Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination

The prevailing view of the nuclear genetic code is that it is largely frozen and unambiguous. Flexibility in the nuclear genetic code has been demonstrated in ciliates that reassign standard stop codons to amino acids, resulting in seven variant genetic codes, including three previously undescribed ones reported here. Surprisingly, in two of these species, we find efficient translation of all 64 codons as standard amino acids and recognition of either one or all three stop codons. How, therefore, does the translation machinery interpret a “stop” codon? We provide evidence, based on ribosomal profiling and “stop” codon depletion shortly before coding sequence ends, that mRNA 3′ ends may contribute to distinguishing stop from sense in a context-dependent manner. We further propose that such context-dependent termination/readthrough suppression near transcript ends enables genetic code evolution.

Eidolyzer: a hardware realization of context-guided picture interpretation.

Cover title.

Graph-based Semi-Supervised Learning in Acoustic Modeling for Automatic Speech Recognition

Thesis (Ph.D.)--University of Washington, 2016-06

Experimental manipulation of prior experience: Effects on item and associative recognition

Frequency of exposure to very low- and high-frequency words was manipulated in a three-phase (familiarisation, study, and test) design. During familiarisation, words were presented with their definition (once, four times, or not presented). One week (Experiment 1) or one day (Experiment 2) later, participants studied a list of homogeneous pairs (i.e., pair members were matched on background and familiarisation frequency). Item and associative recognition of high- and very low-frequency words presented in intact, rearranged, old-new, or new-new pairs were tested in Experiment 1. Associative recognition of very low-frequency words was tested in Experiment 2. Results showed that prior familiaris ation improved associative recognition of very low-frequency pairs, but had no effect on high-frequency pairs. The role of meaning in the formation of item-to-item and item-to-context associations and the implications for current models of memory are discussed.

Is the effect of reading misspellings context dependent?

In 48 university students performing single-item spelling recognition, prior exposure to misspelled words improved slightly the accuracy on correctly spelled words and increased markedly the 'false alarm' rate (classifying a misspelling seen at study as correct). In a group given a dictation test (N = 24) the only effect of exposure to misspellings was a small increment in the number of misspellings that matched the misspelling seen at study. The two test groups showed no advantage of having the same display format at study and test (AA or BB vs AB or BA). Experiment 2 (in progress) investigated a format match at study and test against a condition with a new test context (AA or BB vs AC or BC). The results to date suggest an influence of memory of the study trial rather than simply an updating by the study exposures of abstract lexical representations. [ABSTRACT FROM AUTHOR]

Pretend play, mirror self-recognition and imitation: A longitudinal investigation through the second year

The aim in the current study was to investigate the emergence of pretend play, mirror self-recognition, synchronic imitation and deferred imitation in normally developing human infants. A longitudinal study was conducted with 98 infants seen at three-monthly intervals from 12 through to 24 months of age. At each session the infants were tested on a range of tasks assessing the four target skills. Deferred imitation was found to emerge prior to synchronic imitation, pretend play and mirror self-recognition. In contrast, the latter three skills emerged between 18 and 21 months and followed similar developmental trajectories. Deferred imitation was found to hold a prerequisite relation with these three skills. Synchronic imitation, pretend play and mirror self-recognition were not closely associated and no prerequisite relations were found between these skills. These findings are discussed in the context of current theories regarding the development of pretend play, mirror self-recognition, synchronic imitation and deferred imitation in the second year. (C) 2004 Elsevier Inc. All rights reserved.

The role of context in producing item interactions and false memories

Cued recall with an extralist cue poses a challenge for contemporary memory theory in that there is a need to explain how episodic and semantic information are combined. A parallel activation and intersection approach proposes one such means by assuming that an experimental cue will elicit its preexisting semantic network and a context cue will elicit a list memory. These 2 sources of information are then combined by focusing on information that is common to the 2 sources. Two key predictions of that approach are examined: (a) Combining semantic and episodic information can lead to item interactions and false memories, and (b) these effects are limited to memory tasks that involve an episodic context cue. Five experiments demonstrate such item interactions and false memories in cued recall but not in free association. Links are drawn between the use of context in this setting and in other settings.

Play it again: did this melody occur more frequently or was it heard more recently? The role of stimulus familiarity in episodic recognition of music

Episodic recognition of novel and familiar melodies was examined by asking participants to make judgments about the recency and frequency of presentation of melodies over the course of two days of testing. For novel melodies, recency judgments were poor and participants often confused the number of presentations of a melody with its day of presentation; melodies heard frequently were judged as have been heard more recently than they actually were. For familiar melodies, recency judgments were much more accurate and the number of presentations of a melody helped rather than hindered performance. Frequency judgments were generally more accurate than recency judgments and did not demonstrate the same interaction with musical familiarity. Overall, these findings suggest that (1) episodic recognition of novel melodies is based more on a generalized feeling of familiarity than on a specific episodic memory, (2) frequency information contributes more strongly to this generalized memory than recency information, and (3) the formation of an episodic memory for a melody depends either on the overall familiarity of the stimulus or the availability of a verbal label. (C) 2004 Elsevier B.V. All rights reserved.

Representation and learning of visual information for pose recognition

Recovering position from sensor information is an important problem in mobile robotics, known as localisation. Localisation requires a map or some other description of the environment to provide the robot with a context to interpret sensor data. The mobile robot system under discussion is using an artificial neural representation of position. Building a geometrical map of the environment with a single camera and artificial neural networks is difficult. Instead it would be simpler to learn position as a function of the visual input. Usually when learning images, an intermediate representation is employed. An appropriate starting point for biologically plausible image representation is the complex cells of the visual cortex, which have invariance properties that appear useful for localisation. The effectiveness for localisation of two different complex cell models are evaluated. Finally the ability of a simple neural network with single shot learning to recognise these representations and localise a robot is examined.

Technology valuation within the context of transfer collaborations with Chinese machine tool companies

The point of departure for this study was a recognition of the differences in suppliers' and acquirers' judgements of the value of technology when transferred between the two, and the significant impacts of technology valuation on the establishment of technology partnerships and effectiveness of technology collaborations. The perceptions, transfer strategies and objectives, perceived benefits and assessed technology contributions as well as associated costs and risks of both suppliers and acquirers were seen to be the core to these differences. This study hypothesised that the capability embodied in technology to yield future returns makes technology valuation distinct from the process of valuing manufacturing products. The study hence has gone beyond the dimensions of cost calculation and price determination that have been discussed in the existing literature, by taking a broader view of how to achieve and share future added value from transferred technology. The core of technology valuation was argued as the evaluation of the 'quality' of the capability (technology) in generating future value and the effectiveness of the transfer arrangement for best use of such a capability. A dynamic approach comprising future value generation and realisation within the context of specific forms of collaboration was therefore adopted. The research investigations focused on the UK and China machine tool industries, where there are many technology transfer activities and the value issue has already been recognised in practice. Data were gathered from three groups: machine tool manufacturing technology suppliers in the UK and acquirers in China, and machine tool users in China. Data collecting methods included questionnaire surveys and case studies within all the three groups. The study has focused on identifying and examining the major factors affecting value as well as their interactive effects on technology valuation from both the supplier's and acquirer's point of view. The survey results showed the perceptions and the assessments of the owner's value and transfer value from the supplier's and acquirer's point of view respectively. Benefits, costs and risks related to the technology transfer were the major factors affecting the value of technology. The impacts of transfer payment on the value of technology by the sharing of financial benefits, costs and risks between partners were assessed. The close relationship between technology valuation and transfer arrangements was established by which technical requirements and strategic implications were considered. The case studies reflected the research propositions and revealed that benefits, costs and risks in the financial, technical and strategic dimensions interacted in the process of technology valuation within the context of technology collaboration. Further to the assessment of factors affecting value, a technology valuation framework was developed which suggests that technology attributes for the enhancement of contributory factors and their contributions to the realisation of transfer objectives need to be measured and compared with the associated costs and risks. The study concluded that technology valuation is a dynamic process including the generation and sharing of future value and the interactions between financial, technical and strategic achievements.

A configuration framework of manufacturing strategy paradigm in state owned enterprises within China's petrochemical industry:building context-embedded configurations for the paradigm of strategic manufacturing management from exploratory case studies

The role of the production system as a key determinant of competitive performance of business operations- has long been the subject of industrial organization research, even predating the .explicit conceptua1isation of manufacturing, strategy in the literature. Particular emergent production issues such as the globalisation of production, global supply chain management, management of integrated manufacturing and a growing e~busjness environment are expected to critically influence the overall competitive performance and therefore the strategic success of the organization. More than ever, there is a critical need to configure and improve production system and operations competence in a strategic way so as to contribute to the long-term competitiveness of the organization. In order to operate competitively and profitably, manufacturing companies, no matter how well managed, all need a long-term 'strategic direction' for the development of operations competence in order to consistently produce more market value with less cost towards a leadership position. As to the long-term competitiveness, it is more important to establish a dynamic 'strategic perspective' for continuous operational improvements in pursuit of this direction, as well as ongoing reviews of the direction in relation to the overall operating context. However, it also clear that the 'existing paradigm of manufacturing strategy development' is incapable of adequately responding to the increasing complexities and variations of contemporary business operations. This has been factually reflected as many manufacturing companies are finding that methodologies advocated in the existing paradigm for developing manufacturing strategy have very limited scale and scope for contextual contingency in empirical application. More importantly, there has also emerged a deficiency in the multidimensional and integrative profile from a theoretical perspective when operationalising the underlying concept of strategic manufacturing management established in the literature. The point of departure for this study was a recognition of such contextual and unitary limitations in the existing paradigm of manufacturing strategy development when applied to contemporary industrial organizations in general, and Chinese State Owned Enterprises (SOEs) in particular. As China gradually becomes integrated into the world economy, the relevance of Western management theory and its paradigm becomes a practical matter as much as a theoretical issue. Since China markedly differs from Western countries in terms of culture, society, and political and economic systems, it presents promising grounds to test and refine existing management theories and paradigms with greater contextual contingency and wider theoretical perspective. Under China's ongoing programmes of SOE reform, there has been an increased recognition that strategy development is the very essence of the management task for managers of manufacturing companies in the same way as it is for their counterparts in Western economies. However, the Western paradigm often displays a rather naive and unitary perspective of the nature of strategic management decision-making, one which largely overlooks context-embedded factors and social/political influences on the development of manufacturing strategy. This thesis studies the successful experiences of developing manufacturing strategy from five high-performing large-scale SOEs within China’s petrochemical industry. China’s petrochemical industry constitutes a basic heavy industrial sector, which has always been a strategic focus for reform and development by the Chinese government. Using a confirmation approach, the study has focused on exploring and conceptualising the empirical paradigm of manufacturing strategy development practiced by management. That is examining the ‘empirical specifics’ and surfacing the ‘managerial perceptions’ of content configuration, context of consideration, and process organization for developing a manufacturing strategy during the practice. The research investigation adopts a qualitative exploratory case study methodology with a semi-structural front-end research design. Data collection follows a longitudinal and multiple-case design and triangulates case evidence from sources including qualitative interviews, direct observation, and a search of documentations and archival records. Data analysis follows an investigative progression from a within-case preliminary interpretation of facts to a cross-case search for patterns through theoretical comparison and analytical generalization. The underlying conceptions in both the literature of manufacturing strategy and related studies in business strategy were used to develop theoretical framework and analytical templates applied during data collection and analysis. The thesis makes both empirical and theoretical contributions to our understanding of 'contemporary management paradigm of manufacturing strategy development'. First, it provides a valuable contextual contingency of the 'subject' using the business setting of China's SOEs in petrochemical industry. This has been unpacked into empirical configurations developed for its context of consideration, its content and process respectively. Of special note, a lean paradigm of business operations and production management discovered at case companies has significant implications as an emerging alternative for high-volume capital intensive state manufacturing in China. Second, it provides a multidimensional and integrative theoretical profile of the 'subject' based upon managerial perspectives conceptualised at case companies when operationalising manufacturing strategy. This has been unpacked into conceptual frameworks developed for its context of consideration, its content constructs, and its process patterns respectively. Notably, a synergies perspective towards the operating context, competitive priorities and competence development of business operations and production management has significant implications for implementing a lean manufacturing paradigm. As a whole, in so doing, the thesis established a theoretical platform for future refinement and development of context-specific methodologies for developing manufacturing strategy.

Product design in the context of the social needs in less industrialised economies

This thesis is related to the subject of technical innovation, specifically to the activity of design in microenterprises operating in less industrialised economies. Design here is understood as a process, which is not the sole domain of formally trained categories such as engineers, architects or industrial designers. The 'professional boundary' discussion in this investigation is perceived as secondary as, in this context, products are designed, copied or adapted by workers, entrepreneurs themselves, or directly by the poor community. Design capacity at this level is considered to be important both in relation to the conception of capital and consumer goods and to the building up of technical knowledge. Although professional design emerged in Latin America little over three decades ago, this activity has remained marginalised throughout industry. Design activity tends to be concentrated in some product categories in the formalised industrial sector. For microenterprises operating informally, industrial design appears to be unknown. The existing literature pays little attention to 'informal design' capacity. Other areas of knowledge, such as development economies, recognise the importance of microenterprises and technological capability but neglect the potential role of industrial design in small manufacturing units. The management literature, though it focuses on technical innovation and design, has also paid little attention to 'informal design'. In less industrialised economies this neglect is felt by the lack of programmes specifically tailored to create or stimulate 'informal design'. There is a need for recognition of 'informal design' capacity and for the implementation of programmes which specifically target design as a central activity in the manufacturing firm, independent of their size and technological capability. Addressing 'design by the poor for the poor', requires a down-to-earth approach.

Putting e-commerce adoption in a supply chain context

Purpose – The objective of this paper is to gain a better understanding of the impact of context on the adoption of e-commerce in supply chains. Design/methodology/approach – A literature review, 45 semi-structured interviews in four different supply chains in the UK healthcare sector, involving 16 different organisations, and additional documentation is used in this study. Findings – The adoption of e-commerce in supply chains is simultaneously affected by two contextual meta-variables: external pressure, which is influenced by supply chain structure, demand and industry characteristics; and internal readiness, which is influenced by IT, organisational and buying need characteristics. Different combinations of these two main variables lead to four different trade-off situations affecting adoption or non-adoption. Research limitations/implications – The empirical research has been undertaken in the specific context of the UK healthcare supply chains. It would be useful to test our findings in other sectors and countries. Practical implications – The paper helps to understand the contextual factors that affect e-commerce adoption and concludes with a framework that differentiates four situations that can improve managers' and researchers' understanding of e-commerce adoption in the future. Originality/value – The contribution of this paper is the recognition that the adoption of e-commerce is affected by factors in both an organisational and a supply chain context, which simultaneously lead to trade-off decisions. Also, unlike most other studies which refer to supply chains and are limited to an organisational perspective or at most a dyadic perspective, this paper builds up a supply chain picture of context by including perspectives from multiple actors in a chain.

Speech recognition use in healthcare applications

Speech recognition technology is regarded as a key enabler for increasing the usability of applications deployed on mobile devices -- devices which are becoming increasingly prevalent in modern hospital-based healthcare. Although the use of speech recognition is not new to the hospital-based healthcare domain, its use with mobile devices has thus far been limited. This paper presents the results of a literature review we conducted in order to observe the manner in which speech recognition technology has been used in hospital-based healthcare and to gain an understanding of how this technology is being evaluated, in terms of its dependability and reliability, in healthcare settings. Our intent is that this review will help identify scope for future uses of speech recognition technologies in the healthcare domain, as well as to identify implications for the meaningful evaluation of such technologies given the specific context of use.

Pattern recognition analyses of brain activation elicited by happy and neutral faces in unipolar and bipolar depression

Objectives: Recently, pattern recognition approaches have been used to classify patterns of brain activity elicited by sensory or cognitive processes. In the clinical context, these approaches have been mainly applied to classify groups of individuals based on structural magnetic resonance imaging (MRI) data. Only a few studies have applied similar methods to functional MRI (fMRI) data. Methods: We used a novel analytic framework to examine the extent to which unipolar and bipolar depressed individuals differed on discrimination between patterns of neural activity for happy and neutral faces. We used data from 18 currently depressed individuals with bipolar I disorder (BD) and 18 currently depressed individuals with recurrent unipolar depression (UD), matched on depression severity, age, and illness duration, and 18 age- and gender ratio-matched healthy comparison subjects (HC). fMRI data were analyzed using a general linear model and Gaussian process classifiers. Results: The accuracy for discriminating between patterns of neural activity for happy versus neutral faces overall was lower in both patient groups relative to HC. The predictive probabilities for intense and mild happy faces were higher in HC than in BD, and for mild happy faces were higher in HC than UD (all p < 0.001). Interestingly, the predictive probability for intense happy faces was significantly higher in UD than BD (p = 0.03). Conclusions: These results indicate that patterns of whole-brain neural activity to intense happy faces were significantly less distinct from those for neutral faces in BD than in either HC or UD. These findings indicate that pattern recognition approaches can be used to identify abnormal brain activity patterns in patient populations and have promising clinical utility as techniques that can help to discriminate between patients with different psychiatric illnesses.