Identification Paradigm Research Articles

Modeling and harnessing sparse and low-rank data structure: a new paradigm for structural dynamics, identification, damage detection, and health monitoring

This paper presents a new paradigm of explicitly modeling and harnessing the data structure to address the inverse problems in structural dynamics, identification, and data-driven health monitoring. In particular, it is shown that the structural dynamic features and damage information, intrinsic within the structural vibration response measurement data, possesses sparse and low-rank structure, which can be effectively modeled and processed by emerging mathematical tools such as sparse representation and compressed sensing, low-rank matrix decomposition and completion, as well as the unsupervised multivariate blind source separation. It is also discussed that explicitly modeling and harnessing the sparse and low-rank data structure could benefit future work in developing data-driven approaches toward rapid, unsupervised, and effective system identification, damage detection, as well as massive SHM data sensing and management. Copyright © 2016 John Wiley & Sons, Ltd.

Chipless RFID Tag Exploiting Multifrequency Delta-Phase Quantization Encoding

A novel encoding paradigm for chipless radio frequency identification (RFID) tags based on phase quantization is presented. The most distinctive features of this approach are represented by the low requirement on bandwidth and by the encoding scheme. The former is achieved by using only a multifrequency reading without resorting to ultrawideband systems, whereas the latter relies on linking the information to the quantized difference between the TE and TM phase response of the tag. The encoding mechanism is described as well as the decoding procedure. The reliability of the illustrated approach is experimentally validated by measurements on fabricated prototypes.

Holistic Facial Composite Creation and Subsequent Video Line-up Eyewitness Identification Paradigm.

The paradigm detailed in this manuscript describes an applied experimental method based on real police investigations during which an eyewitness or victim to a crime may create from memory a holistic facial composite of the culprit with the assistance of a police operator. The aim is that the composite is recognized by someone who believes that they know the culprit. For this paradigm, participants view a culprit actor on video and following a delay, participant-witnesses construct a holistic system facial composite. Controls do not construct a composite. From a series of arrays of computer-generated, but realistic faces, the holistic system construction method primarily requires participant-witnesses to select the facial images most closely meeting their memory of the culprit. Variation between faces in successive arrays is reduced until ideally the final image possesses a close likeness to the culprit. Participant-witness directed tools can also alter facial features, configurations between features and holistic properties (e.g., age, distinctiveness, skin tone), all within a whole face context. The procedure is designed to closely match the holistic manner by which humans’ process faces. On completion, based on their memory of the culprit, ratings of composite-culprit similarity are collected from the participant-witnesses. Similar ratings are collected from culprit-acquaintance assessors, as a marker of composite recognition likelihood. Following a further delay, all participants — including the controls — attempt to identify the culprit in either a culprit-present or culprit-absent video line-up, to replicate circumstances in which the police have located the correct culprit, or an innocent suspect. Data of control and participant-witness line-up outcomes are presented, demonstrating the positive influence of holistic composite construction on identification accuracy. Correlational analyses are conducted to measure the relationship between assessor and participant-witness composite-culprit similarity ratings, delay, identification accuracy, and confidence to examine which factors influence video line-up outcomes.

Holistic Facial Composite Creation and Subsequent Video Line-up Eyewitness Identification Paradigm

The paradigm detailed in this manuscript describes an applied experimental method based on real police investigations during which an eyewitness or victim to a crime may create from memory a holistic facial composite of the culprit with the assistance of a police operator. The aim is that the composite is recognized by someone who believes that they know the culprit. For this paradigm, participants view a culprit actor on video and following a delay, participant-witnesses construct a holistic system facial composite. Controls do not construct a composite. From a series of arrays of computer-generated, but realistic faces, the holistic system construction method primarily requires participant-witnesses to select the facial images most closely meeting their memory of the culprit. Variation between faces in successive arrays is reduced until ideally the final image possesses a close likeness to the culprit. Participant-witness directed tools can also alter facial features, configurations between features and holistic properties (e.g., age, distinctiveness, skin tone), all within a whole face context. The procedure is designed to closely match the holistic manner by which humans’ process faces. On completion, based on their memory of the culprit, ratings of composite-culprit similarity are collected from the participant-witnesses. Similar ratings are collected from culprit-acquaintance assessors, as a marker of composite recognition likelihood. Following a further delay, all participants — including the controls — attempt to identify the culprit in either a culprit-present or culprit-absent video line-up, to replicate circumstances in which the police have located the correct culprit, or an innocent suspect. Data of control and participant-witness line-up outcomes are presented, demonstrating the positive influence of holistic composite construction on identification accuracy. Correlational analyses are conducted to measure the relationship between assessor and participant-witness composite-culprit similarity ratings, delay, identification accuracy, and confidence to examine which factors influence video line-up outcomes.

Individualized Map of White Matter Pathways: Connectivity-Based Paradigm for Neurosurgical Planning.

Advances in white matter tractography enhance neurosurgical planning and glioma resection, but white matter tractography is limited by biological variables such as edema, mass effect, and tract infiltration or selection biases related to regions of interest or fractional anisotropy values. To provide an automated tract identification paradigm that corrects for artifacts created by tumor edema and infiltration and provides a consistent, accurate method of fiber bundle identification. An automated tract identification paradigm was developed and evaluated for glioma surgery. A fiber bundle atlas was generated from 6 healthy participants. Fibers of a test set (including 3 healthy participants and 10 patients with brain tumors) were clustered adaptively with this atlas. Reliability of the identified tracts in both groups was assessed by comparison with 2 experts with the Cohen κ used to quantify concurrence. We evaluated 6 major fiber bundles: cingulum bundle, fornix, uncinate fasciculus, arcuate fasciculus, inferior fronto-occipital fasciculus, and inferior longitudinal fasciculus, the last 3 tracts mediating language function. The automated paradigm demonstrated a reliable and practical method to identify white mater tracts, despite mass effect, edema, and tract infiltration. When the tumor demonstrated significant mass effect or shift, the automated approach was useful for providing an initialization to guide the expert with identification of the specific tract of interest. We report a reliable paradigm for the automated identification of white matter pathways in patients with gliomas. This approach should enhance the neurosurgical objective of maximal safe resections. AF, arcuate fasciculusDTI, diffusion tensor imagingIFOF, inferior fronto-occipital fasciculusILF, inferior longitudinal fasciculusROI, region of interestWM, white matter.

A New Paradigm of Organizational Identity and Organizational Identification

A New Paradigm of Organizational Identity and Organizational Identification

Abstract LB-237: Vaccination increases the breadth and diversity of melanoma neoantigen-specific T cells in humans

Abstract Melanoma genomes harbor somatic mutations that are caused by exposure to mutagens such as UV light. Tumor missense mutations (MM), translated into amino acid substitutions (AAS), may provide a form of non-self that elicits tumor specific T cell immunity. Indeed, T cell immunity directed against tumor encoded AAS has been reported in humans with cutaneous melanoma, thus implicating MM as a source of patient specific (private) neoantigens. However, a systematic evaluation of these putative neoantigens as validated targets is lacking and it is unknown whether the immune response directed against tumor encoded AAS can be augmented by vaccination. Here we show that vaccination against melanoma AAS-encoding peptides augments naturally occurring T cell immunity and reveals new HLA class I restricted private neoantigens in patients with advanced melanoma. Neoantigen specific T cells recognized naturally processed and presented antigen but failed to recognize wild type (non-mutated) antigen. The presentation of neoantigens by HLA-A*02:01 in human melanoma was confirmed by mass spectrometry. As determined by TCRβ CDR3 DNA sequencing, vaccination promotes a repertoire of neoantigen-specific T cells that is highly diverse in terms of both TCRβ usage and clonal composition. No evidence of autoimmunity was apparent after vaccination. Our results demonstrate that tumor MM can be targeted as neoantigens and vaccination directed at tumor AAS somatic mutations broadens the antigenic breadth and clonal diversity of anti-tumor immunity. These findings provide a new paradigm for private neoantigen identification in neoplasia and may form the basis of personalized cancer immunotherapies targeting somatic mutations. Citation Format: Beatriz M. Carreno, Vincent Magrini, Michelle Becker-Hapak, Saghar Kaabinejadian, Jasreet Hundal, Allegra A. Petti, Amy Ly, Wen-Rong Lie, William H. Hildebrand, Elaine R. Mardis, Gerald P. Linette. Vaccination increases the breadth and diversity of melanoma neoantigen-specific T cells in humans. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-237. doi:10.1158/1538-7445.AM2015-LB-237

Aligning the 3Rs with new paradigms in the safety assessment of chemicals.

There are currently several factors driving a move away from the reliance on in vivo toxicity testing for the purposes of chemical safety assessment. Progress has started to be made in the development and validation of non-animal methods. However, recent advances in the biosciences provide exciting opportunities to accelerate this process and to ensure that the alternative paradigms for hazard identification and risk assessment deliver lasting 3Rs benefits, whilst improving the quality and relevance of safety assessment. The NC3Rs, a UK-based scientific organisation which supports the development and application of novel 3Rs techniques and approaches, held a workshop recently which brought together over 20 international experts in the field of chemical safety assessment. The aim of this workshop was to review the current scientific, technical and regulatory landscapes, and to identify key opportunities towards reaching these goals. Here, we consider areas where further strategic investment will need to be focused if significant impact on 3Rs is to be matched with improved safety science, and why the timing is right for the field to work together towards an environment where we no longer rely on whole animal data for the accurate safety assessment of chemicals.

A New Paradigm for Known Metabolite Identification in Metabonomics/Metabolomics: Metabolite Identification Efficiency

A new paradigm is proposed for assessing confidence in the identification of known metabolites in metabonomics studies using NMR spectroscopy approaches. This new paradigm is based upon the analysis of the amount of metabolite identification information retrieved from NMR spectra relative to the molecular size of the metabolite. Several new indices are proposed including: metabolite identification efficiency (MIE) and metabolite identification carbon efficiency (MICE), both of which can be easily calculated. These indices, together with some guidelines, can be used to provide a better indication of known metabolite identification confidence in metabonomics studies than existing methods. Since known metabolite identification in untargeted metabonomics studies is one of the key bottlenecks facing the science currently, it is hoped that these concepts based on molecular spectroscopic informatics, will find utility in the field.

Origin replication complex binding, nucleosome depletion patterns, and a primary sequence motif can predict origins of replication in a genome with epigenetic centromeres.

ABSTRACTOrigins of DNA replication are key genetic elements, yet their identification remains elusive in most organisms. In previous work, we found that centromeres contain origins of replication (ORIs) that are determined epigenetically in the pathogenic yeast Candida albicans. In this study, we used origin recognition complex (ORC) binding and nucleosome occupancy patterns in Saccharomyces cerevisiae and Kluyveromyces lactis to train a machine learning algorithm to predict the position of active arm (noncentromeric) origins in the C. albicans genome. The model identified bona fide active origins as determined by the presence of replication intermediates on nondenaturing two-dimensional (2D) gels. Importantly, these origins function at their native chromosomal loci and also as autonomously replicating sequences (ARSs) on a linear plasmid. A “mini-ARS screen” identified at least one and often two ARS regions of ≥100 bp within each bona fide origin. Furthermore, a 15-bp AC-rich consensus motif was associated with the predicted origins and conferred autonomous replicating activity to the mini-ARSs. Thus, while centromeres and the origins associated with them are epigenetic, arm origins are dependent upon critical DNA features, such as a binding site for ORC and a propensity for nucleosome exclusion.

Frequency difference limens and auditory cue trading in CBA/CaJ mice (Mus musculus)

Mice are emerging as an important behavioral model for studies of auditory perception and acoustic communication. These mammals frequently produce ultrasonic vocalizations, although the details of how these vocalizations are used for communication are not entirely understood. An important step in determining how they might be differentiating their calls is to measure discrimination and identification of the dimensions of various acoustic stimuli. Here, behavioral operant conditioning methods were employed to assess frequency difference limens for pure tones. We found that their thresholds were similar to those in other rodents but higher than in humans. We also asked mice, in an identification paradigm, whether they would use frequency or duration differences to classify stimuli varying on those two dimensions. We found that the mice classified the stimuli based on frequency rather than duration.

Besoin de cognition, besoin d’évaluer, besoin de clôture : proposition d’échelles en langue française et approche socio-normative des besoins dits fondamentaux

Introduction and objectivesAfter leading a validation of questionnaires about three fundamental needs in French language (need for cognition, closing and evaluation), we tested in two studies that fundamental needs could be subjected to social constraints and could be considered differently than exclusively like stable personality characteristics and motivational drivers of action. MethodUsing the paradigm of judges (study 1) and the paradigm of identification (study 2), the results argue for a normative approach, at least as regards the need for cognition and assess. ResultsThe results of the first study show that individuals consider more favorably targets with strong need rather than low need and especially in social contexts with high social utility (that is to say, the professional context in comparison with the friendly context). The results of the second study show that when the questionnaires about needs “as would a person having been previously well or poorly assessed” participants get higher scores high on the need for cognition questionnaire in the first case than in the second. The results regarding the need for closure are more mixed. ConclusionThe results are discussed in a socio-normative perspective.

Subspace predictive repetitive control to mitigate periodic loads on large scale wind turbines

Manufacturing and maintenance costs arising out of wind turbine dynamic loading are one of the largest bottlenecks in the roll-out of wind energy. Individual Pitch Control (IPC) is being researched for cost reduction through load alleviation; it poses a challenging mechatronic problem due to its multi-input, multi-output (MIMO) nature and actuation constraints related to the wear of pitch bearings. To address these issues, Subspace Predictive Repetitive Control (SPRC), a novel repetitive control strategy based on the subspace identification paradigm, is presented. First, the Markov parameters of the system are identified online in a recursive manner. These parameters are used to build up the lifted matrices needed to predict the output over the next period. From these matrices an adaptive repetitive control law is derived. To account for actuator limitations, the known shape of wind-induced disturbances is exploited to perform repetitive control in a reduced-dimension basis function subspace. The SPRC methodology is implemented on a high-fidelity numerical aeroelastic environment for wind turbines. Load reductions are achieved similar to those obtained with classical IPC approaches, while considerably limiting the frequency content of the actuator signals.

Effects of stimulus duration and inter-letter spacing on letter-in-string identification

Effects of stimulus duration and inter-letter spacing were studied in a letter-in-string identification paradigm. Participants were shown strings of 5 random consonants (e.g., PGKDM) centered on fixation and were asked to identify the letter that had appeared at a post-cued location. Stimulus duration was manipulated in Experiment 1 (13ms–91ms), and inter-letter spacing manipulated in Experiment 2 (for a fixed stimulus duration of 26ms). We contrasted performance to outer-letters (positions 1 and 5) with non-central inner letters (positions 2 and 4), the first-letter (position 1) with the final letter (position 5), and the central-letter (position 3) with the other inner letters (positions 2 and 4). The outer-letter advantage and the first-letter advantage were present throughout the entire range of exposure durations, whereas the central-letter advantage increased with longer exposures. On the other hand, increased spacing reduced both the outer-letter advantage and the first-letter advantage, whereas it led to a greater central-letter advantage. Changes in acuity and crowding as a function of stimulus exposure and inter-letter spacing, can account for this pattern of results.

Evaluating Vibrotactile Dimensions for the Design of Tactons

Vibrotactile stimuli are defined in terms of their amplitude, frequency, waveform and temporal profile all of which have been varied to create tactons. A number of approaches have been adopted to design tactons including multidimensional scaling, iterative empirical methods and using perceptual processing models. The objective of the present set of experiments was to create sets of tactons based on the properties of the dimensions of vibrotactile stimuli. An absolute identification paradigm was used in which each of nine tactons was presented eight times using a tactor mounted on either the index finger or forearm. It was found that tactons created by varying the frequency, amplitude and temporal profile of the vibrotactile stimuli were correctly identified on 73-83 percent of the trials, with a mean information transfer of 2.41 bits. The latter metric indicates that for these sets of nine tactons between five and six could be reliably identified. The vibrotactile stimuli delivered in the experiments were identified as consistently on the forearm as the hand and the IT values were similar at the two locations. This suggests that sites other than the hand can be used effectively in tactile communication systems and that it is channel capacity that ultimately determines performance on this type of task.

System Identification: New Paradigms, Challenges, and Opportunities

The traditional paradigm of system identification employs prior information on system structures and environments and input/output observation data to derive system models. Extensive research and development on its methodologies, theoretical foundation, algorithms, verifications, and applications over the past half century have established a mature field with a rich literature and substantial benchmark applications. However, rapid advancement in science, technology, engineering, and social medias has ushered in a new era of systems science and control in which challenges and opportunities are abundant for system identification. In this sense, system identification remains an exciting, young, viable, and critical field that mandates new paradigms to meet such challenges. This article points out some potentially important aspects of system identification in these new paradigms, suggests some worthy areas of research focus, and most importantly opens the forum for further discussions.

Is Phenylbutazone a Genotoxic Carcinogen? A Weight-of-Evidence Assessment

Published in silico, in vitro, in vivo laboratory animal and human data, together with information on biotransformation and data from structure-activity analyses with two decision-tree systems (ACToR and Toxtree), have been used in a weight-of-evidence (WoE) assessment to determine whether phenylbutazone (PBZ) is a genotoxic or a non-genotoxic carcinogen. This was undertaken to facilitate the risk assessment of human exposure to this veterinary drug via the consumption of horsemeat from treated animals. Despite problems with data interpretation at all tiers of the database, it was concluded that PBZ behaves like a genotoxic carcinogen with a threshold dose. This conclusion is based mainly on the results of a definitive rodent bioassay, and on the following observations: a) that PBZ has weak in vitro activity only at high concentrations in some genotoxicity assays, accompanied by high levels of cytotoxicity; b) that it (and a major metabolite) is able to cause sister chromatid exchanges in vivo in rodents; and c) that it can induce cytogenetic effects in vivo in humans. It also takes into account the known and predicted activities of the parent drug, some of its metabolites and two structural analogues, and, importantly, several of the drug's other biochemical effects that are unrelated to toxicity. However, this conclusion is not fully supported by all the evidence, and much of the information is based on old papers. Therefore, more studies are required to establish whether the concentration thresholds seen in vitro would translate to dose thresholds for carcinogenicity, such that a safe dose-level could be defined for the purposes of assessing risk. It was disappointing that a WoE approach to evaluating all of the available hazard data, as is increasingly being advocated to improve the hazard identification paradigm, was unable to provide definitive answers in this case, particularly in view of the large numbers of animals that had been used to provide much of the information.

Using multiple methods to characterize the phenotype of individuals with a family history of major depressive disorder

BackgroundUnaffected relatives (URs) of individuals with major depressive disorder (MDD) are biologically more vulnerable to depression. We compare healthy URs and controls at the level of phenotype (symptoms and functioning) and endophenotype (negative emotion bias), and further investigate the interrelation between these and the contribution of environmental early life stress. MethodsURs (n=101), identified using Family History Screen interview methods and matched controls completed written and interview questions assessing symptoms of depression and anxiety, negative cognitive style, life functioning and early life stress. Biases in emotion processing were measured using a facial expression of emotion identification paradigm. ResultsCompared to controls, URs reported higher levels of depression and anxiety, a stronger negative cognitive bias, and poorer functioning and lower satisfaction with life. URs were slower to correctly identify fear and sad facial expressions. A slower response time to identify sad faces was correlated with lower quality of life in the social domain. Early life stress (ELS) did not contribute significantly to any outcome. LimitationsThe methodology relies on accurate reporting of participants' own psychiatric history and that of their family members. The degree of vulnerability varies among URs. ConclusionsA family history of depression accounts for subtle differences in symptom levels and functioning without a necessary role of ELS. A negative emotion bias in processing emotion may be one vulnerability marker for MDD. Biological markers may affect functioning measures before symptoms at the level of experience.

A Small Molecule Screen in Stem-Cell-Derived Motor Neurons Identifies a Kinase Inhibitor as a Candidate Therapeutic for ALS

Amyotrophic lateral sclerosis (ALS) is a rapidly progressing neurodegenerative disease, characterized by motor neuron (MN) death, for which there are no truly effective treatments. Here, we describe a new small molecule survival screen carried out using MNs from both wild-type and mutant SOD1 mouse embryonic stem cells. Among the hits we found, kenpaullone had a particularly impressive ability to prolong the healthy survival of both types of MNs that can be attributed to its dual inhibition of GSK-3 and HGK kinases. Furthermore, kenpaullone also strongly improved the survival of human MNs derived from ALS-patient-induced pluripotent stem cells and was more active than either of two compounds, olesoxime and dexpramipexole, that recently failed in ALS clinical trials. Our studies demonstrate the value of a stem cell approach to drug discovery and point to a new paradigm for identification and preclinical testing of future ALS therapeutics.

Understanding gender bias in face recognition: Effects of divided attention at encoding

Prior research has demonstrated a female own-gender bias in face recognition, with females better at recognizing female faces than male faces. We explored the basis for this effect by examining the effect of divided attention during encoding on females' and males' recognition of female and male faces. For female participants, divided attention impaired recognition performance for female faces to a greater extent than male faces in a face recognition paradigm (Study 1; N=113) and an eyewitness identification paradigm (Study 2; N=502). Analysis of remember–know judgments (Study 2) indicated that divided attention at encoding selectively reduced female participants' recollection of female faces at test. For male participants, divided attention selectively reduced recognition performance (and recollection) for male stimuli in Study 2, but had similar effects on recognition of male and female faces in Study 1. Overall, the results suggest that attention at encoding contributes to the female own-gender bias by facilitating the later recollection of female faces.