3. D PMID:2551666

Interplay Between Innate Immunity and the Plant Microbiota.

PubMed

Hacquard, Stéphane; Spaepen, Stijn; Garrido-Oter, Ruben; Schulze-Lefert, Paul

2017-08-04

The innate immune system of plants recognizes microbial pathogens and terminates their growth. However, recent findings suggest that at least one layer of this system is also engaged in cooperative plant-microbe interactions and influences host colonization by beneficial microbial communities. This immune layer involves sensing of microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs) that initiate quantitative immune responses to control host-microbial load, whereas diversification of MAMPs and PRRs emerges as a mechanism that locally sculpts microbial assemblages in plant populations. This suggests a more complex microbial management role of the innate immune system for controlled accommodation of beneficial microbes and in pathogen elimination. The finding that similar molecular strategies are deployed by symbionts and pathogens to dampen immune responses is consistent with this hypothesis but implies different selective pressures on the immune system due to contrasting outcomes on plant fitness. The reciprocal interplay between microbiota and the immune system likely plays a critical role in shaping beneficial plant-microbiota combinations and maintaining microbial homeostasis.

Involvement of the glucose moiety in the molecular recognition of methyl beta-lactoside by ricin: synthesis, conformational analysis, and binding studies of different derivatives at the C-3 region.

PubMed

Fernández, P; Jiménez-Barbero, J; Martín-Lomas, M; Solís, D; Díaz-Mauriño, T

1994-04-01

Syntheses of the 3-aminodeoxy (4), 3-deoxy-3-methyl (5), and 3-epi (6) derivatives of methyl beta-lactoside (1) have been achieved from 1 in a straightforward way, and their solution conformations in water and dimethyl sulfoxide analysed through molecular mechanics and dynamics calculations and nuclear magnetic resonance data. The overall shape of all the compounds studied is fairly similar and may be described by conformers included in a low energy region with phi = 15 +/- 45 degrees and psi = -25 +/- 30 degrees, that is ca. 5% of the total potential energy surface for the glycosidic linkages of the disaccharides. The binding of the different compounds to ricin, the galactose-specific toxin from Ricinus communis, has been investigated. The results confirm the involvement of the C-3 region in a nonpolar interaction with the protein at the periphery of the combining site.

From Caregivers to Peers: Puberty Shapes Human Face Perception.

PubMed

Picci, Giorgia; Scherf, K Suzanne

2016-11-01

Puberty prepares mammals to sexually reproduce during adolescence. It is also hypothesized to invoke a social metamorphosis that prepares adolescents to take on adult social roles. We provide the first evidence to support this hypothesis in humans and show that pubertal development retunes the face-processing system from a caregiver bias to a peer bias. Prior to puberty, children exhibit enhanced recognition for adult female faces. With puberty, superior recognition emerges for peer faces that match one's pubertal status. As puberty progresses, so does the peer recognition bias. Adolescents become better at recognizing faces with a pubertal status similar to their own. These findings reconceptualize the adolescent "dip" in face recognition by showing that it is a recalibration of the face-processing system away from caregivers toward peers. Thus, in addition to preparing the physical body for sexual reproduction, puberty shapes the perceptual system for processing the social world in new ways. © The Author(s) 2016.

Neurotransmitter and psychostimulant recognition by the dopamine transporter

PubMed Central

Wang, Kevin H.; Penmatsa, Aravind; Gouaux, Eric

2015-01-01

Na+/Cl−-coupled biogenic amine transporters are the primary targets of therapeutic and abused drugs, ranging from antidepressants to the psychostimulants cocaine and amphetamines, and to their cognate substrates. Here we determine x-ray crystal structures of the Drosophila melanogaster dopamine transporter (dDAT) bound to its substrate dopamine (DA), a substrate analogue 3,4-dichlorophenethylamine, the psychostimulants D-amphetamine, methamphetamine, or to cocaine and cocaine analogues. All ligands bind to the central binding site, located approximately halfway across the membrane bilayer, in close proximity to bound sodium and chloride ions. The central binding site recognizes three chemically distinct classes of ligands via conformational changes that accommodate varying sizes and shapes, thus illustrating molecular principles that distinguish substrates from inhibitors in biogenic amine transporters. PMID:25970245

Logic-Gate Functions in Chemomechanical Materials.

PubMed

Schneider, Hans-Jörg

2017-09-06

Chemomechanical polymers that change their shape or volume on stimulation by multiple external chemical signals, particularly on the basis of selective molecular recognition, are discussed. Several examples illustrate how such materials, usually in the form of hydrogels, can be used for the design of chemically triggered valves or artificial muscles and applied, for example, in self-healing materials or drug delivery. The most attractive feature of such materials is that they can combine sensor and actuator within single units, from nano- to macrosize. Simultaneous action of a cofactor allows selective response in the sense of AND logic gates by, for example, amino acids and peptides, which without the presence of a second effector do not induce any changes. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

PubMed Central

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

2016-01-01

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

Adsorption and recognition characteristics of surface molecularly imprinted polymethacrylic acid/silica toward genistein.

PubMed

Zhang, Yanyan; Gao, Baojiao; An, Fuqiang; Xu, Zeqing; Zhang, Tingting

2014-09-12

In this paper, on the basis of surface-initiated graft polymerization, a new surface molecular imprinting technique is established by molecular design. And molecularly imprinted polymer MIP-PMAA/SiO2 is successfully prepared with genistein as template. The adsorption and recognition characteristics of MIP-PMAA/SiO2 for genistein are studied in depth by using static method, dynamic method and competitive adsorption experiment. The experimental results show that MIP-PMAA/SiO2 possesses very strong adsorption affinity and specific recognition for genistein. The saturated adsorption capacity could reach to 0.36mmolg(-1). The selectivity coefficients relative to quercetin and rutin are 5.4 and 11.8, respectively. Besides, MIP-PMAA/SiO2 is regenerated easily and exhibits excellent reusability. Copyright © 2014 Elsevier B.V. All rights reserved.

Supramolecular chemistry-general principles and selected examples from anion recognition and metallosupramolecular chemistry.

PubMed

Albrecht, Markus

2007-12-01

This review gives an introduction into supramolecular chemistry describing in the first part general principles, focusing on terms like noncovalent interaction, molecular recognition, self-assembly, and supramolecular function. In the second part those will be illustrated by simple examples from our laboratories. Supramolecular chemistry is the science that bridges the gap between the world of molecules and nanotechnology. In supramolecular chemistry noncovalent interactions occur between molecular building blocks, which by molecular recognition and self-assembly form (functional) supramolecular entities. It is also termed the "chemistry of the noncovalent bond." Molecular recognition is based on geometrical complementarity based on the "key-and-lock" principle with nonshape-dependent effects, e.g., solvatization, being also highly influential. Self-assembly leads to the formation of well-defined aggregates. Hereby the overall structure of the target ensemble is controlled by the symmetry features of the certain building blocks. Finally, the aggregates can possess special properties or supramolecular functions, which are only found in the ensemble but not in the participating molecules. This review gives an introduction on supramolecular chemistry and illustrates the fundamental principles by recent examples from our group.

Detection of λ-cyhalothrin by a core-shell spherical SiO2-based surface thin fluorescent molecularly imprinted polymer film.

PubMed

Gao, Lin; Han, Wenjuan; Li, Xiuying; Wang, Jixiang; Yan, Yongsheng; Li, Chunxiang; Dai, Jiangdong

2015-12-01

A fluorescent core-shell molecularly imprinted polymer based on the surface of SiO2 beads was synthesized and its application in the fluorescence detection of ultra-trace λ-cyhalothrin (LC) was investigated. The shell was prepared by copolymerization of acrylamide with allyl fluorescein in the presence of LC to form recognition sites. The experimental results showed that the thin fluorescent molecularly imprinted polymer (FMIP) film exhibited better selective recognition ability than fluorescent molecularly non-imprinted polymer (FNIP). A new nonlinear relationship between quenching rate and concentration was found in this work. In addition, the nonlinear relationship allowed a lower concentration range of 0-5.0 nM to be described by the Stern-Volmer equation with a correlation coefficient of 0.9929. The experiment results revealed that the SiO2@FMIP was satisfactory as a recognition element for determination of LC in soda water samples. Therefore this study demonstrated the potential of MIP for the recognition and detection of LC in food.

Transformations in the Recognition of Visual Forms

ERIC Educational Resources Information Center

Charness, Neil; Bregman, Albert S.

1973-01-01

In a study which required college students to learn to recognize four flexible plastic shapes photographed on different backgrounds from different angles, the importance of a context-rich environment for the learning and recognition of visual patterns was illustrated. (Author)

Chinese wine classification system based on micrograph using combination of shape and structure features

NASA Astrophysics Data System (ADS)

Wan, Yi

2011-06-01

Chinese wines can be classification or graded by the micrographs. Micrographs of Chinese wines show floccules, stick and granule of variant shape and size. Different wines have variant microstructure and micrographs, we study the classification of Chinese wines based on the micrographs. Shape and structure of wines' particles in microstructure is the most important feature for recognition and classification of wines. So we introduce a feature extraction method which can describe the structure and region shape of micrograph efficiently. First, the micrographs are enhanced using total variation denoising, and segmented using a modified Otsu's method based on the Rayleigh Distribution. Then features are extracted using proposed method in the paper based on area, perimeter and traditional shape feature. Eight kinds total 26 features are selected. Finally, Chinese wine classification system based on micrograph using combination of shape and structure features and BP neural network have been presented. We compare the recognition results for different choices of features (traditional shape features or proposed features). The experimental results show that the better classification rate have been achieved using the combinational features proposed in this paper.

Molecular recognition in poly(epsilon-caprolactone)-based thermoplastic elastomers.

PubMed

Wisse, Eva; Spiering, A J H; van Leeuwen, Ellen N M; Renken, Raymond A E; Dankers, Patricia Y W; Brouwer, Linda A; van Luyn, Marja J A; Harmsen, Martin C; Sommerdijk, Nico A J M; Meijer, E W

2006-12-01

The molecular recognition properties of the hydrogen bonding segments in biodegradable thermoplastic elastomers were explored, aiming at the further functionalization of these potentially interesting biomaterials. A poly(epsilon-caprolactone)-based poly(urea) 2 was synthesized and characterized in terms of mechanical properties, processibility and histocompatibility. Comparison of the data with those obtained from the structurally related poly(urethane urea) 1 revealed that the difference in hard segment structure does not significantly affect the potency for application as a biomaterial. Nevertheless, the small differences in hard block composition had a strong effect on the molecular recognition properties of the hydrogen bonding segments. High selectivity was found for poly(urea) 2 in which bisureidobutylene-functionalized azobenzene dye 3 was selectively incorporated while bisureidopentylene-functionalized azobenzene dye 4 was completely released. In contrast, the incorporation of both dyes in poly(urethane urea) 1 led in both cases to their gradual release in time. Thermal analysis of the polymers in combination with variable temperature infrared experiments indicated that the hard blocks in 1 showed a sharp melting point, whereas those in 2 showed a very broad melting trajectory. This suggests a more precise organization of the hydrogen bonding segments in the hard blocks of poly(urea) 2 compared to poly(urethane urea) 1 and explains the results from the molecular recognition experiments. Preliminary results revealed that a bisureidobutylene-functionalized GRGDS peptide showed more supramolecular interaction with the PCL-based poly(urea), containing the bisureidobutylene recognition unit, as compared to HMW PCL, lacking this recognition unit.

Human detection in sensitive security areas through recognition of omega shapes using MACH filters

NASA Astrophysics Data System (ADS)

Rehman, Saad; Riaz, Farhan; Hassan, Ali; Liaquat, Muwahida; Young, Rupert

2015-03-01

Human detection has gained considerable importance in aggravated security scenarios over recent times. An effective security application relies strongly on detailed information regarding the scene under consideration. A larger accumulation of humans than the number of personal authorized to visit a security controlled area must be effectively detected, amicably alarmed and immediately monitored. A framework involving a novel combination of some existing techniques allows an immediate detection of an undesirable crowd in a region under observation. Frame differencing provides a clear visibility of moving objects while highlighting those objects in each frame acquired by a real time camera. Training of a correlation pattern recognition based filter on desired shapes such as elliptical representations of human faces (variants of an Omega Shape) yields correct detections. The inherent ability of correlation pattern recognition filters caters for angular rotations in the target object and renders decision regarding the existence of the number of persons exceeding an allowed figure in the monitored area.

Theoretical studies of the mechanism of the action of the neurohypophyseal hormones. I. Molecular electrostatic potential (MEP) and molecular electrostatic field (MEF) maps of some vasopressin analogues

NASA Astrophysics Data System (ADS)

Liwo, Adam; Tempczyk, Anna; Grzonka, Zbigniew

1989-09-01

Continuing our theoretical studies of the oxytocin and vasopressin analogues, we have analysed the molecular electrostatic potential (MEP) and the norm of the molecular electrostatic field (MEF) of [1- β-mercaptopropionic acid]-arginine-vasopressin ([Mpa1]-AVP), [1-( β-mercapto- β,β-cyclopentamethylene)propionic acid]-arginine-vasopressin ([Cpp']-AVP), and [1-thiosalicylic acid]-arginine-vasopressin ([Ths']-AVP) whose low-energy conformations were calculated in our previous work. These compounds are known from experiment to exhibit different biological activity. The scalar fields mentioned determine the energy of interaction with either charged (MEP) or polar (MEF) species, the energy being in the second case either optimal or Boltzmann-averaged over all the possible orientations of the dipole moment versus the electrostatic field. The electrostatic interactions slowly vanish with distance and can therefore be considered to be the factor determining the molecular shape at greater distances, which can help in both predicting the interactions with the receptor at the stage of remote recognition and in finding the preferred directions of solvation by a polar solvent. In the analysis of the fields three techniques have been used: (i) the construction of maps in certain planes; (ii) the construction of maps on spheres centered in the charge center of the molecule under study and of poles chosen according to the main axes of the quadrupole moment; and (iii) the construction of surfaces corresponding to a given value of potential. The results obtained show that the shapes of both MEP and MEF are similar in the case of [Mpa1]-AVP and [Cpp1-AVP (biologically active), while some differences emerge when comparing these compounds with [Ths1]-AVP (inactive). It has also been found that both MEP and MEF depend even more strongly on conformation.

The Development of the Orthographic Consistency Effect in Speech Recognition: From Sublexical to Lexical Involvement

ERIC Educational Resources Information Center

Ventura, Paulo; Morais, Jose; Kolinsky, Regine

2007-01-01

The influence of orthography on children's on-line auditory word recognition was studied from the end of Grade 2 to the end of Grade 4, by examining the orthographic consistency effect [Ziegler, J. C., & Ferrand, L. (1998). Orthography shapes the perception of speech: The consistency effect in auditory recognition. "Psychonomic Bulletin & Review",…

Automatic thoracic anatomy segmentation on CT images using hierarchical fuzzy models and registration

NASA Astrophysics Data System (ADS)

Sun, Kaioqiong; Udupa, Jayaram K.; Odhner, Dewey; Tong, Yubing; Torigian, Drew A.

2014-03-01

This paper proposes a thoracic anatomy segmentation method based on hierarchical recognition and delineation guided by a built fuzzy model. Labeled binary samples for each organ are registered and aligned into a 3D fuzzy set representing the fuzzy shape model for the organ. The gray intensity distributions of the corresponding regions of the organ in the original image are recorded in the model. The hierarchical relation and mean location relation between different organs are also captured in the model. Following the hierarchical structure and location relation, the fuzzy shape model of different organs is registered to the given target image to achieve object recognition. A fuzzy connected delineation method is then used to obtain the final segmentation result of organs with seed points provided by recognition. The hierarchical structure and location relation integrated in the model provide the initial parameters for registration and make the recognition efficient and robust. The 3D fuzzy model combined with hierarchical affine registration ensures that accurate recognition can be obtained for both non-sparse and sparse organs. The results on real images are presented and shown to be better than a recently reported fuzzy model-based anatomy recognition strategy.

The Limits of Shape Recognition following Late Emergence from Blindness.

PubMed

McKyton, Ayelet; Ben-Zion, Itay; Doron, Ravid; Zohary, Ehud

2015-09-21

Visual object recognition develops during the first years of life. But what if one is deprived of vision during early post-natal development? Shape information is extracted using both low-level cues (e.g., intensity- or color-based contours) and more complex algorithms that are largely based on inference assumptions (e.g., illumination is from above, objects are often partially occluded). Previous studies, testing visual acuity using a 2D shape-identification task (Lea symbols), indicate that contour-based shape recognition can improve with visual experience, even after years of visual deprivation from birth. We hypothesized that this may generalize to other low-level cues (shape, size, and color), but not to mid-level functions (e.g., 3D shape from shading) that might require prior visual knowledge. To that end, we studied a unique group of subjects in Ethiopia that suffered from an early manifestation of dense bilateral cataracts and were surgically treated only years later. Our results suggest that the newly sighted rapidly acquire the ability to recognize an odd element within an array, on the basis of color, size, or shape differences. However, they are generally unable to find the odd shape on the basis of illusory contours, shading, or occlusion relationships. Little recovery of these mid-level functions is seen within 1 year post-operation. We find that visual performance using low-level cues is relatively robust to prolonged deprivation from birth. However, the use of pictorial depth cues to infer 3D structure from the 2D retinal image is highly susceptible to early and prolonged visual deprivation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Stereo Viewing Modulates Three-Dimensional Shape Processing During Object Recognition: A High-Density ERP Study

PubMed Central

2017-01-01

The role of stereo disparity in the recognition of 3-dimensional (3D) object shape remains an unresolved issue for theoretical models of the human visual system. We examined this issue using high-density (128 channel) recordings of event-related potentials (ERPs). A recognition memory task was used in which observers were trained to recognize a subset of complex, multipart, 3D novel objects under conditions of either (bi-) monocular or stereo viewing. In a subsequent test phase they discriminated previously trained targets from untrained distractor objects that shared either local parts, 3D spatial configuration, or neither dimension, across both previously seen and novel viewpoints. The behavioral data showed a stereo advantage for target recognition at untrained viewpoints. ERPs showed early differential amplitude modulations to shape similarity defined by local part structure and global 3D spatial configuration. This occurred initially during an N1 component around 145–190 ms poststimulus onset, and then subsequently during an N2/P3 component around 260–385 ms poststimulus onset. For mono viewing, amplitude modulation during the N1 was greatest between targets and distracters with different local parts for trained views only. For stereo viewing, amplitude modulation during the N2/P3 was greatest between targets and distracters with different global 3D spatial configurations and generalized across trained and untrained views. The results show that image classification is modulated by stereo information about the local part, and global 3D spatial configuration of object shape. The findings challenge current theoretical models that do not attribute functional significance to stereo input during the computation of 3D object shape. PMID:29022728

3D automatic anatomy recognition based on iterative graph-cut-ASM

NASA Astrophysics Data System (ADS)

Chen, Xinjian; Udupa, Jayaram K.; Bagci, Ulas; Alavi, Abass; Torigian, Drew A.

2010-02-01

We call the computerized assistive process of recognizing, delineating, and quantifying organs and tissue regions in medical imaging, occurring automatically during clinical image interpretation, automatic anatomy recognition (AAR). The AAR system we are developing includes five main parts: model building, object recognition, object delineation, pathology detection, and organ system quantification. In this paper, we focus on the delineation part. For the modeling part, we employ the active shape model (ASM) strategy. For recognition and delineation, we integrate several hybrid strategies of combining purely image based methods with ASM. In this paper, an iterative Graph-Cut ASM (IGCASM) method is proposed for object delineation. An algorithm called GC-ASM was presented at this symposium last year for object delineation in 2D images which attempted to combine synergistically ASM and GC. Here, we extend this method to 3D medical image delineation. The IGCASM method effectively combines the rich statistical shape information embodied in ASM with the globally optimal delineation capability of the GC method. We propose a new GC cost function, which effectively integrates the specific image information with the ASM shape model information. The proposed methods are tested on a clinical abdominal CT data set. The preliminary results show that: (a) it is feasible to explicitly bring prior 3D statistical shape information into the GC framework; (b) the 3D IGCASM delineation method improves on ASM and GC and can provide practical operational time on clinical images.

All-organic microelectromechanical systems integrating specific molecular recognition--a new generation of chemical sensors.

PubMed

Ayela, Cédric; Dubourg, Georges; Pellet, Claude; Haupt, Karsten

2014-09-03

Cantilever-type all-organic microelectromechanical systems based on molecularly imprinted polymers for specific analyte recognition are used as chemical sensors. They are produced by a simple spray-coating-shadow-masking process. Analyte binding to the cantilever generates a measurable change in its resonance frequency. This allows label-free detection by direct mass sensing of low-molecular-weight analytes at nanomolar concentrations. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Physical and Chemical Strategies for Therapeutic Delivery by Using Polymeric Nanoparticles

PubMed Central

Morachis, José M.; Mahmoud, Enas A.

2012-01-01

A significant challenge that most therapeutic agents face is their inability to be delivered effectively. Nanotechnology offers a solution to allow for safe, high-dose, specific delivery of pharmaceuticals to the target tissue. Nanoparticles composed of biodegradable polymers can be designed and engineered with various layers of complexity to achieve drug targeting that was unimaginable years ago by offering multiple mechanisms to encapsulate and strategically deliver drugs, proteins, nucleic acids, or vaccines while improving their therapeutic index. Targeting of nanoparticles to diseased tissue and cells assumes two strategies: physical and chemical targeting. Physical targeting is a strategy enabled by nanoparticle fabrication techniques. It includes using size, shape, charge, and stiffness among other parameters to influence tissue accumulation, adhesion, and cell uptake. New methods to measure size, shape, and polydispersity will enable this field to grow and more thorough comparisons to be made. Physical targeting can be more economically viable when certain fabrication techniques are used. Chemical targeting can employ molecular recognition units to decorate the surface of particles or molecular units responsive to diseased environments or remote stimuli. In this review, we describe sophisticated nanoparticles designed for tissue-specific chemical targeting that use conjugation chemistry to attach targeting moieties. Furthermore, we describe chemical targeting using stimuli responsive nanoparticles that can respond to changes in pH, heat, and light. PMID:22544864

Exploring the sequence-structure protein landscape in the glycosyltransferase family

PubMed Central

Zhang, Ziding; Kochhar, Sunil; Grigorov, Martin

2003-01-01

To understand the molecular basis of glycosyltransferases’ (GTFs) catalytic mechanism, extensive structural information is required. Here, fold recognition methods were employed to assign 3D protein shapes (folds) to the currently known GTF sequences, available in public databases such as GenBank and Swissprot. First, GTF sequences were retrieved and classified into clusters, based on sequence similarity only. Intracluster sequence similarity was chosen sufficiently high to ensure that the same fold is found within a given cluster. Then, a representative sequence from each cluster was selected to compose a subset of GTF sequences. The members of this reduced set were processed by three different fold recognition methods: 3D-PSSM, FUGUE, and GeneFold. Finally, the results from different fold recognition methods were analyzed and compared to sequence-similarity search methods (i.e., BLAST and PSI-BLAST). It was established that the folds of about 70% of all currently known GTF sequences can be confidently assigned by fold recognition methods, a value which is higher than the fold identification rate based on sequence comparison alone (48% for BLAST and 64% for PSI-BLAST). The identified folds were submitted to 3D clustering, and we found that most of the GTF sequences adopt the typical GTF A or GTF B folds. Our results indicate a lack of evidence that new GTF folds (i.e., folds other than GTF A and B) exist. Based on cases where fold identification was not possible, we suggest several sequences as the most promising targets for a structural genomics initiative focused on the GTF protein family. PMID:14500887

Predicting beta-turns in proteins using support vector machines with fractional polynomials

PubMed Central

2013-01-01

Background β-turns are secondary structure type that have essential role in molecular recognition, protein folding, and stability. They are found to be the most common type of non-repetitive structures since 25% of amino acids in protein structures are situated on them. Their prediction is considered to be one of the crucial problems in bioinformatics and molecular biology, which can provide valuable insights and inputs for the fold recognition and drug design. Results We propose an approach that combines support vector machines (SVMs) and logistic regression (LR) in a hybrid prediction method, which we call (H-SVM-LR) to predict β-turns in proteins. Fractional polynomials are used for LR modeling. We utilize position specific scoring matrices (PSSMs) and predicted secondary structure (PSS) as features. Our simulation studies show that H-SVM-LR achieves Qtotal of 82.87%, 82.84%, and 82.32% on the BT426, BT547, and BT823 datasets respectively. These values are the highest among other β-turns prediction methods that are based on PSSMs and secondary structure information. H-SVM-LR also achieves favorable performance in predicting β-turns as measured by the Matthew's correlation coefficient (MCC) on these datasets. Furthermore, H-SVM-LR shows good performance when considering shape strings as additional features. Conclusions In this paper, we present a comprehensive approach for β-turns prediction. Experiments show that our proposed approach achieves better performance compared to other competing prediction methods. PMID:24565438

Predicting beta-turns in proteins using support vector machines with fractional polynomials.

PubMed

Elbashir, Murtada; Wang, Jianxin; Wu, Fang-Xiang; Wang, Lusheng

2013-11-07

β-turns are secondary structure type that have essential role in molecular recognition, protein folding, and stability. They are found to be the most common type of non-repetitive structures since 25% of amino acids in protein structures are situated on them. Their prediction is considered to be one of the crucial problems in bioinformatics and molecular biology, which can provide valuable insights and inputs for the fold recognition and drug design. We propose an approach that combines support vector machines (SVMs) and logistic regression (LR) in a hybrid prediction method, which we call (H-SVM-LR) to predict β-turns in proteins. Fractional polynomials are used for LR modeling. We utilize position specific scoring matrices (PSSMs) and predicted secondary structure (PSS) as features. Our simulation studies show that H-SVM-LR achieves Qtotal of 82.87%, 82.84%, and 82.32% on the BT426, BT547, and BT823 datasets respectively. These values are the highest among other β-turns prediction methods that are based on PSSMs and secondary structure information. H-SVM-LR also achieves favorable performance in predicting β-turns as measured by the Matthew's correlation coefficient (MCC) on these datasets. Furthermore, H-SVM-LR shows good performance when considering shape strings as additional features. In this paper, we present a comprehensive approach for β-turns prediction. Experiments show that our proposed approach achieves better performance compared to other competing prediction methods.

Role of DNA conformation & energetic insights in Msx-1-DNA recognition as revealed by molecular dynamics studies on specific and nonspecific complexes.

PubMed

Kachhap, Sangita; Singh, Balvinder

2015-01-01

In most of homeodomain-DNA complexes, glutamine or lysine is present at 50th position and interacts with 5th and 6th nucleotide of core recognition region. Molecular dynamics simulations of Msx-1-DNA complex (Q50-TG) and its variant complexes, that is specific (Q50K-CC), nonspecific (Q50-CC) having mutation in DNA and (Q50K-TG) in protein, have been carried out. Analysis of protein-DNA interactions and structure of DNA in specific and nonspecific complexes show that amino acid residues use sequence-dependent shape of DNA to interact. The binding free energies of all four complexes were analysed to define role of amino acid residue at 50th position in terms of binding strength considering the variation in DNA on stability of protein-DNA complexes. The order of stability of protein-DNA complexes shows that specific complexes are more stable than nonspecific ones. Decomposition analysis shows that N-terminal amino acid residues have been found to contribute maximally in binding free energy of protein-DNA complexes. Among specific protein-DNA complexes, K50 contributes more as compared to Q50 towards binding free energy in respective complexes. The sequence dependence of local conformation of DNA enables Q50/Q50K to make hydrogen bond with nucleotide(s) of DNA. The changes in amino acid sequence of protein are accommodated and stabilized around TAAT core region of DNA having variation in nucleotides.

Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin.

PubMed

Fuchs, Julian E; Huber, Roland G; Waldner, Birgit J; Kahler, Ursula; von Grafenstein, Susanne; Kramer, Christian; Liedl, Klaus R

2015-01-01

Biomolecular recognition is crucial in cellular signal transduction. Signaling is mediated through molecular interactions at protein-protein interfaces. Still, specificity and promiscuity of protein-protein interfaces cannot be explained using simplistic static binding models. Our study rationalizes specificity of the prototypic protein-protein interface between thrombin and its peptide substrates relying solely on binding site dynamics derived from molecular dynamics simulations. We find conformational selection and thus dynamic contributions to be a key player in biomolecular recognition. Arising entropic contributions complement chemical intuition primarily reflecting enthalpic interaction patterns. The paradigm "dynamics govern specificity" might provide direct guidance for the identification of specific anchor points in biomolecular recognition processes and structure-based drug design.

Presentations of Shape in Object Recognition and Long-Term Visual Memory

DTIC Science & Technology

1994-04-05

theory of human image understanding . Psychological Review, 94, 115-147. Biederman, I., & Gerhardstein, P. C. (1993). Recognizing depth-rotated...Kybemetik. Submitted to Journal of Experimental Psychology: Human Perception and Performance. REFERENCES Biederman, I. (1987). Recognition-by-components: A

Using molecular recognition of beta-cyclodextrin to determine molecular weights of low-molecular-weight explosives by MALDI-TOF mass spectrometry.

PubMed

Zhang, Min; Shi, Zhen; Bai, Yinjuan; Gao, Yong; Hu, Rongzu; Zhao, Fenqi

2006-02-01

This study presents a novel method for determining the molecular weights of low molecular weight (MW) energetic compounds through their complexes of beta-cyclodextrin (beta-CD) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) in a mass range of 500 to 1700 Da, avoiding matrix interference. The MWs of one composite explosive composed of 2,6-DNT, TNT, and RDX, one propellant with unknown components, and 14 single-compound explosives (RDX, HMX, 3,4-DNT, 2,6-DNT, 2,5-DNT, 2,4,6-TNT, TNAZ, DNI, BTTN, NG, TO, NTO, NP, and 662) were measured. The molecular recognition and inclusion behavior of beta-CD to energetic materials (EMs) were investigated. The results show that (1) the established method is sensitive, simple, accurate, and suitable for determining the MWs of low-MW single-compound explosives and energetic components in composite explosives and propellants; and (2) beta-CD has good inclusion and modular recognition abilities to the above EMs.

Calixarenes in analytical and separation chemistry.

PubMed

Ludwig, R

2000-05-01

Discovered in the 1940's, [1n]metacyclophanes with the common name calix[n]arenes which is derived from for the molecule's shape enjoyed a remarkable interest in almost all fields of chemistry since the 1980's, which is highlighted by several books [1-8]. Over 50 reviews concerning their synthesis, properties and applicabilities were published, many of those with emphasis on organic synthesis and structural properties are cited in [P. 5-6 in 2]. Of interest for analytical chemists are reviews on calixarenes and the structurally related resorcin[n]arenes (or calix[n]resorcarenes) and calixpyrroles concerning potentiometric sensors [9-12], chromo- and fluorophores [13, 14], molecular switches [15], metal ion binding in solution [16-19], redox properties [20] and anion binding [21-24]. Other recent reviews deal with thermodynamic aspects [25], organometallic compounds [26], P-containing calixarenes [27-29], as well as molecular dynamics modeling [30-33]. It is a vital field with over 200 publications per year. Therefore, this article presents only selected results on complexation, solvent extraction and membrane transport with the emphasis on ion and molecular recognition which can be used for analytical purposes, without attempting to cover all available references.

Molecular recognition of 7-(2-octadecyloxycarbonylethyl)guanine to cytidine at the air/water interface and LB film studied by Fourier transform infrared spectroscopy

NASA Astrophysics Data System (ADS)

Miao, Wangen; Luo, Xuzhong; Liang, Yingqiu

2003-03-01

Monolayer behavior of a nucleolipid amphiphile, 7-(2-octadecyloxycarbonylethyl)guanine (ODCG), on aqueous cytidine solution was investigated by means of surface-molecular area ( π- A) isotherms. It indicates that molecular recognition by hydrogen bonding is present between ODCG monolayer and the cytidine in subphase. The Fourier transform infrared (FTIR) transmission spectroscopic result indicates that the cytidine molecules in the subphase can be transferred onto solid substrates by Langmuir-Blodgett (LB) technique as a result of the formation of Watson-Crick base-pairing at the air/water interface. Investigation by rotating polarized FTIR transmission also suggests that the headgroup recognition of this amphiphile to the dissolved cytidine influence the orientation of the tailchains.

Hierarchical human action recognition around sleeping using obscured posture information

NASA Astrophysics Data System (ADS)

Kudo, Yuta; Sashida, Takehiko; Aoki, Yoshimitsu

2015-04-01

This paper presents a new approach for human action recognition around sleeping with the human body parts locations and the positional relationship between human and sleeping environment. Body parts are estimated from the depth image obtained by a time-of-flight (TOF) sensor using oriented 3D normal vector. Issues in action recognition of sleeping situation are the demand of availability in darkness, and hiding of the human body by duvets. Therefore, the extraction of image features is difficult since color and edge features are obscured by covers. Thus, first in our method, positions of four parts of the body (head, torso, thigh, and lower leg) are estimated by using the shape model of bodily surface constructed by oriented 3D normal vector. This shape model can represent the surface shape of rough body, and is effective in robust posture estimation of the body hidden with duvets. Then, action descriptor is extracted from the position of each body part. The descriptor includes temporal variation of each part of the body and spatial vector of position of the parts and the bed. Furthermore, this paper proposes hierarchical action classes and classifiers to improve the indistinct action classification. Classifiers are composed of two layers, and recognize human action by using the action descriptor. First layer focuses on spatial descriptor and classifies action roughly. Second layer focuses on temporal descriptor and classifies action finely. This approach achieves a robust recognition of obscured human by using the posture information and the hierarchical action recognition.

Monkeys recall and reproduce simple shapes from memory.

PubMed

Basile, Benjamin M; Hampton, Robert R

2011-05-10

If you draw from memory a picture of the front of your childhood home, you will have demonstrated recall. You could also recognize this house upon seeing it. Unlike recognition, recall demonstrates memory for things that are not present. Recall is necessary for planning and imagining, and it can increase the flexibility of navigation, social behavior, and other cognitive skills. Without recall, memory is more limited to recognition of the immediate environment. Amnesic patients are impaired on recall tests [1, 2], and recall performance often declines with aging [3]. Despite its importance, we know relatively little about nonhuman animals' ability to recall information; we lack suitable recall tests for them and depend instead on recognition tests to measure nonhuman memory. Here we report that rhesus monkeys can recall simple shapes from memory and reproduce them on a touchscreen. As in humans [4, 5], monkeys remembered less in recall than recognition tests, and their recall performance deteriorated more slowly. Transfer tests showed that monkeys used a flexible memory mechanism rather than memorizing specific actions for each shape. Observation of recall in Old World monkeys suggests that it has been adaptive for over 30 million years [6] and does not depend on language. Copyright © 2011 Elsevier Ltd. All rights reserved.

Recognition intent and visual word recognition.

PubMed

Wang, Man-Ying; Ching, Chi-Le

2009-03-01

This study adopted a change detection task to investigate whether and how recognition intent affects the construction of orthographic representation in visual word recognition. Chinese readers (Experiment 1-1) and nonreaders (Experiment 1-2) detected color changes in radical components of Chinese characters. Explicit recognition demand was imposed in Experiment 2 by an additional recognition task. When the recognition was implicit, a bias favoring the radical location informative of character identity was found in Chinese readers (Experiment 1-1), but not nonreaders (Experiment 1-2). With explicit recognition demands, the effect of radical location interacted with radical function and word frequency (Experiment 2). An estimate of identification performance under implicit recognition was derived in Experiment 3. These findings reflect the joint influence of recognition intent and orthographic regularity in shaping readers' orthographic representation. The implication for the role of visual attention in word recognition was also discussed.

3D face analysis by using Mesh-LBP feature

NASA Astrophysics Data System (ADS)

Wang, Haoyu; Yang, Fumeng; Zhang, Yuming; Wu, Congzhong

2017-11-01

Objective: Face Recognition is one of the widely application of image processing. Corresponding two-dimensional limitations, such as the pose and illumination changes, to a certain extent restricted its accurate rate and further development. How to overcome the pose and illumination changes and the effects of self-occlusion is the research hotspot and difficulty, also attracting more and more domestic and foreign experts and scholars to study it. 3D face recognition fusing shape and texture descriptors has become a very promising research direction. Method: Our paper presents a 3D point cloud based on mesh local binary pattern grid (Mesh-LBP), then feature extraction for 3D face recognition by fusing shape and texture descriptors. 3D Mesh-LBP not only retains the integrity of the 3D geometry, is also reduces the need for recognition process of normalization steps, because the triangle Mesh-LBP descriptor is calculated on 3D grid. On the other hand, in view of multi-modal consistency in face recognition advantage, construction of LBP can fusing shape and texture information on Triangular Mesh. In this paper, some of the operators used to extract Mesh-LBP, Such as the normal vectors of the triangle each face and vertex, the gaussian curvature, the mean curvature, laplace operator and so on. Conclusion: First, Kinect devices obtain 3D point cloud face, after the pretreatment and normalization, then transform it into triangular grid, grid local binary pattern feature extraction from face key significant parts of face. For each local face, calculate its Mesh-LBP feature with Gaussian curvature, mean curvature laplace operator and so on. Experiments on the our research database, change the method is robust and high recognition accuracy.

Molecular Imprinting of Macromolecules for Sensor Applications

PubMed Central

Saylan, Yeşeren; Yilmaz, Fatma; Özgür, Erdoğan; Derazshamshir, Ali; Yavuz, Handan; Denizli, Adil

2017-01-01

Molecular recognition has an important role in numerous living systems. One of the most important molecular recognition methods is molecular imprinting, which allows host compounds to recognize and detect several molecules rapidly, sensitively and selectively. Compared to natural systems, molecular imprinting methods have some important features such as low cost, robustness, high recognition ability and long term durability which allows molecularly imprinted polymers to be used in various biotechnological applications, such as chromatography, drug delivery, nanotechnology, and sensor technology. Sensors are important tools because of their ability to figure out a potentially large number of analytical difficulties in various areas with different macromolecular targets. Proteins, enzymes, nucleic acids, antibodies, viruses and cells are defined as macromolecules that have wide range of functions are very important. Thus, macromolecules detection has gained great attention in concerning the improvement in most of the studies. The applications of macromolecule imprinted sensors will have a spacious exploration according to the low cost, high specificity and stability. In this review, macromolecules for molecularly imprinted sensor applications are structured according to the definition of molecular imprinting methods, developments in macromolecular imprinting methods, macromolecular imprinted sensors, and conclusions and future perspectives. This chapter follows the latter strategies and focuses on the applications of macromolecular imprinted sensors. This allows discussion on how sensor strategy is brought to solve the macromolecules imprinting. PMID:28422082

Molecular Imprinting of Macromolecules for Sensor Applications.

PubMed

Saylan, Yeşeren; Yilmaz, Fatma; Özgür, Erdoğan; Derazshamshir, Ali; Yavuz, Handan; Denizli, Adil

2017-04-19

Molecular recognition has an important role in numerous living systems. One of the most important molecular recognition methods is molecular imprinting, which allows host compounds to recognize and detect several molecules rapidly, sensitively and selectively. Compared to natural systems, molecular imprinting methods have some important features such as low cost, robustness, high recognition ability and long term durability which allows molecularly imprinted polymers to be used in various biotechnological applications, such as chromatography, drug delivery, nanotechnology, and sensor technology. Sensors are important tools because of their ability to figure out a potentially large number of analytical difficulties in various areas with different macromolecular targets. Proteins, enzymes, nucleic acids, antibodies, viruses and cells are defined as macromolecules that have wide range of functions are very important. Thus, macromolecules detection has gained great attention in concerning the improvement in most of the studies. The applications of macromolecule imprinted sensors will have a spacious exploration according to the low cost, high specificity and stability. In this review, macromolecules for molecularly imprinted sensor applications are structured according to the definition of molecular imprinting methods, developments in macromolecular imprinting methods, macromolecular imprinted sensors, and conclusions and future perspectives. This chapter follows the latter strategies and focuses on the applications of macromolecular imprinted sensors. This allows discussion on how sensor strategy is brought to solve the macromolecules imprinting.

Shape Recognition in Infancy: Visual Integration of Sequential Information.

ERIC Educational Resources Information Center

Rose, Susan A

1988-01-01

Investigated infants' integration of visual information across space and time. In four experiments, infants aged 12 months and 6 months viewed objects after watching light trace similar and dissimilar shapes. Infants looked longer at novel shapes, although six-month-olds did not recognize figures taking more than 10 seconds to trace. One-year-old…

Perceptual Effects of Social Salience: Evidence from Self-Prioritization Effects on Perceptual Matching

ERIC Educational Resources Information Center

Sui, Jie; He, Xun; Humphreys, Glyn W.

2012-01-01

We present novel evidence showing that new self-relevant visual associations can affect performance in simple shape recognition tasks. Participants associated labels for themselves, other people, or neutral terms with geometric shapes and then immediately judged whether subsequent label-shape pairings were matched. Across 4 experiments there was a…

Shape Shifting: Local Landmarks Interfere with Navigation By, and Recognition Of, Global Shape

ERIC Educational Resources Information Center

Buckley, Matthew G.; Smith, Alastair D.; Haselgrove, Mark

2014-01-01

An influential theory of spatial navigation states that the boundary shape of an environment is preferentially encoded over and above other spatial cues, such that it is impervious to interference from alternative sources of information. We explored this claim with 3 intradimensional--extradimensional shift experiments, designed to examine the…

Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches.

PubMed

Jiang, Hanlun; Zhu, Lizhe; Héliou, Amélie; Gao, Xin; Bernauer, Julie; Huang, Xuhui

2017-01-01

MicroRNA (miRNA) and Argonaute (AGO) protein together form the RNA-induced silencing complex (RISC) that plays an essential role in the regulation of gene expression. Elucidating the underlying mechanism of AGO-miRNA recognition is thus of great importance not only for the in-depth understanding of miRNA function but also for inspiring new drugs targeting miRNAs. In this chapter we introduce a combined computational approach of molecular dynamics (MD) simulations, Markov state models (MSMs), and protein-RNA docking to investigate AGO-miRNA recognition. Constructed from MD simulations, MSMs can elucidate the conformational dynamics of AGO at biologically relevant timescales. Protein-RNA docking can then efficiently identify the AGO conformations that are geometrically accessible to miRNA. Using our recent work on human AGO2 as an example, we explain the rationale and the workflow of our method in details. This combined approach holds great promise to complement experiments in unraveling the mechanisms of molecular recognition between large, flexible, and complex biomolecules.

Engineering of an Extremely Thermostable Alpha/Beta Barrel Scaffold to Serve as a High Affinity Molecular Recognition Element for Use in Sensor Applications

DTIC Science & Technology

2015-12-23

papers submitted or published that acknowledge ARO support from the start of the project to the date of this printing. List the papers, including...1. Koide, S. & Sidhu, S.S. The importance of being tyrosine: lessons in molecular recognition from minimalist synthetic binding proteins. ACS

Molecular docking of superantigens with class II major histocompatibility complex proteins.

PubMed

Olson, M A; Cuff, L

1997-01-01

The molecular recognition of two superantigens with class II major histocompatibility complex molecules was simulated by using protein-protein docking. Superantigens studied were staphylococcal enterotoxin B (SEB) and toxic shock syndrome toxin-1 (TSST-1) in their crystallographic assemblies with HLA-DR1. Rigid-body docking was performed sampling configurational space of the interfacial surfaces by employing a strategy of partitioning the contact regions on HLA-DR1 into separate molecular recognition units. Scoring of docked conformations was based on an electrostatic continuum model evaluated with the finite-difference Poisson-Boltzmann method. Estimates of nonpolar contributions were derived from the buried molecular surface areas. We found for both superantigens that docking the HLA-DR1 surface complementary with the SEB and TSST-1 contact regions containing a homologous hydrophobic surface loop provided sufficient recognition for the reconstitution of native-like conformers exhibiting the highest-scoring free energies. For the SEB complex, the calculations were successful in reproducing the total association free energy. A comparison of the free-energy determinants of the conserved hydrophobic contact residue indicates functional similarity between the two proteins for this interface. Though both superantigens share a common global association mode, differences in binding topology distinguish the conformational specificities underlying recognition.

Organization of inorganic nanomaterials via programmable DNA self-assembly and peptide molecular recognition.

PubMed

Carter, Joshua D; LaBean, Thomas H

2011-03-22

An interesting alternative to top-down nanofabrication is to imitate biology, where nanoscale materials frequently integrate organic molecules for self-assembly and molecular recognition with ordered, inorganic minerals to achieve mechanical, sensory, or other advantageous functions. Using biological systems as inspiration, researchers have sought to mimic the nanoscale composite materials produced in nature. Here, we describe a combination of self-assembly, molecular recognition, and templating, relying on an oligonucleotide covalently conjugated to a high-affinity gold-binding peptide. After integration of the peptide-coupled DNA into a self-assembling superstructure, the templated peptides recognize and bind gold nanoparticles. In addition to providing new ways of building functional multinanoparticle systems, this work provides experimental proof that a single peptide molecule is sufficient for immobilization of a nanoparticle. This molecular construction strategy, combining DNA assembly and peptide recognition, can be thought of as programmable, granular, artificial biomineralization. We also describe the important observation that the addition of 1-2% Tween 20 surfactant to the solution during gold particle binding allows the gold nanoparticles to remain soluble within the magnesium-containing DNA assembly buffer under conditions that usually lead to the aggregation and precipitation of the nanoparticles.

Crystal structure of RlmAI: Implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site

PubMed Central

Das, Kalyan; Acton, Thomas; Chiang, Yiwen; Shih, Lydia; Arnold, Eddy; Montelione, Gaetano T.

2004-01-01

The RlmA class of enzymes (RlmAI and RlmAII) catalyzes N1-methylation of a guanine base (G745 in Gram-negative and G748 in Gram-positive bacteria) of hairpin 35 of 23S rRNA. We have determined the crystal structure of Escherichia coli RlmAI at 2.8-Å resolution, providing 3D structure information for the RlmA class of RNA methyltransferases. The dimeric protein structure exhibits features that provide new insights into its molecular function. Each RlmAI molecule has a Zn-binding domain, responsible for specific recognition and binding of its rRNA substrate, and a methyltransferase domain. The asymmetric RlmAI dimer observed in the crystal structure has a well defined W-shaped RNA-binding cleft. Two S-adenosyl-l-methionine substrate molecules are located at the two valleys of the W-shaped RNA-binding cleft. The unique shape of the RNA-binding cleft, different from that of known RNA-binding proteins, is highly specific and structurally complements the 3D structure of hairpin 35 of bacterial 23S rRNA. Apart from the hairpin 35, parts of hairpins 33 and 34 also interact with the RlmAI dimer. PMID:14999102

Crystal structure of Clostridium botulinum whole hemagglutinin reveals a huge triskelion-shaped molecular complex.

PubMed

Amatsu, Sho; Sugawara, Yo; Matsumura, Takuhiro; Kitadokoro, Kengo; Fujinaga, Yukako

2013-12-06

Clostridium botulinum HA is a component of the large botulinum neurotoxin complex and is critical for its oral toxicity. HA plays multiple roles in toxin penetration in the gastrointestinal tract, including protection from the digestive environment, binding to the intestinal mucosal surface, and disruption of the epithelial barrier. At least two properties of HA contribute to these roles: the sugar-binding activity and the barrier-disrupting activity that depends on E-cadherin binding of HA. HA consists of three different proteins, HA1, HA2, and HA3, whose structures have been partially solved and are made up mainly of β-strands. Here, we demonstrate structural and functional reconstitution of whole HA and present the complete structure of HA of serotype B determined by x-ray crystallography at 3.5 Å resolution. This structure reveals whole HA to be a huge triskelion-shaped molecule. Our results suggest that whole HA is functionally and structurally separable into two parts: HA1, involved in recognition of cell-surface carbohydrates, and HA2-HA3, involved in paracellular barrier disruption by E-cadherin binding.

Case study of 3D fingerprints applications

PubMed Central

Liu, Feng; Liang, Jinrong; Shen, Linlin; Yang, Meng; Zhang, David; Lai, Zhihui

2017-01-01

Human fingers are 3D objects. More information will be provided if three dimensional (3D) fingerprints are available compared with two dimensional (2D) fingerprints. Thus, this paper firstly collected 3D finger point cloud data by Structured-light Illumination method. Additional features from 3D fingerprint images are then studied and extracted. The applications of these features are finally discussed. A series of experiments are conducted to demonstrate the helpfulness of 3D information to fingerprint recognition. Results show that a quick alignment can be easily implemented under the guidance of 3D finger shape feature even though this feature does not work for fingerprint recognition directly. The newly defined distinctive 3D shape ridge feature can be used for personal authentication with Equal Error Rate (EER) of ~8.3%. Also, it is helpful to remove false core point. Furthermore, a promising of EER ~1.3% is realized by combining this feature with 2D features for fingerprint recognition which indicates the prospect of 3D fingerprint recognition. PMID:28399141

Case study of 3D fingerprints applications.

PubMed

Liu, Feng; Liang, Jinrong; Shen, Linlin; Yang, Meng; Zhang, David; Lai, Zhihui

2017-01-01

Human fingers are 3D objects. More information will be provided if three dimensional (3D) fingerprints are available compared with two dimensional (2D) fingerprints. Thus, this paper firstly collected 3D finger point cloud data by Structured-light Illumination method. Additional features from 3D fingerprint images are then studied and extracted. The applications of these features are finally discussed. A series of experiments are conducted to demonstrate the helpfulness of 3D information to fingerprint recognition. Results show that a quick alignment can be easily implemented under the guidance of 3D finger shape feature even though this feature does not work for fingerprint recognition directly. The newly defined distinctive 3D shape ridge feature can be used for personal authentication with Equal Error Rate (EER) of ~8.3%. Also, it is helpful to remove false core point. Furthermore, a promising of EER ~1.3% is realized by combining this feature with 2D features for fingerprint recognition which indicates the prospect of 3D fingerprint recognition.

Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin

PubMed Central

Fuchs, Julian E.; Huber, Roland G.; Waldner, Birgit J.; Kahler, Ursula; von Grafenstein, Susanne; Kramer, Christian; Liedl, Klaus R.

2015-01-01

Biomolecular recognition is crucial in cellular signal transduction. Signaling is mediated through molecular interactions at protein-protein interfaces. Still, specificity and promiscuity of protein-protein interfaces cannot be explained using simplistic static binding models. Our study rationalizes specificity of the prototypic protein-protein interface between thrombin and its peptide substrates relying solely on binding site dynamics derived from molecular dynamics simulations. We find conformational selection and thus dynamic contributions to be a key player in biomolecular recognition. Arising entropic contributions complement chemical intuition primarily reflecting enthalpic interaction patterns. The paradigm “dynamics govern specificity” might provide direct guidance for the identification of specific anchor points in biomolecular recognition processes and structure-based drug design. PMID:26496636

Design and development of molecularly imprinted polymers for the selective extraction of deltamethrin in olive oil: An integrated computational-assisted approach.

PubMed

Martins, Nuno; Carreiro, Elisabete P; Locati, Abel; Ramalho, João P Prates; Cabrita, Maria João; Burke, Anthony J; Garcia, Raquel

2015-08-28

This work firstly addresses the design and development of molecularly imprinted systems selective for deltamethrin aiming to provide a suitable sorbent for solid phase (SPE) extraction that will be further used for the implementation of an analytical methodology for the trace analysis of the target pesticide in spiked olive oil samples. To achieve this goal, a preliminary evaluation of the molecular recognition and selectivity of the molecularly imprinted polymers has been performed. In order to investigate the complexity of the mechanistic basis for template selective recognition in these polymeric matrices, the use of a quantum chemical approach has been attempted providing new insights about the mechanisms underlying template recognition, and in particular the crucial role of the crosslinker agent and the solvent used. Thus, DFT calculations corroborate the results obtained by experimental molecular recognition assays enabling one to select the most suitable imprinting system for MISPE extraction technique which encompasses acrylamide as functional monomer and ethylene glycol dimethacrylate as crosslinker. Furthermore, an analytical methodology comprising a sample preparation step based on solid phase extraction has been implemented using this "tailor made" imprinting system as sorbent, for the selective isolation/pre-concentration of deltamethrin from olive oil samples. Molecularly imprinted solid phase extraction (MISPE) methodology was successfully applied for the clean-up of spiked olive oil samples, with recovery rates up to 94%. Copyright © 2015 Elsevier B.V. All rights reserved.

Molecular recognition of 7-(2-octadecyloxycarbonylethyl)guanine to cytidine at the air/water interface and LB film studied by Fourier transform infrared spectroscopy.

PubMed

Miao, Wangen; Luo, Xuzhong; Liang, Yingqiu

2003-03-15

Monolayer behavior of a nucleolipid amphiphile, 7-(2-octadecyloxycarbonylethyl)guanine (ODCG), on aqueous cytidine solution was investigated by means of surface-molecular area (pi-A) isotherms. It indicates that molecular recognition by hydrogen bonding is present between ODCG monolayer and the cytidine in subphase. The Fourier transform infrared (FTIR) transmission spectroscopic result indicates that the cytidine molecules in the subphase can be transferred onto solid substrates by Langmuir-Blodgett (LB) technique as a result of the formation of Watson-Crick base-pairing at the air/water interface. Investigation by rotating polarized FTIR transmission also suggests that the headgroup recognition of this amphiphile to the dissolved cytidine influence the orientation of the tailchains. Copyright 2002 Elsevier Science B.V.

Direct recognition of superparamagnetic nanocrystals by macrophage scavenger receptor SR-AI.

PubMed

Chao, Ying; Karmali, Priya P; Mukthavaram, Rajesh; Kesari, Santosh; Kouznetsova, Valentina L; Tsigelny, Igor F; Simberg, Dmitri

2013-05-28

Scavenger receptors (SRs) are molecular pattern recognition receptors that have been shown to mediate opsonin-independent uptake of therapeutic and imaging nanoparticles, underlying the importance of SRs in nanomedicine. Unlike pathogens, engineered nanomaterials offer great flexibility in control of surface properties, allowing addressing specific questions regarding the molecular mechanisms of nanoparticle recognition. Recently, we showed that SR-type AI/II mediates opsonin-independent internalization of dextran superparamagnetic iron oxide (SPIO) nanoparticles via positively charged extracellular collagen-like domain. To understand the mechanism of opsonin-independent SPIO recognition, we tested the binding and uptake of nanoparticles with different surface coatings by SR-AI. SPIO coated with 10 kDa dextran was efficiently recognized and taken up by SR-AI transfected cells and J774 macrophages, while SPIO with 20 kDa dextran coating or cross-linked dextran hydrogel avoided the binding and uptake. Nanoparticle negative charge density and zeta-potential did not correlate with SR-AI binding/uptake efficiency. Additional experiments and computer modeling revealed that recognition of the iron oxide crystalline core by the positively charged collagen-like domain of SR-AI is sterically hindered by surface polymer coating. Importantly, the modeling revealed a strong complementarity between the surface Fe-OH groups of the magnetite crystal and the charged lysines of the collagen-like domain of SR-AI, suggesting a specific recognition of SPIO crystalline surface. These data provide an insight into the molecular recognition of nanocrystals by innate immunity receptors and the mechanisms whereby polymer coatings promote immune evasion.

Enhanced associative memory for colour (but not shape or location) in synaesthesia.

PubMed

Pritchard, Jamie; Rothen, Nicolas; Coolbear, Daniel; Ward, Jamie

2013-05-01

People with grapheme-colour synaesthesia have been shown to have enhanced memory on a range of tasks using both stimuli that induce synaesthesia (e.g. words) and, more surprisingly, stimuli that do not (e.g. certain abstract visual stimuli). This study examines the latter by using multi-featured stimuli consisting of shape, colour and location conjunctions (e.g. shape A+colour A+location A; shape B+colour B+location B) presented in a recognition memory paradigm. This enables distractor items to be created in which one of these features is 'unbound' with respect to the others (e.g. shape A+colour B+location A; shape A+colour A+location C). Synaesthetes had higher recognition rates suggesting an enhanced ability to bind certain visual features together into memory. Importantly, synaesthetes' false alarm rates were lower only when colour was the unbound feature, not shape or location. We suggest that synaesthetes are "colour experts" and that enhanced perception can lead to enhanced memory in very specific ways; but, not for instance, an enhanced ability to form associations per se. The results support contemporary models that propose a continuum between perception and memory. Copyright © 2013 Elsevier B.V. All rights reserved.

Event-related potentials during word mapping to object shape predict toddlers' vocabulary size

PubMed Central

Borgström, Kristina; Torkildsen, Janne von Koss; Lindgren, Magnus

2015-01-01

What role does attention to different object properties play in early vocabulary development? This longitudinal study using event-related potentials in combination with behavioral measures investigated 20- and 24-month-olds' (n = 38; n = 34; overlapping n = 24) ability to use object shape and object part information in word-object mapping. The N400 component was used to measure semantic priming by images containing shape or detail information. At 20 months, the N400 to words primed by object shape varied in topography and amplitude depending on vocabulary size, and these differences predicted productive vocabulary size at 24 months. At 24 months, when most of the children had vocabularies of several hundred words, the relation between vocabulary size and the N400 effect in a shape context was weaker. Detached object parts did not function as word primes regardless of age or vocabulary size, although the part-objects were identified behaviorally. The behavioral measure, however, also showed relatively poor recognition of the part-objects compared to the shape-objects. These three findings provide new support for the link between shape recognition and early vocabulary development. PMID:25762957

Label-free biosensing with functionalized nanopipette probes.

PubMed

Umehara, Senkei; Karhanek, Miloslav; Davis, Ronald W; Pourmand, Nader

2009-03-24

Nanopipette technology can uniquely identify biomolecules such as proteins based on differences in size, shape, and electrical charge. These differences are determined by the detection of changes in ionic current as the proteins interact with the nanopipette tip coated with probe molecules. Here we show that electrostatic, biotin-streptavidin, and antibody-antigen interactions on the nanopipette tip surface affect ionic current flowing through a 50-nm pore. Highly charged polymers interacting with the glass surface modulated the rectification property of the nanopipette electrode. Affinity-based binding between the probes tethered to the surface and their target proteins caused a change in the ionic current due to a partial blockade or an altered surface charge. These findings suggest that nanopipettes functionalized with appropriate molecular recognition elements can be used as nanosensors in biomedical and biological research.

The many sounds of T lymphocyte silence.

PubMed

Melero, Ignacio; Arina, Ainhoa; Chen, Lieping

2005-01-01

It is not unusual for antigens and potentially responsive T cells to co-exist in the same organism while these T cells remain silent and do not mount life-threatening immune responses. A rich array of mechanisms has been proposed to explain these observations. T cell silencing is controlled in multiple levels. Initially, dendritic cells and regulatory T cells appear to play critical roles. In addition, T cell immunity is tightly regulated by a molecular network of cytokines and cell receptor interactions by the opposed surfaces of antigen-presenting cells and T cells. Recognition of a specific antigen is therefore shaped and tuned by co-stimulatory and co-inhibitory receptor-ligand pairs. At last, immunologists are beginning to exploit the rules governing these assorted sounds of T cell silence.

Synthesis, characterization and evaluation of uniformly sized core-shell imprinted microspheres for the separation trans-resveratrol from giant knotweed

NASA Astrophysics Data System (ADS)

Zhang, Zhaohui; Liu, Li; Li, Hui; Yao, Shouzhuo

2009-09-01

A novel core-shell molecularly imprinting microspheres (MIMs) with trans-resveratrol as the template molecule; acrylamide (AA) as functional monomer and ethylene glycol dimethacrylate (EGDMA) as cross-linker, was prepared based on SiO 2 microspheres with surface imprinting technique. These core-shell trans-resveratrol imprinted microspheres were characterized by infrared spectra (IR), scanning electron microscopy (SEM), thermogravimetric analysis (TGA), and high performance liquid chromatography (HPLC). The results showed that these core-shell imprinted microspheres, which take on perfect spherical shape with average shell thickness of 150 nm, exhibit especially selective recognition for trans-resveratrol. These imprinted microspheres were applied as solid-phase extraction materials for selective extraction of trans-resveratrol from giant knotweed extracting solution successfully.

Beyond DNA origami: A look on the bright future of nucleic acid nanotechnology

PubMed Central

Michelotti, Nicole; Johnson-Buck, Alexander; Manzo, Anthony J.

2012-01-01

Nucleic acid nanotechnology exploits the programmable molecular recognition properties of natural and synthetic nucleic acids to assemble structures with nanometer-scale precision. In 2006, DNA origami transformed the field by providing a versatile platform for self-assembly of arbitrary shapes from one long DNA strand held in place by hundreds of short, site-specific (spatially addressable) DNA ”staples”. This revolutionary approach has led to the creation of a multitude of 2D and 3D scaffolds that form the basis for functional nanodevices. Not limited to nucleic acids, these nanodevices can incorporate other structural and functional materials, such as proteins and nanoparticles, making them broadly useful for current and future applications in emerging fields such as nanomedicine, nanoelectronics, and alternative energy. PMID:22131292

Selective involvement of superior frontal cortex during working memory for shapes.

PubMed

Yee, Lydia T S; Roe, Katherine; Courtney, Susan M

2010-01-01

A spatial/nonspatial functional dissociation between the dorsal and ventral visual pathways is well established and has formed the basis of domain-specific theories of prefrontal cortex (PFC). Inconsistencies in the literature regarding prefrontal organization, however, have led to questions regarding whether the nature of the dissociations observed in PFC during working memory are equivalent to those observed in the visual pathways for perception. In particular, the dissociation between dorsal and ventral PFC during working memory for locations versus object identities has been clearly present in some studies but not in others, seemingly in part due to the type of objects used. The current study compared functional MRI activation during delayed-recognition tasks for shape or color, two object features considered to be processed by the ventral pathway for perceptual recognition. Activation for the shape-delayed recognition task was greater than that for the color task in the lateral occipital cortex, in agreement with studies of visual perception. Greater memory-delay activity was also observed, however, in the parietal and superior frontal cortices for the shape than for the color task. Activity in superior frontal cortex was associated with better performance on the shape task. Conversely, greater delay activity for color than for shape was observed in the left anterior insula and this activity was associated with better performance on the color task. These results suggest that superior frontal cortex contributes to performance on tasks requiring working memory for object identities, but it represents different information about those objects than does the ventral frontal cortex.

Aesthetic preference recognition of 3D shapes using EEG.

PubMed

Chew, Lin Hou; Teo, Jason; Mountstephens, James

2016-04-01

Recognition and identification of aesthetic preference is indispensable in industrial design. Humans tend to pursue products with aesthetic values and make buying decisions based on their aesthetic preferences. The existence of neuromarketing is to understand consumer responses toward marketing stimuli by using imaging techniques and recognition of physiological parameters. Numerous studies have been done to understand the relationship between human, art and aesthetics. In this paper, we present a novel preference-based measurement of user aesthetics using electroencephalogram (EEG) signals for virtual 3D shapes with motion. The 3D shapes are designed to appear like bracelets, which is generated by using the Gielis superformula. EEG signals were collected by using a medical grade device, the B-Alert X10 from advance brain monitoring, with a sampling frequency of 256 Hz and resolution of 16 bits. The signals obtained when viewing 3D bracelet shapes were decomposed into alpha, beta, theta, gamma and delta rhythm by using time-frequency analysis, then classified into two classes, namely like and dislike by using support vector machines and K-nearest neighbors (KNN) classifiers respectively. Classification accuracy of up to 80 % was obtained by using KNN with the alpha, theta and delta rhythms as the features extracted from frontal channels, Fz, F3 and F4 to classify two classes, like and dislike.

Shape Adaptive, Robust Iris Feature Extraction from Noisy Iris Images

PubMed Central

Ghodrati, Hamed; Dehghani, Mohammad Javad; Danyali, Habibolah

2013-01-01

In the current iris recognition systems, noise removing step is only used to detect noisy parts of the iris region and features extracted from there will be excluded in matching step. Whereas depending on the filter structure used in feature extraction, the noisy parts may influence relevant features. To the best of our knowledge, the effect of noise factors on feature extraction has not been considered in the previous works. This paper investigates the effect of shape adaptive wavelet transform and shape adaptive Gabor-wavelet for feature extraction on the iris recognition performance. In addition, an effective noise-removing approach is proposed in this paper. The contribution is to detect eyelashes and reflections by calculating appropriate thresholds by a procedure called statistical decision making. The eyelids are segmented by parabolic Hough transform in normalized iris image to decrease computational burden through omitting rotation term. The iris is localized by an accurate and fast algorithm based on coarse-to-fine strategy. The principle of mask code generation is to assign the noisy bits in an iris code in order to exclude them in matching step is presented in details. An experimental result shows that by using the shape adaptive Gabor-wavelet technique there is an improvement on the accuracy of recognition rate. PMID:24696801

Shape adaptive, robust iris feature extraction from noisy iris images.

PubMed

Ghodrati, Hamed; Dehghani, Mohammad Javad; Danyali, Habibolah

2013-10-01

In the current iris recognition systems, noise removing step is only used to detect noisy parts of the iris region and features extracted from there will be excluded in matching step. Whereas depending on the filter structure used in feature extraction, the noisy parts may influence relevant features. To the best of our knowledge, the effect of noise factors on feature extraction has not been considered in the previous works. This paper investigates the effect of shape adaptive wavelet transform and shape adaptive Gabor-wavelet for feature extraction on the iris recognition performance. In addition, an effective noise-removing approach is proposed in this paper. The contribution is to detect eyelashes and reflections by calculating appropriate thresholds by a procedure called statistical decision making. The eyelids are segmented by parabolic Hough transform in normalized iris image to decrease computational burden through omitting rotation term. The iris is localized by an accurate and fast algorithm based on coarse-to-fine strategy. The principle of mask code generation is to assign the noisy bits in an iris code in order to exclude them in matching step is presented in details. An experimental result shows that by using the shape adaptive Gabor-wavelet technique there is an improvement on the accuracy of recognition rate.

Pathogenesis and spectrum of autoimmunity.

PubMed

Perl, Andras

2012-01-01

The immune system specifically recognizes and eliminates foreign antigens and, thus, protects integrity of the host. During maturation of the immune system, tolerance mechanisms develop that prevent or inhibit potentially harmful reactivities to self-antigens. Autoreactive B and T cells that are generated during immune responses are eliminated by apoptosis in the thymus, lymph nodes, or peripheral circulation or actively suppressed by regulatory T cells. However, autoreactive cells may survive due to failure of apoptosis or molecular mimicry, i.e., presentation and recognition of cryptic epitopes of self-antigens, or aberrant lymphokine production. Preservation of the host requires the development of immune responses to foreign antigen and tolerance to self-antigens. Autoimmunity results from a breakdown of tolerance to self-antigens through an interplay of genetic and environmental factors.One of the basic functions of the immune system is to specifically recognize and eliminate foreign antigens and, thus, protect integrity of the host. Through rearrangements and somatic mutations of various gene segments encoding T and B cell receptors and antibody molecules, the immune system acquires tremendous diversity. During maturation of the immune system, recognition of self-antigens plays an important role in shaping the repertoires of immune receptors. Tolerance mechanisms develop that prevent or inhibit potentially harmful reactivities to self-antigens. These self-defense mechanisms are mediated on the levels of central and peripheral tolerance, i.e., autoreactive T cells are either eliminated by apoptosis in the thymus, lymph nodes, or peripheral circulation or actively suppressed by regulatory T cells. Likewise, autoreactive B cells are eliminated in the bone marrow or peripheral lymphoid organs. However, immune responses triggered by foreign antigens may be sustained by molecular mimicry, i.e., presentation and recognition of cryptic epitopes of self-antigens. Further downstream, execution of immune responses depends on the functioning of intracellular signaling networks and the cooperation of many cell types communicating via surface receptors, cytokines, chemokines, and antibody molecules. Therefore, autoimmunity represents the end result of the breakdown of one or multiple basic mechanisms of immune tolerance (Table 1).

Circular blurred shape model for multiclass symbol recognition.

PubMed

Escalera, Sergio; Fornés, Alicia; Pujol, Oriol; Lladós, Josep; Radeva, Petia

2011-04-01

In this paper, we propose a circular blurred shape model descriptor to deal with the problem of symbol detection and classification as a particular case of object recognition. The feature extraction is performed by capturing the spatial arrangement of significant object characteristics in a correlogram structure. The shape information from objects is shared among correlogram regions, where a prior blurring degree defines the level of distortion allowed in the symbol, making the descriptor tolerant to irregular deformations. Moreover, the descriptor is rotation invariant by definition. We validate the effectiveness of the proposed descriptor in both the multiclass symbol recognition and symbol detection domains. In order to perform the symbol detection, the descriptors are learned using a cascade of classifiers. In the case of multiclass categorization, the new feature space is learned using a set of binary classifiers which are embedded in an error-correcting output code design. The results over four symbol data sets show the significant improvements of the proposed descriptor compared to the state-of-the-art descriptors. In particular, the results are even more significant in those cases where the symbols suffer from elastic deformations.

Repair Rate of Clustered Abasic DNA Lesions by Human Endonuclease: Molecular Bases of Sequence Specificity.

PubMed

Gattuso, Hugo; Durand, Elodie; Bignon, Emmanuelle; Morell, Christophe; Georgakilas, Alexandros G; Dumont, Elise; Chipot, Christophe; Dehez, François; Monari, Antonio

2016-10-06

In the present contribution, the interaction between damaged DNA and repair enzymes is examined by means of molecular dynamics simulations. More specifically, we consider clustered abasic DNA lesions processed by the primary human apurinic/apyrimidinic (AP) endonuclease, APE1. Our results show that, in stark contrast with the corresponding bacterial endonucleases, human APE1 imposes strong geometrical constraints on the DNA duplex. As a consequence, the level of recognition and, hence, the repair rate is higher. Important features that guide the DNA/protein interactions are the presence of an extended positively charged region and of a molecular tweezers that strongly constrains DNA. Our results are on very good agreement with the experimentally determined repair rate of clustered abasic lesions. The lack of repair for one particular arrangement of the two abasic sites is also explained considering the peculiar destabilizing interaction between the recognition region and the second lesion, resulting in a partial opening of the molecular tweezers and, thus, a less stable complex. This contribution cogently establishes the molecular bases for the recognition and repair of clustered DNA lesions by means of human endonucleases.

Boronic acid based imprinted electrochemical sensor for rutin recognition and detection.

PubMed

Wang, Chunlei; Wang, Qi; Zhong, Min; Kan, Xianwen

2016-10-21

Multi-walled carbon nanotubes (MWNTs) and boronic acid based molecular imprinting polymer (MIP) were successively modified on a glassy carbon electrode surface to fabricate a novel electrochemical sensor for rutin recognition and detection. 3-Aminophenylboronic acid (APBA) was chosen as a monomer for the electropolymerization of MIP film in the presence of rutin. In addition to the imprinted cavities in MIP film to complement the template molecule in shape and functional groups, the high affinity between the boronic acid group of APBA and vicinal diols of rutin also enhanced the selectivity of the sensor, which made the sensor display a good selectivity to rutin. Moreover, the modified MWNTs improved the sensitivity of the sensor for rutin detection. The mole ratios of rutin and APBA, electropolymerized scan cycles and rates, and pH value of the detection solution were optimized. Under optimal conditions, the sensor was used to detect rutin in a linear range from 4.0 × 10 -7 to 1.0 × 10 -5 mol L -1 with a detection limit of 1.1 × 10 -7 mol L -1 . The sensor has also been applied to assay rutin in tablets with satisfactory results.

A Study Regarding the Spontaneous Use of Geometric Shapes in Young Children's Drawings

ERIC Educational Resources Information Center

Villarroel, José Domingo; Sanz Ortega, Olga

2017-01-01

The studies regarding how the comprehension of geometric shapes evolves in childhood are largely based on the assessment of children's responses during the course of tasks linked to the recognition, classification or explanation of prototypes and models. Little attention has been granted to the issue as to what extent the geometric shape turns out…

Recognition of Double Stranded RNA by Guanidine-Modified Peptide Nucleic Acids (GPNA)

PubMed Central

Gupta, Pankaj; Muse, Oluwatoyosi; Rozners, Eriks

2011-01-01

Double helical RNA has become an attractive target for molecular recognition because many non-coding RNAs play important roles in control of gene expression. Recently, we discovered that short peptide nucleic acids (PNA) bind strongly and sequence selectively to a homopurine tract of double helical RNA via triple helix formation. Herein we tested if the molecular recognition of RNA can be enhanced by α-guanidine modification of PNA. Our study was motivated by the discovery of Ly and co-workers that the guanidine modification greatly enhances the cellular delivery of PNA. Isothermal titration calorimetry showed that the guanidine-modified PNA (GPNA) had reduced affinity and sequence selectivity for triple helical recognition of RNA. The data suggested that in contrast to unmodified PNA, which formed a 1:1 PNA-RNA triple helix, GPNA preferred a 2:1 GPNA-RNA triplex-invasion complex. Nevertheless, promising results were obtained for recognition of biologically relevant double helical RNA. Consistent with enhanced strand invasion ability, GPNA derived from D-arginine recognized the transactivation response element (TAR) of HIV-1 with high affinity and sequence selectivity, presumably via Watson-Crick duplex formation. On the other hand, strong and sequence selective triple helices were formed by unmodified and nucelobase-modified PNAs and the purine rich strand of bacterial A-site. These results suggest that appropriate chemical modifications of PNA may enhance molecular recognition of complex non-coding RNAs. PMID:22146072

The Potato Chip Really Does Look Like Elvis! Neural Hallmarks of Conceptual Processing Associated with Finding Novel Shapes Subjectively Meaningful

PubMed Central

Federmeier, Kara D.; Paller, Ken A.

2012-01-01

Clouds and inkblots often compellingly resemble something else—faces, animals, or other identifiable objects. Here, we investigated illusions of meaning produced by novel visual shapes. Individuals found some shapes meaningful and others meaningless, with considerable variability among individuals in these subjective categorizations. Repetition for shapes endorsed as meaningful produced conceptual priming in a priming test along with concurrent activity reductions in cortical regions associated with conceptual processing of real objects. Subjectively meaningless shapes elicited robust activity in the same brain areas, but activity was not influenced by repetition. Thus, all shapes were conceptually evaluated, but stable conceptual representations supported neural priming for meaningful shapes only. During a recognition memory test, performance was associated with increased frontoparietal activity, regardless of meaningfulness. In contrast, neural conceptual priming effects for meaningful shapes occurred during both priming and recognition testing. These different patterns of brain activation as a function of stimulus repetition, type of memory test, and subjective meaningfulness underscore the distinctive neural bases of conceptual fluency versus episodic memory retrieval. Finding meaning in ambiguous stimuli appears to depend on conceptual evaluation and cortical processing events similar to those typically observed for known objects. To the brain, the vaguely Elvis-like potato chip truly can provide a substitute for the King himself. PMID:22079921

Application of syntactic methods of pattern recognition for data mining and knowledge discovery in medicine

NASA Astrophysics Data System (ADS)

Ogiela, Marek R.; Tadeusiewicz, Ryszard

2000-04-01

This paper presents and discusses possibilities of application of selected algorithms belonging to the group of syntactic methods of patten recognition used to analyze and extract features of shapes and to diagnose morphological lesions seen on selected medical images. This method is particularly useful for specialist morphological analysis of shapes of selected organs of abdominal cavity conducted to diagnose disease symptoms occurring in the main pancreatic ducts, upper segments of ureters and renal pelvis. Analysis of the correct morphology of these organs is possible with the application of the sequential and tree method belonging to the group of syntactic methods of pattern recognition. The objective of this analysis is to support early diagnosis of disease lesions, mainly characteristic for carcinoma and pancreatitis, based on examinations of ERCP images and a diagnosis of morphological lesions in ureters as well as renal pelvis based on an analysis of urograms. In the analysis of ERCP images the main objective is to recognize morphological lesions in pancreas ducts characteristic for carcinoma and chronic pancreatitis, while in the case of kidney radiogram analysis the aim is to diagnose local irregularities of ureter lumen and to examine the morphology of renal pelvis and renal calyxes. Diagnosing the above mentioned lesion has been conducted with the use of syntactic methods of pattern recognition, in particular the languages of description of features of shapes and context-free sequential attributed grammars. These methods allow to recognize and describe in a very efficient way the aforementioned lesions on images obtained as a result of initial image processing of width diagrams of the examined structures. Additionally, in order to support the analysis of the correct structure of renal pelvis a method using the tree grammar for syntactic pattern recognition to define its correct morphological shapes has been presented.

Recognition memory across the lifespan: the impact of word frequency and study-test interval on estimates of familiarity and recollection

PubMed Central

Meier, Beat; Rey-Mermet, Alodie; Rothen, Nicolas; Graf, Peter

2013-01-01

The goal of this study was to investigate recognition memory performance across the lifespan and to determine how estimates of recollection and familiarity contribute to performance. In each of three experiments, participants from five groups from 14 up to 85 years of age (children, young adults, middle-aged adults, young-old adults, and old-old adults) were presented with high- and low-frequency words in a study phase and were tested immediately afterwards and/or after a one day retention interval. The results showed that word frequency and retention interval affected recognition memory performance as well as estimates of recollection and familiarity. Across the lifespan, the trajectory of recognition memory followed an inverse u-shape function that was neither affected by word frequency nor by retention interval. The trajectory of estimates of recollection also followed an inverse u-shape function, and was especially pronounced for low-frequency words. In contrast, estimates of familiarity did not differ across the lifespan. The results indicate that age differences in recognition memory are mainly due to differences in processes related to recollection while the contribution of familiarity-based processes seems to be age-invariant. PMID:24198796

Perception of biological motion from size-invariant body representations.

PubMed

Lappe, Markus; Wittinghofer, Karin; de Lussanet, Marc H E

2015-01-01

The visual recognition of action is one of the socially most important and computationally demanding capacities of the human visual system. It combines visual shape recognition with complex non-rigid motion perception. Action presented as a point-light animation is a striking visual experience for anyone who sees it for the first time. Information about the shape and posture of the human body is sparse in point-light animations, but it is essential for action recognition. In the posturo-temporal filter model of biological motion perception posture information is picked up by visual neurons tuned to the form of the human body before body motion is calculated. We tested whether point-light stimuli are processed through posture recognition of the human body form by using a typical feature of form recognition, namely size invariance. We constructed a point-light stimulus that can only be perceived through a size-invariant mechanism. This stimulus changes rapidly in size from one image to the next. It thus disrupts continuity of early visuo-spatial properties but maintains continuity of the body posture representation. Despite this massive manipulation at the visuo-spatial level, size-changing point-light figures are spontaneously recognized by naive observers, and support discrimination of human body motion.

Feature binding and attention in working memory: a resolution of previous contradictory findings.

PubMed

Allen, Richard J; Hitch, Graham J; Mate, Judit; Baddeley, Alan D

2012-01-01

We aimed to resolve an apparent contradiction between previous experiments from different laboratories, using dual-task methodology to compare effects of a concurrent executive load on immediate recognition memory for colours or shapes of items or their colour-shape combinations. Results of two experiments confirmed previous evidence that an irrelevant attentional load interferes equally with memory for features and memory for feature bindings. Detailed analyses suggested that previous contradictory evidence arose from limitations in the way recognition memory was measured. The present findings are inconsistent with an earlier suggestion that feature binding takes place within a multimodal episodic buffer Baddeley, ( 2000 ) and support a subsequent account in which binding takes place automatically prior to information entering the episodic buffer Baddeley, Allen, & Hitch, ( 2011 ). Methodologically, the results suggest that different measures of recognition memory performance (A', d', corrected recognition) give a converging picture of main effects, but are less consistent in detecting interactions. We suggest that this limitation on the reliability of measuring recognition should be taken into account in future research so as to avoid problems of replication that turn out to be more apparent than real.

Signal recognition efficiencies of artificial neural-network pulse-shape discrimination in HPGe -decay searches

NASA Astrophysics Data System (ADS)

Caldwell, A.; Cossavella, F.; Majorovits, B.; Palioselitis, D.; Volynets, O.

2015-07-01

A pulse-shape discrimination method based on artificial neural networks was applied to pulses simulated for different background, signal and signal-like interactions inside a germanium detector. The simulated pulses were used to investigate variations of efficiencies as a function of used training set. It is verified that neural networks are well-suited to identify background pulses in true-coaxial high-purity germanium detectors. The systematic uncertainty on the signal recognition efficiency derived using signal-like evaluation samples from calibration measurements is estimated to be 5 %. This uncertainty is due to differences between signal and calibration samples.

Effects of Iris Surface Curvature on Iris Recognition

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

Thompson, Joseph T; Flynn, Patrick J; Bowyer, Kevin W

To focus on objects at various distances, the lens of the eye must change shape to adjust its refractive power. This change in lens shape causes a change in the shape of the iris surface which can be measured by examining the curvature of the iris. This work isolates the variable of iris curvature in the recognition process and shows that differences in iris curvature degrade matching ability. To our knowledge, no other work has examined the effects of varying iris curvature on matching ability. To examine this degradation, we conduct a matching experiment across pairs of images with varyingmore » degrees of iris curvature differences. The results show a statistically signi cant degradation in matching ability. Finally, the real world impact of these ndings is discussed« less

Resolution of Site-Specific Conformational Heterogeneity in Proline-Rich Molecular Recognition by Src Homology 3 Domains.

PubMed

Horness, Rachel E; Basom, Edward J; Mayer, John P; Thielges, Megan C

2016-02-03

Conformational heterogeneity and dynamics are increasingly evoked in models of protein molecular recognition but are challenging to experimentally characterize. Here we combine the inherent temporal resolution of infrared (IR) spectroscopy with the spatial resolution afforded by selective incorporation of carbon-deuterium (C-D) bonds, which provide frequency-resolved absorptions within a protein IR spectrum, to characterize the molecular recognition of the Src homology 3 (SH3) domain of the yeast protein Sho1 with its cognate proline-rich (PR) sequence of Pbs2. The IR absorptions of C-D bonds introduced at residues along a peptide of the Pbs2 PR sequence report on the changes in the local environments upon binding to the SH3 domain. Interestingly, upon forming the complex the IR spectra of the peptides labeled with C-D bonds at either of the two conserved prolines of the PXXP consensus recognition sequence show more absorptions than there are C-D bonds, providing evidence for the population of multiple states. In contrast, the NMR spectra of the peptides labeled with (13)C at the same residues show only single resonances, indicating rapid interconversion on the NMR time scale. Thus, the data suggest that the SH3 domain recognizes its cognate peptide with a component of induced fit molecular recognition involving the adoption of multiples states, which have previously gone undetected due to interconversion between the populated states that is too fast to resolve using conventional methods.

Context and Spoken Word Recognition in a Novel Lexicon

ERIC Educational Resources Information Center

Revill, Kathleen Pirog; Tanenhaus, Michael K.; Aslin, Richard N.

2008-01-01

Three eye movement studies with novel lexicons investigated the role of semantic context in spoken word recognition, contrasting 3 models: restrictive access, access-selection, and continuous integration. Actions directed at novel shapes caused changes in motion (e.g., looming, spinning) or state (e.g., color, texture). Across the experiments,…

Molecular recognition of microbial lipid-based antigens by T cells.

PubMed

Gras, Stephanie; Van Rhijn, Ildiko; Shahine, Adam; Le Nours, Jérôme

2018-05-01

The immune system has evolved to protect hosts from pathogens. T cells represent a critical component of the immune system by their engagement in host defence mechanisms against microbial infections. Our knowledge of the molecular recognition by T cells of pathogen-derived peptidic antigens that are presented by the major histocompatibility complex glycoproteins is now well established. However, lipids represent an additional, distinct chemical class of molecules that when presented by the family of CD1 antigen-presenting molecules can serve as antigens, and be recognized by specialized subsets of T cells leading to antigen-specific activation. Over the past decades, numerous CD1-presented self- and bacterial lipid-based antigens have been isolated and characterized. However, our understanding at the molecular level of T cell immunity to CD1 molecules presenting microbial lipid-based antigens is still largely unexplored. Here, we review the insights and the molecular basis underpinning the recognition of microbial lipid-based antigens by T cells.

Influence of Molecular Shape on the Thermal Stability and Molecular Orientation of Vapor-Deposited Organic Semiconductors

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

Walters, Diane M; Antony, Lucas; de Pablo, Juan

High thermal stability and anisotropic molecular orientation enhance the performance of vapor-deposited organic semiconductors, but controlling these properties is a challenge in amorphous materials. To understand the influence of molecular shape on these properties, vapor-deposited glasses of three disk-shaped molecules were prepared. For all three systems, enhanced thermal stability is observed for glasses prepared over a wide range of substrate temperatures and anisotropic molecular orientation is observed at lower substrate temperatures. For two of the disk-shaped molecules, atomistic simulations of thin films were also performed and anisotropic molecular orientation was observed at the equilibrium liquid surface. We find that themore » structure and thermal stability of these vapor-deposited glasses results from high surface mobility and partial equilibration toward the structure of the equilibrium liquid surface during the deposition process. For the three molecules studied, molecular shape is a dominant factor in determining the anisotropy of vapor-deposited glasses.« less

Association, intrinsic shape, and molecular recognition: Elucidating DNA biophysics through coarse-grained simulation

NASA Astrophysics Data System (ADS)

Freeman, Gordon Samuel

DNA is of central importance in biology as it is responsible for carrying, copying, and translating the genetic code into the building blocks that comprise life. In order to accomplish these tasks, the DNA molecule must be versatile and robust. Indeed, the underlying molecular interactions that allow DNA to execute these tasks are complex and their origins are only beginning to be understood. While experiments are able to elucidate many key biophysical phenomena, there remain many unanswered questions. Molecular simulation is able to shed light on phenomena at the molecular scale and provide information that is missing from experimental views of DNA behavior. In this dissertation I use state-of-the-art coarse-grained DNA models to address two key problems. In the first, metadynamics calculations are employed to uncover the free energy surface of two complimentary DNA strands. This free energy surface takes on the appearance of a hybridization funnel and reveals candidates for intermediate states in the hybridization of short DNA oligomers. Such short oligomers are important building blocks for DNA-driven self-assembly and the mechanism of hybridization in this regime is not well understood. The second problem is that of nucleosome formation. Nucleosomes are the fundamental subunit of genome compaction in the nucleus of a cell. As such, nucleosomes are a key epigenetic factor and affect gene expression and the ability of DNA-binding proteins to locate and bind to the appropriate position in the genome. However, the factors that drive nucleosome positioning are not well understood. While DNA sequence is known to affect nucleosome formation, the mechanism by which it does so has not been established and a number of hypotheses explaining this sequence-dependence exist in the literature. I demonstrate that DNA shape dominates this process with contributions arising from both intrinsic DNA curvature as well as DNA-protein interactions driven by sequence-dependent variations in minor groove dimensions.

Molecular Recognition Involving Anthraquinone Derivatives and Molecular Clips

NASA Astrophysics Data System (ADS)

Alaparthi, Madhubabu

In the past, we have demonstrated that 1,8-anthraquinone-18-crown-5 (1) and its heterocyclic derivatives act as luminescent hosts for a variety of cations of environmental and clinical concern. We report here a series of heteroatom-substituted macrocycles containing an anthraquinone moiety as a fluorescent signaling unit and a cyclic polyheteroether chain as the receptor. Sulfur, selenium, and tellurium derivatives of 1,8-anthraquinone-18-crown-5 (1) were synthesized by reacting sodium sulfide (Na2S), sodium selenide (Na2Se) and sodium telluride (Na2Te) with 1,8-bis(2-bromoethylethyleneoxy)anthracene - 9,10-dione in a 1:1 ratio (2,3, and 6). These sensors bind metal ions in a 1:1 ratio (7 and 8), and the optical properties of the new complexes were examined and the sulfur and selenium analogues show that selectivity for Pb(II) is markedly improved as compared to the oxygen analogue 1 which was competitive for Ca(II) ion. Selective reduction of 1 yields secondary alcohols where either one or both of the anthraquinone carbonyl groups has been reduced ( 15 and 9). A new mechanism for the fluorescence detection of metal cations in solution is introduced involving a unique keto-enol tautomerization. Reduction of 1 yields the doubly reduced secondary alcohol, 9. 9 acts as a chemodosimeter for Al(III) ion producing a strong blue emission due to the formation of the anthracene fluorophore, 10, via dehydration of the internal secondary alcohol in DMSO/aqueous solution. The enol form is not the most thermodynamically stable form under these conditions however, and slowly converts to the keto form 11.. Currently we are focusing on cucurbituril derivatives, also described as molecular clips due to their folded geometry used as molecular recognition hosts. We first investigated the synthesis and characterization of aromatic methoxy/catechol terminated cucurbituril units that act as hosts for small solvent molecules, such as CH2Cl2, CH3CN, DMF, and MeOH, through dual pi...H-C T-shaped interactions. We have calculated the single-point interaction energies of these non-covalent interactions and compared them to the dihedral angle formed from the molecular clip. We have also synthesized a molecular clip that contains terminal chelating phenanthroline ligands. This tetradentate ligand shows 2:3 metal:ligand binding with Fe(II) and 1:2 metal:ligand binding with Co(II) and Ni(II) cations.

Sentence Recognition Prediction for Hearing-impaired Listeners in Stationary and Fluctuation Noise With FADE

PubMed Central

Schädler, Marc René; Warzybok, Anna; Meyer, Bernd T.; Brand, Thomas

2016-01-01

To characterize the individual patient’s hearing impairment as obtained with the matrix sentence recognition test, a simulation Framework for Auditory Discrimination Experiments (FADE) is extended here using the Attenuation and Distortion (A+D) approach by Plomp as a blueprint for setting the individual processing parameters. FADE has been shown to predict the outcome of both speech recognition tests and psychoacoustic experiments based on simulations using an automatic speech recognition system requiring only few assumptions. It builds on the closed-set matrix sentence recognition test which is advantageous for testing individual speech recognition in a way comparable across languages. Individual predictions of speech recognition thresholds in stationary and in fluctuating noise were derived using the audiogram and an estimate of the internal level uncertainty for modeling the individual Plomp curves fitted to the data with the Attenuation (A-) and Distortion (D-) parameters of the Plomp approach. The “typical” audiogram shapes from Bisgaard et al with or without a “typical” level uncertainty and the individual data were used for individual predictions. As a result, the individualization of the level uncertainty was found to be more important than the exact shape of the individual audiogram to accurately model the outcome of the German Matrix test in stationary or fluctuating noise for listeners with hearing impairment. The prediction accuracy of the individualized approach also outperforms the (modified) Speech Intelligibility Index approach which is based on the individual threshold data only. PMID:27604782

Demonstration of Removal, Separation, and Recovery of Heavy Metals from Industrial Wastestreams Using Molecular Recognition Technology (MRT)

DTIC Science & Technology

2002-11-01

Treatment Plant”, TM-2123-ENV, April 1995. 3. Ford, K.H., 1996, “ Heavy Metal Adsorption/ Biosorption Studies for Zero Discharge Industrial Wastewater...SEPARATION, AND RECOVERY OF HEAVY METALS FROM INDUSTRIAL WASTESTREAMS USING MOLECULAR RECOGNITION TECHNOLOGY (MRT) Final Report by Dr. Katherine...GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER DEMONSTRATION OF REMOVAL, SEPARATION, AND RECOVERY OF HEAVY METALS FROM INDUSTRIAL WASTEWATERS USING

Spherical harmonics coefficients for ligand-based virtual screening of cyclooxygenase inhibitors.

PubMed

Wang, Quan; Birod, Kerstin; Angioni, Carlo; Grösch, Sabine; Geppert, Tim; Schneider, Petra; Rupp, Matthias; Schneider, Gisbert

2011-01-01

Molecular descriptors are essential for many applications in computational chemistry, such as ligand-based similarity searching. Spherical harmonics have previously been suggested as comprehensive descriptors of molecular structure and properties. We investigate a spherical harmonics descriptor for shape-based virtual screening. We introduce and validate a partially rotation-invariant three-dimensional molecular shape descriptor based on the norm of spherical harmonics expansion coefficients. Using this molecular representation, we parameterize molecular surfaces, i.e., isosurfaces of spatial molecular property distributions. We validate the shape descriptor in a comprehensive retrospective virtual screening experiment. In a prospective study, we virtually screen a large compound library for cyclooxygenase inhibitors, using a self-organizing map as a pre-filter and the shape descriptor for candidate prioritization. 12 compounds were tested in vitro for direct enzyme inhibition and in a whole blood assay. Active compounds containing a triazole scaffold were identified as direct cyclooxygenase-1 inhibitors. This outcome corroborates the usefulness of spherical harmonics for representation of molecular shape in virtual screening of large compound collections. The combination of pharmacophore and shape-based filtering of screening candidates proved to be a straightforward approach to finding novel bioactive chemotypes with minimal experimental effort.

Role of the α clamp in the protein translocation mechanism of anthrax toxin

PubMed Central

Brown, Michael J.; Thoren, Katie L.; Krantz, Bryan A.

2015-01-01

Membrane-embedded molecular machines are utilized to move water-soluble proteins across these barriers. Anthrax toxin forms one such machine through the self-assembly of its three component proteins—protective antigen (PA), lethal factor (LF), and edema factor (EF). Upon endocytosis into host cells, acidification of the endosome induces PA to form a membrane-inserted channel, which unfolds LF and EF and translocates them into the host cytosol. Translocation is driven by the proton motive force, comprised of the chemical potential, the proton-gradient (ΔpH), and the membrane potential (ΔΨ). A crystal structure of the lethal toxin core complex revealed an “α clamp” structure that binds to substrate helices nonspecifically. Here we test the hypothesis that through the recognition of unfolding helical structure the α clamp can accelerate the rate of translocation. We produced a synthetic PA mutant in which an α helix was crosslinked into the α clamp to block its function. This synthetic construct impairs translocation by raising a yet uncharacterized translocation barrier shown to be much less force dependent than the known unfolding barrier. We also report that the α clamp more stably binds substrates that can form helices than those, such as polyproline, that cannot. Hence the α clamp recognizes substrates by a general shape-complementarity mechanism. Substrates that are incapable of forming compact secondary structure (due to the introduction of a polyproline track) are severely deficient for translocation. Therefore, the α clamp and its recognition of helical structure in the translocating substrate play key roles in the molecular mechanism of protein translocation. PMID:26344833

Dissecting ant recognition systems in the age of genomics.

PubMed

Tsutsui, Neil D

2013-01-01

Hamilton is probably best known for his seminal work demonstrating the role of kin selection in social evolution. His work made it clear that, for individuals to direct their altruistic behaviours towards appropriate recipients (kin), mechanisms must exist for kin recognition. In the social insects, colonies are typically comprised of kin, and colony recognition cues are used as proxies for kinship cues. Recent years have brought rapid advances in our understanding of the genetic and molecular mechanisms that are used for this process. Here, I review some of the most notable advances, particularly the contributions from recent ant genome sequences and molecular biology.

Molecularly imprinted titania nanoparticles for selective recognition and assay of uric acid

NASA Astrophysics Data System (ADS)

Mujahid, Adnan; Khan, Aimen Idrees; Afzal, Adeel; Hussain, Tajamal; Raza, Muhammad Hamid; Shah, Asma Tufail; uz Zaman, Waheed

2015-06-01

Molecularly imprinted titania nanoparticles are su ccessfully synthesized by sol-gel method for the selective recognition of uric acid. Atomic force microscopy is used to study the morphology of uric acid imprinted titania nanoparticles with diameter in the range of 100-150 nm. Scanning electron microscopy images of thick titania layer indicate the formation of fine network of titania nanoparticles with uniform distribution. Molecular imprinting of uric acid as well as its subsequent washing is confirmed by Fourier transformation infrared spectroscopy measurements. Uric acid rebinding studies reveal the recognition capability of imprinted particles in the range of 0.01-0.095 mmol, which is applicable in monitoring normal to elevated levels of uric acid in human blood. The optical shift (signal) of imprinted particles is six times higher in comparison with non-imprinted particles for the same concentration of uric acid. Imprinted titania particles have shown substantially reduced binding affinity toward interfering and structurally related substances, e.g. ascorbic acid and guanine. These results suggest the possible application of titania nanoparticles in uric acid recognition and quantification in blood serum.

Data encoding based on the shape of the ferroelectric domains produced by a scanning probe microscopy tip

DOE PAGES

Ievlev, Anton; Kalinin, Sergei V.

2015-05-28

Ferroelectric materials are broadly considered for information storage due to extremely high storage and information processing densities they enable. To date, ferroelectric based data storage has invariably relied on formation of cylindrical domains, allowing for binary information encoding. Here we demonstrate and explore the potential of high-density encoding based on domain morphology. We explore the domain morphogenesis during the tip-induced polarization switching by sequences of positive and negative pulses in a lithium niobate single-crystal and demonstrate the principal of information coding by shape and size of the domains. We applied cross-correlation and neural network approaches for recognition of the switchingmore » sequence by the shape of the resulting domains and establish optimal parameters for domain shape recognition. These studies both provide insight into the highly non-trivial mechanism of domain switching and potentially establish a new paradigm for multilevel information storage and content retrieval memories. Furthermore, this approach opens a pathway to exploration of domain switching mechanisms via shape analysis.« less

LGBT Family Lawyers and Same-Sex Marriage Recognition: How Legal Change Shapes Professional Identity and Practice.

PubMed

Baumle, Amanda K

2018-01-10

Lawyers who practice family law for LGBT clients are key players in the tenuous and evolving legal environment surrounding same-sex marriage recognition. Building on prior research on factors shaping the professional identities of lawyers generally, and activist lawyers specifically, I examine how practice within a rapidly changing, patchwork legal environment shapes professional identity for this group of lawyers. I draw on interviews with 21 LGBT family lawyers to analyze how the unique features of LGBT family law shape their professional identities and practice, as well as their predictions about the development of the practice in a post-Obergefell world. Findings reveal that the professional identities and practice of LGBT family lawyers are shaped by uncertainty, characteristics of activist lawyering, community membership, and community service. Individual motivations and institutional forces work to generate a professional identity that is resilient and dynamic, characterized by skepticism and distrust coupled with flexibility and creativity. These features are likely to play a role in the evolution of the LGBT family lawyer professional identity post-marriage equality.

Multidimensional brain activity dictated by winner-take-all mechanisms.

PubMed

Tozzi, Arturo; Peters, James F

2018-06-21

A novel demon-based architecture is introduced to elucidate brain functions such as pattern recognition during human perception and mental interpretation of visual scenes. Starting from the topological concepts of invariance and persistence, we introduce a Selfridge pandemonium variant of brain activity that takes into account a novel feature, namely, demons that recognize short straight-line segments, curved lines and scene shapes, such as shape interior, density and texture. Low-level representations of objects can be mapped to higher-level views (our mental interpretations): a series of transformations can be gradually applied to a pattern in a visual scene, without affecting its invariant properties. This makes it possible to construct a symbolic multi-dimensional representation of the environment. These representations can be projected continuously to an object that we have seen and continue to see, thanks to the mapping from shapes in our memory to shapes in Euclidean space. Although perceived shapes are 3-dimensional (plus time), the evaluation of shape features (volume, color, contour, closeness, texture, and so on) leads to n-dimensional brain landscapes. Here we discuss the advantages of our parallel, hierarchical model in pattern recognition, computer vision and biological nervous system's evolution. Copyright © 2018 Elsevier B.V. All rights reserved.

Conformational Smear Characterization and Binning of Single-Molecule Conductance Measurements for Enhanced Molecular Recognition.

PubMed

Korshoj, Lee E; Afsari, Sepideh; Chatterjee, Anushree; Nagpal, Prashant

2017-11-01

Electronic conduction or charge transport through single molecules depends primarily on molecular structure and anchoring groups and forms the basis for a wide range of studies from molecular electronics to DNA sequencing. Several high-throughput nanoelectronic methods such as mechanical break junctions, nanopores, conductive atomic force microscopy, scanning tunneling break junctions, and static nanoscale electrodes are often used for measuring single-molecule conductance. In these measurements, "smearing" due to conformational changes and other entropic factors leads to large variances in the observed molecular conductance, especially in individual measurements. Here, we show a method for characterizing smear in single-molecule conductance measurements and demonstrate how binning measurements according to smear can significantly enhance the use of individual conductance measurements for molecular recognition. Using quantum point contact measurements on single nucleotides within DNA macromolecules, we demonstrate that the distance over which molecular junctions are maintained is a measure of smear, and the resulting variance in unbiased single measurements depends on this smear parameter. Our ability to identify individual DNA nucleotides at 20× coverage increases from 81.3% accuracy without smear analysis to 93.9% with smear characterization and binning (SCRIB). Furthermore, merely 7 conductance measurements (7× coverage) are needed to achieve 97.8% accuracy for DNA nucleotide recognition when only low molecular smear measurements are used, which represents a significant improvement over contemporary sequencing methods. These results have important implications in a broad range of molecular electronics applications from designing robust molecular switches to nanoelectronic DNA sequencing.

Online Farsi digit recognition using their upper half structure

NASA Astrophysics Data System (ADS)

Ghods, Vahid; Sohrabi, Mohammad Karim

2015-03-01

In this paper, we investigated the efficiency of upper half Farsi numerical digit structure. In other words, half of data (upper half of the digit shapes) was exploited for the recognition of Farsi numerical digits. This method can be used for both offline and online recognition. Half of data is more effective in speed process, data transfer and in this application accuracy. Hidden Markov model (HMM) was used to classify online Farsi digits. Evaluation was performed by TMU dataset. This dataset contains more than 1200 samples of online handwritten Farsi digits. The proposed method yielded more accuracy in recognition rate.

Qualitative Differences in the Representation of Spatial Relations for Different Object Classes

ERIC Educational Resources Information Center

Cooper, Eric E.; Brooks, Brian E.

2004-01-01

Two experiments investigated whether the representations used for animal, produce, and object recognition code spatial relations in a similar manner. Experiment 1 tested the effects of planar rotation on the recognition of animals and nonanimal objects. Response times for recognizing animals followed an inverted U-shaped function, whereas those…

Face Recognition Is Shaped by the Use of Sign Language

ERIC Educational Resources Information Center

Stoll, Chloé; Palluel-Germain, Richard; Caldara, Roberto; Lao, Junpeng; Dye, Matthew W. G.; Aptel, Florent; Pascalis, Olivier

2018-01-01

Previous research has suggested that early deaf signers differ in face processing. Which aspects of face processing are changed and the role that sign language may have played in that change are however unclear. Here, we compared face categorization (human/non-human) and human face recognition performance in early profoundly deaf signers, hearing…

Two-dimensional shape recognition using oriented-polar representation

NASA Astrophysics Data System (ADS)

Hu, Neng-Chung; Yu, Kuo-Kan; Hsu, Yung-Li

1997-10-01

To deal with such a problem as object recognition of position, scale, and rotation invariance (PSRI), we utilize some PSRI properties of images obtained from objects, for example, the centroid of the image. The corresponding position of the centroid to the boundary of the image is invariant in spite of rotation, scale, and translation of the image. To obtain the information of the image, we use the technique similar to Radon transform, called the oriented-polar representation of a 2D image. In this representation, two specific points, the centroid and the weighted mean point, are selected to form an initial ray, then the image is sampled with N angularly equispaced rays departing from the initial rays. Each ray contains a number of intersections and the distance information obtained from the centroid to the intersections. The shape recognition algorithm is based on the least total error of these two items of information. Together with a simple noise removal and a typical backpropagation neural network, this algorithm is simple, but the PSRI is achieved with a high recognition rate.

Peptidoglycan microarray as a novel tool to explore protein-ligand recognition.

PubMed

Wang, Ning; Hirata, Akiyoshi; Nokihara, Kiyoshi; Fukase, Koichi; Fujimoto, Yukari

2016-11-04

Peptidoglycan is a giant bag-shaped molecule essential for bacterial cell shape and resistance to osmotic stresses. The activity of a large number of bacterial surface proteins involved in cell growth and division requires binding to this macromolecule. Recognition of peptidoglycan by immune effectors is also crucial for the establishment of the immune response against pathogens. The availability of pure and chemically defined peptidoglycan fragments is a major technical bottleneck that has precluded systematic studies of the mechanisms underpinning protein-mediated peptidoglycan recognition. Here, we report a microarray strategy suitable to carry out comprehensive studies to characterize proteins-peptidoglycan interactions. We describe a method to introduce a functional group on peptidoglycan fragments allowing their stable immobilization on amorphous carbon chip plates to minimize nonspecific binding. Such peptidoglycan microarrays were used with a model peptidoglycan binding protein-the human peptidoglycan recognition protein-S (hPGRP-S). We propose that this strategy could be implemented to carry out high-throughput analyses to study peptidoglycan binding proteins. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 422-429, 2016. © 2016 Wiley Periodicals, Inc.

Neural networks for data compression and invariant image recognition

NASA Technical Reports Server (NTRS)

Gardner, Sheldon

1989-01-01

An approach to invariant image recognition (I2R), based upon a model of biological vision in the mammalian visual system (MVS), is described. The complete I2R model incorporates several biologically inspired features: exponential mapping of retinal images, Gabor spatial filtering, and a neural network associative memory. In the I2R model, exponentially mapped retinal images are filtered by a hierarchical set of Gabor spatial filters (GSF) which provide compression of the information contained within a pixel-based image. A neural network associative memory (AM) is used to process the GSF coded images. We describe a 1-D shape function method for coding of scale and rotationally invariant shape information. This method reduces image shape information to a periodic waveform suitable for coding as an input vector to a neural network AM. The shape function method is suitable for near term applications on conventional computing architectures equipped with VLSI FFT chips to provide a rapid image search capability.

Dynamic representation of partially occluded objects in primate prefrontal and visual cortex

PubMed Central

Choi, Hannah; Shea-Brown, Eric

2017-01-01

Successful recognition of partially occluded objects is presumed to involve dynamic interactions between brain areas responsible for vision and cognition, but neurophysiological evidence for the involvement of feedback signals is lacking. Here, we demonstrate that neurons in the ventrolateral prefrontal cortex (vlPFC) of monkeys performing a shape discrimination task respond more strongly to occluded than unoccluded stimuli. In contrast, neurons in visual area V4 respond more strongly to unoccluded stimuli. Analyses of V4 response dynamics reveal that many neurons exhibit two transient response peaks, the second of which emerges after vlPFC response onset and displays stronger selectivity for occluded shapes. We replicate these findings using a model of V4/vlPFC interactions in which occlusion-sensitive vlPFC neurons feed back to shape-selective V4 neurons, thereby enhancing V4 responses and selectivity to occluded shapes. These results reveal how signals from frontal and visual cortex could interact to facilitate object recognition under occlusion. PMID:28925354

Neural correlates of facilitations in face learning by selective caricaturing of facial shape or reflectance.

PubMed

Itz, Marlena L; Schweinberger, Stefan R; Schulz, Claudia; Kaufmann, Jürgen M

2014-11-15

Spatially caricatured faces were recently shown to benefit face learning (Schulz et al., 2012a). Moreover, spatial information may be particularly important for encoding unfamiliar faces, but less so for recognizing familiar faces (Kaufmann et al., 2013). To directly test the possibility of a major role of reflectance information for the recognition of familiar faces, we compared effects of selective photorealistic caricaturing in either shape or reflectance on face learning and recognition. Participants learned 3D-photographed faces across different viewpoints, and different images were presented at learning and test. At test, performance benefits for both types of caricatures were modulated by familiarity: Benefits for learned faces were substantially larger for reflectance caricatures, whereas benefits for novel faces were numerically larger for shape caricatures. ERPs confirmed a consistent reduction of the occipitotemporal P200 (200-240 ms) by shape caricaturing, whereas the most prominent effect of reflectance caricaturing was seen in an enhanced posterior N250 (240-400 ms), a component that has been related to the activation of acquired face representations. Our results suggest that performance benefits for face learning caused by distinctive spatial versus reflectance information are mediated by different neural processes with different timing and support a prominent role of reflectance for the recognition of learned faces. Copyright © 2014 Elsevier Inc. All rights reserved.

Deep neural network using color and synthesized three-dimensional shape for face recognition

NASA Astrophysics Data System (ADS)

Rhee, Seon-Min; Yoo, ByungIn; Han, Jae-Joon; Hwang, Wonjun

2017-03-01

We present an approach for face recognition using synthesized three-dimensional (3-D) shape information together with two-dimensional (2-D) color in a deep convolutional neural network (DCNN). As 3-D facial shape is hardly affected by the extrinsic 2-D texture changes caused by illumination, make-up, and occlusions, it could provide more reliable complementary features in harmony with the 2-D color feature in face recognition. Unlike other approaches that use 3-D shape information with the help of an additional depth sensor, our approach generates a personalized 3-D face model by using only face landmarks in the 2-D input image. Using the personalized 3-D face model, we generate a frontalized 2-D color facial image as well as 3-D facial images (e.g., a depth image and a normal image). In our DCNN, we first feed 2-D and 3-D facial images into independent convolutional layers, where the low-level kernels are successfully learned according to their own characteristics. Then, we merge them and feed into higher-level layers under a single deep neural network. Our proposed approach is evaluated with labeled faces in the wild dataset and the results show that the error rate of the verification rate at false acceptance rate 1% is improved by up to 32.1% compared with the baseline where only a 2-D color image is used.

Perception of pathogenic or beneficial bacteria and their evasion of host immunity: pattern recognition receptors in the frontline

PubMed Central

Trdá, Lucie; Boutrot, Freddy; Claverie, Justine; Brulé, Daphnée; Dorey, Stephan; Poinssot, Benoit

2015-01-01

Plants are continuously monitoring the presence of microorganisms to establish an adapted response. Plants commonly use pattern recognition receptors (PRRs) to perceive microbe- or pathogen-associated molecular patterns (MAMPs/PAMPs) which are microorganism molecular signatures. Located at the plant plasma membrane, the PRRs are generally receptor-like kinases (RLKs) or receptor-like proteins (RLPs). MAMP detection will lead to the establishment of a plant defense program called MAMP-triggered immunity (MTI). In this review, we overview the RLKs and RLPs that assure early recognition and control of pathogenic or beneficial bacteria. We also highlight the crucial function of PRRs during plant-microbe interactions, with a special emphasis on the receptors of the bacterial flagellin and peptidoglycan. In addition, we discuss the multiple strategies used by bacteria to evade PRR-mediated recognition. PMID:25904927

Cavitand-grafted silicon microcantilevers as a universal probe for illicit and designer drugs in water.

PubMed

Biavardi, Elisa; Federici, Stefania; Tudisco, Cristina; Menozzi, Daniela; Massera, Chiara; Sottini, Andrea; Condorelli, Guglielmo G; Bergese, Paolo; Dalcanale, Enrico

2014-08-25

The direct, clean, and unbiased transduction of molecular recognition into a readable and reproducible response is the biggest challenge associated to the use of synthetic receptors in sensing. All possible solutions demand the mastering of molecular recognition at the solid-liquid interface as prerequisite. The socially relevant issue of screening amine-based illicit and designer drugs is addressed by nanomechanical recognition at the silicon-water interface. The methylamino moieties of different drugs are all first recognized by a single cavitand receptor through a synergistic set of weak interactions. The peculiar recognition ability of the cavitand is then transferred with high fidelity and robustness on silicon microcantilevers and harnessed to realize a nanomechanical device for label-free detection of these drugs in water. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

3D palmprint data fast acquisition and recognition

NASA Astrophysics Data System (ADS)

Wang, Xiaoxu; Huang, Shujun; Gao, Nan; Zhang, Zonghua

2014-11-01

This paper presents a fast 3D (Three-Dimension) palmprint capturing system and develops an efficient 3D palmprint feature extraction and recognition method. In order to fast acquire accurate 3D shape and texture of palmprint, a DLP projector triggers a CCD camera to realize synchronization. By generating and projecting green fringe pattern images onto the measured palm surface, 3D palmprint data are calculated from the fringe pattern images. The periodic feature vector can be derived from the calculated 3D palmprint data, so undistorted 3D biometrics is obtained. Using the obtained 3D palmprint data, feature matching test have been carried out by Gabor filter, competition rules and the mean curvature. Experimental results on capturing 3D palmprint show that the proposed acquisition method can fast get 3D shape information of palmprint. Some initial experiments on recognition show the proposed method is efficient by using 3D palmprint data.

The influence of averaging and noisy decision strategies on the recognition memory ROC.

PubMed

Malmberg, Kenneth J; Xu, Jing

2006-02-01

Many single- and dual-process models of recognition memory predict that the ratings and remember-know receiver operating characteristics (ROCs) are the same, but Rotello, Macmillan, and Reeder (2004) reported that the slopes of the remember-know and ratings z-transformed ROCs (zROCs) are different The authors show that averaging introduces nonlinearities to the form of the zROC and that ratings and remember-know zROCs are indistinguishable when constructed in a conventional manner. The authors show, further, that some nonoptimal decision strategies have a distinctive, nonlinear effect on the form of the single-process continuous-state zROC. The conclusion is that many factors having nothing to do with the nature of recognition memory can affect the shape of zROCs, and that therefore, the shape of the zROC does not, alone, characterize different memory models.

Molecular Docking and Drug Discovery in β-Adrenergic Receptors.

PubMed

Vilar, Santiago; Sobarzo-Sanchez, Eduardo; Santana, Lourdes; Uriarte, Eugenio

2017-01-01

Evolution in computer engineering, availability of increasing amounts of data and the development of new and fast docking algorithms and software have led to improved molecular simulations with crucial applications in virtual high-throughput screening and drug discovery. Moreover, analysis of protein-ligand recognition through molecular docking has become a valuable tool in drug design. In this review, we focus on the applicability of molecular docking on a particular class of G protein-coupled receptors: the β-adrenergic receptors, which are relevant targets in clinic for the treatment of asthma and cardiovascular diseases. We describe the binding site in β-adrenergic receptors to understand key factors in ligand recognition along with the proteins activation process. Moreover, we focus on the discovery of new lead compounds that bind the receptors, on the evaluation of virtual screening using the active/ inactive binding site states, and on the structural optimization of known families of binders to improve β-adrenergic affinity. We also discussed strengths and challenges related to the applicability of molecular docking in β-adrenergic receptors. Molecular docking is a valuable technique in computational chemistry to deeply analyze ligand recognition and has led to important breakthroughs in drug discovery and design in the field of β-adrenergic receptors. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Molecularly Imprinted Nanomaterials for Sensor Applications

PubMed Central

Irshad, Muhammad; Iqbal, Naseer; Mujahid, Adnan; Afzal, Adeel; Hussain, Tajamal; Sharif, Ahsan; Ahmad, Ejaz; Athar, Muhammad Makshoof

2013-01-01

Molecular imprinting is a well-established technology to mimic antibody-antigen interaction in a synthetic platform. Molecularly imprinted polymers and nanomaterials usually possess outstanding recognition capabilities. Imprinted nanostructured materials are characterized by their small sizes, large reactive surface area and, most importantly, with rapid and specific analysis of analytes due to the formation of template driven recognition cavities within the matrix. The excellent recognition and selectivity offered by this class of materials towards a target analyte have found applications in many areas, such as separation science, analysis of organic pollutants in water, environmental analysis of trace gases, chemical or biological sensors, biochemical assays, fabricating artificial receptors, nanotechnology, etc. We present here a concise overview and recent developments in nanostructured imprinted materials with respect to various sensor systems, e.g., electrochemical, optical and mass sensitive, etc. Finally, in light of recent studies, we conclude the article with future perspectives and foreseen applications of imprinted nanomaterials in chemical sensors. PMID:28348356

Aminoglycosides: Molecular Insights on the Recognition of RNA and Aminoglycoside Mimics

PubMed Central

Chittapragada, Maruthi; Roberts, Sarah; Ham, Young Wan

2009-01-01

RNA is increasingly recognized for its significant functions in biological systems and has recently become an important molecular target for therapeutics development. Aminoglycosides, a large class of clinically significant antibiotics, exert their biological functions by binding to prokaryotic ribosomal RNA (rRNA) and interfering with protein translation, resulting in bacterial cell death. They are also known to bind to viral mRNAs such as HIV-1 RRE and TAR. Consequently, aminoglycosides are accepted as the single most important model in understanding the principles that govern small molecule-RNA recognition, which is essential for the development of novel antibacterial, antiviral or even anti-oncogenic agents. This review outlines the chemical structures and mechanisms of molecular recognition and antibacterial activity of aminoglycosides and various aminoglycoside mimics that have recently been devised to improve biological efficacy, binding affinity and selectivity, or to circumvent bacterial resistance. PMID:19812740

Synthesis of a specific monolithic column with artificial recognition sites for L-glutamic acid via cryo-crosslinking of imprinted nanoparticles.

PubMed

Göktürk, Ilgım; Üzek, Recep; Uzun, Lokman; Denizli, Adil

2016-06-01

In this study, a new molecular imprinting (MIP)-based monolithic cryogel column was prepared using chemically crosslinked molecularly imprinted nanoparticles, to achieve a simplified chromatographic separation (SPE) for a model compound, L-glutamic acid (L-Glu). Cryogelation through crosslinking of imprinted nanoparticles forms stable monolithic cryogel columns. This technique reduces the leakage of nanoparticles and increases the surface area, while protecting the structural features of the cryogel for stable and efficient recognition of the template molecule. A non-imprinted monolithic cryogel column (NIP) was also prepared, using non-imprinted nanoparticles produced without the addition of L-Glu during polymerization. The molecularly imprinted monolithic cryogel column (MIP) indicates apparent recognition selectivity and a good adsorption capacity compared to the NIP. Also, we have achieved a significant increase in the adsorption capacity, using the advantage of high surface area of the nanoparticles.

Molecular Recognition of Methyl α-d-Mannopyranoside by Antifreeze (Glyco)Proteins

PubMed Central

2015-01-01

Antifreeze proteins and glycoproteins [AF(G)Ps] have been well-known for more than three decades for their ability to inhibit the growth and recrystallization of ice through binding to specific ice crystal faces, and they show remarkable structural compatibility with specific ice crystal faces. Here, we show that the crystal growth faces of methyl α-d-mannopyranoside (MDM), a representative pyranose sugar, also show noteworthy structural compatibility with the known periodicities of AF(G)Ps. We selected fish AFGPs (AFGP8, AFGP1–5), and a beetle AFP (DAFP1) with increasing antifreeze activity as potential additives for controlling MDM crystal growth. Similar to their effects on ice growth, the AF(G)Ps can inhibit MDM crystal growth and recrystallization, and more significantly, the effectiveness for the AF(G)Ps are well correlated with their antifreeze activity. MDM crystals grown in the presence of AF(G)Ps are smaller and have better defined shapes and are of higher quality as indicated by single crystal X-ray diffraction and polarized microscopy than control crystals, but no new polymorphs of MDM were identified by single crystal X-ray diffraction, solid-state NMR, and attenuated total reflectance infrared spectroscopy. The observed changes in the average sizes of the MDM crystals can be related to the changes in the number of the MDM nuclei in the presence of the AF(G)Ps. The critical free energy change differences of the MDM nucleation in the absence and presence of the additives were calculated. These values are close to those of the ice nucleation in the presence of AF(G)Ps suggesting similar interactions are involved in the molecular recognition of MDM by the AF(G)Ps. To our knowledge this is the first report where AF(G)Ps have been used to control crystal growth of carbohydrates and on AFGPs controlling non-ice-like crystals. Our finding suggests MDM might be a possible alternative to ice for studying the detailed mechanism of AF(G)P–crystal interactions. The relationships between AF(G)Ps and carbohydrate binding proteins are also discussed. The structural compatibility between AF(G)Ps and growing crystal faces demonstrated herein adds to the repertoire of molecular recognition by AF(G)Ps, which may have potential applications in the sugar, food, pharmaceutical, and materials industries. PMID:24918258

A Gromov-Hausdorff Framework with Diffusion Geometry for Topologically-Robust Non-Rigid Shape Matching

DTIC Science & Technology

2009-02-01

topology changes. We used a subset of the TOSCA shape database , [10], consisting of four different objects: cat, dog, male, and female. Each of the...often encountered as acquisition imperfections when the shapes are acquired using a 3D scanner. We used a subset of the TOSCA shape database , consisting...object recognition, Point Based Graphics, Prague, 2007. 18 44. A. Spira and R. Kimmel, An efficient solution to the eikonal equation on parametric

Label-free biosensing with functionalized nanopipette probes

PubMed Central

Umehara, Senkei; Karhanek, Miloslav; Davis, Ronald W.; Pourmand, Nader

2009-01-01

Nanopipette technology can uniquely identify biomolecules such as proteins based on differences in size, shape, and electrical charge. These differences are determined by the detection of changes in ionic current as the proteins interact with the nanopipette tip coated with probe molecules. Here we show that electrostatic, biotin-streptavidin, and antibody-antigen interactions on the nanopipette tip surface affect ionic current flowing through a 50-nm pore. Highly charged polymers interacting with the glass surface modulated the rectification property of the nanopipette electrode. Affinity-based binding between the probes tethered to the surface and their target proteins caused a change in the ionic current due to a partial blockade or an altered surface charge. These findings suggest that nanopipettes functionalized with appropriate molecular recognition elements can be used as nanosensors in biomedical and biological research. PMID:19264962

Triazine herbicide imprinted monolithic column for capillary electrochromatography.

PubMed

Aşır, Süleyman; Derazshamshir, Ali; Yılmaz, Fatma; Denizli, Adil

2015-12-01

Trietazine was selectively separated from aqueous solution containing the competitor molecule cyanazine, which is similar in size and shape to the template molecule. Structural features of the molecularly imprinted column were figured out by SEM. The influence of the mobile-phase composition, applied electrical field, and pH of the mobile phase on the recognition of trietazine by the imprinted monolithic polymer has been evaluated, and the imprint effect in the trietazine-imprinted monolithic polymer was demonstrated by an imprinting factor. The optimized monolithic column resulted in separation of trietazine from a structurally related competitor molecule, cyanazine. In addition, fast separation was obtained within 6 min by applying higher electrical field, with the electrophoretic mobility of 2.97 × 10(-8) m(2) V(-1) s(-1) at pH 11.0. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Assembly, Thermodynamics, and Structure of a Two-Wheeled Composite of a Dumbbell-Shaped Molecule and Cylindrical Molecules with Different Edges.

PubMed

Matsuno, Taisuke; Kamata, Sho; Sato, Sota; Yokoyama, Atsutoshi; Sarkar, Parantap; Isobe, Hiroyuki

2017-11-20

A carbonaceous dumbbell was able to spontaneously glue two tubular receptors to form a unique two-wheeled composite through van der Waals interactions, thus forcing the wheel components into contact with each other at the edges. In the present study, two tubular receptors with enantiomeric carbon networks were assembled on the dumbbell joint, and the handedness of the receptors was discriminated, thus leading to the self-sorting of homomeric receptors from a mixture of enantiomeric tubes. The crystal structures of the composites revealed the structural origins of the molecular recognition driven by van der Waals forces as well as the presence of a columnar array of C 120 molecules in a 1:1 composite. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Three-dimensional deformable-model-based localization and recognition of road vehicles.

PubMed

Zhang, Zhaoxiang; Tan, Tieniu; Huang, Kaiqi; Wang, Yunhong

2012-01-01

We address the problem of model-based object recognition. Our aim is to localize and recognize road vehicles from monocular images or videos in calibrated traffic scenes. A 3-D deformable vehicle model with 12 shape parameters is set up as prior information, and its pose is determined by three parameters, which are its position on the ground plane and its orientation about the vertical axis under ground-plane constraints. An efficient local gradient-based method is proposed to evaluate the fitness between the projection of the vehicle model and image data, which is combined into a novel evolutionary computing framework to estimate the 12 shape parameters and three pose parameters by iterative evolution. The recovery of pose parameters achieves vehicle localization, whereas the shape parameters are used for vehicle recognition. Numerous experiments are conducted in this paper to demonstrate the performance of our approach. It is shown that the local gradient-based method can evaluate accurately and efficiently the fitness between the projection of the vehicle model and the image data. The evolutionary computing framework is effective for vehicles of different types and poses is robust to all kinds of occlusion.

Cholesterol accelerates the binding of Alzheimer's β-amyloid peptide to ganglioside GM1 through a universal hydrogen-bond-dependent sterol tuning of glycolipid conformation

PubMed Central

Fantini, Jacques; Yahi, Nouara; Garmy, Nicolas

2013-01-01

Age-related alterations of membrane lipids in brain cell membranes together with high blood cholesterol are considered as major risk factors for Alzheimer's disease. Yet the molecular mechanisms by which these factors increase Alzheimer's risk are mostly unknown. In lipid raft domains of the plasma membrane, neurotoxic Alzheimer's beta-amyloid (Abeta) peptides interact with both cholesterol and ganglioside GM1. Recent data also suggested that cholesterol could stimulate the binding of Abeta to GM1 through conformational modulation of the ganglioside headgroup. Here we used a combination of physicochemical and molecular modeling approaches to decipher the mechanisms of cholesterol-assisted binding of Abeta to GM1. With the aim of decoupling the effect of cholesterol on GM1 from direct Abeta-cholesterol interactions, we designed a minimal peptide (Abeta5-16) containing the GM1-binding domain but lacking the amino acid residues involved in cholesterol recognition. Using the Langmuir technique, we showed that cholesterol (but not phosphatidylcholine or sphingomyelin) significantly accelerates the interaction of Abeta5-16 with GM1. Molecular dynamics simulations suggested that Abeta5-16 interacts with a cholesterol-stabilized dimer of GM1. The main structural effect of cholesterol is to establish a hydrogen-bond between its own OH group and the glycosidic-bond linking ceramide to the glycone part of GM1, thereby inducing a tilt in the glycolipid headgroup. This fine conformational tuning stabilizes the active conformation of the GM1 dimer whose headgroups, oriented in two opposite directions, form a chalice-shaped receptacle for Abeta. These data give new mechanistic insights into the stimulatory effect of cholesterol on Abeta/GM1 interactions. They also support the emerging concept that cholesterol is a universal modulator of protein-glycolipid interactions in the broader context of membrane recognition processes. PMID:23772214

A Novel Phonology- and Radical-Coded Chinese Sign Language Recognition Framework Using Accelerometer and Surface Electromyography Sensors

PubMed Central

Cheng, Juan; Chen, Xun; Liu, Aiping; Peng, Hu

2015-01-01

Sign language recognition (SLR) is an important communication tool between the deaf and the external world. It is highly necessary to develop a worldwide continuous and large-vocabulary-scale SLR system for practical usage. In this paper, we propose a novel phonology- and radical-coded Chinese SLR framework to demonstrate the feasibility of continuous SLR using accelerometer (ACC) and surface electromyography (sEMG) sensors. The continuous Chinese characters, consisting of coded sign gestures, are first segmented into active segments using EMG signals by means of moving average algorithm. Then, features of each component are extracted from both ACC and sEMG signals of active segments (i.e., palm orientation represented by the mean and variance of ACC signals, hand movement represented by the fixed-point ACC sequence, and hand shape represented by both the mean absolute value (MAV) and autoregressive model coefficients (ARs)). Afterwards, palm orientation is first classified, distinguishing “Palm Downward” sign gestures from “Palm Inward” ones. Only the “Palm Inward” gestures are sent for further hand movement and hand shape recognition by dynamic time warping (DTW) algorithm and hidden Markov models (HMM) respectively. Finally, component recognition results are integrated to identify one certain coded gesture. Experimental results demonstrate that the proposed SLR framework with a vocabulary scale of 223 characters can achieve an averaged recognition accuracy of 96.01% ± 0.83% for coded gesture recognition tasks and 92.73% ± 1.47% for character recognition tasks. Besides, it demonstrats that sEMG signals are rather consistent for a given hand shape independent of hand movements. Hence, the number of training samples will not be significantly increased when the vocabulary scale increases, since not only the number of the completely new proposed coded gestures is constant and limited, but also the transition movement which connects successive signs needs no training samples to model even though the same coded gesture performed in different characters. This work opens up a possible new way to realize a practical Chinese SLR system. PMID:26389907

A Novel Phonology- and Radical-Coded Chinese Sign Language Recognition Framework Using Accelerometer and Surface Electromyography Sensors.

PubMed

Cheng, Juan; Chen, Xun; Liu, Aiping; Peng, Hu

2015-09-15

Sign language recognition (SLR) is an important communication tool between the deaf and the external world. It is highly necessary to develop a worldwide continuous and large-vocabulary-scale SLR system for practical usage. In this paper, we propose a novel phonology- and radical-coded Chinese SLR framework to demonstrate the feasibility of continuous SLR using accelerometer (ACC) and surface electromyography (sEMG) sensors. The continuous Chinese characters, consisting of coded sign gestures, are first segmented into active segments using EMG signals by means of moving average algorithm. Then, features of each component are extracted from both ACC and sEMG signals of active segments (i.e., palm orientation represented by the mean and variance of ACC signals, hand movement represented by the fixed-point ACC sequence, and hand shape represented by both the mean absolute value (MAV) and autoregressive model coefficients (ARs)). Afterwards, palm orientation is first classified, distinguishing "Palm Downward" sign gestures from "Palm Inward" ones. Only the "Palm Inward" gestures are sent for further hand movement and hand shape recognition by dynamic time warping (DTW) algorithm and hidden Markov models (HMM) respectively. Finally, component recognition results are integrated to identify one certain coded gesture. Experimental results demonstrate that the proposed SLR framework with a vocabulary scale of 223 characters can achieve an averaged recognition accuracy of 96.01% ± 0.83% for coded gesture recognition tasks and 92.73% ± 1.47% for character recognition tasks. Besides, it demonstrats that sEMG signals are rather consistent for a given hand shape independent of hand movements. Hence, the number of training samples will not be significantly increased when the vocabulary scale increases, since not only the number of the completely new proposed coded gestures is constant and limited, but also the transition movement which connects successive signs needs no training samples to model even though the same coded gesture performed in different characters. This work opens up a possible new way to realize a practical Chinese SLR system.

Specific recognition of polyphenols by molecularly imprinted polymers based on a ternary deep eutectic solvent.

PubMed

Fu, Najing; Li, Liteng; Liu, Xiao; Fu, Nian; Zhang, Chenchen; Hu, Liandong; Li, Donghao; Tang, Baokun; Zhu, Tao

2017-12-29

Typically, a target compound is selected as a template for a molecularly imprinted polymer (MIP); however, some target compounds are not suitable as templates because of their poor solubility. Using the tailoring properties of a deep eutectic solvent (DES), the insoluble target compound caffeic acid was transformed into a ternary choline chloride-caffeic acid-ethylene glycol (ChCl-CA-EG) DES, which was then employed as a template to prepare MIPs. The ternary DES-based MIPs were characterized by Fourier transform infrared spectroscopy, elemental analysis, scanning electron microscopy, and atomic force microscopy. The effects of time, temperature, ionic strength, and pH on the recognition processes for four polyphenols (caffeic acid, protocatechuic acid, catechin, and epicatechin) by 13 ChCl-CA-EG ternary DES-based MIPs was investigated using high-performance liquid chromatography. The recognition specificity of the MIPs for CA was significantly better than that for the other polyphenols, and the MIPs exhibited obvious characteristics of chromatographic packing materials. In addition, the recognition processes mainly followed a second-order kinetics model and the Freundlich isotherm model, which together indicated that the MIPs mainly recognized the polyphenols by chemical interactions including ion exchange, electron exchange, and new bond formation. Furthermore, the specific recognition ability of the MIPs for polyphenols, which was better than those of C 18 , C 8 , or non-molecularly imprinted polymer adsorbents, was successfully applied to the recognition of polyphenols in a Radix asteris sample. The transformation of an insoluble target compound in a polymeric DES for MIP preparation and recognition is a novel and feasible strategy suitable for use in further MIP research developments. Copyright © 2017 Elsevier B.V. All rights reserved.

Exploring the energy landscape of antibody-antigen complexes: protein dynamics, flexibility, and molecular recognition.

PubMed

Thielges, Megan C; Zimmermann, Jörg; Yu, Wayne; Oda, Masayuki; Romesberg, Floyd E

2008-07-08

The production of antibodies that selectively bind virtually any foreign compound is the hallmark of the immune system. While much is understood about how sequence diversity contributes to this remarkable feat of molecular recognition, little is known about how sequence diversity impacts antibody dynamics, which is also expected to contribute to molecular recognition. Toward this goal, we examined a panel of antibodies elicited to the chromophoric antigen fluorescein. On the basis of isothermal titration calorimetry, we selected six antibodies that bind fluorescein with diverse binding entropies, suggestive of varying contributions of dynamics to molecular recognition. Sequencing revealed that two pairs of antibodies employ homologous heavy chains that were derived from common germline genes, while the other two heavy chains and all six of the light chains were derived from different germline genes and are not homologous. Interestingly, more than half of all the somatic mutations acquired during affinity maturation among the six antibodies are located in positions unlikely to contact fluorescein directly. To quantify and compare the dynamics of the antibody-fluorescein complexes, three-pulse photon echo peak shift and transient grating spectroscopy were employed. All of the antibodies exhibited motions on three distinct time scales, ultrafast motions on the <100 fs time scale, diffusive motions on the picosecond time scale, and motions that occur on time scales longer than nanoseconds and thus appear static. However, the exact frequency of the picosecond time scale motion and the relative contribution of the different motions vary significantly among the antibody-chromophore complexes, revealing a high level of dynamic diversity. Using a hierarchical model, we relate the data to features of the antibodies' energy landscapes as well as their flexibility in terms of elasticity and plasticity. In all, the data provide a consistent picture of antibody flexibility, which interestingly appears to be correlated with binding entropy as well as with germline gene use and the mutations introduced during affinity maturation. The data also provide a gauge of the dynamic diversity of the antibody repertoire and suggest that this diversity might contribute to molecular recognition by facilitating the recognition of the broadest range of foreign molecules.

Variety of geologic silhouette shapes distinguishable by multiple rotations method of quantitative shape analysis text

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

Collins, D.G.; Parks, J.M.

1984-04-01

Silhouette shapes are two-dimensional projections of three-dimensional objects such as sand grains, gravel, and fossils. Within-the-margin markings such as chamber boundaries, sutures, or ribs are ignored. Comparisons between populations of objects from similar and differential origins (i.e., environments, species or genera, growth series, etc) is aided by quantifying the shapes. The Multiple Rotations Method (MRM) uses a variation of ''eigenshapes'', which is capable of distinguishing most of the subtle variations that the ''trained eye'' can detect. With a video-digitizer and microcomputer, MRM is fast, more accurate, and more objective than the human eye. The resulting shape descriptors comprise 5 ormore » 6 numbers per object that can be stored and retrieved to compare with similar descriptions of other objects. The original-shape outlines can be reconstituted sufficiently for gross recognition from these few numerical descriptors. Thus, a semi-automated data-retrieval system becomes feasible, with silhouette-shape descriptions as one of several recognition criteria. MRM consists of four ''rotations'': rotation about a center to a comparable orientation; a principal-components rotation to reduce the many original shape descriptors to a few; a VARIMAX orthogonal-factor rotation to achieve simple structure; and a rotation to achieve factor scores on individual objects. A variety of subtly different shapes includes sand grains from several locations, ages, and environments, and fossils of several types. This variety illustrates the feasibility of quantitative comparisons by MRM.« less

Sentence Recognition Prediction for Hearing-impaired Listeners in Stationary and Fluctuation Noise With FADE: Empowering the Attenuation and Distortion Concept by Plomp With a Quantitative Processing Model.

PubMed

Kollmeier, Birger; Schädler, Marc René; Warzybok, Anna; Meyer, Bernd T; Brand, Thomas

2016-09-07

To characterize the individual patient's hearing impairment as obtained with the matrix sentence recognition test, a simulation Framework for Auditory Discrimination Experiments (FADE) is extended here using the Attenuation and Distortion (A+D) approach by Plomp as a blueprint for setting the individual processing parameters. FADE has been shown to predict the outcome of both speech recognition tests and psychoacoustic experiments based on simulations using an automatic speech recognition system requiring only few assumptions. It builds on the closed-set matrix sentence recognition test which is advantageous for testing individual speech recognition in a way comparable across languages. Individual predictions of speech recognition thresholds in stationary and in fluctuating noise were derived using the audiogram and an estimate of the internal level uncertainty for modeling the individual Plomp curves fitted to the data with the Attenuation (A-) and Distortion (D-) parameters of the Plomp approach. The "typical" audiogram shapes from Bisgaard et al with or without a "typical" level uncertainty and the individual data were used for individual predictions. As a result, the individualization of the level uncertainty was found to be more important than the exact shape of the individual audiogram to accurately model the outcome of the German Matrix test in stationary or fluctuating noise for listeners with hearing impairment. The prediction accuracy of the individualized approach also outperforms the (modified) Speech Intelligibility Index approach which is based on the individual threshold data only. © The Author(s) 2016.

Shape-specific perceptual learning in a figure-ground segregation task.

PubMed

Yi, Do-Joon; Olson, Ingrid R; Chun, Marvin M

2006-03-01

What does perceptual experience contribute to figure-ground segregation? To study this question, we trained observers to search for symmetric dot patterns embedded in random dot backgrounds. Training improved shape segmentation, but learning did not completely transfer either to untrained locations or to untrained shapes. Such partial specificity persisted for a month after training. Interestingly, training on shapes in empty backgrounds did not help segmentation of the trained shapes in noisy backgrounds. Our results suggest that perceptual training increases the involvement of early sensory neurons in the segmentation of trained shapes, and that successful segmentation requires perceptual skills beyond shape recognition alone.

Magnetic deep eutectic solvents molecularly imprinted polymers for the selective recognition and separation of protein.

PubMed

Liu, Yanjin; Wang, Yuzhi; Dai, Qingzhou; Zhou, Yigang

2016-09-14

A novel and facile magnetic deep eutectic solvents (DES) molecularly imprinted polymers (MIPs) for the selective recognition and separation of Bovine hemoglobin (BHb) was prepared. The new-type DES was adopted as the functional monomer which would bring molecular imprinted technology to a new direction. The amounts of DES were optimized. The obtained magnetic DES-MIPs were characterized with fourier transform infrared spectrometry (FT-IR), thermogravimetric analysis (TGA), field emission scanning electron microscope (FESEM), dynamic light scattering (DLS), elemental analysis and vibrating sample magnetometer (VSM). The results suggested that the imprinted polymers were successfully formed and possessed a charming magnetism. The maximum adsorption capability (Qmax) and dissociation constant (KL) were analyzed by Langmuir isotherms (R(2) = 0.9983) and the value were estimated to be 175.44 mg/g and 0.035 mg/mL for the imprinted particles. And the imprinted particles showed a high imprinting factor of 4.77. In addition, the magnetic DES-MIPs presented outstanding recognition specificity and selectivity so that it can be utilized to separate template protein from the mixture of proteins and real samples. Last but not least, the combination of deep eutectic solvents and molecular imprinted technology in this paper provides a new perspective for the recognition and separation of proteins. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular Basis for Phosphorylation-dependent SUMO Recognition by the DNA Repair Protein RAP80.

PubMed

Anamika; Spyracopoulos, Leo

2016-02-26

Recognition and repair of double-stranded DNA breaks (DSB) involves the targeted recruitment of BRCA tumor suppressors to damage foci through binding of both ubiquitin (Ub) and the Ub-like modifier SUMO. RAP80 is a component of the BRCA1 A complex, and plays a key role in the recruitment process through the binding of Lys(63)-linked poly-Ub chains by tandem Ub interacting motifs (UIM). RAP80 also contains a SUMO interacting motif (SIM) just upstream of the tandem UIMs that has been shown to specifically bind the SUMO-2 isoform. The RAP80 tandem UIMs and SIM function collectively for optimal recruitment of BRCA1 to DSBs, although the molecular basis of this process is not well understood. Using NMR spectroscopy, we demonstrate that the RAP80 SIM binds SUMO-2, and that both specificity and affinity are enhanced through phosphorylation of the canonical CK2 site within the SIM. The affinity increase results from an enhancement of electrostatic interactions between the phosphoserines of RAP80 and the SIM recognition module within SUMO-2. The NMR structure of the SUMO-2·phospho-RAP80 complex reveals that the molecular basis for SUMO-2 specificity is due to isoform-specific sequence differences in electrostatic SIM recognition modules. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Preparation and evaluation of a macroporous molecularly imprinted hybrid silica monolithic column for recognition of proteins by high performance liquid chromatography.

PubMed

Lin, Zian; Yang, Fan; He, Xiwen; Zhao, Xiaomiao; Zhang, Yukui

2009-12-04

A novel type of macroporous molecularly imprinted hybrid silica monolithic column was first developed for recognition of proteins. The macroporous silica-based monolithic skeleton was synthesized in a 4.6mm i.d. stainless steel column by a mild sol-gel process with methyltrimethoxysilane (MTMS) as a sole precursor, and then vinyl groups were introduced onto the surface of the silica skeleton by chemical modification of gamma-methacryloxypropyltrimethoxysilane (gamma-MAPS). Subsequently, the molecularly imprinted polymer (MIP) coating was copolymerized and anchored onto the surface of the silica monolith. Bovine serum albumin (BSA) and lysozyme (Lyz), which differ greatly in molecular size, isoelectric point, and charge, were representatively selected for imprinted templates to evaluate recognition property of the hybrid silica-based MIP monolith. Some important factors, such as template-monomer molar ratio, total monomer concentration and crosslinking density, were systematically investigated. Under the optimum conditions, the obtained hybrid silica-based MIP monolith showed higher binding affinity for template than its corresponding non-imprinted (NIP) monolith. The imprinted factor (IF) for BSA and Lyz reached 9.07 and 6.52, respectively. Moreover, the hybrid silica-based MIP monolith displayed favorable binding characteristics for template over competitive protein. Compared with the imprinted silica beads for stationary phase and in situ organic polymer-based hydrogel MIP monolith, the hybrid silica MIP monolith exhibited higher recognition, stability and lifetime.

Support vector machine for automatic pain recognition

NASA Astrophysics Data System (ADS)

Monwar, Md Maruf; Rezaei, Siamak

2009-02-01

Facial expressions are a key index of emotion and the interpretation of such expressions of emotion is critical to everyday social functioning. In this paper, we present an efficient video analysis technique for recognition of a specific expression, pain, from human faces. We employ an automatic face detector which detects face from the stored video frame using skin color modeling technique. For pain recognition, location and shape features of the detected faces are computed. These features are then used as inputs to a support vector machine (SVM) for classification. We compare the results with neural network based and eigenimage based automatic pain recognition systems. The experiment results indicate that using support vector machine as classifier can certainly improve the performance of automatic pain recognition system.

A positional code and anisotropic forces control tissue remodeling in Drosophila

NASA Astrophysics Data System (ADS)

Zallen, Jennifer

A major challenge in developmental biology is to understand how tissue-scale changes in organism structure arise from events that occur on a cellular and molecular level. We are using cell biological, biophysical, and quantitative live-embryo imaging approaches to understand how genes encode the forces that shape tissues, and to identify the mechanisms that modulate cell behavior in response to local forces. In many animals, the elongated head-to-tail body axis is achieved by rapid and coordinated movements of hundreds of cells. We found that in the fruit fly, these cell movements are regulated by subcellular asymmetries in the localization of proteins that generate contractile and adhesive forces between cells. Asymmetries in the force-generating machinery are in turn controlled by a positional code of spatial information provided by an ancient family of Toll-related receptors that are widely used for pathogen recognition by the innate immune system. I will describe how this spatial system systematically orients local cell movements and collective rosette-like clusters in the Drosophila embryo. Rosettes have now also been shown to shape the body axis in chicks, frogs, and mice, demonstrating that rosette behaviors are a general mechanism linking cellular asymmetry to tissue reorganization.

Compact optical processor for Hough and frequency domain features

NASA Astrophysics Data System (ADS)

Ott, Peter

1996-11-01

Shape recognition is necessary in a broad band of applications such as traffic sign or work piece recognition. It requires not only neighborhood processing of the input image pixels but global interconnection of them. The Hough transform (HT) performs such a global operation and it is well suited in the preprocessing stage of a shape recognition system. Translation invariant features can be easily calculated form the Hough domain. We have implemented on the computer a neural network shape recognition system which contains a HT, a feature extraction, and a classification layer. The advantage of this approach is that the total system can be optimized with well-known learning techniques and that it can explore the parallelism of the algorithms. However, the HT is a time consuming operation. Parallel, optical processing is therefore advantageous. Several systems have been proposed, based on space multiplexing with arrays of holograms and CGH's or time multiplexing with acousto-optic processors or by image rotation with incoherent and coherent astigmatic optical processors. We took up the last mentioned approach because 2D array detectors are read out line by line, so a 2D detector can achieve the same speed and is easier to implement. Coherent processing can allow the implementation of tilers in the frequency domain. Features based on wedge/ring, Gabor, or wavelet filters have been proven to show good discrimination capabilities for texture and shape recognition. The astigmatic lens system which is derived form the mathematical formulation of the HT is long and contains a non-standard, astigmatic element. By methods of lens transformation s for coherent applications we map the original design to a shorter lens with a smaller number of well separated standard elements and with the same coherent system response. The final lens design still contains the frequency plane for filtering and ray-tracing shows diffraction limited performance. Image rotation can be done optically by a rotating prism. We realize it on a fast FLC- SLM of our lab as input device. The filters can be implemented on the same type of SLM with 128 by 128 square pixels of size, resulting in a total length of the lens of less than 50cm.

Molecular recognition of naphthalene diimide ligands by telomeric quadruplex-DNA: the importance of the protonation state and mediated hydrogen bonds.

PubMed

Spinello, A; Barone, G; Grunenberg, J

2016-01-28

In depth Monte Carlo conformational scans in combination with molecular dynamics (MD) simulations and electronic structure calculations were applied in order to study the molecular recognition process between tetrasubstituted naphthalene diimide (ND) guests and G-quadruplex (G4) DNA receptors. ND guests are a promising class of telomere stabilizers due to which they are used in novel anticancer therapeutics. Though several ND guests have been studied experimentally in the past, the protonation state under physiological conditions is still unclear. Based on chemical intuition, in the case of N-methyl-piperazine substitution, different protonation states are possible and might play a crucial role in the molecular recognition process by G4-DNA. Depending on the proton concentration, different nitrogen atoms of the N-methyl-piperazine might (or might not) be protonated. This fact was considered in our simulation in terms of a case by case analysis, since the process of molecular recognition is determined by possible donor or acceptor positions. The results of our simulations show that the electrostatic interactions between the ND ligands and the G4 receptor are maximized in the case of the protonation of the terminal nitrogen atoms, forming compact ND G4 complexes inside the grooves. The influence of different protonation states in terms of the ability to form hydrogen bonds with the sugar-phosphate backbone, as well as the importance of mediated vs. direct hydrogen bonding, was analyzed in detail by MD and relaxed force constant (compliance constant) simulations.

Molecular imprinting at walls of silica nanotubes for TNT recognition.

PubMed

Xie, Chenggen; Liu, Bianhua; Wang, Zhenyang; Gao, Daming; Guan, Guijian; Zhang, Zhongping

2008-01-15

This paper reports the molecular imprinting at the walls of highly uniform silica nanotubes for the recognition of 2,4,6-trinitrotoluene (TNT). It has been demonstrated that TNT templates were efficiently imprinted into the matrix of silica through the strong acid-base pairing interaction between TNT and 3-aminopropyltriethoxysilane (APTS). TNT-imprinted silica nanotubes were synthesized by the gelation reaction between APTS and tetraethylorthosilicate (TEOS), selectively occurring at the porous walls of APTS-modified alumina membranes. The removal of the original TNT templates leaves the imprinted cavities with covalently anchored amine groups at the cavity walls. A high density of recognition sites with molecular selectivity to the TNT analyte was created at the wall of silica nanotubes. Furthermore, most of these recognition sites are situated at the inside and outside surfaces of tubular walls and in the proximity of the two surfaces due to the ultrathin wall thickness of only 15 nm, providing a better site accessibility and lower mass-transfer resistance. Therefore, greater capacity and faster kinetics of uptaking target species were achieved. The silica nanotube reported herein is an ideal form of material for imprinting various organic or biological molecules toward applications in chemical/biological sensors and bioassay.

Evaluation of Ochratoxin Recognition by Peptides Using Explicit Solvent Molecular Dynamics

PubMed Central

Thyparambil, Aby A.; Bazin, Ingrid; Guiseppi-Elie, Anthony

2017-01-01

Biosensing platforms based on peptide recognition provide a cost-effective and stable alternative to antibody-based capture and discrimination of ochratoxin-A (OTA) vs. ochratoxin-B (OTB) in monitoring bioassays. Attempts to engineer peptides with improved recognition efficacy require thorough structural and thermodynamic characterization of the binding-competent conformations. Classical molecular dynamics (MD) approaches alone do not provide a thorough assessment of a peptide’s recognition efficacy. In this study, in-solution binding properties of four different peptides, a hexamer (SNLHPK), an octamer (CSIVEDGK), NFO4 (VYMNRKYYKCCK), and a 13-mer (GPAGIDGPAGIRC), which were previously generated for OTA-specific recognition, were evaluated using an advanced MD simulation approach involving accelerated configurational search and predictive modeling. Peptide configurations relevant to ochratoxin binding were initially generated using biased exchange metadynamics and the dynamic properties associated with the in-solution peptide–ochratoxin binding were derived from Markov State Models. Among the various peptides, NFO4 shows superior in-solution OTA sensing and also shows superior selectivity for OTA vs. OTB due to the lower penalty associated with solvating its bound complex. Advanced MD approaches provide structural and energetic insights critical to the hapten-specific recognition to aid the engineering of peptides with better sensing efficacies. PMID:28505090

Sonographic Diagnosis of Tubal Cancer with IOTA Simple Rules Plus Pattern Recognition

PubMed Central

Tongsong, Theera; Wanapirak, Chanane; Tantipalakorn, Charuwan; Tinnangwattana, Dangcheewan

2017-01-01

Objective: To evaluate diagnostic performance of IOTA simple rules plus pattern recognition in predicting tubal cancer. Methods: Secondary analysis was performed on prospective database of our IOTA project. The patients recruited in the project were those who were scheduled for pelvic surgery due to adnexal masses. The patients underwent ultrasound examinations within 24 hours before surgery. On ultrasound examination, the masses were evaluated using the well-established IOTA simple rules plus pattern recognition (sausage-shaped appearance, incomplete septum, visible ipsilateral ovaries) to predict tubal cancer. The gold standard diagnosis was based on histological findings or operative findings. Results: A total of 482 patients, including 15 cases of tubal cancer, were evaluated by ultrasound preoperatively. The IOTA simple rules plus pattern recognition gave a sensitivity of 86.7% (13 in 15) and specificity of 97.4%. Sausage-shaped appearance was identified in nearly all cases (14 in 15). Incomplete septa and normal ovaries could be identified in 33.3% and 40%, respectively. Conclusion: IOTA simple rules plus pattern recognition is relatively effective in predicting tubal cancer. Thus, we propose the simple scheme in diagnosis of tubal cancer as follows. First of all, the adnexal masses are evaluated with IOTA simple rules. If the B-rules could be applied, tubal cancer is reliably excluded. If the M-rules could be applied or the result is inconclusive, careful delineation of the mass with pattern recognition should be performed. PMID:29172273

Sonographic Diagnosis of Tubal Cancer with IOTA Simple Rules Plus Pattern Recognition

PubMed

Tongsong, Theera; Wanapirak, Chanane; Tantipalakorn, Charuwan; Tinnangwattana, Dangcheewan

2017-11-26

Objective: To evaluate diagnostic performance of IOTA simple rules plus pattern recognition in predicting tubal cancer. Methods: Secondary analysis was performed on prospective database of our IOTA project. The patients recruited in the project were those who were scheduled for pelvic surgery due to adnexal masses. The patients underwent ultrasound examinations within 24 hours before surgery. On ultrasound examination, the masses were evaluated using the well-established IOTA simple rules plus pattern recognition (sausage-shaped appearance, incomplete septum, visible ipsilateral ovaries) to predict tubal cancer. The gold standard diagnosis was based on histological findings or operative findings. Results: A total of 482 patients, including 15 cases of tubal cancer, were evaluated by ultrasound preoperatively. The IOTA simple rules plus pattern recognition gave a sensitivity of 86.7% (13 in 15) and specificity of 97.4%. Sausage-shaped appearance was identified in nearly all cases (14 in 15). Incomplete septa and normal ovaries could be identified in 33.3% and 40%, respectively. Conclusion: IOTA simple rules plus pattern recognition is relatively effective in predicting tubal cancer. Thus, we propose the simple scheme in diagnosis of tubal cancer as follows. First of all, the adnexal masses are evaluated with IOTA simple rules. If the B-rules could be applied, tubal cancer is reliably excluded. If the M-rules could be applied or the result is inconclusive, careful delineation of the mass with pattern recognition should be performed. Creative Commons Attribution License

Textual and shape-based feature extraction and neuro-fuzzy classifier for nuclear track recognition

NASA Astrophysics Data System (ADS)

Khayat, Omid; Afarideh, Hossein

2013-04-01

Track counting algorithms as one of the fundamental principles of nuclear science have been emphasized in the recent years. Accurate measurement of nuclear tracks on solid-state nuclear track detectors is the aim of track counting systems. Commonly track counting systems comprise a hardware system for the task of imaging and software for analysing the track images. In this paper, a track recognition algorithm based on 12 defined textual and shape-based features and a neuro-fuzzy classifier is proposed. Features are defined so as to discern the tracks from the background and small objects. Then, according to the defined features, tracks are detected using a trained neuro-fuzzy system. Features and the classifier are finally validated via 100 Alpha track images and 40 training samples. It is shown that principle textual and shape-based features concomitantly yield a high rate of track detection compared with the single-feature based methods.

Imaging and Force Recognition of Single Molecular Behaviors Using Atomic Force Microscopy

PubMed Central

Li, Mi; Dang, Dan; Liu, Lianqing; Xi, Ning; Wang, Yuechao

2017-01-01

The advent of atomic force microscopy (AFM) has provided a powerful tool for investigating the behaviors of single native biological molecules under physiological conditions. AFM can not only image the conformational changes of single biological molecules at work with sub-nanometer resolution, but also sense the specific interactions of individual molecular pair with piconewton force sensitivity. In the past decade, the performance of AFM has been greatly improved, which makes it widely used in biology to address diverse biomedical issues. Characterizing the behaviors of single molecules by AFM provides considerable novel insights into the underlying mechanisms guiding life activities, contributing much to cell and molecular biology. In this article, we review the recent developments of AFM studies in single-molecule assay. The related techniques involved in AFM single-molecule assay were firstly presented, and then the progress in several aspects (including molecular imaging, molecular mechanics, molecular recognition, and molecular activities on cell surface) was summarized. The challenges and future directions were also discussed. PMID:28117741

Molecularly Imprinted Intelligent Scaffolds for Tissue Engineering Applications.

PubMed

Neves, Mariana I; Wechsler, Marissa E; Gomes, Manuela E; Reis, Rui L; Granja, Pedro L; Peppas, Nicholas A

2017-02-01

The development of molecularly imprinted polymers (MIPs) using biocompatible production methods enables the possibility to further exploit this technology for biomedical applications. Tissue engineering (TE) approaches use the knowledge of the wound healing process to design scaffolds capable of modulating cell behavior and promote tissue regeneration. Biomacromolecules bear great interest for TE, together with the established recognition of the extracellular matrix, as an important source of signals to cells, both promoting cell-cell and cell-matrix interactions during the healing process. This review focuses on exploring the potential of protein molecular imprinting to create bioactive scaffolds with molecular recognition for TE applications based on the most recent approaches in the field of molecular imprinting of macromolecules. Considerations regarding essential components of molecular imprinting technology will be addressed for TE purposes. Molecular imprinting of biocompatible hydrogels, namely based on natural polymers, is also reviewed here. Hydrogel scaffolds with molecular memory show great promise for regenerative therapies. The first molecular imprinting studies analyzing cell adhesion report promising results with potential applications for cell culture systems, or biomaterials for implantation with the capability for cell recruitment by selectively adsorbing desired molecules.

Solubility Interactions and the Design of Chemically Selective Sorbent Coatings for Chemical Sensors and Arrays

DTIC Science & Technology

1990-07-27

sorptionpiezoelectric sorption 63 detector, surface acoustic wave, pattern recognition, array, 16. PRICE CODE molecular recognition , 17. SECURITY...1 PIEZOELECTRIC SORPTION DETECTORS ........................................................... 6 SOLUBILITY... SORPTION AND LINEAR SOLVATION ENERGY RELATIONSHIPS (LSER) ................................................................................... 9

Student award for outstanding research winner in the Ph.D. category for the 2017 society for biomaterials annual meeting and exposition, april 5-8, 2017, Minneapolis, Minnesota: Characterization of protein interactions with molecularly imprinted hydrogels that possess engineered affinity for high isoelectric point biomarkers.

PubMed

Clegg, John R; Zhong, Justin X; Irani, Afshan S; Gu, Joann; Spencer, David S; Peppas, Nicholas A

2017-06-01

Molecularly imprinted polymers (MIPs) with selective affinity for protein biomarkers could find extensive utility as environmentally robust, cost-efficient biomaterials for diagnostic and therapeutic applications. In order to develop recognitive, synthetic biomaterials for prohibitively expensive protein biomarkers, we have developed a molecular imprinting technique that utilizes structurally similar, analogue proteins. Hydrogel microparticles synthesized by molecular imprinting with trypsin, lysozyme, and cytochrome c possessed an increased affinity for alternate high isoelectric point biomarkers both in isolation and plasma-mimicking adsorption conditions. Imprinted and non-imprinted P(MAA-co-AAm-co-DEAEMA) microgels containing PMAO-PEGMA functionalized polycaprolactone nanoparticles were net-anionic, polydisperse, and irregularly shaped. MIPs and control non-imprinted polymers (NIPs) exhibited regions of Freundlich and BET isotherm adsorption behavior in a range of non-competitive protein solutions, where MIPs exhibited enhanced adsorption capacity in the Freundlich isotherm regions. In a competitive condition, imprinting with analogue templates (trypsin, lysozyme) increased the adsorption capacity of microgels for cytochrome c by 162% and 219%, respectively, as compared to a 122% increase provided by traditional bulk imprinting with cytochrome c. Our results suggest that molecular imprinting with analogue protein templates is a viable synthetic strategy for enhancing hydrogel-biomarker affinity and promoting specific protein adsorption behavior in biological fluids. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 1565-1574, 2017. © 2017 Wiley Periodicals, Inc.

Influence of Geometries on the Assembly of Snowman-Shaped Janus Nanoparticles.

PubMed

Kang, Chengjun; Honciuc, Andrei

2018-04-24

The self-assembly of micro/nanoparticles into suprastructures is a promising way to develop reconfigurable materials and to gain insights into the fundamental question of how matter organizes itself. The geometry of particles, especially those deviating from perfectly spherical shapes, is of significant importance in colloidal assembly because it influences the particle "recognition", determines the particle packing, and ultimately dictates the formation of assembled suprastructures. In order to organize particles into desired structures, it is of vital importance to understand the relationship between the shape of the colloidal building blocks and the assembled suprastructures. This fundamental issue is an enduring topic in the assembly of molecular surfactants, but it remained elusive in colloidal assembly. To address this issue, we use snowman-shaped Janus nanoparticles (JNPs) as a model to systematically study the effect of colloidal geometries on their assembled suprastructures. Ten types of JNPs with identical chemical compositions but with different geometries were synthesized. Specifically, the synthesized JNPs differ in their lobe size ratios, phase separation degrees, and overall sizes. We show that by altering these parameters, both finite suprastructures, such as capsules with different curvatures, and nonfinite suprastructures, including free-standing single-layered or double-layered JNPs sheets, can be obtained via self-assembly. All these different types of suprastructures are constituted by highly oriented and hexagonally packed JNPs. These findings demonstrate the significance of geometries in colloidal assembly, such that slightly changing the building block geometries could result in a large variety of very different assembled structures, without altering the chemistry of the particles.

Introducing MINA--The Molecularly Imprinted Nanoparticle Assay.

PubMed

Shutov, Roman V; Guerreiro, Antonio; Moczko, Ewa; de Vargas-Sansalvador, Isabel Perez; Chianella, Iva; Whitcombe, Michael J; Piletsky, Sergey A

2014-03-26

A new ELISA- (enzyme-linked immunosorbent assay)-like assay is demonstrated in which no elements of biological origin are used for molecular recognition or signaling. Composite imprinted nanoparticles that contain a catalytic core and which are synthesized by using a solid-phase approach can simultaneously act as recognition/signaling elements, and be used with minimal modifications to standard assay protocols. This assay provides a new route towards replacement of unstable biomolecules in immunoassays. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ventral-stream-like shape representation: from pixel intensity values to trainable object-selective COSFIRE models

PubMed Central

Azzopardi, George; Petkov, Nicolai

2014-01-01

The remarkable abilities of the primate visual system have inspired the construction of computational models of some visual neurons. We propose a trainable hierarchical object recognition model, which we call S-COSFIRE (S stands for Shape and COSFIRE stands for Combination Of Shifted FIlter REsponses) and use it to localize and recognize objects of interests embedded in complex scenes. It is inspired by the visual processing in the ventral stream (V1/V2 → V4 → TEO). Recognition and localization of objects embedded in complex scenes is important for many computer vision applications. Most existing methods require prior segmentation of the objects from the background which on its turn requires recognition. An S-COSFIRE filter is automatically configured to be selective for an arrangement of contour-based features that belong to a prototype shape specified by an example. The configuration comprises selecting relevant vertex detectors and determining certain blur and shift parameters. The response is computed as the weighted geometric mean of the blurred and shifted responses of the selected vertex detectors. S-COSFIRE filters share similar properties with some neurons in inferotemporal cortex, which provided inspiration for this work. We demonstrate the effectiveness of S-COSFIRE filters in two applications: letter and keyword spotting in handwritten manuscripts and object spotting in complex scenes for the computer vision system of a domestic robot. S-COSFIRE filters are effective to recognize and localize (deformable) objects in images of complex scenes without requiring prior segmentation. They are versatile trainable shape detectors, conceptually simple and easy to implement. The presented hierarchical shape representation contributes to a better understanding of the brain and to more robust computer vision algorithms. PMID:25126068

Molecular recognition in myxobacterial outer membrane exchange: functional, social and evolutionary implications.

PubMed

Wall, Daniel

2014-01-01

Through cooperative interactions, bacteria can build multicellular communities. To ensure that productive interactions occur, bacteria must recognize their neighbours and respond accordingly. Molecular recognition between cells is thus a fundamental behaviour, and in bacteria important discoveries have been made. This MicroReview focuses on a recently described recognition system in myxobacteria that is governed by a polymorphic cell surface receptor called TraA. TraA regulates outer membrane exchange (OME), whereby myxobacterial cells transiently fuse their OMs to efficiently transfer proteins and lipids between cells. Unlike other transport systems, OME is rather indiscriminate in what OM goods are transferred. In contrast, the recognition of partnering cells is discriminatory and only occurs between cells that bear identical or closely related TraA proteins. Therefore TraA functions in kin recognition and, in turn, OME helps regulate social interactions between myxobacteria. Here, I discuss and speculate on the social and evolutionary implications of OME and suggest it helps to guide their transition from free-living cells into coherent and functional populations. © 2013 John Wiley & Sons Ltd.

The Word Shape Hypothesis Re-Examined: Evidence for an External Feature Advantage in Visual Word Recognition

ERIC Educational Resources Information Center

Beech, John R.; Mayall, Kate A.

2005-01-01

This study investigates the relative roles of internal and external letter features in word recognition. In Experiment 1 the efficacy of outer word fragments (words with all their horizontal internal features removed) was compared with inner word fragments (words with their outer features removed) as primes in a forward masking paradigm. These…

Representations of Shape in Object Recognition and Long-Term Visual Memory

DTIC Science & Technology

1993-02-11

in anything other than linguistic terms ( Biederman , 1987 , for example). STATUS 1. Viewpoint-Dependent Features in Object Representation Tarr and...is object- based orientation-independent representations sufficient for "basic-level" categorization ( Biederman , 1987 ; Corballis, 1988). Alternatively...space. REFERENCES Biederman , I. ( 1987 ). Recognition-by-components: A theory of human image understanding. Psychological Review, 94,115-147. Cooper, L

Biomimetic synthesis of noble metal nanocrystals

NASA Astrophysics Data System (ADS)

Chiu, Chin-Yi

At the nanometer scale, the physical and chemical properties of materials heavily depend on their sizes and shapes. This fact has triggered considerable efforts in developing controllable nanomaterial synthesis. The controlled growth of colloidal nanocrystal is a kinetic process, in which high-energy facets grow faster and then vanish, leading to a nanocrystal enclosed by low-energy facets. Identifying a surfactant that can selectively bind to a particular crystal facet and thus lower its surface energy, is critical and challenging in shape controlled synthesis of nanocrystals. Biomolecules exhibiting exquisite molecular recognition properties can be exploited to precisely engineer nanostructured materials. In the first part of my thesis, we employed the phage display technique to select a specific multifunctional peptide sequence which can bind on Pd surface and mediate Pd crystal nucleation and growth, achieving size controlled synthesis of Pd nanocrystals in aqueous solution. We further demonstrated a rational biomimetic approach to the predictable synthesis of nanocrystals enclosed by a particular facet in the case of Pt. Specifically, Pt {100} and Pt {111} facet-specific peptides were identified and used to synthesize Pt nanocubes and Pt nano-tetrahedrons, respectively. The mechanistic studies of Pt {111} facet-specific peptide had led us to study the facet-selective adsorption of aromatic molecules on noble metal surfaces. The discoveries had achieved the development of design strategies to select facet-selective molecules which can synthesize nanocrystals with expected shapes in both Pt and Pd system. At last, we exploited Pt facet-specific peptides and controlled the molecular interaction to produce one- and three- dimensional nanostructures composed of anisotropic nanoparticles in synthetic conditions without supramolecular pre-organization, demonstrating the full potential of biomolecules in mediating material formation process. My research on biomimetic synthesis of nanocrystals with shape control and nanostructures with control over the anisotropy are unprecedented, representing a step forward in achieving the goal of producing complex nanostructures with required properties. The fundamental studies on the biomolecule-inorganic interfaces have contributed to advancing the synthesis tool of colloidal nanomaterials and enriching understating of organic-inorganic interface, impacting many applications.

Neural network classification technique and machine vision for bread crumb grain evaluation

NASA Astrophysics Data System (ADS)

Zayas, Inna Y.; Chung, O. K.; Caley, M.

1995-10-01

Bread crumb grain was studied to develop a model for pattern recognition of bread baked at Hard Winter Wheat Quality Laboratory (HWWQL), Grain Marketing and Production Research Center (GMPRC). Images of bread slices were acquired with a scanner in a 512 multiplied by 512 format. Subimages in the central part of the slices were evaluated by several features such as mean, determinant, eigen values, shape of a slice and other crumb features. Derived features were used to describe slices and loaves. Neural network programs of MATLAB package were used for data analysis. Learning vector quantization method and multivariate discriminant analysis were applied to bread slices from what of different sources. A training and test sets of different bread crumb texture classes were obtained. The ranking of subimages was well correlated with visual judgement. The performance of different models on slice recognition rate was studied to choose the best model. The recognition of classes created according to human judgement with image features was low. Recognition of arbitrarily created classes, according to porosity patterns, with several feature patterns was approximately 90%. Correlation coefficient was approximately 0.7 between slice shape features and loaf volume.

Tolerance for distorted faces: challenges to a configural processing account of familiar face recognition.

PubMed

Sandford, Adam; Burton, A Mike

2014-09-01

Face recognition is widely held to rely on 'configural processing', an analysis of spatial relations between facial features. We present three experiments in which viewers were shown distorted faces, and asked to resize these to their correct shape. Based on configural theories appealing to metric distances between features, we reason that this should be an easier task for familiar than unfamiliar faces (whose subtle arrangements of features are unknown). In fact, participants were inaccurate at this task, making between 8% and 13% errors across experiments. Importantly, we observed no advantage for familiar faces: in one experiment participants were more accurate with unfamiliars, and in two experiments there was no difference. These findings were not due to general task difficulty - participants were able to resize blocks of colour to target shapes (squares) more accurately. We also found an advantage of familiarity for resizing other stimuli (brand logos). If configural processing does underlie face recognition, these results place constraints on the definition of 'configural'. Alternatively, familiar face recognition might rely on more complex criteria - based on tolerance to within-person variation rather than highly specific measurement. Copyright © 2014 Elsevier B.V. All rights reserved.

Automatic recognition of surface landmarks of anatomical structures of back and posture

NASA Astrophysics Data System (ADS)

Michoński, Jakub; Glinkowski, Wojciech; Witkowski, Marcin; Sitnik, Robert

2012-05-01

Faulty postures, scoliosis and sagittal plane deformities should be detected as early as possible to apply preventive and treatment measures against major clinical consequences. To support documentation of the severity of deformity and diminish x-ray exposures, several solutions utilizing analysis of back surface topography data were introduced. A novel approach to automatic recognition and localization of anatomical landmarks of the human back is presented that may provide more repeatable results and speed up the whole procedure. The algorithm was designed as a two-step process involving a statistical model built upon expert knowledge and analysis of three-dimensional back surface shape data. Voronoi diagram is used to connect mean geometric relations, which provide a first approximation of the positions, with surface curvature distribution, which further guides the recognition process and gives final locations of landmarks. Positions obtained using the developed algorithms are validated with respect to accuracy of manual landmark indication by experts. Preliminary validation proved that the landmarks were localized correctly, with accuracy depending mostly on the characteristics of a given structure. It was concluded that recognition should mainly take into account the shape of the back surface, putting as little emphasis on the statistical approximation as possible.

Computational Design of Ligand Binding Proteins with High Affinity and Selectivity

PubMed Central

Dou, Jiayi; Doyle, Lindsey; Nelson, Jorgen W.; Schena, Alberto; Jankowski, Wojciech; Kalodimos, Charalampos G.; Johnsson, Kai; Stoddard, Barry L.; Baker, David

2014-01-01

The ability to design proteins with high affinity and selectivity for any given small molecule would have numerous applications in biosensing, diagnostics, and therapeutics, and is a rigorous test of our understanding of the physiochemical principles that govern molecular recognition phenomena. Attempts to design ligand binding proteins have met with little success, however, and the computational design of precise molecular recognition between proteins and small molecules remains an “unsolved problem”1. We describe a general method for the computational design of small molecule binding sites with pre-organized hydrogen bonding and hydrophobic interfaces and high overall shape complementary to the ligand, and use it to design protein binding sites for the steroid digoxigenin (DIG). Of 17 designs that were experimentally characterized, two bind DIG; the highest affinity design has the lowest predicted interaction energy and the most pre-organized binding site in the set. A comprehensive binding-fitness landscape of this design generated by library selection and deep sequencing was used to guide optimization of binding affinity to a picomolar level, and two X-ray co-crystal structures of optimized complexes show atomic level agreement with the design models. The designed binder has a high selectivity for DIG over the related steroids digitoxigenin, progesterone, and β-estradiol, which can be reprogrammed through the designed hydrogen-bonding interactions. Taken together, the binding fitness landscape, co-crystal structures, and thermodynamic binding parameters illustrate how increases in binding affinity can result from distal sequence changes that limit the protein ensemble to conformers making the most energetically favorable interactions with the ligand. The computational design method presented here should enable the development of a new generation of biosensors, therapeutics, and diagnostics. PMID:24005320

Changes in the electric dipole vector of human serum albumin due to complexing with fatty acids.

PubMed Central

Scheider, W; Dintzis, H M; Oncley, J L

1976-01-01

The magnitude of the electric dipole vector of human serum albumin, as measured by the dielectric increment of the isoionic solution, is found to be a sensitive, monotonic indicator of the number of moles (up to at least 5) of long chain fatty acid complexed. The sensitivity is about three times as great as it is in bovine albumin. New methods of analysis of the frequency dispersion of the dielectric constant were developed to ascertain if molecular shape changes also accompany the complexing with fatty acid. Direct two-component rotary diffusion constant analysis is found to be too strongly affected by cross modulation between small systematic errors and physically significant data components to be a reliable measure of structural modification. Multicomponent relaxation profiles are more useful as recognition patterns for structural comparisons, but the equations involved are ill-conditioned and solutions based on standard least-squares regression contain mathematical artifacts which mask the physically significant spectrum. By constraining the solution to non-negative coefficients, the magnitude of the artifacts is reduced to well below the magnitudes of the spectral components. Profiles calculated in this way show no evidence of significant dipole direction or molecular shape change as the albumin is complexed with 1 mol of fatty acid. In these experiments albumin was defatted by incubation with adipose tissue at physiological pH, which avoids passing the protein through the pH of the N-F transition usually required in defatting. Addition of fatty acid from soluion in small amounts of ethanol appears to form a complex indistinguishable from the "native" complex. PMID:6087

Influence of Stimulus Symmetry and Complexity upon Haptic Scanning Strategies During Detection, Learning and Recognition Tasks.

ERIC Educational Resources Information Center

Locher, Paul J.; Simmons, Roger W.

Two experiments were conducted to investigate the perceptual processes involved in haptic exploration of randomly generated shapes. Experiment one required subjects to detect symmetrical or asymmetrical characteristics of individually presented plastic shapes, also varying in complexity. Scanning time for both symmetrical and asymmetrical shapes…

MToS: A Tree of Shapes for Multivariate Images.

PubMed

Carlinet, Edwin; Géraud, Thierry

2015-12-01

The topographic map of a gray-level image, also called tree of shapes, provides a high-level hierarchical representation of the image contents. This representation, invariant to contrast changes and to contrast inversion, has been proved very useful to achieve many image processing and pattern recognition tasks. Its definition relies on the total ordering of pixel values, so this representation does not exist for color images, or more generally, multivariate images. Common workarounds, such as marginal processing, or imposing a total order on data, are not satisfactory and yield many problems. This paper presents a method to build a tree-based representation of multivariate images, which features marginally the same properties of the gray-level tree of shapes. Briefly put, we do not impose an arbitrary ordering on values, but we only rely on the inclusion relationship between shapes in the image definition domain. The interest of having a contrast invariant and self-dual representation of multivariate image is illustrated through several applications (filtering, segmentation, and object recognition) on different types of data: color natural images, document images, satellite hyperspectral imaging, multimodal medical imaging, and videos.

A New Minimum Trees-Based Approach for Shape Matching with Improved Time Computing: Application to Graphical Symbols Recognition

NASA Astrophysics Data System (ADS)

Franco, Patrick; Ogier, Jean-Marc; Loonis, Pierre; Mullot, Rémy

Recently we have developed a model for shape description and matching. Based on minimum spanning trees construction and specifics stages like the mixture, it seems to have many desirable properties. Recognition invariance in front shift, rotated and noisy shape was checked through median scale tests related to GREC symbol reference database. Even if extracting the topology of a shape by mapping the shortest path connecting all the pixels seems to be powerful, the construction of graph induces an expensive algorithmic cost. In this article we discuss on the ways to reduce time computing. An alternative solution based on image compression concepts is provided and evaluated. The model no longer operates in the image space but in a compact space, namely the Discrete Cosine space. The use of block discrete cosine transform is discussed and justified. The experimental results led on the GREC2003 database show that the proposed method is characterized by a good discrimination power, a real robustness to noise with an acceptable time computing.

Two-dimensional shape classification using generalized Fourier representation and neural networks

NASA Astrophysics Data System (ADS)

Chodorowski, Artur; Gustavsson, Tomas; Mattsson, Ulf

2000-04-01

A shape-based classification method is developed based upon the Generalized Fourier Representation (GFR). GFR can be regarded as an extension of traditional polar Fourier descriptors, suitable for description of closed objects, both convex and concave, with or without holes. Explicit relations of GFR coefficients to regular moments, moment invariants and affine moment invariants are given in the paper. The dual linear relation between GFR coefficients and regular moments was used to compare shape features derive from GFR descriptors and Hu's moment invariants. the GFR was then applied to a clinical problem within oral medicine and used to represent the contours of the lesions in the oral cavity. The lesions studied were leukoplakia and different forms of lichenoid reactions. Shape features were extracted from GFR coefficients in order to classify potentially cancerous oral lesions. Alternative classifiers were investigated based on a multilayer perceptron with different architectures and extensions. The overall classification accuracy for recognition of potentially cancerous oral lesions when using neural network classifier was 85%, while the classification between leukoplakia and reticular lichenoid reactions gave 96% (5-fold cross-validated) recognition rate.

Classification of C2C12 cells at differentiation by convolutional neural network of deep learning using phase contrast images.

PubMed

Niioka, Hirohiko; Asatani, Satoshi; Yoshimura, Aina; Ohigashi, Hironori; Tagawa, Seiichi; Miyake, Jun

2018-01-01

In the field of regenerative medicine, tremendous numbers of cells are necessary for tissue/organ regeneration. Today automatic cell-culturing system has been developed. The next step is constructing a non-invasive method to monitor the conditions of cells automatically. As an image analysis method, convolutional neural network (CNN), one of the deep learning method, is approaching human recognition level. We constructed and applied the CNN algorithm for automatic cellular differentiation recognition of myogenic C2C12 cell line. Phase-contrast images of cultured C2C12 are prepared as input dataset. In differentiation process from myoblasts to myotubes, cellular morphology changes from round shape to elongated tubular shape due to fusion of the cells. CNN abstract the features of the shape of the cells and classify the cells depending on the culturing days from when differentiation is induced. Changes in cellular shape depending on the number of days of culture (Day 0, Day 3, Day 6) are classified with 91.3% accuracy. Image analysis with CNN has a potential to realize regenerative medicine industry.

TD-M06-2X insights into the absorption and emission spectra of dichlorvos and its molecularly imprinted recognition by methacrylic acid.

PubMed

Cheng, Xueli

2016-11-01

The absorption and emission spectra of dichlorvos and the dichlorvos-MAA complex in methanol, water, and chloroform in the molecularly imprinted recognition were investigated systematically. The M06-2X results revealed that: 1) the hydroxyl groups in polar solvents such as methanol and water may markedly influence the weak interactions, and then alter the adsorption and emission spectra; 2) the electronic excitation in absorption spectra of dichlorvos is dominated by the configuration HOMO → LUMO, but in the most stable dichlorvos-MAA it becomes the ππ* excitation of HOMO → LUMO + 1; 3) Mulliken charges reveal that dichlorvos almost dissociates to Cl - and a cation in its S 1 excitation state; 4) the phosphorescence spectra of dichlorvos-MAA are relatively weak. Graphical Abstract The absorption and emission spectra of dichlorvos and the dichlorvos-MAA complex in the molecularly imprinted recognition of dichlorvos were investigated systematically in methanol, water, and chloroform as solvents.

Tunneling readout of hydrogen-bonding based recognition

PubMed Central

Chang, Shuai; He, Jin; Kibel, Ashley; Lee, Myeong; Sankey, Otto; Zhang, Peiming; Lindsay, Stuart

2009-01-01

Hydrogen bonding has a ubiquitous role in electron transport1,2 and in molecular recognition, with DNA base-pairing being the best known example.3 Scanning tunneling microscope (STM) images4 and measurements of the decay of tunnel-current as a molecular junction is pulled apart by the STM tip, 5 are sensitive to hydrogen-bonded interactions. Here we show that these tunnel-decay signals can be used to measure the strength of hydrogen bonding in DNA basepairs. Junctions that are held together by three hydrogen bonds per basepair (e.g., guanine-cytosine interactions) are stiffer than junctions held together by two hydrogen bonds per basepair (e.g., adenine-thymine interactions). Similar, but less-pronounced, effects are observed on the approach of the tunneling probe, implying that hydrogen-bond dependent attractive forces also have a role in determining the rise of current. These effects provide new mechanisms for making sensors that transduce a molecular recognition event into an electronic signal. PMID:19421214

An expanded framework for biomolecular visualization in the classroom: Learning goals and competencies.

PubMed

Dries, Daniel R; Dean, Diane M; Listenberger, Laura L; Novak, Walter R P; Franzen, Margaret A; Craig, Paul A

2017-01-02

A thorough understanding of the molecular biosciences requires the ability to visualize and manipulate molecules in order to interpret results or to generate hypotheses. While many instructors in biochemistry and molecular biology use visual representations, few indicate that they explicitly teach visual literacy. One reason is the need for a list of core content and competencies to guide a more deliberate instruction in visual literacy. We offer here the second stage in the development of one such resource for biomolecular three-dimensional visual literacy. We present this work with the goal of building a community for online resource development and use. In the first stage, overarching themes were identified and submitted to the biosciences community for comment: atomic geometry; alternate renderings; construction/annotation; het group recognition; molecular dynamics; molecular interactions; monomer recognition; symmetry/asymmetry recognition; structure-function relationships; structural model skepticism; and topology and connectivity. Herein, the overarching themes have been expanded to include a 12th theme (macromolecular assemblies), 27 learning goals, and more than 200 corresponding objectives, many of which cut across multiple overarching themes. The learning goals and objectives offered here provide educators with a framework on which to map the use of molecular visualization in their classrooms. In addition, the framework may also be used by biochemistry and molecular biology educators to identify gaps in coverage and drive the creation of new activities to improve visual literacy. This work represents the first attempt, to our knowledge, to catalog a comprehensive list of explicit learning goals and objectives in visual literacy. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(1):69-75, 2017. © 2016 The Authors Biochemistry and Molecular Biology Education published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology.

Vision-based object detection and recognition system for intelligent vehicles

NASA Astrophysics Data System (ADS)

Ran, Bin; Liu, Henry X.; Martono, Wilfung

1999-01-01

Recently, a proactive crash mitigation system is proposed to enhance the crash avoidance and survivability of the Intelligent Vehicles. Accurate object detection and recognition system is a prerequisite for a proactive crash mitigation system, as system component deployment algorithms rely on accurate hazard detection, recognition, and tracking information. In this paper, we present a vision-based approach to detect and recognize vehicles and traffic signs, obtain their information, and track multiple objects by using a sequence of color images taken from a moving vehicle. The entire system consist of two sub-systems, the vehicle detection and recognition sub-system and traffic sign detection and recognition sub-system. Both of the sub- systems consist of four models: object detection model, object recognition model, object information model, and object tracking model. In order to detect potential objects on the road, several features of the objects are investigated, which include symmetrical shape and aspect ratio of a vehicle and color and shape information of the signs. A two-layer neural network is trained to recognize different types of vehicles and a parameterized traffic sign model is established in the process of recognizing a sign. Tracking is accomplished by combining the analysis of single image frame with the analysis of consecutive image frames. The analysis of the single image frame is performed every ten full-size images. The information model will obtain the information related to the object, such as time to collision for the object vehicle and relative distance from the traffic sings. Experimental results demonstrated a robust and accurate system in real time object detection and recognition over thousands of image frames.

Ball-scale based hierarchical multi-object recognition in 3D medical images

NASA Astrophysics Data System (ADS)

Bağci, Ulas; Udupa, Jayaram K.; Chen, Xinjian

2010-03-01

This paper investigates, using prior shape models and the concept of ball scale (b-scale), ways of automatically recognizing objects in 3D images without performing elaborate searches or optimization. That is, the goal is to place the model in a single shot close to the right pose (position, orientation, and scale) in a given image so that the model boundaries fall in the close vicinity of object boundaries in the image. This is achieved via the following set of key ideas: (a) A semi-automatic way of constructing a multi-object shape model assembly. (b) A novel strategy of encoding, via b-scale, the pose relationship between objects in the training images and their intensity patterns captured in b-scale images. (c) A hierarchical mechanism of positioning the model, in a one-shot way, in a given image from a knowledge of the learnt pose relationship and the b-scale image of the given image to be segmented. The evaluation results on a set of 20 routine clinical abdominal female and male CT data sets indicate the following: (1) Incorporating a large number of objects improves the recognition accuracy dramatically. (2) The recognition algorithm can be thought as a hierarchical framework such that quick replacement of the model assembly is defined as coarse recognition and delineation itself is known as finest recognition. (3) Scale yields useful information about the relationship between the model assembly and any given image such that the recognition results in a placement of the model close to the actual pose without doing any elaborate searches or optimization. (4) Effective object recognition can make delineation most accurate.

Facial patterns in a tropical social wasp correlate with colony membership

NASA Astrophysics Data System (ADS)

Baracchi, David; Turillazzi, Stefano; Chittka, Lars

2016-10-01

Social insects excel in discriminating nestmates from intruders, typically relying on colony odours. Remarkably, some wasp species achieve such discrimination using visual information. However, while it is universally accepted that odours mediate a group level recognition, the ability to recognise colony members visually has been considered possible only via individual recognition by which wasps discriminate `friends' and `foes'. Using geometric morphometric analysis, which is a technique based on a rigorous statistical theory of shape allowing quantitative multivariate analyses on structure shapes, we first quantified facial marking variation of Liostenogaster flavolineata wasps. We then compared this facial variation with that of chemical profiles (generated by cuticular hydrocarbons) within and between colonies. Principal component analysis and discriminant analysis applied to sets of variables containing pure shape information showed that despite appreciable intra-colony variation, the faces of females belonging to the same colony resemble one another more than those of outsiders. This colony-specific variation in facial patterns was on a par with that observed for odours. While the occurrence of face discrimination at the colony level remains to be tested by behavioural experiments, overall our results suggest that, in this species, wasp faces display adequate information that might be potentially perceived and used by wasps for colony level recognition.

DNA Nanotechnology for Precise Control over Drug Delivery and Gene Therapy.

PubMed

Angell, Chava; Xie, Sibai; Zhang, Liangfang; Chen, Yi

2016-03-02

Nanomedicine has been growing exponentially due to its enhanced drug targeting and reduced drug toxicity. It uses the interactions where nanotechnological components and biological systems communicate with each other to facilitate the delivery performance. At this scale, the physiochemical properties of delivery systems strongly affect their capacities. Among current delivery systems, DNA nanotechnology shows many advantages because of its unprecedented engineering abilities. Through molecular recognition, DNA nanotechnology can be used to construct a variety of nanostructures with precisely controllable size, shape, and surface chemistry, which can be appreciated in the delivery process. In this review, different approaches that are currently used for the construction of DNA nanostructures are reported. Further, the utilization of these DNA nanostructures with the well-defined parameters for the precise control in drug delivery and gene therapy is discussed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dynamically correlated mutations drive human Influenza A evolution.

PubMed

Tria, F; Pompei, S; Loreto, V

2013-01-01

Human Influenza A virus undergoes recurrent changes in the hemagglutinin (HA) surface protein, primarily involved in the human antibody recognition. Relevant antigenic changes, enabling the virus to evade host immune response, have been recognized to occur in parallel to multiple mutations at antigenic sites in HA. Yet, the role of correlated mutations (epistasis) in driving the molecular evolution of the virus still represents a challenging puzzle. Further, though circulation at a global geographic level is key for the survival of Influenza A, its role in shaping the viral phylodynamics remains largely unexplored. Here we show, through a sequence based epidemiological model, that epistatic effects between amino acids substitutions, coupled with a reservoir that mimics worldwide circulating viruses, are key determinants that drive human Influenza A evolution. Our approach explains all the up-to-date observations characterizing the evolution of H3N2 subtype, including phylogenetic properties, nucleotide fixation patterns, and composition of antigenic clusters.

Direct patterning of a cyclotriveratrylene derivative for directed self-assembly of C60

NASA Astrophysics Data System (ADS)

Osner, Zachary R.; Nyamjav, Dorjderem; Holz, Richard C.; Becker, Daniel P.

2011-07-01

A novel apex-modified cyclotriveratrylene (CTV) derivative with an attached thiolane-containing lipoic acid linker was directly patterned onto gold substrates via dip-pen nanolithography (DPN). The addition of a dithiolane-containing linker to the apex of CTV provides a molecule that can adhere to a gold surface with its bowl-shaped cavity directed away from the surface, thereby providing a surface-bound CTV host that can be used for the directed assembly of guest molecules. Subsequent exposure of these CTV microarrays to C60 in toluene resulted in the directed assembly of predesigned, spatially controlled, high-density microarrays of C60. The molecular recognition capabilities of this CTV template toward C60 provides proof-of-concept that supramolecular CTV scaffolds can be directly patterned onto surfaces providing a foundation for the development of organic electronic and optoelectronic materials.

S-layers: principles and applications

PubMed Central

Sleytr, Uwe B; Schuster, Bernhard; Egelseer, Eva-Maria; Pum, Dietmar

2014-01-01

Monomolecular arrays of protein or glycoprotein subunits forming surface layers (S-layers) are one of the most commonly observed prokaryotic cell envelope components. S-layers are generally the most abundantly expressed proteins, have been observed in species of nearly every taxonomical group of walled bacteria, and represent an almost universal feature of archaeal envelopes. The isoporous lattices completely covering the cell surface provide organisms with various selection advantages including functioning as protective coats, molecular sieves and ion traps, as structures involved in surface recognition and cell adhesion, and as antifouling layers. S-layers are also identified to contribute to virulence when present as a structural component of pathogens. In Archaea, most of which possess S-layers as exclusive wall component, they are involved in determining cell shape and cell division. Studies on structure, chemistry, genetics, assembly, function, and evolutionary relationship of S-layers revealed considerable application potential in (nano)biotechnology, biomimetics, biomedicine, and synthetic biology. PMID:24483139

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

DOE PAGES

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

2017-10-16

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

Crystal Structure of a Plant Multidrug and Toxic Compound Extrusion Family Protein.

PubMed

Tanaka, Yoshiki; Iwaki, Shigehiro; Tsukazaki, Tomoya

2017-09-05

The multidrug and toxic compound extrusion (MATE) family of proteins consists of transporters responsible for multidrug resistance in prokaryotes. In plants, a number of MATE proteins were identified by recent genomic and functional studies, which imply that the proteins have substrate-specific transport functions instead of multidrug extrusion. The three-dimensional structure of eukaryotic MATE proteins, including those of plants, has not been reported, preventing a better understanding of the molecular mechanism of these proteins. Here, we describe the crystal structure of a MATE protein from the plant Camelina sativa at 2.9 Å resolution. Two sets of six transmembrane α helices, assembled pseudo-symmetrically, possess a negatively charged internal pocket with an outward-facing shape. The crystal structure provides insight into the diversity of plant MATE proteins and their substrate recognition and transport through the membrane. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Precise and Efficient Identification of Medical Order Forms Using Shape Trees

NASA Astrophysics Data System (ADS)

Henker, Uwe; Petersohn, Uwe; Ultsch, Alfred

A powerful and flexible technique to identify, classify and process documents using images from a scanning process is presented. The types of documents can be described to the system as a set of differentiating features in a case base using shape trees. The features are filtered and abstracted from an extremely reduced scanner image of the document. Classification rules are stored with the cases to enable precise recognition and further mark reading and Optical Character Recognition (OCR) process. The method is implemented in a system which actually processes the majority of requests for medical lab procedures in Germany. A large practical experiment with data from practitioners was performed. An average of 97% of the forms were correctly identified; none were identified incorrectly. This meets the quality requirements for most medical applications. The modular description of the recognition process allows for a flexible adaptation of future changes to the form and content of the document’s structures.

The interplay of holistic shape, local feature and color information in object categorization.

PubMed

Rokszin, Adrienn Aranka; Győri-Dani, Dóra; Linnert, Szilvia; Krajcsi, Attila; Tompa, Tamás; Csifcsák, Gábor

2015-07-01

Although it is widely accepted that colors facilitate object and scene recognition under various circumstances, several studies found no effects of color removal in tasks requiring categorization of briefly presented animals in natural scenes. In this study, three experiments were performed to test the assumption that the discrepancy between empirical data is related to variations of the available meaningful global information such as object shapes and contextual cues. Sixty-one individuals categorized chromatic and achromatic versions of intact and scrambled images containing either cars or birds. While color removal did not affect the classification of intact stimuli, the recognition of moderately scrambled achromatic images was more difficult. This effect was accompanied by amplitude modulations of occipital event-related potentials emerging from approximately 150ms post-stimulus. Our results indicate that colors facilitate stimulus classification, but this effect becomes prominent only in cases when holistic processing is not sufficient for stimulus recognition. Copyright © 2015 Elsevier B.V. All rights reserved.

Mechanism of Origin DNA Recognition and Assembly of an Initiator-Helicase Complex by SV40 Large Tumor Antigen

PubMed Central

Chang, Y. Paul; Xu, Meng; Machado, Ana Carolina Dantas; Yu, Xian Jessica; Rohs, Remo; Chen, Xiaojiang S.

2013-01-01

SUMMARY The DNA tumor virus Simian virus 40 (SV40) is a model system for studying eukaryotic replication. SV40 large tumor antigen (LTag) is the initiator/helicase that is essential for genome replication. LTag recognizes and assembles at the viral replication origin. We determined the structure of two multidomain LTag subunits bound to origin DNA. The structure reveals that the origin binding domains (OBDs) and Zn and AAA+ domains are involved in origin recognition and assembly. Notably, the OBDs recognize the origin in an unexpected manner. The histidine residues of the AAA+ domains insert into a narrow minor groove region with enhanced negative electrostatic potential. Computational analysis indicates that this region is intrinsically narrow, demonstrating the role of DNA shape readout in origin recognition. Our results provide important insights into the assembly of the LTag initiator/ helicase at the replication origin and suggest that histidine contacts with the minor groove serve as a mechanism of DNA shape readout. PMID:23545501

RIG-I in RNA virus recognition

PubMed Central

Kell, Alison M.; Gale, Michael

2015-01-01

Antiviral immunity is initiated upon host recognition of viral products via non-self molecular patterns known as pathogen-associated molecular patterns (PAMPs). Such recognition initiates signaling cascades that induce intracellular innate immune defenses and an inflammatory response that facilitates development of the acquired immune response. The retinoic acid-inducible gene I (RIG-I) and the RIG-I-like receptor (RLR) protein family are key cytoplasmic pathogen recognition receptors that are implicated in the recognition of viruses across genera and virus families, including functioning as major sensors of RNA viruses, and promoting recognition of some DNA viruses. RIG-I, the charter member of the RLR family, is activated upon binding to PAMP RNA. Activated RIG-I signals by interacting with the adapter protein MAVS leading to a signaling cascade that activates the transcription factors IRF3 and NF-κB. These actions induce the expression of antiviral gene products and the production of type I and III interferons that lead to an antiviral state in the infected cell and surrounding tissue. RIG-I signaling is essential for the control of infection by many RNA viruses. Recently, RIG-I crosstalk with other pathogen recognition receptors and components of the inflammasome has been described. In this review, we discuss the current knowledge regarding the role of RIG-I in recognition of a variety of virus families and its role in programming the adaptive immune response through cross-talk with parallel arms of the innate immune system, including how RIG-I can be leveraged for antiviral therapy. PMID:25749629

The effect of molecular shape on oligomerization of hydrophobic drugs: Molecular simulations of ciprofloxacin and nutlin

NASA Astrophysics Data System (ADS)

Li, Jianguo; Beuerman, Roger; Verma, Chandra

2018-03-01

Molecular aggregation plays a significant role in modulating the solubility, permeability, and bioactivity of drugs. The propensity to aggregate depends on hydrophobicity and on molecular shape. Molecular dynamics simulations coupled with enhanced sampling methods are used to explore the early stages of oligomerization of two drug molecules which have a strong aggregation propensity, but with contrasting molecule shapes: the antibiotic ciprofloxacin and the anticancer drug Nutlin-3A. The planar shape of ciprofloxacin induces the formation of stable oligomers at all cluster sizes. The aggregation of ciprofloxacin is driven by two-body interactions, and transferring one ciprofloxacin molecule to an existing cluster involves the desolvation of two faces and the concomitant hydrophobic interactions between the two faces; thus, the corresponding free energy of oligomerization weakly depends on the oligomer size. By contrast, Nutlin-3A has a star-shape and hence can only form stable oligomers when the cluster size is greater than 8. Free energy simulations further confirmed that the free energy of oligomer formation for Nutlin-3A becomes more favorable as the oligomer becomes larger. The aggregation of star-shaped Nutlin-3A results from many-body interactions and hence the free energy of cluster formation is strongly dependent on the size. The findings of this study provide atomistic insights into how molecular shape modulates the aggregation behavior of molecules and may be factored into the design of drugs or nano-particles.

Interrupted Monosyllabic Words: The Effects of Ten Interruption Locations on Recognition Performance by Older Listeners with Sensorineural Hearing Loss.

PubMed

Wilson, Richard H; Sharrett, Kadie C

2017-01-01

Two previous experiments from our laboratory with 70 interrupted monosyllabic words demonstrated that recognition performance was influenced by the temporal location of the interruption pattern. The interruption pattern (10 interruptions/sec, 50% duty cycle) was always the same and referenced word onset; the only difference between the patterns was the temporal location of the on- and off-segments of the interruption cycle. In the first study, both young and older listeners obtained better recognition performances when the initial on-segment coincided with word onset than when the initial on-segment was delayed by 50 msec. The second experiment with 24 young listeners detailed recognition performance as the interruption pattern was incremented in 10-msec steps through the 0- to 90-msec onset range. Across the onset conditions, 95% of the functions were either flat or U-shaped. To define the effects that interruption pattern locations had on word recognition by older listeners with sensorineural hearing loss as the interruption pattern incremented, re: word onset, from 0 to 90 msec in 10-msec steps. A repeated-measures design with ten interruption patterns (onset conditions) and one uninterruption condition. Twenty-four older males (mean = 69.6 yr) with sensorineural hearing loss participated in two 1-hour sessions. The three-frequency pure-tone average was 24.0 dB HL and word recognition was ≥80% correct. Seventy consonant-vowel nucleus-consonant words formed the corpus of materials with 25 additional words used for practice. For each participant, the 700 interrupted stimuli (70 words by 10 onset conditions), the 70 words uninterrupted, and two practice lists each were randomized and recorded on compact disc in 33 tracks of 25 words each. The data were analyzed at the participant and word levels and compared to the results obtained earlier on 24 young listeners with normal hearing. The mean recognition performance on the 70 words uninterrupted was 91.0% with an overall mean performance on the ten interruption conditions of 63.2% (range: 57.9-69.3%), compared to 80.4% (range: 73.0-87.7%) obtained earlier on the young adults. The best performances were at the extremes of the onset conditions. Standard deviations ranged from 22.1% to 28.1% (24 participants) and from 9.2% to 12.8% (70 words). An arithmetic algorithm categorized the shapes of the psychometric functions across the ten onset conditions. With the older participants in the current study, 40% of the functions were flat, 41.4% were U-shaped, and 18.6% were inverted U-shaped, which compared favorably to the function shapes by the young listeners in the earlier study of 50.0%, 41.4%, and 8.6%, respectively. There were two words on which the older listeners had 40% better performances. Collectively, the data are orderly, but at the individual word or participant level, the data are somewhat volatile, which may reflect auditory processing differences between the participant groups. The diversity of recognition performances by the older listeners on the ten interruption conditions with each of the 70 words supports the notion that the term hearing loss is inclusive of processes well beyond the filtering produced by end-organ sensitivity deficits. American Academy of Audiology

Characterization of QCM sensor surfaces coated with molecularly imprinted nanoparticles.

PubMed

Reimhult, Kristina; Yoshimatsu, Keiichi; Risveden, Klas; Chen, Si; Ye, Lei; Krozer, Anatol

2008-07-15

Molecularly imprinted polymers (MIPs) are gaining great interest as tailor-made recognition materials for the development of biomimetic sensors. Various approaches have been adopted to interface MIPs with different transducers, including the use of pre-made imprinted particles and the in situ preparation of thin polymer layers directly on transducer surfaces. In this work we functionalized quartz crystal microbalance (QCM) sensor crystals by coating the sensing surfaces with pre-made molecularly imprinted nanoparticles. The nanoparticles were immobilized on the QCM transducers by physical entrapment in a thin poly(ethylene terephthalate) (PET) layer that was spin-coated on the transducer surface. By controlling the deposition conditions, it was possible to gain a high nanoparticle loading in a stable PET layer, allowing the recognition sites in nanoparticles to be easily accessed by the test analytes. In this work, different sensor surfaces were studied by micro-profilometry and atomic force microscopy and the functionality was evaluated using quartz crystal microbalance with dissipation (QCM-D). The molecular recognition capability of the sensors were also confirmed using radioligand binding analysis by testing their response to the presence of the test compounds, (R)- and (S)-propranolol in aqueous buffer.

Neural network application for thermal image recognition of low-resolution objects

NASA Astrophysics Data System (ADS)

Fang, Yi-Chin; Wu, Bo-Wen

2007-02-01

In the ever-changing situation on a battle field, accurate recognition of a distant object is critical to a commander's decision-making and the general public's safety. Efficiently distinguishing between an enemy's armoured vehicles and ordinary civilian houses under all weather conditions has become an important research topic. This study presents a system for recognizing an armoured vehicle by distinguishing marks and contours. The characteristics of 12 different shapes and 12 characters are used to explore thermal image recognition under the circumstance of long distance and low resolution. Although the recognition capability of human eyes is superior to that of artificial intelligence under normal conditions, it tends to deteriorate substantially under long-distance and low-resolution scenarios. This study presents an effective method for choosing features and processing images. The artificial neural network technique is applied to further improve the probability of accurate recognition well beyond the limit of the recognition capability of human eyes.

Detection and recognition of targets by using signal polarization properties

NASA Astrophysics Data System (ADS)

Ponomaryov, Volodymyr I.; Peralta-Fabi, Ricardo; Popov, Anatoly V.; Babakov, Mikhail F.

1999-08-01

The quality of radar target recognition can be enhanced by exploiting its polarization signatures. A specialized X-band polarimetric radar was used for target recognition in experimental investigations. The following polarization characteristics connected to the object geometrical properties were investigated: the amplitudes of the polarization matrix elements; an anisotropy coefficient; depolarization coefficient; asymmetry coefficient; the energy of a backscattering signal; object shape factor. A large quantity of polarimetric radar data was measured and processed to form a database of different object and different weather conditions. The histograms of polarization signatures were approximated by a Nakagami distribution, then used for real- time target recognition. The Neyman-Pearson criterion was used for the target detection, and the criterion of the maximum of a posterior probability was used for recognition problem. Some results of experimental verification of pattern recognition and detection of objects with different electrophysical and geometrical characteristics urban in clutter are presented in this paper.

Basics of identification measurement technology

NASA Astrophysics Data System (ADS)

Klikushin, Yu N.; Kobenko, V. Yu; Stepanov, P. P.

2018-01-01

All available algorithms and suitable for pattern recognition do not give 100% guarantee, therefore there is a field of scientific night activity in this direction, studies are relevant. It is proposed to develop existing technologies for pattern recognition in the form of application of identification measurements. The purpose of the study is to identify the possibility of recognizing images using identification measurement technologies. In solving problems of pattern recognition, neural networks and hidden Markov models are mainly used. A fundamentally new approach to the solution of problems of pattern recognition based on the technology of identification signal measurements (IIS) is proposed. The essence of IIS technology is the quantitative evaluation of the shape of images using special tools and algorithms.

Understanding selective molecular recognition in integrated carbon nanotube-polymer sensors by simulating physical analyte binding on carbon nanotube-polymer scaffolds.

PubMed

Lin, Shangchao; Zhang, Jingqing; Strano, Michael S; Blankschtein, Daniel

2014-08-28

Macromolecular scaffolds made of polymer-wrapped single-walled carbon nanotubes (SWCNTs) have been explored recently (Zhang et al., Nature Nanotechnology, 2013) as a new class of molecular-recognition motifs. However, selective analyte recognition is still challenging and lacks the underlying fundamental understanding needed for its practical implementation in biological sensors. In this report, we combine coarse-grained molecular dynamics (CGMD) simulations, physical adsorption/binding theories, and photoluminescence (PL) experiments to provide molecular insight into the selectivity of such sensors towards a large set of biologically important analytes. We find that the physical binding affinities of the analytes on a bare SWCNT partially correlate with their distribution coefficients in a bulk water/octanol system, suggesting that the analyte hydrophobicity plays a key role in determining the binding affinities of the analytes considered, along with the various specific interactions between the analytes and the polymer anchor groups. Two distinct categories of analytes are identified to demonstrate a complex picture for the correlation between optical sensor signals and the simulated binding affinities. Specifically, a good correlation was found between the sensor signals and the physical binding affinities of the three hormones (estradiol, melatonin, and thyroxine), the neurotransmitter (dopamine), and the vitamin (riboflavin) to the SWCNT-polymer scaffold. The four amino acids (aspartate, glycine, histidine, and tryptophan) and the two monosaccharides (fructose and glucose) considered were identified as blank analytes which are unable to induce sensor signals. The results indicate great success of our physical adsorption-based model in explaining the ranking in sensor selectivities. The combined framework presented here can be used to screen and select polymers that can potentially be used for creating synthetic molecular recognition motifs.

Characterization of the interaction of interleukin-8 with hyaluronan, chondroitin sulfate, dermatan sulfate and their sulfated derivatives by spectroscopy and molecular modeling.

PubMed

Pichert, Annelie; Samsonov, Sergey A; Theisgen, Stephan; Thomas, Lars; Baumann, Lars; Schiller, Jürgen; Beck-Sickinger, Annette G; Huster, Daniel; Pisabarro, M Teresa

2012-01-01

The interactions between glycosaminoglycans (GAGs), important components of the extracellular matrix, and proteins such as growth factors and chemokines play critical roles in cellular regulation processes. Therefore, the design of GAG derivatives for the development of innovative materials with bio-like properties in terms of their interaction with regulatory proteins is of great interest for tissue engineering and regenerative medicine. Previous work on the chemokine interleukin-8 (IL-8) has focused on its interaction with heparin and heparan sulfate, which regulate chemokine function. However, the extracellular matrix contains other GAGs, such as hyaluronic acid (HA), dermatan sulfate (DS) and chondroitin sulfate (CS), which have so far not been characterized in terms of their distinct molecular recognition properties towards IL-8 in relation to their length and sulfation patterns. NMR and molecular modeling have been in great part the methods of choice to study the structural and recognition properties of GAGs and their protein complexes. However, separately these methods have challenges to cope with the high degree of similarity and flexibility that GAGs exhibit. In this work, we combine fluorescence spectroscopy, NMR experiments, docking and molecular dynamics simulations to study the configurational and recognition properties of IL-8 towards a series of HA and CS derivatives and DS. We analyze the effects of GAG length and sulfation patterns in binding strength and specificity, and the influence of GAG binding on IL-8 dimer formation. Our results highlight the importance of combining experimental and theoretical approaches to obtain a better understanding of the molecular recognition properties of GAG-protein systems.

Carbohydrate recognition by the antiviral lectin cyanovirin-N

PubMed Central

Fujimoto, Yukiji K.; Green, David F.

2012-01-01

Cyanovirin-N is a cyanobacterial lectin with potent antiviral activity, and has been the focus of extensive pre-clinical investigation as a potential prophylactic for the prevention of the sexual transmission of the human immunodeficiency virus (HIV). Here we present a detailed analysis of carbohydrate recognition by this important protein, using a combination of computational methods, including extensive molecular dynamics simulations and Molecular-Mechanics/ Poisson–Boltzmann/Surface-Area (MM/PBSA) energetic analysis. The simulation results strongly suggest that the observed tendency of wildtype CVN to form domain-swapped dimers is the result of a previously unidentified cis-peptide bond present in the monomeric state. The energetic analysis additionally indicates that the highest-affinity ligand for CVN characterized to date (α-Man-(1,2)-α-Man-(1,2)-α-Man) is recognized asymmetrically by the two binding sites. Finally, we are able to provide a detailed map of the role of all binding site functional groups (both backbone and side chain) to various aspects of molecular recognition: general affinity for cognate ligands, specificity for distinct oligosaccharide targets and the asymmetric recognition of α-Man-(1,2)-α-Man-(1,2)-α-Man. Taken as a whole, these results complement past experimental characterization (both structural and thermodynamic) to provide the most complete understanding of carbohydrate recognition by CVN to date. The results also provide strong support for the application of similar approaches to the understanding of other protein–carbohydrate complexes. PMID:23057413

Molecular mechanisms of substrate recognition and specificity of botulinum neurotoxin serotype F.

PubMed

Chen, Sheng; Wan, Hoi Ying

2011-01-15

BoNTs (botulinum neurotoxins) are both deadly neurotoxins and natural toxins that are widely used in protein therapies to treat numerous neurological disorders of dystonia and spinal spasticity. Understanding the mechanism of action and substrate specificity of BoNTs is a prerequisite to develop antitoxin and novel BoNT-derived protein therapy. To date, there is a lack of detailed information with regard to how BoNTs recognize and hydrolyse the substrate VAMP-2 (vesicle-associated membrane protein 2), even though it is known to be cleaved by four of the seven BoNT serotypes, B, D, F, G and TeNT (tetanus neurotoxin). In the present study we dissected the molecular mechanisms of VAMP-2 recognition by BoNT serotype F for the first time. The initial substrate recognition was mediated through sequential binding of VAMP-2 to the B1, B2 and B3 pockets in LC/F (light chain of BoNT serotype F), which directed VAMP-2 to the active site of LC/F and stabilized the active site substrate recognition, where the P2, P1' and P2' sites of VAMP-2 were specifically recognized by the S2, S1' and S2' pockets of LC/F to promote substrate hydrolysis. The understanding of the molecular mechanisms of LC/F substrate recognition provides insights into the development of antitoxins and engineering novel BoNTs to optimize current therapy and extend therapeutic interventions.

Structural correlates of carrier protein recognition in tetanus toxoid-conjugated bacterial polysaccharide vaccines.

PubMed

Lockyer, Kay; Gao, Fang; Derrick, Jeremy P; Bolgiano, Barbara

2015-03-10

An analysis of structure-antibody recognition relationships in nine licenced polysaccharide-tetanus toxoid (TT) conjugate vaccines was performed. The panel of conjugates used included vaccine components to protect against disease caused by Haemophilus influenzae type b, Neisseria meningitidis groups A, C, W and Y and Streptococcus pneumoniae serotype 18C. Conformation and structural analysis included size exclusion chromatography with multi-angle light scattering to determine size, and intrinsic fluorescence spectroscopy and fluorescence quenching to evaluate the protein folding and exposure of Trp residues. A capture ELISA measured the recognition of TT epitopes in the conjugates, using four rat monoclonal antibodies: 2 localised to the HC domain, and 2 of which were holotoxoid conformation-dependent. The conjugates had a wide range of average molecular masses ranging from 1.8×10(6) g/mol to larger than 20×10(6) g/mol. The panel of conjugates were found to be well folded, and did not have spectral features typical of aggregated TT. A partial correlation was found between molecular mass and epitope recognition. Recognition of the epitopes either on the HC domain or the whole toxoid was not necessarily hampered by the size of the molecule. Correlation was also found between the accessibility of Trp side chains and polysaccharide loading, suggesting also that a higher level of conjugated PS does not necessarily interfere with toxoid accessibility. There were different levels of carrier protein Trp side-chain and epitope accessibility that were localised to the HC domain; these were related to the saccharide type, despite the conjugates being independently manufactured. These findings extend our understanding of the molecular basis for carrier protein recognition in TT conjugate vaccines. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Structural correlates of carrier protein recognition in tetanus toxoid-conjugated bacterial polysaccharide vaccines

PubMed Central

Lockyer, Kay; Gao, Fang; Derrick, Jeremy P.; Bolgiano, Barbara

2015-01-01

An analysis of structure-antibody recognition relationships in nine licenced polysaccharide-tetanus toxoid (TT) conjugate vaccines was performed. The panel of conjugates used included vaccine components to protect against disease caused by Haemophilus influenzae type b, Neisseria meningitidis groups A, C, W and Y and Streptococcus pneumoniae serotype 18C. Conformation and structural analysis included size exclusion chromatography with multi-angle light scattering to determine size, and intrinsic fluorescence spectroscopy and fluorescence quenching to evaluate the protein folding and exposure of Trp residues. A capture ELISA measured the recognition of TT epitopes in the conjugates, using four rat monoclonal antibodies: 2 localised to the HC domain, and 2 of which were holotoxoid conformation-dependent. The conjugates had a wide range of average molecular masses ranging from 1.8 × 106 g/mol to larger than 20 × 106 g/mol. The panel of conjugates were found to be well folded, and did not have spectral features typical of aggregated TT. A partial correlation was found between molecular mass and epitope recognition. Recognition of the epitopes either on the HC domain or the whole toxoid was not necessarily hampered by the size of the molecule. Correlation was also found between the accessibility of Trp side chains and polysaccharide loading, suggesting also that a higher level of conjugated PS does not necessarily interfere with toxoid accessibility. There were different levels of carrier protein Trp side-chain and epitope accessibility that were localised to the HC domain; these were related to the saccharide type, despite the conjugates being independently manufactured. These findings extend our understanding of the molecular basis for carrier protein recognition in TT conjugate vaccines. PMID:25640334

Molecular recognition of pre-tRNA by Arabidopsis protein-only Ribonuclease P.

PubMed

Klemm, Bradley P; Karasik, Agnes; Kaitany, Kipchumba J; Shanmuganathan, Aranganathan; Henley, Matthew J; Thelen, Adam Z; Dewar, Allison J L; Jackson, Nathaniel D; Koutmos, Markos; Fierke, Carol A

2017-12-01

Protein-only ribonuclease P (PRORP) is an enzyme responsible for catalyzing the 5' end maturation of precursor transfer ribonucleic acids (pre-tRNAs) encoded by various cellular compartments in many eukaryotes. PRORPs from plants act as single-subunit enzymes and have been used as a model system for analyzing the function of the metazoan PRORP nuclease subunit, which requires two additional proteins for efficient catalysis. There are currently few molecular details known about the PRORP-pre-tRNA complex. Here, we characterize the determinants of substrate recognition by the single subunit Arabidopsis thaliana PRORP1 and PRORP2 using kinetic and thermodynamic experiments. The salt dependence of binding affinity suggests 4-5 contacts with backbone phosphodiester bonds on substrates, including a single phosphodiester contact with the pre-tRNA 5' leader, consistent with prior reports of short leader requirements. PRORPs contain an N-terminal pentatricopeptide repeat (PPR) domain, truncation of which results in a >30-fold decrease in substrate affinity. While most PPR-containing proteins have been implicated in single-stranded sequence-specific RNA recognition, we find that the PPR motifs of PRORPs recognize pre-tRNA substrates differently. Notably, the PPR domain residues most important for substrate binding in PRORPs do not correspond to positions involved in base recognition in other PPR proteins. Several of these residues are highly conserved in PRORPs from algae, plants, and metazoans, suggesting a conserved strategy for substrate recognition by the PRORP PPR domain. Furthermore, there is no evidence for sequence-specific interactions. This work clarifies molecular determinants of PRORP-substrate recognition and provides a new predictive model for the PRORP-substrate complex. © 2017 Klemm et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Increased Alpha-Band Power during the Retention of Shapes and Shape-Location Associations in Visual Short-Term Memory

PubMed Central

Johnson, Jeffrey S.; Sutterer, David W.; Acheson, Daniel J.; Lewis-Peacock, Jarrod A.; Postle, Bradley R.

2011-01-01

Studies exploring the role of neural oscillations in cognition have revealed sustained increases in alpha-band (~8–14 Hz) power during the delay period of delayed-recognition short-term memory tasks. These increases have been proposed to reflect the inhibition, for example, of cortical areas representing task-irrelevant information, or of potentially interfering representations from previous trials. Another possibility, however, is that elevated delay-period alpha-band power (DPABP) reflects the selection and maintenance of information, rather than, or in addition to, the inhibition of task-irrelevant information. In the present study, we explored these possibilities using a delayed-recognition paradigm in which the presence and task relevance of shape information was systematically manipulated across trial blocks and electroencephalographic was used to measure alpha-band power. In the first trial block, participants remembered locations marked by identical black circles. The second block featured the same instructions, but locations were marked by unique shapes. The third block featured the same stimulus presentation as the second, but with pretrial instructions indicating, on a trial-by-trial basis, whether memory for shape or location was required, the other dimension being irrelevant. In the final block, participants remembered the unique pairing of shape and location for each stimulus. Results revealed minimal DPABP in each of the location-memory conditions, whether locations were marked with identical circles or with unique task-irrelevant shapes. In contrast, alpha-band power increases were observed in both the shape-memory condition, in which location was task irrelevant, and in the critical final condition, in which both shape and location were task relevant. These results provide support for the proposal that alpha-band oscillations reflect the retention of shape information and/or shape–location associations in short-term memory. PMID:21713012

Integration trumps selection in object recognition.

PubMed

Saarela, Toni P; Landy, Michael S

2015-03-30

Finding and recognizing objects is a fundamental task of vision. Objects can be defined by several "cues" (color, luminance, texture, etc.), and humans can integrate sensory cues to improve detection and recognition [1-3]. Cortical mechanisms fuse information from multiple cues [4], and shape-selective neural mechanisms can display cue invariance by responding to a given shape independent of the visual cue defining it [5-8]. Selective attention, in contrast, improves recognition by isolating a subset of the visual information [9]. Humans can select single features (red or vertical) within a perceptual dimension (color or orientation), giving faster and more accurate responses to items having the attended feature [10, 11]. Attention elevates neural responses and sharpens neural tuning to the attended feature, as shown by studies in psychophysics and modeling [11, 12], imaging [13-16], and single-cell and neural population recordings [17, 18]. Besides single features, attention can select whole objects [19-21]. Objects are among the suggested "units" of attention because attention to a single feature of an object causes the selection of all of its features [19-21]. Here, we pit integration against attentional selection in object recognition. We find, first, that humans can integrate information near optimally from several perceptual dimensions (color, texture, luminance) to improve recognition. They cannot, however, isolate a single dimension even when the other dimensions provide task-irrelevant, potentially conflicting information. For object recognition, it appears that there is mandatory integration of information from multiple dimensions of visual experience. The advantage afforded by this integration, however, comes at the expense of attentional selection. Copyright © 2015 Elsevier Ltd. All rights reserved.

Integration trumps selection in object recognition

PubMed Central

Saarela, Toni P.; Landy, Michael S.

2015-01-01

Summary Finding and recognizing objects is a fundamental task of vision. Objects can be defined by several “cues” (color, luminance, texture etc.), and humans can integrate sensory cues to improve detection and recognition [1–3]. Cortical mechanisms fuse information from multiple cues [4], and shape-selective neural mechanisms can display cue-invariance by responding to a given shape independent of the visual cue defining it [5–8]. Selective attention, in contrast, improves recognition by isolating a subset of the visual information [9]. Humans can select single features (red or vertical) within a perceptual dimension (color or orientation), giving faster and more accurate responses to items having the attended feature [10,11]. Attention elevates neural responses and sharpens neural tuning to the attended feature, as shown by studies in psychophysics and modeling [11,12], imaging [13–16], and single-cell and neural population recordings [17,18]. Besides single features, attention can select whole objects [19–21]. Objects are among the suggested “units” of attention because attention to a single feature of an object causes the selection of all of its features [19–21]. Here, we pit integration against attentional selection in object recognition. We find, first, that humans can integrate information near-optimally from several perceptual dimensions (color, texture, luminance) to improve recognition. They cannot, however, isolate a single dimension even when the other dimensions provide task-irrelevant, potentially conflicting information. For object recognition, it appears that there is mandatory integration of information from multiple dimensions of visual experience. The advantage afforded by this integration, however, comes at the expense of attentional selection. PMID:25802154

Pattern recognition for Space Applications Center director's discretionary fund

NASA Technical Reports Server (NTRS)

Singley, M. E.

1984-01-01

Results and conclusions are presented on the application of recent developments in pattern recognition to spacecraft star mapping systems. Sensor data for two representative starfields are processed by an adaptive shape-seeking version of the Fc-V algorithm with good results. Cluster validity measures are evaluated, but not found especially useful to this application. Recommendations are given two system configurations worthy of additional study,

Object/Shape Recognition Technology: An Assessment of the Feasibility of Implementation at Defense Logistics Agency Disposition Services

DTIC Science & Technology

2015-02-25

provide efficiency and effectively manufacture or inventory items. The industries that benefit from Cognex technology are automotive, food and beverage ...recognition tedmology, Tedmology Readiness Level, PAGES Cost Benefit Analysis, Tedmology Commercialization, Technology Transition 139 16. PRICE CODE 17...Technology Development & Transition Strategy Guidebook xvii UD Ultimate Disposal U.S. United States USAF United States Air Force xviii THIS

Application of biomolecular recognition via magnetic nanoparticle in nanobiotechnology

NASA Astrophysics Data System (ADS)

Shen, Wei-Zheng; Cetinel, Sibel; Montemagno, Carlo

2018-05-01

The marriage of biomolecular recognition and magnetic nanoparticle creates tremendous opportunities in the development of advanced technology both in academic research and in industrial sectors. In this paper, we review current progress on the magnetic nanoparticle-biomolecule hybrid systems, particularly employing the recognition pairs of DNA-DNA, DNA-protein, protein-protein, and protein-inorganics in several nanobiotechnology application areas, including molecular biology, diagnostics, medical treatment, industrial biocatalysts, and environmental separations.

Molecular moment similarity between several nucleoside analogs of thymidine and thymidine. sil@watson.ibm.com.

PubMed

Silverman, B D; Pitman, M C; Platt, D E

1999-06-01

Molecular moment descriptors of the shape and charge distributions of twenty five nucleoside structures have been examined. The structures include thymidine as well as the difluorotoluene nucleoside analog which has been found to pair efficiently with adenine by polymerase catalysis. The remaining twenty three structures have been chosen to be as structurally similar to thymidine and to the difluorotoluene nucleoside analog as possible. The moment descriptors which include a description of the relationship of molecular charge to shape show the difluorotoluene nucleoside to be one of the most proximate molecules to thymidine in the space of the molecular moments. The calculations, therefore, suggest that polymerase specificity might be not only a consequence of molecular steric features alone but also of the molecular electrostatic environment and its registration with molecular shape.

Structure-wise discrimination of cytosine, thymine, and uracil by proteins in terms of their nonbonded interactions.

PubMed

Usha, S; Selvaraj, S

2014-01-01

The molecular recognition and discrimination of very similar ligand moieties by proteins are important subjects in protein-ligand interaction studies. Specificity in the recognition of molecules is determined by the arrangement of protein and ligand atoms in space. The three pyrimidine bases, viz. cytosine, thymine, and uracil, are structurally similar, but the proteins that bind to them are able to discriminate them and form interactions. Since nonbonded interactions are responsible for molecular recognition processes in biological systems, our work attempts to understand some of the underlying principles of such recognition of pyrimidine molecular structures by proteins. The preferences of the amino acid residues to contact the pyrimidine bases in terms of nonbonded interactions; amino acid residue-ligand atom preferences; main chain and side chain atom contributions of amino acid residues; and solvent-accessible surface area of ligand atoms when forming complexes are analyzed. Our analysis shows that the amino acid residues, tyrosine and phenyl alanine, are highly involved in the pyrimidine interactions. Arginine prefers contacts with the cytosine base. The similarities and differences that exist between the interactions of the amino acid residues with each of the three pyrimidine base atoms in our analysis provide insights that can be exploited in designing specific inhibitors competitive to the ligands.

Label-Free Bioanalyte Detection from Nanometer to Micrometer Dimensions-Molecular Imprinting and QCMs †.

PubMed

Mujahid, Adnan; Mustafa, Ghulam; Dickert, Franz L

2018-06-01

Modern diagnostic tools and immunoassay protocols urges direct analyte recognition based on its intrinsic behavior without using any labeling indicator. This not only improves the detection reliability, but also reduces sample preparation time and complexity involved during labeling step. Label-free biosensor devices are capable of monitoring analyte physiochemical properties such as binding sensitivity and selectivity, affinity constants and other dynamics of molecular recognition. The interface of a typical biosensor could range from natural antibodies to synthetic receptors for example molecular imprinted polymers (MIPs). The foremost advantages of using MIPs are their high binding selectivity comparable to natural antibodies, straightforward synthesis in short time, high thermal/chemical stability and compatibility with different transducers. Quartz crystal microbalance (QCM) resonators are leading acoustic devices that are extensively used for mass-sensitive measurements. Highlight features of QCM devices include low cost fabrication, room temperature operation, and most importantly ability to monitor extremely low mass shifts, thus potentially a universal transducer. The combination of MIPs with quartz QCM has turned out as a prominent sensing system for label-free recognition of diverse bioanalytes. In this article, we shall encompass the potential applications of MIP-QCM sensors exclusively label-free recognition of bacteria and virus species as representative micro and nanosized bioanalytes.

Efficient synthesis of molecularly imprinted polymers with bio-recognition sites for the selective separation of bovine hemoglobin.

PubMed

Zhang, Zulei; Li, Lei

2018-06-01

We developed a facile approach to the construction of bio-recognition sites in silica nanoparticles for efficient separation of bovine hemoglobin based on amino-functionalized silica nanoparticles grafting by 3-aminopropyltriethoxylsilane providing hydrogen bonds with bovine hemoglobin through surface molecularly imprinting technology. The resulting amino-functionalized silica surface molecularly imprinted polymers were characterized using scanning electron microscope, transmission electronic microscopy, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and thermogravimetric analysis. Results showed that the as-synthesized imprinted polymers exhibited spherical morphology and favorable thermal stability. The binding adsorption experiments showed that the imprinted polymers can reach equilibrium within 1 h. The Langmuir isotherm and pseudo-second-order kinetic model fitted the adsorption data well. Meanwhile, the imprinted polymers possessed a maximum binding capacity up to 90.3 mg/g and highly selectivity for the recognition of bovine hemoglobin. Moreover, such high binding capacity and selectivity retained after eight cycles, indicating the good stability and reusability of the imprinted polymers. Finally, successful application in the selective recognition of bovine hemoglobin from a real bovine blood sample indicated that the imprinted polymers displayed great potentials in efficient purification and separation of target proteins. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

On the optimal design of molecular sensing interfaces with lipid bilayer assemblies - A knowledge based approach

NASA Astrophysics Data System (ADS)

Siontorou, Christina G.

2012-12-01

Biosensors are analytic devices that incorporate a biochemical recognition system (biological, biologicalderived or biomimic: enzyme, antibody, DNA, receptor, etc.) in close contact with a physicochemical transducer (electrochemical, optical, piezoelectric, conductimetric, etc.) that converts the biochemical information, produced by the specific biological recognition reaction (analyte-biomolecule binding), into a chemical or physical output signal, related to the concentration of the analyte in the measuring sample. The biosensing concept is based on natural chemoreception mechanisms, which are feasible over/within/by means of a biological membrane, i.e., a structured lipid bilayer, incorporating or attached to proteinaceous moieties that regulate molecular recognition events which trigger ion flux changes (facilitated or passive) through the bilayer. The creation of functional structures that are similar to natural signal transduction systems, correlating and interrelating compatibly and successfully the physicochemical transducer with the lipid film that is self-assembled on its surface while embedding the reconstituted biological recognition system, and at the same time manage to satisfy the basic conditions for measuring device development (simplicity, easy handling, ease of fabrication) is far from trivial. The aim of the present work is to present a methodological framework for designing such molecular sensing interfaces, functioning within a knowledge-based system built on an ontological platform for supplying sub-systems options, compatibilities, and optimization parameters.

Permutation coding technique for image recognition systems.

PubMed

Kussul, Ernst M; Baidyk, Tatiana N; Wunsch, Donald C; Makeyev, Oleksandr; Martín, Anabel

2006-11-01

A feature extractor and neural classifier for image recognition systems are proposed. The proposed feature extractor is based on the concept of random local descriptors (RLDs). It is followed by the encoder that is based on the permutation coding technique that allows to take into account not only detected features but also the position of each feature on the image and to make the recognition process invariant to small displacements. The combination of RLDs and permutation coding permits us to obtain a sufficiently general description of the image to be recognized. The code generated by the encoder is used as an input data for the neural classifier. Different types of images were used to test the proposed image recognition system. It was tested in the handwritten digit recognition problem, the face recognition problem, and the microobject shape recognition problem. The results of testing are very promising. The error rate for the Modified National Institute of Standards and Technology (MNIST) database is 0.44% and for the Olivetti Research Laboratory (ORL) database it is 0.1%.

StreetScenes: Towards Scene Understanding in Still Images

DTIC Science & Technology

2006-05-01

Riesenhuber and Poggio’s C1 features from their Standard Model [91], Berg and Malik’s geometric blur [7], Belongie et al.’s shape context [5], and Dalal and...images was performed by payed employees of the Center for Biological and Computational Learning (CBCL) during the period between January 2003 and July...single example by feature replacement. In CVPR, 2005. [5] S. Belongie , J. Malik, and J. Puzicha. Shape matching and object recognition using shape

Genetic dissection of the maize (Zea mays L.) MAMP response

USDA-ARS?s Scientific Manuscript database

Microbe-associated molecular patterns (MAMPs) are highly conserved molecules commonly found in microbes which can be recognized by plant pattern recognition receptors (PRRs). Recognition triggers a suite of responses including production of reactive oxygen species (ROS) and nitric oxide (NO) and ex...

A bacterial tyrosine phosphatase inhibits plant pattern recognition receptor activation

USDA-ARS?s Scientific Manuscript database

Perception of pathogen-associated molecular patterns (PAMPs) by surface-localised pattern-recognition receptors (PRRs) is a key component of plant innate immunity. Most known plant PRRs are receptor kinases and initiation of PAMP-triggered immunity (PTI) signalling requires phosphorylation of the PR...

The Design of Molecular Hosts, Guests, and Their Complexes.

ERIC Educational Resources Information Center

Cram, Donald J.

1988-01-01

Describes the origins, definitions, tools, and principles of host-guest chemistry. Gives examples of chiral recognition in complexation, of partial transacylase mimics, of caviplexes, and of a synthetic molecular cell. (Author/RT)

A requirement for the immediate early gene zif268 in reconsolidation of recognition memory after retrieval.

PubMed

Bozon, Bruno; Davis, Sabrina; Laroche, Serge

2003-11-13

Recent research has revived interest in the possibility that previously consolidated memories need to reconsolidate when recalled to return to accessible long-term memory. Evidence suggests that both consolidation and reconsolidation of certain types of memory require protein synthesis, but whether similar molecular mechanisms are involved remains unclear. Here, we explore whether zif268, an activity-dependent inducible immediate early gene (IEG) required for consolidation of new memories, is also recruited for reconsolidation of recognition memory following reactivation. We show that when a consolidated memory for objects is recalled, zif268 mutant mice are impaired in further long-term but not short-term recognition memory. The impairment is specific to reactivation with the previously memorized objects in the relevant context, occurs in delayed recall, and does not recover over several days. These findings indicate that IEG-mediated transcriptional regulation in neurons is one common molecular mechanism for the storage of newly formed and reactivated recognition memories.

Conformational selection in a protein-protein interaction revealed by dynamic pathway analysis

DOE PAGES

Chakrabarti, Kalyan S.; Agafonov, Roman V.; Pontiggia, Francesco; ...

2015-12-24

Molecular recognition plays a central role in biology, and protein dynamics has been acknowledged to be important in this process. However, it is highly debated whether conformational changes happen before ligand binding to produce a binding-competent state (conformational selection) or are caused in response to ligand binding (induced fit). Proposals for both mechanisms in protein/protein recognition have been primarily based on structural arguments. However, the distinction between them is a question of the probabilities of going via these two opposing pathways. Here we present a direct demonstration of exclusive conformational selection in protein/protein recognition by measuring the flux for rhodopsinmore » kinase binding to its regulator recoverin, an important molecular recognition in the vision system. Using NMR spectroscopy, stopped-flow kinetics and isothermal titration calorimetry we show that recoverin populates a minor conformation in solution that exposes a hydrophobic binding pocket responsible for binding rhodopsin kinase. Lastly, protein dynamics in free recoverin limits the overall rate of binding.« less

Molecular recognition on a cavitand-functionalized silicon surface.

PubMed

Biavardi, Elisa; Favazza, Maria; Motta, Alessandro; Fragalà, Ignazio L; Massera, Chiara; Prodi, Luca; Montalti, Marco; Melegari, Monica; Condorelli, Guglielmo G; Dalcanale, Enrico

2009-06-03

A Si(100) surface featuring molecular recognition properties was obtained by covalent functionalization with a tetraphosphonate cavitand (Tiiii), able to complex positively charged species. Tiiii cavitand was grafted onto the Si by photochemical hydrosilylation together with 1-octene as a spatial spectator. The recognition properties of the Si-Tiiii surface were demonstrated through two independent analytical techniques, namely XPS and fluorescence spectroscopy, during the course of reversible complexation-guest exchange-decomplexation cycles with specifically designed ammonium and pyridinium salts. Control experiments employing a Si(100) surface functionalized with a structurally similar, but complexation inactive, tetrathiophosphonate cavitand (TSiiii) demonstrated no recognition events. This provides evidence for the complexation properties of the Si-Tiiii surface, ruling out the possibility of nonspecific interactions between the substrate and the guests. The residual Si-O(-) terminations on the surface replace the guests' original counterions, thus stabilizing the complex ion pairs. These results represent a further step toward the control of self-assembly of complex supramolecular architectures on surfaces.

Conformational selection in a protein-protein interaction revealed by dynamic pathway analysis

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

Chakrabarti, Kalyan S.; Agafonov, Roman V.; Pontiggia, Francesco

Molecular recognition plays a central role in biology, and protein dynamics has been acknowledged to be important in this process. However, it is highly debated whether conformational changes happen before ligand binding to produce a binding-competent state (conformational selection) or are caused in response to ligand binding (induced fit). Proposals for both mechanisms in protein/protein recognition have been primarily based on structural arguments. However, the distinction between them is a question of the probabilities of going via these two opposing pathways. Here we present a direct demonstration of exclusive conformational selection in protein/protein recognition by measuring the flux for rhodopsinmore » kinase binding to its regulator recoverin, an important molecular recognition in the vision system. Using NMR spectroscopy, stopped-flow kinetics and isothermal titration calorimetry we show that recoverin populates a minor conformation in solution that exposes a hydrophobic binding pocket responsible for binding rhodopsin kinase. Lastly, protein dynamics in free recoverin limits the overall rate of binding.« less

Magnetic molecularly imprinted polymer for aspirin recognition and controlled release

NASA Astrophysics Data System (ADS)

Kan, Xianwen; Geng, Zhirong; Zhao, Yao; Wang, Zhilin; Zhu, Jun-Jie

2009-04-01

Core-shell structural magnetic molecularly imprinted polymers (magnetic MIPs) with combined properties of molecular recognition and controlled release were prepared and characterized. Magnetic MIPs were synthesized by the co-polymerization of methacrylic acid (MAA) and trimethylolpropane trimethacrylate (TRIM) around aspirin (ASP) at the surface of double-bond-functionalized Fe3O4 nanoparticles in chloroform. The obtained spherical magnetic MIPs with diameters of about 500 nm had obvious superparamagnetism and could be separated quickly by an external magnetic field. Binding experiments were carried out to evaluate the properties of magnetic MIPs and magnetic non-molecularly imprinted polymers (magnetic NIPs). The results demonstrated that the magnetic MIPs had high adsorption capacity and selectivity to ASP. Moreover, release profiles and release rate of ASP from the ASP-loaded magnetic MIPs indicated that the magnetic MIPs also had potential applications in drug controlled release.

Variations in Recollection: The Effects of Complexity on Source Recognition

ERIC Educational Resources Information Center

Parks, Colleen M.; Murray, Linda J.; Elfman, Kane; Yonelinas, Andrew P.

2011-01-01

Whether recollection is a threshold or signal detection process is highly controversial, and the controversy has centered in part on the shape of receiver operating characteristics (ROCs) and z-transformed ROCs (zROCs). U-shaped zROCs observed in tests thought to rely heavily on recollection, such as source memory tests, have provided evidence in…

Structural elements and organization of the ancestral translational machinery

NASA Technical Reports Server (NTRS)

Rein, R.; Srinivasan, S.; Mcdonald, J.; Raghunathan, G.; Shibata, M.

1987-01-01

The molecular mechanisms of the primitive translational apparatus are discussed in the framework of present-day protein biosynthesis. The structural necessities of an early adaptor and the multipoint recognition properties of such an adaptor are investigated on the basis of structure/function relationships found in a contemporary system and a molecular model of the contemporary transpeptidation complex. A model of the tRNA(Tyr)-tyrosyl tRNA synthetase complex including the positioning of the disordered region is proposed; the model is used to illustrate the required recognition properties of the ancestor aminoacyl synthetase.

Amplifying Electrochemical Indicators

NASA Technical Reports Server (NTRS)

Fan, Wenhong; Li, Jun; Han, Jie

2004-01-01

Dendrimeric reporter compounds have been invented for use in sensing and amplifying electrochemical signals from molecular recognition events that involve many chemical and biological entities. These reporter compounds can be formulated to target specific molecules or molecular recognition events. They can also be formulated to be, variously, hydrophilic or amphiphilic so that they are suitable for use at interfaces between (1) aqueous solutions and (2) electrodes connected to external signal-processing electronic circuits. The invention of these reporter compounds is expected to enable the development of highly miniaturized, low-power-consumption, relatively inexpensive, mass-producible sensor units for diverse applications.

Molecular recognition in chiral smectic liquid crystals: the effect of core-core interactions and chirality transfer on polar order.

PubMed

Lemieux, Robert P

2007-12-01

This critical review focuses on the induction of polar order in smectic liquid crystal phases by dopants with axially chiral cores, and should be of interest to all practitioners of supramolecular chemistry. The variations in polarization power of these dopants with the core structure of the liquid crystal hosts is a manifestation of molecular recognition that reflects the nanosegregation of aromatic cores from paraffinic side-chains in smectic phases, and the collective effect of core-core interactions that enable the propagation of chiral perturbations.

Recognition of the genus Thaumatophyllum Schott − formerly Philodendron subg. Meconostigma (Araceae) − based on molecular and morphological evidence

PubMed Central

Sakuragui, Cassia Mônica; Calazans, Luana Silva Braucks; de Oliveira, Leticia Loss; de Morais, Érica Barroso; Benko-Iseppon, Ana Maria; Vasconcelos, Santelmo; Schrago, Carlos Eduardo Guerra; Mayo, Simon Joseph

2018-01-01

Abstract Philodendron subgenus Meconostigma has been a well-circumscribed group since 1829. Members of this group are easily distinguished by diagnostic morphological characters as well as by a distinct ecology and geographical distribution. Based on molecular, morphological and cytological evidence, we propose the recognition of P. subg. Meconostigma as a distinct genus, Thaumatophyllum Schott. We also present the necessary new combinations, an emended key and some nomenclatural and taxonomic corrections regarding 21 names of Thaumatophyllum. PMID:29750071

Use of pattern recognition and neural networks for non-metric sex diagnosis from lateral shape of calvarium: an innovative model for computer-aided diagnosis in forensic and physical anthropology.

PubMed

Cavalli, Fabio; Lusnig, Luca; Trentin, Edmondo

2017-05-01

Sex determination on skeletal remains is one of the most important diagnosis in forensic cases and in demographic studies on ancient populations. Our purpose is to realize an automatic operator-independent method to determine the sex from the bone shape and to test an intelligent, automatic pattern recognition system in an anthropological domain. Our multiple-classifier system is based exclusively on the morphological variants of a curve that represents the sagittal profile of the calvarium, modeled via artificial neural networks, and yields an accuracy higher than 80 %. The application of this system to other bone profiles is expected to further improve the sensibility of the methodology.

Ensemble training to improve recognition using 2D ear

NASA Astrophysics Data System (ADS)

Middendorff, Christopher; Bowyer, Kevin W.

2009-05-01

The ear has gained popularity as a biometric feature due to the robustness of the shape over time and across emotional expression. Popular methods of ear biometrics analyze the ear as a whole, leaving these methods vulnerable to error due to occlusion. Many researchers explore ear recognition using an ensemble, but none present a method for designing the individual parts that comprise the ensemble. In this work, we introduce a method of modifying the ensemble shapes to improve performance. We determine how different properties of an ensemble training system can affect overall performance. We show that ensembles built from small parts will outperform ensembles built with larger parts, and that incorporating a large number of parts improves the performance of the ensemble.

Object Recognition using Feature- and Color-Based Methods

NASA Technical Reports Server (NTRS)

Duong, Tuan; Duong, Vu; Stubberud, Allen

2008-01-01

An improved adaptive method of processing image data in an artificial neural network has been developed to enable automated, real-time recognition of possibly moving objects under changing (including suddenly changing) conditions of illumination and perspective. The method involves a combination of two prior object-recognition methods one based on adaptive detection of shape features and one based on adaptive color segmentation to enable recognition in situations in which either prior method by itself may be inadequate. The chosen prior feature-based method is known as adaptive principal-component analysis (APCA); the chosen prior color-based method is known as adaptive color segmentation (ACOSE). These methods are made to interact with each other in a closed-loop system to obtain an optimal solution of the object-recognition problem in a dynamic environment. One of the results of the interaction is to increase, beyond what would otherwise be possible, the accuracy of the determination of a region of interest (containing an object that one seeks to recognize) within an image. Another result is to provide a minimized adaptive step that can be used to update the results obtained by the two component methods when changes of color and apparent shape occur. The net effect is to enable the neural network to update its recognition output and improve its recognition capability via an adaptive learning sequence. In principle, the improved method could readily be implemented in integrated circuitry to make a compact, low-power, real-time object-recognition system. It has been proposed to demonstrate the feasibility of such a system by integrating a 256-by-256 active-pixel sensor with APCA, ACOSE, and neural processing circuitry on a single chip. It has been estimated that such a system on a chip would have a volume no larger than a few cubic centimeters, could operate at a rate as high as 1,000 frames per second, and would consume in the order of milliwatts of power.

Improving of Mechanical and Shape-Memory Properties in Hyperbranched Epoxy Shape-Memory Polymers

NASA Astrophysics Data System (ADS)

Santiago, David; Fabregat-Sanjuan, Albert; Ferrando, Francesc; De la Flor, Silvia

2016-09-01

A series of shape-memory epoxy polymers were synthesized using an aliphatic amine and two different commercial hyperbranched poly(ethyleneimine)s with different molecular weights as crosslinking agents. Thermal, mechanical, and shape-memory properties in materials modified with different hyperbranched polymers were analyzed and compared in order to establish the effect of the structure and the molecular weight of the hyperbranched polymers used. The presence of hyperbranched polymers led to more heterogeneous networks, and the crosslinking densities of which increase as the hyperbranched polymer content increases. The transition temperatures can be tailored from 56 to 117 °C depending on the molecular weight and content of the hyperbranched polymer. The mechanical properties showed excellent values in all formulations at room temperature and, specially, at T_{{g}}^{{E^' with stress at break as high as 15 MPa and strain at break as high as 60 %. The shape-memory performances revealed recovery ratios around 95 %, fixity ratios around 97 %, and shape-recovery velocities as high as 22 %/min. The results obtained in this study reveal that hyperbranched polymers with different molecular weights can be used to enhance the thermal and mechanical properties of epoxy-based SMPs while keeping excellent shape-memory properties.

"Soft docking": matching of molecular surface cubes.

PubMed

Jiang, F; Kim, S H

1991-05-05

Molecular recognition is achieved through the complementarity of molecular surface structures and energetics with, most commonly, associated minor conformational changes. This complementarity can take many forms: charge-charge interaction, hydrogen bonding, van der Waals' interaction, and the size and shape of surfaces. We describe a method that exploits these features to predict the sites of interactions between two cognate molecules given their three-dimensional structures. We have developed a "cube representation" of molecular surface and volume which enables us not only to design a simple algorithm for a six-dimensional search but also to allow implicitly the effects of the conformational changes caused by complex formation. The present molecular docking procedure may be divided into two stages. The first is the selection of a population of complexes by geometric "soft docking", in which surface structures of two interacting molecules are matched with each other, allowing minor conformational changes implicitly, on the basis of complementarity in size and shape, close packing, and the absence of steric hindrance. The second is a screening process to identify a subpopulation with many favorable energetic interactions between the buried surface areas. Once the size of the subpopulation is small, one may further screen to find the correct complex based on other criteria or constraints obtained from biochemical, genetic, and theoretical studies, including visual inspection. We have tested the present method in two ways. First is a control test in which we docked the components of a molecular complex of known crystal structure available in the Protein Data Bank (PDB). Two molecular complexes were used: (1) a ternary complex of dihydrofolate reductase, NADPH and methotrexate (3DFR in PDB) and (2) a binary complex of trypsin and trypsin inhibitor (2PTC in PDB). The components of each complex were taken apart at an arbitrary relative orientation and then docked together again. The results show that the geometric docking alone is sufficient to determine the correct docking solutions in these ideal cases, and that the cube representation of the molecules does not degrade the docking process in the search for the correct solution. The second is the more realistic experiment in which we docked the crystal structures of uncomplexed molecules and then compared the structures of docked complexes with the crystal structures of the corresponding complexes. This is to test the capability of our method in accommodating the effects of the conformational changes in the binding sites of the molecules in docking.(ABSTRACT TRUNCATED AT 400 WORDS)

Document image retrieval through word shape coding.

PubMed

Lu, Shijian; Li, Linlin; Tan, Chew Lim

2008-11-01

This paper presents a document retrieval technique that is capable of searching document images without OCR (optical character recognition). The proposed technique retrieves document images by a new word shape coding scheme, which captures the document content through annotating each word image by a word shape code. In particular, we annotate word images by using a set of topological shape features including character ascenders/descenders, character holes, and character water reservoirs. With the annotated word shape codes, document images can be retrieved by either query keywords or a query document image. Experimental results show that the proposed document image retrieval technique is fast, efficient, and tolerant to various types of document degradation.

A new look at emotion perception: Concepts speed and shape facial emotion recognition.

PubMed

Nook, Erik C; Lindquist, Kristen A; Zaki, Jamil

2015-10-01

Decades ago, the "New Look" movement challenged how scientists thought about vision by suggesting that conceptual processes shape visual perceptions. Currently, affective scientists are likewise debating the role of concepts in emotion perception. Here, we utilized a repetition-priming paradigm in conjunction with signal detection and individual difference analyses to examine how providing emotion labels-which correspond to discrete emotion concepts-affects emotion recognition. In Study 1, pairing emotional faces with emotion labels (e.g., "sad") increased individuals' speed and sensitivity in recognizing emotions. Additionally, individuals with alexithymia-who have difficulty labeling their own emotions-struggled to recognize emotions based on visual cues alone, but not when emotion labels were provided. Study 2 replicated these findings and further demonstrated that emotion concepts can shape perceptions of facial expressions. Together, these results suggest that emotion perception involves conceptual processing. We discuss the implications of these findings for affective, social, and clinical psychology. (c) 2015 APA, all rights reserved).

Bypassing adverse injection reactions to nanoparticles through shape modification and attachment to erythrocytes

NASA Astrophysics Data System (ADS)

Wibroe, Peter Popp; Anselmo, Aaron C.; Nilsson, Per H.; Sarode, Apoorva; Gupta, Vivek; Urbanics, Rudolf; Szebeni, Janos; Hunter, Alan Christy; Mitragotri, Samir; Mollnes, Tom Eirik; Moghimi, Seyed Moein

2017-07-01

Intravenously injected nanopharmaceuticals, including PEGylated nanoparticles, induce adverse cardiopulmonary reactions in sensitive human subjects, and these reactions are highly reproducible in pigs. Although the underlying mechanisms are poorly understood, roles for both the complement system and reactive macrophages have been implicated. Here, we show the dominance and importance of robust pulmonary intravascular macrophage clearance of nanoparticles in mediating adverse cardiopulmonary distress in pigs irrespective of complement activation. Specifically, we show that delaying particle recognition by macrophages within the first few minutes of injection overcomes adverse reactions in pigs using two independent approaches. First, we changed the particle geometry from a spherical shape (which triggers cardiopulmonary distress) to either rod- or disk-shape morphology. Second, we physically adhered spheres to the surface of erythrocytes. These strategies, which are distinct from commonly leveraged stealth engineering approaches such as nanoparticle surface functionalization with poly(ethylene glycol) and/or immunological modulators, prevent robust macrophage recognition, resulting in the reduction or mitigation of adverse cardiopulmonary distress associated with nanopharmaceutical administration.

Biophysical exploration of protein-flavonol recognition: effects of molecular properties and conformational flexibility.

PubMed

Ding, Fei; Peng, Wei; Peng, Yu-Kui

2016-04-28

The current work explores the biomolecular recognition of a series of flavonols by a protein and then uncovers the influences of the structural features of flavonols and the protein's own characteristics, e.g. the dynamics and flexibility, on the bioavailability of flavonols by using the pivotal biomacromolecule hemoglobin as a model. The experimental results revealed that flavonol may lead to a notable decrease in the steady-state fluorescence intensity of the β-37 Trp residue, and in the meantime the R-T transition of the protein transpired. Such noncovalent recognition forms the ground-state adduct, with an association intensity of 3.991 × 10(4) M(-1) in the reaction process, which has already been authenticated by the detailed analysis of time-resolved fluorescence and UV/vis absorption spectra. Furthermore, flavonol can form hydrogen bonds and π-conjugation effects with several amino acid residues on the polypeptide chain, for example, Trp-37, Arg-40, Asp-99 and Asn-102, and this event would induce self-regulation of the compact, regular conformation of the protein to a certain extent, which explicitly corroborates the results of circular dichroism. According to the study of molecular docking and structure-activity relationships, we could see that the recognition capacities of the protein-flavonols are inversely interrelated with the C log P values of the flavonol molecules. Moreover, the properties of the substituents in the structural B-ring unit of flavonols, i.e. polarity, position and number, will also prominently affect the degree of affinity and bioavailability of the protein-flavonol complexes. The analytical results of molecular dynamics (MD) simulation testified that the discussions of the structure-activity relationships are entirely logical, and the conformations of the amino acid residues forming noncovalent interactions tend to be stable in the MD simulation, as further elucidated from the dynamics data. Plainly, molecular recognition of the protein-flavonols might noticeably cause relatively large changes in protein flexibility, and then manifest different recognition strengths and corresponding biological activities. This issue will be carefully validated by the interpretation of root-mean-square fluctuation.

Results using the OPAL strategy in Mandarin speaking cochlear implant recipients.

PubMed

Vandali, Andrew E; Dawson, Pam W; Arora, Komal

2017-01-01

To evaluate the effectiveness of an experimental pitch-coding strategy for improving recognition of Mandarin lexical tone in cochlear implant (CI) recipients. Adult CI recipients were tested on recognition of Mandarin tones in quiet and speech-shaped noise at a signal-to-noise ratio of +10 dB; Mandarin sentence speech-reception threshold (SRT) in speech-shaped noise; and pitch discrimination of synthetic complex-harmonic tones in quiet. Two versions of the experimental strategy were examined: (OPAL) linear (1:1) mapping of fundamental frequency (F0) to the coded modulation rate; and (OPAL+) transposed mapping of high F0s to a lower coded rate. Outcomes were compared to results using the clinical ACE™ strategy. Five Mandarin speaking users of Nucleus® cochlear implants. A small but significant benefit in recognition of lexical tones was observed using OPAL compared to ACE in noise, but not in quiet, and not for OPAL+ compared to ACE or OPAL in quiet or noise. Sentence SRTs were significantly better using OPAL+ and comparable using OPAL to those using ACE. No differences in pitch discrimination thresholds were observed across strategies. OPAL can provide benefits to Mandarin lexical tone recognition in moderately noisy conditions and preserve perception of Mandarin sentences in challenging noise conditions.

[Visual Texture Agnosia in Humans].

PubMed

Suzuki, Kyoko

2015-06-01

Visual object recognition requires the processing of both geometric and surface properties. Patients with occipital lesions may have visual agnosia, which is impairment in the recognition and identification of visually presented objects primarily through their geometric features. An analogous condition involving the failure to recognize an object by its texture may exist, which can be called visual texture agnosia. Here we present two cases with visual texture agnosia. Case 1 had left homonymous hemianopia and right upper quadrantanopia, along with achromatopsia, prosopagnosia, and texture agnosia, because of damage to his left ventromedial occipitotemporal cortex and right lateral occipito-temporo-parietal cortex due to multiple cerebral embolisms. Although he showed difficulty matching and naming textures of real materials, he could readily name visually presented objects by their contours. Case 2 had right lower quadrantanopia, along with impairment in stereopsis and recognition of texture in 2D images, because of subcortical hemorrhage in the left occipitotemporal region. He failed to recognize shapes based on texture information, whereas shape recognition based on contours was well preserved. Our findings, along with those of three reported cases with texture agnosia, indicate that there are separate channels for processing texture, color, and geometric features, and that the regions around the left collateral sulcus are crucial for texture processing.

Real-time color/shape-based traffic signs acquisition and recognition system

NASA Astrophysics Data System (ADS)

Saponara, Sergio

2013-02-01

A real-time system is proposed to acquire from an automotive fish-eye CMOS camera the traffic signs, and provide their automatic recognition on the vehicle network. Differently from the state-of-the-art, in this work color-detection is addressed exploiting the HSI color space which is robust to lighting changes. Hence the first stage of the processing system implements fish-eye correction and RGB to HSI transformation. After color-based detection a noise deletion step is implemented and then, for the classification, a template-based correlation method is adopted to identify potential traffic signs, of different shapes, from acquired images. Starting from a segmented-image a matching with templates of the searched signs is carried out using a distance transform. These templates are organized hierarchically to reduce the number of operations and hence easing real-time processing for several types of traffic signs. Finally, for the recognition of the specific traffic sign, a technique based on extraction of signs characteristics and thresholding is adopted. Implemented on DSP platform the system recognizes traffic signs in less than 150 ms at a distance of about 15 meters from 640x480-pixel acquired images. Tests carried out with hundreds of images show a detection and recognition rate of about 93%.

Body-Earth Mover's Distance: A Matching-Based Approach for Sleep Posture Recognition.

PubMed

Xu, Xiaowei; Lin, Feng; Wang, Aosen; Hu, Yu; Huang, Ming-Chun; Xu, Wenyao

2016-10-01

Sleep posture is a key component in sleep quality assessment and pressure ulcer prevention. Currently, body pressure analysis has been a popular method for sleep posture recognition. In this paper, a matching-based approach, Body-Earth Mover's Distance (BEMD), for sleep posture recognition is proposed. BEMD treats pressure images as weighted 2D shapes, and combines EMD and Euclidean distance for similarity measure. Compared with existing work, sleep posture recognition is achieved with posture similarity rather than multiple features for specific postures. A pilot study is performed with 14 persons for six different postures. The experimental results show that the proposed BEMD can achieve 91.21% accuracy, which outperforms the previous method with an improvement of 8.01%.

Face recognition using 3D facial shape and color map information: comparison and combination

NASA Astrophysics Data System (ADS)

Godil, Afzal; Ressler, Sandy; Grother, Patrick

2004-08-01

In this paper, we investigate the use of 3D surface geometry for face recognition and compare it to one based on color map information. The 3D surface and color map data are from the CAESAR anthropometric database. We find that the recognition performance is not very different between 3D surface and color map information using a principal component analysis algorithm. We also discuss the different techniques for the combination of the 3D surface and color map information for multi-modal recognition by using different fusion approaches and show that there is significant improvement in results. The effectiveness of various techniques is compared and evaluated on a dataset with 200 subjects in two different positions.

Character context: a shape descriptor for Arabic handwriting recognition

NASA Astrophysics Data System (ADS)

Mudhsh, Mohammed; Almodfer, Rolla; Duan, Pengfei; Xiong, Shengwu

2017-11-01

In the handwriting recognition field, designing good descriptors are substantial to obtain rich information of the data. However, the handwriting recognition research of a good descriptor is still an open issue due to unlimited variation in human handwriting. We introduce a "character context descriptor" that efficiently dealt with the structural characteristics of Arabic handwritten characters. First, the character image is smoothed and normalized, then the character context descriptor of 32 feature bins is built based on the proposed "distance function." Finally, a multilayer perceptron with regularization is used as a classifier. On experimentation with a handwritten Arabic characters database, the proposed method achieved a state-of-the-art performance with recognition rate equal to 98.93% and 99.06% for the 66 and 24 classes, respectively.

Study of Molecular-Shape Selectivity of Zeolites by Gas Chromatography

ERIC Educational Resources Information Center

Chao, Pei-Yu; Chuang, Yao-Yuan; Ho, Grace Hsiuying; Chuang, Shiow-Huey; Tsai, Tseng-Chang; Lee, Chi-Young; Tsai, Shang-Tien; Huang, Jun-Fu

2008-01-01

A sorption experiment using a gas chromatograph is described that can help students understand the "molecular-shape selectivity" behavior of zeolites in the subnano regime. Hexane isomers are used as probe molecules to demonstrate the sorption phenomena. In the experiment, a zeolite adsorbs certain hexane isomers with molecular sizes smaller than…

When apperceptive agnosia is explained by a deficit of primary visual processing.

PubMed

Serino, Andrea; Cecere, Roberto; Dundon, Neil; Bertini, Caterina; Sanchez-Castaneda, Cristina; Làdavas, Elisabetta

2014-03-01

Visual agnosia is a deficit in shape perception, affecting figure, object, face and letter recognition. Agnosia is usually attributed to lesions to high-order modules of the visual system, which combine visual cues to represent the shape of objects. However, most of previously reported agnosia cases presented visual field (VF) defects and poor primary visual processing. The present case-study aims to verify whether form agnosia could be explained by a deficit in basic visual functions, rather that by a deficit in high-order shape recognition. Patient SDV suffered a bilateral lesion of the occipital cortex due to anoxia. When tested, he could navigate, interact with others, and was autonomous in daily life activities. However, he could not recognize objects from drawings and figures, read or recognize familiar faces. He was able to recognize objects by touch and people from their voice. Assessments of visual functions showed blindness at the centre of the VF, up to almost 5°, bilaterally, with better stimulus detection in the periphery. Colour and motion perception was preserved. Psychophysical experiments showed that SDV's visual recognition deficits were not explained by poor spatial acuity or by the crowding effect. Rather a severe deficit in line orientation processing might be a key mechanism explaining SDV's agnosia. Line orientation processing is a basic function of primary visual cortex neurons, necessary for detecting "edges" of visual stimuli to build up a "primal sketch" for object recognition. We propose, therefore, that some forms of visual agnosia may be explained by deficits in basic visual functions due to widespread lesions of the primary visual areas, affecting primary levels of visual processing. Copyright © 2013 Elsevier Ltd. All rights reserved.

A Novel Receptor-Like Kinase Involved in Fungal Pathogen Defense in Arabidopsis thaliana

USDA-ARS?s Scientific Manuscript database

Plants are under constant attack from a variety of disease causing organisms. Lacking an adaptive immune system, plants repel pathogen attack via an array of pathogen recognition machinery. Receptor-like kinases (RLKs) are involved in the recognition of pathogen-associated molecular patterns (PAMPs)...

Molecular basis of mycobacterial lipid antigen presentation by CD1c and its recognition by αβ T cells

PubMed Central

Roy, Sobhan; Ly, Dalam; Li, Nan-Sheng; Altman, John D.; Piccirilli, Joseph A.; Moody, D. Branch; Adams, Erin J.

2014-01-01

CD1c is a member of the group 1 CD1 family of proteins that are specialized for lipid antigen presentation. Despite high cell surface expression of CD1c on key antigen-presenting cells and the discovery of its mycobacterial lipid antigen presentation capability, the molecular basis of CD1c recognition by T cells is unknown. Here we present a comprehensive functional and molecular analysis of αβ T-cell receptor (TCR) recognition of CD1c presenting mycobacterial phosphomycoketide antigens. Our structure of CD1c with the mycobacterial phosphomycoketide (PM) shows similarities to that of CD1c-mannosyl-β1-phosphomycoketide in that the A' pocket accommodates the mycoketide alkyl chain; however, the phosphate head-group of PM is shifted ∼6 Å in relation to that of mannosyl-β1-PM. We also demonstrate a bona fide interaction between six human TCRs and CD1c-mycoketide complexes, measuring high to moderate affinities. The crystal structure of the DN6 TCR and mutagenic studies reveal a requirement of five complementarity determining region (CDR) loops for CD1c recognition. Furthermore, mutagenesis of CD1c reveals residues in both the α1 and α2 helices involved in TCR recognition, yet not entirely overlapping among the examined TCRs. Unlike patterns for MHC I, no archetypical binding footprint is predicted to be shared by CD1c-reactive TCRs, even when recognizing the same or similar antigens. PMID:25298532

A model based method for recognizing psoas major muscles in torso CT images

NASA Astrophysics Data System (ADS)

Kamiya, Naoki; Zhou, Xiangrong; Chen, Huayue; Hara, Takeshi; Yokoyama, Ryujiro; Kanematsu, Masayuki; Hoshi, Hiroaki; Fujita, Hiroshi

2010-03-01

In aging societies, it is important to analyze age-related hypokinesia. A psoas major muscle has many important functional capabilities such as capacity of balance and posture control. These functions can be measured by its cross sectional area (CSA), volume, and thickness. However, these values are calculated manually in the clinical situation. The purpose of our study is to propose an automated recognition method of psoas major muscles in X-ray torso CT images. The proposed recognition process involves three steps: 1) determination of anatomical points such as the origin and insertion of the psoas major muscle, 2) generation of a shape model for the psoas major muscle, and 3) recognition of the psoas major muscles by use of the shape model. The model was built using quadratic function, and was fit to the anatomical center line of psoas major muscle. The shape model was generated using 20 CT cases and tested by 20 other CT cases. The applied database consisted of 12 male and 8 female cases from the ages of 40's to 80's. The average value of Jaccard similarity coefficient (JSC) values employed in the evaluation was 0.7. Our experimental results indicated that the proposed method was effective for a volumetric analysis and could be possible to be used for a quantitative measurement of psoas major muscles in CT images.

Is Word Shape Still in Poor Shape for the Race to the Lexicon?

ERIC Educational Resources Information Center

Hill, Jessica C.

2010-01-01

Current models of normal reading behavior emphasize not only the recognition and processing of the word being fixated (n) but also processing of the upcoming parafoveal word (n + 1). Gaze contingent displays employing the boundary paradigm often mask words in order to understand how much and what type of processing is completed on the parafoveal…

3D-shape recognition and size measurement of irregular rough particles using multi-views interferometric out-of-focus imaging.

PubMed

Ouldarbi, L; Talbi, M; Coëtmellec, S; Lebrun, D; Gréhan, G; Perret, G; Brunel, M

2016-11-10

We realize simplified-tomography experiments on irregular rough particles using interferometric out-of-focus imaging. Using two angles of view, we determine the global 3D-shape, the dimensions, and the 3D-orientation of irregular rough particles whose morphologies belong to families such as sticks, plates, and crosses.

Defense Against Pathogens: Structural Insights into the Mechanism of Chitin Induced Activation of Innate Immunity.

PubMed

Squeglia, Flavia; Berisio, Rita; Shibuya, Naoto; Kaku, Hanae

2017-11-24

Pattern recognition receptors on the plant cell surface mediate the recognition of microbe-associated molecular patterns, in a process which activates downstream immune signaling. These receptors are plasma membrane-localized kinases which need to be autophosphorylated to activate downstream responses. Perception of attacks from fungi occurs through recognition of chitin, a polymer of an N-acetylglucosamine which is a characteristic component of the cell walls of fungi. This process is regulated in Arabidopsis by chitin elicitor receptor kinase CERK1. A more complex process characterizes rice, in which regulation of chitin perception is operated by a complex composed of OsCERK1, a homolog of CERK1, and the chitin elicitor binding protein OsCEBiP. Recent literature has provided a mechanistic description of the complex regulation of activation of innate immunity in rice and an advance in the structural description of molecular players involved in this process. This review describes the current status of the understanding of molecular events involved in innate immunity activation in rice. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

mpMoRFsDB: a database of molecular recognition features in membrane proteins.

PubMed

Gypas, Foivos; Tsaousis, Georgios N; Hamodrakas, Stavros J

2013-10-01

Molecular recognition features (MoRFs) are small, intrinsically disordered regions in proteins that undergo a disorder-to-order transition on binding to their partners. MoRFs are involved in protein-protein interactions and may function as the initial step in molecular recognition. The aim of this work was to collect, organize and store all membrane proteins that contain MoRFs. Membrane proteins constitute ∼30% of fully sequenced proteomes and are responsible for a wide variety of cellular functions. MoRFs were classified according to their secondary structure, after interacting with their partners. We identified MoRFs in transmembrane and peripheral membrane proteins. The position of transmembrane protein MoRFs was determined in relation to a protein's topology. All information was stored in a publicly available mySQL database with a user-friendly web interface. A Jmol applet is integrated for visualization of the structures. mpMoRFsDB provides valuable information related to disorder-based protein-protein interactions in membrane proteins. http://bioinformatics.biol.uoa.gr/mpMoRFsDB

Application of virtual screening and molecular dynamics for the analysis of selectivity of inhibitors of HU proteins targeted to the DNA-recognition site

NASA Astrophysics Data System (ADS)

Talyzina, A. A.; Agapova, Yu. K.; Podshivalov, D. D.; Timofeev, V. I.; Sidorov-Biryukov, D. D.; Rakitina, T. V.

2017-11-01

DNA-Binding HU proteins are essential for the maintenance of genomic DNA supercoiling and compaction in prokaryotic cells and are promising pharmacological targets for the design of new antibacterial agents. The virtual screening for low-molecular-weight compounds capable of specifically interacting with the DNA-recognition loop of the HU protein from the mycoplasma Spiroplasma melliferum was performed. The ability of the initially selected ligands to form stable complexes with the protein target was assessed by molecular dynamics simulation. One compound, which forms an unstable complex, was eliminated by means of a combination of computational methods, resulting in a decrease in the number of compounds that will pass to the experimental test phase. This approach can be used to solve a wide range of problems related to the search for and validation of low-molecular-weight inhibitors specific for a particular protein target.

Entropy in molecular recognition by proteins

PubMed Central

Caro, José A.; Harpole, Kyle W.; Kasinath, Vignesh; Lim, Jackwee; Granja, Jeffrey; Valentine, Kathleen G.; Sharp, Kim A.

2017-01-01

Molecular recognition by proteins is fundamental to molecular biology. Dissection of the thermodynamic energy terms governing protein–ligand interactions has proven difficult, with determination of entropic contributions being particularly elusive. NMR relaxation measurements have suggested that changes in protein conformational entropy can be quantitatively obtained through a dynamical proxy, but the generality of this relationship has not been shown. Twenty-eight protein–ligand complexes are used to show a quantitative relationship between measures of fast side-chain motion and the underlying conformational entropy. We find that the contribution of conformational entropy can range from favorable to unfavorable, which demonstrates the potential of this thermodynamic variable to modulate protein–ligand interactions. For about one-quarter of these complexes, the absence of conformational entropy would render the resulting affinity biologically meaningless. The dynamical proxy for conformational entropy or “entropy meter” also allows for refinement of the contributions of solvent entropy and the loss in rotational-translational entropy accompanying formation of high-affinity complexes. Furthermore, structure-based application of the approach can also provide insight into long-lived specific water–protein interactions that escape the generic treatments of solvent entropy based simply on changes in accessible surface area. These results provide a comprehensive and unified view of the general role of entropy in high-affinity molecular recognition by proteins. PMID:28584100

Entropy in molecular recognition by proteins.

PubMed

Caro, José A; Harpole, Kyle W; Kasinath, Vignesh; Lim, Jackwee; Granja, Jeffrey; Valentine, Kathleen G; Sharp, Kim A; Wand, A Joshua

2017-06-20

Molecular recognition by proteins is fundamental to molecular biology. Dissection of the thermodynamic energy terms governing protein-ligand interactions has proven difficult, with determination of entropic contributions being particularly elusive. NMR relaxation measurements have suggested that changes in protein conformational entropy can be quantitatively obtained through a dynamical proxy, but the generality of this relationship has not been shown. Twenty-eight protein-ligand complexes are used to show a quantitative relationship between measures of fast side-chain motion and the underlying conformational entropy. We find that the contribution of conformational entropy can range from favorable to unfavorable, which demonstrates the potential of this thermodynamic variable to modulate protein-ligand interactions. For about one-quarter of these complexes, the absence of conformational entropy would render the resulting affinity biologically meaningless. The dynamical proxy for conformational entropy or "entropy meter" also allows for refinement of the contributions of solvent entropy and the loss in rotational-translational entropy accompanying formation of high-affinity complexes. Furthermore, structure-based application of the approach can also provide insight into long-lived specific water-protein interactions that escape the generic treatments of solvent entropy based simply on changes in accessible surface area. These results provide a comprehensive and unified view of the general role of entropy in high-affinity molecular recognition by proteins.

Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement.

PubMed

Jiang, Hanlun; Sheong, Fu Kit; Zhu, Lizhe; Gao, Xin; Bernauer, Julie; Huang, Xuhui

2015-07-01

Argonaute (Ago) proteins and microRNAs (miRNAs) are central components in RNA interference, which is a key cellular mechanism for sequence-specific gene silencing. Despite intensive studies, molecular mechanisms of how Ago recognizes miRNA remain largely elusive. In this study, we propose a two-step mechanism for this molecular recognition: selective binding followed by structural re-arrangement. Our model is based on the results of a combination of Markov State Models (MSMs), large-scale protein-RNA docking, and molecular dynamics (MD) simulations. Using MSMs, we identify an open state of apo human Ago-2 in fast equilibrium with partially open and closed states. Conformations in this open state are distinguished by their largely exposed binding grooves that can geometrically accommodate miRNA as indicated in our protein-RNA docking studies. miRNA may then selectively bind to these open conformations. Upon the initial binding, the complex may perform further structural re-arrangement as shown in our MD simulations and eventually reach the stable binary complex structure. Our results provide novel insights in Ago-miRNA recognition mechanisms and our methodology holds great potential to be widely applied in the studies of other important molecular recognition systems.

Novel hybrid structure silica/CdTe/molecularly imprinted polymer: synthesis, specific recognition, and quantitative fluorescence detection of bovine hemoglobin.

PubMed

Li, Dong-Yan; He, Xi-Wen; Chen, Yang; Li, Wen-You; Zhang, Yu-Kui

2013-12-11

This work presented a novel strategy for the synthesis of the hybrid structure silica/CdTe/molecularly imprinted polymer (Si-NP/CdTe/MIP) to recognize and detect the template bovine hemoglobin (BHb). First, amino-functionalized silica nanoparticles (Si-NP) and carboxyl-terminated CdTe quantum dots (QDs) were assembled into composite nanoparticles (Si-NP/CdTe) using the EDC (1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride) chemistry. Next, Si-NP/CdTe/MIP was synthesized by anchoring molecularly imprinted polymer (MIP) layer on the surface of Si-NP/CdTe through the sol-gel technique and surface imprinting technique. The hybrid structure possessed the selectivity of molecular imprinting technique and the sensitivity of CdTe QDs as well as well-defined morphology. The binding experiment and fluorescence method demonstrated its special recognition performance toward the template BHb. Under the optimized conditions, the fluorescence intensity of the Si-NP/CdTe/MIP decreased linearly with the increase of BHb in the concentration range 0.02-2.1 μM, and the detection limit was 9.4 nM. Moreover, the reusability and reproducibility and the successful applications in practical samples indicated the synthesis of Si-NP/CdTe/MIP provided an alternative solution for special recognition and determination of protein from real samples.

MOLECULAR ARCHITECTURE OF THE HUMAN SPERM IZUMO1 AND EGG JUNO FERTILIZATION COMPLEX

PubMed Central

Aydin, Halil; Sultana, Azmiri; Li, Sheng; Thavalingam, Annoj; Lee, Jeffrey E.

2017-01-01

Fertilization is an essential biological process in sexual reproduction and comprises a series of molecular interactions between the sperm and egg1,2. The fusion of haploid spermatozoon and oocyte is the culminating event in mammalian fertilization, enabling the creation of a new genetically distinct diploid organism3,4. The merger of two gametes is achieved through a two-step mechanism where the sperm Izumo1 on the equatorial segment of the acrosome-reacted sperm recognizes its receptor Juno, on the egg surface4–6. This is followed by the fusion of two plasma membranes. Izumo1 and Juno proteins are indispensable for fertilization as constitutive knockout of either Izumo1 or Juno result in mice that are healthy but infertile5,6. Despite their central importance in reproductive medicine, the molecular architectures and the details of their functional roles in fertilization are not known. Here, we present the crystal structures of the human Izumo1 and Juno in unbound and bound conformations. The human Izumo1 structure exhibits a distinct boomerang shape and provides the first structural insights into the Izumo family of proteins7. Human Izumo1 forms a high-affinity complex with Juno and undergoes a major conformational change within its N-terminal domain upon binding to the egg-surface receptor. Our results provide new insights into the molecular basis of sperm-egg recognition, cross-species fertilization, and barrier to polyspermy, thus promising benefits for the rational development of novel non-hormonal contraceptives and fertility treatments for humans and other species of mammals. PMID:27309818

Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease.

PubMed

Alvizo, Oscar; Mittal, Seema; Mayo, Stephen L; Schiffer, Celia A

2012-07-01

HIV-1 protease recognizes and cleaves more than 12 different substrates leading to viral maturation. While these substrates share no conserved motif, they are specifically selected for and cleaved by protease during viral life cycle. Drug resistant mutations evolve within the protease that compromise inhibitor binding but allow the continued recognition of all these substrates. While the substrate envelope defines a general shape for substrate recognition, successfully predicting the determinants of substrate binding specificity would provide additional insights into the mechanism of altered molecular recognition in resistant proteases. We designed a variant of HIV protease with altered specificity using positive computational design methods and validated the design using X-ray crystallography and enzyme biochemistry. The engineered variant, Pr3 (A28S/D30F/G48R), was designed to preferentially bind to one out of three of HIV protease's natural substrates; RT-RH over p2-NC and CA-p2. In kinetic assays, RT-RH binding specificity for Pr3 increased threefold compared to the wild-type (WT), which was further confirmed by isothermal titration calorimetry. Crystal structures of WT protease and the designed variant in complex with RT-RH, CA-p2, and p2-NC were determined. Structural analysis of the designed complexes revealed that one of the engineered substitutions (G48R) potentially stabilized heterogeneous flap conformations, thereby facilitating alternate modes of substrate binding. Our results demonstrate that while substrate specificity could be engineered in HIV protease, the structural pliability of protease restricted the propagation of interactions as predicted. These results offer new insights into the plasticity and structural determinants of substrate binding specificity of the HIV-1 protease. Copyright © 2012 The Protein Society.

An expanded framework for biomolecular visualization in the classroom: Learning goals and competencies

PubMed Central

Dries, Daniel R.; Dean, Diane M.; Listenberger, Laura L.; Novak, Walter R.P.

2016-01-01

Abstract A thorough understanding of the molecular biosciences requires the ability to visualize and manipulate molecules in order to interpret results or to generate hypotheses. While many instructors in biochemistry and molecular biology use visual representations, few indicate that they explicitly teach visual literacy. One reason is the need for a list of core content and competencies to guide a more deliberate instruction in visual literacy. We offer here the second stage in the development of one such resource for biomolecular three‐dimensional visual literacy. We present this work with the goal of building a community for online resource development and use. In the first stage, overarching themes were identified and submitted to the biosciences community for comment: atomic geometry; alternate renderings; construction/annotation; het group recognition; molecular dynamics; molecular interactions; monomer recognition; symmetry/asymmetry recognition; structure‐function relationships; structural model skepticism; and topology and connectivity. Herein, the overarching themes have been expanded to include a 12th theme (macromolecular assemblies), 27 learning goals, and more than 200 corresponding objectives, many of which cut across multiple overarching themes. The learning goals and objectives offered here provide educators with a framework on which to map the use of molecular visualization in their classrooms. In addition, the framework may also be used by biochemistry and molecular biology educators to identify gaps in coverage and drive the creation of new activities to improve visual literacy. This work represents the first attempt, to our knowledge, to catalog a comprehensive list of explicit learning goals and objectives in visual literacy. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(1):69–75, 2017. PMID:27486685

Infrared/Terahertz Double Resonance for Chemical Remote Sensing: Signatures and Performance Predictions

DTIC Science & Technology

2011-01-01

remote sensing , such as Fourier-transform infrared spectroscopy, has limited recognition specificity because of atmospheric pressure broadening. Active interrogation techniques promise much greater chemical recognition that can overcome the limits imposed by atmospheric pressure broadening. Here we introduce infrared - terahertz (IR/THz) double resonance spectroscopy as an active means of chemical remote sensing that retains recognition specificity through rare, molecule-unique coincidences between IR molecular absorption and a line-tunable CO2

Evolution of kin recognition mechanisms in a fish.

PubMed

Hain, Timothy J A; Garner, Shawn R; Ramnarine, Indar W; Neff, Bryan D

2017-03-01

Both selection and phylogenetic history can influence the evolution of phenotypic traits. Here we used recently characterized variation in kin recognition mechanisms among six guppy populations to explore the phylogenetic history of this trait. Guppies can use two different kin recognition mechanisms: either phenotype matching, in which individuals are identified based on comparison with a recognition template, or familiarity, in which individuals are remembered based on previous interactions. Across the six populations, we identified four transitions in recognition mechanism: phenotype matching evolved once and was subsequently lost in a single population, whereas familiarity evolved twice. Based on a molecular clock, these transitions occurred among populations that had diverged on a timescale of hundreds of thousands of years, which is two orders of magnitude faster than previously documented transitions in recognition mechanisms. A randomization test provided no evidence that recognition mechanisms were constrained by phylogeny, suggesting that recognition mechanisms have the capacity to evolve rapidly, although the specific selection pressures that may be contributing to variation in recognition mechanisms across populations remain unknown.

Study on road sign recognition in LabVIEW

NASA Astrophysics Data System (ADS)

Panoiu, M.; Rat, C. L.; Panoiu, C.

2016-02-01

Road and traffic sign identification is a field of study that can be used to aid the development of in-car advisory systems. It uses computer vision and artificial intelligence to extract the road signs from outdoor images acquired by a camera in uncontrolled lighting conditions where they may be occluded by other objects, or may suffer from problems such as color fading, disorientation, variations in shape and size, etc. An automatic means of identifying traffic signs, in these conditions, can make a significant contribution to develop an Intelligent Transport Systems (ITS) that continuously monitors the driver, the vehicle, and the road. Road and traffic signs are characterized by a number of features which make them recognizable from the environment. Road signs are located in standard positions and have standard shapes, standard colors, and known pictograms. These characteristics make them suitable for image identification. Traffic sign identification covers two problems: traffic sign detection and traffic sign recognition. Traffic sign detection is meant for the accurate localization of traffic signs in the image space, while traffic sign recognition handles the labeling of such detections into specific traffic sign types or subcategories [1].

Orchestration of Molecular Information through Higher Order Chemical Recognition

NASA Astrophysics Data System (ADS)

Frezza, Brian M.

Broadly defined, higher order chemical recognition is the process whereby discrete chemical building blocks capable of specifically binding to cognate moieties are covalently linked into oligomeric chains. These chains, or sequences, are then able to recognize and bind to their cognate sequences with a high degree of cooperativity. Principally speaking, DNA and RNA are the most readily obtained examples of this chemical phenomenon, and function via Watson-Crick cognate pairing: guanine pairs with cytosine and adenine with thymine (DNA) or uracil (RNA), in an anti-parallel manner. While the theoretical principles, techniques, and equations derived herein apply generally to any higher-order chemical recognition system, in practice we utilize DNA oligomers as a model-building material to experimentally investigate and validate our hypotheses. Historically, general purpose information processing has been a task limited to semiconductor electronics. Molecular computing on the other hand has been limited to ad hoc approaches designed to solve highly specific and unique computation problems, often involving components or techniques that cannot be applied generally in a manner suitable for precise and predictable engineering. Herein, we provide a fundamental framework for harnessing high-order recognition in a modular and programmable fashion to synthesize molecular information process networks of arbitrary construction and complexity. This document provides a solid foundation for routinely embedding computational capability into chemical and biological systems where semiconductor electronics are unsuitable for practical application.

Automatic recognition of ship types from infrared images using superstructure moment invariants

NASA Astrophysics Data System (ADS)

Li, Heng; Wang, Xinyu

2007-11-01

Automatic object recognition is an active area of interest for military and commercial applications. In this paper, a system addressing autonomous recognition of ship types in infrared images is proposed. Firstly, an approach of segmentation based on detection of salient features of the target with subsequent shadow removing is proposed, as is the base of the subsequent object recognition. Considering the differences between the shapes of various ships mainly lie in their superstructures, we then use superstructure moment functions invariant to translation, rotation and scale differences in input patterns and develop a robust algorithm of obtaining ship superstructure. Subsequently a back-propagation neural network is used as a classifier in the recognition stage and projection images of simulated three-dimensional ship models are used as the training sets. Our recognition model was implemented and experimentally validated using both simulated three-dimensional ship model images and real images derived from video of an AN/AAS-44V Forward Looking Infrared(FLIR) sensor.

Network Analysis Reveals the Recognition Mechanism for Mannose-binding Lectins

NASA Astrophysics Data System (ADS)

Zhao, Yunjie; Jian, Yiren; Zeng, Chen; Computational Biophysics Lab Team

The specific carbohydrate binding of mannose-binding lectin (MBL) protein in plants makes it a very useful molecular tool for cancer cell detection and other applications. The biological states of most MBL proteins are dimeric. Using dynamics network analysis on molecular dynamics (MD) simulations on the model protein of MBL, we elucidate the short- and long-range driving forces behind the dimer formation. The results are further supported by sequence coevolution analysis. We propose a general framework for deciphering the recognition mechanism underlying protein-protein interactions that may have potential applications in signaling pathways.

π-Cation Interactions in Molecular Recognition: Perspectives on Pharmaceuticals and Pesticides.

PubMed

Liang, Zhibin; Li, Qing X

2018-04-04

The π-cation interaction that differs from the cation-π interaction is a valuable concept in molecular design of pharmaceuticals and pesticides. In this Perspective we present an up-to-date review (from 1995 to 2017) on bioactive molecules involving π-cation interactions with the recognition site, and categorize into systems of inhibitor-enzyme, ligand-receptor, ligand-transporter, and hapten-antibody. The concept of π-cation interactions offers use of π systems in a small molecule to enhance the binding affinity, specificity, selectivity, lipophilicity, bioavailability, and metabolic stability, which are physiochemical features desired for drugs and pesticides.

The rational development of molecularly imprinted polymer-based sensors for protein detection.

PubMed

Whitcombe, Michael J; Chianella, Iva; Larcombe, Lee; Piletsky, Sergey A; Noble, James; Porter, Robert; Horgan, Adrian

2011-03-01

The detection of specific proteins as biomarkers of disease, health status, environmental monitoring, food quality, control of fermenters and civil defence purposes means that biosensors for these targets will become increasingly more important. Among the technologies used for building specific recognition properties, molecularly imprinted polymers (MIPs) are attracting much attention. In this critical review we describe many methods used for imprinting recognition for protein targets in polymers and their incorporation with a number of transducer platforms with the aim of identifying the most promising approaches for the preparation of MIP-based protein sensors (277 references).

The role of lines and corners of geometric figures in recognition performance.

PubMed

Shevelev, Igor A; Kamenkovich, Viktorina M; Sharaev, George A

2003-01-01

A relative role of lines and corners of images of outline geometric figures in recognition performance was studied psychophysically. Probability of correct response to the shape of the whole figure (control) and figures with lines or corners masked to a different extent was compared. Increase in the extent of masking resulted in a drop of recognition performance that was significantly lower for figures without corners, than for figures without part of their lines. The whole 3D figures were recognized better than 2D ones, whereas the opposite relations were observed under conditions of masking. Significant gender difference in a recognition performance was found: men recognize entire and partly masked figures better than women. Possible mechanisms of relatively better recognition of figures with corners than with lines are discussed in connection with finding of high sensitivity of many neurons in the primary visual cortex to line crossing and branching.

Handwritten recognition of Tamil vowels using deep learning

NASA Astrophysics Data System (ADS)

Ram Prashanth, N.; Siddarth, B.; Ganesh, Anirudh; Naveen Kumar, Vaegae

2017-11-01

We come across a large volume of handwritten texts in our daily lives and handwritten character recognition has long been an important area of research in pattern recognition. The complexity of the task varies among different languages and it so happens largely due to the similarity between characters, distinct shapes and number of characters which are all language-specific properties. There have been numerous works on character recognition of English alphabets and with laudable success, but regional languages have not been dealt with very frequently and with similar accuracies. In this paper, we explored the performance of Deep Belief Networks in the classification of Handwritten Tamil vowels, and conclusively compared the results obtained. The proposed method has shown satisfactory recognition accuracy in light of difficulties faced with regional languages such as similarity between characters and minute nuances that differentiate them. We can further extend this to all the Tamil characters.

Building Hierarchical Representations for Oracle Character and Sketch Recognition.

PubMed

Jun Guo; Changhu Wang; Roman-Rangel, Edgar; Hongyang Chao; Yong Rui

2016-01-01

In this paper, we study oracle character recognition and general sketch recognition. First, a data set of oracle characters, which are the oldest hieroglyphs in China yet remain a part of modern Chinese characters, is collected for analysis. Second, typical visual representations in shape- and sketch-related works are evaluated. We analyze the problems suffered when addressing these representations and determine several representation design criteria. Based on the analysis, we propose a novel hierarchical representation that combines a Gabor-related low-level representation and a sparse-encoder-related mid-level representation. Extensive experiments show the effectiveness of the proposed representation in both oracle character recognition and general sketch recognition. The proposed representation is also complementary to convolutional neural network (CNN)-based models. We introduce a solution to combine the proposed representation with CNN-based models, and achieve better performances over both approaches. This solution has beaten humans at recognizing general sketches.

A depictive neural model for the representation of motion verbs.

PubMed

Rao, Sunil; Aleksander, Igor

2011-11-01

In this paper, we present a depictive neural model for the representation of motion verb semantics in neural models of visual awareness. The problem of modelling motion verb representation is shown to be one of function application, mapping a set of given input variables defining the moving object and the path of motion to a defined output outcome in the motion recognition context. The particular function-applicative implementation and consequent recognition model design presented are seen as arising from a noun-adjective recognition model enabling the recognition of colour adjectives as applied to a set of shapes representing objects to be recognised. The presence of such a function application scheme and a separately implemented position identification and path labelling scheme are accordingly shown to be the primitives required to enable the design and construction of a composite depictive motion verb recognition scheme. Extensions to the presented design to enable the representation of transitive verbs are also discussed.

Advances in image compression and automatic target recognition; Proceedings of the Meeting, Orlando, FL, Mar. 30, 31, 1989

NASA Technical Reports Server (NTRS)

Tescher, Andrew G. (Editor)

1989-01-01

Various papers on image compression and automatic target recognition are presented. Individual topics addressed include: target cluster detection in cluttered SAR imagery, model-based target recognition using laser radar imagery, Smart Sensor front-end processor for feature extraction of images, object attitude estimation and tracking from a single video sensor, symmetry detection in human vision, analysis of high resolution aerial images for object detection, obscured object recognition for an ATR application, neural networks for adaptive shape tracking, statistical mechanics and pattern recognition, detection of cylinders in aerial range images, moving object tracking using local windows, new transform method for image data compression, quad-tree product vector quantization of images, predictive trellis encoding of imagery, reduced generalized chain code for contour description, compact architecture for a real-time vision system, use of human visibility functions in segmentation coding, color texture analysis and synthesis using Gibbs random fields.

SHAPEMOL: the companion to SHAPE in the molecular era of ALMA and HERSCHEL

NASA Astrophysics Data System (ADS)

Santander-García, M.; Bujarrabal, V.; Alcolea, J.

2013-05-01

Modern instrumentation in radioastronomy constitutes a valuable tool for studying the Universe: ALMA will reach unprecedented sensitivities and spatial resolution, while Herschel/HIFI has opened a new window (most of the sub-mm and far infrared ranges are only accessible from space) for probing molecular warm gas (˜50-1000 K), complementing ground-based telescopes, which are better suited to study molecular molecular gas with temperatures under ˜100 K. On the other hand, the SHAPE software has emerged in the last few years as the standard tool for determinging the morphology and velocity field of different kinds of gaseous nebulae (mainly planetary nebulae, protoplanetary nebulae and nebulae around massive stars, although it can also be applied to H II regions and molecular clouds) via spatio-kinematical modelling. Standard SHAPE implements radiative transfer solving, but it is only available for atomic species and not for molecules. Being aware of the growing importance of the development of tools for easying the analyses of molecular data from new era observatories, we introduce the computer code shapemol, a plug-in for SHAPE with which we intend to fill the so far empty molecular niche. shapemol enables spatio-kinematic modeling with accurate non-LTE calculations of line excitation and radiative transfer in molecular species. This code has been succesfully tested in the study of the excitation conditions of the molecular envelope of the planetary nebula NGC 7027 using data from Herschel/HIFI and IRAM 30m. Currently, it allows radiative transfer solving in the ^{12}CO and ^{13}CO J=1-0 to J=17-16 lines. shapemol, used along SHAPE, allows to easily generate synthetic maps to test against interferometric observations, as well as synthetic line profiles to match single-dish observations.

Ligand recognition by RAR and RXR receptors: binding and selectivity.

PubMed

Sussman, Fredy; de Lera, Angel R

2005-10-06

Fundamental biological functions, most notably embriogenesis, cell growth, cell differentiation, and cell apoptosis, are in part regulated by a complex genomic network that starts with the binding (and activation) of retinoids to their cognate receptors, members of the superfamily of nuclear receptors. We have studied ligand recognition of retinoic receptors (RXRalpha and RARgamma) using a molecular-mechanics-based docking method. The protocol used in this work is able to rank the affinity of pairs of ligands for a single retinoid receptor, the highest values corresponding to those that adapt better to the shape of the binding site and generate the optimal set of electrostatic and apolar interactions with the receptor. Moreover, our studies shed light onto some of the energetic contributions to retinoid receptor ligand selectivity. In this regard we show that there is a difference in polarity between the binding site regions that anchor the carboxylate in RAR and RXR, which translates itself into large differences in the energy of interaction of both receptors with the same ligand. We observe that the latter energy change is canceled off by the solvation energy penalty upon binding. This energy compensation is borne out as well by experiments that address the effect of site-directed mutagenesis on ligand binding to RARgamma. The hypothesis that the difference in binding site polarity might be exploited to build RXR-selective ligands is tested with some compounds having a thiazolidinedione anchoring group.

PSPP: A Protein Structure Prediction Pipeline for Computing Clusters

DTIC Science & Technology

2009-07-01

Evanseck JD, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B 102...dimensional (3-D) protein structures are critical for the understanding of molecular mechanisms of living systems. Traditionally, X-ray crystallography...disordered proteins are often responsible for molecular recognition, molecular assembly, protein modifica- tion, and entropic chain activities in organisms [26

Detecting objects in radiographs for homeland security

NASA Astrophysics Data System (ADS)

Prasad, Lakshman; Snyder, Hans

2005-05-01

We present a general scheme for segmenting a radiographic image into polygons that correspond to visual features. This decomposition provides a vectorized representation that is a high-level description of the image. The polygons correspond to objects or object parts present in the image. This characterization of radiographs allows the direct application of several shape recognition algorithms to identify objects. In this paper we describe the use of constrained Delaunay triangulations as a uniform foundational tool to achieve multiple visual tasks, namely image segmentation, shape decomposition, and parts-based shape matching. Shape decomposition yields parts that serve as tokens representing local shape characteristics. Parts-based shape matching enables the recognition of objects in the presence of occlusions, which commonly occur in radiographs. The polygonal representation of image features affords the efficient design and application of sophisticated geometric filtering methods to detect large-scale structural properties of objects in images. Finally, the representation of radiographs via polygons results in significant reduction of image file sizes and permits the scalable graphical representation of images, along with annotations of detected objects, in the SVG (scalable vector graphics) format that is proposed by the world wide web consortium (W3C). This is a textual representation that can be compressed and encrypted for efficient and secure transmission of information over wireless channels and on the Internet. In particular, our methods described here provide an algorithmic framework for developing image analysis tools for screening cargo at ports of entry for homeland security.

Exploration of the binding modes of buffalo PGRP1 receptor complexed with meso-diaminopimelic acid and lysine-type peptidoglycans by molecular dynamics simulation and free energy calculation.

PubMed

Sahoo, Bikash Ranjan; Dubey, Praveen Kumar; Goyal, Shubham; Bhoi, Gopal Krushna; Lenka, Santosh Kumar; Maharana, Jitendra; Pradhan, Sukanta Kumar; Kataria, Ranjit Singh

2014-09-05

The peptidoglycan recognition proteins (PGRPs) are the key components of innate-immunity, and are highly specific for the recognition of bacterial peptidoglycans (PGN). Among different mammalian PGRPs, the PGRP1 binds to murein PGN of Gram-positive bacteria (lysine-type) and also have bactericidal activity towards Gram-negative bacteria (diaminopimelic acid or Dap-type). Buffaloes are the major sources of milk and meat in Asian sub-continents and are highly exposed to bacterial infections. The PGRP activates the innate-immune signaling, but their studies has been confined to limited species due to lack of structural and functional information. So, to understand the structural constituents, 3D model of buffalo PGRP1 (bfPGRP1) was constructed and conformational and dynamics properties of bfPGRP1 was studied. The bfPGRP1 model highly resembled human and camel PGRP structure, and shared a highly flexible N-terminus and centrally placed L-shaped cleft. Docking simulation of muramyl-tripeptide, tetrapeptide, pentapeptide-Dap-(MTP-Dap, MTrP-Dap and MPP-Dap) and lysine-type (MTP-Lys, MTrP-Lys and MPP-Lys) in AutoDock 4.2 and ArgusLab 4.0.1 anticipated β1, α2, α4, β4, and loops connecting β1-α2, α2-β2, β3-β4 and α4-α5 as the key interacting domains. The bfPGRP1-ligand complex molecular dynamics simulation followed by free binding energy (BE) computation conceded BE values of -18.30, -35.53, -41.80, -25.03, -24.62 and -22.30 kJ mol(-1) for MTP-Dap, MTrP-Dap, MPP-Dap, MTP-Lys, MTrP-Lys and MPP-Lys, respectively. The groove-surface and key binding residues involved in PGN-Dap and Lys-type interaction intended by the molecular docking, and were also accompanied by significant BE values directed their importance in pharmacogenomics, and warrants further in vivo studies for drug targeting and immune signaling pathways exploration. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

System for face recognition under expression variations of neutral-sampled individuals using recognized expression warping and a virtual expression-face database

NASA Astrophysics Data System (ADS)

Petpairote, Chayanut; Madarasmi, Suthep; Chamnongthai, Kosin

2018-01-01

The practical identification of individuals using facial recognition techniques requires the matching of faces with specific expressions to faces from a neutral face database. A method for facial recognition under varied expressions against neutral face samples of individuals via recognition of expression warping and the use of a virtual expression-face database is proposed. In this method, facial expressions are recognized and the input expression faces are classified into facial expression groups. To aid facial recognition, the virtual expression-face database is sorted into average facial-expression shapes and by coarse- and fine-featured facial textures. Wrinkle information is also employed in classification by using a process of masking to adjust input faces to match the expression-face database. We evaluate the performance of the proposed method using the CMU multi-PIE, Cohn-Kanade, and AR expression-face databases, and we find that it provides significantly improved results in terms of face recognition accuracy compared to conventional methods and is acceptable for facial recognition under expression variation.

Color constancy in 3D-2D face recognition

NASA Astrophysics Data System (ADS)

Meyer, Manuel; Riess, Christian; Angelopoulou, Elli; Evangelopoulos, Georgios; Kakadiaris, Ioannis A.

2013-05-01

Face is one of the most popular biometric modalities. However, up to now, color is rarely actively used in face recognition. Yet, it is well-known that when a person recognizes a face, color cues can become as important as shape, especially when combined with the ability of people to identify the color of objects independent of illuminant color variations. In this paper, we examine the feasibility and effect of explicitly embedding illuminant color information in face recognition systems. We empirically examine the theoretical maximum gain of including known illuminant color to a 3D-2D face recognition system. We also investigate the impact of using computational color constancy methods for estimating the illuminant color, which is then incorporated into the face recognition framework. Our experiments show that under close-to-ideal illumination estimates, one can improve face recognition rates by 16%. When the illuminant color is algorithmically estimated, the improvement is approximately 5%. These results suggest that color constancy has a positive impact on face recognition, but the accuracy of the illuminant color estimate has a considerable effect on its benefits.

Crystallization of micrometer-sized particles with molecular contours.

PubMed

Song, Pengcheng; Olmsted, Brian K; Chaikin, Paul; Ward, Michael D

2013-11-12

The crystallization of micrometer-sized particles with shapes mimicking those of tetrabenzoheptacene (TBH) and 1,2:5,6-dibenzanthracene (DBT), both flat polyacenes, in an electric field results in the formation of ordered 2D packings that mimic the plane group symmetries in their respective molecular crystal equivalents. Whereas the particles packed in low-density disordered arrangements under a gravitational gradient, dielectrophoresis (under an ac electric field) produced ordered high-density packings with readily identifiable plane group symmetry. The ordered colloidal assemblies were stable for hours, with the packing density decreasing slowly but with recognizable symmetry for up to 12 h for the TBH-shaped particles and up to 4 h for the DBT-shaped particles. This unexpected stability is attributed to jamming behavior associated with interlocking of the dogbone-shaped (TBH) and Z-block (DBT) particles, contrasting with the more rapid reduction of packing density and loss of hexagonal symmetry for disk-shaped particles upon removal of the electric field. The TBH-shaped and DBT-shaped particles assemble into the p2 plane group, which corresponds to the densest particle packing among the possible close-packed plane groups for these particle symmetries. The p2 symmetry observed for the TBH-shaped and DBT-shaped colloid crystal emulates the p2 symmetry of the (010) layers in their respective molecular crystals, which crystallize in monoclinic lattices. Notably, DBT-shaped particles also form ordered domains with pgg symmetry, replicating the plane group symmetry of the (100) layer in the orthorhombic polymorph of DBT. These observations illustrate that the 2D ordering of colloid particles can mimic the packing of molecules with similar shapes, demonstrating that packing can transcend length scales from the molecular to the colloidal.

Application of morphological associative memories and Fourier descriptors for classification of noisy subsurface signatures

NASA Astrophysics Data System (ADS)

Ortiz, Jorge L.; Parsiani, Hamed; Tolstoy, Leonid

2004-02-01

This paper presents a method for recognition of Noisy Subsurface Images using Morphological Associative Memories (MAM). MAM are type of associative memories that use a new kind of neural networks based in the algebra system known as semi-ring. The operations performed in this algebraic system are highly nonlinear providing additional strength when compared to other transformations. Morphological associative memories are a new kind of neural networks that provide a robust performance with noisy inputs. Two representations of morphological associative memories are used called M and W matrices. M associative memory provides a robust association with input patterns corrupted by dilative random noise, while the W associative matrix performs a robust recognition in patterns corrupted with erosive random noise. The robust performance of MAM is used in combination of the Fourier descriptors for the recognition of underground objects in Ground Penetrating Radar (GPR) images. Multiple 2-D GPR images of a site are made available by NASA-SSC center. The buried objects in these images appear in the form of hyperbolas which are the results of radar backscatter from the artifacts or objects. The Fourier descriptors of the prototype hyperbola-like and shapes from non-hyperbola shapes in the sub-surface images are used to make these shapes scale-, shift-, and rotation-invariant. Typical hyperbola-like and non-hyperbola shapes are used to calculate the morphological associative memories. The trained MAMs are used to process other noisy images to detect the presence of these underground objects. The outputs from the MAM using the noisy patterns may be equal to the training prototypes, providing a positive identification of the artifacts. The results are images with recognized hyperbolas which indicate the presence of buried artifacts. A model using MATLAB has been developed and results are presented.

Geometrical eigen-subspace framework based molecular conformation representation for efficient structure recognition and comparison

NASA Astrophysics Data System (ADS)

Li, Xiao-Tian; Yang, Xiao-Bao; Zhao, Yu-Jun

2017-04-01

We have developed an extended distance matrix approach to study the molecular geometric configuration through spectral decomposition. It is shown that the positions of all atoms in the eigen-space can be specified precisely by their eigen-coordinates, while the refined atomic eigen-subspace projection array adopted in our approach is demonstrated to be a competent invariant in structure comparison. Furthermore, a visual eigen-subspace projection function (EPF) is derived to characterize the surrounding configuration of an atom naturally. A complete set of atomic EPFs constitute an intrinsic representation of molecular conformation, based on which the interatomic EPF distance and intermolecular EPF distance can be reasonably defined. Exemplified with a few cases, the intermolecular EPF distance shows exceptional rationality and efficiency in structure recognition and comparison.

Robust wafer identification recognition based on asterisk-shape filter and high-low score comparison method.

PubMed

Hsu, Wei-Chih; Yu, Tsan-Ying; Chen, Kuan-Liang

2009-12-10

Wafer identifications (wafer ID) can be used to identify wafers from each other so that wafer processing can be traced easily. Wafer ID recognition is one of the problems of optical character recognition. The process to recognize wafer IDs is similar to that used in recognizing car license-plate characters. However, due to some unique characteristics, such as the irregular space between two characters and the unsuccessive strokes of wafer ID, it will not get a good result to recognize wafer ID by directly utilizing the approaches used in car license-plate character recognition. Wafer ID scratches are engraved by a laser scribe almost along the following four fixed directions: horizontal, vertical, plus 45 degrees , and minus 45 degrees orientations. The closer to the center line of a wafer ID scratch, the higher the gray level will be. These and other characteristics increase the difficulty to recognize the wafer ID. In this paper a wafer ID recognition scheme based on an asterisk-shape filter and a high-low score comparison method is proposed to cope with the serious influence of uneven luminance and make recognition more efficiently. Our proposed approach consists of some processing stages. Especially in the final recognition stage, a template-matching method combined with stroke analysis is used as a recognizing scheme. This is because wafer IDs are composed of Semiconductor Equipment and Materials International (SEMI) standard Arabic numbers and English alphabets, and thus the template ID images are easy to obtain. Furthermore, compared with the approach that requires prior training, such as a support vector machine, which often needs a large amount of training image samples, no prior training is required for our approach. The testing results show that our proposed scheme can efficiently and correctly segment out and recognize the wafer ID with high performance.

Basic perceptual changes that alter meaning and neural correlates of recognition memory

PubMed Central

Gao, Chuanji; Hermiller, Molly S.; Voss, Joel L.; Guo, Chunyan

2015-01-01

It is difficult to pinpoint the border between perceptual and conceptual processing, despite their treatment as distinct entities in many studies of recognition memory. For instance, alteration of simple perceptual characteristics of a stimulus can radically change meaning, such as the color of bread changing from white to green. We sought to better understand the role of perceptual and conceptual processing in memory by identifying the effects of changing a basic perceptual feature (color) on behavioral and neural correlates of memory in circumstances when this change would be expected to either change the meaning of a stimulus or to have no effect on meaning (i.e., to influence conceptual processing or not). Abstract visual shapes (“squiggles”) were colorized during study and presented during test in either the same color or a different color. Those squiggles that subjects found to resemble meaningful objects supported behavioral measures of conceptual priming, whereas meaningless squiggles did not. Further, changing color from study to test had a selective effect on behavioral correlates of priming for meaningful squiggles, indicating that color change altered conceptual processing. During a recognition memory test, color change altered event-related brain potential (ERP) correlates of memory for meaningful squiggles but not for meaningless squiggles. Specifically, color change reduced the amplitude of frontally distributed N400 potentials (FN400), implying that these potentials indicated conceptual processing during recognition memory that was sensitive to color change. In contrast, color change had no effect on FN400 correlates of recognition for meaningless squiggles, which were overall smaller in amplitude than for meaningful squiggles (further indicating that these potentials signal conceptual processing during recognition). Thus, merely changing the color of abstract visual shapes can alter their meaning, changing behavioral and neural correlates of memory. These findings are relevant to understanding similarities and distinctions between perceptual and conceptual processing as well as the functional interpretation of neural correlates of recognition memory. PMID:25717298

Characterization of two porcine macrophage cell lines for the expression of pathogen-recognition receptors, defensins, cytokines, chemokines, and surface sialic acid

USDA-ARS?s Scientific Manuscript database

Macrophages express various pathogen-recognition receptors (PRRs) which recognize pathogen-associated molecular patterns (PAMPs) and activate genes responsible for host defense. The aim of this study was to characterize two porcine macrophage cell lines (Cdelta+ and Cdelta–) for the expression of P...

Molecular recognition of halogen-tagged aromatic VOCs at the air-silicon interface.

PubMed

Condorelli, Guglielmo G; Motta, Alessandro; Favazza, Maria; Gurrieri, Ettore; Betti, Paolo; Dalcanale, Enrico

2010-01-14

Selective and reversible complexation of halogen-tagged aromatic VOCs by a quinoxaline cavitand-decorated Si surface is demonstrated. The specific host-guest interactions of the Si-bonded receptors are proved to be responsible of the surface recognition properties, while extracavity non specific adsorptions are totally suppressed compared to the bulk material.

Molecular self-recognition: a chiral [Mn(II)6] wheel via donor-acceptor π···π contacts and H-bonds.

PubMed

Barrios, L A; Salinas-Uber, J; Roubeau, O; Teat, S J; Aromí, G

2015-03-18

A multinucleating ligand capable of establishing different types of intermolecular interactions, when combined with acetate groups leads to the assembly of a chiral [Mn(II)3] cluster poised for a process of self-recognition through a combination of perfectly complementary weak forces.

Molecular recognition principles and stationary-phase characteristics of topoisomer-selective chemoaffinity materials for chromatographic separation of circular plasmid DNA topoisomers.

PubMed

Mahut, Marek; Lindner, Wolfgang; Lämmerhofer, Michael

2012-01-18

We recently discovered the molecular recognition capability of a quinine carbamate ligand attached to silica as a powerful chemoaffinity material for the chromatographic separation of circular plasmid topoisomers of different linking numbers. In this paper we develop structure-selectivity relationship studies to figure out the essential structural features for topoisomer recognition. By varying different moieties of the original cinchonan-derived selector, it was shown that intercalation by the quinoline moiety of the ligand as assumed initially as the working hypothesis is not an essential feature for topoisomer recognition during chromatography. We found that the key elements for topoisomer selectivity are the presence of a rigid weak anion-exchange site and a H-donor site separated from each other in a defined distance by a 4-atom spacer. Additionally, incorporation of the weak anion-exchange site into a cyclic ring structure provides greater rigidity of the ligand molecule and turned out to be advantageous, if not mandatory, for (close to) baseline separation. © 2011 American Chemical Society

Method for traffic-sign detection within a picture by color identification and external shape recognition

NASA Astrophysics Data System (ADS)

Falcoff, Daniel E.; Canali, Luis R.

1999-08-01

This work present one method aimed to individualization and recognition of vial signs in route and city. It is based fundamentally on the identification by means of color and form of the vial sing, located in the border of the route or street in city, and then recognition. To do so the obtained RGB image is processed, carrying out diverse filtrates in the sequence of input image, or intensifying the colors of the same ones otherwise, recognizing their silhouette and then segmenting the sign and comparing the symbology of them with the previously stored and classified database.

Contrasted evolutionary histories of two Toll-like receptors (Tlr4 and Tlr7) in wild rodents (MURINAE)

PubMed Central

2013-01-01

Background In vertebrates, it has been repeatedly demonstrated that genes encoding proteins involved in pathogen-recognition by adaptive immunity (e.g. MHC) are subject to intensive diversifying selection. On the other hand, the role and the type of selection processes shaping the evolution of innate-immunity genes are currently far less clear. In this study we analysed the natural variation and the evolutionary processes acting on two genes involved in the innate-immunity recognition of Microbe-Associated Molecular Patterns (MAMPs). Results We sequenced genes encoding Toll-like receptor 4 (Tlr4) and 7 (Tlr7), two of the key bacterial- and viral-sensing receptors of innate immunity, across 23 species within the subfamily Murinae. Although we have shown that the phylogeny of both Tlr genes is largely congruent with the phylogeny of rodents based on a comparably sized non-immune sequence dataset, we also identified several potentially important discrepancies. The sequence analyses revealed that major parts of both Tlrs are evolving under strong purifying selection, likely due to functional constraints. Yet, also several signatures of positive selection have been found in both genes, with more intense signal in the bacterial-sensing Tlr4 than in the viral-sensing Tlr7. 92% and 100% of sites evolving under positive selection in Tlr4 and Tlr7, respectively, were located in the extracellular domain. Directly in the Ligand-Binding Region (LBR) of TLR4 we identified two rapidly evolving amino acid residues and one site under positive selection, all three likely involved in species-specific recognition of lipopolysaccharide of gram-negative bacteria. In contrast, all putative sites of LBRTLR7 involved in the detection of viral nucleic acids were highly conserved across rodents. Interspecific differences in the predicted 3D-structure of the LBR of both Tlrs were not related to phylogenetic history, while analyses of protein charges clearly discriminated Rattini and Murini clades. Conclusions In consequence of the constraints given by the receptor protein function purifying selection has been a dominant force in evolution of Tlrs. Nevertheless, our results show that episodic diversifying parasite-mediated selection has shaped the present species-specific variability in rodent Tlrs. The intensity of diversifying selection was higher in Tlr4 than in Tlr7, presumably due to structural properties of their ligands. PMID:24028551

Spline curve matching with sparse knot sets: applications to deformable shape detection and recognition

Treesearch

Sang-Mook Lee; A. Lynn Abbott; Neil A. Clark; Philip A. Araman

2003-01-01

Splines can be used to approximate noisy data with a few control points. This paper presents a new curve matching method for deformable shapes using two-dimensional splines. In contrast to the residual error criterion, which is based on relative locations of corresponding knot points such that is reliable primarily for dense point sets, we use deformation energy of...

Dielectric properties of crystalline organic molecular films in the limit of zero overlap

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

D’Avino, Gabriele, E-mail: gabriele.davino@gmail.com; Vanzo, Davide; Soos, Zoltán G., E-mail: soos@princeton.edu

2016-01-21

We present the calculation of the static dielectric susceptibility tensor and dipole field sums in thin molecular films in the well-defined limit of zero intermolecular overlap. Microelectrostatic and charge redistribution approaches are applied to study the evolution of dielectric properties from one to a few molecular layers in films of different conjugated molecules with organic electronics applications. Because of the conditional convergence of dipolar interactions, dipole fields depend on the shape of the sample and different values are found in the middle layer of a thick film and in the bulk. The shape dependence is eliminated when depolarization is takenmore » into account, and the dielectric tensor of molecular films converges to the bulk limit within a few molecular layers. We quantify the magnitude of surface effects and interpret general trends among different systems in terms of molecular properties, such as shape, polarizability anisotropy, and supramolecular organization. A connection between atomistic models for molecular dielectrics and simpler theories for polarizable atomic lattices is also provided.« less

Prediction of quantum interference in molecular junctions using a parabolic diagram: Understanding the origin of Fano and anti- resonances

NASA Astrophysics Data System (ADS)

Nozaki, Daijiro; Avdoshenko, Stanislav M.; Sevinçli, Hâldun; Gutierrez, Rafael; Cuniberti, Gianaurelio

2013-03-01

Recently the interest in quantum interference (QI) phenomena in molecular devices (molecular junctions) has been growing due to the unique features observed in the transmission spectra. In order to design single molecular devices exploiting QI effects as desired, it is necessary to provide simple rules for predicting the appearance of QI effects such as anti-resonances or Fano line shapes and for controlling them. In this study, we derive a transmission function of a generic molecular junction with a side group (T-shaped molecular junction) using a minimal toy model. We developed a simple method to predict the appearance of quantum interference, Fano resonances or anti- resonances, and its position in the conductance spectrum by introducing a simple graphical representation (parabolic model). Using it we can easily visualize the relation between the key electronic parameters and the positions of normal resonant peaks and anti-resonant peaks induced by quantum interference in the conductance spectrum. We also demonstrate Fano and anti-resonance in T-shaped molecular junctions using a simple tight-binding model. This parabolic model enables one to infer on-site energies of T-shaped molecules and the coupling between side group and main conduction channel from transmission spectra.

Exploring the molecular basis of RNA recognition by the dimeric RNA-binding protein via molecular simulation methods.

PubMed

Chang, Shan; Zhang, Da-Wei; Xu, Lei; Wan, Hua; Hou, Ting-Jun; Kong, Ren

2016-11-01

RNA-binding protein with multiple splicing (RBPMS) is critical for axon guidance, smooth muscle plasticity, and regulation of cancer cell proliferation and migration. Recently, different states of the RNA-recognition motif (RRM) of RBPMS, one in its free form and another in complex with CAC-containing RNA, were determined by X-ray crystallography. In this article, the free RRM domain, its wild type complex and 2 mutant complex systems are studied by molecular dynamics (MD) simulations. Through comparison of free RRM domain and complex systems, it's found that the RNA binding facilitates stabilizing the RNA-binding interface of RRM domain, especially the C-terminal loop. Although both R38Q and T103A/K104A mutations reduce the binding affinity of RRM domain and RNA, the underlining mechanisms are different. Principal component analysis (PCA) and Molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) methods were used to explore the dynamical and recognition mechanisms of RRM domain and RNA. R38Q mutation is positioned on the homodimerization interface and mainly induces the large fluctuations of RRM domains. This mutation does not directly act on the RNA-binding interface, but some interfacial hydrogen bonds are weakened. In contrast, T103A/K104A mutations are located on the RNA-binding interface of RRM domain. These mutations obviously break most of high occupancy hydrogen bonds in the RNA-binding interface. Meanwhile, the key interfacial residues lose their favorable energy contributions upon RNA binding. The ranking of calculated binding energies in 3 complex systems is well consistent with that of experimental binding affinities. These results will be helpful in understanding the RNA recognition mechanisms of RRM domain.

Molecular evolution of the CYP2D subfamily in primates: purifying selection on substrate recognition sites without the frequent or long-tract gene conversion.

PubMed

Yasukochi, Yoshiki; Satta, Yoko

2015-03-25

The human cytochrome P450 (CYP) 2D6 gene is a member of the CYP2D gene subfamily, along with the CYP2D7P and CYP2D8P pseudogenes. Although the CYP2D6 enzyme has been studied extensively because of its clinical importance, the evolution of the CYP2D subfamily has not yet been fully understood. Therefore, the goal of this study was to reveal the evolutionary process of the human drug metabolic system. Here, we investigate molecular evolution of the CYP2D subfamily in primates by comparing 14 CYP2D sequences from humans to New World monkey genomes. Window analysis and statistical tests revealed that entire genomic sequences of paralogous genes were extensively homogenized by gene conversion during molecular evolution of CYP2D genes in primates. A neighbor-joining tree based on genomic sequences at the nonsubstrate recognition sites showed that CYP2D6 and CYP2D8 genes were clustered together due to gene conversion. In contrast, a phylogenetic tree using amino acid sequences at substrate recognition sites did not cluster the CYP2D6 and CYP2D8 genes, suggesting that the functional constraint on substrate specificity is one of the causes for purifying selection at the substrate recognition sites. Our results suggest that the CYP2D gene subfamily in primates has evolved to maintain the regioselectivity for a substrate hydroxylation activity between individual enzymes, even though extensive gene conversion has occurred across CYP2D coding sequences. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Exploring the molecular basis of RNA recognition by the dimeric RNA-binding protein via molecular simulation methods

PubMed Central

Chang, Shan; Zhang, Da-Wei; Xu, Lei; Wan, Hua; Hou, Ting-Jun; Kong, Ren

2016-01-01

ABSTRACT RNA-binding protein with multiple splicing (RBPMS) is critical for axon guidance, smooth muscle plasticity, and regulation of cancer cell proliferation and migration. Recently, different states of the RNA-recognition motif (RRM) of RBPMS, one in its free form and another in complex with CAC-containing RNA, were determined by X-ray crystallography. In this article, the free RRM domain, its wild type complex and 2 mutant complex systems are studied by molecular dynamics (MD) simulations. Through comparison of free RRM domain and complex systems, it's found that the RNA binding facilitates stabilizing the RNA-binding interface of RRM domain, especially the C-terminal loop. Although both R38Q and T103A/K104A mutations reduce the binding affinity of RRM domain and RNA, the underlining mechanisms are different. Principal component analysis (PCA) and Molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) methods were used to explore the dynamical and recognition mechanisms of RRM domain and RNA. R38Q mutation is positioned on the homodimerization interface and mainly induces the large fluctuations of RRM domains. This mutation does not directly act on the RNA-binding interface, but some interfacial hydrogen bonds are weakened. In contrast, T103A/K104A mutations are located on the RNA-binding interface of RRM domain. These mutations obviously break most of high occupancy hydrogen bonds in the RNA-binding interface. Meanwhile, the key interfacial residues lose their favorable energy contributions upon RNA binding. The ranking of calculated binding energies in 3 complex systems is well consistent with that of experimental binding affinities. These results will be helpful in understanding the RNA recognition mechanisms of RRM domain. PMID:27592836

Molecular recognition of a model globular protein apomyoglobin by synthetic receptor cyclodextrin: effect of fluorescence modification of the protein and cavity size of the receptor in the interaction.

PubMed

Saha, Ranajay; Rakshit, Surajit; Pal, Samir Kumar

2013-11-01

Labelling of proteins with some extrinsic probe is unavoidable in molecular biology research. Particularly, spectroscopic studies in the optical region require fluorescence modification of native proteins by attaching polycyclic aromatic fluoroprobe with the proteins under investigation. Our present study aims to address the consequence of the attachment of a fluoroprobe at the protein surface in the molecular recognition of the protein by selectively small model receptor. A spectroscopic study involving apomyoglobin (Apo-Mb) and cyclodextrin (CyD) of various cavity sizes as model globular protein and synthetic receptors, respectively, using steady-state and picosecond-resolved techniques, is detailed here. A study involving Förster resonance energy transfer, between intrinsic amino acid tryptophan (donor) and N, N-dimethyl naphthalene moiety of the extrinsic dansyl probes at the surface of Apo-Mb, precisely monitor changes in donor acceptor distance as a consequence of interaction of the protein with CyD having different cavity sizes (β and γ variety). Molecular modelling studies on the interaction of tryptophan and dansyl probe with β-CyD is reported here and found to be consistent with the experimental observations. In order to investigate structural aspects of the interacting protein, we have used circular dichroism spectroscopy. Temperature-dependent circular dichroism studies explore the change in the secondary structure of Apo-Mb in association with CyD, before and after fluorescence modification of the protein. Overall, the study well exemplifies approaches to protein recognition by CyD as a synthetic receptor and offers a cautionary note on the use of hydrophobic fluorescent labels for proteins in biochemical studies involving recognition of molecules. Copyright © 2013 John Wiley & Sons, Ltd.

Selective Nitrate Recognition by a Halogen‐Bonding Four‐Station [3]Rotaxane Molecular Shuttle

PubMed Central

Barendt, Timothy A.; Docker, Andrew; Marques, Igor; Félix, Vítor

2016-01-01

Abstract The synthesis of the first halogen bonding [3]rotaxane host system containing a bis‐iodo triazolium‐bis‐naphthalene diimide four station axle component is reported. Proton NMR anion binding titration experiments revealed the halogen bonding rotaxane is selective for nitrate over the more basic acetate, hydrogen carbonate and dihydrogen phosphate oxoanions and chloride, and exhibits enhanced recognition of anions relative to a hydrogen bonding analogue. This elaborate interlocked anion receptor functions via a novel dynamic pincer mechanism where upon nitrate anion binding, both macrocycles shuttle from the naphthalene diimide stations at the periphery of the axle to the central halogen bonding iodo‐triazolium station anion recognition sites to form a unique 1:1 stoichiometric nitrate anion–rotaxane sandwich complex. Molecular dynamics simulations carried out on the nitrate and chloride halogen bonding [3]rotaxane complexes corroborate the 1H NMR anion binding results. PMID:27436297

A molecular mechanism of chaperone-client recognition

PubMed Central

He, Lichun; Sharpe, Timothy; Mazur, Adam; Hiller, Sebastian

2016-01-01

Molecular chaperones are essential in aiding client proteins to fold into their native structure and in maintaining cellular protein homeostasis. However, mechanistic aspects of chaperone function are still not well understood at the atomic level. We use nuclear magnetic resonance spectroscopy to elucidate the mechanism underlying client recognition by the adenosine triphosphate-independent chaperone Spy at the atomic level and derive a structural model for the chaperone-client complex. Spy interacts with its partially folded client Im7 by selective recognition of flexible, locally frustrated regions in a dynamic fashion. The interaction with Spy destabilizes a partially folded client but spatially compacts an unfolded client conformational ensemble. By increasing client backbone dynamics, the chaperone facilitates the search for the native structure. A comparison of the interaction of Im7 with two other chaperones suggests that the underlying principle of recognizing frustrated segments is of a fundamental nature. PMID:28138538

Protein-targeted corona phase molecular recognition

PubMed Central

Bisker, Gili; Dong, Juyao; Park, Hoyoung D.; Iverson, Nicole M.; Ahn, Jiyoung; Nelson, Justin T.; Landry, Markita P.; Kruss, Sebastian; Strano, Michael S.

2016-01-01

Corona phase molecular recognition (CoPhMoRe) uses a heteropolymer adsorbed onto and templated by a nanoparticle surface to recognize a specific target analyte. This method has not yet been extended to macromolecular analytes, including proteins. Herein we develop a variant of a CoPhMoRe screening procedure of single-walled carbon nanotubes (SWCNT) and use it against a panel of human blood proteins, revealing a specific corona phase that recognizes fibrinogen with high selectivity. In response to fibrinogen binding, SWCNT fluorescence decreases by >80% at saturation. Sequential binding of the three fibrinogen nodules is suggested by selective fluorescence quenching by isolated sub-domains and validated by the quenching kinetics. The fibrinogen recognition also occurs in serum environment, at the clinically relevant fibrinogen concentrations in the human blood. These results open new avenues for synthetic, non-biological antibody analogues that recognize biological macromolecules, and hold great promise for medical and clinical applications. PMID:26742890

Dynamic nanoplatforms in biosensor and membrane constitutional systems.

PubMed

Mahon, Eugene; Aastrup, Teodor; Barboiu, Mihail

2012-01-01

Molecular recognition in biological systems occurs mainly at interfacial environments such as membrane surfaces, enzyme active sites, or the interior of the DNA double helix. At the cell membrane surface, carbohydrate-protein recognition principles apply to a range of specific non-covalent interactions including immune response, cell proliferation, adhesion and death, cell-cell interaction and communication. Protein-protein recognition meanwhile accounts for signalling processes and ion channel structure. In this chapter we aim to describe such constitutional dynamic interfaces for biosensing and membrane transport applications. Constitutionally adaptive interfaces may mimic the recognition capabilities intrinsic to natural recognition processes. We present some recent examples of 2D and 3D constructed sensors and membranes of this type and describe their sensing and transport capabilities.

Structural basis of recognition of pathogen-associated molecular patterns and inhibition of proinflammatory cytokines by camel peptidoglycan recognition protein.

PubMed

Sharma, Pradeep; Dube, Divya; Singh, Amar; Mishra, Biswajit; Singh, Nagendra; Sinha, Mau; Dey, Sharmistha; Kaur, Punit; Mitra, Dipendra K; Sharma, Sujata; Singh, Tej P

2011-05-06

Peptidoglycan recognition proteins (PGRPs) are involved in the recognition of pathogen-associated molecular patterns. The well known pathogen-associated molecular patterns include LPS from Gram-negative bacteria and lipoteichoic acid (LTA) from Gram-positive bacteria. In this work, the crystal structures of two complexes of the short form of camel PGRP (CPGRP-S) with LPS and LTA determined at 1.7- and 2.1-Å resolutions, respectively, are reported. Both compounds were held firmly inside the complex formed with four CPGRP-S molecules designated A, B, C, and D. The binding cleft is located at the interface of molecules C and D, which is extendable to the interface of molecules A and C. The interface of molecules A and B is tightly packed, whereas that of molecules B and D forms a wide channel. The hydrophilic moieties of these compounds occupy a common region, whereas hydrophobic chains interact with distinct regions in the binding site. The binding studies showed that CPGRP-S binds to LPS and LTA with affinities of 1.6 × 10(-9) and 2.4 × 10(-8) M, respectively. The flow cytometric studies showed that both LPS- and LTA-induced expression of the proinflammatory cytokines TNF-α and IL-6 was inhibited by CPGRP-S. The results of animal studies using mouse models indicated that both LPS- and LTA-induced mortality rates decreased drastically when CPGRP-S was administered. The recognition of both LPS and LTA, their high binding affinities for CPGRP-S, the significant decrease in the production of LPS- and LTA-induced TNF-α and IL-6, and the drastic reduction in the mortality rates in mice by CPGRP-S indicate its useful properties as an antibiotic agent.

Interdependence of Inhibitor Recognition in HIV-1 Protease

PubMed Central

2017-01-01

Molecular recognition is a highly interdependent process. Subsite couplings within the active site of proteases are most often revealed through conditional amino acid preferences in substrate recognition. However, the potential effect of these couplings on inhibition and thus inhibitor design is largely unexplored. The present study examines the interdependency of subsites in HIV-1 protease using a focused library of protease inhibitors, to aid in future inhibitor design. Previously a series of darunavir (DRV) analogs was designed to systematically probe the S1′ and S2′ subsites. Co-crystal structures of these analogs with HIV-1 protease provide the ideal opportunity to probe subsite interdependency. All-atom molecular dynamics simulations starting from these structures were performed and systematically analyzed in terms of atomic fluctuations, intermolecular interactions, and water structure. These analyses reveal that the S1′ subsite highly influences other subsites: the extension of the hydrophobic P1′ moiety results in 1) reduced van der Waals contacts in the P2′ subsite, 2) more variability in the hydrogen bond frequencies with catalytic residues and the flap water, and 3) changes in the occupancy of conserved water sites both proximal and distal to the active site. In addition, one of the monomers in this homodimeric enzyme has atomic fluctuations more highly correlated with DRV than the other monomer. These relationships intricately link the HIV-1 protease subsites and are critical to understanding molecular recognition and inhibitor binding. More broadly, the interdependency of subsite recognition within an active site requires consideration in the selection of chemical moieties in drug design; this strategy is in contrast to what is traditionally done with independent optimization of chemical moieties of an inhibitor. PMID:28358514

Interdependence of Inhibitor Recognition in HIV-1 Protease.

PubMed

Paulsen, Janet L; Leidner, Florian; Ragland, Debra A; Kurt Yilmaz, Nese; Schiffer, Celia A

2017-05-09

Molecular recognition is a highly interdependent process. Subsite couplings within the active site of proteases are most often revealed through conditional amino acid preferences in substrate recognition. However, the potential effect of these couplings on inhibition and thus inhibitor design is largely unexplored. The present study examines the interdependency of subsites in HIV-1 protease using a focused library of protease inhibitors, to aid in future inhibitor design. Previously a series of darunavir (DRV) analogs was designed to systematically probe the S1' and S2' subsites. Co-crystal structures of these analogs with HIV-1 protease provide the ideal opportunity to probe subsite interdependency. All-atom molecular dynamics simulations starting from these structures were performed and systematically analyzed in terms of atomic fluctuations, intermolecular interactions, and water structure. These analyses reveal that the S1' subsite highly influences other subsites: the extension of the hydrophobic P1' moiety results in 1) reduced van der Waals contacts in the P2' subsite, 2) more variability in the hydrogen bond frequencies with catalytic residues and the flap water, and 3) changes in the occupancy of conserved water sites both proximal and distal to the active site. In addition, one of the monomers in this homodimeric enzyme has atomic fluctuations more highly correlated with DRV than the other monomer. These relationships intricately link the HIV-1 protease subsites and are critical to understanding molecular recognition and inhibitor binding. More broadly, the interdependency of subsite recognition within an active site requires consideration in the selection of chemical moieties in drug design; this strategy is in contrast to what is traditionally done with independent optimization of chemical moieties of an inhibitor.

Automatic Recognition of Road Signs

NASA Astrophysics Data System (ADS)

Inoue, Yasuo; Kohashi, Yuuichirou; Ishikawa, Naoto; Nakajima, Masato

2002-11-01

The increase in traffic accidents is becoming a serious social problem with the recent rapid traffic increase. In many cases, the driver"s carelessness is the primary factor of traffic accidents, and the driver assistance system is demanded for supporting driver"s safety. In this research, we propose the new method of automatic detection and recognition of road signs by image processing. The purpose of this research is to prevent accidents caused by driver"s carelessness, and call attention to a driver when the driver violates traffic a regulation. In this research, high accuracy and the efficient sign detecting method are realized by removing unnecessary information except for a road sign from an image, and detect a road sign using shape features. At first, the color information that is not used in road signs is removed from an image. Next, edges except for circular and triangle ones are removed to choose sign shape. In the recognition process, normalized cross correlation operation is carried out to the two-dimensional differentiation pattern of a sign, and the accurate and efficient method for detecting the road sign is realized. Moreover, the real-time operation in a software base was realized by holding down calculation cost, maintaining highly precise sign detection and recognition. Specifically, it becomes specifically possible to process by 0.1 sec(s)/frame using a general-purpose PC (CPU: Pentium4 1.7GHz). As a result of in-vehicle experimentation, our system could process on real time and has confirmed that detection and recognition of a sign could be performed correctly.

Mapping a protein recognition centre with chiral photoactive ligands. An integrated approach combining photophysics, reactivity, proteomics and molecular dynamics simulation studies.

PubMed

Limones-Herrero, Daniel; Pérez-Ruiz, Raúl; Lence, Emilio; González-Bello, Concepción; Miranda, Miguel A; Jiménez, M Consuelo

2017-04-01

A multidisciplinary strategy to obtain structural information on the intraprotein region is described here. As probe ligands, ( S )- and ( R )- CPFMe (the methyl esters of the chiral drug carprofen) have been selected, while bovine α 1 -acid glycoprotein (BAAG) has been chosen as a biological host. The procedure involves the separate irradiation of the BAAG/( S )- CPFMe and BAAG/( R )- CPFMe complexes, coupled with fluorescence spectroscopy, laser flash photolysis, proteomic analysis, docking and molecular dynamics simulations. Thus, irradiation of the BAAG/ CPFMe complexes at λ = 320 nm was followed by fluorescence spectroscopy. The intensity of the emission band obtained after irradiation indicated photodehalogenation, whereas its structureless shape suggested covalent binding of the resulting radical CBZMe˙ to the biopolymer. After gel filtration chromatography, the spectra still displayed emission, in agreement with covalent attachment of CBZMe˙ to BAAG. Stereodifferentiation was observed in this process. After trypsin digestion and ESI-MS/MS, the incorporation of CBZMe was detected at Phe68. Docking and molecular dynamics simulation studies, which were carried out using a homology model of BAAG, reveal that the closer proximity of the aromatic moiety of the ( S )-enantiomer to the phenyl group of Phe68 would be responsible for the experimentally observed, more effective chemical modification of the protein. The proposed tridimensional structure of BAAG covalently modified by the two enantiomers is also provided. In principle, this approach can be extended to a variety of protein/ligand complexes.

Can You See Me Now Visualizing Battlefield Facial Recognition Technology in 2035

DTIC Science & Technology

2010-04-01

County Sheriff’s Department, use certain measurements such as the distance between eyes, the length of the nose, or the shape of the ears. 8 However...captures multiple frames of video and composites them into an appropriately high-resolution image that can be processed by the facial recognition software...stream of data. High resolution video systems, such as those described below will be able to capture orders of magnitude more data in one video frame

Clustering of Farsi sub-word images for whole-book recognition

NASA Astrophysics Data System (ADS)

Soheili, Mohammad Reza; Kabir, Ehsanollah; Stricker, Didier

2015-01-01

Redundancy of word and sub-word occurrences in large documents can be effectively utilized in an OCR system to improve recognition results. Most OCR systems employ language modeling techniques as a post-processing step; however these techniques do not use important pictorial information that exist in the text image. In case of large-scale recognition of degraded documents, this information is even more valuable. In our previous work, we proposed a subword image clustering method for the applications dealing with large printed documents. In our clustering method, the ideal case is when all equivalent sub-word images lie in one cluster. To overcome the issues of low print quality, the clustering method uses an image matching algorithm for measuring the distance between two sub-word images. The measured distance with a set of simple shape features were used to cluster all sub-word images. In this paper, we analyze the effects of adding more shape features on processing time, purity of clustering, and the final recognition rate. Previously published experiments have shown the efficiency of our method on a book. Here we present extended experimental results and evaluate our method on another book with totally different font face. Also we show that the number of the new created clusters in a page can be used as a criteria for assessing the quality of print and evaluating preprocessing phases.

Road Signs Detection and Recognition Utilizing Images and 3d Point Cloud Acquired by Mobile Mapping System

NASA Astrophysics Data System (ADS)

Li, Y. H.; Shinohara, T.; Satoh, T.; Tachibana, K.

2016-06-01

High-definition and highly accurate road maps are necessary for the realization of automated driving, and road signs are among the most important element in the road map. Therefore, a technique is necessary which can acquire information about all kinds of road signs automatically and efficiently. Due to the continuous technical advancement of Mobile Mapping System (MMS), it has become possible to acquire large number of images and 3d point cloud efficiently with highly precise position information. In this paper, we present an automatic road sign detection and recognition approach utilizing both images and 3D point cloud acquired by MMS. The proposed approach consists of three stages: 1) detection of road signs from images based on their color and shape features using object based image analysis method, 2) filtering out of over detected candidates utilizing size and position information estimated from 3D point cloud, region of candidates and camera information, and 3) road sign recognition using template matching method after shape normalization. The effectiveness of proposed approach was evaluated by testing dataset, acquired from more than 180 km of different types of roads in Japan. The results show a very high success in detection and recognition of road signs, even under the challenging conditions such as discoloration, deformation and in spite of partial occlusions.