bluuebunny/crossref_metadata_2025_split huggingface dataset:
SATCHMO: sequence alignment and tree construction using hidden Markov models
Authors: Edgar Robert C. , Sjölander Kimmen 
Published: July 2003

Abstract
Motivation:Aligning multiple proteins based on sequence information alone is challenging if sequence identity is low or there is a significant degree of structural divergence. We present a novel algorithm (SATCHMO) that is designed to address this challenge. SATCHMO simultaneously constructs a tree and a set of multiple sequence alignments, one for each internal node of the tree. The alignment at a given node contains all sequences within its sub-tree, and predicts which positions in those sequences are alignable and which are not. Aligned regions therefore typically get shorter on a path from a leaf to the root as sequences diverge in structure. Current methods either regard all positions as alignable (e.g. ClustalW), or align only those positions believed to be homologous across all sequences (e.g. profile HMM methods); by contrast SATCHMO makes different predictions of alignable regions in different subgroups. SATCHMO generates profile hidden Markov models at each node; these are used to determine branching order, to align sequences and to predict structurally alignable regions.
Results: In experiments on the BAliBASE benchmark alignment database, SATCHMO is shown to perform comparably to ClustalW and the UCSC SAM HMM software. Results using SATCHMO to identify protein domains are demonstrated on potassium channels, with implications for the mechanism by which tumor necrosis factor alpha affects potassium current.
Availability: The software is available for download from http://www.drive5.com/lobster/index.htm
Contact: bob@drive5.com
* To whom correspondence should be addressed.
Identifying property based sequence motifs in protein
families and superfamilies: application to DNase-1 related
endonucleases
Authors: Mathura Venkatarajan S. , Schein Catherine H. , Braun Werner 
Published: July 2003

Abstract
Motivation: Identification of short conserved sequence motifs common to a protein family or superfamily can be more useful than overall sequence similarity in suggesting the function of novel gene products. Locating motifs still requires expert knowledge, as automated methods using stringent criteria may not differentiate subtle similarities from statistical noise.
Results: We have developed a novel automatic method, based on patterns of conservation of 237 physical–chemical properties of amino acids in aligned protein sequences, to find related motifs in proteins with little or no overall sequence similarity. As an application, our web-server MASIA identified 12 property-based motifs in the apurinic/apyrimidinic endonuclease (APE) family of DNA-repair enzymes of the DNase-I superfamily. Searching with these motifs located distantly related representatives of the DNase-I superfamily, such as Inositol 5′-polyphosphate phosphatases in the ASTRAL40 database, using a Bayesian scoring function. Other proteins containing APE motifs had no overall sequence or structural similarity. However, all were phosphatases and/or had a metal ion binding active site. Thus our automated method can identify discrete elements in distantly related proteins that define local structure and aspects of function. We anticipate that our method will complement existing ones to functionally annotate novel protein sequences from genomic projects.
Availability: MASIA WEB site: http://www.scsb.utmb.edu/masia/masia.html
Contact: werner@newton.utmb.edu
Supplementary information: The dendrogram of 42 APE sequences used to derive motifs is available on http://www.scsb.utmb.edu/comp_biol.html/DNA_repair/publication.html
* To whom correspondence should be addressed.
Exact significance levels for the maximumχ
2
method of detecting recombination
Authors: Spencer M. 
Published: July 2003

Abstract
Summary:Maynard Smith’s maximum χ2 method is a useful tool for detecting recombination. Significance testing is usually carried out by random permutation, which may require a large amount of computer time. I describe an exact algorithm.
Availability: Matlab source code from http://www.bioc.cam.ac.uk/UTOs/howe/
Contact: ms379@cam.ac.uk
Which genetic loci have greater population assignment power?
Authors: Banks Michael A. , Eichert Will , Olsen Jeffrey B. 
Published: July 2003

Abstract
Summary: WHICHLOCI is a program that determines the relative discriminatory power of alternate genetic loci and loci combinations for population assignment of individuals.
Availability: http://www.oregonstate.edu/dept/comes/genetics/software.htm
Contact: Michael.Banks@oregonstate.edu
* To whom correspondence should be addressed.
An adjustable-threshold algorithm for the identification of objects
in three-dimensional images
Authors: Ponomarev Artem L. , Davis Ronald L. 
Published: July 2003

Abstract
Motivation:To develop a highly accurate, practical and fast automated segmentation algorithm for three-dimensional images containing biological objects. To test the algorithm on images of the Drosophila brain, and identify, count and determine the locations of neurons in the images.
Results: A new adjustable-threshold algorithm was developed to efficiently segment fluorescently labeled objects contained within three-dimensional images obtained from laser scanning confocal microscopy, or two-photon microscopy. The result of the test segmentation with Drosophila brain images showed that the algorithm is extremely accurate and provided detailed information about the locations of neurons in the Drosophila brain. Centroids of each object (nucleus of each neuron) were also recorded into an algebraic matrix that describes the locations of the neurons.
Availability: Interested parties should send their request for the NeuronMapper™ program with the segmentation algorithm to artemp@bcm.tmc.edu.
Contact: artemp@bcm.tmc.edu
* To whom correspondence should be addressed.
Orchestrating debate: a multimodal analysis of classroom interaction
Authors: Bourne Jill , Jewitt Carey 
Published: July 2003

AbstractThis paper examines the ways in which the interpretation of a literary text is constructed through social interaction in a multi‐ethnic urban secondary school English classroom. The focus is on the literacy experiences of Year 10 students (age 14 to 15 years). We take a multimodal approach to understanding social interaction around texts and show that higher‐order literacy skills are realised and constructed through the configuration of talk and writing with a range of other representational and communicational modes, such as gesture, gaze, movement, and posture. We suggest that despite the exhaustive regulation of literacy and school English, some English teachers, while still curriculum and examination focused, have found strategies that give them space to make connections between texts and the experiences of their particular student intake. They do so in ways that link to wider social and moral issues, drawing on their own and their students' life experiences, to make cultural connections with the texts studied. The paper shows how a multimodal analysis of social interaction facilitates and extends understanding of the teaching that is taking place.
Unequal Plurality: Towards an Asymmetric Power Model of British Politics
Authors: Marsh David , Richards David , Smith Martin 
Published: July 2003

AbstractUntil recently, Rhodes's ‘Differentiate Polity Model’ (DPM) has been the most analytically-developed model of the British political system, but it is not without its problems. Here, we argue that the DPM over-stresses the diffuse nature of power in Britain and the extent to which the state has been hollowed out. Instead, we contend that the British political system is more closed and elitist than the DPM acknowledges; rather than being hollowed-out, the state has been reconstituted and the core executive still remains the most powerful actor in the policy process. These themes are reflected in our own ‘Asymmetric Power model’.
Evaluation of Range Searching Methods for Contact Searching in Mechanical Engineering
Authors: Fjällström Per-Olof , Petersson Jan , Nilsson Larsgunnar , Zhong Zhi-Hua 
Published: July 2003

Contact searching is an important and time-consuming part of computer simulation of certain deformation processes. Contact searching can be facilitated by orthogonal range searching. We have experimentally evaluated four methods for orthogonal range searching: the projection method, the cell method, the k-d tree method, and the range tree method. The results of our experiments indicate that two of these methods, the cell and k-d tree methods, have practical significance. The cell method is in most cases faster than the k-d tree method.
Stable Computation of the 2D Medial Axis Transform
Authors: Evans Guy , Middleditch Alan , Miles Nick 
Published: July 2003

The medial axis transform of a 2D region was introduced by Blum in the 1960's as an aid to the description of biological shape. It is an alternative representation of a region which is often more amenable to analysis. This property has led to its use in diverse fields including pattern recognition and automatic finite element mesh generation. There are two widely agreed mathematical definitions for the medial axis transform which are closely related. It is shown that these definitions are not in general equivalent, despite being so far many types of region. In this paper, precise mathematical definitions of the medial axis transform and its key points (atoms) are given, and an O(n2) algorithm for its computation via those atoms presented. This algorithm is described in terms of simple polygons whose sole boundary consists of circular arcs and straight line segments, then extended to polygons with holes. It is shown how more complex edges could be accommodated. In comparison with existing algorithms it is simple to implement and stable in the presence of geometric degeneracy.
FROM FLATLAND TO FRACTALAND: NEW GEOMETRIES IN RELATIONSHIP TO ARTISTIC AND SCIENTIFIC REVOLUTIONS
Authors: SHEARER RHONDA ROLAND 
Published: July 2003

Abbott’s 19th century book, Flatland, continues to be popularly interpreted as both a social commentary and a way of visualizing the 4th-dimension by analogy. I attempt here to integrate these two seemingly disparate readings. Flatland is better interpreted as a story with a central theme that social, perceptual, and conceptual innovations are linked to changes in geometry. In such cases as the shift from the two-dimensional world of Flatland to a three-dimensional Spaceland, the taxonomic restructuring of human importance from Linnaeaus to Darwin, or the part/whole proportional shift from Ptolemy’s earth as the center of the universe to Copernicus’s sun, new geometries have changed our thinking, seeing, and social values, and lie at the heart of innovations in both art and science. For example, the two greatest innovations in art — the Renaissance with geometric perspective, and the birth of modern art at the beginning of this century with n-dimensional and non-Euclidean geometries — were developed by artists who were thinking within new geometries. When we view the history of scientific revolutions as new geometries, rather than only as new ideas, we gain direct access to potential manipulations of the structures of human innovation itself. I will discuss the seven historical markers of scientific revolutions (suggested by Kuhn, Cohen, and Popper), and how these seven traits correlate and can now be seen within the new paradigm of fractals and nonlinear sciences.
Experimental Characterization of Interlaminar Shear Strengths of Graphite/Epoxy Laminated Composites
Authors: Zhang Chao , Hoa Suong V. , Ganesan R. 
Published: July 2003

An investigation is conducted to study the effects of fiber orientations on the interlaminar shear (ILS) strengths of CYTEC® G40-800/5276-1 graphite/epoxy laminated composites. The results of this investigation are going to be reported in two separate parts; experimental characterization and stochastic simulation. The present paper demonstrates the experimental program and the experimental results. The ILS strengths at the θ-interfaces (θ=0, 10, 20, 30, 40, 50, 60, 70, 80 and 90°), around which the two neighboring plies have a fiber orientation difference angle, are experimentally measured using the modified double notch shear specimens with an elaborately designed lay-up. Because of the potentially considerable scatter in the matrix-dominated ILS strengths, each data set at a specified interface is obtained through a larger sample with 35 specimens. A 3D finite element analysis is also performed to aid in the design of the multi-directional laminated composite specimens, so as to minimize the edge effects and obtain a relatively uniform stress state in the specimen gage sections. The experimental results show that not only the mean values but also the probability distribution forms of ILS strengths depend on the fiber orientations of the neighboring plies around the interfaces. Five failure modes are also found by observing the fracture surfaces; i.e., interface crack, in-ply crack, crack jumping, fiber bridging, and fiber breakage. The inherent relationships between the failure modes and the probability distributions of ILS strengths are studied on the basis of rank-sum test. The general forms of the individual probability density functions corresponding to each experimental data set are determined by means of the maximum entropy technique and verified by Kolmogorov–Smirnov good-of-fit test.
A Methodology to Obtain a Desired Filling Pattern during Resin Transfer Molding
Authors: Minaie B. , Chen Y. F. , Mescher A. M. 
Published: July 2003

In Resin Transfer Molding (RTM), dry spot formation and air entrapment during the filling stage often lead to defective parts and high scrap rate. These problems are usually caused by improper design of inlet conditions and vent locations that prevent the Last Point to Fill (LPF) location from coinciding with the preset vent location. Use of direct filling simulation as a design tool for the RTM process often involves trial-and-error procedures in order to find the appropriate inlet conditions and locations as well as exit vent locations. This design procedure becomes complex when adesign involving multiple inlet gates is being considered, especially in large parts. There may also be uncertainty as to whether the final design (obtained using trial-and-error simulation procedures) is indeed the optimum design. This paper presents a methodology to design the RTM process with a desired filling pattern free of dry spots and knitlines. Unlike the traditional filling simulation that predicts the filling pattern using prescribed inlet conditions and the specification of the preform permeability field, this methodology calculates the optimum inlet conditions based on the specification of the desired filling pattern and the prescription of preform permeability. The use of this algorithm greatly enhances
Prediction of the Residual Tensile Strength after Solid Particle Erosion of UD-GF/PP Composites
Authors: Barkoula N.-M. , Karger-Kocsis J. , Papanicolaou G. C. 
Published: July 2003

In the present work the residual tensile strength of unidirectional (UD) glass fibre (GF) reinforced thermoplastic polypropylene (PP) composites after oblique (30) solid particle erosion was investigated as a function of the impact time and relative fibre orientation (parallel, Pa and perpendicular, Pe). A semi-empirical approach initially developed to predict the residual tensile strength after single normal impact [1] and latest successfully adopted for thermo-setting carbon fibre/epoxy (CF/EP) composites [2] worked well for the thermoplastic UD-GF/PP composites studied. A very good agreement was found between the experimental results at 30 erosion angle and the theoretical prediction in both Pa and Pe erosion directions. A comparison of the strength degradation behaviour of UD-GF/PP and CF/EP composites showed that UD-GF/PP presented the onset of its strength degradation considerably earlier but it preserved a higher relative residual tensile strength than CF/EP. The erosion direction in UD-GF/PP had marginal effect on the energy threshold resulting in severe strength degradation, whereas it showed a pronounced effect on the residual tensile strength.
Single‐Dose and Steady‐State Pharmacokinetic and Pharmacodynamic Evaluation of Therapeutically Clinically Equivalent Doses of Inhaled Fluticasone Propionate and Budesonide, Given as Diskus® or Turbohaler® Dry‐Powder Inhalers to Healthy Subjects
Authors: Möllmann Helmut , Wagner Melanie , Krishnaswami Sriram , Dimova Hristina , Tang Yufei , Falcoz Christine , Daley‐Yates Peter T. , Krieg Michael , Stöckmann Ricarda , Barth Jürgen , Lawlor Ms. Caroline , Möllmann Anja C. , Derendorf Hartmut , Hochhaus Günther 
Published: July 2003

Direct comparisons of the pharmacokinetic (PK) and systemic pharmacodynamic (PD) properties of inhaled corticosteroids after single and multiple dosing in the same subjects are scarce. The objective of this study was to compare the PK/PD properties of clinically equivalent, single, and multiple doses of dry‐powder formulations of inhaled fluticasone propionate (FP, 200 and 500 μg via Diskus®) and budesonide (BUD, 400 and 1000 μg via Turbohaler®). Fourteen healthy subjects completed a double‐blind, doubledummy, randomized, placebo‐controlled, five‐way crossover study consisting of a single dose administered at 8 a.m. on day 1 followed by 4 days of twice‐daily dosing at 8 a.m. and 8 p.m. on days 2 to 5. Serum concentrations of FP and BUD were measured using validated liquid chromatography/mass spectrometry assays. The 24‐hour cumulative cortisol suppression (CCS) in serum was monitored as the pharmacodynamic surrogate marker. Peak serum concentrations following single and multiple dosing were observed 10 to 30 minutes after inhalation for BUD and 30 to 90 minutes after inhalation of FP with no influence of dose or dosing regimen. After a single dose of 1000 vg BUD and 500 Vg FP, the median estimates of terminal half‐life and mean residence time were3.5 and 3.9 hours for BUD and 10.1 and 12.0 hours for FP, respectively. Using previously reported intravenousdata, the mean absorption times (MAT) were calculated to be around 2 hours and 7 hours for BUD and FP, respectively. On average, the area underthe curve (AUC) at steady state (day 5) was up to 30% higher for BUD compared to that over a 12‐hour period following the first dose on day 1, whereas AUC estimates were 50% to 80% higher for FP at steady state, indicating accumulation. However, the steady‐state Cmax values were seven to eight times and AUC values three to four times higher for BUD than for FP Comparison of active treatment data with placebo showed that CCS after a single dose was not pronounced for any of the doses/drugs studied. On day 5, both doses of BUD caused statistically significant suppression (CCS of 19% for the 400 μg dose and 36% for the 1000 μg dose). For FP, only the high dose had a statistically significant effect on serum cortisol (CCS of 14% for the 200 g dose and 27% forthe 500 μg dose). Compared to BUD, FP has slower pulmonary absorption and slower elimination kinetics. However, following inhalation of therapeutically equipotent, multiple twice‐daily doses in healthy subjects, the systemic effects of FP delivered via Diskus® on AUC24 serum cortisol were relatively low and similar to those of BUD delivered via Turbohaler®.
Characteristics of MML/EAP Parameter Estimates in the Generalized Graded Unfolding Model
Authors: Roberts James S. , Donoghue John R. , Laughlin James E. 
Published: July 2003

The generalized graded unfolding model (GGUM) is a very general parametric, unidimensional item response theory model for unfolding either binary or polytomous responses to test items. Roberts, Donoghue, and Laughlin have described a marginal maximum likelihood (MML) approach to estimate item parameters in the GGUM along with an expected a posteriori (EAP) method to estimate person parameters. This article examines the data demands required to produce accurate parameter estimates using these techniques under ideal conditions. It also examines the robustness of parameter estimates under nonideal conditions, in which there are inconsistencies between the prior distribution of person parameters that must be speci.ed when using either the MML or EAP approaches and the true distribution of person parameters. Results from two simulation studies show that accurate item parameter estimates can generally be obtained with approximately 750 to 1,000 respondents. Similarly, responses to approximately 15 to 20, equally spaced, six-category items can yield accurate EAP estimates of person parameters under static testing conditions. The results also suggest that MML item parameter estimates are quite robust to discrepancies between the prior and true distributions of person parameters. EAP parameter estimates are also fairly robust as long as the item response patterns in question are not too extreme. Finally, 20 quadrature points are generally sufficient to integrate over the prior distribution in both the MML and EAP methods when test and sample characteristics are like those simulated. Thus, the MML/EAP approach to parameter estimation in the general graded unfolding model can produce accurate estimates in an ef.cient manner even when there is uncertainty about the true distribution of person parameters.
Mechanically Implementable Accommodation Matrices for Passive Force Control
Authors: Goswami Ambarish , Peshkin Michael 
Published: July 2003

Robot force control implemented by means of passive mechanical devices has inherent advantages over active implementations with regard to stability, response rapidity, and physical robustness. The class of devices considered in this paper consists of a Stewart platform-type mechanism interconnected with a network of adjustable mechanical elements such as springs and dampers. The control law repertoire of such a device, imagined as a robot wrist, is given by the range of admittance matrices that it may be programmed to possess. This paper focuses on wrists incorporating damper networks for which the admittance matrices reduce to accommodation or inverse-damping matrices. We show that a hydraulic network of fully adjustable damper elements may attain any diagonally dominant accommodation matrix. We describe the technique of selecting the individual damping coefficients to design a desired matrix. We identify the set of dominant matrices as a polyhedral convex cone in the space of matrix entries, and show that each dominant matrix can be composed of a positive linear combination of a fixed set of basis matrices. The overall wrist-accommodation matrix is obtained by projecting the accommodation matrix of the damper network through the wrist kinematics. The linear combination of the dominant basis matrices projected through the wrist kinematics generates the entire space of mechanically implementable force-control laws. We quantify the versatility of mechanically implementable force-control laws by comparing this space to the space of all matrices.