bluuebunny/crossref_metadata_2025_split huggingface dataset:
Torsional dependence of molecular electrical properties and long-range interactions: CH3OH–rare gas systems
Authors: Davis Stephen L. , Dennison Elizabeth C. 
Published: July 2002

Self-consistent-field (SCF) values are reported for all Cartesian tensor components of the dipole, quadrupole, and octupole moments (μ,Θ,Ω) and polarizabilities α and A of the methanol molecule in its staggered, eclipsed, and three intermediate conformations. The methanol geometry was held rigid except for a single internal rotation angle γ, describing the relative orientation of the methyl rotor and the hydroxyl framework. Three different basis sets were used, including a 110 contracted Gaussian set based on the electrical properties (ELP) basis of Dykstra et al. [Adv. Chem. Phys. 75, 37 (1989), and references therein]. It was found that the tensor components Ωxxx, Ωxyy, Axxx, Axyy, and Ayxy vary as cos 3γ, while the components Ωyyy, Ωyxx, Ayyy, Ayxx, and Axyx vary as sin 3γ. All other components of Ω and A, as well as all components of μ, Θ, show little variation with γ. This dependence was explained using a simple model that treats each property as a sum of a constant, hydroxyl framework contribution and a conformation-dependent, methyl rotor contribution. Torsional averages of these properties were computed from torsional wave functions obtained by diagonalization of the internal axis method (IAM) Hamiltonian.
It was found that the large amplitude internal rotation in methanol gives rise to large vibrational effects on the Axxx, Axyy, and Ayxy polarizability components. The conformational dependence of the electrical properties was used to describe the conformational dependence of long-range interactions involving a near-symmetric, nonrigid molecule such as methanol. The leading γ-dependent interaction term was shown to vary as R−8 and R−7 for the induction and dispersion interactions (respectively) between a methanol molecule and a structureless atom. Cartesian tensor expressions are given for the long-range dispersion interaction within second-order perturbation theory, and the leading torsionally dependent interaction is shown to vary as sin3 θ cos 3(φ−γ), where θ,φ are the spherical coordinates of the atom.
Vibrational mode selectivity in the unimolecular decomposition of CH2NNO2
Authors: Rice Betsy M. , Grosh John , Thompson Donald L. 
Published: July 2002

Vibrational mode selectivity has been investigated for the unimolecular decomposition of methylene nitramine (MN), CH2NNO2, by using classical trajectories computed on a (previously reported) potential-energy surface (PES) that is based on ab initio results. The PES allows for the two known primary decomposition pathways: (I) N–N bond scission to form H2CN and NO2 and (II) concerted molecular elimination giving HONO and HCN. Of particular interest in this study is the influence of selective vibrational mode excitations on the rates and branching of the decomposition via the competing reaction channels, which have barrier heights that differ by only 2 kcal/mol. Rates were computed for 57.7 kcal/mol above the zero-point energy for initial conditions corresponding to overtone excitations of each of the 15 normal modes. In each case, zero-point energy was assigned to each of the normal modes, and then one of the modes was assigned 57.7 kcal/mol excitation energy giving a total of 85.0 kcal/mol. One calculation was done at this energy with initial conditions corresponding to a microcanonical (statistical) distribution in which the energy was randomly distributed among all of the vibrational modes. Comparisons of the mode selective results with this statistical rate show that there is substantial enhancement of the decomposition rates for the two reactions for excitation of three of the normal modes (those with frequencies of 275, 442, and 753 cm−1).
Excitation of the other 12 modes yielded rates in accord with the statistical rates for the 2 reactions. The eigenvectors of the normal modes of the molecule that give mode selectivity in the reaction rates project onto the reaction coordinates for the two pathways. One other mode (with frequency 606 cm−1) also projects strongly onto the reaction path for II), but there is no enhancement of the rate when it is excited. However, we found that energy transfers out of this mode to other modes not coupled to either reaction coordinate. The remaining 11 modes do not project to any significant extent onto either reaction coordinate. The results show that projection of a vibrational mode onto the reaction coordinate is necessary for mode selective reaction, but is not sufficient since energy transfer into the reaction coordinate must compete with energy flow to other modes that do not project onto (i.e., are uncoupled from) the reaction coordinates.
Dissection of Complex Molecular Interactions of Neurofascin with Axonin-1, F11, and Tenascin-R, Which Promote Attachment and Neurite Formation of Tectal Cells
Authors: Volkmer Hansjürgen , Zacharias Ute , Nörenberg Ursel , Rathjen Fritz G. 
Published: July 2002

Neurofascin is a member of the L1 subgroup of the Ig superfamily that promotes axon outgrowth by interactions with neuronal NgCAM-related cell adhesion molecule (NrCAM). We used a combination of cellular binding assays and neurite outgrowth experiments to investigate mechanisms that might modulate the interactions of neurofascin. In addition to NrCAM, we here demonstrate that neurofascin also binds to the extracellular matrix glycoprotein tenascin-R (TN-R) and to the Ig superfamily members axonin-1 and F11.
Isoforms of neurofascin that are generated by alternative splicing show different preferences in ligand binding. While interactions of neurofascin with F11 are only slightly modulated, binding to axonin-1 and TN-R is strongly regulated by alternatively spliced stretches located in the NH2-terminal half, and by the proline-alanine-threonine-rich segment.
In vitro neurite outgrowth and cell attachment assays on a neurofascin-Fc substrate reveal a shift of cellular receptor usage from NrCAM to axonin-1, F11, and at least one additional protein in the presence of TN-R, presumably due to competition of the neurofascin– NrCAM interaction. Thereby, F11 binds to TN-R of the neurofascin/TN-R complex, but not to neurofascin, whereas axonin-1 is not able to bind directly to the neurofascin/TN-R complex as shown by competition binding assays.
In conclusion, these investigations indicate that the molecular interactions of neurofascin are regulated at different levels, including alternative splicing and by the presence of interacting proteins.
Association between Ozone and Hospitalization for Acute Respiratory Diseases in Children Less than 2 Years of Age
Authors: Burnett Richard T. , Smith-Doiron Marc , Stieb Dave , Raizenne Mark E. , Brook Jeffrey R. , Dales Robert E. , Leech Judy A. , Cakmak Sabit , Krewski Daniel 
Published: July 2002

Abstract
To clarify the health effects of ozone exposure in young children, the authors studied the association between air pollution and hospital admissions for acute respiratory problems in children less than 2 years of age during the 15-year period from 1980 to 1994 in Toronto, Canada. The daily time series of admissions was adjusted for the influences of day of the week, season, and weather. A 35% (95% confidence interval: 19%, 52%) increase in the daily hospitalization rate for respiratory problems was associated with a 5-day moving average of the daily 1-hour maximum ozone concentration of 45 parts per billion, the May–August average value. The ozone effect persisted after adjustment for other ambient air pollutants or weather variables. Ozone was not associated with hospital admissions during the September–April period. Ambient ozone levels in the summertime should be considered a risk factor for respiratory problems in children less than 2 years of age.
Risk Factors for Proximal Humerus, Forearm, and Wrist Fractures in Elderly Men and Women The Dubbo Osteoporosis Epidemiology Study
Authors: Nguyen Tuan V. , Center Jacqueline R. , Sambrook Philip N. , Eisman John A. 
Published: July 2002

Abstract
Fractures of the proximal humerus, forearm, and wrist account for approximately one third of total osteoporotic fractures in the elderly. Several risk factors for these fractures were evaluated in this prospective study of 739 men and 1,105 women aged ≥60 years in Dubbo, Australia. During follow-up (1989–1996), the respective incidences of humerus and of forearm and wrist fractures, per 10,000 person-years, were 22.6 and 33.8 for men and 54.8 and 124.6 for women. Independent predictors of humerus fracture were femoral neck bone mineral density (FNBMD) (relative risk (RR) = 2.3, 95% confidence interval (CI): 1.2, 4.5) in men and FNBMD (RR = 2.4, 95% CI: 1.7, 3.5) and height loss (RR = 1.1, 95% CI: 1.0, 1.2) in women. For forearm and wrist fractures, risk factors were FNBMD (men: RR = 1.5, 95% CI: 1.0, 2.3; women: RR = 1.5, 95% CI: 1.2, 1.9) and height loss (men: RR = 1.2, 95% CI: 1.0, 1.3; women: RR = 1.1, 95% CI: 1.0, 1.2). In addition, dietary calcium (men: RR = 2.0, 95% CI: 1.0, 3.6) and a history of falls (women: RR = 1.9, 95% CI: 1.4, 2.6) were also significant. These data suggest that elderly men and women largely share common risk factors for upper limb fractures and that FNBMD is the primary risk factor.
Estimation and filtering of potential protein-protein docking positions.
Authors: Ackermann F , Herrmann G , Posch S , Sagerer G 
Published: July 2002

Abstract
MOTIVATION: Software systems predicting automatically whether and how two proteins may interact are highly desirable, both for understanding biological processes and for the rational design of new proteins. As a part of a future complete solution to this problem, a bundle of programs is presented designed (i) to estimate initial docking positions for a given pair of docking candidates, (ii) to adjust them, and (iii) to filter them, thus preparing more detailed computations of free energies. RESULTS: The system is evaluated on a test set of 51 co-crystallized complexes aiming at redocking the subunits. It works completely automatically and the evaluation is performed using one single set of parameters for all complexes in the test set. The number of solutions is fixed to 50 positions with a median CPU time of 26 min. For 30 complexes, these contain a near-correct solution with root mean square deviation ( RMSD ) &lt;/=5.0 A, which is ranked first in five cases. For all complexes, the best solution is scored on rank 16 as the worst case, and has a median RMSD of 4.3 A. Alternatively to this initial estimation of docking positions, a global sampling of rotations was tested. Whereas this yields top-ranked solutions with RMSD &lt;/=3.0 A for all 51 complexes, the median CPU time increases to 11 h. This shows that this blind sampling is not feasible for most applications. AVAILABILITY: The system and its components are available on request from the authors. Contact: friedric@techfak.uni-bielefeld or posch@techfak.uni-bielefeld.de
An NMR assignment module implemented in the Gifa NMR processing program.
Authors: Malliavin T E , Pons J L , Delsuc M A 
Published: July 2002

Abstract
MOTIVATION: Peptide and protein structures are determined daily using NMR spectroscopy. Assignment of the NMR spectra is an important step within the procedure and is usually the limiting one. Computer-aided assignment tools should be user friendly with open architecture to communicate with other programs involved in the structure determination. RESULTS: Here we present an interactive NMR assignment module which provides numerous graphic tools for the user. The module is composed of a database management system-handling peaks, spins and spin-systems. The assignment information is maintained as a set of interrelated associative arrays, which serve as generic high-level data structures. The module is developed in the macro language embedded in the Gifa NMR processing program (Pons et al. , J. Biomol. NMR, 8 , 445-452, 1996). This provides the user with a consistent interface, a set of sophisticated tools, and an easily extendible and customizable environment. AVAILABILITY: The program is available on request from the authors. The Gifa package can be accessed at: ((http://www.cbs. univ-montp1.fr/GIFA)) CONTACT: Marc-Andre.Delsuc@cbs.univ-montp1.fr
Motif-based searching in TOPS protein topology databases.
Authors: Gilbert D , Westhead D , Nagano N , Thornton J 
Published: July 2002

Abstract
MOTIVATION: TOPS cartoons are a schematic ion of protein three-dimensional structures in two dimensions, and are used for understanding and manual comparison of protein folds. Recently, an algorithm that produces the cartoons automatically from protein structures has been devised and cartoons have been generated to represent all the structures in the structural databank. There is now a need to be able to define target topological patterns and to search the database for matching domains. RESULTS: We have devised a formal language for describing TOPS diagrams and patterns, and have designed an efficient algorithm to match a pattern to a set of diagrams. A pattern-matching system has been implemented, and tested on a database derived from all the current entries in the Protein Data Bank (15,000 domains). Users can search on patterns selected from a library of motifs or, alternatively, they can define their own search patterns. AVAILABILITY: The system is accessible over the Web at http://tops.ebi.ac.uk/tops
STRAP: editor for STRuctural Alignments of Proteins
Authors: Gille Christoph , Frömmel Cornelius 
Published: July 2002

Abstract
Summary: STRAP is a comfortable and extensible tool for the generation and refinement of multiple alignments of protein sequences. Various sequence ordered input file formats are supported. These are the SwissProt-,GenBank-, EMBL-, DSSP- PDB-, MSF-, and plain ASCII text format. The special feature of STRAP is the simple visualization of spatial distances of \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(C_{{\alpha}}\) \end{document}-atoms within the alignment. Thus structural information can easily be incorporated into the sequence alignment and can guide the alignment process in cases of low sequence similarities. Further STRAP is able to manage huge alignments comprising a lot of sequences. The protein viewers and modeling programs INSIGHT, RASMOL and WEBMOL are embedded into STRAP. STRAP is written in Java. The well-documented source code can be adapted easily to special requirements. STRAP may become the basis for complex alignment tools in the future.
Availability: The tool is available to academic institutions at http://www.charite.de/bioinf. The source code can be requested via e-mail.
Contact: christoph.gille@charite.de
* To whom correspondence should be addressed.
A data-mining approach to spacer oligonucleotide typing of
Mycobacterium tuberculosis
Authors: Sebban M. , Mokrousov I. , Rastogi N. , Sola C. 
Published: July 2002

Abstract
Motivation: The Direct Repeat (DR) locus of Mycobacterium tuberculosis is a suitable model to study (i) molecular epidemiology and (ii) the evolutionary genetics of tuberculosis. This is achieved by a DNA analysis technique (genotyping), called sp acer oligo nucleotide typing (spoligotyping ). In this paper, we investigated data analysis methods to discover intelligible knowledge rules from spoligotyping, that has not yet been applied on such representation. This processing was achieved by applying the C4.5 induction algorithm and knowledge rules were produced. Finally, a Prototype Selection (PS) procedure was applied to eliminate noisy data. This both simplified decision rules, as well as the number of spacers to be tested to solve classification tasks. In the second part of this paper, the contribution of 25 new additional spacers and the knowledge rules inferred were studied from a machine learning point of view. From a statistical point of view, the correlations between spacers were analyzed and suggested that both negative and positive ones may be related to potential structural constraints within the DR locus that may shape its evolution directly or indirectly.
Results: By generating knowledge rules induced from decision trees, it was shown that not only the expert knowledge may be modeled but also improved and simplified to solve automatic classification tasks on unknown patterns. A practical consequence of this study may be a simplification of the spoligotyping technique, resulting in a reduction of the experimental constraints and an increase in the number of samples processed.
Contact: csola@pasteur.gp
* To whom correspondence should be addressed.
An integrated approach utilizing artificial neural networks and
SELDI mass spectrometry for the classification of human tumours and
rapid identification of potential biomarkers
Authors: Ball G. , Mian S. , Holding F. , Allibone R. O. , Lowe J. , Ali S. , Li G. , McCardle S. , Ellis I. O. , Creaser C. , Rees R. C. 
Published: July 2002

Abstract
Motivation: MALDI mass spectrometry is able to elicit macromolecular expression data from cellular material and when used in conjunction with Ciphergen protein chip technology (also referred to as SELDI—Surface Enhanced Laser Desorption/Ionization), it permits a semi-high throughput approach to be taken with respect to sample processing and data acquisition. Due to the large array of data that is generated from a single analysis (8–10000 variables using a mass range of 2–15 kDa—this paper) it is essential to implement the use of algorithms that can detect expression patterns from such large volumes of data correlating to a given biological/pathological phenotype from multiple samples. If successful, the methodology could be extrapolated to larger data sets to enable the identification of validated biomarkers correlating strongly to disease progression. This would not only serve to enable tumours to be classified according to their molecular expression profile but could also focus attention upon a relatively small number of molecules that might warrant further biochemical/molecular characterization to assess their suitability as potential therapeutic targets.
Results: Using a multi-layer perceptron Artificial Neural Network (ANN) (Neuroshell 2) with a back propagation algorithm we have developed a prototype approach that uses a model system (comprising five low and seven high-grade human astrocytomas) to identify mass spectral peaks whose relative intensity values correlate strongly to tumour grade. Analyzing data derived from MALDI mass spectrometry in conjunction with Ciphergen protein chip technology we have used relative importance values, determined from the weights of trained ANNs (Balls et al. , Water, Air Soil Pollut. , 85, 1467–1472, 1996), to identify masses that accurately predict tumour grade. Implementing a three-stage procedure, we have screened a population of approximately 100000–120000 variables and identified two ions (m/zvalues of 13454 and 13457) whose relative intensity pattern was significantly reduced in high-grade astrocytoma. The data from this initial study suggests that application of ANN-based approaches can identify molecular ion patterns which strongly associate with disease grade and that its application to larger cohorts of patient material could potentially facilitate the rapid identification of validated biomarkers having significant clinical (i.e. diagnostic/prognostic) potential for the field of cancer biology.
Availability: Neuroshell 2 is commercially available from ward systems.
Contact: graham.balls@ntu.ac.uk
* To whom correspondence should be addressed.
Refolding kinetics of cytochrome c551 reveals a mechanistic difference between urea and guanidine
Authors: Gianni Stefano , Brunori Maurizio , Travaglini‐Allocatelli Carlo 
Published: July 2002

AbstractThe energetic parameters for the folding of small globular proteins can be very different if derived from guanidine hydrochloride (GdnHCl) or urea denaturation experiments. A study of the equilibrium and kinetics of the refolding of wild‐type (wt) cytochrome c551 (cyt c551) from Pseudomonas aeruginosa and of two site‐directed mutants (E70Q and E70V) shows that the nonionic nature of urea reveals the role of a salt bridge between residues E70 and K10 on the transition state, which is otherwise completely masked in GdnHCl experiments. Mixed denaturant refolding experiments allow us to conclude that the masking effect of GdnHCl is complete at fairly low GdnHCl concentrations (≅0.1 M). The fact that potassium chloride is unable to reproduce this quenching effect, together with the results obtained on the mutants, suggests a specific binding of the Gdn+ cation, which involves the E70–K10 ion pair in wt cyt c551. We propose, therefore, a simple kinetic test to obtain a mechanistic interpretation of nonlinear dependences of ΔGw on GdnHCl concentration on the basis of kinetic refolding experiments in the presence of both denaturants.
Comparison of Distal Radius Fracture Outcomes in Older Adults Stratified by Chronologic vs Physiologic Age Managed With Casting vs Surgery
Authors: Jayaram Mayank , Wu Hao , Yoon Alfred P. , Kane Robert L. , Wang Lu , Chung Kevin C. 
Published: February 2023

ImportanceCasting is recommended for adults older than 65 years with distal radius fractures (DRFs) because similar long-term outcomes are achieved regardless of treatment. However, physiologically younger adults could benefit from operative DRF management despite advanced chronologic age.ObjectiveTo examine how chronologic age compares with measures of physiologic age in DRF treatment recovery.Design, Setting, and ParticipantsThis retrospective secondary analysis of the Wrist and Radius Injury Surgical Trial (WRIST) was performed from May 1 to August 31, 2022. WRIST was a 24-center randomized clinical trial that enrolled participants older than 60 years with unstable DRFs from April 1, 2012, to December 31, 2016.InterventionsParticipants selected casting or surgery. Patients who selected surgery were randomly assigned to volar lock plating, percutaneous pinning, or external fixation. Participants were stratified by chronologic age, number of comorbidities, and activity status.Main Outcomes and MeasuresThe primary outcome was Michigan Hand Outcomes Questionnaire (MHQ) score assessed at 6 weeks, 3 months, 6 months, and 1 year. Partial correlation (PC) analysis adjusted for confounding.ResultsThe final cohort consisted of 293 participants (mean [SD] age, 71.1 [8.89] years; 255 [87%] female; 247 [85%] White), with 109 receiving casting and 184 receiving surgery. Increased chronologic age was associated with increased MHQ scores in the surgery group at all time points but decreased MHQ scores in the casting group at 12 months (mean [SD] score, −0.46 [0.21]; P = .03). High activity was associated with improved MHQ scores in the surgical cohort at 6 weeks (mean [SD] score, 12.21 [5.18]; PC = 0.27; P = .02) and 12 months (mean [SD] score, 13.25 [5.77]; PC = 0.17; P = .02). Comorbidities were associated with decreased MHQ scores at all time points in the casting group. Clinically significant differences in MHQ scores were associated with low physical activity, 4 or more comorbidities, or increased age by 15 years.Conclusions and RelevanceIn this retrospective secondary analysis of WRIST, chronologic age was not associated with functional demand. These findings suggest that physicians should counsel active older adults with few comorbidities on earlier return to daily activities after surgery compared with casting.Trial RegistrationClinicalTrials.gov Identifier: NCT01589692