Specialization of Perceptual Processes

In this report, I discuss the use of vision to support concrete, everyday activity. I will argue that a variety of interesting tasks can be solved using simple and inexpensive vision systems. I will provide a number of working examples in the form of a state-of-the-art mobile robot, Polly, which uses vision to give primitive tours of the seventh floor of the MIT AI Laboratory. By current standards, the robot has a broad behavioral repertoire and is both simple and inexpensive (the complete robot was built for less than $20,000 using commercial board-level components). The approach I will use will be to treat the structure of the agent's activity---its task and environment---as positive resources for the vision system designer. By performing a careful analysis of task and environment, the designer can determine a broad space of mechanisms which can perform the desired activity. My principal thesis is that for a broad range of activities, the space of applicable mechanisms will be broad enough to include a number mechanisms which are simple and economical. The simplest mechanisms that solve a given problem will typically be quite specialized to that problem. One thus worries that building simple vision systems will be require a great deal of {it ad-hoc} engineering that cannot be transferred to other problems. My second thesis is that specialized systems can be analyzed and understood in a principled manner, one that allows general lessons to be extracted from specialized systems. I will present a general approach to analyzing specialization through the use of transformations that provably improve performance. By demonstrating a sequence of transformations that derive a specialized system from a more general one, we can summarize the specialization of the former in a compact form that makes explicit the additional assumptions that it makes about its environment. The summary can be used to predict the performance of the system in novel environments. Individual transformations can be recycled in the design of future systems.

Analysis of the estrogenic components in kudzu root by bioassay and high performance liquid chromatography

The estrogenic activity of the Chinese herb kudzu root was investigated by a recombinant yeast screening assay (YES). Isoflavones are the main components in the plant, of which puerarin is the most abundant one. The kudzu root extract was separated into four fractions according to the polarity. The crude extract and its sub-fractions, except the water fraction, showed clear estrogenic activity and the potencies were in the range of 10(-3) to 10(-1) g/l. The ligand potency was used to compare the estrogenic activity of these fractions. The crude extract and its sub-fractions were further analyzed by high performance liquid chromatography (HPLC) to correlate the activity and the active components. Bioassay and chemical analysis showed that theoretical estrogenic activity expressed as equivalent 17 beta-estradiol concentration or the cumulative effects are comparable to that experimentally determined by YES. The results showed that the high content of isoflavones as well as the high estrogenic activity could make kudzu root extract an interesting candidate for hormone replacement therapy. (c) 2005 Elsevier Ltd. All rights reserved.

Analysis of the mechanism and regulation of lactose transport and metabolism in Clostridium acetobutylicum ATCC 824.

Although the acetone-butanol-ethanol (ABE) fermentation of Clostridium acetobutylicum is currently uneconomic, the ability of the bacterium to metabolise a wide range of carbohydrates offers the potential for revival based on the use of cheap, low grade substrates. We have investigated the uptake and metabolism of lactose, the major sugar in industrial whey waste, by C. acetobutylicum ATCC 824. Lactose is taken up via a phosphoenolpyruvate (PEP)-dependent phosphotransferase system (PTS) comprising both soluble and membrane-associated components, and the resulting phosphorylated derivative is hydrolysed by a phospho--galactosidase. These activities are induced during growth on lactose, but are absent in glucose-grown cells. Analysis of the C. acetobutylicum genome sequence identified a gene system, lacRFEG, encoding a transcriptional regulator of the DeoR family, IIA and IICB components of a lactose PTS, and phospho--galactosidase. During growth in medium containing both glucose and lactose, C. acetobutylicum exhibited a classical diauxic growth, and the lac operon was not expressed until glucose was exhausted from the medium. The presence upstream of lacR of a potential catabolite responsive element (cre) encompassing the transcriptional start site is indicative of the mechanism of carbon catabolite repression characteristic of low-GC Gram-positive bacteria. A pathway for the uptake and metabolism of lactose by this industrially important organism is proposed.

BLID: an Application of Logical Information Systems in Bioinformatics

Ferr?, S. and King, R. D. (2004) BLID: an Application of Logical Information Systems in Bioinformatics. In P. Eklund (editor), 2nd International Conference on Formal Concept Analysis (ICFCA), Feb 2004. LNCS 2961, Springer.

Homology Induction: the use of machine learning to improve sequence similarity searches

Karwath, A. King, R. Homology induction: the use of machine learning to improve sequence similarity searches. BMC Bioinformatics. 23rd April 2002. 3:11 Additional File Describes the title organims species declaration in one string [http://www.biomedcentral.com/content/supplementary/1471- 2105-3-11-S1.doc] Sponsorship: Andreas Karwath and Ross D. King were supported by the EPSRC grant GR/L62849.

Learning styles and performance in the introductory programming sequence

Thomas, L., Ratcliffe, M., Woodbury, J., and Jarman, E. 2002. Learning styles and performance in the introductory programming sequence. SIGCSE Bull. 34, 1 (Mar. 2002), 33-37.

Analysis of Sequence Periodicity in E. coli Proteins: Empirical Investigation of the ?Duplication and Divergence? Theory of Protein Evolution

Gatherer, D., and McEwan, N.R. (2003). Analysis of sequence periodicity in E. coli proteins: empirical investigation of the 'duplication and divergence' theory of protein evolution. Journal of Molecular Evolution 57, 149-158. RAE2008

A Phylogenetic Mixture Model for Detecting Pattern-Heterogeneity in Gene Sequence or Character-State Data

Mark Pagel, Andrew Meade (2004). A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Systematic Biology, 53(4), 571-581. RAE2008

A role for LH in the regulation of expression of mRNAs encoding components of the insulin-like growth factor (IGF) system in the ovine corpus luteum

P.M. Hastie and W. Haresign (2006). A role for LH in the regulation of expression of mRNAs encoding components of the insulin-like growth factor (IGF) system in the ovine corpus luteum. Animal Reproduction Science, 96(1-2), 196-209. Sponsorship: DEFRA RAE2008

Biobased additives as biodegradability enhancers with application in TPU-based footwear components

Among the wide variety of materials employed in the manufacture of shoes, thermoplastic polyurethanes (TPUs) are one of the most widely used. Given its widespread use, and associated waste management problems, the development of more biodegradable and evironmentally compatible solutions is needed. In this work, a polyester-based TPU used in the footwear industry for outsoles production was modified by compounding with lignin, starch and cellulose at content of 4% (w/w). The biodegradability was evaluated by using agar plate tests with the fungi Aspergillus niger ATCC16404, the Gram-negative bacteria Pseudomonas aeruginosa ATCC9027 and an association of both (consortium), and soil tests at 37 °C and 58 °C. The obtained results evidenced a positive effect of the tested biobased additives, the most favourable results being registered with lignin. These results were corroborated by the structural modifications observed by FTIR analysis. Additionally, mechanical tests prove the suitability of using the lignin modified TPUs for footwear outsoles production.

A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study

BACKGROUND:Blood lipid levels including low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and triglycerides (TG) are highly heritable. Genome-wide association is a promising approach to map genetic loci related to these heritable phenotypes.METHODS:In 1087 Framingham Heart Study Offspring cohort participants (mean age 47 years, 52% women), we conducted genome-wide analyses (Affymetrix 100K GeneChip) for fasting blood lipid traits. Total cholesterol, HDL-C, and TG were measured by standard enzymatic methods and LDL-C was calculated using the Friedewald formula. The long-term averages of up to seven measurements of LDL-C, HDL-C, and TG over a ~30 year span were the primary phenotypes. We used generalized estimating equations (GEE), family-based association tests (FBAT) and variance components linkage to investigate the relationships between SNPs (on autosomes, with minor allele frequency [greater than or equal to]10%, genotypic call rate [greater than or equal to]80%, and Hardy-Weinberg equilibrium p [greater than or equal to] 0.001) and multivariable-adjusted residuals. We pursued a three-stage replication strategy of the GEE association results with 287 SNPs (P < 0.001 in Stage I) tested in Stage II (n ~1450 individuals) and 40 SNPs (P < 0.001 in joint analysis of Stages I and II) tested in Stage III (n~6650 individuals).RESULTS:Long-term averages of LDL-C, HDL-C, and TG were highly heritable (h2 = 0.66, 0.69, 0.58, respectively; each P < 0.0001). Of 70,987 tests for each of the phenotypes, two SNPs had p < 10-5 in GEE results for LDL-C, four for HDL-C, and one for TG. For each multivariable-adjusted phenotype, the number of SNPs with association p < 10-4 ranged from 13 to 18 and with p < 10-3, from 94 to 149. Some results confirmed previously reported associations with candidate genes including variation in the lipoprotein lipase gene (LPL) and HDL-C and TG (rs7007797; P = 0.0005 for HDL-C and 0.002 for TG). The full set of GEE, FBAT and linkage results are posted at the database of Genotype and Phenotype (dbGaP). After three stages of replication, there was no convincing statistical evidence for association (i.e., combined P < 10-5 across all three stages) between any of the tested SNPs and lipid phenotypes.CONCLUSION:Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., < 1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.

Recognition of Human Action Using Moment-Based Feature

The performance of different classification approaches is evaluated using a view-based approach for motion representation. The view-based approach uses computer vision and image processing techniques to register and process the video sequence. Two motion representations called Motion Energy Images and Motion History Image are then constructed. These representations collapse the temporal component in a way that no explicit temporal analysis or sequence matching is needed. Statistical descriptions are then computed using moment-based features and dimensionality reduction techniques. For these tests, we used 7 Hu moments, which are invariant to scale and translation. Principal Components Analysis is used to reduce the dimensionality of this representation. The system is trained using different subjects performing a set of examples of every action to be recognized. Given these samples, K-nearest neighbor, Gaussian, and Gaussian mixture classifiers are used to recognize new actions. Experiments are conducted using instances of eight human actions (i.e., eight classes) performed by seven different subjects. Comparisons in the performance among these classifiers under different conditions are analyzed and reported. Our main goals are to test this dimensionality-reduced representation of actions, and more importantly to use this representation to compare the advantages of different classification approaches in this recognition task.

From Parallel Sequence Representations to Calligraphic Control: A Conspiracy of Neural Circuits

Calligraphic writing presents a rich set of challenges to the human movement control system. These challenges include: initial learning, and recall from memory, of prescribed stroke sequences; critical timing of stroke onsets and durations; fine control of grip and contact forces; and letter-form invariance under voluntary size scaling, which entails fine control of stroke direction and amplitude during recruitment and derecruitment of musculoskeletal degrees of freedom. Experimental and computational studies in behavioral neuroscience have made rapid progress toward explaining the learning, planning and contTOl exercised in tasks that share features with calligraphic writing and drawing. This article summarizes computational neuroscience models and related neurobiological data that reveal critical operations spanning from parallel sequence representations to fine force control. Part one addresses stroke sequencing. It treats competitive queuing (CQ) models of sequence representation, performance, learning, and recall. Part two addresses letter size scaling and motor equivalence. It treats cursive handwriting models together with models in which sensory-motor tmnsformations are performed by circuits that learn inverse differential kinematic mappings. Part three addresses fine-grained control of timing and transient forces, by treating circuit models that learn to solve inverse dynamics problems.

SOVEREIGN: An Autonomous Neural System for Incrementally Learning Planned Action Sequence to Navigate Towards a Rewarded Goal

How do reactive and planned behaviors interact in real time? How are sequences of such behaviors released at appropriate times during autonomous navigation to realize valued goals? Controllers for both animals and mobile robots, or animats, need reactive mechanisms for exploration, and learned plans to reach goal objects once an environment becomes familiar. The SOVEREIGN (Self-Organizing, Vision, Expectation, Recognition, Emotion, Intelligent, Goaloriented Navigation) animat model embodies these capabilities, and is tested in a 3D virtual reality environment. SOVEREIGN includes several interacting subsystems which model complementary properties of cortical What and Where processing streams and which clarify similarities between mechanisms for navigation and arm movement control. As the animat explores an environment, visual inputs are processed by networks that are sensitive to visual form and motion in the What and Where streams, respectively. Position-invariant and sizeinvariant recognition categories are learned by real-time incremental learning in the What stream. Estimates of target position relative to the animat are computed in the Where stream, and can activate approach movements toward the target. Motion cues from animat locomotion can elicit head-orienting movements to bring a new target into view. Approach and orienting movements are alternately performed during animat navigation. Cumulative estimates of each movement are derived from interacting proprioceptive and visual cues. Movement sequences are stored within a motor working memory. Sequences of visual categories are stored in a sensory working memory. These working memories trigger learning of sensory and motor sequence categories, or plans, which together control planned movements. Predictively effective chunk combinations are selectively enhanced via reinforcement learning when the animat is rewarded. Selected planning chunks effect a gradual transition from variable reactive exploratory movements to efficient goal-oriented planned movement sequences. Volitional signals gate interactions between model subsystems and the release of overt behaviors. The model can control different motor sequences under different motivational states and learns more efficient sequences to rewarded goals as exploration proceeds.

Laminar Cortical Dynamics of Cognitive and Motor Working Memory, Sequence Learning and Performance: Toward a Unified Theory of How the Cerebral Cortex Works

How do the layered circuits of prefrontal and motor cortex carry out working memory storage, sequence learning, and voluntary sequential item selection and performance? A neural model called LIST PARSE is presented to explain and quantitatively simulate cognitive data about both immediate serial recall and free recall, including bowing of the serial position performance curves, error-type distributions, temporal limitations upon recall, and list length effects. The model also qualitatively explains cognitive effects related to attentional modulation, temporal grouping, variable presentation rates, phonemic similarity, presentation of non-words, word frequency/item familiarity and list strength, distracters and modality effects. In addition, the model quantitatively simulates neurophysiological data from the macaque prefrontal cortex obtained during sequential sensory-motor imitation and planned performance. The article further develops a theory concerning how the cerebral cortex works by showing how variations of the laminar circuits that have previously clarified how the visual cortex sees can also support cognitive processing of sequentially organized behaviors.