Sat, 26 Jul 2008 04:27:23 BST CiteULike: Author Woods http://www.citeulike.org/author/Woods CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/group/2608/article/2834549 <i>Nature (25 May 2008)</i> Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins Nathan Joh Andrew Min Salem Faham Julian Whitelegge Duan Yang Virgil Woods James Bowie doi:10.1038/nature06977 Nature (25 May 2008) 2008-05-26T13:58:20-00:00 2008 Nature 0028-0836 Nature Publishing Group protein_engineering protein_folding structure http://www.citeulike.org/user/burcusumer/article/3036692 <i>European Journal of Communication, Vol. 16, No. 4. (1 December 2001), pp. 477-504.</i><br /><br />European Community audiovisual policy, and particularly public service broadcasting (PSB), exhibit tensions between different types of policy objectives: the social, political and cultural on the one hand and economic on the other. Thus, while the Community recognizes the importance of PSB as a public good (i.e. non-individualized goods or benefits, which are for the benefit of, and enjoyed by, the community), which has democratic potential, it also subjects any state funding for PSB to the limitation that `such funding does not affect trading conditions and competition in the Community to an extent which would be contrary to the common interest'. This article aims to identify the Community view of PSB as necessitated by its perceived role in society and juxtapose those requirements against the operation of Community competition policy. 10.1177/0267323101016004003 Defining European Public Service Broadcasting J Harrison LM Woods doi:10.1177/0267323101016004003 European Journal of Communication, Vol. 16, No. 4. (1 December 2001), pp. 477-504. 2008-07-23T11:24:32-00:00 2001 European Journal of Communication 16 4 477 504 no-tag http://www.citeulike.org/user/EschenbaecherS/article/1272776 <i>Arch Insect Biochem Physiol, Vol. 55, No. 3. (March 2004), pp. 153-168.</i><br /><br />Although phosphorus has long been considered an important factor in the growth of diverse biota such as bacteria, algae, and zooplankton, insect nutrition has classically focused on dietary protein and energy content. However, research in elemental stoichiometry has suggested that primary producer biomass has similar N:P ratios in aquatic and terrestrial systems, and phosphorus-rich herbivores in freshwater systems frequently face phosphorus-limited nutritional conditions. Therefore, herbivorous insects should also be prone to phosphorus limitation. We tested this prediction by rearing Manduca sexta larvae on artificial and natural (Datura wrightii leaves) diets containing varying levels of phosphorus (approximately 0.20, 0.55, or 1.2% phosphorus by dry weight). For both artificial and natural diets, increased dietary phosphorus significantly increased growth rates and body phosphorus contents, and shortened the time to the final instar molt. Caterpillars did not consistently exhibit compensatory feeding for phosphorus on either type of diet. The growth and body phosphorus responses were not explicable by changes in amounts of potassium or calcium, which co-varied with phosphorus in the diets. Concentrations of phosphorus in D. wrightii leaves collected in the field varied over a range in which leaf phosphorus is predicted to affect M. sexta's growth rates. These results suggest that natural variation in dietary phosphorus is likely to affect the growth rate and population dynamics of M. sexta, and perhaps larval insects more generally. Dietary phosphorus affects the growth of larval Manduca sexta. MC Perkins HA Woods JF Harrison JJ Elser doi:10.1002/arch.10133 Arch Insect Biochem Physiol, Vol. 55, No. 3. (March 2004), pp. 153-168. 2007-05-02T22:36:55-00:00 2004 Arch Insect Biochem Physiol 0739-4462 55 3 153 168 larvae http://www.citeulike.org/user/austin/article/804401 <i>Bioinformatics, Vol. 22, No. 14. (15 July 2006)</i><br /><br />MOTIVATION: For several decades, free energy minimization methods have been the dominant strategy for single sequence RNA secondary structure prediction. More recently, stochastic context-free grammars (SCFGs) have emerged as an alternative probabilistic methodology for modeling RNA structure. Unlike physics-based methods, which rely on thousands of experimentally-measured thermodynamic parameters, SCFGs use fully-automated statistical learning algorithms to derive model parameters. Despite this advantage, however, probabilistic methods have not replaced free energy minimization methods as the tool of choice for secondary structure prediction, as the accuracies of the best current SCFGs have yet to match those of the best physics-based models. RESULTS: In this paper, we present CONTRAfold, a novel secondary structure prediction method based on conditional log-linear models (CLLMs), a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. In a series of cross-validation experiments, we show that grammar-based secondary structure prediction methods formulated as CLLMs consistently outperform their SCFG analogs. Furthermore, CONTRAfold, a CLLM incorporating most of the features found in typical thermodynamic models, achieves the highest single sequence prediction accuracies to date, outperforming currently available probabilistic and physics-based techniques. Our result thus closes the gap between probabilistic and thermodynamic models, demonstrating that statistical learning procedures provide an effective alternative to empirical measurement of thermodynamic parameters for RNA secondary structure prediction. AVAILABILITY: Source code for CONTRAfold is available at http://contra.stanford.edu/contrafold/. CONTACT: chuongdo@cs.stanford.edu. CONTRAfold: RNA secondary structure prediction without physics-based models. CB Do DA Woods S Batzoglou doi:10.1093/bioinformatics/btl246 Bioinformatics, Vol. 22, No. 14. (15 July 2006) 2006-08-17T18:46:12-00:00 2006 Bioinformatics 1460-2059 22 14 folding prediction rna secondary structure http://www.citeulike.org/user/smarchesini/article/3007076 <i>Appl. Opt., Vol. 47, No. 10. (1 April 2008), pp. 1673-1683.</i><br /><br />We describe a camera to record coherent scattering patterns with a soft-x-ray free-electron laser (FEL). The camera consists of a laterally graded multilayer mirror, which reflects the diffraction pattern onto a CCD detector. The mirror acts as a bandpass filter for both the wavelength and the angle, which isolates the desired scattering pattern from nonsample scattering or incoherent emission from the sample. The mirror also solves the particular problem of the extreme intensity of the FEL pulses, which are focused to greater than 10 14 W/cm 2 . The strong undiffracted pulse passes through a hole in the mirror and propagates onto a beam dump at a distance behind the instrument rather than interacting with a beam stop placed near the CCD. The camera concept is extendable for the full range of the fundamental wavelength of the free electron laser in Hamburg (FLASH) FEL (i.e., between 6 and 60 nm) and into the water window. We have fabricated and tested various multilayer mirrors for wavelengths of 32, 16, 13.5, and 4.5 nm. At the shorter wavelengths mirror roughness must be minimized to reduce scattering from the mirror. We have recorded over 30,000 diffraction patterns at the FLASH FEL with no observable mirror damage or degradation of performance. Camera for coherent diffractive imaging and holography with a soft-x-ray free-electron laser Sa?a Bajt Henry Chapman Eberhard Spiller Jennifer Alameda Bruce Woods Matthias Frank Michael Bogan Anton Barty Sebastien Boutet Stefano Marchesini Stefan Hau-Riege Janos Hajdu David Shapiro Appl. Opt., Vol. 47, No. 10. (1 April 2008), pp. 1673-1683. 2008-07-15T22:25:41-00:00 2008 Appl. Opt. 47 10 1673 1683 OSA diffractive holography imaging http://www.citeulike.org/user/matjes/article/2341798 <i>(11 May 2008)</i><br /><br />Digital Image Processing is a third generation book that builds on two highly successful earlier editions and the authors' twenty years of academic and industrial experience in image processing. The book provides an introduction to basic concepts and methodologies for image processing and develops the foundation for further study in this diverse and rapidly evolving field. The topics covered range from enhancement and restoration to image encoding, segmentation, description, recognition, and interpretation. These topics are illustrated by numerous computer-processed images. Digital Image Processing Rafael Gonzalez Richard Woods (11 May 2008) 2008-02-06T14:24:16-00:00 2008 Addison-Wesley Pub (Sd) book http://www.citeulike.org/user/Oleksandr/article/2973893 <i>Brain Research, Vol. 848, No. 1-2. (27 November 1999), pp. 114-123.</i><br /><br />Insulin and leptin are hypothesized to be [`]adiposity signals' for the long-term regulation of body weight by the brain. Accordingly, a change in the plasma levels of leptin or insulin indicates a state of altered energy homeostasis and adiposity, and the brain responds by adjusting food intake to restore adipose tissue mass to a regulated level. The candidate site for the brain's detection of leptin adiposity signaling is the hypothalamic arcuate nucleus, where leptin inhibits expression neuropeptide Y and increases expression of the pro-opiomelanocortin (POMC) precursor of [alpha]MSH. Insulin also inhibits arcuate nucleus expression of neuropeptide Y but its effects on other hypothalamic signaling systems are not known. Leptin-responsive neurons in the arcuate nucleus are hypothesized to project to the paraventricular nucleus and lateral hypothalamic area where they are proposed to influence the expression of peptides that regulate food intake. Future development of this model will incorporate brain pathways for integration of leptin and insulin adiposity signaling to the hypothalamus with meal-related signals that act in the caudal brainstem. Recent research showing that leptin and insulin enhance the satiety action of peripheral CCK, thereby causing meals to be terminated earlier and reducing cumulative food intake, suggests that hypothalamic pathways that are sensitive to leptin and insulin adiposity signals have anatomical connections with caudal brainstem neurons that respond to meal-related signals and regulate meal size. The recent findings that insulin alters the expression and function of neural transporters for dopamine and norepinephrine indicate that adiposity signals may influence food intake by acting on non-peptide neurotransmitter systems. Insulin and leptin: dual adiposity signals to the brain for the regulation of food intake and body weight Denis Baskin Figlewicz Randy Seeley Stephen Woods Daniel Porte Michael Schwartz doi:10.1016/S0006-8993(99)01974-5 Brain Research, Vol. 848, No. 1-2. (27 November 1999), pp. 114-123. 2008-07-08T22:28:07-00:00 1999 Brain Research 848 1-2 114 123 insulin leptin http://www.citeulike.org/user/kndiaye/article/2518575 <i>Cereb. Cortex, Vol. 17, No. 7. (1 July 2007), pp. 1550-1560.</i><br /><br />Findings from previous magnetic resonance imaging studies of sex differences in gray matter have been inconsistent, with some showing proportionally increased gray matter in women and some showing no differences between the sexes. Regional sex differences in gray matter thickness have not yet been mapped over the entire cortical surface in a large sample of subjects spanning the age range from early childhood to old age. We applied algorithms for cortical pattern matching and techniques for measuring cortical thickness to the structural magnetic resonance images of 176 healthy individuals between the ages of 7 and 87 years. We also mapped localized differences in brain size. Maps of sex differences in cortical thickness revealed thicker cortices in women in right inferior parietal and posterior temporal regions even without correcting for total brain volume. In these regions, the cortical mantle is up to 0.45 mm thicker, on average, in women than in men. Analysis of a subset of 18 female and 18 male subjects matched for age and brain volume confirmed the significance of thicker gray matter in temporal and parietal cortices in females, independent of brain size differences. Further analyses were conducted in the adult subjects where gender differences were evaluated using height as a covariate, and similar sex differences were observed even when body size differences between the sexes were controlled. Together, these results suggest that greater cortical thickness in posterior temporal inferior parietal regions in females relative to males are independent of differences in brain or body size. Age-by-sex interactions were not significant in the temporoparietal region, suggesting that sex differences in these regions are present from at least late childhood and then are maintained throughout life. Male brains were larger than female brains in all locations, though male enlargement was most prominent in the frontal and occipital poles, bilaterally. Given the large sample and the large range of ages studied, these results help to address controversies in the study of central nervous system sexual dimorphisms. 10.1093/cercor/bhl066 Sex Differences in Cortical Thickness Mapped in 176 Healthy Individuals between 7 and 87 Years of Age Elizabeth Sowell Bradley Peterson Eric Kan Roger Woods June Yoshii Ravi Bansal Dongrong Xu Hongtu Zhu Paul Thompson Arthur Toga doi:10.1093/cercor/bhl066 Cereb. Cortex, Vol. 17, No. 7. (1 July 2007), pp. 1550-1560. 2008-03-12T08:11:48-00:00 2007 Cereb. Cortex 17 7 1550 1560 brain brain-asymmetry mri sexual-dimorphism http://www.citeulike.org/user/cgravlee/article/2449632 <i>Field Methods, Vol. 18, No. 4. (1 November 2006), pp. 382-397.</i><br /><br />This article evaluates the use of handheld computers for systematic observation of the social and physical environments. Handheld computers, also known as personal digital assistants (PDAs), make the advantages of computer-assisted data collection (CADC) more accessible to field-based researchers. In particular, CADC with handheld computers may improve data quality, reduce turnaround time, and enhance research capacity for community-academic partnerships. Here, we describe our experiences using handheld computers for the Healthy Environments Partnership's Neighborhood Observational Checklist, an instrument for systematic observation of the social and physical environments. We discuss hardware and software considerations, observer training and implementation strategies, and observer attitudes toward using handhelds in the field. We conclude that handheld computers are a feasible alternative to pen-and-paper forms, and we identify ways that future researchers can maximize the advantages of CADC with handheld computers to advance our understanding of how neighborhood context relates to individual-level outcomes. 10.1177/1525822X06293067 Handheld Computers for Direct Observation of the Social and Physical Environment Clarence Gravlee Shannon Zenk Sachiko Woods Zachary Rowe Amy Schulz doi:10.1177/1525822X06293067 Field Methods, Vol. 18, No. 4. (1 November 2006), pp. 382-397. 2008-02-29T23:50:37-00:00 2006 Field Methods 18 4 382 397 handhelds mcapi methods http://www.citeulike.org/user/domt/article/2963537 <i>(24 July 2007)</i><br /><br />* Corporations have finally realized the value of collaboration tools for knowledge sharing and Wiki is the open source technology for creating collaborative Web sites, as either a public site on the Internet or on a private intranet site * Shows readers how to set up Wikis in a corporate setting or on a personal site so that users can retrieve information, post information, and edit the content * Covers everything from choosing a Wiki engine to administration and maintenance * Discusses the advantages of using Wiki in a corporate environment, which companies such as Microsoft, Boeing, Disney, and Motorola have already discovered Wikis for Dummies (For Dummies (Computers)) Dan Woods Peter Thoeny (24 July 2007) 2008-07-04T09:58:28-00:00 2007 Wiley & Sons collaboration ub wiki http://www.citeulike.org/user/paulschlesinger/article/2946222 <i>J. Biol. Chem., Vol. 283, No. 27. (4 July 2008), pp. 19112-19118.</i><br /><br />Bif-1 interacts with Bax and enhances its conformational rearrangement, resulting in apoptosis. However, the molecular mechanism governing the interaction between Bif-1 and Bax is poorly defined. Here we provide evidence that Bif-1 is phosphorylated, an event that can be repressed by apoptotic stimuli. The protein kinase c-Src binds to and directly phosphorylates Bif-1 on tyrosine 80. Moreover, Src phosphorylation of Bif-1 suppresses the interaction between Bif-1 and Bax, resulting in the inhibition of Bax activation during anoikis. Together, these results suggest that phosphorylation of Bif-1 impairs its binding to Bax and represses apoptosis, providing another mechanism by which Src oncogenic signaling can prevent cell death. 10.1074/jbc.M709882200 Src Directly Phosphorylates Bif-1 and Prevents Its Interaction with Bax and the Initiation of Anoikis Hirohito Yamaguchi Nicholas Woods Jay Dorsey Yoshinori Takahashi Nicole Gjertsen Timothy Yeatman Jie Wu Hong-Gang Wang doi:10.1074/jbc.M709882200 J. Biol. Chem., Vol. 283, No. 27. (4 July 2008), pp. 19112-19118. 2008-07-01T01:38:57-00:00 2008 J. Biol. Chem. 283 27 19112 19118 activation bax bif phsophrylation http://www.citeulike.org/user/bernardjb/article/2929475 <i>Optometry and vision science : official publication of the American Academy of Optometry, Vol. 81, No. 3. (March 2004), pp. 205-213.</i><br /><br />BACKGROUND: Electronic display devices hold the potential to improve access to written material by people with low vision. For those with central field loss, the optimal form of electronic text presentation may vary according to the location of the preferred retinal locus, but this has never been investigated. In this study, we examined the relationship between preferred retinal locus location and reading rate for four electronic display formats (rapid serial visual presentation, horizontal scroll, vertical scroll, and page). METHODS: Short sentences were presented in each format to 35 low-vision (most with central field loss) and 14 age-matched control subjects. Subjects read aloud to determine maximum oral reading rate and read silently to determine preferred silent reading rate. RESULTS: With the exception of page format, maximum oral reading rates were faster than silent preferred reading rates for both groups of subjects. For the low-vision group, there was no significant difference in maximum oral reading rates between the four display formats; and when reading at a preferred silent rate, page format was faster than the other three formats. Though page format was read more quickly, half of the low-vision subjects preferred the horizontal-scroll format. Contrary to our predictions, there was no significant effect of preferred retinal locus location (vertical vs. lateral) on reading rate and no significant interaction between preferred retinal locus location and display format. CONCLUSIONS: The differences between maximum oral and preferred silent reading rates and the lack of a relationship between reading rates and preferred display format reinforce the importance of patient preference in the evaluation and selection of a device or display format during rehabilitation. Preferred retinal locus and reading rate with four dynamic text presentation formats. AR Bowers RL Woods E Peli Optometry and vision science : official publication of the American Academy of Optometry, Vol. 81, No. 3. (March 2004), pp. 205-213. 2008-06-26T09:52:58-00:00 2004 Optometry and vision science : official publication of the American Academy of Optometry 1040-5488 81 3 205 213 no-tag http://www.citeulike.org/user/drivard/article/2926539 <i>Pattern Analysis and Machine Intelligence, IEEE Transactions on, Vol. 19, No. 4. (1997), pp. 405-410.</i><br /><br />This paper presents a method for combining classifiers that uses estimates of each individual classifier's local accuracy in small regions of feature space surrounding an unknown test sample. An empirical evaluation using five real data sets confirms the validity of our approach compared to some other combination of multiple classifiers algorithms. We also suggest a methodology for determining the best mix of individual classifiers Combination of multiple classifiers using local accuracy estimates K Woods WP Kegelmeyer K Bowyer doi:10.1109/34.588027 Pattern Analysis and Machine Intelligence, IEEE Transactions on, Vol. 19, No. 4. (1997), pp. 405-410. 2008-06-25T17:47:51-00:00 1997 Pattern Analysis and Machine Intelligence, IEEE Transactions on 19 4 405 410 classifier_ensemble http://www.citeulike.org/user/bhamcnil/article/444875 <i>Science, Vol. 286, No. 5449. (24 December 1999), pp. 2526-2528.</i> Cortical Mechanisms of Human Imitation Marco Iacoboni Roger Woods Marcel Brass Harold Bekkering John Mazziotta Giacomo Rizzolatti doi:10.1126/science.286.5449.2526 Science, Vol. 286, No. 5449. (24 December 1999), pp. 2526-2528. 2005-12-19T22:39:21-00:00 1999 Science 286 5449 2526 2528 no-tag http://www.citeulike.org/user/adilson_mohr/article/355441 <i>J Comput Chem, Vol. 26, No. 16. (December 2005), pp. 1668-1688.</i><br /><br />We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates. (c) 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1668-1688, 2005. The Amber biomolecular simulation programs. DA Case TE Cheatham T Darden H Gohlke R Luo KM Merz A Onufriev C Simmerling B Wang RJ Woods doi:10.1002/jcc.20290 J Comput Chem, Vol. 26, No. 16. (December 2005), pp. 1668-1688. 2005-10-19T23:51:42-00:00 2005 J Comput Chem 0192-8651 26 16 1668 1688 no-tag http://www.citeulike.org/user/fiacobelli/article/452279 <i>(2004), pp. 194-201.</i> Caring for Agents and Agents that Care: Building Empathic Relations with Synthetic Agents Ana Paiva Joao Dias Daniel Sobral Ruth Aylett Polly Sobreperez Sarah Woods Carsten Zoll Lynne Hall doi:10.1109/AAMAS.2004.82 (2004), pp. 194-201. 2005-12-28T21:13:20-00:00 2004 194 201 IEEE Computer Society no-tag http://www.citeulike.org/user/napvasconcelos/article/131501 <i>(15 January 2002)</i> Digital Image Processing (2nd Edition) Rafael Gonzalez Richard Woods (15 January 2002) 2005-03-17T20:14:20-00:00 2002 Prentice Hall no-tag http://www.citeulike.org/user/RamuAnandakrishnan/article/2902878 <i>Molecular Simulation, Vol. 34, No. 4. (2008), pp. 349-364.</i><br /><br />GLYCAM06 is a generalisable biomolecular force field that is extendible to diverse molecular classes in the spirit of a small-molecule force field. Here we report parameters for lipids, lipid bilayers and glycolipids for use with GLYCAM06. Only three lipid-specific atom types have been introduced, in keeping with the general philosophy of transferable parameter development. Bond stretching, angle bending, and torsional force constants were derived by fitting to quantum mechanical data for a collection of minimal molecular fragments and related small molecules. Partial atomic charges were computed by fitting to ensemble-averaged quantum-computed molecular electrostatic potentials. In addition to reproducing quantum mechanical internal rotational energies and experimental valence geometries for an array of small molecules, condensed-phase simulations employing the new parameters are shown to reproduce the bulk physical properties of a DMPC lipid bilayer. The new parameters allow for molecular dynamics simulations of complex systems containing lipids, lipid bilayers, glycolipids, and carbohydrates, using an internally consistent force field. By combining the AMBER parameters for proteins with the GLYCAM06 parameters, it is also possible to simulate proteinlipid complexes and proteins in biologically relevant membrane-like environments. Extension of the GLYCAM06 biomolecular force field to lipids, lipid bilayers and glycolipids MB Tessier ML Demarco AB Yongye RJ Woods doi:10.1080/08927020701710890 Molecular Simulation, Vol. 34, No. 4. (2008), pp. 349-364. 2008-06-17T17:13:26-00:00 2008 Molecular Simulation 34 4 349 364 Taylor & Francis amber force_field ligand http://www.citeulike.org/user/laposalucci/article/2879818 <i>Comparative Politics, Vol. 27, No. 2. (1995), pp. 187-203.</i><br /><br />The long-term effects of urbanization and secularization, the end of the Cold War, and the European Community's escalation of demands on the Italian state to rationalize its bureaucracy and bring its budget deficit under control have rendered the postwar pattern of center-periphery integration in Italy obsolete. As a new type of social movement, the Northern League is attempting to constitute a new political identity in Italy by contraposing the crisis of the political center with the purported vitality of the periphery. The Crisis of Center-Periphery Integration in Italy and the Rise of Regional Populism: The Lombard League Dwayne Woods doi:10.2307/422164 Comparative Politics, Vol. 27, No. 2. (1995), pp. 187-203. 2008-06-10T14:34:44-00:00 1995 Comparative Politics 27 2 187 203 Ph.D. Program in Political Science of the City University of New York italy lega right http://www.citeulike.org/user/abcxyzooo/article/1915927 <i>(21 August 2007)</i><br /><br /><B></B> <I>THE</I> leader in the field for more than twenty years, this introduction to basic concepts and methodologies for digital image processing continues its cutting-edge focus on <I>contemporary</I> developments in <I>all</I> mainstream areas of image processing. Completely self-contained, heavily illustrated, and mathematically accessible, it has a scope of application that is not limited to the solution of specialized problems. <B></B> Digital Image Fundamentals. Image Enhancement in the Spatial Domain. Image Enhancement in the Frequency Domain. Image Restoration. Color Image Processing. Wavelets and Multiresolution Processing. Image Compression. Morphological Image Processing. Image Segmentation. Representation and Description. Object Recognition. <B></B> For technicians interested in the fundamentals and contemporary applications of digital imaging processing Digital Image Processing (3rd Edition) Rafael Gonzalez Richard Woods (21 August 2007) 2007-11-14T20:52:38-00:00 2007 Prentice Hall no-tag http://www.citeulike.org/user/mebrown/article/147649 <i>International Affairs, Vol. 81, No. 2. (March 2005), pp. 393-409.</i> The shifting politics of foreign aid Ngair Woods doi:10.1111/j.1468-2346.2005.00457.x International Affairs, Vol. 81, No. 2. (March 2005), pp. 393-409. 2005-04-02T10:36:10-00:00 2005 International Affairs 0020-5850 81 2 393 409 Blackwell Publishing no-tag http://www.citeulike.org/user/EschenbaecherS/article/278640 <i>Australian Journal of Entomology, Vol. 44, No. 3. (August 2005), pp. 233-243.</i> Wing shape versus asymmetry as an indicator of changing environmental conditions in insects Ary Hoffmann Richard Woods Eveline Collins Kathleen Wallin Andrea White John Mckenzie doi:10.1111/j.1440-6055.2005.00469.x Australian Journal of Entomology, Vol. 44, No. 3. (August 2005), pp. 233-243. 2005-08-11T10:42:38-00:00 2005 Australian Journal of Entomology 1326-6756 44 3 233 243 Blackwell Publishing fluctuating_asymmetry wing_shape http://www.citeulike.org/group/1660/article/1562081 <i>(20 April 2005)</i><br /><br /><P>The field of software architecture continues to grow in acceptance and</P><P>importance. However, this burgeoning discipline has thus far lacked an</P><P>authoritative treatment that helps its practitioners gain valuable perspective and</P><P>a thorough understanding of the disparate viewpoints that project stakeholders</P><P>bring to the project. In this new book written by two practicing software</P><P>architects, the field of software architecture now has an invaluable resource for</P><P>designing and implementing successful software architectures.</P><P>Colleagues, business management, and ultimately customers appreciate the</P><P>benefit of solid software systems architecture, and this new book helps the</P><P>architect deliver it. This software architecture handbook will be referred to time</P><P>and again. It is a single source of proven practices and valuable advice that will</P><P>help the software architect shepherd a project through its entire lifecycle.</P> Software Systems Architecture: Working With Stakeholders Using Viewpoints and Perspectives Nick Rozanski Eóin Woods (20 April 2005) 2007-08-15T07:33:13-00:00 2005 Addison-Wesley Professional architect documentation software-architecture software-engineering view viewpoint http://www.citeulike.org/user/EschenbaecherS/article/2860978 <i>Environmental Entomology (December 2002), pp. 965-971.</i><br /><br />Changes in the mean, variance and developmental instability of morphological traits have often been used to detect environmental stress in insects. Studies have focused on linear measurements, whereas modern morphometric techniques allow the separation of shape and size effects. To examine stress effects on shape we assessed wings of Helicoverpa punctigera moths exposed to two stresses (pesticide, low temperature). The pyrethroid esfenvelerate applied in larval medium increased development time but did not affect viability, whereas low culture temperatures (7-18°C) influenced both fitness traits. Neither stress affected mean wing size, but both stresses had a marked influence on wing shape. Changes in shape were stress-specific and detectable despite moderate sample sizes. The variance in wing size was altered by low temperature stress but not pesticide exposure. Neither stress increased the asymmetry of wing shape or size; in fact cold stress decreased asymmetry for centroid size. However, measurement error of asymmetry could not be accurately assessed in these wings because scales of both wings could only be removed once. Shape changes therefore appear to be more sensitive to stress in this moth species than other morphological measures, and stress effects on variation among individuals appear to be different than those on asymmetry. Wing Shape and Wing Size Changes as Indicators of Environmental Stress in Helicoverpa punctigera (Lepidoptera: Noctuidae) Moths: Comparing Shifts in Means, Variances, and Asymmetries Ary Hoffmann Eveline Collins Richard Woods Environmental Entomology (December 2002), pp. 965-971. 2008-06-04T12:19:15-00:00 2002 Environmental Entomology 0046-225X 965 971 Entomological Society of America fluctuating_asymmetry moth wing_shape wing_size http://www.citeulike.org/user/paulschlesinger/article/2838072 <i>Biochemistry (24 May 2008)</i><br /><br />Abstract: Deuterium exchange mass spectrometric evaluation of the cobra venom (Naja naja naja) group IA phospholipase A2 (GIA PLA2) was carried out in the presence of metal ions Ca2+ and Ba2+ and phospholipid vesicles. Novel conditions for digesting highly disulfide bonded proteins and a methodology for studying proteinlipid interactions using deuterium exchange have been developed. The enzyme exhibits unexpectedly slow rates of exchange in the two large ±-helices of residues 4353 and 89101, which suggests that these ±-helices are highly rigidified by the four disulfide bonds in this region. The binding of Ca2+ or Ba2+ ions decreased the deuterium exchange rates for five regions of the protein (residues 2427, 2940, 4353, 103110, and 111114). The magnitude of the changes was the same for both ions with the exception of regions of residues 2427 and 103110 which showed greater changes for Ca2+. The crystal structure of the N. naja naja GIA PLA2 contains a single Ca2+ bound in the catalytic site, but the crystal structures of related PLA2s contain a second Ca2+ binding site. The deuterium exchange studies reported here clearly show that in solution the GIA PLA2 does in fact bind two Ca2+ ions. With dimyristoylphosphatidylcholine (DMPC) phospholipid vesicles with 100 ¼M Ca2+ present at 0 °C, significant areas on the i-face of the enzyme showed decreases in the rate of exchange. These areas included regions of residues 38, 1821, and 5664 which include Tyr-3, Trp-61, Tyr-63, and Phe-64 proposed to penetrate the membrane surface. These regions also contained Phe-5 and Trp-19, proposed to bind the fatty acyl tails of substrate. Interaction of Group IA Phospholipase A2 with Metal Ions and Phospholipid Vesicles Probed with Deuterium Exchange Mass Spectrometry John Burke Mark Karbarz Raymond Deems Sheng Li Virgil Woods Edward Dennis doi:10.1021/bi8000962 Biochemistry (24 May 2008) 2008-05-27T18:55:39-00:00 2008 Biochemistry a2 binding membrane metals phospholipase http://www.citeulike.org/user/mattions/article/2837890 <i>Brain Research Reviews, Vol. 55, No. 1. (August 2007), pp. 55-67.</i><br /><br />[`]Local module' is a fundamental functional unit of the central nervous system that can be defined as the minimal portion of one or more neurons and/or one or more glial cells that operates as an independent integrative unit. This review focuses on the importance of neurotransmitter receptor heteromers for the operation of local modules. To illustrate this, we use the striatal spine module (SSM), comprised of the dendritic spine of the medium spiny neuron (MSN), its glutamatergic and dopaminergic terminals and astroglial processes. The SSM is found in the striatum, and although aspects such as neurotransmitters and receptors will be specific to the SSM, some general principles should apply to any local module in the brain. The analysis of some of the receptor heteromers in the SSM shows that receptor heteromerization is associated with particular elaborated functions in this local module. Adenosine A2A receptor-dopamine D2 receptor-glutamate metabotropic mGlu5 receptor heteromers are located adjacent to the glutamatergic synapse of the dendritic spine of the enkephalin MSN, and their cross-talk within the receptor heteromers helps to modulate postsynaptic plastic changes at the glutamatergic synapse. A1 receptor-A2A receptor heteromers are found in the glutamatergic terminals and the molecular cross-talk between the two receptors in the heteromer helps to modulate glutamate release. Finally, dopamine D2 receptor-non-[alpha]7 nicotinic acetylcholine receptor heteromers, which are located in dopaminergic terminals, introduce the new concept of autoreceptor heteromer. Neurotransmitter receptor heteromers and their integrative role in [`]local modules': The striatal spine module Sergi Ferré Luigi Agnati Francisco Ciruela Carme Lluis Amina Woods Kjell Fuxe Rafael Franco doi:10.1016/j.brainresrev.2007.01.007 Brain Research Reviews, Vol. 55, No. 1. (August 2007), pp. 55-67. 2008-05-27T16:18:02-00:00 2007 Brain Research Reviews 55 1 55 67 anatomical msn http://www.citeulike.org/user/pauly123/article/2837787 <i>Tissue engineering. Part C, Methods (14 May 2008)</i><br /><br />Recent studies have shown that mesenchymal stem cells (MSC) with the potential for cell-mediated therapies and tissue engineering applications can be isolated from extracted dental tissues. Here, we investigated the collection, processing, and cryobiological characteristics of MSC from human teeth processed under current good tissue practices (cGTP). Viable dental pulp-derived MSC (DPSC) cultures were isolated from 31 of 40 teeth examined. Of eight DPSC cultures examined more thoroughly, all expressed appropriate cell surface markers and underwent osteogenic, adipogenic, and chondrogenic differentiation in appropriate differentiation medium, thus meeting criteria to be called MSC. Viable DPSC were obtained up to 120 h postextraction. Efficient recovery of DPSC from cryopreserved intact teeth and second-passage DPSC cultures was achieved. These studies indicate that DPSC isolation is feasible for at least 5 days after tooth extraction, and imply that processing immediately after extraction may not be required for successful banking of DPSC. Further, the recovery of viable DPSC after cryopreservation of intact teeth suggests that minimal processing may be needed for the banking of samples with no immediate plans for expansion and use. These initial studies will facilitate the development of future cGTP protocols for the clinical banking of MSC. Collection, Cryopreservation, and Characterization of Human Dental Pulp-Derived Mesenchymal Stem Cells for Banking and Clinical Use. Brandon C Perry Dan Zhou Xiaohua Wu Feng-Chun Yang Michael A Byers T-M Gabriel Chu J Jeffrey Hockema Erik J Woods W Scott Goebel doi:10.1089/ten.tec.2008.0031 Tissue engineering. Part C, Methods (14 May 2008) 2008-05-27T15:19:18-00:00 2008 Tissue engineering. Part C, Methods 1937-3384 pulp stem-cell http://www.citeulike.org/user/ANB/article/2834601 <i>BMJ (Clinical research ed.), Vol. 318, No. 7191. (24 April 1999), pp. 1099-1103.</i><br /><br />OBJECTIVES: To determine whether preoperative optimisation of oxygen delivery improves outcome after major elective surgery, and to determine whether the inotropes, adrenaline and dopexamine, used to enhance oxygen delivery influence outcome. DESIGN: Randomised controlled trial with double blinding between inotrope groups. Setting: York District Hospital, England. SUBJECTS: 138 patients undergoing major elective surgery who were at risk of developing postoperative complications either because of the surgery or the presence of coexistent medical conditions. Interventions: Patients were randomised into three groups. Two groups received invasive haemodynamic monitoring, fluid, and either adrenaline or dopexamine to increase oxygen delivery. Inotropic support was continued during surgery and for at least 12 hours afterwards. The third group (control) received routine perioperative care. MAIN OUTCOME MEASURES: Hospital mortality and morbidity. RESULTS: Overall, 3/92 (3%) preoptimised patients died compared with 8/46 controls (17%) (P=0.007). There were no differences in mortality between the treatment groups, but 14/46 (30%) patients in the dopexamine group developed complications compared with 24/46 (52%) patients in the adrenaline group (difference 22%, 95% confidence interval 2% to 41%) and 28 patients (61%) in the control group (31%, 11% to 50%). The use of dopexamine was associated with a decreased length of stay in hospital. CONCLUSION: Routine preoperative optimisation of patients undergoing major elective surgery would be a significant and cost effective improvement in perioperative care. Reducing the risk of major elective surgery: randomised controlled trial of preoperative optimisation of oxygen delivery. J Wilson I Woods J Fawcett R Whall W Dibb C Morris E McManus BMJ (Clinical research ed.), Vol. 318, No. 7191. (24 April 1999), pp. 1099-1103. 2008-05-26T14:13:53-00:00 1999 BMJ (Clinical research ed.) 0959-8138 318 7191 1099 1103 no-tag http://www.citeulike.org/user/marcia/article/2140094 <i>(2005), pp. 25-35.</i> Using Architectural Perspectives Eoin Woods Nick Rozanski doi:10.1109/WICSA.2005.74 (2005), pp. 25-35. 2007-12-18T09:13:44-00:00 2005 25 35 IEEE Computer Society 2005 architecture views http://www.citeulike.org/user/nguizard/article/1295813 <i>J Comput Assist Tomogr, Vol. 25, No. 5. (t 2001), pp. 805-816.</i><br /><br />PURPOSE: The purpose of this work was to develop methods for defining, constructing, and evaluating a "minimal deformation target" (MDT) brain for multisubject studies based on analysis of the entire group. The goal is to provide a procedure that will create a standard, reproducible target brain image based on common features of a group of three-dimensional MR brain images. METHOD: The average deformation and dispersion distance, derived from discrete three-dimensional deformation fields (DFs), are used to identify the best individual target (BIT) brain. This brain is assumed to be the one with the minimal deformation bias within a group of MR brain images. The BIT brain is determined as the one with the minimal target quality score, our cost function based on the deformation displacement and dispersion distance. The BIT brain is then transformed to the MDT brain using an average DF to create an optimized target brain. This analysis requires the calculation of a large number of DFs. To overcome this limitation, we developed an analysis method (the fast method) that reduces the task from order N2 complexity to one of order N, a tremendous advantage for large-N studies. RESULTS: Multiscale correlation analysis in a group of 20 subjects demonstrated the superiority of warping using the MDT target brain, made from the BIT brain, over several individual and MDT-transformed target brains also from the group. CONCLUSION: Analysis of three-dimensional DF provides a means to quickly create a reproducible MDT target brain for any set of subjects. Warping to the MDT target was shown by an independent multiscale correlation method to produce superior results. Regional spatial normalization: toward an optimal target. P Kochunov JL Lancaster P Thompson R Woods J Mazziotta J Hardies P Fox J Comput Assist Tomogr, Vol. 25, No. 5. (t 2001), pp. 805-816. 2007-05-14T19:33:52-00:00 2001 J Comput Assist Tomogr 0363-8715 25 5 805 816 atlas initial template http://www.citeulike.org/user/Petersarkies/article/2814270 <i>Cancer Cell, Vol. 13, No. 5. (6 May 2008), pp. 454-463.</i><br /><br />Summary We have carried out a cell-based screen aimed at discovering small molecules that activate p53 and have the potential to decrease tumor growth. Here, we describe one of our hit compounds, tenovin-1, along with a more water-soluble analog, tenovin-6. Via a yeast genetic screen, biochemical assays, and target validation studies in mammalian cells, we show that tenovins act through inhibition of the protein-deacetylating activities of SirT1 and SirT2, two important members of the sirtuin family. Tenovins are active on mammalian cells at one-digit micromolar concentrations and decrease tumor growth in vivo as single agents. This underscores the utility of these compounds as biological tools for the study of sirtuin function as well as their potential therapeutic interest. Discovery, In Vivo Activity, and Mechanism of Action of a Small-Molecule p53 Activator Sonia Lain Jonathan Hollick Johanna Campbell Oliver Staples Maureen Higgins Mustapha Aoubala Anna Mccarthy Virginia Appleyard Karen Murray Lee Baker Alastair Thompson Joanne Mathers Stephen Holland Michael Stark Georgia Pass Julie Woods David Lane Nicholas Westwood doi:10.1016/j.ccr.2008.03.004 Cancer Cell, Vol. 13, No. 5. (6 May 2008), pp. 454-463. 2008-05-19T21:10:26-00:00 2008 Cancer Cell 13 5 454 463 cancer p53 therapy http://www.citeulike.org/user/maralena/article/974000 <i>J Biol Chem (29 November 2006)</i><br /><br />MicroRNAs (miRNAs) are a class of non-coding RNAs that post-transcriptionally regulate gene expression via the RNA interference (RNAi) pathway. In addition to roles in normal development, miRNAs have recently been implicated in a range of human diseases, including cancer. We recently demonstrated that a polycistronic cluster of miRNAs, miR-17~92, is oncogenic in a mouse model for Burkitt's lymphoma. This is due, in part, to a reduced apoptotic program. In an effort to understand the regulation of miR-17~92, we have studied the promoter structure of this miRNA cluster. The primary transcript initiates from a consensus initiator sequence downstream of a nonconsensus TATA box. The core promoter region contains two functional E2F transcription factor binding sites. Chromatin immunoprecipitation demonstrates that E2F3 is the primary E2F family member that occupies the promoter. These data place miR-17~92 in a regulatory loop between E2F3 and the miR-17 target E2F1. We propose a model whereby miR-17~92 promotes cell proliferation by shifting the E2F transcriptional balance away from the pro-apoptotic E2F1 and towards the proliferative E2F3 transcriptional network. Direct regulation of an oncogenic microRNA cluster by E2F transcription factors. Keith Woods J Michael Thomson Scott M Hammond doi:10.1074/jbc.C600252200 J Biol Chem (29 November 2006) 2006-12-05T00:28:05-00:00 2006 J Biol Chem 0021-9258 e2f microrna mir-17-92 tf http://www.citeulike.org/group/1024/article/2800612 <i>Clinical Case Studies, Vol. 6, No. 2. (1 April 2007), pp. 181-189.</i><br /><br />Habit reversal (HR) is a multicomponent treatment for tic disorders. This case study incorporated elements of HR (awareness training, self-monitoring, response competition), combined with relaxation, as an intervention for vocal and motor tics in a 10-year-old boy with Tourette's syndrome (TS). Therapy was provided on an outpatient basis at a pediatric clinic. In-home data collection by the boy's mother documented decreased tic frequency during the course of treatment. Clinical improvement was maintained at a 3-month follow-up. These results support previous research demonstrating efficacy of simplified HR in controlling multiple tics associated with TS. 10.1177/1534650106286865 Habit Reversal Treatment of Vocal and Motor Tics in a Child With Tourette's Syndrome Jessica Woods James Luiselli doi:10.1177/1534650106286865 Clinical Case Studies, Vol. 6, No. 2. (1 April 2007), pp. 181-189. 2008-05-15T03:47:43-00:00 2007 Clinical Case Studies 6 2 181 189 case-reports child tic treatment http://www.citeulike.org/user/bhamcnil/article/2797452 <i>Proceedings of the National Academy of Sciences, Vol. 98, No. 24. (20 November 2001), pp. 13995-13999.</i><br /><br />Imitation is a complex phenomenon, the neural mechanisms of which are still largely unknown. When individuals imitate an action that already is present in their motor repertoire, a mechanism matching the observed action onto an internal motor representation of that action should suffice for the purpose. When one has to copy a new action, however, or to adjust an action present in one's motor repertoire to a different observed action, an additional mechanism is needed that allows the observer to compare the action made by another individual with the sensory consequences of the same action made by himself. Previous experiments have shown that a mechanism that directly matches observed actions on their motor counterparts exists in the premotor cortex of monkeys and humans. Here we report the results of functional magnetic resonance experiments, suggesting that in the superior temporal sulcus, a higher order visual region, there is a sector that becomes active both during hand action observation and during imitation even in the absence of direct vision of the imitator's hand. The motor-related activity is greater during imitation than during control motor tasks. This newly identified region has all the requisites for being the region at which the observed actions, and the reafferent motor-related copies of actions made by the imitator, interact. 10.1073/pnas.241474598 Reafferent copies of imitated actions in the right superior temporal cortex Marco Iacoboni Lisa Koski Marcel Brass Harold Bekkering Roger Woods Marie-Charlotte Dubeau John Mazziotta Giacomo Rizzolatti doi:10.1073/pnas.241474598 Proceedings of the National Academy of Sciences, Vol. 98, No. 24. (20 November 2001), pp. 13995-13999. 2008-05-14T10:46:48-00:00 2001 Proceedings of the National Academy of Sciences 98 24 13995 13999 no-tag http://www.citeulike.org/user/briordan/article/2784100 <i>Developmental Science, Vol. 11, No. 3. (May 2008), pp. 361-370.</i> Hemodynamic response to featural changes in the occipital and inferior temporal cortex in infants: a preliminary methodological exploration Wilcox Teresa Bortfeld Heather Woods Rebecca Wruck Eric Boas A David doi:10.1111/j.1467-7687.2008.00681.x Developmental Science, Vol. 11, No. 3. (May 2008), pp. 361-370. 2008-05-11T10:12:08-00:00 2008 Developmental Science 1363-755X 11 3 361 370 Blackwell Publishing optical-imaging semantic-features http://www.citeulike.org/user/dbellmd/article/862086 <i>Medical Education, Vol. 40, No. 10. (October 2006), pp. 973-979.</i> Speed kills? Speed, accuracy, encapsulations and causal understanding Woods N Nicole Howey A Elizabethh Brooks R Lee Norman R Geoffrey doi:10.1111/j.1365-2929.2006.02556.x Medical Education, Vol. 40, No. 10. (October 2006), pp. 973-979. 2006-09-22T21:55:36-00:00 2006 Medical Education 0308-0110 40 10 973 979 Blackwell Publishing causal-knowledge educational-psych learning med-students norman-geoff http://www.citeulike.org/user/carmenv/article/2776588 <i>The Biochemical journal (3 April 2008)</i><br /><br />The LKB1 tumour suppressor phosphorylates and activates AMPK when cellular energy levels are low, thereby suppressing growth through multiple pathways, including inhibiting the mTORC1 kinase that is activated in the majority of human cancers. Blood glucose lowering type-2 diabetes drugs also induce LKB1 to activate AMPK, indicating that these compounds could be used to suppress growth of tumour cells. In this study we investigated the importance of the LKB1-AMPK pathway in regulating tumourigenesis in mice resulting from deficiency of the PTEN tumour suppressor, which drives cell growth through over-activation of the Akt and mTOR kinases. We demonstrate that inhibition of AMPK resulting from a hypomorphic mutation that decreases LKB1 expression does not lead to tumourigenesis on its own, but markedly accelerated tumour development in PTEN+/- mice. In contrast, activating the AMPK pathway by administration of PTEN+/- mice metformin, phenformin or A-769662, significantly delayed tumour onset. We demonstrate that LKB1 is required for activators of AMPK to inhibit mTORC1 signalling as well as cell growth in PTEN deficient cells. Our findings highlight in an animal model relevant to understanding human cancer, the vital role that the LKB1-AMPK pathway plays in suppressing tumourigenesis resulting from loss of PTEN tumour suppressor. They also suggest that pharmacological inhibition of LKB1 and/or AMPK would be undesirable, at least for the treatment of cancers in which the mTORC1-pathway is activated. Most importantly our data demonstrate the potential of AMPK activators such as clinically approved metformin as anti-cancer agents, which will suppress tumour development by triggering a physiological signalling pathway that potently inhibits cell growth. Important role of the LKB1-AMPK pathway in suppressing tumourigenesis in PTEN deficient mice. Xu Huang Stephan Wullschleger Natalia Shpiro Victoria McGuire Kei Sakamoto Yvonne Woods Wendy McBurnie Stewart Fleming Dario Alessi doi:10.1042/BJ20080557 The Biochemical journal (3 April 2008) 2008-05-09T20:36:26-00:00 2008 The Biochemical journal 1470-8728 http://www.citeulike.org/user/IrinaMoreira/article/2767535 <i>TheScientificWorldJournal, Vol. 7 (2007), pp. 48-57.</i><br /><br />Until recently, heptahelical G-protein-coupled receptors (GPCRs) were considered to be expressed as monomers on the cell surface of neuronal and non-neuronal cells. It is now becoming evident that this view must be overtly changed since these receptors can form homodimers, heterodimers, and higher-order oligomers on the plasma membrane. Here we discuss some of the basics and some new concepts of receptor homo- and heteromerization. Dimers-oligomers modify pharmacology, trafficking, and signaling of receptors. First of all, GPCR dimers must be considered as the main molecules that are targeted by neurotransmitters or by drugs. Thus, binding data must be fitted to dimer-based models. In these models, it is considered that the conformational changes transmitted within the dimer molecule lead to cooperativity. Cooperativity must be taken into account in the binding of agonists-antagonists-drugs and also in the binding of the so-called allosteric modulators. Cooperativity results from the intramolecular cross-talk in the homodimer. As an intramolecular cross-talk in the heterodimer, the binding of one neurotransmitter to one receptor often affects the binding of the second neurotransmitter to the partner receptor. Coactivation of the two receptors in a heterodimer can change completely the signaling pathway triggered by the neurotransmitter as well as the trafficking of the receptors. Heterodimer-specific drugs or dual drugs able to activate the two receptors in the heterodimer simultaneously emerge as novel and promising drugs for a variety of central nervous system (CNS) therapeutic applications. Basic concepts in G-protein-coupled receptor homo- and heterodimerization. R Franco V Casadó A Cortés C Ferrada J Mallol A Woods C Lluis EI Canela S Ferré doi:10.1100/tsw.2007.197 TheScientificWorldJournal, Vol. 7 (2007), pp. 48-57. 2008-05-07T22:25:19-00:00 2007 TheScientificWorldJournal 1537-744X 7 48 57 dopamine http://www.citeulike.org/user/miwismith/article/2754233 <i>Journal of Cognitive Engineering and Decision Making, pp. 75-97.</i><br /><br />Intelligence analysis is a high-stakes domain that poses challenges to effective individual and collaborative cognition. The design of support tools and analytical pedagogy could benefit from an understanding of how challenges that are reported in other decision-making literature generalize and are manifested in more naturalistic settings. The objective of this research was to elicit challenges for cognition in collaborative intelligence analysis. Two complementary research methods were used: unstructured interviews with 46 analysts and supervisors, and observations of eight teams of military intelligence analysts conducting a training scenario. Interviews with designers, educators, and practitioners in the intelligence community revealed trends in unsupported cognitive work and cultural challenges, whereas observations from a training exercise for army intelligence analysts instantiated other cognitive challenges of collaborative analysis. This study indicates that analytical style (part tradition and part due to individual reasoning tendencies) can result in premature narrowing, difficulty in reframing, and getting lost in the details. The study also illustrates the effects of friction within and across federated teams, how variable tempo can produce inexpert behavior, and considerations for the design of analytical support tools. This work suggests the value of complementary research methods in the study of other domains involving collaborative work. It is likely that these cognitive challenges affect other domains involving collaborative analysis. Finally, this study suggests that the effects of individual cognitive challenges are difficult to isolate in naturalistic settings and should most likely be considered collectively rather than independently. Challenges for Cognition in Intelligence Analysis Stoney Trent Emily Patterson David Woods Journal of Cognitive Engineering and Decision Making, pp. 75-97. 2008-05-04T16:16:01-00:00 Journal of Cognitive Engineering and Decision Making 1555-3434 75 97 Human Factors and Ergonomics Society no-tag http://www.citeulike.org/user/thenose/article/1824 <i>Nature Neuroscience, Vol. 7, No. 12. (07 November 2004), 1310.</i> Math1 regulates development of the sensory epithelium in the mammalian cochlea Chad Woods Mireille Montcouquiol Matthew Kelley doi:10.1038/nn1349 Nature Neuroscience, Vol. 7, No. 12. (07 November 2004), 1310. 2004-12-06T02:31:58-00:00 2004 Nature Neuroscience 7 12 1310 math1 http://www.citeulike.org/user/bhamcnil/article/2729518 <i>Proceedings of the National Academy of Sciences, Vol. 99, No. 23. (12 November 2002), pp. 15164-15169.</i><br /><br />Visual perception involves the grouping of individual elements into coherent patterns that reduce the descriptive complexity of a visual scene. The physiological basis of this perceptual simplification remains poorly understood. We used functional MRI to measure activity in a higher object processing area, the lateral occipital complex, and in primary visual cortex in response to visual elements that were either grouped into objects or randomly arranged. We observed significant activity increases in the lateral occipital complex and concurrent reductions of activity in primary visual cortex when elements formed coherent shapes, suggesting that activity in early visual areas is reduced as a result of grouping processes performed in higher areas. These findings are consistent with predictive coding models of vision that postulate that inferences of high-level areas are subtracted from incoming sensory information in lower areas through cortical feedback. 10.1073/pnas.192579399 Shape perception reduces activity in human primary visual cortex Scott Murray Daniel Kersten Bruno Olshausen Paul Schrater David Woods doi:10.1073/pnas.192579399 Proceedings of the National Academy of Sciences, Vol. 99, No. 23. (12 November 2002), pp. 15164-15169. 2008-04-28T10:02:47-00:00 2002 Proceedings of the National Academy of Sciences 99 23 15164 15169 no-tag http://www.citeulike.org/user/bhamcnil/article/2717341 <i>J. Cognitive Neuroscience, Vol. 9, No. 1. (January 1997), pp. 133-142.</i> A locus in human extrastriate cortex for visual shape analysis Nancy Kanwisher Roger Woods Marco Iacoboni John Mazziotta J. Cognitive Neuroscience, Vol. 9, No. 1. (January 1997), pp. 133-142. 2008-04-25T10:42:01-00:00 1997 J. Cognitive Neuroscience 9 1 133 142 MIT Press no-tag http://www.citeulike.org/user/meeri/article/2713305 <i>American journal of critical care : an official publication, American Association of Critical-Care Nurses, Vol. 15, No. 2. (March 2006), pp. 206-216.</i><br /><br />BACKGROUND: In patients with aneurysmal subarachnoid hemorrhage, elevation of the head of the bed during vasospasm has been limited in an attempt to minimize vasospasm or its sequelae or both. Consequently, some patients have remained on bed rest for weeks. OBJECTIVES: To determine how elevations of the head of the bed of 20 degrees and 45 degrees affect cerebrovascular dynamics in adult patients with mild or moderate vasospasm after aneurysmal subarachnoid hemorrhage and to describe the response of mild or moderate vasospasm to head-of-bed elevations of 20 degrees and 45 degrees with respect to variables such as grade of subarachnoid hemorrhage and degree of vasospasm. METHODS: A within-patient repeated-measures design was used. The head of the bed was positioned in the sequence of 0 degrees -20 degrees -45 degrees -0 degrees in 20 patients with mild or moderate vasospasm between days 3 and 14 after aneurysmal subarachnoid hemorrhage. Continuous transcranial Doppler recordings were obtained for 2 to 5 minutes after allowing approximately 2 minutes for stabilization in each position. RESULTS: No patterns or trends indicated that having the head of the bed elevated increases vasospasm. As a group, there were no significant differences within patients at the different positions of the head of the bed. Utilizing repeated-measures analysis of variance, P values ranged from .34 to .97, well beyond .05. No neurological deterioration occurred. CONCLUSIONS: In general, elevation of the head of the bed did not cause harmful changes in cerebral blood flow related to vasospasm. Cerebrovascular dynamics with head-of-bed elevation in patients with mild or moderate vasospasm after aneurysmal subarachnoid hemorrhage. PA Blissitt PH Mitchell DW Newell SL Woods B Belza American journal of critical care : an official publication, American Association of Critical-Care Nurses, Vol. 15, No. 2. (March 2006), pp. 206-216. 2008-04-24T15:08:06-00:00 2006 American journal of critical care : an official publication, American Association of Critical-Care Nurses 1062-3264 15 2 206 216 hob neurotrauma tcd http://www.citeulike.org/user/pmendes/article/1412 <i>J Math Biol, Vol. 45, No. 2. (August 2002), pp. 153-181.</i><br /><br />Elementary flux modes (direct reaction routes) are minimal sets of enzymes that can operate at steady state, with all irreversible reactions used in the appropriate direction. They can be interpreted as component pathways of a (bio)chemical reaction network. Here, two different definitions of elementary modes are given and their equivalence is proved. Several algebraic properties of elementary modes are then presented and proved. This concerns, amongst other features, the minimal number of enzymes of the network not used in an elementary mode and the situations where irreversible reactions are replaced by reversible ones. Based on these properties, a refined algorithm is presented, and it is formally proved that this algorithm will exclusively generate all the elementary flux modes of an arbitrary network containing reversible or irreversible reactions or both. The algorithm is illustrated by a biochemical example relevant in nucleotide metabolism. The computer implementation in two different programming languages is discussed. Reaction routes in biochemical reaction systems: algebraic properties, validated calculation procedure and example from nucleotide metabolism. S Schuster C Hilgetag JH Woods DA Fell doi:10.1007/s002850200143 J Math Biol, Vol. 45, No. 2. (August 2002), pp. 153-181. 2004-12-02T01:46:09-00:00 2002 J Math Biol 0303-6812 45 2 153 181 elementary-modes metabolism network-structure http://www.citeulike.org/user/schmoutz/article/2702681 <i>Journal of the experimental analysis of behavior, Vol. 89, No. 2. (March 2008), pp. 209-224.</i><br /><br />The generalized matching law provides precise descriptions of choice, but has not been used to characterize choice between different doses of drugs or different classes of drugs. The current study examined rhesus monkeys' drug self-administration choices between identical drug doses, different doses, different drugs (cocaine, remifentanil, and methohexital), and between drug and drug-paired stimuli. The bias parameter of the generalized matching law was used to quantify preference for one reinforcer over another. Choice between identical drug doses yielded undermatching. Choices between 0.3 microg/kg/injection remifentanil and either 0.1 microg/kg/injection remifentanil or saline plus drug-paired stimuli revealed bias for the 0.3 microg/kg/injection dose. Choice was relatively insensitive to differences in random interval schedule value when one reinforcer was replaced with drug-paired stimulus presentations. Bias for 0.3 microg/kg/injection remifentanil over 10 microg/kg/injection cocaine was seen in one subject, and indifference was generally observed between 0.1 microg/kg/injection remifentanil and 56 microg/kg/injection cocaine and between 30 microg/kg/injection cocaine and 320 microg/kg/injection methohexital. These findings suggest the bias parameter may be useful in quantitatively measuring level of preference, which would be an advantage over concurrent FR procedures that often result in exclusive choice. Quantification of drug choice with the generalized matching law in rhesus monkeys. MN Koffarnus JH Woods Journal of the experimental analysis of behavior, Vol. 89, No. 2. (March 2008), pp. 209-224. 2008-04-22T18:21:30-00:00 2008 Journal of the experimental analysis of behavior 0022-5002 89 2 209 224 no-tag http://www.citeulike.org/user/mvermaat/article/2678033 <i>Journal of the Interest Group in Pure and Applied Logics, Vol. 9 (2) (2001), pp. 157-190.</i><br /><br />Syntax with Variable Binding Murdoch J. Gabbay and Andrew M. Pitts Cambridge University Computer Laboratory, Cambridge, UK Keywords: Abstract syntax; Alpha-conversion; Permutation actions; Set theory; Structural induction Abstract. The permutation model of set theory with atoms (FM-sets), devised by Fraenkel and Mostowski in the 1930s, supports notions of `name-abstraction' and `fresh name' that provide a new way to represent, compute with, and reason about the syntax of formal systems... A New Approach to Abstract Syntax with Variable Binding DM Gabbay J Woods Journal of the Interest Group in Pure and Applied Logics, Vol. 9 (2) (2001), pp. 157-190. 2008-04-16T13:50:38-00:00 2001 Journal of the Interest Group in Pure and Applied Logics 9 (2) 157 190 binding lambda-calculus set-theory http://www.citeulike.org/user/alphabetagamma/article/2676360 <i>Software Engineering, 1996., Proceedings of the 18th International Conference on (1996), pp. 6-15.</i><br /><br />Program understanding is the process of making sense of a complex source code. This process has been considered as computationally difficult and conceptually complex. So far no formal complexity results have been presented, and conceptual models differ from one researcher to the next. We formally prove that program understanding is NP hard. Furthermore, we show that even a much simpler subproblem remains NP hard. However we do not despair by this result, but rather offer an attractive problem solving model for the program understanding problem. Our model is built on a framework for solving constraint satisfaction problems, or CSPs, which are known to have interesting heuristic solutions. Specifically, we can represent and heuristically address previous and new heuristic approaches to the program understanding problem with both existing and specially designed constraint propagation and search algorithms The program understanding problem: analysis and a heuristic approach S Woods Qiang Yang doi:10.1109/ICSE.1996.493397 Software Engineering, 1996., Proceedings of the 18th International Conference on (1996), pp. 6-15. 2008-04-16T07:52:27-00:00 1996 Software Engineering, 1996., Proceedings of the 18th International Conference on 6 15 constraint_programming program_understanding http://www.citeulike.org/user/hannibal_07/article/2670735 <i>Advanced Research in Asynchronous Circuits and Systems, 2000. (ASYNC 2000) Proceedings. Sixth International Symposium on (2000), pp. 162-175.</i><br /><br />AMULET3i is the third generation asynchronous ARM-compatible microprocessor subsystem developed at the University of Manchester. It is internally modular being based around the MARBLE asynchronous on-chip bus, and is also extensible through the addition of conventional clocked synthesizable peripherals via an on-chip synchronous peripheral bus. As such it is capable of forming the core of a wide range of system-on-chip applications, bringing asynchronous design into commercial use in a flexible and easy-to-use configuration. Its performance and area are comparable with clocked equivalents, and its low-power and electromagnetic emission characteristics give it unique capabilities in appropriate applications AMULET3i-an asynchronous system-on-chip JD Garside WJ Bainbridge A Bardsley DM Clark DA Edwards SB Furber J Liu DW Lloyd S Mohammadi S Mohammadi JS Pepper A10 O Petlin A11 S Temple A12 JV Woods A13 doi:10.1109/ASYNC.2000.836999 Advanced Research in Asynchronous Circuits and Systems, 2000. (ASYNC 2000) Proceedings. Sixth International Symposium on (2000), pp. 162-175. 2008-04-14T22:23:57-00:00 2000 Advanced Research in Asynchronous Circuits and Systems, 2000. (ASYNC 2000) Proceedings. Sixth International Symposium on 162 175 asynchronous processors http://www.citeulike.org/user/hannibal_07/article/2670695 <i>Compcon Spring '94, Digest of Papers. (1994), pp. 476-485.</i><br /><br />A fully asynchronous implementation of the ARM microprocessor has been developed in order to investigate the potential of asynchronous logic for low-power applications. The work demonstrates the feasibility of complex asynchronous design and shows that the cost and performance characteristics are similar to clocked designs. AMULET1 is the first attempt at applying asynchronous techniques to a design of this complexity and as such there is much room for improvement. The authors introduce the design approach and organisation of the chip; they then cover the lessons learned from the first design and point towards future strategies for its enhancement and the likely benefits which will accrue from mature asynchronous technology AMULET1: a micropipelined ARM SB Furber P Day JD Garside NC Paver JV Woods doi:10.1109/CMPCON.1994.282880 Compcon Spring '94, Digest of Papers. (1994), pp. 476-485. 2008-04-14T22:04:45-00:00 1994 Compcon Spring '94, Digest of Papers. 476 485 asynchronous processors http://www.citeulike.org/user/pverstra/article/2669745 <i>Ann. Softw. Eng., Vol. 9, No. 1-4. (2000), pp. 5-33.</i> Toward a discipline of scenario-based architectural engineering Rick Kazman Jeromy Carrière Steven Woods Ann. Softw. Eng., Vol. 9, No. 1-4. (2000), pp. 5-33. 2008-04-14T16:45:10-00:00 2000 Ann. Softw. Eng. 1022-7091 9 1-4 5 33 J. C. Baltzer AG, Science Publishers architecture simulation