bluuebunny/crossref_metadata_2025_split huggingface dataset:
Density-functional modeling of structure and forces in thin micellar liquid films
Authors: Pollard Maria L. , Radke C. J. 
Published: July 2002

Recent equilibrium force measurements on aqueous films of surfactant above the critical micelle concentration show oscillations for film thicknesses up to 50 nm. To model this phenomenon we express the micellar contribution to the disjoining pressure in terms of thickness-dependent inhomogeneous micelle number density distributions through the film. Density functional theory is used to calculate micelle density profiles, presuming the micelles to behave as charged spheres interacting with each other, and with the film interfaces, through screened-Coulomb potentials. The background electrolyte permits dilute micellar solutions to act as concentrated systems exhibiting pronounced layering in the film. For a 0.1 M sodium dodecylsulfate (SDS) film we find up to five micellar layers for a film thickness equal to ten micelle diameters (d), the layer separation scaling with the effective diameter (deff/d=1.86) which includes the micelle Debye atmosphere. The peaks are largest near the interfaces and decay toward the bulk density at the film midplane. The corresponding disjoining pressures show oscillations with the same distance scaling between the branches as in the density profiles; these values are consistent with experiment. With decreasing film thickness, the (meta-)stable disjoining pressure regions represent micellar layers in the film being forced closer together, raising the pressure until the interior layer is expelled, allowing more space between the remaining micellar layers at that thickness.
Repulsive (positive) disjoining pressures result from layer separations less than the corresponding bulk value whereas attractive (negative) regions represent more distance between layers than that in the bulk. The 0.2 M SDS disjoining pressure isotherm exhibits one additional layer than the 0.1 M case for thicknesses up to 50 nm. The pressure magnitudes of the former case are about twice that of the latter. Addition of ionic salts greatly inhibits the long-range micellar structuring. For SDS foam films, predicted disjoining pressures are much higher than measured values. Comparison with cetyltrimethyl-ammonium bromide (CTAB) micellar films in the surface forces apparatus, however, shows near quantitative agreement. The nature of the confining interfaces thus plays a key role in supporting the internal micellar structuring.
The thermal energy dependence (10–20 eV) of electron impact induced fragmentation of C60 in molecular beams: Experiment and model calculations
Authors: Kolodney E. , Tsipinyuk B. , Budrevich A. 
Published: July 2002

We have studied the dependence of electron impact induced ionization and fragmentation of C60 molecules in effusive molecular beams upon the initial thermal excitation in the temperature range of 1190–1875 K, corresponding to an average vibrational energy of 10–20 eV. This is the largest energy range of parent molecule thermal excitation ever reported for electron-impact mass-spectrometric studies. The normalized curves of electron energy (Ee) dependent ion currents of C+60 and C+58 were measured and analyzed for the temperatures (T0) of 1190, 1435, 1570, 1695, and 1875 K. Similar measurements were done for C+2n (n=26–28) fragments for T0=1190 and 1875 K. We have developed an expression for the dependence of C+58 fragment ion current i58(Ee,T0), formed via the decay process C+60→C+58+C2, on electron energy and initial temperature. Using this expression and the strong temperature dependence observed, we have proposed a simple experimental method for estimating the energy deposition function—the probability density of vibrational excitation ε by an ionizing electron of energy Ee. The effective (apparent) value of maximum deposited energy was found to be εm(Ee)=Ee−E*, where E*=30±5 eV. Possible interpretations for this surprisingly low value are discussed. Comparing the experimental i58(Ee,T0) curves with the calculated ones over the range of Ee=30–80 eV we find that for T0≤1600 K, good agreement is obtained assuming that the C60 initial internal excitation is determined by the source temperature alone.
For the higher temperature range 1600 K≤T0≤1900 K, we had to use a modified calculation taking into account radiative cooling and ensemble evaporative cooling processes along the molecular beam flight path. As a result, we have obtained an accurate simulation of the complete family of i58(Ee,T0) curves over all the temperature range measured, using a single set of independently measured physical quantities, and without any adjustable parameter. Uniqueness and sensitivity were thoroughly checked and demonstrated. The good agreement between experiment and calculation basically confirms our description of the underlying process and provides an additional support for the values of the independent physical parameters used. We have used maximum energy deposition parameter of E*=31 eV, an activation energy of E0=4.3–4.5 eV for the neutral fragmentation channel C60→C58+C2 and E1=4.0 eV for the ion fragmentation channel C+60→C+58+C2, and pre-exponential factors of A0=A1=2.5×1013 s−1. These values are very close to former ones obtained by us from analysis of time-of-flight distributions and integrated flux decay measurements of hot C60 molecular beams. Correspondence with other results reported in the literature is discussed and a two-step dissociation mechanism is proposed.
Cannabis use in relation to illicit drug use and health problems among opiate misusers in treatment
Authors: BEST DAVID , GOSSOP MICHAEL , GREENWOOD JUDY , MARSDEN JOHN , LEHMANN PETRA , STRANG JOHN 
Published: July 2002

AbstractThe study investigated cannabis use among 200 opiate misusers attending out‐patient treatment services at two sites. Three groups were classified according to the frequency of their cannabis use in the previous month; 40.5% were non‐users, 40% daily users and the remaining 19.5% were classified as occasional users (they had used on between 1 and 29 days in the previous month). Non‐users of cannabis had used heroin in the previous month on more occasions than either daily or occasional users (p < 0.001). Non‐cannabis users also reported the highest average frequencies of use of alcohol (p < 0.01) and crack cocaine (p < 0.05). In contrast, daily users of cannabis reported more symptoms of anxiety (p < 0.01) and depression (p < 0.01) than either of the other groups. Finally, daily cannabis users were more likely to report dietary problems than either occasional users or non‐users of cannabis. While cannabis use is highly prevalent among opiate misusers in treatment, its relationship to treatment outcome is complex and requires greater research scrutiny.
Effect of low doses of ethanol on spontaneous locomotor activity in UChB and UChA rats
Authors: QUINTANILLA MARIA ELENA 
Published: July 2002

AbstractThe effects of low to moderate doses of ethanol on spontaneous locomotor activity were studied in the selectively bred high‐ethanol drinking (UChB) and the low‐ethanol drinking (UChA) strain of rats. Alcohol‐naive rats had food and water available ad libitum, although food was removed 24 hours before and during activity testing. After an injection of c.15 M NaCl or ethanol (0.25–1.0 g/kg), spontaneous locomotor activity was monitored every 5 minutes for 20 minutes in an open field apparatus. The UChB rats exhibited increased locomotor activity after doses of 0.25 and 0.50 g/kg of ethanol, while UChA rats failed to show increased locomotor activity at any ethanol dose. Moreover, the UChA rats appeared to be more sensitive to the sedating effects of 1.0 g/kg of ethanol than the UChB rats. These differences were not the result of different brain‐blood alcohol levels. Ethanol intakes by the UChB and UChA rats determined at the conclusion of activity testing averaged 5.0 ± 0.5 and 1.9 ± 0.4 g/kg/day, respectively. The data suggest that ethanol‐induced locomotor stimulation may be associated with ethanol preference and that hyperactivity may be an expression of the positive reinforcing effect of ethanol in UChB rats.
A Role for Cdc42 in Macrophage Chemotaxis
Authors: Allen William E. , Zicha Daniel , Ridley Anne J. , Jones Gareth E. 
Published: July 2002

Three members of the Rho family, Cdc42, Rac, and Rho are known to regulate the organization of actin-based cytoskeletal structures. In Bac1.2F5 macrophages, we have shown that Rho regulates cell contraction, whereas Rac and Cdc42 regulate the formation of lamellipodia and filopodia, respectively. We have now tested the roles of Cdc42, Rac, and Rho in colony stimulating factor-1 (CSF-1)–induced macrophage migration and chemotaxis using the Dunn chemotaxis chamber. Microinjection of constitutively activated RhoA, Rac1, or Cdc42 inhibited cell migration, presumably because the cells were unable to polarize significantly in response to CSF-1. Both Rho and Rac were required for CSF-1–induced migration, since migration speed was reduced to background levels in cells injected with C3 transferase, an inhibitor of Rho, or with the dominant-negative Rac mutant, N17Rac1. In contrast, cells injected with the dominant-negative Cdc42 mutant, N17Cdc42, were able to migrate but did not polarize in the direction of the gradient, and chemotaxis towards CSF-1 was abolished.
We conclude that Rho and Rac are required for the process of cell migration, whereas Cdc42 is required for cells to respond to a gradient of CSF-1 but is not essential for cell locomotion.
Fast evaluation of internal loops in RNA secondary structure prediction.
Authors: Lyngs√∏ R B , Zuker M , Pedersen C N 
Published: July 2002

Abstract
MOTIVATION: Though not as abundant in known biological processes as proteins, RNA molecules serve as more than mere intermediaries between DNA and proteins. Research in the last 15 years demonstrates that RNA molecules serve in many roles, including catalysis. Furthermore, RNA secondary structure prediction based on free energy rules for stacking and loop formation remains one of the few major breakthroughs in the field of structure prediction, as minimum free energy structures and related quantities can be computed with full mathematical rigor. However, with the current energy parameters, the algorithms used hitherto suffer the disadvantage of either employing heuristics that risk (though highly unlikely) missing the optimal structure or becoming prohibitively time consuming for moderate to large sequences. RESULTS: We present a new method to evaluate internal loops utilizing currently used energy rules. This method reduces the time complexity of this part of the structure prediction from O(n4) to O(n3), thus reducing the overall complexity to O(n3). Even when the size of evaluated internal loops is bounded by k (a commonly used heuristic), the method presented has a competitive edge by reducing the time complexity of internal loop evaluation from O(k2n2) to O(kn2). The method also applies to the calculation of the equilibrium partition function. AVAILABILITY: Source code for an RNA secondary structure prediction program implementing this method is available at ftp://www.ibc.wustl.edu/pub/zuker/zuker .tar.Z
Oligonucleotide frequency matrices addressed to recognizing functional DNA sites.
Authors: Ponomarenko M P , Ponomarenko J V , Frolov A S , Podkolodnaya O A , Vorobyev D G , Kolchanov N A , Overton G C 
Published: July 2002

Abstract
MOTIVATION: Recognition of functional sites remains a key event in the course of genomic DNA annotation. It is well known that a number of sites have their own specific oligonucleotide content. This pinpoints the fact that the preference of the site-specific nucleotide combinations at adjacent positions within an analyzed functional site could be informative for this site recognition. Hence, Web-available resources describing the site-specific oligonucleotide content of the functional DNA sites and applying the above approach for site recognition are needed. However, they have been poorly developed up to now. RESULTS: To describe the specific oligonucleotide content of the functional DNA sites, we introduce the oligonucleotide alphabets, out of which the frequency matrix for a given site could be constructed in addition to a traditional nucleotide frequency matrix. Thus, site recognition accuracy increases. This approach was implemented in the activated MATRIX database accumulating oligonucleotide frequency matrices of the functional DNA sites. We have demonstrated that the false-positive error of the functional site recognition decreases if the oligonucleotide frequency matrixes are added to the nucleotide frequency matrixes commonly used. AVAILABILITY: The MATRIX database is available on the Web, http://wwwmgs.bionet.nsc.ru/Dbases/MATRIX/ and the mirror site, http://www.cbil.upenn.edu/mgs/systems/c onsfreq/.
SISEQ: manipulation of multiple sequence and large database
files for common platforms
Authors: Sato Naoki 
Published: July 2002

Abstract
Summary: A multiple sequence file converter for common platforms, SISEQ, is described, which performs extraction of DNA sequences that correspond to CDS or RNA field of a large database file as well as subsequent multi-sequence conversions for phylogenetic or molecular biological analysis. Command-line interface as well as a GUI and a script-driven operation mode are provided.
Availability: The program is freely available to academic users in the form of Macintosh FAT binary, DOS executable, or UNIX source code at http://www.molbiol.saitama-u.ac.jp/~naoki/Software.html.
Contact: naokisat@molbiol.saitama-u.ac.jp
Systemic properties of ensembles of metabolic networks:
application of graphical and statistical methods to simple
unbranched pathways
Authors: Alves Rui , Savageau Michael A. 
Published: July 2002

Abstract
Motivation: Mathematical models are the only realistic method for representing the integrated dynamic behavior of complex biochemical networks. However, it is difficult to obtain a consistent set of values for the parameters that characterize such a model. Even when a set of parameter values exists, the accuracy of the individual values is questionable. Therefore, we were motivated to explore statistical techniques for analyzing the properties of a given model when knowledge of the actual parameter values is lacking.
Results: The graphical and statistical methods presented in the previous paper are applied here to simple unbranched biosynthetic pathways subject to control by feedback inhibition. We represent these pathways within a canonical nonlinear formalism that provides a regular structure that is convenient for randomly sampling the parameter space. After constructing a large ensemble of randomly generated sets of parameter values, the structural and behavioral properties of the model with these parameter sets are examined statistically and classified. The results of our analysis demonstrate that certain properties of these systems are strongly correlated, thereby revealing aspects of organization that are highly probable independent of selection. Finally, we show how specification of a given behavior affects the distribution of acceptable parameter values.
Contact: Savageau@umich.edu
* To whom correspondence should be addressed.
Identifying target sites for cooperatively binding factors
Authors: GuhaThakurta Debraj , Stormo Gary D. 
Published: July 2002

Abstract
Motivation: Transcriptional activation in eukaryotic organisms normally requires combinatorial interactions of multiple transcription factors. Though several methods exist for identification of individual protein binding site patterns in DNA sequences, there are few methods for discovery of binding site patterns for cooperatively acting factors. Here we present an algorithm, Co-Bind (for COperative BINDing), for discovering DNA target sites for cooperatively acting transcription factors. The method utilizes a Gibbs sampling strategy to model the cooperativity between two transcription factors and defines position weight matrices for the binding sites. Sequences from both the training set and the entire genome are taken into account, in order to discriminate against commonly occurring patterns in the genome, and produce patterns which are significant only in the training set.
Results: We have tested Co-Bind on semi-synthetic and real data sets to show it can efficiently identify DNA target site patterns for cooperatively binding transcription factors. In cases where binding site patterns are weak and cannot be identified by other available methods, Co-Bind, by virtue of modeling the cooperativity between factors, can identify those sites efficiently. Though developed to model protein–DNA interactions, the scope of Co-Bind may be extended to combinatorial, sequence specific, interactions in other macromolecules.
Availability: The program is available upon request from the authors or may be downloaded from http://ural.wustl.edu.
Contact: dg@genetics.wustl.edu; stormo@genetics.wustl.edu
Exploring the pathway structure of metabolism: decomposition
into subnetworks and application to Mycoplasma pneumoniae
Authors: Schuster S. , Pfeiffer T. , Moldenhauer F. , Koch I. , Dandekar T. 
Published: July 2002

Abstract
Motivation: Reconstructing and analyzing the metabolic map of microorganisms is an important challenge in bioinformatics. Pathway analysis of large metabolic networks meets with the problem of combinatorial explosion of pathways. Therefore, appropriate algorithms for an automated decomposition of these networks into smaller subsystems are needed.
Results: A decomposition algorithm for metabolic networks based on the local connectivity of metabolites is presented. Interrelations of this algorithm with alternative methods proposed in the literature and the theory of small world networks are discussed. The applicability of our method is illustrated by an analysis of the metabolism of Mycoplasma pneumoniae , which is an organism of considerable medical interest. The decomposition gives rise to 19 subnetworks. Three of these are here discussed in biochemical terms: arginine degradation, the tetrahydrofolate system, and nucleotide metabolism. The interrelations of pathway analysis of biochemical networks with Petri net theory are outlined.
Availability: Metatoolis available from ftp://mudshark.brookes.ac.uk/pub/software/ibmpc or http://www.bioinf.mdc-berlin.de/metabolic/. The program Separatorfor decomposing metabolic networks is available from http://www.bioinf.mdc-berlin.de/metabolic/.
Supplementary information: http://www.bioinf.mdc-berlin.de/metabolic/metatool/http://www.bork.embl-heidelberg.de/Annot/MP/ (re-annotation of M. pneumoniae genome)
Contact: dandekar@embl-heidelberg.de; koch_i@molgen.mpg.de; pfeiffer@eco.umnw.ethz.ch; stschust@mdc-berlin.de
A material system with integrated fault diagnosis and feedback controlled self‐healing
Authors: Kuponu Oluwafemi Sedoten , Kadirkamanathan Visakan , Bhattacharya Bishakh , Pope Simon Alexander 
Published: June 2022

SummaryTwo significant drawbacks of current self‐healing materials are that they are: (1) Passive and as such do not guarantee a match between the healing and damage rate; (2) Not monitored during and after healing, so that the performance of the healed material is not known without retrospective offline testing. As a consequence their application is currently limited in some sectors, such as the aerospace sector where high performance needs to be guaranteed within strict guidelines. This article proposes the first active self‐healing material that integrates with control and fault diagnosis to provide a system with a desired healing response. A fault diagnosis algorithm using supervised regression is used to estimate the measure of damage. Then based on this estimate, adaptive feedback control is used to ensure a match between the healing response and the damage rate, while taking into account the nonlinear system dynamics and uncertainty. The system is demonstrated in simulation using a self‐healing material based on piezoelectricity and electrolysis. This shows the ability of the integrated subsystems to tackle these two significant drawbacks of most current self‐healing systems and will benefit applications with strict performance requirements, or systems operating under harsh conditions or that are remotely accessed.
Improve the Photocatalytic Hydrogen Production Using ZnS@ZnO Twin‐Junction Structure with Isoelectronic Traps
Authors: Li Zehan , Huang Meiling , Li Yanlu , Ai Zizheng , Zhang Kang , Yao Xiaogang , Kong Zhen , Shao Yongliang , Wu Yongzhong , Hao Xiaopeng 
Published: June 2022

AbstractThe effective separation of carriers with prolonged lifetime is important to improve the activity of photocatalytic water splitting hydrogen production. In this work, the separation of electron‐hole pairs is achieved by ZnS@ZnO twin‐junction with isoelectronic traps, with which the corresponding doubled fluorescence lifetime is achieved. The existence of isoelectronic traps is further confirmed by the first principles calculations that prove the coincidence between impurity level position and Fermi level. The all‐important role of isoelectronic traps has almost never been mentioned and demonstrated in photocatalysis so far. Moreover, it is favorable for photocatalysis that the migration direction of carriers in II‐type ZnS@ZnO is consistent with the trapped behavior under the effect of isoelectronic traps, which shows a leading H2 production activity of 1628 µmol h‐1 g‐1 under simulated sunlight. What's more, the impurity levels formed by sulfur in the middle part ZnO1‐xSx enable visible light to be absorbed, neither ZnS nor ZnO would otherwise absorb visible light, and the H2 production activity reaches 380 µmol h‐1 g‐1. This will provide guidance to construct composite structure for wide bandgap semiconductors in the future.
Chemical Control Over Optical Trapping Force at an Interface
Authors: Bresolí‐Obach Roger , Nonell Santi , Masuhara Hiroshi , Hofkens Johan 
Published: June 2022

AbstractSo far, the optical trapping potential is controlled by tuning the physical conditions of the system. Herein, for the first time, an approach, in which the induced optical force or optical potential is controlled, by an external chemical stimulus, is reported. The key to realize this is to design an optical trapping condition in conjunction with resonant excitation, the so‐called optical resonance effect (ORE). For this purpose, phenalenone, a well‐known triplet photosensitizer, is embedded inside polystyrene particles. The optical resonance effect is achieved through a two‐laser system: a 405 nm widefield laser to excite the phenalenone molecules to T1 state and a 488 nm trapping laser to induce the T1–Tn–T1 resonance cycle. Thus, the triplet state is mainly responsible for the optical force enhancement. Since oxygen is an excellent triplet quencher, the triplet populations, and hence, the optical force is controlled by changing the dissolved oxygen concentration. The results presented here pave the way to chemically control the optical force through ORE with promising applications in several research fields ranging from physics to biology.