bluuebunny/crossref_metadata_2025_split huggingface dataset:
Infrared intensities of liquids. XVII. Infrared refractive indices from 8000 to 350 cm−1, absolute integrated absorption intensities, transition moments, and dipole moment derivatives of methan-d3-ol and methanol-d4 at 25 °C
Authors: Bertie John E. , Zhang Shuliang L. 
Published: July 2002

This paper reports absolute infrared absorption intensities of liquids methan-d3-ol (CD3OH) and methanol-d4 (CD3OD) at 25 °C between 8000 and 350 cm−1. Measurements were made by multiple attenuated total reflection spectroscopy with the CIRCLE cell, and by transmission spectroscopy with transmission cells fitted with calcium fluoride windows. In both cases, the spectra were converted to infrared real and imaginary refractive index spectra. The refractive indices obtained by these two methods agreed excellently and were combined to yield an imaginary refractive index spectrum k(ν̃) between 7244 and 350 cm−1 for CD3OH and between 5585 and 350 cm−1 for CD3OD. The imaginary refractive index spectrum was arbitrarily set to zero from 8000 to 7244 cm−1 (CD3OH) or 5585 cm−1 (CD3OD), where k is always less than 4×10−6, in order that the real refractive index can be calculated below 8000 cm−1 by Kramers–Krönig transformation. The results are reported as graphs and tables of the refractive indices between 8000 and 350 cm−1, from which all other infrared properties of the two liquids can be calculated. The estimated accuracy, not precision, of the imaginary refractive index is ±3%, except for ±10%, where k is less than 4×10−5. The estimated accuracy of the real refractive index is better than ±0.5%.
In order to obtain molecular information from the measurements, the spectra of the imaginary polarizability multiplied by wave number ν̃αm″ were calculated under the assumption of the Lorentz local field. The area under these ν̃αm″ spectra was separated into the integrated intensities of different vibrations. The magnitudes of the transition moments were calculated from the integrated intensities, and the double harmonic approximation was used to calculate the magnitudes of the dipole moment derivatives of the liquid-state molecules with respect to the normal coordinates. Dipole moment derivatives with respect to internal coordinates were calculated under the simplest approximations, the validity of which is demonstrated by the experimental data in many cases. The consistency of the dipole moment derivatives with respect to internal coordinates obtained for different isotopomers is shown through their relative rotational corrections. Results are presented for the O–H, O–D, C–H, and C–D stretches; the C–O–H in-plane bending; and the D–C–O–H and D–C–O–D torsion vibrations.
Photophysics and dynamics of the lowest excited singlet state in long substituted polyenes with implications to the very long-chain limit
Authors: Andersson Per Ola , Gillbro Tomas 
Published: July 2002

In this paper we explore the intramolecular relaxation processes within two long carotenoids, namely decapreno-β-carotene (M15) and dodecapreno-β-carotene (M19) with 15 and 19 conjugated double bonds (N), respectively. Amplified 200 fs pulses at 590 nm were used to excite the optically allowed S0→S2 (1 1Ag→1 1Bu) transition of the two carotenoids. The excited state dynamics were probed by continuum light between 400–890 nm in solvents with different polarizabilities. The transient absorption spectra consist of a bleaching region, due to loss of ground state absorption, and of an excited state absorption region at longer wavelengths, due to the S1→Sn transition. The Sn state was assigned to an n 1Bu state. The overall wavelength dependence of the measured kinetics could be well described by introducing three decay time constants. One reflects the S1 lifetime (τ1) and was determined to 1.1 and 0.5 ps for M15 and M19, respectively. A second lifetime, between 5 and 15 ps, was attributed to vibrational cooling in the ground state. A third decay time was in the subpicosecond range, and was ascribed to the vibrational redistribution and relaxation of the S1 potential surface after being populated by the subpicosecond S2–S1 internal conversion. No significant change of the decay constants was observed for M15 embedded in a 77 K matrix. This shows that the relaxation rates are only influenced by intramolecular processes.
The S2 lifetime was shorter than the pulse duration and was estimated to be in the order of 100 fs. The S0→S2 transition of M15 in the liquid phase exhibits a 0.39 anisotropy at short times, while the S1→Sn transition has an initial value of only 0.31. This corresponds to an angle of 23° between the transition dipoles. The measured S1 rate constants were analyzed, together with decay constants of shorter carotenes, in terms of the energy gap law. When going from the shortest (N=5) to the longest (N=19) polyene, τ1 decreases about 6000 times, i.e., from 3 ns to 0.5 ps. By using an empirical form of the energy gap law the 0–0 transition of S1(2 1Ag)→S0 was estimated to be located at 11 300 and 10 200±1 000 cm−1 for M15 and M19, respectively. By fitting the excitation energies of all carotenes in the series (3≤N≤19) with a truncated two or three term expansion of a power series in 1/N the long-chain limit values were extrapolated to be 11 000 and 3 500 cm−1 for the 1 1Bu and 2 1Ag state, respectively. The implication of these limit values on the electronic structure of polyacetylene are discussed.
Analysis of viscous dissipation in disk storage systems and similar flow configurations
Authors: Humphrey J. A. C. , Schuler C. A. , Iglesias I. 
Published: July 2002

Flows in rotating magnetic disk storage systems and similar devices are prone to instabilities and the viscous generation of heat. Serious degradation in the performance of disk storage systems occurs when differential thermal expansion, due to the maldistribution of heat, and flow-induced vibrations result in track misregistration by the magnetic read/write heads. Submicron flying heights and micron track widths exacerbate such alignment difficulties. High rotation speeds, also characterizing the emerging disk storage technology, impose significant torque requirements. Experimental measurements of torque obtained by Daily and Nece [J. Basic Eng. Trans ASME 82, 217 (1960)] for a single disk, and by Hudson and Eibeck [J. Fluids Eng. 113, 648 (1991)] for a disk stack with and without obstructions, both in cylindrical enclosures, are found in this study to be correctly correlated by the analytically derived equation, TNo≡Ttotρ/Nμ2R2 = (2C1 + C2H/R2) × [Re/(1 − tL/HR2)]3/2+m, where TNo is a newly defined dimensionsless torque number, Re is the Reynolds number of the interdisk flow; H, R2, t, and L are geometrical length scales; and, C1, C2, and m are experimentally determined constants of order unity.
Regressions to the experimental data of these authors yield values for C1, C2, and m in this equation which offer a combination of accuracy and universality not previously available. Moderate amounts of imposed radially directed flows in the spaces between unobstructed pairs of corotating disks are shown, via numerical calculation, to affect the interdisk flow fields quite notably. Analysis of results obtained solving the Navier–Stokes equations, assuming unsteady, axisymmetric, streamlined flow at low speeds of rotation shows that sucking air radially inward in the interdisk space, rather than blowing it radially outwards, substantially reduces the torque required to rotate the disks relative to the unventilated condition. Notwithstanding, depending on how the sucking condition is implemented, in obstructed geometries the reduction in torque may come at the expense of flow instabilities that could affect magnetic head read/write performance, a problem requiring close attention in the application of present findings to the improved design of disk storage systems.
Needle and syringe provision and disposal in an Australian regional centre
Authors: MILLER PETER G. 
Published: July 2002

AbstractThe aim of this study was to investigate the provision and disposal of needles and syringes in Geelong, Victoria, supplying a comparison of needles provided to needles returned through needle and syringe programmes (NSPs), needles disposed of in ‘Sharpsafe’ bins and needles discarded. This study combined quantitative data obtained from a number of sources and qualitative data obtained from 60 interviews. An average of 18,337 (SD = 2796) per month were dispensed from NSPs and an average of 5576 needles are returned to NSP sites in Geelong per month. For the current year, 450 needles and syringes per month were placed in publicly located disposal bins. On average there were 19 callouts to discarded needles per month in the Geelong region and these needles constituted 0.38% of the monthly average of needles provided through NSPs. It was concluded that, while discarded needles are of major community concern, the vast majority of needles and syringes provided in this regional centre are not discarded. Findings are discussed in relation to the current laws surrounding the possession of injecting equipment.
Cortical Num1p Interacts with the Dynein Intermediate Chain Pac11p and Cytoplasmic Microtubules in Budding Yeast
Authors: Farkasovsky Marian , Küntzel Hans 
Published: July 2002

Num1p, a cortical 313-kD protein, controls cytoplasmic microtubule (cMT) functions and nuclear migration through the bud neck in anaphase cells. A green fluorescent protein (GFP)-Num1p fusion protein localizes at the bud tip and the distal mother pole of living cells, apparently forming cMT capture sites at late anaphase. In addition, galactose-induced GFP-Num1p is seen at the bud neck and in lateral regions of the mother cortex. The bud tip location of Num1p depends on Bni1p but does not require Kar9p, Dyn1p, or cMTs, whereas cMT contacts with polar Num1p dots are reduced in cells lacking Dyn1p. Num1p associates with the dynein intermediate chain Pac11p in the presence of Dyn1p, and with the α-tubulin Tub3p, as shown by coimmune precipitation of tagged proteins. Num1p also forms a complex with Bni1p and Kar9p, although Num1p is not required for Bni1p- and Kar9p-dependent nuclear migration to the bud neck in preanaphase cells.
Our data suggest that Num1p controls nuclear migration during late anaphase by forming dynein-interacting cortical cMT capture sites at both cellular poles. In addition, Num1p may transiently cooperate with an associated Bni1p–Kar9p complex at the bud tip of early anaphase cells.
GeneDn: for high-level expression design of heterologous genes in a prokaryotic system.
Authors: Ju L W , Xing L H , Hong P W , Jin W J 
Published: July 2002

Abstract
RESULTS: Based on the mathematical model of high-level expression of heterologous genes in prokaryotic vector pBV220, we developed a program GeneDn for high-level expression design of natural and synthetic genes. AVAILIBILITY: The program is written in Turbo Pascal 7.0. The source code and related material are available upon request. CONTACT: wujj@nic.bmi.ac.cn
Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12.
Authors: Thieffry D , Salgado H , Huerta A M , Collado-Vides J 
Published: July 2002

Abstract
MOTIVATION: As one of the best-characterized free-living organisms, Escherichia coli and its recently completed genomic sequence offer a special opportunity to exploit systematically the variety of regulatory data available in the literature in order to make a comprehensive set of regulatory predictions in the whole genome. RESULTS: The complete genome sequence of E.coli was analyzed for the binding of transcriptional regulators upstream of coding sequences. The biological information contained in RegulonDB (Huerta, A.M. et al., Nucleic Acids Res.,26,55-60, 1998) for 56 different transcriptional proteins was the support to implement a stringent strategy combining string search and weight matrices. We estimate that our search included representatives of 15-25% of the total number of regulatory binding proteins in E.coli. This search was performed on the set of 4288 putative regulatory regions, each 450 bp long. Within the regions with predicted sites, 89% are regulated by one protein and 81% involve only one site. These numbers are reasonably consistent with the distribution of experimental regulatory sites. Regulatory sites are found in 603 regions corresponding to 16% of operon regions and 10% of intra-operonic regions. Additional evidence gives stronger support to some of these predictions, including the position of the site, biological consistency with the function of the downstream gene, as well as genetic evidence for the regulatory interaction. The predictions described here were incorporated into the map presented in the paper describing the complete E.coli genome (Blattner,F.R. et al., Science, 277, 1453-1461, 1997). AVAILABILITY: The complete set of predictions in GenBank format is available at the url: http://www. cifn.unam.mx/Computational_Biology/E.coli-predictions CONTACT: ecoli-reg@cifn.unam.mx, collado@cifn.unam.mx
Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis.
Authors: Mendoza L , Thieffry D , Alvarez-Buylla E R 
Published: July 2002

Abstract
MOTIVATION: A large number of molecular mechanisms at the basis of gene regulation have been described during the last few decades. It is now becoming possible to address questions dealing with both the structure and the dynamics of genetic regulatory networks, at least in the case of some of the best-characterized organisms. Most recent attempts to address these questions deal with microbial or animal model systems. In contrast, we analyze here a gene network involved in the control of the morphogenesis of flowers in a model plant, Arabidopsis thaliana. RESULTS: The genetic control of flower morphogenesis in Arabidopsis involves a large number of genes, of which 10 are considered here. The network topology has been derived from published genetic and molecular data, mainly relying on mRNA expression patterns under wild-type and mutant backgrounds. Using a 'generalized logical formalism', we provide a qualitative model and derive the parameter constraints accounting for the different patterns of gene expression found in the four floral organs of Arabidopsis (sepals, petals, stamens and carpels), plus a 'non-floral' state. This model also allows the simulation or the prediction of various mutant phenotypes. On the basis of our model analysis, we predict the existence of a sixth stable pattern of gene expression, yet to be characterized experimentally. Moreover, our dynamical analysis leads to the prediction of at least one more regulator of the gene LFY, likely to be involved in the transition from the non-flowering state to the flowering pathways. Finally, this work, together with other theoretical and experimental considerations, leads us to propose some general conclusions about the structure of gene networks controlling development.
TEXtopo: shaded membrane protein topology plots in LaTEX2ε
Authors: Beitz Eric 
Published: July 2002

Abstract
Summary: TEXtopo is a LaTEX2ε macro package for plotting topology data directly from PHD predictions or SwissProt database files in publication-ready quality. The plot can be shaded automatically to emphasize conserved residues or functional properties of the residue sidechains. The addition of rich decorations, such as labels, annotations and legends, is easily accomplished.
Availability: The TEXtopo macro package and a full on-line documentation are freely available at http://homepages.uni-tuebingen.de/beitz/
Contact: eric.beitz@uni-tuebingen.de
SPLASH: structural pattern localization analysis by sequential
histograms
Authors: Califano Andrea 
Published: July 2002

Abstract
Motivation: The discovery of sparse amino acid patterns that match repeatedly in a set of protein sequences is an important problem in computational biology. Statistically significant patterns, that is patterns that occur more frequently than expected, may identify regions that have been preserved by evolution and which may therefore play a key functional or structural role. Sparseness can be important because a handful of non-contiguous residues may play a key role, while others, in between, may be changed without significant loss of function or structure. Similar arguments may be applied to conserved DNA patterns. Available sparse pattern discovery algorithms are either inefficient or impose limitations on the type of patterns that can be discovered.
Results: This paper introduces a deterministic pattern discovery algorithm, called Splash, which can find sparse amino or nucleic acid patterns matching identically or similarly in a set of protein or DNA sequences. Sparse patterns of any length, up to the size of the input sequence, can be discovered without significant loss in performances.
Splash is extremely efficient and embarrassingly parallel by nature. Large databases, such as a complete genome or the non-redundant SWISS-PROT database can be processed in a few hours on a typical workstation. Alternatively, a protein family or superfamily, with low overall homology, can be analyzed to discover common functional or structural signatures. Some examples of biologically interesting motifs discovered by Splash are reported for the histone I and for the G-Protein Coupled Receptor families. Due to its efficiency, Splash can be used to systematically and exhaustively identify conserved regions in protein family sets. These can then be used to build accurate and sensitive PSSM or HMM models for sequence analysis.
Availability: Splash is available to non-commercial research centers upon request, conditional on the signing of a test field agreement.
Contact: acal@us.ibm.com, Splash main page http://www.research.ibm.com/splash
Genomic Microsatellites as Evolutionary Chronometers: A Test in Wild Cats
Authors: Driscoll Carlos A. , Menotti-Raymond Marilyn , Nelson George , Goldstein David , O'Brien Stephen J. 
Published: July 2002

Nuclear microsatellite loci (2- to 5-bp tandem repeats) would seem to be ideal markers for population genetic monitoring because of their abundant polymorphism, wide dispersal in vertebrate genomes, near selective neutrality, and ease of assessment; however, questions about their mode of generation, mutation rates and ascertainment bias have limited interpretation considerably. We have assessed the patterns of genomic diversity for ninety feline microsatellite loci among previously characterized populations of cheetahs, lions and pumas in recapitulating demographic history. The results imply that the microsatellite diversity measures (heterozygosity, allele reconstitution and microsatellite allele variance) offer proportionate indicators, albeit with large variance, of historic population bottlenecks and founder effects. The observed rate of reconstruction of new alleles plus the growth in the breadth of microsatellite allele size (variance) was used here to develop genomic estimates of time intervals following historic founder events in cheetahs (12,000 yr ago), in North American pumas (10,000–17,000 yr ago), and in Asiatic lions of the Gir Forest (1000–4000 yr ago).[Supplemental material available online at http://rex.nci.nih.gov/lgd/front_page.htm and athttp://www.genome.org.]
Hydrogen‐bonding classes in proteins and their contribution to the unfolding reaction
Authors: Ragone Raffaele 
Published: July 2002

AbstractThis paper proposes to assess hydrogen‐bonding contributions to the protein stability, using a set of model proteins for which both X‐ray structures and calorimetric unfolding data are known. Pertinent thermodynamic quantities are first estimated according to a recent model of protein energetics based on the dissolution of alkyl amides. Then it is shown that the overall free energy of hydrogen‐bond formation accounts for a hydrogen‐bonding propensity close to helix‐forming tendencies previously found for individual amino acids. This allows us to simulate the melting curve of an alanine‐rich helical 50‐mer with good precision. Thereafter, hydrogen‐bonding enthalpies and entropies are expressed as linear combinations of backbone‐backbone, backbone–side‐chain, side‐chain–backbone, and side‐chain–side‐chain donor‐acceptor contributions. On this basis, each of the four components shows a different free energy versus temperature trend. It appears that structural preference for side‐chain–side‐chain hydrogen bonding plays a major role in stabilizing proteins at elevated temperatures.
Examination of the folding of E. coli CspA through tryptophan substitutions
Authors: Vu Dung M. , Reid Katherine L. , Rodriguez Hector M. , Gregoret Lydia M. 
Published: July 2002

AbstractEscherichia coli cold shock protein, CspA, folds very rapidly (time constant, τ = 4 msec) by an apparent two‐state mechanism. However, recent time‐resolved infrared (IR) temperature‐jump experiments indicate that the folding trajectory of CspA may be more complicated. The sole tryptophan of wild‐type CspA (Trp11), which is used to monitor the folding process by fluorescence spectroscopy, is located in an unusual aromatic cluster on the surface of CspA within the nucleic acid binding site. To gain a more global picture of the folding kinetics of CspA and to determine if there are any previously undetected intermediates, we have introduced a second tryptophan at three different surface locations in the protein. The three mutations did not significantly alter the tertiary structure of CspA, although two of the substitutions were found to be slightly stabilizing. Two‐state folding, as detected by stopped‐flow fluorescence spectroscopy, is preserved in all three mutants. These results indicate that the fast folding of CspA is driven by a concerted mechanism.