Origin and early evolution of vertebrate skeletonization

Data from living and extinct faunas of primitive vertebrates imply very different scenarios for the origin and evolution of the dermal and oral skeletal developmental system. A direct reading of the evolutionary relationships of living primitive vertebrates implies that the dermal scales, teeth, and jaws arose synchronously with a cohort of other characters that could be considered unique to jawed vertebrates: the dermoskeleton is primitively composed of numerous scales, each derived from an individual dental papilla; teeth are primitively patterned such that they are replaced in a classical conveyor-belt system. The paleontological record provides a unique but complementary perspective in that: 1) the organisms in which the skeletal system evolved are extinct and we have no recourse but to fossils if we aim to address this problem; 2) extinct organisms can be classified among, and in the same way as, living relatives; 3) a holistic approach to the incorporation of all data provides a more complete perspective on early vertebrate evolution. This combined approach is of no greater significance than in dealing with the origin of the skeleton and, combined with recent discoveries and new phylogenetic analyses, we have been able to test and reject existing hypotheses for the origin of the skeleton and erect a new model in their place.     

Deconvolution estimation of nerve conduction velocity distribution

A conduction velocity distribution (CVD) estimator that incorporates volume conductor modeling of the nerve-evoked response is introduced in this paper. The CVD estimates are obtained from two compound nerve action potentials (CNAP) recorded at the skin surface. A third channel is introduced in order to assess the estimator performance in the experimental case. The relevance of using an accurate signal model is shown by comparing the performance of the proposed estimator with a previous approach based on a different CNAP model. The performance of the proposed estimator is evaluated for simulated and experimental data. The study assesses signal-to-noise ratio immunity and sensitivity to errors in the model parameters.     

Method detection limit determination and application of a convenient headspace analysis method for methyl tert-butyl ether in water

Methyl tert-butyl ether (MTBE) is a common groundwater contaminant, introduced to the environment by leaking petroleum storage tanks, urban runoff, and motorized watercraft. In this study. a simplified (static) headspace analysis method was adapted for determination of MTBE in water samples and soil water extracts. The MDL of the headspace method was calculated to be 2.0 microg L(-1) by the EPA single-concentration design method(1) and 1.2 microg L(-1) by a calibration method developed by Hubaux and Vos (Hubaux, A.; Vos, G. Anal. Chem. 1970,42, 849-855). The MDL calculated with the Hubaux and Vos method was favored because it considers both a true positive and a false positive. The static headspace method was applied to analysis of a tap water sample and a monitoring well sample from a gasoline service station, a river sample, and aqueous extracts from soil excavated during removal of a leaking underground storage tank (LUST). The water samples examined in this study had MTTBE concentrations ranging from 6 to 19 microg L(-1). Aqueous extracts of a soil sample taken from the LUST site had 8 microg L(-1) MTBE.     

Functional assays for identifying ligands at orphan G protein-coupled receptors

The superfamily of G protein-coupled receptors (GPCRs; 7TMs) is one of the largest families of genes identified in humans, and has a proven history of being an excellent source of drug targets. The near completion of the human genome sequencing project has allowed the identification of a plethora of sequences encoding "orphan" GPCRs--putative receptors whose natural ligand(s) remain to be discovered. In many cases, the level of sequence homology with known receptors is insufficient to be able to predict the natural ligand for these orphan receptors, although it is usually possible to determine the likely nature of the cognate ligand e.g. peptide, lipid, nucleotide etc. Deorphanizing these novel GPCRs and evaluating their biological function has become a major target of many of the major pharmaceutical companies as well as several academic groups. Since 1995 more than 50 ligands for orphan GPCRs have been discovered by using the orphan receptor as a biosensor and screening candidate compounds looking for a biological response (the so-called "reverse pharmacology" approach). Identification of the natural ligands for these receptors marks the beginning of the process of understanding the biology of these newly discovered signalling systems and the development of novel therapies targeted at them. This article will focus on the functional assays which have been used to discover ligands for orphan GPCRs.     

Electrokinetic chromatography utilizing two pseudostationary phases providing ion-exchange and hydrophobic interactions

The electrokinetic chromatographic separation of a series of inorganic and organic anions was achieved by utilizing an electrolyte system comprising a cationic soluble polymer (poly(diallydimethylammonium chloride, PDDAC) and a neutral beta-cyclodextrin (beta-CD) as pseudostationary phases. The separation mechanism was a combination of electrophoresis, ion-exchange (IE) interactions with PDDAC, and hydrophobic interactions with beta-CD. The extent of each chromatographic interaction was independently variable, allowing for control of the separation selectivity of the system. IE interactions could be varied by changing either the PDDAC concentration or the concentration of a competing ion (e.g., chloride) in the BGE, while the hydrophobic interactions could be varied by changing the concentration of beta-CD. The separation system was very robust, with the reproducibility of the migration times being <0.7% RSD. A mathematical model that predicted the mobilities of analytes under varying experimental conditions was derived and was shown to give good correlation (r2 = 0.9804) between predicted and experimental migration times. Parameters derived from the model were in good agreement with the ion-exchange and hydrophobic characteristics of the analytes. The model was also applied successfully to the optimization of conditions for the separation of a mixture of analytes or for conditions under which particular analytes migrated in a desired order. That is, the opportunity to tune the separation selectivity has been demonstrated.     

Detection of hydrogen peroxide at mesoporous platinum microelectrodes

Mesoporous (H(I)-ePt) platinum microelectrodes electrodeposited from the hexagonal (H(I)) lyotropic liquid crystalline phase are shown to be excellent amperometric sensors for the detection of hydrogen peroxide over a wide range of concentrations. Good reproducibility, high precision, and accuracy of measurements are demonstrated. Mesoporous microelectrodes retain the high rates of mass transport typical of conventional microelectrodes, and their high real surface area greatly enhances their catalytic activity. This unique combination of properties overcomes the limitations of previous amperometric hydrogen peroxide sensors and yields outstanding qualitative and quantitative results.     

Conversion of carbon into CF4 for SI-traceable measurements of absolute carbon isotope amount ratios: a feasibility study

The feasibility of performing SI-traceable carbon isotope amount ratio measurements following conversion of carbon into CF4 was studied. A procedure for the direct fluorination of carbon with elemental fluorine was developed, and the conversion step was checked for losses, blank contributions, and the absence of systematic isotope effects. Gas chromatography was used to identify and quantify the gaseous fluorination products and to isolate CF4 from byproducts. After fluorination of graphite carbon, CF4 and perfluoroalkanes with up to six carbon atoms were observed as reaction products. Within an uncertainty of 10%, the graphite carbon was fully recovered in the gaseous carbon fluorides, with the main product being CF4 (80-90%) and C2F6 as the major byproduct. The fluorination and GC procedures were found to introduce an alteration not bigger than 0.03 +/- 0.04/1000 on the isotopic composition of CF4. Carbon blank contributions introduced during the fluorination procedure were below 0.5% relative to a typical sample of 4 mg of carbon. For two of the materials investigated, the carbon isotope ratios measured on a differential mass spectrometer were reproducible within a standard deviation of approximately 0.1/1000 for several individual fluorinations. For these materials, the developed fluorination procedure is a straightforward process, which can be used as a foundation to establish SI-traceable measurements of carbon isotope amount ratios. However, for the third graphite material the formation of byproducts (C2F6-C6F14) was found to induce significant isotopic fractionation.     

Re-illuminating single images using Albedo estimation

Predicting the appearance of a scene under novel lighting conditions is of growing interest at the convergence of vision, graphics and virtual reality. In this paper, we develop a method for appearance prediction from a single image using the apparatus of shape from shading (SFS). We re-visit the reflectance estimation process first proposed by Blake (Graphics Image Process. 32 (1985) 314), and develop a novel approach to parameter selection within the Blake method based on the quality of images which can be produced by re-illuminating the recovered needle-map. Combining Blake's method with recent advances in SFS is demonstrated to yield significant improvements in the appearance prediction of real images under varying lighting conditions.     

Query indexing with containment-encoded intervals for efficient stream processing

Many continual range queries can be issued against data streams. To efficiently evaluate continual queries against a stream, a main memory-based query index with a small storage cost and a fast search time is needed, especially if the stream is rapid. In this paper, we study a CEI-based query index that meets both criteria for efficient processing of continual interval queries. This new query index is an indirect indexing approach. It centres around a set of predefined virtual containment-encoded intervals, or CEIs. The CEIs are used to first decompose query intervals and then perform efficient search operations. The CEIs are defined and labeled such that containment relationships among them are encoded in their IDs. The containment encoding makes decomposition and search operations efficient; from the encoding of the smallest CEI containing a data point, the encodings of other containing CEIs can be easily derived. Closed-form formulae for the bounds of the average index storage cost are derived. Simulations are conducted to evaluate the effectiveness of the CEI-based query index and to compare it with alternative approaches. The results show that the CEI-based query index significantly outperforms existing approaches in terms of both storage cost and search time. Kun-Lung Wu received the B.S. degree in electrical engineering from the National Taiwan University, Taipei, Taiwan, the M.S. and Ph.D. degrees in computer science from the University of Illinois at Urbana–Champaign. He is with the IBM Thomas J. Watson Research Center, currently a member of the Software Tools and Techniques Group. His current research interests include data streams, continual queries, mobile computing, Internet technologies and applications, database systems and distributed and parallel computing. He has published extensively and holds various patents in these areas. Dr. Wu is a Senior Member of the IEEE Computer Society and a member of the ACM. He was an Associate Editor for the IEEE Transactions on Knowledge and Data Engineering, 2000–2004. He was the general chair for the 3rd International Workshop on e-Commerce and Web-Based Information Systems (WECWIS 2001). He has served as an organising and program committee member on various conferences. He has received various IBM awards, including IBM Corporate Environmental Affair Excellence Award, Research Division Award and Invention Achievement Awards. He received a best paper award from IEEE EEE 2004. He is an IBM Master Inventor. Shyh-Kwei Chen received the B.S. degree in computer science and information engineering from National Taiwan University, Taipei, Taiwan, in 1983, the M.S. degree in computer science from the University of Minnesota, Minneapolis, in 1987, and the Ph.D. degree in computer science from University of Illinois at Urbana–Champaign, in 1994. Dr. Chen has been with the IBM Thomas J. Watson Research Center, Yorktown Heights, New York since October 1994, where he is currently a research staff member. His current research interests include XML, electronic commerce, business performance management, data engineering and compilers. He is a member of the ACM, the IEEE and the IEEE Computer Society. Philip S. Yu received the B.S. degree in electrical engineering from National Taiwan University, the M.S. and Ph.D. degrees in electrical engineering from Stanford University, and the M.B.A. degree from New York University. He is with the IBM Thomas J. Watson Research Center and is currently manager of the Software Tools and Techniques group. His research interests include data mining, Internet applications and technologies, database systems, multimedia systems, parallel and distributed processing and performance modelling. Dr. Yu has published more than 400 papers in refereed journals and conferences. He holds or has applied for more than 250 US patents. Dr. Yu is a Fellow of the ACM and a Fellow of the IEEE. He is an associate editor of ACM Transactions on Internet Technology. He is a member of the IEEE Data Engineering steering committee and is also on the steering committee of IEEE Conference on Data Mining. He was the Editor-in-Chief of IEEE Transactions on Knowledge and Data Engineering (2001–2004), an editor and advisory board member of IEEE Transactions on Knowledge and Data Engineering and also a guest coeditor of the special issue on mining of databases. He had also served as an associate editor of Knowledge and Information Systems. In addition to serving as program committee member on various conferences, he was the program cochair of the 11th International Conference on Data Engineering, the 6th Pacific Area Conference on Knowledge Discovery and Data Mining, and the 9th ACM SIGMOD Workshop on Research Issues in Data Mining and Knowledge Discovery, and the program chair of the 2nd International Workshop on Research Issues on Data Engineering: Transaction and Query Processing, the PAKDD Workshop on Knowledge Discovery from Advanced Databases and the 2nd International Workshop on Advanced Issues of E-Commerce and Web-based Information Systems. He served as the general chair of the 14th International Conference on Data Engineering and the general cochair of the 2nd IEEE International Conference on Data Mining. He has received several IBM honours, including two IBM Outstanding Innovation Awards, an Outstanding Technical Achievement Award, two Research Division Awards and the 81st Plateau of Invention Achievement Awards. He received an Outstanding Contributions Award from IEEE International Conference on Data Mining in 2003 and also an IEEE Region 1 Award for “promoting and perpetuating numerous new electrical engineering concepts” in 1999. Dr. Yu is an IBM Master Inventor and was recognised as one of the IBM's 10 top leading inventors in 1999.