bluuebunny/crossref_metadata_2025_split huggingface dataset:
Active emmetropization — evidence for its existence and ramifications for clinical practice
Authors: Wildsoet C. F. 
Published: July 2002

SummaryThere is increasing evidence from animal studies in support of the concept of an active emmetropization mechanism which has potentially important clinical ramifications for the management of refractive errors.Recent research into retractive development and emmetropization is reviewed, with emphasis given to work involving the chick, tree shrew and monkey, which represent the three most widely used animal models in this field. The findings of this research are reviewed in a clinical context.Compensatory eye growth responses to focusing errors imposed by lenses represent the most compelling evidence for active emmetropization. These observations are complemented by other evidence showing recovery from induced refractive errors such as form‐deprivation myopia. Of the animals listed above, chicks show the most impressive emmetropization, being able to compensate fully (using choroidal and scleral mechanisms) to lens powers ranging from +15 D to ‐10 D. The range of lens powers eliciting appropriate compensatory responses is narrower in the tree shrew and monkey, and the response patterns generally are also more complex to interpret. These data relate to young animals and together indicate refractive plasticity during development. Extrapolation of these findings to humans predicts that natural emmetropization will be inhibited in neonates by early intervention with prescription lenses, and that refractive correction of myopia will lead to accelerated progression.This convincing evidence for active emmetropization warrants due consideration in developing clinical management strategies for refractive errors.
Ammonia dimer: Further structural studies
Authors: Nelson D. D. , Klemperer W. , Fraser G. T. , Lovas F. J. , Suenram R. D. 
Published: July 2002

New experimental results on the structural and dynamical properties of NH3 dimer are reported in this work. J=1–0, K=0 transitions of 14NH3–15NH3, 15NH3–14NH3, ND3 dimer, and ND3–ND2H have been measured at high resolution and 14N electric quadrupole coupling constants are reported for each of these species. The NH3 subunits comprising the dimer are inequivalent. The quadrupole coupling constant associated with the first ammonia subunit eqQ1aa, is measured in 14NH3–15NH3 [−627(8)kHz], in ND3 dimer [−531(15) kHz], and in ND3–ND2H [−991(18) kHz]. For the other subunit, eqQ2aa is reported in 15NH3–14NH3 [892(8)kHz], in ND3 dimer [745(13) kHz], and in NH3–ND2H [1013(18) kHz]. These numbers can be used to estimate the vibrationally averaged polar angles of these isotopomers of NH3 dimer. The result is (including the primary isotopomer) θ1 for 14NH3–14NH3 is 48.6°, for 14NH3–15NH3 is 48.7°, for ND3 dimer is 49.6° and for ND3–ND2H is 45.3°; while θ2 for 14NH3–14NH3 is 64.5°, for 15NH3–14NH3 is 64.3°, for ND3 dimer is 62.6°, and for ND3–ND2H is 65.8°. The remarkable invariance of these values rules out the possibility of large vibrational averaging or tunneling averaging in this system and establishes that the angles θ1=49° and θ2=65° are near equilibrium. The isotope effect in the
component of the electric dipole moment along the a inertial axis μa, is shown to correlate well with the trend in polar angles given by the quadrupole coupling constants. The absence of interchange tunneling effects in the observed states of NH3 dimer implies that these states are asymmetrically excited internal rotor states of the complex. These experimental structural results are in disagreement with all previous theoretically determined structures for NH3 dimer except one. A recent electronic structure calculation which incorporates correlation through the coupled pair functional approach (while systematically varying geometry) obtains a compact, asymmetric structure for the dimer in close accord to observations.
Cluster impact chemistry. High-energy collisions of I2ArN clusters with a Pt surface
Authors: Schek Israel , Raz Tamar , Levine R. D. , Jortner Joshua 
Published: July 2002

In this paper, we explore cluster–surface impact induced dissociation of an I2 molecule initially embedded within an I2ArN (N=11–553) cluster, which collides with a Pt surface. Molecular dynamics simulations of high-energy I2ArN–Pt surface collisions (with initial center of mass velocities v=0.2–10 km s−1 and initial kinetic energies E0K=1 eV−1.2×104 eV) provide information on the yields and time scales for energy acquisition by the cluster and by the surface and energy deposition to the guest molecule via the formation of an intracluster microscopic shock wave, as well as on the I2 dissociation dynamics. The intracluster shock wave is characterized by a temporal peak in the cluster potential energy and in the saturation of the cluster temperature, with the sum of the yields for potential and kinetic energy deposition into the cluster being 0.5–0.6. The cluster residence time (τ=50–800 fs over our velocity and cluster size domain) coincides (within 20%) with the time scale for the cluster energy acquisition, decreasing linearly with v−1 and obeying a dynamic size equation τ∝(N+2.9)1/3. The characteristic time tp for energy deposition to the I2 molecule via a local mechanism involving pair interactions is also close to τ.
The initial cluster kinetic energy dependence of the dissociation yields YD of I2 reveals a gradual increase of YD towards unity above a threshold at the energy Et. For smaller (N=11,53) clusters, Et/N is close to the dissociation energy of bare I2, while for larger clusters Et exhibits an exponential N dependence. Cluster impact dissociation of I2 in I2ArN results in higher YD values (≳0.4) than the high-energy collision of bare I2 with the Pt surface for which YD saturates at 0.35. The I2 dissociation times 〈τD〉, which were characterized by averaging over the first passage times for the attainment of the turning point of the I–I intramolecular Morse potential for reactive trajectories, fall in the range 170–800 fs, exhibiting a marked inverse kinetic energy dependence, revealing an increase with increasing cluster size and obeying the rough relation 〈τD〉≂2τ, i.e., being proportional to the cluster radius. Energy acquisition and dissociation times are comparable to or even shorter than the vibrational time [τ(I2)=156 fs] of the I2 molecule, opening up a new research area of thermal femtosecond chemistry.
Generalized Burgers equations and Euler–Painlevé transcendents. III
Authors: Sachdev P. L. , Nair K. R. C. , Tikekar V. G. 
Published: July 2002

It was proposed earlier [P. L. Sachdev, K. R. C. Nair, and V. G. Tikekar, J. Math. Phys. 27, 1506 (1986); P. L. Sachdev and K. R. C. Nair, ibid. 28, 977 (1987)] that the Euler–Painlevé equations  y(d2y/dη2)+a(dy/dη)2 +f(η)y(dy/dη)+g(η)y2+b(dy/dη) +c=0 represent generalized Burgers equations (GBE’s) in the same way as Painlevé equations represent the Korteweg–de Vries type of equations. The earlier studies were carried out in the context of GBE’s with damping and those with spherical and cylindrical symmetry. In the present paper, GBE’s with variable coefficients of viscosity and those with inhomogeneous terms are considered for their possible connection to Euler–Painlevé equations. It is found that the Euler–Painlevé equation, which represents the GBE ut+uβux=(δ/2)g(t)uxx, g(t)=(1+t)n, β&gt;0, has solutions, which either decay or oscillate at η=±∞, only when −1&lt;n&lt;1. The solutions are shocklike when n=1. On the other hand, they oscillate over the whole real line when n=−1. Furthermore, the solutions monotonically decay both at η=+∞ and η=−∞, that is, they have a single hump form if β≥βn=(1−n)/(1+n). For β&lt;βn, the solutions have an oscillatory behavior either at η=+∞ or at η=−∞, or at η=+∞ and η=−∞. For β=βn, there exists a single parameter family of exact single hump solutions, similar to those found for the nonplanar Burgers equations in Paper II. Thus the parametric value β=βn seems to bifurcate the families of solutions, which remain bounded at η=±∞. Other GBE’s considered here are also found to be reducible to Euler–Painlevé equations.
The scope of these equations is broadened by relating them to a large number of nonlinear DE’s selected from the compendia of Kamke [Differential Gleichungen : Lösungsmethoden und Lösungen (Akademische Verlagsgesellschaft, Leipzig, 1943)] and Murphy [Ordinary Differential Equations and their Solutions (Van Nostrand, Princeton, NJ, 1960)]. These latter equations arise from a wide range of physical applications and are of some historical interest as well. They are all special cases of a slightly generalized form of the Euler–Painlevé equation.
The international drug control system in the post‐Cold War era. Managing markets or fighting a war?
Authors: Room Robin , Paglia Angela 
Published: July 2002

AbstractThe core institutions and scope of the international drug control system are described. The system has grown in participation and particularly in scope and ambitions since it was studied in the early 1970s by Bruun and colleagues. Its premises are notably in conflict with the currently dominant ideologies of a free‐market global economy although, as earlier, the United States plays a dominant role in the drug control system. At a time when it is seen as a failure in its primary aims both from inside and from outside, defenses of the system have ranged from rousing rhetorical appeals to efforts to “de‐sensationalize” the issues.
Mitochondria in the Programmed Death Phenomena; A Principle of Biology: “It Is Better to Die than to be Wrong”
Authors: Skulachev Vladimir P. 
Published: July 2002

AbstractThe very fact that mitochondria participate in amplification of the cell suicide signals has stimulated interest in the mechanism of this and related phenomena. It seems probable that mitochondria possess an autonomic system that allows them to commit suicide. This mitoptosis is mediated by reactive oxygen species (ROS), causing opening of the permeability transition pores (PTP) in the inner mitochondrial membrane. Mitoptosis can purify the mitochondrial population in a cell from the ROS‐overproducing organelles. Massive mitoptosis can result in apoptosis (programmed cell death) because of the release of proapoptotic proteins from the mitochondrial intermembrane space, a mechanism purifying tissues from the ROS‐overproducing and other unwanted cells. Large‐scale apoptosis can be used by organisms to eliminate some organs during ontogenesis (organoptosis). In adult organisms, organoptosis of organs of vital importance may entail a programmed death of individuals (phenoptosis). This mechanism might purify kins, communities, and populations from individuals becoming dangerous because of, for example, heavy infection (septic shock). It is hypothesized that aging represents a slow ROS‐linked phenoptosis that eliminates individuals with damaged genomes and gives reproductive advantage to those who succeeded in a better preservation of their genomes from damage.
LI-Cadherin–mediated Cell–Cell Adhesion Does Not Require Cytoplasmic Interactions
Authors: Kreft Bertolt , Berndorff Dietmar , Böttinger Anja , Finnemann Silvia , Wedlich Doris , Hortsch Michael , Tauber Rudolf , Geßner Reinhard 
Published: July 2002

The adhesive function of classical cadherins depends on the association with cytoplasmic proteins, termed catenins, which serve as a link between cadherins and the actin cytoskeleton. LI-cadherin, a structurally different member of the cadherin family, mediates Ca2+-dependent cell–cell adhesion, although its markedly short cytoplasmic domain exhibits no homology to this highly conserved region of classical cadherins. We now examined whether the adhesive function of LI-cadherin depends on the interaction with catenins, the actin cytoskeleton or other cytoplasmic components. In contrast to classical cadherins, LI-cadherin, when expressed in mouse L cells, was neither associated with catenins nor did it induce an upregulation of β-catenin. Consistent with these findings, LI-cadherin was not resistant to detergent extraction and did not induce a reorganization of the actin cytoskeleton. However, LI-cadherin was still able to mediate Ca2+dependent cell–cell adhesion.
To analyze whether this function requires any interaction with proteins other than catenins, a glycosyl phosphatidylinositol–anchored form of LI-cadherin (LI-cadherinGPI) was constructed and expressed in Drosophila S2 cells. The mutant protein was able to induce Ca2+-dependent, homophilic cell–cell adhesion, and its adhesive properties were indistinguishable from those of wild type LI-cadherin. These findings indicate that the adhesive function of LI-cadherin is independent of any interaction with cytoplasmic components, and consequently should not be sensitive to regulatory mechanisms affecting the binding of classical cadherins to catenins and to the cytoskeleton. Thus, we postulate that the adhesive function of LI-cadherin is complementary to that of coexpressed classical cadherins ensuring cell–cell contacts even under conditions that downregulate the function of classical cadherins.
Semi-classical limit of wave functions
Authors: Truman A. , Zhao H. 
Published: July 2002

We study in one dimension the semi-classical limit of the exact eigenfunctionΨE(N,h)h\Psi _{E(N,h)}^{h}of the HamiltonianH=−12h2Δ+V(x)H=-\frac {1}{2} h^{2} \Delta +V(x), for a potentialVVbeing analytic, bounded below andlim|x|→∞V(x)=+∞\lim _{|x|\to \infty }V(x)=+\infty. The main result of this paper is that, for any givenE>minx∈R1V(x)E>\min _{x\in R^{1}} V(x)with two turning points, the exactL2L^{2}normalized eigenfunction|ΨE(N,h)h(q)|2|\Psi ^{h}_{E(N,h)}(q)|^{2}converges to the classical probability density, and the momentum distribution|Ψ^E(N,h)h(p)|2|\hat \Psi ^{h}_{E(N,h)}(p)|^{2}converges to the classical momentum density in the sense of distribution, ash→0h\to 0andN→∞N\to \inftywith(N+12)h=1π∫V(x)>E2(E−V(x))dx(N+\frac {1}{2} )h =\frac {1}{\pi } \int _{V(x)>E} \sqrt {2(E-V(x))}dxfixed. In this paper we only consider the harmonic oscillator Hamiltonian. By studying the semi-classical limit of the Wigner’s quasi-probability density and using the generating function of the Laguerre polynomials, we give a complete mathematical proof of the Correspondence Principle.
Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm.
Authors: Rigoutsos I , Floratos A 
Published: July 2002

Abstract
MOTIVATION: The discovery of motifs in biological sequences is an important problem. RESULTS: This paper presents a new algorithm for the discovery of rigid patterns (motifs) in biological sequences. Our method is combinatorial in nature and able to produce all patterns that appear in at least a (user-defined) minimum number of sequences, yet it manages to be very efficient by avoiding the enumeration of the entire pattern space. Furthermore, the reported patterns are maximal: any reported pattern cannot be made more specific and still keep on appearing at the exact same positions within the input sequences. The effectiveness of the proposed approach is showcased on a number of test cases which aim to: (i) validate the approach through the discovery of previously reported patterns; (ii) demonstrate the capability to identify automatically highly selective patterns particular to the sequences under consideration. Finally, experimental analysis indicates that the algorithm is output sensitive, i.e. its running time is quasi-linear to the size of the generated output.
Incremental threading optimization (TITO) to help alignment and modelling of remote homologues.
Authors: Labesse G , Mornon J 
Published: July 2002

Abstract
MOTIVATION: Protein sequence comparison has become a major tool for biologists. Various methods have been designed in order to reveal even remote homologies among proteins. Sequence analyses are powerful, but the lower the identity score, the more skill and time are required to perform them accurately. While necessary to confirm the sequence comparison through the potential of mean force, sequence alignment and molecular modelling are still tedious and time-consuming tasks. RESULTS: In order to help sequence threading onto known three-dimensional (3D) structures, we have developed a new program, named TITO (Tool for Incremental Threading Optimization), which uses a multiple alignment to validate and help the refinement of a sequence/structure comparison. It measures the compatibility of a family of related sequences with a known 3D structure. The coordinates of the common core are extracted, allowing further molecular modelling and 3D survey. AVAILABILITY: TITO is available by anonymous ftp at: ftp://lmcp.jussieu. fr/pub/tito CONTACT: labesse@lmcp.jussieu.fr Supplementary information: http://www.lmcp.jussieu.fr/ approximately labesse/TITO/TITO.html
GeneNet: a gene network database and its automated visualization.
Authors: Kolpakov F A , Ananko E A , Kolesov G B , Kolchanov N A 
Published: July 2002

Abstract
MOTIVATION: Gene networks that provide the regulation of physiological processes are the basic feature of organisms. Information regarding the regulation of gene expression and signal transduction pathways is increasing rapidly. However, the information is hard to formalize and systematize. Ways and means for automated visualization of the gene networks based on their formalized description are needed. RESULTS: The object-oriented database GeneNet and the software for its automated visualization have been developed. The main principles of a formalized description of the gene network have been worked out. Antiviral response and erythropoiesis are provided as examples to show how this is achieved. The GeneNet graphical user interface written in Java provides automated generation of the gene network diagrams and allows visualization and exploration of the GeneNet database through the Internet. A system of filters allows the selection of particular components of the network for visualization. AVAILABILITY: The GeneNet database and its graphical user interface are available at http://wwwmgs.bionet.nsc.ru/systems/MGL/GeneN et/ CONTACT: fedor@bionet.nsc.ru
Sausage: protein threading with flexible force fields
Authors: Huber Thomas , J.Russell Anthony , Ayers Daniel , E.Torda Andrew 
Published: July 2002

Abstract
Summary: Sausage is a protein sequence threading program, but with remarkable run-time flexibility. Using different scripts, it can calculate protein sequence-structure alignments, search structure libraries, swap force fields, create models from alignments, convert file formats and analyse results. There are several different force fields which might be classed as knowledge-based, although they do not rely on Boltzmann statistics. Different force fields are used for alignment calculations and subsequent ranking of calculated models.
Availability: Freely available to academics at ftp://ftp.rsc.anu.edu.au/pub/torda/sausage/README
Contact: Andrew.Torda@anu.edu.au
MASIA: recognition of common patterns and properties in
multiple aligned protein sequences
Authors: Zhu H. , Schein C. H. , Braun W. 
Published: July 2002

Abstract
Summary: MASIA is a software tool for pattern recognition in multiple aligned protein sequences. MASIA converts a sequence to a properties matrix that can be scanned in both vertical and horizontal steps. Consistent patterns are recognized based on the statistical significance of their occurrence. Preset macros can be altered on-line to seek any combination of amino acid properties or sequence characteristics. MASIA output can be used directly by our programs to predict the 3D structure of proteins.
Availability: Access MASIA at http://www.scsb.utmb.edu/masia/masia.html.
Contact: werner@newton.utmb.edu
To whom correspondence should be addressed.
Biochemical systems analysis of genome-wide expression data
Authors: Voit Eberhard O. , Radivoyevitch Tomas 
Published: July 2002

Abstract
Motivation: Modern methods of genomics have produced an unprecedented amount of raw data. The interpretation and explanation of these data constitute a major, well-recognized challenge.
Results: Biochemical Systems Theory (BST) is the mathematical basis of a well-established methodological framework for analyzing networks of biochemical reactions. An existing BST model of yeast glycolysis is used here to explain and interpret the glycolytic gene expression pattern of heat shocked yeast. Our analysis demonstrates that the observed gene expression profile satisfies the primary goals of increased ATP, trehalose, and NADPH production, while maintaining intermediate metabolites at reasonable levels. Based on a systematic exploration of alternative, hypothetical expression profiles, we show that the observed profile outperforms other profiles.
Conclusion: BST is a useful framework for combining DNA microarray data with enzymatic process information to yield new insights into metabolic pathway regulation.
Availability: All analyses were executed with the software PLAS©, which is freely available at http://correio.cc.fc.ul.pt/~aenf/plas.html for academic use.
Contact: VoitEO@MUSC.edu
To whom correspondence should be addressed.
PatSearch: a pattern matcher software that finds functional
elements in nucleotide and protein sequences and assesses their
statistical significance
Authors: Pesole Graziano , Liuni Sabino , D’Souza Mark 
Published: July 2002

Abstract
* To whom correspondence should be addressed.
Motivation: The identification of sequence patterns involved in gene regulation and expression is a major challenge in molecular biology. In this paper we describe a novel algorithm and the software for searching nucleotide and protein sequences for complex nucleotide patterns including potential secondary structure elements, also allowing for mismatches/mispairings below a user-fixed threshold, and assessing the statistical significance of their occurrence through a Markov chain simulation.
Results: The application of the proposed algorithm allowed the identification of some functional elements, such as the Iron Responsive Element, the Histone stem-loop structure and the Selenocysteine Insertion Sequence, located in the mRNA untranslated regions of post-transcriptionally regulated genes with the assessment of sensitivity and selectivity of the searching method.
Availability: A Web interface is available at: http://bigarea.area.ba.cnr.it:8000/EmbIT/Patsearch.html.
Contact: graziano.pesole@unimi.it