Academic literature on the topic 'FEATURE ENCODING'
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Journal articles on the topic "FEATURE ENCODING"
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Lathroum, Amanda. "Feature encoding by neural nets." Phonology 6, no. 2 (August 1989): 305–16. http://dx.doi.org/10.1017/s0952675700001044.
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While the use of categorical features seems to be the appropriate way to express sound patterns within languages, these features do not seem adequate to describe the sounds actually produced by speakers. Examination of the speech signal fails to reveal objective, discrete phonological segments. Similarly, segments are not directly observable in the flow of articulatory movements, and vary slightly according to an individual speaker's articulatory strategies. Because of the lack of a reliable relationship between segments and speech sounds, a plausible transition from feature representation to the actual acoustic signal has proven elusive. This paper utilises a theory of information processing, known as PARALLEL DISTRIBUTED PROCESSING (PDP) NETWORKS (also called neural networks), to propose a model which begins to express this transition: translating the feature bundles indicated in a broad phonetic transcription into continuous, potentially variable articulator behaviour.
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Jaswal, Snehlata, and Robert H. Logie. "Configural encoding in visual feature binding." Journal of Cognitive Psychology 23, no. 5 (August 2011): 586–603. http://dx.doi.org/10.1080/20445911.2011.570256.
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Wu, Pengxiang, Chao Chen, Jingru Yi, and Dimitris Metaxas. "Point Cloud Processing via Recurrent Set Encoding." Proceedings of the AAAI Conference on Artificial Intelligence 33 (July 17, 2019): 5441–49. http://dx.doi.org/10.1609/aaai.v33i01.33015441.
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We present a new permutation-invariant network for 3D point cloud processing. Our network is composed of a recurrent set encoder and a convolutional feature aggregator. Given an unordered point set, the encoder firstly partitions its ambient space into parallel beams. Points within each beam are then modeled as a sequence and encoded into subregional geometric features by a shared recurrent neural network (RNN). The spatial layout of the beams is regular, and this allows the beam features to be further fed into an efficient 2D convolutional neural network (CNN) for hierarchical feature aggregation. Our network is effective at spatial feature learning, and competes favorably with the state-of-the-arts (SOTAs) on a number of benchmarks. Meanwhile, it is significantly more efficient compared to the SOTAs.
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Eurich, Christian W., and Stefan D. Wilke. "Multidimensional Encoding Strategy of Spiking Neurons." Neural Computation 12, no. 7 (July 1, 2000): 1519–29. http://dx.doi.org/10.1162/089976600300015240.
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Neural responses in sensory systems are typically triggered by a multitude of stimulus features. Using information theory, we study the encoding accuracy of a population of stochastically spiking neurons characterized by different tuning widths for the different features. The optimal encoding strategy for representing one feature most accurately consists of narrow tuning in the dimension to be encoded, to increase the single-neuron Fisher information, and broad tuning in all other dimensions, to increase the number of active neurons. Extremely narrow tuning without sufficient receptive field overlap will severely worsen the coding. This implies the existence of an optimal tuning width for the feature to be encoded. Empirically, only a subset of all stimulus features will normally be accessible. In this case, relative encoding errors can be calculated that yield a criterion for the function of a neural population based on the measured tuning curves.
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Shinomiya, Yuki, and Yukinobu Hoshino. "A Quantitative Quality Measurement for Codebook in Feature Encoding Strategies." Journal of Advanced Computational Intelligence and Intelligent Informatics 21, no. 7 (November 20, 2017): 1232–39. http://dx.doi.org/10.20965/jaciii.2017.p1232.
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Nowadays, a feature encoding strategy is a general approach to represent a document, an image or audio as a feature vector. In image recognition problems, this approach treats an image as a set of partial feature descriptors. The set is then converted to a feature vector based on basis vectors called codebook. This paper focuses on a prior probability, which is one of codebook parameters and analyzes dependency for the feature encoding. In this paper, we conducted the following two experiments, analysis of prior probabilities in state-of-the-art encodings and control of prior probabilities. The first experiment investigates the distribution of prior probabilities and compares recognition performances of recent techniques. The results suggest that recognition performance probably depends on the distribution of prior probabilities. The second experiment tries further statistical analysis by controlling the distribution of prior probabilities. The results show a strong negative linear relationship between a standard deviation of prior probabilities and recognition accuracy. From these experiments, the quality of codebook used for feature encoding can be quantitatively measured, and recognition performances can be improved by optimizing codebook. Besides, the codebook is created at an offline step. Therefore, optimizing codebook does not require any additional computational cost for practical applications.
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Ronran, Chirawan, Seungwoo Lee, and Hong Jun Jang. "Delayed Combination of Feature Embedding in Bidirectional LSTM CRF for NER." Applied Sciences 10, no. 21 (October 27, 2020): 7557. http://dx.doi.org/10.3390/app10217557.
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Named Entity Recognition (NER) plays a vital role in natural language processing (NLP). Currently, deep neural network models have achieved significant success in NER. Recent advances in NER systems have introduced various feature selections to identify appropriate representations and handle Out-Of-the-Vocabulary (OOV) words. After selecting the features, they are all concatenated at the embedding layer before being fed into a model to label the input sequences. However, when concatenating the features, information collisions may occur and this would cause the limitation or degradation of the performance. To overcome the information collisions, some works tried to directly connect some features to latter layers, which we call the delayed combination and show its effectiveness by comparing it to the early combination. As feature encodings for input, we selected the character-level Convolutional Neural Network (CNN) or Long Short-Term Memory (LSTM) word encoding, the pre-trained word embedding, and the contextual word embedding and additionally designed CNN-based sentence encoding using a dictionary. These feature encodings are combined at early or delayed position of the bidirectional LSTM Conditional Random Field (CRF) model according to each feature’s characteristics. We evaluated the performance of this model on the CoNLL 2003 and OntoNotes 5.0 datasets using the F1 score and compared the delayed combination model with our own implementation of the early combination as well as the previous works. This comparison convinces us that our delayed combination is more effective than the early one and also highly competitive.
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James, Melissa S., Stuart J. Johnstone, and William G. Hayward. "Event-Related Potentials, Configural Encoding, and Feature-Based Encoding in Face Recognition." Journal of Psychophysiology 15, no. 4 (October 2001): 275–85. http://dx.doi.org/10.1027//0269-8803.15.4.275.
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Abstract The effects of manipulating configural and feature information on the face recognition process were investigated by recording event-related potentials (ERPs) from five electrode sites (Fz, Cz, Pz, T5, T6), while 17 European subjects performed an own-race and other-race face recognition task. A series of upright faces were presented in a study phase, followed by a test phase where subjects indicated whether inverted and upright faces were studied or novel via a button press response. An inversion effect, illustrating the disruption of upright configural information, was reflected in accuracy measures and in greater lateral N2 amplitude to inverted faces, suggesting that structural encoding is harder for inverted faces. An own-race advantage was found, which may reflect the use of configural encoding for the more frequently experienced own-race faces, and feature-based encoding for the less familiar other-race faces, and was reflected in accuracy measures and ERP effects. The midline N2 was larger to configurally encoded faces (i. e., own-race and upright), possibly suggesting configural encoding involves more complex processing than feature-based encoding. An N400-like component was sensitive to feature manipulations, with greater amplitude to other-race than own-race faces and to inverted than upright faces. This effect was interpreted as reflecting increased activation of incompatible representations activated by a feature-based strategy used in processing of other-race and inverted faces. The late positive complex was sensitive to configural manipulation with larger amplitude to other-race than own-race faces, and was interpreted as reflecting the updating of an own-race norm used in face recognition, to incorporate other-race information.
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S RAO, VIBHA, and P. RAMESH NAIDU. "Periocular and Iris Feature Encoding - A Survey." International Journal of Innovative Research in Computer and Communication Engineering 03, no. 01 (January 30, 2015): 368–74. http://dx.doi.org/10.15680/ijircce.2015.0301023.
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HUO, Lu, and Leijie ZHANG. "Combined feature compression encoding in image retrieval." TURKISH JOURNAL OF ELECTRICAL ENGINEERING & COMPUTER SCIENCES 27, no. 3 (May 15, 2019): 1603–18. http://dx.doi.org/10.3906/elk-1803-3.
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Lee, Hui-Jin, Ki-Sang Hong, Henry Kang, and Seungyong Lee. "Photo Aesthetics Analysis via DCNN Feature Encoding." IEEE Transactions on Multimedia 19, no. 8 (August 2017): 1921–32. http://dx.doi.org/10.1109/tmm.2017.2687759.
Full textDissertations / Theses on the topic "FEATURE ENCODING"
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Gollnick, Clare Ann. "Probabilistic encoding and feature selectivity in the somatosensory pathway." Diss., Georgia Institute of Technology, 2014. http://hdl.handle.net/1853/54025.
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Our sensory experiences are encoded in the patterns of activity of the neurons in our brain. While we know we are capable of sensing and responding to a constantly changing sensory environment, we often study neural activity by repeatedly presenting the same stimulus and analyzing the average neural response. It is not understood how the average neural response represents the dynamic neural activity that produces our perceptions. In this work, we use functional imaging of the rodent primary somatosensory cortex, specifically the whisker representations, and apply classic signal-detection methods to test the predictive power of the average neural response. Stimulus features such as intensity are thought to be perceptually separable from the average representation; however, we show that stimulus intensity cannot be reliably decoded from neural activity from only a single experience. Instead, stimulus intensity was encoded only across many experiences. We observed this probabilistic neural code in multiple classic sensory paradigms including complex temporal stimuli (pairs of whisker deflections) and multi-whisker stimuli. These data suggest a novel framework for the encoding of stimulus features in the presence of high-neural variability. Specifically we suggest that our brains can compensate for unreliability by encoding information redundantly across cortical space. This thesis predicts that a somatosensory stimulus is not encoded identically each time it is experienced; instead, our brains use multiple redundant pathways to create a reliable sensory percept.
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Seger, Cedric. "An investigation of categorical variable encoding techniques in machine learning: binary versus one-hot and feature hashing." Thesis, KTH, Skolan för elektroteknik och datavetenskap (EECS), 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-237426.
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Machine learning methods can be used for solving important binary classification tasks in domains such as display advertising and recommender systems. In many of these domains categorical features are common and often of high cardinality. Using one-hot encoding in such circumstances lead to very high dimensional vector representations, causing memory and computability concerns for machine learning models. This thesis investigated the viability of a binary encoding scheme in which categorical values were mapped to integers that were then encoded in a binary format. This binary scheme allowed for representing categorical features using log2(d)-dimensional vectors, where d is the dimension associated with a one-hot encoding. To evaluate the performance of the binary encoding, it was compared against one-hot and feature hashed representations with the use of linear logistic regression and neural networks based models. These models were trained and evaluated using data from two publicly available datasets: Criteo and Census. The results showed that a one-hot encoding with a linear logistic regression model gave the best performance according to the PR-AUC metric. This was, however, at the expense of using 118 and 65,953 dimensional vector representations for Census and Criteo respectively. A binary encoding led to a lower performance but used only 35 and 316 dimensions respectively. For Criteo, binary encoding suffered significantly in performance and feature hashing was perceived as a more viable alternative. It was also found that employing a neural network helped mitigate any loss in performance associated with using binary and feature hashed representations.Maskininlärningsmetoder kan användas för att lösa viktiga binära klassificeringsuppgifter i domäner som displayannonsering och rekommendationssystem. I många av dessa domäner är kategoriska variabler vanliga och ofta av hög kardinalitet. Användning av one-hot-kodning under sådana omständigheter leder till väldigt högdimensionella vektorrepresentationer. Detta orsakar minnesoch beräkningsproblem för maskininlärningsmodeller. Denna uppsats undersökte användbarheten för ett binärt kodningsschema där kategoriska värden var avbildade på heltalvärden som sedan kodades i ett binärt format. Detta binära system tillät att representera kategoriska värden med hjälp av log2(d) -dimensionella vektorer, där d är dimensionen förknippad med en one-hot kodning. För att utvärdera prestandan för den binära kodningen jämfördes den mot one-hot och en hashbaserad kodning. En linjär logistikregression och ett neuralt nätverk tränades med hjälp av data från två offentligt tillgängliga dataset: Criteo och Census, och den slutliga prestandan jämfördes. Resultaten visade att en one-hot kodning med en linjär logistisk regressionsmodell gav den bästa prestandan enligt PR-AUC måttet. Denna metod använde dock 118 och 65,953 dimensionella vektorrepresentationer för Census respektive Criteo. En binär kodning ledde till en lägre prestanda generellt, men använde endast 35 respektive 316 dimensioner. Den binära kodningen presterade väsentligt sämre specifikt för Criteo datan, istället var hashbaserade kodningen en mer attraktiv lösning. Försämringen i prestationen associerad med binär och hashbaserad kodning kunde mildras av att använda ett neuralt nätverk.
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Zhang, Cuicui. "Quad-Tree based Image Encoding Methods for Data-Adaptive Visual Feature Learning." 京都大学 (Kyoto University), 2015. http://hdl.handle.net/2433/199435.
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Chambers, Anna. "Progressive Recovery of Cortical and Midbrain Sound Feature Encoding Following Profound Cochlear Neuropathy." Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:14226064.
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To enable the identification and localization of sounds in our environment, auditory brain centers must form representations that accurately encode distinct acoustic properties, but also integrate those properties to support a unified percept of an auditory object. These parallel operations of decomposition and integration are carried out by hierarchically organized processing regions which progressively reformat peripheral electrical impulses into signals that may be integrated into higher order brain circuits. To investigate the nature of these transformations and their vulnerability to hearing loss, I recorded extracellular responses in the auditory midbrain and cortex of awake mice. The first aim of this project was to study the multiparametric tuning characteristics of single neurons using an online stimulus optimization algorithm. Closed-loop stimulus tailoring rapidly revealed diverse multiparametric tuning, and further revealed the conservation of response sparseness between the two areas. I then tracked the recovery of central feature encoding in mice with profound cochlear neuropathy. I recorded from midbrain and cortex at two timepoints after nerve degeneration, observing a progressive recovery of responsiveness in both areas, which occurred earlier and was more robust in the cortex. Concurrently, several aspects of the once-precise temporal response properties in midbrain were persistently degraded, and classification of speech tokens in the cortex did not recover to control levels of accuracy. I hypothesize that compensatory central plasticity may support the recovery of feature encoding in the auditory pathway to a large extent, although various aspects of temporal encoding remain impaired. This may underlie the observation that some human patients with auditory neuropathy have profound deficits in speech comprehension despite having normal hearing thresholds. Finally, I tested the effect of AUT3, a novel positive modulator of the Kv3.1 potassium channel, on the encoding and classification of pulse trains and speech tokens in the midbrain. I observed that adjusting the excitability of central auditory neurons with this compound can partially restore the precision and reliability of spiking responses after hearing loss.
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Moallem, Theodore M. 1976. "Articulatory feature encoding and sensorimotor training for tactually supplemented speech reception by the hearing-impaired." Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/68454.
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Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2011.Cataloged from PDF version of thesis.
Includes bibliographical references (p. 150-159).
This thesis builds on previous efforts to develop tactile speech-reception aids for the hearing-impaired. Whereas conventional hearing aids mainly amplify acoustic signals, tactile speech aids convert acoustic information into a form perceptible via the sense of touch. By facilitating visual speechreading and providing sensory feedback for vocal control, tactile speech aids may substantially enhance speech communication abilities in the absence of useful hearing. Research for this thesis consisted of several lines of work. First, tactual detection and temporal order discrimination by congenitally deaf adults were examined, in order to assess the practicability of encoding acoustic speech information as temporal relationships among tactual stimuli. Temporal resolution among most congenitally deaf subjects was deemed adequate for reception of tactually-encoded speech cues. Tactual offset-order discrimination thresholds substantially exceeded those measured for onset-order, underscoring fundamental differences between stimulus masking dynamics in the somatosensory and auditory systems. Next, a tactual speech transduction scheme was designed with the aim of extending the amount of articulatory information conveyed by an earlier vocoder-type tactile speech display strategy. The novel transduction scheme derives relative amplitude cues from three frequency-filtered speech bands, preserving the cross-channel timing information required for consonant voicing discriminations, while retaining low-frequency modulations that distinguish voiced and aperiodic signal components. Additionally, a sensorimotor training approach ("directed babbling") was developed with the goal of facilitating tactile speech acquisition through frequent vocal imitation of visuo-tactile speech stimuli and attention to tactual feedback from one's own vocalizations. A final study evaluated the utility of the tactile speech display in resolving ambiguities among visually presented consonants, following either standard or enhanced sensorimotor training. Profoundly deaf and normal-hearing participants trained to exploit tactually-presented acoustic information in conjunction with visual speechreading to facilitate consonant identification in the absence of semantic context. Results indicate that the present transduction scheme can enhance reception of consonant manner and voicing information and facilitate identification of syllableinitial and syllable-final consonants. The sensorimotor training strategy proved selectively advantageous for subjects demonstrating more gradual tactual speech acquisition. Simple, low-cost tactile devices may prove suitable for widespread distribution in developing countries, where hearing aids and cochlear implants remain unaffordable for most severely and profoundly deaf individuals. They have the potential to enhance verbal communication with minimal need for clinical intervention.
by Theodore M. Moallem.
Ph.D.
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Laczik, Tamás. "Encoding Temporal Healthcare Data for Machine Learning." Thesis, KTH, Skolan för elektroteknik och datavetenskap (EECS), 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-299433.
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This thesis contains a review of previous work in the fields of encoding sequential healthcare data and predicting graft- versus- host disease, a medical condition, based on patient history using machine learning. A new encoding of such data is proposed for machine learning purposes. The proposed encoding, called bag of binned weighted events, is a combination of two strategies proposed in previous work, called bag of binned events and bag of weighted events. An empirical experiment is designed to evaluate the predictive performance of the proposed encoding over various binning windows to that of the previous encodings, based on the area under the receiver operating characteristic curve (AUC) metric. The experiment is carried out on real- world healthcare data obtained from Swedish registries, using the random forest and the logistic regression algorithms. After filtering the data, solving quality issues and tuning hyperparameters of the models, final results are obtained. These results indicate that the proposed encoding strategy performs on par, or slightly better than the bag of weighted events, and outperforms the bag of binned events in most cases. However, differences in metrics show small differences. It is also observed that the proposed encoding usually performs better with longer binning windows which may be attributed to data noise. Future work is proposed in the form of repeating the experiment with different datasets and models, as well as changing the binning window length of the baseline algorithms.Denna avhandling innehåller en recension av tidigare arbete inom områden av kodning av sekventiell sjukvårdsdata och förutsägelse av transplantat- mot- värdsjukdom, ett medicinskt tillstånd, baserat på patienthistoria med maskininlärning. En ny kodning av sådan data föreslås i maskininlärningssyfte. Den föreslagna kodningen, kallad bag of binned weighted events, är en kombination av två strategier som föreslagits i tidigare arbete, kallad bag of binned events och bag of weighted events. Ett empiriskt experiment är utformat för att utvärdera den föreslagna prestandan för den föreslagna kodningen över olika binningfönster jämfört med tidigare kodningar, baserat på AUC- måttet. Experimentet utförs på verkliga sjukvårdsdata som erhållits från svenska register, med random forest och logistic regression. Efter filtrering av data, lösning av kvalitetsproblem och justering av hyperparametrar för modellerna, erhålls slutliga resultat. Dessa resultat indikerar att den föreslagna kodningsstrategin presterar i nivå med, eller något bättre än bag of weighted events, och överträffar i de flesta fall bag of binned events. Skillnader i mått är dock små. Det observeras också att den föreslagna kodningen vanligtvis fungerar bättre med längre binningfönster som kan tillskrivas dataljud. Framtida arbete föreslås i form av att upprepa experimentet med olika datamängder och modeller, samt att ändra binningfönstrets längd för basalgoritmerna.
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Dulas, Michael Robert. "The effect of explicitly directing attention toward item-feature relationships on source memory and aging: an erp study." Thesis, Georgia Institute of Technology, 2011. http://hdl.handle.net/1853/41187.
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Previous evidence has shown that older adults may have specific declines in prefrontal cortex (PFC)-mediated processes supported source memory retrieval, such as strategic retrieval and post-retrieval monitoring. This decline may manifest in the form of attenuated late-frontal ERP effects. Behavioral research suggests that explicitly integrating a target context, or source, with a stimulus during encoding will improve subsequent source memory performance for both younger and older adults. Explicit item-feature binding instructions during encoding may alleviate source memory impairments, in part, by reducing the need for strategic processing during episodic retrieval. The present ERP study investigated whether explicit direction of attention toward item-feature integration may reduce age-related deficits in source memory by alleviating the necessity of frontally-mediated strategic processing at retrieval. Results demonstrated that explicit direction of attention improved source memory accuracy for both young and older adults, but older adults benefited less than the young, indicating additional age-related deficits. ERPs revealed that explicit encoding support attenuated post-retrieval monitoring effects in the young. In the old, explicit encoding instruction resulted in earlier onset of early frontal effects, possibly related to familiarity. Results suggest explicit direction of attention toward item-source integration at encoding may improve source memory by alleviating the need for strategic retrieval, but age-related deficits persist.
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Pauzin, François Philippe [Verfasser], Patrick [Gutachter] Krieger, and Stephan [Gutachter] Herlitze. "A corticothalamic circuit for refining tactile encoding : a switch between feature detection and discrimination / François Philippe Pauzin ; Gutachter: Patrick Krieger, Stephan Herlitze ; International Graduate School of Neuroscience." Bochum : Ruhr-Universität Bochum, 2018. http://d-nb.info/117520496X/34.
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Bisso, Paul W. (Paul William). "Leveraging features of nanoscale particulates for information encoding, quantitative sensing and drug delivery." Thesis, Massachusetts Institute of Technology, 2017. http://hdl.handle.net/1721.1/115691.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, February 2018.Cataloged from PDF version of thesis. "February 2017." Handwritten on title page "February 2018."
Includes bibliographical references.
It is both uncontroversial and unassailable to assert that small things can often go where big things cannot. It is similarly prosaic to note that at smaller length scales, matter behaves differently than at larger length scales. This thesis exploits these intuitive and simple axioms to yield advances in three independent lines of enquiry: (i) robust and practically accessible encoding of information within microparticles, (ii) rapid, quantitative sensing of hydrophobic colloids and (iii) immunologically-focused drug delivery. Specifically, upconversion nanocrystals are used as the foundation of a novel spatial-spectral patterning motif to produce polymer microparticles with unique, decodable identities. With large single-particle encoding capacities (>10-⁶), an ultralow decoding false alarm rate (<10-⁹), and pronounced insensitivity to both particle chemistry and harsh processing conditions, this architecture enables practical deployment of encoded microparticles in applications with orthogonal requirements, including multiplexed bioassays and covert labeling of objects and packaging for anti-counterfeiting. Next, the large specific surface area of nanoscale objects is exploited by a family of zwitterionic, surfactant-like molecular rotors to develop a broadly applicable tool for sensitive, quantitative, and accessible nanoscale metrology. This tool is shown to address multiple challenges in nanometrology of self-assembled structures, including (i) quantification of surfactant adsorption isotherms on metal oxide surfaces, (ii) determination of self-assembly onset concentration, and (iii) high-throughput readout of drug delivery nanoparticle mass concentration. Finally, the combination of small size and large interfacial area was exploited to design nanoscale formulations for (i) ex vivo delivery to human neutrophils, a significant element of the innate immune system and (ii) targeted delivery of therapeutics to the asthmatic lung.
by Paul W. Bisso.
Ph. D.
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Kundu, Benjamin Ina Annesha. "Imaging platforms for detecting and analyzing skin features and Its stability : with applications in skin health and in using the skin as a body-relative position-encoding system." Thesis, Massachusetts Institute of Technology, 2015. http://hdl.handle.net/1721.1/100114.
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Thesis: S.M., Massachusetts Institute of Technology, Department of Mechanical Engineering, 2015.Cataloged from PDF version of thesis.
Includes bibliographical references (pages 121-124).
Skin imaging is a powerful, noninvasive method used with potential to aid in the diagnosis of various dermatological diseases and assess overall skin health. This thesis discusses imaging platforms that were developed to aid in studying skin features and characteristics at different time and length scales to characterize and monitor skin. Two applications are considered: (1) using natural skin features as a position encoding system and an aid for volume reconstruction of ultrasound imaging and (2) studying natural skin feature evolution or stability over time to aid in assessing skin health. A 5-axis, rigid translational scanning system was developed to capture images at specific locations and to validate skin based body registration algorithms. We show that natural skin features could be used to perform ultrasound based reconstruction accurate to 0.06 mm. A portable, handheld scanning device was designed to study skin characteristics at different time and length scales. With this imaging platform, we analyze skin features at different length scales: [mu]m (for microreliefs), mm (for moles and pores), and cm (for distances between microreliefs and other features). Preliminary algorithms are used to automatically identify microreliefs. Further work in image processing is required to assess skin variation using these images.
by Ina Annesha Kundu.
S.M.
Books on the topic "FEATURE ENCODING"
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Botly, Leigh Cortland Perry. Cholinergic influences on the encoding, but not retrieval, of crossmodal sensory feature binding in rats. 2005.
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Jeshion, Robin. Slurs, Dehumanization, and the Expression of Contempt. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198758655.003.0005.
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A theory of slurring terms must explain how and why uses of slurs function to dehumanize. On extant expressivist views, speakers express contempt for targets on account of being in the group. This chapter argues that explaining how slurs dehumanize requires more than encoding the speaker’s contempt toward the target and group. It requires appreciating the intricate moral-psychological structure of contempt, in particular that contempt, as a moral emotion, involves taking those properties that are the basis for regarding the target contemptuously as fundamental to the targets’ identity as a person. This feature of contempt is reflected in slurs’ semantics. Understanding contempt is also needed to defend expressivism from important objections.
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Völgyi, Béla, Garrett T. Kenyon, David W. Marshak, and Botir Sagdullaev, eds. Encoding Visual Features by Parallel Ganglion Cell Initiated Pathways in the Healthy, Diseased and Artificial Retina. Frontiers Media SA, 2019. http://dx.doi.org/10.3389/978-2-88963-105-6.
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Bjorkman, Bronwyn M., and Daniel Currie Hall, eds. Contrast and Representations in Syntax. Oxford University Press, 2020. http://dx.doi.org/10.1093/oso/9780198817925.001.0001.
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Syntactic contrasts, the systems of grammatical oppositions that exist within individual languages, are typically formally encoded in terms of features. The nature of syntactic contrast is tied to a fundamental question in generative syntactic theory: What is universal in syntax (and in language more generally), and what is variable? This volume explores the dual role of features, on the one hand defining a set of paradigmatic contrasts, and other the other hand acting as the building blocks of syntactic structures and the drivers of syntactic operations. In both roles, features are increasingly seen as the locus of parametric variation. The identification of parameters with features has opened up new possibilities for exploring connections between the morphological system of a language and its syntax, and suggests a new role for featural contrast in syntactic theory. The papers collected here represent a diversity of topics, perspectives, and concerns, but are united by an interest in morphosyntactic representations, and in the formal encoding of syntactic contrasts.
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Kuhlmann, Beatrice G., and Ute J. Bayen. Metacognitive Aspects of Source Monitoring. Edited by John Dunlosky and Sarah (Uma) K. Tauber. Oxford University Press, 2015. http://dx.doi.org/10.1093/oxfordhb/9780199336746.013.8.
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Source monitoring involves attributing remembered information to a source, such as determining who told you something. Source-monitoring is a highly inferential process, involving the evaluation of memory for contextual features but also drawing onto more general knowledge and beliefs (Johnson, Hashtroudi, and Lindsay, 1993). After an introduction to the typical laboratory paradigm of source monitoring and the measurement of the cognitive states involved through multinomial modeling, we review research on metacognitive influences on this inferential source-monitoring process. We also consider means of metacognitive control over source encoding through encoding strategies. Moving on to metacognitive monitoring processes, we review research on predictions of later source memory (judgments of source) and on the monitoring of source-attribution accuracy at test. The chapter concludes with questions for future research.
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Mitchell, Karen J. The Cognitive Neuroscience of Source Monitoring. Edited by John Dunlosky and Sarah (Uma) K. Tauber. Oxford University Press, 2015. http://dx.doi.org/10.1093/oxfordhb/9780199336746.013.2.
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Source monitoring is a metamemory function that includes processes for encoding and organizing the content of memories, and processes that selectively revive, cumulate, and evaluate that content in the service of making attributions about the origin of the information (e.g., perception vs imagination). Neuroimaging techniques, especially functional magnetic resonance imaging (fMRI), are encouraging rapid developments in understanding the neural mechanisms supporting source monitoring. This chapter reviews current findings, placing them in historical context. It highlights key issues of particular relevance, including: neural reinstatement—the match between brain activity at encoding and later remembering; the role of lateral parietal cortex in cumulating multiple features and attending to information during remembering; functional specificity of the prefrontal cortex with respect to cognitive control; and identifying functional networks that support source monitoring. Suggestions are made for clarifying the big picture and increasing the specificity of our understanding of source monitoring and its neural architecture.
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Gilad-Gutnick, Sharon, and Pawan Sinha. The Presidential Illusion. Oxford University Press, 2017. http://dx.doi.org/10.1093/acprof:oso/9780199794607.003.0090.
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The effectiveness of the presidential illusion underscores the important point that by excluding external facial features, such as the head and hair shape, we lose critical information about the way faces are represented in real life. This chapter considers the question of whether whole-head processing is a general principle that can be extended to all face processes or if it specifically reflects the nature of facial encoding used by the visual system for the identification of individuals. For example, would supplementing the internal features of one face with those of another affect the perception of other common facial attributes, such as gender, race, or age? The eyes, nose, and mouth are believed to be the primary purveyors of facial identity. The presidential illusion challenges this dogma and suggests that external head features (the hair and jawline) are also crucial constituents of facial representation and strongly influence identity judgments.
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Ünal, Ercenur, and Anna Papafragou. The relation between language and mental state reasoning. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789710.003.0008.
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This chapter discusses how children’s conceptual representations of the mind make contact with language. It focuses on two domains: the understanding of the conditions that lead to knowledge, and the ability to attribute knowledge to oneself and others. Specifically, it asks whether language provides the representational resources necessary for representing mental states and whether cross-linguistic differences in encoding of mental states influence sensitivity to the features that distinguish the conditions that allow people to gain knowledge. Empirical findings in these domains strongly suggest that language scaffolds the development of these cognitive abilities without altering the underlying conceptual representations of mental states.
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Bailey, Matthew A. An overview of tubular function. Edited by Robert Unwin. Oxford University Press, 2015. http://dx.doi.org/10.1093/med/9780199592548.003.0020.
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This chapter provides an overview of transport processes, describing both the membrane proteins that effect transepithelial solute flux and the systems that allow integrated regulation of electrolyte transport. The emphasis is on the physiological mechanisms but links to human diseases are made in order to illuminate fundamental principles of control. The key transport proteins and encoding genes are listed. First, the major transport pathways and regulatory features for each nephron segment are described. The focus here is on the transepithelial flux of sodium, potassium, and water. In the second part, other important aspects of renal homeostasis, including urine concentration and acid–base balance, are summarized.
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Nordlinger, Rachel. The Languages of the Daly River Region (Northern Australia). Edited by Michael Fortescue, Marianne Mithun, and Nicholas Evans. Oxford University Press, 2017. http://dx.doi.org/10.1093/oxfordhb/9780199683208.013.44.
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This chapter surveys the polysynthetic characteristics of the languages of the Daly River region of Australia’s Northern Territory. Although they are not all closely related, these languages share many typological features typical of polysynthesis, including the encoding of core arguments in the verbal word; noun incorporation; applicatives; and complex templatic verbal morphology. In addition the Daly languages exhibit complex verbal predicates composed of two discontinuous stems, one functioning broadly to classify the event type and the other providing more specific lexical semantics. These properties are surveyed across a range of Daly languages, considering both their similarities and their differences, and the implications they have for a cross-linguistic typology of polysynthesis.
Book chapters on the topic "FEATURE ENCODING"
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Langendoen, D. Terence, and Gary F. Simons. "A Rationale for the TEI Recommendations for Feature-Structure Markup." In Text Encoding Initiative, 191–209. Dordrecht: Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-011-0325-1_16.
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Avants, Brian, Elliot Greenblatt, Jacob Hesterman, and Nicholas Tustison. "Deep Volumetric Feature Encoding for Biomedical Images." In Biomedical Image Registration, 91–100. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-50120-4_9.
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Pang, Xiaolin, Kexin Xie, Yuxi Zhang, Max Fleming, Damian Chen Xu, and Wei Liu. "Adversarial Active Learning with Guided BERT Feature Encoding." In Advances in Knowledge Discovery and Data Mining, 508–20. Cham: Springer Nature Switzerland, 2023. http://dx.doi.org/10.1007/978-3-031-33377-4_39.
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Liu, Yang, Yuehuan Wang, and Jun Wang. "An Improved MEEM Tracker via Adaptive Binary Feature Encoding." In Communications in Computer and Information Science, 413–25. Singapore: Springer Singapore, 2016. http://dx.doi.org/10.1007/978-981-10-3002-4_35.
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Nakajima, Shin. "Non-clausal Encoding of Feature Diagram for Automated Diagnosis." In Software Product Lines: Going Beyond, 420–24. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-15579-6_29.
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Venugopalan, Shreyas, and Marios Savvides. "Iris Spoofing: Reverse Engineering the Daugman Feature Encoding Scheme." In Handbook of Iris Recognition, 355–66. London: Springer London, 2012. http://dx.doi.org/10.1007/978-1-4471-4402-1_18.
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Dai, Qiang, Xi Cheng, and Li Zhang. "Multi-spectral Dynamic Feature Encoding Network for Image Demoiréing." In Lecture Notes in Computer Science, 151–62. Cham: Springer Nature Switzerland, 2022. http://dx.doi.org/10.1007/978-3-031-15937-4_13.
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Xing, Dong, Xianzhong Wang, and Hongtao Lu. "Action Recognition Using Hybrid Feature Descriptor and VLAD Video Encoding." In Computer Vision - ACCV 2014 Workshops, 99–112. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-16628-5_8.
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Dai, Longqi, Bo Xu, and Hui Song. "Feature-Level Attention Based Sentence Encoding for Neural Relation Extraction." In Natural Language Processing and Chinese Computing, 184–96. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-32233-5_15.
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Li, Shuyi, Haigang Zhang, Guimin Jia, and Jinfeng Yang. "Finger Vein Recognition Based on Weighted Graph Structural Feature Encoding." In Biometric Recognition, 29–37. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-97909-0_4.
Full textConference papers on the topic "FEATURE ENCODING"
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Li, Ning, and Youfu Li. "Feature encoding for color image segmentation." In Multispectral Image Processing and Pattern Recognition, edited by Tianxu Zhang, Bir Bhanu, and Ning Shu. SPIE, 2001. http://dx.doi.org/10.1117/12.441437.
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Noor, Jumana, Muneeba Daud, Raima Rashid, Hira Mir, Saima Nazir, and Sergio A. Velastin. "Facial Expression Recognition using Hand-Crafted Features and Supervised Feature Encoding." In 2020 International Conference on Electrical, Communication, and Computer Engineering (ICECCE). IEEE, 2020. http://dx.doi.org/10.1109/icecce49384.2020.9179473.
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Shatnawi, Hazim, and H. Conrad Cunningham. "Encoding feature models using mainstream JSON technologies." In ACM SE '21: 2021 ACM Southeast Conference. New York, NY, USA: ACM, 2021. http://dx.doi.org/10.1145/3409334.3452048.
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Zhou, Yao, Jiamin Ren, Jingyu Li, Litong Feng, Shi Qiu, and Ping Luo. "Video Classification via Relational Feature Encoding Networks." In the Workshop. New York, New York, USA: ACM Press, 2017. http://dx.doi.org/10.1145/3134263.3134265.
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Wang, Yu, and Jien Kato. "Good Choices for Deep Convolutional Feature Encoding." In 2019 IEEE Winter Conference on Applications of Computer Vision (WACV). IEEE, 2019. http://dx.doi.org/10.1109/wacv.2019.00039.
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Li, Lin, Zhaoxiang Zhang, Yan Huang, and Liang Wang. "Deep Temporal Feature Encoding for Action Recognition." In 2018 24th International Conference on Pattern Recognition (ICPR). IEEE, 2018. http://dx.doi.org/10.1109/icpr.2018.8546263.
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Rahimpour, Alireza, Ali Taalimi, and Hairong Qi. "Feature encoding in band-limited distributed surveillance systems." In 2017 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP). IEEE, 2017. http://dx.doi.org/10.1109/icassp.2017.7952457.
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Shi, Yunxiao, Haoyu Fang, Jing Zhu, and Yi Fang. "Pairwise Attention Encoding for Point Cloud Feature Learning." In 2019 International Conference on 3D Vision (3DV). IEEE, 2019. http://dx.doi.org/10.1109/3dv.2019.00024.
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Ando, Shin. "Latent feature encoding using dyadic and relational data." In the 20th ACM international conference. New York, New York, USA: ACM Press, 2011. http://dx.doi.org/10.1145/2063576.2063926.
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Jin, Mengsi, JianHong Ye, JiLiang Luo, and Yan Lin. "Predictive Monitoring Algorithm Based on Global Feature Encoding." In 2020 IEEE International Conference on Networking, Sensing and Control (ICNSC). IEEE, 2020. http://dx.doi.org/10.1109/icnsc48988.2020.9238130.
Full textReports on the topic "FEATURE ENCODING"
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Lers, Amnon, and Pamela J. Green. LX Senescence-Induced Ribonuclease in Tomato: Function and Regulation. United States Department of Agriculture, September 2003. http://dx.doi.org/10.32747/2003.7586455.bard.
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Natural leaf senescence, which occurs even when growth conditions are near optimal, has a negative influence on yield. Postharvest induced senescence contributes to the losses of quality in flowers, foliage, and vegetables. Strategies designed to control the senescence process in crop plants could therefore have great applied significance. However, the successful design of such strategies requires a better insight into the senescence machinery and control in higher plants. A main feature of senescence is the hydrolysis of macromolecules by hydrolases of various types such as ribonucleases (RNases) and proteases. Previously we had identified and characterized the tomato LX RNase gene demonstrating its transcript to be highly and specifically induced during senescence. This reported study was focused on LX but also had broadened our research to other senescence-associated nucleic acids degrading enzymes to learn about their function and the regulation of their encoding genes. Beside tomato we used parsley and Arabidopsis for the study of: the bi-functional nuclease which has a role in senescence. The study of different senescence- associated nucleases in few plant systems will allow a more general view on function and regulation of these enzymes in senescence. The specific original proposed objectives included: 1. Study the consequences of alterations in LX RNase level on tomato leaf senescence and general development; 2. Analyze stimuli which may participate in senescence-specific activation of the LX gene; 3. Clone the senescence-associated BFNI nuclease gene homologue from tomato. 4. Further characterize the sequences required for senescence-specific gene expression. Homozygous transgenic plants in which LX gene was either inhibited or over-expressed were generated. In both of these LX mutated plants no major phenotypic consequences were observed, which may suggests that LX is not essential for plant growth under optimal growth conditions. Lack of any abnormalities in the LX over-expressing lines suggests that special system exist to allow function of the RNase only when needed. Detailed analyses of growth under stress and consequences to RNA metabolism are underway. We have analyzed LX expression on the protein level demonstrating that it is involved also in petal senescing. Our results suggest that LX is responding to complex regulation involving developmental, organ dependent factors and responds differently to hormonal or environmental stimuli in the different plant organs. The cloned 1.4 kb promoter was cloned and its analysis revealed that probably not all required elements for senescence induction are included. Biochemical analysis of senescence-associated be-functional nucleases in the different plants, tomato, parsley and Arabidopsis, suggests they belong to a sub-class within the type I plant nucleases. The parsley PcNUC1/2 nuclease protein was purified from senescing leaves its and activity was studied in vitro revealing endo-, double strand, nucleolytic activity and exo-nucleolytic activity. Its encoding gene was cloned and found to be induced on the mRNA level. The promoter of the related Arabidopsis BFNI nuclease was shown in both tomato and Arabidopsis to be able and direct senescence-specific expression suggesting that, at least part, the gene is regulated on the transcriptional level and that the mechanism for this senescence-specific regulation is conserved between different plants. Few plants in which the BFNI gene is mutated were identified which are subjected now to detailed analysis. Our results suggest that the senescence-related nucleic acid degrading enzymes share similarities in both function and regulation between different plants and possibly have important functions in processes un-related to senescence. Still, the function of these enzymes, at least in some cases is not essential to plant development under optimal growth conditions. We are now at the stage which permits in depth investigation of the specific functions and mode of molecular regulation of senescence-associated nucleases with the aid of the research tools developed. The isolated senescence-specific promoter, shown to be active in heterologous plant system, could be utilized in agricultural-related biotechnological applications for retardation of senescence.
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Ostersetzer-Biran, Oren, and Jeffrey Mower. Novel strategies to induce male sterility and restore fertility in Brassicaceae crops. United States Department of Agriculture, January 2016. http://dx.doi.org/10.32747/2016.7604267.bard.
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Abstract Mitochondria are the site of respiration and numerous other metabolic processes required for plant growth and development. Increased demands for metabolic energy are observed during different stages in the plants life cycle, but are particularly ample during germination and reproductive organ development. These activities are dependent upon the tight regulation of the expression and accumulation of various organellar proteins. Plant mitochondria contain their own genomes (mtDNA), which encode for rRNAs, tRNAs and some mitochondrial proteins. Although all mitochondria have probably evolved from a common alpha-proteobacterial ancestor, notable genomic reorganizations have occurred in the mtDNAs of different eukaryotic lineages. Plant mtDNAs are notably larger and more variable in size (ranging from 70~11,000 kbp in size) than the mrDNAs in higher animals (16~19 kbp). Another unique feature of plant mitochondria includes the presence of both circular and linear DNA fragments, which undergo intra- and intermolecular recombination. DNA-seq data indicate that such recombination events result with diverged mitochondrial genome configurations, even within a single plant species. One common plant phenotype that emerges as a consequence of altered mtDNA configuration is cytoplasmic male sterility CMS (i.e. reduced production of functional pollen). The maternally-inherited male sterility phenotype is highly valuable agriculturally. CMS forces the production of F1 hybrids, particularly in predominantly self-pollinating crops, resulting in enhanced crop growth and productivity through heterosis (i.e. hybrid vigor or outbreeding enhancement). CMS lines have been implemented in some cereal and vegetables, but most crops still lack a CMS system. This work focuses on the analysis of the molecular basis of CMS. We also aim to induce nuclear or organellar induced male-sterility in plants, and to develop a novel approach for fertility restoration. Our work focuses on Brassicaceae, a large family of flowering plants that includes Arabidopsis thaliana, a key model organism in plant sciences, as well as many crops of major economic importance (e.g., broccoli, cauliflower, cabbage, and various seeds for oil production). In spite of the genomic rearrangements in the mtDNAs of plants, the number of genes and the coding sequences are conserved among different mtDNAs in angiosperms (i.e. ~60 genes encoding different tRNAs, rRNAs, ribosomal proteins and subunits of the respiratory system). Yet, in addition to the known genes, plant mtDNAs also harbor numerous ORFs, most of which are not conserved among species and are currently of unknown function. Remarkably, and relevant to our study, CMS in plants is primarily associated with the expression of novel chimericORFs, which likely derive from recombination events within the mtDNAs. Whereas the CMS loci are localized to the mtDNAs, the factors that restore fertility (Rfs) are identified as nuclear-encoded RNA-binding proteins. Interestingly, nearly all of the Rf’s are identified as pentatricopeptide repeat (PPR) proteins, a large family of modular RNA-binding proteins that mediate several aspects of gene expression primarily in plant organelles. In this project we proposed to develop a system to test the ability of mtORFs in plants, which are closely related to known CMS factors. We will induce male fertility in various species of Brassicaceae, and test whether a down-relation in the expression of the recombinantCMS-genes restores fertility, using synthetically designed PPR proteins.
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Elizur, Abigail, Amir Sagi, Gideon Hulata, Clive Jones, and Wayne Knibb. Improving Crustacean Aquaculture Production Efficiencies through Development of Monosex Populations Using Endocrine and Molecular Manipulations. United States Department of Agriculture, June 2010. http://dx.doi.org/10.32747/2010.7613890.bard.
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Background Most of Australian prawn aquaculture production is based on P. monodon. However, the Australian industry is under intense competition from lower priced overseas imports. The availability of all-female monosex populations, by virtue of their large size and associated premium prize, will offer competitive advantage to the industry which desperately needs to counteract competitors within this market. As for the redclaw production in Israel, although it is at its infancy, the growers realized that the production of males is extremely advantageous and that such management strategy will change the economic assumptions and performances of this aquaculture to attract many more growers. Original objectives (as in original proposal) Investigating the sex inheritance mechanism in the tiger prawn. Identification of genes expressed uniquely in the androgenic gland (AG) of prawns and crayfish. The above genes and/or their products will be used to localize the AG in the prawn and manipulate the AG activity in both species. Production of monosex populations through AG manipulation. In the prawn, production of all-female populations and in the crayfish, all-male populations. Achievements In the crayfish, the AG cDNA library was further screened and a third AG specific transcript, designated Cq-AG3, had been identified. Simultaneously the two AG specific genes, which were previously identified, were further characterized. Tissue specificity of one of those genes, termed Cq-AG2, was demonstrated by northern blot hybridization and RNA in-situ hybridization. Bioinformatics prediction, which suggested a 42 amino acid long signal anchor at the N-terminus of the deduced Cq-AG2, was confirmed by immunolocalization of a recombinant protein. Cq-IAG's functionality was demonstrated by dsRNA in-vivo injections to intersex crayfish. Cq-IAGsilencing induced dramatic sex-related alterations, including male feature feminization, reduced sperm production, extensive testicular apoptosis, induction of the vitellogeningene expression and accumulation of yolk proteins in the ovaries. In the prawn, the AG was identified and a cDNA library was created. The putative P. monodonAG hormone encoding gene (Pm-IAG) was identified, isolated and characterized for time of expression and histological localization. Implantation of the AG into prawn post larvae (PL) and juveniles resulted in phenotypic transformation which included the appearance of appendix masculina and enlarged petasma. The transformation however did not result in sex change or the creation of neo males thus the population genetics stage to be executed with Prof. Hulata did not materialized. Repeated AG implantation is currently being trialed. Major conclusions and Implications, both scientific and agricultural Cq-IAG's involvement in male sexual differentiation had been demonstrated and it is strongly suggested that this gene encodes an AG hormone in this crayfish. A thorough screening of the AG cDNA library shows Cq-IAG is the prominent transcript within the library. However, the identification of two additional transcripts hints that Cq-IAG is not the only gene mediating the AG effects. The successful gene silencing of Cq-IAG, if performed at earlier developmental stages, might accomplish full and functional sex reversal which will enable the production of all-male crayfish populations. Pm-IAG is likely to play a similar role in prawns. It is possible that repeated administration of the AG into prawn will lead to the desired full sex reversal, so that WZ neo males, crossed with WZ females can result in WW females, which will form the basis for monosex all-female population.
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Lers, Amnon, E. Lomaniec, S. Burd, A. Khalchitski, L. Canetti, and Pamela J. Green. Analysis of Senescence Inducible Ribonuclease in Tomato: Gene Regulation and Function. United States Department of Agriculture, February 2000. http://dx.doi.org/10.32747/2000.7570563.bard.
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Natural leaf senescence has a negative influence on yield. Postharvest induced senescence contributes to the losses of quality in flowers, foliage, and vegetables. Strategies designed to control the senescence process in crop plants could therefore have great applied significance. Senescence is regulated by differential gene expression yet, functional characterization of the genes specifically induced and study of their expression control, is still in its infancy. Study of senescence-specific genes is required to allow identification of regulatory elements participating in senescence-induced expression and thus provide insights into the genetic regulation of senescence. A main feature of senescence is the hydrolysis of macromolecules by hydrolases of various types such as RNases and proteases. This study was aimed a analysis of senescence-inducible RNases in tomato with the following objectives: Isolation of senescence-inducible RNase cDNA clones; Expression analyses of RNase genes during senescence; Identification of sequences required for senescence-induced gene expression; Functional analyses of senescence-inducible RNases. We narrowed our aims somewhat to focus on the first three objectives because the budget we were awarded was reduced from that requested. We have expanded our research for identification senescence-related RNase/nuclease activities as we thought it will direct us to new RNase/nuclease genes. We have also carried out research in Arabidopsis and parsley, which enabled us to draw mire general conclusions. We completed the first and second objectives and have made considerable progress on the remaining two. We have defined growth conditions suitable for this research and defined the physiological and biochemical parameters characteristic to the advance of leaf senescence. In tomato and arabidopsis we have focused on natural leaf senescence. Parsley was used mainly for study of postharvest senescence in detached leaves. We have identified a 41-kD a tomato nuclease, LeNUCI, specifically induced during senescence which can degrade both RNA and DNA. This activity could be induced by ethylene in young leaves and was subjected to detailed analysis, which enabled its classification as Nuclease I enzyme. LeNUCI may be involved in nucleic acid metabolism during tomato leaf senescence. In parsley senescing leaves we identified 2 main senescence-related nuclease activities of 41 and 39-kDa. These activities were induced in both naturally or artificially senescing leaves, could degrade both DNA and RNA and were very similar in their characteristics to the LeNUCI. Two senescence-induced RNase cDNAs were cloned from tomato. One RNase cDNA was identical to the tomato LX RNase while the second corresponded to the LE RNase. Both were demonstrated before to be induced following phosphate starvation of tomato cell culture but nothing was known about their expression or function in plants. LX gene expression was much more senescence specific and ethylene could activate it in detached young leaves. LE gene expression, which could be transiently induced by wounding, appeared to be activated by abscisic acid. We suggest that the LX RNase has a role in RNA catabolism in the final stage of senescence, and LE may be a defense-related protein. Transgenic plants were generated for altering LX gene expression. No major visible alterations in the phenotype were observed so far. Detailed analysis of senescence in these plants is performed currently. The LX promoter was cloned and its analysis is performed currently for identification of senescence-specific regulatory elements. In Arabidopsis we have identified and characterized a senescence-associated nuclease 1 gene, BFN1, which is highly expressed during leaf and stem senescence. BFN1, is the first example of a senescence- associated gene encoding a nuclease I enzyme as well as the first nuclease I cloned and characterized from Arabidopsis. Our progress should provide excellent tools for the continued analysis of regulation and function of senescence-inducible ribonucleases and nucleases in plants. The cloned genes can be used in reverse genetic approaches, already initiated, which can yield a more direct evidence for the function of these enzymes. Another contribution of this research will be in respect to the molecular mechanism, which controls senescence. We had already initiated in this project and will continue to identify and characterize regulatory elements involved in senescence-specific expression of the genes isolated in this work.
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Morrison, Mark, Joshuah Miron, Edward A. Bayer, and Raphael Lamed. Molecular Analysis of Cellulosome Organization in Ruminococcus Albus and Fibrobacter Intestinalis for Optimization of Fiber Digestibility in Ruminants. United States Department of Agriculture, March 2004. http://dx.doi.org/10.32747/2004.7586475.bard.
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Improving plant cell wall (fiber) degradation remains one of the highest priority research goals for all ruminant enterprises dependent on forages, hay, silage, or other fibrous byproducts as energy sources, because it governs the provision of energy-yielding nutrients to the host animal. Although the predominant species of microbes responsible for ruminal fiber degradation are culturable, the enzymology and genetics underpinning the process are poorly defined. In that context, there were two broad objectives for this proposal. The first objective was to identify the key cellulosomal components in Ruminococcus albus and to characterize their structural features as well as regulation of their expression, in response to polysaccharides and (or) P AA/PPA. The second objective was to evaluate the similarities in the structure and architecture of cellulosomal components between R. albus and other ruminal and non-ruminal cellulolytic bacteria. The cooperation among the investigators resulted in the identification of two glycoside hydrolases rate-limiting to cellulose degradation by Ruminococcus albus (Cel48A and CeI9B) and our demonstration that these enzymes possess a novel modular architecture specific to this bacterium (Devillard et al. 2004). We have now shown that the novel X-domains in Cel48A and Cel9B represent a new type of carbohydrate binding module, and the enzymes are not part of a ceiluiosome-like complex (CBM37, Xu et al. 2004). Both Cel48A and Cel9B are conditionally expressed in response to P AA/PPA, explaining why cellulose degradation in this bacterium is affected by the availability of these compounds, but additional studies have shown for the first time that neither PAA nor PPA influence xylan degradation by R. albus (Reveneau et al. 2003). Additionally, the R. albus genome sequencing project, led by the PI. Morrison, has supported our identification of many dockerin containing proteins. However, the identification of gene(s) encoding a scaffoldin has been more elusive, and recombinant proteins encoding candidate cohesin modules are now being used in Israel to verify the existence of dockerin-cohesin interactions and cellulosome production by R. albus. The Israeli partners have also conducted virtually all of the studies specific to the second Objective of the proposal. Comparative blotting studies have been conducted using specific antibodies prepare against purified recombinant cohesins and X-domains, derived from cellulosomal scaffoldins of R. flavefaciens 17, a Clostridium thermocellum mutant-preabsorbed antibody preparation, or against CbpC (fimbrial protein) of R. albus 8. The data also suggest that additional cellulolytic bacteria including Fibrobacter succinogenes S85, F. intestinalis DR7 and Butyrivibrio fibrisolvens Dl may also employ cellulosomal modules similar to those of R. flavefaciens 17. Collectively, our work during the grant period has shown that R. albus and other ruminal bacteria employ several novel mechanisms for their adhesion to plant surfaces, and produce both cellulosomal and non-cellulosomal forms of glycoside hydrolases underpinning plant fiber degradation. These improvements in our mechanistic understanding of bacterial adhesion and enzyme regulation now offers the potential to: i) optimize ruminal and hindgut conditions by dietary additives to maximize fiber degradation (e.g. by the addition of select enzymes or PAA/PPA); ii) identify plant-borne influences on adhesion and fiber-degradation, which might be overcome (or improved) by conventional breeding or transgenic plant technologies and; iii) engineer or select microbes with improved adhesion capabilities, cellulosome assembly and fiber degradation. The potential benefits associated with this research proposal are likely to be realized in the medium term (5-10 years).
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McElwain, Terry F., Eugene Pipano, Guy H. Palmer, Varda Shkap, Stephn A. Hines, and Wendy C. Brown. Protection of Cattle against Babesiosis: Immunization against Babesia bovis with an Optimized RAP-1/Apical Complex Construct. United States Department of Agriculture, September 1999. http://dx.doi.org/10.32747/1999.7573063.bard.
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Previous research and current efforts at control of babesiosis fall short of meeting the needs of countries where the disease is endemic, such as Israel, as well as the needs of exporting countries and countries bordering on endemic areas, such as the U.S. Our long-term goal is to develop improved methods of immunization against bovine babesiosis based on an understanding of the molecular mechanisms of immune protection and parasite targets of a protective immune response. In our previous BARD project, we established the basis for focusing on rhoptry antigens as components of a subunit vaccine against bovine babesiosis, and for additional research to better characterize rhoptry associated protein-1 (RAP-1) as a target of protective immunity. In this continuation BARD project, our objectives were to [1] optimize the immune response against RAP-1, and [2] identify additional rhoptry candidate vaccine antigens. The entire locus encoding B. bovis RAP-1 was sequenced, and the rap-1 open reading frame compared among several strains. Unlike B. bigemina, in which multiple gene copies with variant domains encode RAP-1, the B. bovis RAP-1 locus contains only two identical genes which are conserved among strains. Through testing of multiple truncated constructs of rRAP-1, one or more immunodominant T cell epitopes were mapped to the amino terminal half of RAP-1. At least one linear and one conformational B cell epitope have been demonstrated in the same amino terminal construct, which in B. bigemina RAP-1 also contains an epitope recognized by neutralizing antibody. The amine terminal half of the molecule represents the most highly conserved part of the gene family and contains motifs conserved broadly among the apicomplexa. In contrast, the carboxy terminal half of B. bovis RAP-1 is less well conserved and contains multiple repeats encoding a linear B cell epitope potentially capable of inducing an ineffective, T cell independent, type 2 immune response. Therefore, we are testing an amino terminal fragment of RAP-1 (RAP-1N) in an immunization trial in cattle. Cattle have beer immunized with RAP-1N or control antigen, and IL-12 with Ribi adjuvant. Evaluation of the immune response is ongoing, and challenge with virulent B. bovis will occur in the near future. While no new rhoptry antigens were identified, our studies did identify and characterize a new spherical body antigen (SBP3), and several heat shock proteins (HSP's). The SBP3 and HSP21 antigens stimulate T cells from immune cattle and are considered new vaccine candidates worthy of further testing. Overall, we conclude that a single RAP-1 vaccine construct representing the conserved amino terminal region of the molecule should be sufficient for immunization against all strains of B. bovis. While results of the ongoing immunization trial will direct our next research steps, results at this time are consistent with our long term goal of designing a subunit vaccine which contains only the epitopes relevant to induction of protective immunity. Parallel studies are defining the mechanisms of protective immunity. Apicomplexan protozoa, including babesiosis and malaria, cause persistent diseases for which control is inadequate. The apical organelles are defining features of these complex protozoa, and have been conserved through the evolutionary process, Past and current BARD projects on babesiosis have established the validity and potential of exploiting these conserved organelles in developing improved control methods applicable to all apicomplexan diseases.
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Minz, Dror, Stefan J. Green, Noa Sela, Yitzhak Hadar, Janet Jansson, and Steven Lindow. Soil and rhizosphere microbiome response to treated waste water irrigation. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7598153.bard.
Full textAbstract:
Research objectives : Identify genetic potential and community structure of soil and rhizosphere microbial community structure as affected by treated wastewater (TWW) irrigation. This objective was achieved through the examination soil and rhizosphere microbial communities of plants irrigated with fresh water (FW) and TWW. Genomic DNA extracted from soil and rhizosphere samples (Minz laboratory) was processed for DNA-based shotgun metagenome sequencing (Green laboratory). High-throughput bioinformatics was performed to compare both taxonomic and functional gene (and pathway) differences between sample types (treatment and location). Identify metabolic pathways induced or repressed by TWW irrigation. To accomplish this objective, shotgun metatranscriptome (RNA-based) sequencing was performed. Expressed genes and pathways were compared to identify significantly differentially expressed features between rhizosphere communities of plants irrigated with FW and TWW. Identify microbial gene functions and pathways affected by TWW irrigation*. To accomplish this objective, we will perform a metaproteome comparison between rhizosphere communities of plants irrigated with FW and TWW and selected soil microbial activities. Integration and evaluation of microbial community function in relation to its structure and genetic potential, and to infer the in situ physiology and function of microbial communities in soil and rhizospere under FW and TWW irrigation regimes. This objective is ongoing due to the need for extensive bioinformatics analysis. As a result of the capabilities of the new PI, we have also been characterizing the transcriptome of the plant roots as affected by the TWW irrigation and comparing the function of the plants to that of the microbiome. *This original objective was not achieved in the course of this study due to technical issues, especially the need to replace the American PIs during the project. However, the fact we were able to analyze more than one plant system as a result of the abilities of the new American PI strengthened the power of the conclusions derived from studies for the 1ˢᵗ and 2ⁿᵈ objectives. Background: As the world population grows, more urban waste is discharged to the environment, and fresh water sources are being polluted. Developing and industrial countries are increasing the use of wastewater and treated wastewater (TWW) for agriculture practice, thus turning the waste product into a valuable resource. Wastewater supplies a year- round reliable source of nutrient-rich water. Despite continuing enhancements in TWW quality, TWW irrigation can still result in unexplained and undesirable effects on crops. In part, these undesirable effects may be attributed to, among other factors, to the effects of TWW on the plant microbiome. Previous studies, including our own, have presented the TWW effect on soil microbial activity and community composition. To the best of our knowledge, however, no comprehensive study yet has been conducted on the microbial population associated BARD Report - Project 4662 Page 2 of 16 BARD Report - Project 4662 Page 3 of 16 with plant roots irrigated with TWW – a critical information gap. In this work, we characterize the effect of TWW irrigation on root-associated microbial community structure and function by using the most innovative tools available in analyzing bacterial community- a combination of microbial marker gene amplicon sequencing, microbial shotunmetagenomics (DNA-based total community and gene content characterization), microbial metatranscriptomics (RNA-based total community and gene content characterization), and plant host transcriptome response. At the core of this research, a mesocosm experiment was conducted to study and characterize the effect of TWW irrigation on tomato and lettuce plants. A focus of this study was on the plant roots, their associated microbial communities, and on the functional activities of plant root-associated microbial communities. We have found that TWW irrigation changes both the soil and root microbial community composition, and that the shift in the plant root microbiome associated with different irrigation was as significant as the changes caused by the plant host or soil type. The change in microbial community structure was accompanied by changes in the microbial community-wide functional potential (i.e., gene content of the entire microbial community, as determined through shotgun metagenome sequencing). The relative abundance of many genes was significantly different in TWW irrigated root microbiome relative to FW-irrigated root microbial communities. For example, the relative abundance of genes encoding for transporters increased in TWW-irrigated roots increased relative to FW-irrigated roots. Similarly, the relative abundance of genes linked to potassium efflux, respiratory systems and nitrogen metabolism were elevated in TWW irrigated roots when compared to FW-irrigated roots. The increased relative abundance of denitrifying genes in TWW systems relative FW systems, suggests that TWW-irrigated roots are more anaerobic compare to FW irrigated root. These gene functional data are consistent with geochemical measurements made from these systems. Specifically, the TWW irrigated soils had higher pH, total organic compound (TOC), sodium, potassium and electric conductivity values in comparison to FW soils. Thus, the root microbiome genetic functional potential can be correlated with pH, TOC and EC values and these factors must take part in the shaping the root microbiome. The expressed functions, as found by the metatranscriptome analysis, revealed many genes that increase in TWW-irrigated plant root microbial population relative to those in the FW-irrigated plants. The most substantial (and significant) were sodium-proton antiporters and Na(+)-translocatingNADH-quinoneoxidoreductase (NQR). The latter protein uses the cell respiratory machinery to harness redox force and convert the energy for efflux of sodium. As the roots and their microbiomes are exposed to the same environmental conditions, it was previously hypothesized that understanding the soil and rhizospheremicrobiome response will shed light on natural processes in these niches. This study demonstrate how newly available tools can better define complex processes and their downstream consequences, such as irrigation with water from different qualities, and to identify primary cues sensed by the plant host irrigated with TWW. From an agricultural perspective, many common practices are complicated processes with many ‘moving parts’, and are hard to characterize and predict. Multiple edaphic and microbial factors are involved, and these can react to many environmental cues. These complex systems are in turn affected by plant growth and exudation, and associated features such as irrigation, fertilization and use of pesticides. However, the combination of shotgun metagenomics, microbial shotgun metatranscriptomics, plant transcriptomics, and physical measurement of soil characteristics provides a mechanism for integrating data from highly complex agricultural systems to eventually provide for plant physiological response prediction and monitoring. BARD Report