bluuebunny/crossref_metadata_2025_split huggingface dataset:
The erbium-impurity interaction and its effects on the 1.54 μm luminescence of Er3+ in crystalline silicon
Authors: Priolo F. , Franzò G. , Coffa S. , Polman A. , Libertino S. , Barklie R. , Carey D. 
Published: July 2002

We have studied the effect of erbium-impurity interactions on the 1.54 μm luminescence of Er3+ in crystalline Si. Float-zone and Czochralski-grown (100) oriented Si wafers were implanted with Er at a total dose of ∼1×1015/cm2. Some samples were also coimplanted with O, C, and F to realize uniform concentrations (up to 1020/cm3) of these impurities in the Er-doped region. Samples were analyzed by photoluminescence spectroscopy (PL) and electron paramagnetic resonance (EPR). Deep-level transient spectroscopy (DLTS) was also performed on p-n diodes implanted with Er at a dose of 6×1011/cm2 and codoped with impurities at a constant concentration of 1×1018/cm3. It was found that impurity codoping reduces the temperature quenching of the PL yield and that this reduction is more marked when the impurity concentration is increased. An EPR spectrum of sharp, anisotropic, lines is obtained for the sample codoped with 1020 O/cm3 but no clear EPR signal is observed without this codoping. The spectrum for the magnetic field B parallel to the [100] direction is similar to that expected for Er3+ in an approximately octahedral crystal field. DLTS analyses confirmed the formation of new Er3+ sites in the presence of the codoping impurities. In particular, a reduction in the density of the deepest levels has been observed and an impurity+Er-related level at ∼0.15 eV below the conduction band has been identified.
This level is present in Er+O-, Er+F-, and Er+C-doped Si samples while it is not observed in samples solely doped with Er or with the codoping impurity only. We suggest that this new level causes efficient excitation of Er through the recombination of e-h pairs bound to this level. Temperature quenching is ascribed to the thermalization of bound electrons to the conduction band. We show that the attainment of well-defined impurity-related luminescent Er centers is responsible for both the luminescence enhancement at low temperatures and for the reduction of the temperature quenching of the luminescence. A quantitative model for the excitation and deexcitation processes of Er in Si is also proposed and shows good agreement with the experimental results.
Statistical thermodynamics of molecular organization in mixed micelles and bilayers
Authors: Szleifer I. , Ben-Shaul A. , Gelbart W. M. 
Published: July 2002

The conformational and thermodynamic characteristics of molecular organization in mixed amphiphilic aggregates of different compositions and geometries are analyzed theoretically. Our mean-field theory of chain conformational statistics in micelles and bilayer membranes is extended from pure to mixed aggregates, without invoking any additional assumptions or adjustable parameters. We consider specifically binary aggregates comprised of long-chain and short-chain surfactants, packed in spherical micelles, cylindrical rods, and planar bilayers. Numerical results are presented for mixtures of 11- and 5-carbon chain amphiphiles. The probability distribution functions (pdfs) of the (different types of) chains are determined by minimizing the conformational free energy, subject to packing constraints which reflect the segment density distribution within the hydrophobic core. In order to analyze the relative thermodynamic stabilities of mixed aggregates of different compositions (long/short chain ratios) and different geometries, the aggregate’s free energy is expressed as a sum of conformational, surface, and mixing contributions. The conformational free energy is determined by the pdfs of the chains and the surface term is modeled in terms of the ‘‘opposing forces’’ operative at the hydrocarbon–water interface. An interesting coupling between these terms arises from the special geometric (surface/volume) limitations associated with packing short and long chains in a given ratio within a given aggregate. In particular, it is found that the minimal area per surfactant head group in a mixed spherical micelle is significantly lower than that in a pure micelle (similarly, though less drastically so, for cylindrical micelles). The most important qualitative conclusion of our thermodynamic analysis is that the preferred aggregation geometry may vary with composition. For example, we find that under certain conditions (areas per head group, chain lengths) the preferred micellar geometry of pure long or short-chain aggregates is that of a planar bilayer, whereas at intermediate compositions spherical micelles are more stable. Our analysis of chain conformational properties provides quantitative
information on the extent of long (or short) chain distortion attendant upon chain mixing. For example, the results for bond order parameter profiles and segment density distributions reveal enhanced stretching of the long chain towards the central regions of the hydrophophic core as the fraction of short chains is increased.
Cluster expansion of the wave function. Valence and Rydberg excitations and ionizations of benzene
Authors: Kitao O. , Nakatsuji H. 
Published: July 2002

The SAC (symmetry-adapted cluster) expansion and the SAC-CI theory are applied to the calculations of the valence and Rydberg excitations and the ionizations of benzene. The active space consists of 80 MO’s including both π and σ spaces; viz., 35π+45σ for the valence excitations and ionizations and 29π+51σ for the Rydberg excitations. For the lower six valence excited states, 3B1u(T1), 3E1u(T2), 1B2u(S1), 3B2u(T3), 1B1u(S2), and 1E1u(S3), generated from the π(e1g)→π*(e2u) transitions, the excitation energies are reproduced to within 0.5 eV of the experimental values with the average discrepancy being 0.34 eV. The first three states are explainable within the π electron space. For the other three states, the σ-reorganization effect is very important; viz., 0.6, 0.7, and 0.8 eV for the T3, S2, and S3 states, respectively. The polarization
d π function also works to lower the T3 and S2 states by 0.3 and 0.4 eV, respectively. The total lowerings from the SDT π-CI of Hay and Shavitt to the 35π+45σ SAC-CI are about 1 eV for these three states. With including the σ-reorganization effect, the diffuse nature of the S3 state, a typical V state, decrease from 〈x2〉=62 (π SAC-CI) to 41 (π+σ SAC-CI) a.u., in comparison with the ground state value of 30 a.u. Accordingly, the oscillator strength changes from 0.61 (π SAC-CI) to 1.03 (π+σ SAC-CI). The first systematic theoretical study is given for the Rydberg excitations including both π and σ states. With the aid of the recent experimental studies due to the MPI (multiphoton ionization) spectroscopy, the lower Rydberg excited states are almost completely identified. The SAC-CI results agree with the experimental values to within 0.3 eV for all the Rydberg states studied here. The σ-reorganization effect on the Rydberg transitions is about 0.3 eV. The SAC-CI calculation further gives satisfactory results for the outer and inner valence ionizations and their satellite peaks. The theoretical ionization spectrum well reproduces the general trends of the observed ESCA spectrum.
Thermodynamics far from equilibrium: Reactions with multiple stationary states
Authors: Ross John , Hunt Katharine L. C. , Hunt Paul M. 
Published: July 2002

We present a thermodynamic analysis of global validity for effectively one-variable, irreversible chemical systems with multiple steady states. A hypothetical reaction chamber is held at constant temperature and volume and is connected by selectively permeable membranes to reservoirs of reactant(s) and product(s), each at constant selected pressures. An appropriate free energy function, which yields criteria of evolution to equilibrium for the composite system of reaction chamber and reservoirs, is a hybrid of Gibbs and Helmholtz free energies. The one variable in the reaction chamber is the pressure of a chemical intermediate which varies in time according to a given reaction mechanism. With the hybrid free energy, the kinetics for a given mechanism, and a concept of instantaneous indistinguishability of systems with different mechanisms, we establish a thermodynamic driving force, or species-specific affinity, for the intermediate. The species-specific affinity vanishes at steady states, and upon its differentiation we obtain necessary and sufficient conditions for the stability of steady states and for critical points. The integral of the species-specific affinity globally provides valid Liapunov functions for the evolution of the intermediate. These results are independent of the number of steady states of the system, and they hold both near to and far from equilibrium. For a large class of mechanisms with a single intermediate, the integral of the species-specific affinity appears in the irreversible part
of the time-dependent transition probability of the single-variable Master equation and in its stationary solution. Hence for these mechanisms we obtain a direct interpretation of the stochastic results in terms of thermodynamic quantities. The time rate of change in the pressure of the intermediate multiplied by its species-specific affinity yields a species-specific term in the dissipation. The total system dissipation (or entropy production) is not in general a minimum at a nonequilibrium steady state, but the species-specific term is minimized at every such state. The expression of the stationary solution of the master equation in terms of the species-specific affinity provides a generalization of the Einstein relation for the probability of equilibrium fluctuations to far-from-equilibrium conditions. The functional form of the species-specific term in the dissipation parallels a form that appears in Boltzmann’s H theorem for the momentum relaxation of a dilute gas.
Hyper‐Fractionated Radiotherapy for Soft Tissue Sarcoma: Results of theSecond Study of Hyper‐Fractionated Radiotherapy
Authors: Jacob R. , Gilligan D. , Robinson M. , Harmer C. 
Published: July 2002

Purpose and Method. Hyper‐fractionated radiotherapy for treatment
of soft tissue sarcomas is designed to deliver a higher total dose of radiation without an
increase in late normal tissue damage. In a previous study at the Royal Marsden Hospital,
a total dose of 75 Gy using twice daily 1.25 Gy fractions resulted in a higher incidence of late
damage than conventional radiotherapy using 2 Gy daily fractions treating to a total of 60 Gy.
The current trial therefore used a lower dose per fraction of 1.2 Gy and lower total dose of 72
Gy, with 60 fractions given over a period of 6 weeks.Subjects. A total of 37 patients (22 males and 15 females) with a median
age of 56 years (range 19–88 years) were treated.Results. Of eight patients treated pre‐operatively, six showed a
partial response and in two the tumour was static. The maximum acute toxicities were grade
1 in eight, grade 2 in 14 and grade 3 in 15 patients. Late toxicities of the skin were
graded 1 in 10 and grade 2 in nine patients. Five patients complained of pain in the irradiated
bone and soft tissues, which was of moderate severity (grade 2). Stiffness was graded 2 in
three patients and severe (grade 3) in one.Three patients had moderate and one patient had
severe lymphoedema following treatment. The 5‐year recurrence‐free survival probability of
patients treated radically was 76%. Following excision of local recurrences the study group
had a disease‐free survival probability of 86% at 5 years.Discussion. The regime is well tolerated with comparable local control
and late complication rates to standard daily fractionated therapy.The potential benefit of this
regime needs to be defined in a prospective randomized trial.
Digital Metastases of Giant Cell Rich Malignant Fibrous Histiocytoma
Authors: Brownlow Harry C. , Ioannidis George , Gibbons Max C. L. M. H. , Jones Adrian C. , Athanasou Nick 
Published: July 2002

Background. Metastatic spread of soft tissue sarcomas to the digits is
extremely rare and metastasis of MFH to the fingers and toes has not been documented.Purpose. We present two case reports of metastatic spread from a giant
cell rich malignant fibrous histiocytoma to the digits and discuss their management.
Lack of Activity of Docetaxel in Soft Tissue Sarcomas:Results of a Phase II Study of the Italian Group on Rare Tumors
Authors: Santoro Armando , Romanini Antonella , Rosso Alberto , Frustaci Sergio , Comandone Alessandro , Apice Gaetano , De Toma Domenico , Dogliotti Luigi , Lionetto Rita , Dani Carla , Bruzzi Paolo , Piolini Marco , Bergnolo Paola , Verusio Claudio 
Published: July 2002

Purpose. The prognosis of advanced soft tissue sarcoma is poor, only
a few drugs showing some activity with response rates around 15– 25%. Consequently drug
development seems mandatory to improve treatment outcome. Following previous
favourable EORTC experience, the Italian Group on Rare Tumors started a phase II study
with docetaxel to confirm the activity of this drug in soft tissue sarcoma.Patients and methods. Thirty‐seven patients with soft tissue sarcoma
resistant to at least one anthracyclinecontaining regimen were enrolled in a phase II multicenter
study evaluating docetaxel 100 mg/m2
in a 1‐h i.v. infusion q3
weeks.Results.Thirty‐seven patients were enrolled onto this phase II study and
36 were evaluable for response. Only one partial remission was observed [2.8% with 95%
confidence interval (CI) 0.1– 16.2%]. Median progression‐free and overall survival
were 42 and 350 days, respectively. Neutropenia and leukopenia as well as cutaneous
manifestations were the most common toxicities.Discussion. The results of this phase II study do not confirm a previous
EORTC repor t on the activity of docetaxel in soft tissue sarcoma, but are consistent with
other more recent phase II studies. The accumulated evidence does not justify the use of this
drug in the management of patients suffering from this disease, resistant to
anthracyclinecontaining regimens.
Quality of Life in Survivors of a Primary Bone Tumour:A Systematic Review
Authors: Eiser Christine , Grimer Robert J. 
Published: July 2002

Purpose. We conducted a systematic search of published literature,
to assess (i) quality of life (QoL) for survivors of a bone tumour compared with the normal
population; (ii) QoL implications following amputation, successful or failed limb salvage;
(iii) adaptation of young children to amputation compared with older children or
adolescents.Methods. Electronic databases were searched including Medline,
PsycLIT and Cinahl covering the years 1982– 1998.Results. We identified 11 studies. Regardless of treatment, physical
functioning was poor compared with population norms or healthy siblings.There was less
consistent evidence regarding emotional functioning. Seven studies compared functioning
in amputees and limb salvage patients.Two reported advantages in physical function for the
limb salvage group, one for the amputees and the rest no differences. Evidence about social
functioning or marriage is inconclusive, but there are suggestions that amputees report more
job discrimination.Discussion. The literature is inconclusive, largely because of
methodological problems. These include small and non‐representative samples, and lack of
sensitive and appropriate measures. Specific gaps in the literature include very little
work concerned with psychological outcomes for children, or for those experiencing failed
limb salvage. More attention needs to be given to gender differences in emotional response
to traumatic surgery.The implications of the results for helping families balance the merits of
different treatments are discussed.
Caspase Recruitment Domain (Card-Dependent) Cytoplasmic Filaments Mediate Bcl10-Induced Nf-κb Activation
Authors: Guiet Chantal , Vito Pasquale 
Published: July 2002

Mucosa-associated lymphoid tissue (MALT) lymphomas are associated with overexpression and constitutive activity of bcl10, a caspase recruitment domain (CARD)-containing protein that activates NF-κB. Here, we show that arrangement of overexpressed bcl10 protein in cytoplasmic filaments is essential for recruitment of signal transducer molecules-involved NF-κB activation. We also show that cytoskeleton elements regulate bcl10 signaling.
Thus, organized assemblage of proteins in ordered structures linked to the cytoskeleton network may represent a general mechanism for intracellular signaling.
Decision tree-based formation of consensus protein secondary
structure prediction
Authors: Selbig Joachim , Mevissen Theo , Lengauer Thomas 
Published: July 2002

Abstract
Motivation: Prediction of protein secondary structure provides information that is useful for other prediction methods like fold recognition and ab initio 3D prediction. A consensus prediction constructed from the output of several methods should yield more reliable results than each of the individual methods.
Method: We present an approach that reveals subtle but systematic differences in the output of different secondary structure prediction methods allowing the derivation of coherent consensus predictions. The method uses a machine learning technique that builds decision trees from existing data.
Results: The first results of our analysis show that consensus prediction of protein secondary structure may be improved both quantitatively and qualitatively.
Availability: Our method for consensus secondary structure prediction CoDe (Consensus formation by Decision tree learning) is based on machine learning and will be integrated into the ToPLign system (Toolbox for Protein aLignment) which can be accessed at http://cartan.gmd.de/ToPLign.html.
Contact: {mevissen,selbig}@gmd.de
A simple probabilistic scoring method for protein domain

identification
Authors: Murvai János , Vlahovic̆ek Kristian , Pongor Sándor 
Published: July 2002

Abstract
Summary: A simple heuristic scoring method is described for assigning sequences to known domain types based on BLAST search outputs. The scoring is based on the score distribution of the known domain groups determined from a database versus database comparison and is directly applicable to BLAST output processing.
Availability: The scoring system will be incorporated into the server www.icgeb.trieste.it/sbase/
Contact: murvai@icgeb.trieste.it; pongor@icgeb.trieste.it
Net Nearest Neighbor Analysis (NNNA) summarizes non-compensated
dinucleotides within gene sequences
Authors: Lang Dorothy M. 
Published: July 2002

Abstract
*Address for correspondence: 2538 Great Highway, San Francisco, CA 94116, USA.
Motivation: Net Nearest Neighbor Analysis (NNNA) measures a previously unexamined aspect of dinucleotide frequency—the non-compensated, non-repetitive dinucleotides in a sequence. Non-compensated dinucleotides are those in excess of their corresponding reverse dinucleotides.
Results: NNNA regards dinucleotides as vector quantities, making it possible to summarize any sequence as a group of circuits and tags. The results of NNNA are found to be consistent with traditional analytic methods, yet reveal additional characteristics of the sequences. The NNNA circuits and tags uniquely identify each tRNA in Escherichia coli K-12 and certain structural components of each tRNA, extract function-specific characteristics for each of the sequences involved in the formation of insulin from preinsulin, and exhibit species-specific phylogenetic characterization (demonstrated with Monilinia ).
Availability: Nearest neighbor analysis software has been available for many years and is a component of most gene analysis software packages, including the Staden Package which is available at no charge to academic users (http://www.mrc-1mb.cam.ac.uk/pubseq/).
Combinatorial motif analysis and hypothesis generation on a
genomic scale
Authors: Hu Yuh-Jyh , Sandmeyer Suzanne , McLaughlin Calvin , Kibler Dennis 
Published: July 2002

Abstract
3Now with Tatung University, Taipei, Taiwan. To whom correspondence should be addressed.
Motivation: Computer-assisted methods are essential for the analysis of biosequences. Gene activity is regulated in part by the binding of regulatory molecules (transcription factors) to combinations of short motifs. The goal of our analysis is the development of algorithms to identify regulatory motifs and to predict the activity of combinations of those motifs.
Approach: Our research begins with a new motif-finding method, using multiple objective functions and an improved stochastic iterative sampling strategy. Combinatorial motif analysis is accomplished by constructive induction that analyzes potential motif combinations. The hypothesis is generated by applying standard inductive learning algorithms.
Results: Tests using 10 previously identified regulons from budding yeast and 14 artificial families of sequences demonstrated the effectiveness of the new motif-finding method. Motif combination and classification approaches were used in the analysis of a sample DNA array data set derived from genome-wide gene expression analysis.
Availability: Programs will be available as executable files upon request.
Contact: yhu@ics.uci.eduor yhu@cse.ttu.edu.tw
An ontology for biological function based on molecular
interactions
Authors: Karp Peter D. 
Published: July 2002

Abstract
Motivations: A number of important bioinformatics computations involve computing with function: executing computational operations whose inputs or outputs are descriptions of the functions of biomolecules. Examples include performing functional queries to sequence and pathway databases, and determining functional equality to evaluate algorithms that predict function from sequence. A prerequisite to computing with function is the existence of an ontology that provides a structured semantic encoding of function. Functional bioinformatics is an emerging subfield of bioinformatics that is concerned with developing ontologies and algorithms for computing with biological function.
Results: The article explores the notion of computing with function, and explains the importance of ontologies of function to bioinformatics. The functional ontology developed for the EcoCyc database is presented. This ontology can encode a diverse array of biochemical processes, including enzymatic reactions involving small-molecule substrates and macromolecular substrates, signal-transduction processes, transport events, and mechanisms of regulation of gene expression. The ontology is validated through its use to express complex functional queries for the EcoCyc DB.
Contact: pkarp@ai.sri.com
PRoMT: inferring demographic history from DNA sequences
Authors: Wooding Stephen 
Published: July 2002

Abstract
Summary: I describe a parallel implementation of Rogers’ mismatch algorithm, a method for making inferences about demographic history from DNA sequence data. The program is distributed on clusters of workstations, providing a substantial speedup and low execution times on large numbers of nodes.
Availability: Source code and documentation are available at http://mombasa.anthro.utah.edu/wooding/
Contact: stephen.wooding@anthro.utah.edu