CiteULike: Author Koehler

A system for traffic sign detection, tracking, and recognition using color, shape, and motion information

C Bahlmann — 2008-07-15T03:38:07-00:00

Intelligent Vehicles Symposium, 2005. Proceedings. IEEE (2005), pp. 255-260.

This paper describes a computer vision based system for real-time robust traffic sign detection, tracking, and recognition. Such a framework is of major interest for driver assistance in an intelligent automotive cockpit environment. The proposed approach consists of two components. First, signs are detected using a set of Haar wavelet features obtained from AdaBoost training. Compared to previously published approaches, our solution offers a generic, joint modeling of color and shape information without the need of tuning free parameters. Once detected, objects are efficiently tracked within a temporal information propagation framework. Second, classification is performed using Bayesian generative modeling. Making use of the tracking information, hypotheses are fused over multiple frames. Experiments show high detection and recognition accuracy and a frame rate of approximately 10 frames per second on a standard PC.

Formation of dense partonic matter in relativistic nucleus-nucleus collisions at RHIC: Experimental evaluation by the PHENIX Collaboration

K Adcox — 2008-07-02T09:39:16-00:00

Nuclear Physics A, Vol. 757, No. 1-2. (8 August 2005), pp. 184-283.

Extensive experimental data from high-energy nucleus-nucleus collisions were recorded using the PHENIX detector at the Relativistic Heavy Ion Collider (RHIC). The comprehensive set of measurements from the first three years of RHIC operation includes charged particle multiplicities, transverse energy, yield ratios and spectra of identified hadrons in a wide range of transverse momenta (pT), elliptic flow, two-particle correlations, nonstatistical fluctuations, and suppression of particle production at high pT. The results are examined with an emphasis on implications for the formation of a new state of dense matter. We find that the state of matter created at RHIC cannot be described in terms of ordinary color neutral hadrons.

Rheology of Steady-State Draining Foams

Raenell Soller — 2008-06-06T18:00:34-00:00

Physical Review Letters, Vol. 100, No. 20. (2008)

We developed the foam drainage rheology technique in order to perform rheological measurements of aqueous foams at a set liquid fraction and fixed bubble radius R without the usual difficulties associated with fluid drainage and bubble coarsening. The shear stress exhibits a power-law dependence on strain-rate, ~n where n0.2. The stress exhibits an inverse dependence on liquid content, ~(1+h)-1, where h=(10) exhibits a diminishing logarithmic trend with . We propose a model based upon film shearing as the dominant source of viscous dissipation.

Web page change and persistence---a four-year longitudinal study

Wallace Koehler — 2008-05-24T01:03:29-00:00

J. Am. Soc. Inf. Sci. Technol., Vol. 53, No. 2. (January 2002), pp. 162-171.

Multicolor spectral karyotyping of rat chromosomes.

A Buwe — 2008-05-27T18:43:22-00:00

Cytogenetic and genome research, Vol. 103, No. 1-2. (2003), pp. 163-168.

Rat and mouse have become important animal models to study various human diseases such as cancer. Cytogenetic analysis of the respective karyotypes is frequently required to investigate the causative genetic defects and especially neoplastic cells often show complex chromosome aberrations and many different marker chromosomes. However, structural homogeneity of the chromosomes in these species as well as less pronounced differences in banding patterns make it difficult to assign genetic abnormalities to certain chromosomes by conventional banding techniques. Here we report for the first time the successful application of multicolor spectral karyotyping (SKY) to rat chromosomes, which allows unequivocal identification of all rat chromosomes with the exception of chromosomes 13 and 14 in different colors, thus enabling the elucidation of even complex rearrangements in the rat karyotype. Flow-sorted chromosome specific painting probes for all 22 rat chromosomes (20 autosomes, X, and Y) were combinatorially labeled by a set of five different fluorochromes and hybridized in situ to metaphase spreads of a healthy rat, to diakineses from testicular material, and to cells from a rat FAO hepatoma cell line. Measuring the complete spectrum at each image point by using the SpectraCube((R)) spectral imaging system and respective computer software allowed identification of the individual rat chromosomes by their specific emission spectra. Classification algorithms in the analysis software can then display the rat chromosomes in specific pseudo-colors and automatically order them in a karyotype table. After its successful application to human and mouse chromosomes, spectral karyotyping of rat chromosomes now also allows cytogenetic screening of the complete rat genome by a single hybridization.

Bacteremia, fever, and splenomegaly caused by a newly recognized bartonella species.

ME Eremeeva — 2008-05-23T03:19:52-00:00

The New England journal of medicine, Vol. 356, No. 23. (7 June 2007), pp. 2381-2387.

Bartonella species cause serious human infections globally, including bacillary angiomatosis, Oroya fever, trench fever, and endocarditis. We describe a patient who had fever and splenomegaly after traveling to Peru and also had bacteremia from an organism that resembled Bartonella bacilliformis, the causative agent of Oroya fever, which is endemic to Peru. However, genetic analyses revealed that this fastidious bacterium represented a previously uncultured and unnamed bartonella species, closely related to B. clarridgeiae and more distantly related to B. bacilliformis. We characterized this isolate, including its ability to cause fever and sustained bacteremia in a rhesus macaque. The route of infection and burden of human disease associated with this newly described pathogen are currently unknown.

Scaling vertical drag forces in granular media

G Hill — 2008-05-02T23:58:00-00:00

EPL (Europhysics Letters), Vol. 72, No. 1. (2005), pp. 137-143.

The average drag forces on intruders slowly plunging into and withdrawing from shallow beds of monodisperse smooth glass beads and of sifted rough sand scale with the immersion depth and lateral dimensions of the intruder. The withdrawal forces are comparable for both types of media; however, the plunging forces for sand are substantially greater than for smooth glass beads. Furthermore, for glass beads, the rescaled plunging and withdrawal forces have two different power law dependences on the immersion depth, with exponents greater than unity.

An optimized embryonic stem cell model for consistent gene expression and developmental studies: a fundamental study.

C Gissel — 2008-04-28T09:15:37-00:00

Thrombosis and haemostasis, Vol. 94, No. 4. (October 2005), pp. 719-727.

In vitro differentiation of embryonic stem (ES) cells results in generation of tissue-specific somatic cells and may represent a powerful tool for general understanding of cellular differentiation and development in vivo. Culturing of most ES cell lines requires murine embryonic fibroblasts (MEF), which may influence adventitiously the genetic differentiation program of ES cells. We compared the expression profile of key developmental genes in the MEF-independent CGR8 ES cell line and in the MEF-dependent D3 ES cell line. Using neomycin-resistant MEFs we demonstrated that MEFs are able to contaminate the D3 ES cells even after removing the MEFs. Subsequently, optimal differentiation conditions were established for the differentiation of CGR8 ES cells into various germ layer cells. Detailed gene expression studies in differentiating CGR8 cells were done by RT-PCR analysis and by microarray analysis demonstrating a general trend of the assessed genes to be expressed either in 3 days- or 10-days old embryoid bodies (EBs) when compared to undifferentiated ES cells. Subsets within the various functional gene classes were defined that are specifically up- or down-regulated in concert. Interestingly, the present results demonstrate that developmental processes toward germ layer formation are irreversible and mostly independent of the culture conditions. Notably, apoptotic and mitochondrial ribosomal genes were down- and up-regulated in 10-days old EBs, respectively, whereas compared to the 3-days old EBs whereas the activity of the extracellular signal-regulated kinase (ERK) 1/2 decreased with progressive development. This article defines a platform for ES cell differentiation and gene expression studies.

Continuous Time-Domain Analysis of Cerebrovascular Autoregulation Using Near-Infrared Spectroscopy

Ken Brady — 2008-04-24T17:03:35-00:00

Stroke, Vol. 38, No. 10. (1 October 2007), pp. 2818-2825.

Background and Purpose-- Assessment of autoregulation in the time domain is a promising monitoring method for actively optimizating cerebral perfusion pressure (CPP) in critically ill patients. The ability to detect loss of autoregulatory vasoreactivity to spontaneous fluctuations in CPP was tested with a new time-domain method that used near-infrared spectroscopic measurements of tissue oxyhemoglobin saturation in an infant animal model. Methods-- Piglets were made progressively hypotensive over 4 to 5 hours by inflation of a balloon catheter in the inferior vena cava, and the breakpoint of autoregulation was determined using laser-Doppler flowmetry. The cerebral oximetry index (COx) was determined as a moving linear correlation coefficient between CPP and INVOS cerebral oximeter waveforms during 300-second periods. A laser-Doppler derived time-domain analysis of spontaneous autoregulation with the same parameters (LDx) was also determined. Results-- An increase in the correlation coefficient between cerebral oximetry values and dynamic CPP fluctuations, indicative of a pressure-passive relationship, occurred when CPP was below the steady state autoregulatory breakpoint. This COx had 92% sensitivity (73% to 99%) and 63% specificity (48% to 76%) for detecting loss of autoregulation attributable to hypotension when COx was above a threshold of 0.36. The area under the receiver-operator characteristics curve for the COx was 0.89. COx correlated with LDx when values were sorted and averaged according to the CPP at which they were obtained (r=0.67). Conclusions-- The COx is sensitive for loss of autoregulation attributable to hypotension and is a promising monitoring tool for determining optimal CPP for patients with acute brain injury. 10.1161/STROKEAHA.107.485706

From business process model to consistent implementation: A case for formal verification methods

J Koehler — 2008-04-23T20:27:55-00:00

(2002)

Today's business applications and their underlying process models are becoming more and more complicated, making the implementation of these processes an increasingly challenging task. On the one hand, tools and methods exist to describe the business processes. On the other hand, different tools and method exist to describe the IT artifacts implementing them. But a significant gap exists between the two. To overcome this gap, new methodologies are sought.

The SNPlex genotyping system: a flexible and scalable platform for SNP genotyping.

AR Tobler — 2008-03-31T12:44:58-00:00

J Biomol Tech, Vol. 16, No. 4. (December 2005), pp. 398-406.

We developed the SNPlex Genotyping System to address the need for accurate genotyping data, high sample throughput, study design flexibility, and cost efficiency. The system uses oligonucleotide ligation/polymerase chain reaction and capillary electrophoresis to analyze bi-allelic single nucleotide polymorphism genotypes. It is well suited for single nucleotide polymorphism genotyping efforts in which throughput and cost efficiency are essential. The SNPlex Genotyping System offers a high degree of flexibility and scalability, allowing the selection of custom-defined sets of SNPs for medium- to high-throughput genotyping projects. It is therefore suitable for a broad range of study designs. In this article we describe the principle and applications of the SNPlex Genotyping System, as well as a set of single nucleotide polymorphism selection tools and validated assay resources that accelerate the assay design process. We developed the control pool, an oligonucleotide ligation probe set for training and quality-control purposes, which interrogates 48 SNPs simultaneously. We present performance data from this control pool obtained by testing genomic DNA samples from 44 individuals. in addition, we present data from a study that analyzed 521 SNPs in 92 individuals. Combined, both studies show the SNPlex Genotyping system to have a 99.32% overall call rate, 99.95% precision, and 99.84% concordance with genotypes analyzed by TaqMan probe-based assays. The SNPlex Genotyping System is an efficient and reliable tool for a broad range of genotyping applications, supported by applications for study design, data analysis, and data management.

Testing Videotape Education for Heart Failure

Carol Smith — 2008-03-28T21:25:10-00:00

Clin Nurs Res, Vol. 14, No. 2. (1 May 2005), pp. 191-205.

This pilot study tested a videotape intervention designed to improve patient selfmanagement of heart failure (HF). Content of the video series (produced professionally under a federal grant) is based on national, scientifically validated guidelines for HF home management. Outcomes tested were HF knowledge, symptom reporting, and functional status. Participants were 10 newly diagnosed HF patients (mean age 67). After viewing the tapes, data indicated participants had a clinically relevant improvement in HF knowledge, and improved or maintained HF health status. None were rehospitalized during the 60-day follow-up period. One patient contacted his/her physician to report weight gain, as prompted by the videotapes. The cost data indicated that patients paid $177 out of pocket monthly for medications and all were low income. These results indicate the need for further testing of the videotape as a potentially cost-effective method of teaching aboutHFself-management and daily home self-monitoring. 10.1177/1054773804273276

The Coming Paradigm Shift in Forensic Identification Science

Michael Saks — 2005-08-05T09:36:22-00:00

Science, Vol. 309, No. 5736. (05 August 2005), pp. 892-895.

Converging legal and scientific forces are pushing the traditional forensic identification sciences toward fundamental change. The assumption of discernible uniqueness that resides at the core of these fields is weakened by evidence of errors in proficiency testing and in actual cases. Changes in the law pertaining to the admissibility of expert evidence in court, together with the emergence of DNA typing as a model for a scientifically defensible approach to questions of shared identity, are driving the older forensic sciences toward a new scientific paradigm.

Science for Kids Outreach Programs: College Students Teaching Science to Elementary School Students and Their Parents.

Birgit Koehler — 2008-02-05T09:24:03-00:00

Journal of Chemical Education, Vol. 76, No. 11. (0 1999), pp. 1505-1509.

Describes an outreach program in which college students plan, develop, and present hands-on workshops to fourth-grade students and their parents. Provides an overview of the pedagogical aims of this approach and a sense of the timeline for putting the program together. (CCM)

Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalised Data Structures.

J Koehler — 2006-06-20T16:55:52-00:00

In Silico Biol, Vol. 5, No. 1. (2005), pp. 33-44.

The structure of a closely integrated data warehouse is described that is designed to link different types and varying numbers of biological networks, sequence analysis methods and experimental results such as those coming from microarrays. The data schema is inspired by a combination of graph based methods and generalised data structures and makes use of ontologies and meta-data. The core idea is to consider and store biological networks as graphs, and to use generalised data structures (GDS) for the storage of further relevant information. This is possible because many biological networks can be stored as graphs: protein interactions, signal transduction networks, metabolic pathways, gene regulatory networks etc. Nodes in biological graphs represent entities such as promoters, proteins, genes and transcripts whereas the edges of such graphs specify how the nodes are related. The semantics of the nodes and edges are defined using ontologies of node and relation types. Besides generic attributes that most biological entities possess (name, attribute description), further information is stored using generalised data structures. By directly linking to underlying sequences (exons, introns, promoters, amino acid sequences) in a systematic way, close interoperability to sequence analysis methods can be achieved. This approach allows us to store, query and update a wide variety of biological information in a way that is semantically compact without requiring changes at the database schema level when new kinds of biological information is added. We describe how this datawarehouse is being implemented by extending the text-mining framework ONDEX to link, support and complement different bioinformatics applications and research activities such as microarray analysis, sequence analysis and modelling/simulation of biological systems. The system is developed under the GPL license and can be downloaded from http://sourceforge.net/projects/ondex/

Genetic Variants Within the LPIN1 Gene, Encoding Lipin, Are Influencing Phenotypes of the Metabolic Syndrome in Humans

Silke Wiedmann — 2008-01-02T04:33:06-00:00

Diabetes, Vol. 57, No. 1. (1 January 2008), pp. 209-217.

OBJECTIVE Lipin, a novel molecular protein expressed by adipocytes, has marked effects on adipose tissue mass, insulin sensitivity, and glucose homeostasis. Thus, we hypothesized that genetic variants within LPIN1 are associated with traits of the metabolic syndrome. RESEARCH DESIGN AND METHODS A total of 15 single nucleotide polymorphisms (SNPs) covering the LPIN1 gene region were genotyped in an age- and sex-stratified sample of the general population (Monitoring Trends and Determinants on Cardiovascular Diseases Study Augsburg; DNA and phenotypes of 1,416 Caucasians). Ten SNPs were also genotyped for replication in an independent sample of 1,030 subjects recruited throughout Germany. The metabolic syndrome was defined via the sum of its core components and, additionally, by a factor score derived from factor analysis. Permutation-based methods were used to test the association between genetic LPIN1 variants and metabolic traits for empirical significance. RESULTS Linkage disequilibrium (LD) analysis revealed three LD blocks encompassing LPIN1. We identified three associated three-marker haplotypes: one common haplotype (26.8% frequency) increases the risk for the metabolic syndrome (odds ratio 1.6 [95% CI 1.22.2]), while the other two, being less common (5.7 and 4.0%), are strongly associated with lower blood pressure levels (systolic blood pressure 127 +/- 18 vs. 135 +/- 20 mmHg; P = 0.0001), a lower BMI (24.6 +/- 3.6 vs. 26.9 +/- 4.1 kg/m2; P = 3.7 x 107) and waist circumference (82 +/- 12 vs. 90 +/- 12 cm; P = 3.2 x 108), lower A1C levels (5.1 +/- 0.7 vs. 5.3 +/- 0.9%; P = 0.0002), as well as a lower metabolic syndrome factor score (0.67 +/- 1.00 vs. 0.04 +/- 1.24; P = 1.4 x 107). Furthermore, the frequencies of arterial hypertension (23.7 vs. 46.4%; P = 0.00001), obesity (12.9 vs. 30.8%; P = 0.0003), diabetes (2.2 vs. 8.2%; P = 0.041), and the presence of three or more metabolic syndrome components (3.3 vs. 13.7%; P = 0.002) were significantly lower than in subjects not carrying one of these protective haplotypes. Strong associations were also observed in the replication sample using the same haplotypes but with effects in the opposite direction. CONCLUSIONS These data suggest that allelic variants of the LPIN1 gene have significant effects in human metabolic traits and thus implicate lipin in the pathophysiology of the metabolic syndrome. 10.2337/db07-0083

Treatment of word-finding deficits in fluent aphasia through the manipulation of spatial attention: Preliminary findings

Vonetta Dotson — 2007-11-15T17:44:12-00:00

Aphasiology, Vol. 22, No. 1. (2008), pp. 1-11.

Background: Attention, the processing of one source of information to the exclusion of others, is important for most cognitive processes, including language. Evidence suggests not only that dysfunctional attention mechanisms contribute to language deficits after stroke, but also that orienting attention to a patient's ipsilesional hemispace recruits attention mechanisms in the intact hemisphere and improves language functions in some persons with aphasia. Aims: The aim of the current research was to offer proof of concept for the strategy of improving picture-naming performance in fluent aphasia by moving stimuli into the left hemispace. It was hypothesised that repeated orientation of attention to the ipsilesional hemispace during picture naming would lead to improved naming accuracy for participants with fluent aphasia. Methods & Procedures: Three participants with stable fluent aphasia received daily treatment sessions that consisted of naming simple line drawings presented 45 degrees to the left of body midline on a computer monitor. Naming probes were administered before initiation of the treatment protocol to establish a baseline, and before each treatment session to measure change during treatment. The C statistic was used to establish the stability of baseline performance and to determine whether the slope of the treatment phases differed significantly from the slope of the baseline. Outcomes & Results: Two of the three participants showed significant improvement over baseline performance in the percent correct of naming probes. One participant showed no improvement over baseline accuracy. Conclusions: Results suggest that engaging right-hemisphere attention mechanisms may improve naming accuracy in some people with fluent aphasia. Findings justify further investigation of this treatment in a larger controlled study.

Classifying Web sites and Web pages: the use of metrics and URL characteristics as markers

Wallace Koehler — 2007-10-17T12:28:25-00:00

Journal of Librarianship and Information Science, Vol. 31, No. 1. (1 March 1999), pp. 21-31.

Points to the way in which computer scientists and librarians working with the World Wide Web are turning to traditional library and information science techniques, such as cataloguing and classification, to bring order to the chaos of the Web. Explores cataloguing opportunities offered by the ephemeral nature of materials on the Web and examines several of the latter's unique characteristics. Suggests the coupling of automated filtering and measuring to the Web record cataloguing process, with particular reference to the ephemeral nature of Web documents and the ability to measure Uniform Resource Locator (URL) and Web document characteristics and migrate them to catalogue records using automated procedures. Reports results of an ongoing longitudinal study of 361 randomly selected Web pages and their Web sites, the data being collected weekly using the Flashsite 1.01 software package. Four basic approaches to ordering information on the Web were studied: postcoordinate keyword and full-text indexes; application of both precoordinate and postcoordinate filters or identifiers to the native document by either authors or indexers; use of thesauri and other classification schemes; and bibliometric techniques employing mapping of hypertext links and other citation systems. Concludes that off-the-shelf technology exists that allows the monitoring of Web sites and Web pages to measure' Web page and Web site characteristics, to process quantified changes, and to write those changes to bibliographic records. Capturing semantic or meaningful change is more complex, but these can be approximated using existing software. 10.1177/096100069903100103

Foam drainage on the microscale II. Imaging flow through single Plateau borders

SA Koehler — 2007-09-20T04:35:11-00:00

Journal of Colloid and Interface Science, Vol. 276, No. 2. (15 August 2004), pp. 439-449.

The liquid in foam forms an interconnected network, which is composed of Plateau borders, nodes, and films. One of the dominant pathways for foam drainage is flow through Plateau borders, and we use confocal microscopy to obtain experimental results for the flow fields inside individual Plateau borders. For three types of surfactants detailed comparisons are made with a model based upon the influence of surface viscosity at free boundaries between the gas in the bubbles and the liquid in the Plateau borders. The model describes the flows well, and we find good agreement between the surface viscosity predicted by this model and representative values found in the literature. We also give a qualitative description of the flow in the nodes.

Drainage of single Plateau borders: Direct observation of rigid and mobile interfaces

Stephan Koehler — 2007-09-20T04:26:50-00:00

Physical Review E, Vol. 66, No. 4. (October 2002), pp. 040601-040601.

Foam drainage varies with surfactant. We present direct measurements of the flow velocity profiles across single Plateau borders; which make up the interconnected channel-like network for liquid flow. For protein foams the interface is rigid; whereas small-surfactant foams show significant interfacial mobility. The results agree with a model that takes into account the shearing of the liquid-gas interface transverse to the flow direction. A significant consequence is that bubble size and liquid volume fraction in a foam affect the relative importance of surface rheology on the drainage behavior.

Two-Particle Microrheology of Quasi-2D Viscous Systems

V Prasad — 2007-09-19T16:35:40-00:00

Physical Review Letters, Vol. 97, No. 17. (2006), 176001.

We study the spatially correlated motions of colloidal particles in a quasi-2D system (human serum albumin protein molecules at an air-water interface) for different surface viscosities s. We observe a transition in the behavior of the correlated motion, from 2D interface dominated at high s to bulk fluid dependent at low s. The correlated motions can be scaled onto a master curve which captures the features of this transition. This master curve also characterizes the spatial dependence of the flow field of a viscous interface in response to a force. The scale factors used for the master curve allow for the calculation of the surface viscosity s that can be compared to one-particle measurements.

Betrayal aversion: When agents of protection become agents of harm

Jonathan Koehler — 2007-09-11T17:59:33-00:00

Organizational Behavior and Human Decision Processes, Vol. 90, No. 2. (March 2003), pp. 244-261.

A form of betrayal occurs when agents of protection cause the very harm that they are entrusted to guard against. Examples include the military leader who commits treason and the exploding automobile air bag. We conducted five studies that examined how people respond to criminal betrayals, safety product betrayals, and the risk of future betrayal by safety products. We found that people reacted more strongly (in terms of punishment assigned and negative emotions felt) to acts of betrayal than to identical bad acts that do not violate a duty or promise to protect. We also found that, when faced with a choice among pairs of safety devices (air bags, smoke alarms, and vaccines), most people preferred inferior options (in terms of risk exposure) to options that included a slim (0.01%) risk of betrayal. However, when the betrayal risk was replaced by an equivalent non-betrayal risk, the choice pattern was reversed. Apparently, people are willing to incur greater risks of the very harm they seek protection from to avoid the mere possibility of betrayal.

An integrated framework of vision-based vehicle detection with knowledge fusion

Y Zhu — 2007-09-06T15:29:00-00:00

Intelligent Vehicles Symposium, 2005. Proceedings. IEEE (2005), pp. 199-204.

This paper describes an integrated framework of on-road vehicle detection through knowledge fusion. In contrast to appearance-based detectors that make instant decisions, the proposed detection framework fuses appearance, geometry and motion information over multiple image frames. The knowledge of vehicle/non-vehicle appearance, scene geometry and vehicle motion is utilized through prior models obtained by learning, modeling and estimation algorithms. It is shown that knowledge fusion largely improves the robustness and reliability of the detection system.

Nutrient Composition, Protein Quality, and Sensory Properties of Thirty-Six Cultivars of Dry Beans (Phaseolus vulgaris L.)

HH Koehler — 2007-08-18T14:32:45-00:00

Journal of Food Science, Vol. 52, No. 5. (1987), pp. 1335-1340.

ABSTRACT Thirty-six cultivars representing eight types of dry beans (Phaseolus vulgaris L) were analyzed chemically for content of moisture, fat, ash, total nitrogen, iron, zinc, calcium, magnesium, potassium, phosphorus, thiamin, riboflavin, and amino acids. Protein quality was evaluated using Tetrahymena pyriformis W. Cooked beans were subjected to sensory evaluation and shear-force measurement. Nutrient concentrations were similar to values reported by earlier investigators. Protein quality ranged from 60% (Red Kidneys) to 90% (Pintos) that of casein. Pintos Nodak and Fiesta and Hyden Navy beans were most acceptable in flavor and texture; Bonus Small White was least acceptable. Cooperation between bean breeders and nutritionists will enable early screening of segregating hybrid populations for desirable nutritional and sensory qualities.

The "bioeffect assessment index" (BAI): A concept for the quantification of effects of marine pollution by an integrated biomarker approach

K Broeg — 2007-08-17T08:45:19-00:00

Marine Pollution Bulletin, Vol. 50, No. 5. (May 2005), pp. 495-503.

The "bioeffect assessment index" (BAI) is based on the integration of several pathological endpoints measured in the liver of European flounder (Platichthys flesus (L.)) during a long term study of biological effects of pollution in the German Bight. The BAI represents a modification of the "health assessment index" since it includes solely validated biomarkers reflecting toxically induced alterations at different levels of biological organisation in order to quantify the effects of environmental pollution. The concept of the BAI is based on the observation of progressive deleterious effects from early responses to late effects. Specific "key events" were detected, representing progressive stages of functional deterioration. The biomarkers selected from a whole battery of cellular markers for the BAI calculation reflect deleterious effects of various classes of contaminants such as heavy metals, organochlorines, pesticides, PAHs, and therefore reflect general toxicity in an integrative manner. Selected biomarkers were: lysosomal perturbations (reduced membrane stability), storage disorders (lipid accumulation) as early markers for toxic effects of liver cells, and the size of macrophage aggregates and their acid phosphatase activity. The latter two markers are indicative for the modulation of non-specific immune response which represents longer time scale responses after chronic exposure.

Another look at measures of forecast accuracy

Rob Hyndman — 2007-08-14T16:38:59-00:00

International Journal of Forecasting, Vol. 22, No. 4. ( 2006), pp. 679-688.

We discuss and compare measures of accuracy of univariate time series forecasts. The methods used in the M-competition as well as the M3-competition, and many of the measures recommended by previous authors on this topic, are found to be degenerate in commonly occurring situations. Instead, we propose that the mean absolute scaled error become the standard measure for comparing forecast accuracy across multiple time series.

A high-quality catalog of the Drosophila melanogaster proteome

Erich Brunner — 2007-05-05T13:02:17-00:00

Nature Biotechnology, Vol. 25, No. 5. (22 April 2007), pp. 576-583.

An AI-based Approach to Destination Control in Elevators

Jana Koehler — 2007-06-05T03:01:18-00:00

Not widely known by the AI community, elevator control has become a major field of application for AI technologies. Techniques such as neural networks, genetic algorithms, fuzzy rules, and, recently, multi-agent systems and AI planning have been adopted by leading elevator companies not only to improve the transportation capacity of conventional elevator systems, but also to revolutionize the way in which elevators interact with and serve passengers.

Reflections on the Discovery and Significance of Estrogen Receptor beta

Konrad Koehler — 2007-05-27T09:02:56-00:00

Endocr Rev, Vol. 26, No. 3. (1 May 2005), pp. 465-478.

We have known for many years that estrogen is more than the female hormone. It is essential in the male gonads, and in both sexes, estrogen has functions in the skeleton and central nervous system, on behavior, and in the cardiovascular and immune systems. An important aspect of the discovery of estrogen receptor (ER) beta is that the diverse functions of estrogen can now be divided into those mediated by ERalpha and those mediated by ERbeta. Pharmacological exploitation of this division of the labors of estrogen is facilitated by the ligand-binding specificity and selective tissue distribution of the two ERs. Because the ligand binding domains of ERalpha and ERbeta are significantly different from each other, selective ligands can be (and have been) developed to target the estrogenic pathway that is malfunctioning, without interfering with the other estrogen-regulated pathways. Because of the absence of ERbeta from the adult pituitary and endometrium, ERbeta agonists can be used to target ERbeta with no risk of adverse effects from chemical castration and uterine cancer. Some of the diseases in which there is hope that ERbeta agonists will be of benefit are prostate cancer, autoimmune diseases, colon cancer, malignancies of the immune system, and neurodegeneration. 10.1210/er.2004-0027

Explanation, imagination, and confidence in judgment.

DJ Koehler — 2007-05-25T22:15:46-00:00

Psychol Bull, Vol. 110, No. 3. (November 1991), pp. 499-519.

This article concerns a class of experimental manipulations that require people to generate explanations or imagine scenarios. A review of studies using such manipulations indicates that people who explain or imagine a possibility then express greater confidence in the truth of that possibility. It is argued that this effect results from the approach people take in the explanation or imagination task: They temporarily assume that the hypothesis is true and assess how plausibly it can account for the relevant evidence. From this view, any task that requires that a hypothesis be treated as if it were true is sufficient to increase confidence in the truth of that hypothesis. Such tasks cause increased confidence in the hypothesis at the expense of viable alternatives because of changes in problem representation, evidence evaluation, and information search that take place when the hypothesis is temporarily treated as if it were true.

Small Molecules, Big Players: the National Cancer Institute's Initiative for Chemical Genetics

Nicola Tolliday — 2007-04-23T02:39:50-00:00

Cancer Res, Vol. 66, No. 18. (15 September 2006), pp. 8935-8942.

In 2002, the National Cancer Institute created the Initiative for Chemical Genetics (ICG), to enable public research using small molecules to accelerate the discovery of cancer-relevant small-molecule probes. The ICG is a public-access research facility consisting of a tightly integrated team of synthetic and analytical chemists, assay developers, high-throughput screening and automation engineers, computational scientists, and software developers. The ICG seeks to facilitate the cross-fertilization of synthetic chemistry and cancer biology by creating a research environment in which new scientific collaborations are possible. To date, the ICG has interacted with 76 biology laboratories from 39 institutions and more than a dozen organic synthetic chemistry laboratories around the country and in Canada. All chemistry and screening data are deposited into the ChemBank web site (http://chembank.broad.harvard.edu/) and are available to the entire research community within a year of generation. ChemBank is both a data repository and a data analysis environment, facilitating the exploration of chemical and biological information across many different assays and small molecules. This report outlines how the ICG functions, how researchers can take advantage of its screening, chemistry and informatic capabilities, and provides a brief summary of some of the many important research findings. (Cancer Res 2006; 66(18): 8935-42) 10.1158/0008-5472.CAN-06-2552

Role of astrocytes in cerebrovascular regulation.

RC Koehler — 2007-01-19T03:00:52-00:00

J Appl Physiol, Vol. 100, No. 1. (January 2006), pp. 307-317.

Astrocytes send processes to synapses and blood vessels, communicate with other astrocytes through gap junctions and by release of ATP, and thus are an integral component of the neurovascular unit. Electrical field stimulations in brain slices demonstrate an increase in intracellular calcium in astrocyte cell bodies transmitted to perivascular end-feet, followed by a decrease in vascular smooth muscle calcium oscillations and arteriolar dilation. The increase in astrocyte calcium after neuronal activation is mediated, in part, by activation of metabotropic glutamate receptors. Calcium signaling in vitro can also be influenced by adenosine acting on A2B receptors and by epoxyeicosatrienoic acids (EETs) shown to be synthesized in astrocytes. Prostaglandins, EETs, arachidonic acid, and potassium ions are candidate mediators of communication between astrocyte end-feet and vascular smooth muscle. In vivo evidence supports a role for cyclooxygenase-2 metabolites, EETs, adenosine, and neuronally derived nitric oxide in the coupling of increased blood flow to increased neuronal activity. Combined inhibition of the EETs, nitric oxide, and adenosine pathways indicates that signaling is not by parallel, independent pathways. Indirect pharmacological results are consistent with astrocytes acting as intermediaries in neurovascular signaling within the neurovascular unit. For specific stimuli, astrocytes are also capable of transmitting signals to pial arterioles on the brain surface for ensuring adequate inflow pressure to parenchymal feeding arterioles. Therefore, evidence from brain slices and indirect evidence in vivo with pharmacological approaches suggest that astrocytes play a pivotal role in regulating the fundamental physiological response coupling dynamic changes in cerebral blood flow to neuronal synaptic activity. Future work using in vivo imaging and genetic manipulation will be required to provide more direct evidence for a role of astrocytes in neurovascular coupling.

Suppression of perception in migraine: evidence for reduced inhibition in the visual cortex.

WM Mulleners — 2007-01-06T00:33:06-00:00

Neurology, Vol. 56, No. 2. (23 January 2001), pp. 178-183.

BACKGROUND: Results from transcranial magnetic stimulation (TMS) studies of visual cortex have confirmed visual cortical hyperexcitability in patients with migraine. It has been speculated that this may be due to deficient intracortical inhibitory tone. However, the TMS induction of phosphenes relies on the reporting of a subjective experience, and may thus be subject to bias. METHODS: Seven migraineurs with visual aura and seven sex- and age-matched controls were studied. Fifty-four different three-letter combinations were briefly displayed and followed by a magnetic pulse at 40, 70, 100, 130, 160, and 190 msec. Subjects were required to report as many letters as they thought they had recognized. RESULTS: In the migraine group, the mean proportion of correctly identified letters was significantly higher at 100 msec, as was the proportion of trials with two or three letters correctly reported. The time window in which perceptual suppression could be introduced was narrower in migraineurs compared to controls. CONCLUSION: These findings suggest that inhibitory systems are activated to a lesser extent by TMS pulses in patients. This observation is in agreement with the hypothesized deficiency of intracortical inhibition of the visual cortex, at least in migraineurs with aura.

Mutations of the TGF-beta type II receptor BMPR2 in pulmonary arterial hypertension.

Rajiv D Machado — 2006-01-25T10:28:30-00:00

Hum Mutat, Vol. 27, No. 2. (20 January 2006), pp. 121-132.

Pulmonary arterial hypertension (PAH) is clinically characterized by a sustained elevation in mean pulmonary artery pressure leading to significant morbidity and mortality. The disorder is typically sporadic, and in such cases the term idiopathic PAH (IPAH) is used. However, cases that occur within families (familial PAH (FPAH)) display similar clinical and histopathological features, suggesting a common etiology. Heterozygous mutations of a type II member of the TGF-beta cell signaling superfamily known as BMPR2 on chromosome 2q33 have been identified in many kindreds with FPAH, yet display both reduced penetrance and sex bias. This report presents the compilation of data for 144 distinct mutations that alter the coding sequence of the BMPR2 gene identified in 210 independent PAH subjects. This large data set characterizes the extent of sequence variation and reveals that the majority (71%) of mutations in FPAH and IPAH comprise nonsense, frameshift, and splice-site defects, and gene rearrangements. These predict premature termination of the transcript with likely loss through the process of nonsense-mediated decay (NMD). A total of 44 missense mutations were identified that substitute amino acid residues at highly conserved sites within recognized functional domains of the mature receptor. We assess this category of mutations in the context of their heterogeneous effects on cell signaling when assayed by in vitro cell-based systems. Disease-causing mutation hot-spots within BMPR2 are summarized. Taken together, these observations are likely to aid in the development of targeted mutation detection strategies relevant for patient management. Finally, we examine the age- and sex-dependent reduced penetrance of BMPR2 mutations by reviewing bmpr2 animal models and the requirement for additional genetic and/or environmental modifiers of disease. In conclusion, these data provide compelling genetic evidence that haploinsufficiency is the predominant molecular mechanism underlying disease predisposition, and support the concept of a critical threshold of signaling activity below which disease may be precipitated. Hum Mutat 27(2), 121-132, 2006. (c) 2006 Wiley-Liss, Inc.

Origins of PDZ domain ligand specificity. Structure determination and mutagenesis of the Erbin PDZ domain.

NJ Skelton — 2006-11-07T22:10:27-00:00

J Biol Chem, Vol. 278, No. 9. (28 February 2003), pp. 7645-7654.

The LAP (leucine-rich repeat and PDZ-containing) family of proteins play a role in maintaining epithelial and neuronal cell size, and mutation of these proteins can have oncogenic consequences. The LAP protein Erbin has been implicated previously in a number of cellular activities by virtue of its PDZ domain-dependent association with the C termini of both ERB-B2 and the p120-catenins. The present work describes the NMR structure of Erbin PDZ in complex with a high affinity peptide ligand and includes a comprehensive energetic analysis of both the ligand and PDZ domain side chains responsible for binding. C-terminal phage display has been used to identify preferred ligands, whereas binding affinity measurements provide precise details of the energetic importance of each ligand side chain to binding. Alanine and homolog scanning mutagenesis (in a combinatorial phage display format) identifies Erbin side chains that make energetically important contacts with the ligand. The structure of a phage-optimized peptide (Ac-TGW(-4)ETW(-1)V; IC(50) = approximately 0.15 microm) in complex with Erbin PDZ provides a structural context to understand the binding energetics. In particular, the very favorable interactions with Trp(-1) are not Erbin side chain-mediated (and therefore may be generally applicable to many PDZ domains), whereas the beta2-beta3 loop provides a binding site for the Trp(-4) side chain (specific to Erbin because it has an unusually long loop). These results contribute to a growing appreciation for the importance of at least five ligand C-terminal side chains in determining PDZ domain binding energy and highlight the mechanisms of ligand discrimination among the several hundred PDZ domains present in the human genome.

Ramsey interferometry with atoms and molecules: two-body versus many-body phenomena

Krzysztof Goral — 2006-10-13T09:30:58-00:00

(10 Feb 2005)

We discuss the frequency and visibility of atom-molecule Ramsey fringes observed in recent experiments by Claussen et al.[Phys. Rev. A 67, 060701 (2003)]. In these experiments a 85Rb Bose-Einstein condensate was exposed to a sequence of magnetic field pulses on the high field side of the 155 G Feshbach resonance. The observed oscillation frequencies largely agree with the theoretically predicted magnetic field dependence of the binding energy of the highest excited diatomic vibrational state, except for a small region very close to the singularity of the scattering length. Our analytic treatment of the experiment, as well as our dynamical simulations, follow the magnitude of the measured oscillation frequencies as well as the visibilities of the Ramsey fringes. We show that significant deviations from a purely binary dynamics, with an associated binding frequency, occur when the spatial extent of the molecular wave function becomes comparable with the mean distance between the atoms in the dilute gas. The experiments thus clearly identify the conditions under which diatomic molecules may be identified as a separate entity of the gas or, conversely, when the concept of binary physics in a many-body environment is bound to break down.

A caching compiler for C

B Koehler — 2006-10-10T04:54:09-00:00

Communications, Computers, and Signal Processing, 1995. Proceedings. IEEE Pacific Rim Conference on (1995), pp. 141-144.

Breaking the source text of a contemporary C program into separate compilation units and employing aggressive selective compilation schemes can greatly reduce the amount of time spent compiling programs. However, much redundant processing still occurs when a single compilation unit is compiled repeatedly, during the repetitive edit-compile-debug cycle, for example, or when a large number of compilation units are selected for compilation. We investigate the benefits of retaining internal representations of header files for reuse in subsequent invocations of the compiler, thus speeding up compilation. Our general, transparent, adaptive approach experimentally achieves a 60% reduction in compilation time in the average repetitive case, and a 40% reduction in the average massive case

A natural language understanding system combining syntactic and semantic techniques.

P Haug — 2006-09-01T11:57:13-00:00

Proc Annu Symp Comput Appl Med Care (1994), pp. 247-251.

A large proportion of the medical record currently available in computerized medical information systems is in the form of free text reports. While the accessibility of this source of data is improved through inclusion in the computerized record, it remains unavailable for automated decision support, medical research, and management of medical delivery systems. Natural language understanding systems (NLUS) designed to encode free text reports represent one approach to making this information available for these uses. Below we describe an experimental NLUS designed to parse the reports of chest radiographs and store the clinical data extracted in a medical data base.

Experience with a mixed semantic/syntactic parser.

PJ Haug — 2006-09-01T11:52:35-00:00

Proc Annu Symp Comput Appl Med Care (1995), pp. 284-288.

The value of the computerized medical record is derived in part from the availability of medical information in a coded form accessible to manipulation by processes designed for automated decision support, medical research, and computer assistance in the management of health care delivery. To meet these needs medical reports captured and stored as natural language documents must be encoded. Below we discuss an ongoing formative process aimed at developing a natural language understanding system for chest x-ray reports. Comparative data showing the progress of this process is presented.

Web page change and persistence---a four-year longitudinal study

Wallace Koehler — 2006-06-23T17:13:50-00:00

J. Am. Soc. Inf. Sci. Technol., Vol. 53, No. 2. (January 2002), pp. 162-171.

DNA-directed assembly of bienzymic complexes from in vivo biotinylated NAD(P)H:FMN oxidoreductase and luciferase.

CM Niemeyer — 2006-05-15T21:31:51-00:00

Chembiochem, Vol. 3, No. 2-3. (1 March 2002), pp. 242-245.

Some Thoughts on the Meaning of Open Access for University Library Technical Services

Amy Koehler — 2006-03-31T13:39:01-00:00

Serials Review, Vol. 32, No. 1. (March 2006), pp. 17-21.

Many studies of the Open Access (OA) movement analyze the problems of cost, author, and publisher reactions to OA, or the fluidity of the movement. Very few, however, investigate how library technical services have already been impacted by OA. How do collection development librarians identify and select material in these models? How do acquisitions librarians license or otherwise gain access to the materials? How are these materials to be maintained and preserved? The author surveys how OA in its various forms impacts the primary functions of technical services in academic libraries.

Parallel Symbolic Computation of Curvature Invariants in General Relativity

KR Koehler — 2006-02-23T19:37:46-00:00

(19 Feb 2006)

We present a practical application of parallel symbolic computation in General Relativity: the calculation of curvature invariants for large dimension. We discuss the structure of the calculations, an implementation of the technique and scaling of the computation with spacetime dimension for various invariants.

Issue definition, political discourse and the politics of nationality reform in France and Germany

Randall Hansen — 2005-07-26T17:24:34-00:00

European Journal of Political Research, Vol. 44, No. 5. (August 2005), pp. 623-644.

Dilution and confirmation of probability judgments based on nondiagnostic evidence.

C LaBella — 2005-11-01T14:05:37-00:00

Mem Cognit, Vol. 32, No. 7. (October 2004), pp. 1076-1089.

Previous research has shown that probability judgments based on a mix of diagnostic and nondiagnostic information are less extreme than judgments based on the diagnostic information alone. Results of the present experiments suggest that this dilution effect holds only under a limited set of conditions. When judgments based on a mix of diagnostic and nondiagnostic information are compared with separately elicited judgments based on the diagnostic information alone, the dilution effect is consistently observed. When judgments based on the diagnostic evidence are revised in light of additional, nondiagnostic evidence, by contrast, the dilution effect is eliminated or even reversed (yielding a confirmation effect) depending on the type of nondiagnostic evidence under evaluation.

Higher-Dimensional Packing with Order Constraints

Sandor Fekete — 2005-07-29T12:20:36-00:00

(28 Jul 2005)

We present a first exact study on higher-dimensional packing problems with order constraints. Problems of this type occur naturally in applications such as logistics or computer architecture and can be interpreted as higher-dimensional generalizations of scheduling problems. Using graph-theoretic structures to describe feasible solutions, we develop a novel exact branch-and-bound algorithm. This extends previous work by Fekete and Schepers; a key tool is a new order-theoretic characterization of feasible extensions of a partial order to a given complementarity graph that is tailor-made for use in a branch-and-bound environment. The usefulness of our approach is validated by computational results.

Linking Experimental Results, Biological Networks and Sequence Analysis Methods Using Ontologies and Generalised Data Structures

Jacob Koehler — 2005-06-04T12:38:07-00:00

In Silico Biology, Vol. 5, No. 1. (January 2005), pp. 33-44.

The structure of a closely integrated data warehouse is described that is designed to link different types and varying numbers of biological networks, sequence analysis methods and experimental results such as those coming from microarrays. The data schema is inspired by a combination of graph based methods and generalised data structures and makes use of ontologies and meta-data. The core idea is to consider and store biological networks as graphs, and to use generalised data structures (GDS) for the storage of further relevant information. This is possible because many biological networks can be stored as graphs: protein interactions, signal transduction networks, metabolic pathways, gene regulatory networks etc. Nodes in biological graphs represent entities such as promoters, proteins, genes and transcripts whereas the edges of such graphs specify how the nodes are related. The semantics of the nodes and edges are defined using ontologies of node and relation types. Besides generic attributes that most biological entities possess (name, attribute description), further information is stored using generalised data structures. By directly linking to underlying sequences (exons, introns, promoters, amino acid sequences) in a systematic way, close interoperability to sequence analysis methods can be achieved. This approach allows us to store, query and update a wide variety of biological information in a way that is semantically compact without requiring changes at the database schema level when new kinds of biological information is added. We describe how this datawarehouse is being implemented by extending the text-mining framework ONDEX to link, support and complement different bioinformatics applications and research activities such as microarray analysis, sequence analysis and modelling/simulation of biological systems. The system is developed under the GPL license and can be downloaded from http://sourceforge.net/projects/ondex/

Patterns that define the four domains conserved in known and novel isoforms of the protein import receptor Tom20.

VA Likić — 2005-03-23T03:38:03-00:00

J Mol Biol, Vol. 347, No. 1. (18 March 2005), pp. 81-93.

Tom20 is the master receptor for protein import into mitochondria. Analysis of motifs present in Tom20 sequences from fungi and animals found several highly conserved regions, including features of the transmembrane segment, the ligand-binding domain and functionally important flexible segments at the N terminus and the C terminus of the protein. Hidden Markov model searches of genome sequence data revealed novel isoforms of Tom20 in vertebrate and invertebrate animals. A three-dimensional comparative model of the novel type I Tom20, based on the structurally characterized type II isoform, shows important differences in the amino acid residues lining the ligand-binding groove, where the type I protein from animals is more similar to the fungal form of Tom20. Given that the two receptor types from mouse interact with the same set of precursor protein substrates, comparative analysis of the substrate-binding site provides unique insight into the mechanism of substrate recognition. No Tom20-related protein was found in genome sequence data from plants or protozoans, suggesting the receptor Tom20 evolved after the split of animals and fungi from the main lineage of eukaryotes.