A tool for the qualitative comparison of membrane-embedded and detergent-solubilized membrane protein structures in projection

The calculation of projection structures (PSs) from Protein Data Bank (PDB)-coordinate files of membrane proteins is not well-established. Reports on such attempts exist but are rare. In addition, the different procedures are barely described and thus difficult if not impossible to reproduce. Here we present a simple, fast and well-documented method for the calculation and visualization of PSs from PDB-coordinate files of membrane proteins: the projection structure visualization (PSV)-method. The PSV-method was successfully validated using the PS of aquaporin-1 (AQP1) from 2D crystals and cryo-transmission electron microscopy, and the PDB-coordinate file of AQP1 determined from 3D crystals and X-ray crystallography. Besides AQP1, which is a relatively rigid protein, we also studied a flexible membrane transport protein, i.e. the L-arginine/agmatine antiporter AdiC. Comparison of PSs calculated from the existing PDB-coordinate files of substrate-free and L-arginine-bound AdiC indicated that conformational changes are detected in projection. Importantly, structural differences were found between the PSV-method calculated PSs of the detergent-solubilized AdiC proteins and the PS from cryo-TEM of membrane-embedded AdiC. These differences are particularly exciting since they may reflect a different conformation of AdiC induced by the lateral pressure in the lipid bilayer.

Moving along the mental number line: Interactions between whole-body motion and numerical cognition

Active head turns to the left and right have recently been shown to influence numerical cognition by shifting attention along the mental number line. In the present study, we found that passive whole-body motion influences numerical cognition. In a random-number generation task (Experiment 1), leftward and downward displacement of participants facilitated small number generation, whereas rightward and upward displacement facilitated the generation of large numbers. Influences of leftward and rightward motion were also found for the processing of auditorily presented numbers in a magnitude-judgment task (Experiment 2). Additionally, we investigated the reverse effect of the number-space association (Experiment 3). Participants were displaced leftward or rightward and asked to detect motion direction as fast as possible while small or large numbers were auditorily presented. When motion detection was difficult, leftward motion was detected faster when hearing small number and rightward motion when hearing large number. We provide new evidence that bottom-up vestibular activation is sufficient to interact with the higher-order spatial representation underlying numerical cognition. The results show that action planning or motor activity is not necessary to influence spatial attention. Moreover, our results suggest that self-motion perception and numerical cognition can mutually influence each other.

Human and embodied energy analysis applied to water source protection and household water treatment interventions used in Mali, West Africa

As water quality interventions are scaled up to meet the Millennium Development Goal of halving the proportion of the population without access to safe drinking water by 2015 there has been much discussion on the merits of household- and source-level interventions. This study furthers the discussion by examining specific interventions through the use of embodied human and material energy. Embodied energy quantifies the total energy required to produce and use an intervention, including all upstream energy transactions. This model uses material quantities and prices to calculate embodied energy using national economic input/output-based models from China, the United States and Mali. Embodied energy is a measure of aggregate environmental impacts of the interventions. Human energy quantifies the caloric expenditure associated with the installation and operation of an intervention is calculated using the physical activity ratios (PARs) and basal metabolic rates (BMRs). Human energy is a measure of aggregate social impacts of an intervention. A total of four household treatment interventions – biosand filtration, chlorination, ceramic filtration and boiling – and four water source-level interventions – an improved well, a rope pump, a hand pump and a solar pump – are evaluated in the context of Mali, West Africa. Source-level interventions slightly out-perform household-level interventions in terms of having less total embodied energy. Human energy, typically assumed to be a negligible portion of total embodied energy, is shown to be significant to all eight interventions, and contributing over half of total embodied energy in four of the interventions. Traditional gender roles in Mali dictate the types of work performed by men and women. When the human energy is disaggregated by gender, it is seen that women perform over 99% of the work associated with seven of the eight interventions. This has profound implications for gender equality in the context of water quality interventions, and may justify investment in interventions that reduce human energy burdens.

Expert-novice Differences in Geologic Field Mapping and Related Cognition

The geosciences are often characterized as a visuospatial field - that is, one in which success depends upon the ability to mentally manipulate, rotate, project, and bend objects. To what extent is the assumption of strong spatial visualization skills among geoscientists correct? This talk will discuss two studies that investigated geoscience expert and novice spatial visualization, both in laboratory experiments and in a novel field study.

The subjective present and its modulation in clinical contexts

Time is a basic dimension in psychology, underlying behavior and experience. Timing and time perception constitute implicit processes that are often inaccessible to the individual person. Research in this field has shown that timing is involved in many areas of clinical significance. In the projects presented here, we combine timing with seemingly different fields of research, such as psychopathology, perceptual grouping, and embodied cognition. Focusing on the time scale of the subjective present, we report findings from three different clinical studies: (1) We studied perceived causality in schizophrenia patients, finding that perceptual grouping (‘binding’, ‘Gestalt formation’), which leads to visual causality perceptions, did not distinguish between patients and healthy controls. Patients however did integrate context (provided by the temporal distribution of auditory context stimuli) less into perceptions, in significant contrast to controls. This is consistent with reports of higher inaccuracy in schizophrenia patients’ temporal processing. (2) In a project on auditory Gestalt perception we investigated auditory perceptual grouping in schizophrenia patients. The mean dwell time was positively related to how much patients were prone to auditory hallucinations. Dwell times of auditory Gestalts may be regarded as operationalizations of the subjective present; findings thus suggested that patients with hallucinations had a shorter present. (3) The movement correlations of interacting individuals were used to study the non-verbal synchrony between therapist and patient in psychotherapy sessions. We operationalized the duration of an embodied ‘social present’ by the statistical significance of such associations, finding a window of roughly 5.7 seconds in conversing dyads.We discuss that temporal scales of nowness may be modifiable, e.g., by mindfulness. This yields promising goals for future research on timing in the clinical context: psychotherapeutic techniques may alter binding processes, hence the subjective present of individuals, and may affect the social present in therapeutic interactions.

Bodily and Embodied: Being Human in the Tradition of the Hebrew Bible

A depiction of the ancient Hebrew understanding of the human being must take into account the fact that the Bible does not contain a systematic anthropology, but unfolds the multiplicity of human existence inductively, aspectively, and in narrative fashion. In comparison to Greek body/soul dualism, but also in the context of body-(de-)construction and gender debates, this circumstance makes it a treasure trove of interesting, often contrasting recollections and insights with liberating potential. This assertion will be illustrated concretely in terms of the nexus points of the human body (throat, heart, and womb), the relationship of humans to animals and angels, and the questions of the power and value of a human being.

Dreams: A tool for the design of dynamically reconfigurable embedded and modular systems

Dynamically Reconfigurable Systems are attracting a growing interest, mainly due to the emergence of novel applications based on this technology. However, commercial tools do not provide enough flexibility to design solutions, while keeping an acceptable design productivity. In this paper, a novel design flow is proposed, targeting dynamically reconfigurable systems. It is fully supported by a tool called Dreams, which is able to implement flexible systems, starting from a set of netlists corresponding to the modules, as well as a system description provided by the user. The tool automatically post-processes the nets, implementing a solution for the communications between reconfigurable regions, as well as the handling of routing conflicts, by means of a custom router. Since the design process of every module and the static system are independent, the proposed flow is compatible with system upgrade at run-time. In this paper, a use case corresponding to the design of a highly regular and parallel mesh-type architecture is described, in order to show the architectural flexibility offered by the tool.

An Empirical Comparison of Reuse in Embedded and Nonembedded Systems

High-quality software, delivered on time and budget, constitutes a critical part of most products and services in modern society. Our government has invested billions of dollars to develop software assets, often to redevelop the same capability many times. Recognizing the waste involved in redeveloping these assets, in 1992 the Department of Defense issued the Software Reuse Initiative. The vision of the Software Reuse Initiative was "To drive the DoD software community from its current "re-invent the software" cycle to a process-driven, domain-specific, architecture-centric, library-based way of constructing software.'' Twenty years after issuing this initiative, there is evidence of this vision beginning to be realized in nonembedded systems. However, virtually every large embedded system undertaken has incurred large cost and schedule overruns. Investigations into the root cause of these overruns implicates reuse. Why are we seeing improvements in the outcomes of these large scale nonembedded systems and worse outcomes in embedded systems? This question is the foundation for this research. The experiences of the Aerospace industry have led to a number of questions about reuse and how the industry is employing reuse in embedded systems. For example, does reuse in embedded systems yield the same outcomes as in nonembedded systems? Are the outcomes positive? If the outcomes are different, it may indicate that embedded systems should not use data from nonembedded systems for estimation. Are embedded systems using the same development approaches as nonembedded systems? Does the development approach make a difference? If embedded systems develop software differently from nonembedded systems, it may mean that the same processes do not apply to both types of systems. What about the reuse of different artifacts? Perhaps there are certain artifacts that, when reused, contribute more or are more difficult to use in embedded systems. Finally, what are the success factors and obstacles to reuse? Are they the same in embedded systems as in nonembedded systems? The research in this dissertation is comprised of a series of empirical studies using professionals in the aerospace and defense industry as its subjects. The main focus has been to investigate the reuse practices of embedded systems professionals and nonembedded systems professionals and compare the methods and artifacts used against the outcomes. The research has followed a combined qualitative and quantitative design approach. The qualitative data were collected by surveying software and systems engineers, interviewing senior developers, and reading numerous documents and other studies. Quantitative data were derived from converting survey and interview respondents' answers into coding that could be counted and measured. From the search of existing empirical literature, we learned that reuse in embedded systems are in fact significantly different from nonembedded systems, particularly in effort in model based development approach and quality where the development approach was not specified. The questionnaire showed differences in the development approach used in embedded projects from nonembedded projects, in particular, embedded systems were significantly more likely to use a heritage/legacy development approach. There was also a difference in the artifacts used, with embedded systems more likely to reuse hardware, test products, and test clusters. Nearly all the projects reported using code, but the questionnaire showed that the reuse of code brought mixed results. One of the differences expressed by the respondents to the questionnaire was the difficulty in reuse of code for embedded systems when the platform changed. The semistructured interviews were performed to tell us why the phenomena in the review of literature and the questionnaire were observed. We asked respected industry professionals, such as senior fellows, fellows and distinguished members of technical staff, about their experiences with reuse. We learned that many embedded systems used heritage/legacy development approaches because their systems had been around for many years, before models and modeling tools became available. We learned that reuse of code is beneficial primarily when the code does not require modification, but, especially in embedded systems, once it has to be changed, reuse of code yields few benefits. Finally, while platform independence is a goal for many in nonembedded systems, it is certainly not a goal for the embedded systems professionals and in many cases it is a detriment. However, both embedded and nonembedded systems professionals endorsed the idea of platform standardization. Finally, we conclude that while reuse in embedded systems and nonembedded systems is different today, they are converging. As heritage embedded systems are phased out, models become more robust and platforms are standardized, reuse in embedded systems will become more like nonembedded systems.

A PHENOMENOLOGY OF MIMETIC LEARNING AND MULTIMODAL COGNITION: INTEGRATING EXPERIENTIAL KNOWLEDGE INTO PROGRAMS IN RHETORIC, COMPOSITION, AND TECHNICAL COMMUNICATION

My dissertation emphasizes a cognitive account of multimodality that explicitly integrates experiential knowledge work into the rhetorical pedagogy that informs so many composition and technical communication programs. In these disciplines, multimodality is widely conceived in terms of what Gunther Kress calls “socialsemiotic” modes of communication shaped primarily by culture. In the cognitive and neurolinguistic theories of Vittorio Gallese and George Lakoff, however, multimodality is described as a key characteristic of our bodies’ sensory-motor systems which link perception to action and action to meaning, grounding all communicative acts in knowledge shaped through body-engaged experience. I argue that this “situated” account of cognition – which closely approximates Maurice Merleau-Ponty’s phenomenology of perception, a major framework for my study – has pedagogical precedence in the mimetic pedagogy that informed ancient Sophistic rhetorical training, and I reveal that training’s multimodal dimensions through a phenomenological exegesis of the concept mimesis. Plato’s denigration of the mimetic tradition and his elevation of conceptual contemplation through reason, out of which developed the classic Cartesian separation of mind from body, resulted in a general degradation of experiential knowledge in Western education. But with the recent introduction into college classrooms of digital technologies and multimedia communication tools, renewed emphasis is being placed on the “hands-on” nature of inventive and productive praxis, necessitating a revision of methods of instruction and assessment that have traditionally privileged the acquisition of conceptual over experiential knowledge. The model of multimodality I construct from Merleau-Ponty’s phenomenology, ancient Sophistic rhetorical pedagogy, and current neuroscientific accounts of situated cognition insists on recognizing the significant role knowledges we acquire experientially play in our reading and writing, speaking and listening, discerning and designing practices.

The embodied embedded character of system 1 processing

In the last thirty years, a relatively large group of cognitive scientists have begun characterising the mind in terms of two distinct, relatively autonomous systems. To account for paradoxes in empirical results of studies mainly on reasoning, Dual Process Theories were developed. Such Dual Process Theories generally agree that System 1 is rapid, automatic, parallel, and heuristic-based and System 2 is slow, capacity-demanding, sequential, and related to consciousness. While System 2 can still be decently understood from a traditional cognitivist approach, I will argue that it is essential for System 1 processing to be comprehended in an Embodied Embedded approach to Cognition.© MSM 2013.