bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wavelets in bioinformatics and computational biology:
state of art and perspectives
Authors: Liò Pietro 
Published: December 2002

Abstract
Motivation: At a recent meeting†, the wavelet transform was depicted as a small child kicking back at its father, the Fourier transform. Wavelets are more efficient and faster than Fourier methods in capturing the essence of data. Nowadays there is a growing interest in using wavelets in the analysis of biological sequences and molecular biology-related signals.
Results: This review is intended to summarize the potential of state of the art wavelets, and in particular wavelet statistical methodology, in different areas of molecular biology: genome sequence, protein structure and microarray data analysis. I conclude by discussing the use of wavelets in modeling biological structures.
Contact: plio@hgmp.mrc.ac.uk
† XIX SMC 2001 ‘Wavelets in Statistics’, Vico Equense, Naples, I, 2–7 April 2001.
Simple rules underlying gene expression profiles
of more than six subtypes of acute lymphoblastic leukemia (ALL)
patients
Authors: Li Jinyan , Liu Huiqing , Downing James R. , Yeoh Allen Eng-Juh , Wong Limsoon 
Published: December 2002

Abstract
Motivations and Results: For classifying gene expression profiles or other types of medical data, simple rules are preferable to non-linear distance or kernel functions. This is because rules may help us understand more about the application in addition to performing an accurate classification. In this paper, we discover novel rules that describe the gene expression profiles of more than six subtypes of acute lymphoblastic leukemia (ALL) patients. We also introduce a new classifier, named PCL, to make effective use of the rules. PCL is accurate and can handle multiple parallel classifications. We evaluate this method by classifying 327 heterogeneous ALL samples. Our test error rate is competitive to that of support vector machines, and it is 71% better than C4.5, 50% better than Naive Bayes, and 43% better than k-nearest neighbour. Experimental results on another independent data sets are also presented to show the strength of our method.
Availability: Under http://sdmc.lit.org.sg/GEDatasets/, click on Supplementary Information.
Contact: jinyan@lit.a-star.edu.sg
* To whom correspondence should be addressed.
pfcrt
Polymorphism and Chloroquine Resistance in
Plasmodium falciparum
Strains Isolated in Cambodia
Authors: Lim Pharath , Chy Sophy , Ariey Frédéric , Incardona Sandra , Chim Pektra , Sem Rithy , Denis Mey Bouth , Hewitt Sean , Hoyer Stefan , Socheat Doung , Merecreau-Puijalon Odile , Fandeur Thierry 
Published: December 2002

ABSTRACT

Plasmodium falciparum
chloroquine resistance was first detected in Cambodia in the early sixties. Treatment with chloroquine was abandoned 20 years ago. In vitro chloroquine sensitivity monitoring indicates that all eastern Cambodian isolates were sensitive to chloroquine, whereas most isolates collected from western provinces displayed reduced susceptibility to chloroquine. This indicates that the rate of chloroquine resistance remains high and stable in this region in the absence of chloroquine pressure. Characterization of codons 72 to 78 and 218 to 220 of
pfcrt
revealed six distinct haplotypes, four of which had never been described. The frequency of each haplotype depended on the geographical origin of the samples. The CVIETIF//ISS haplotype was detected in 92% of western Cambodian isolates and in 11% of isolates collected from the eastern province, where CVMNKIF//ISA and CVIDTIF//ISS predominate. The detection of an intermediate haplotype from a susceptible area with 76T/220A, suggests that acquisition of chloroquine resistance might be a stepwise process, during which accumulation of point mutations modulates the response to chloroquine. The association of the K76T mutation with chloroquine resistance was not clear. The mutation was detected in resistant and susceptible samples, suggesting that additional factors are involved in chloroquine resistance. By contrast, the
pfcrt
D/N75E mutation was strongly associated with the in vitro chloroquine resistance in Cambodian isolates. The N86 allelic form of
pfmdr1
was detected in all isolates, consistent with a poor association with resistance to chloroquine. This indicates that in vitro resistance to chloroquine was associated with accumulation of point mutations in
pfcrt
.
Transient scattering of SH waves from an inclusion with a unilateral frictional interface—a 2D time domain boundary element analysis
Authors: Feng Yang‐De , Wang Yue‐Sheng , Zhang Zi‐Mao 
Published: December 2002

AbstractThis paper develops a 2D time domain boundary element method (BEM) to solve the transient SH‐wave scattering from an inclusion with a unilateral frictional interface. The incident SH‐wave is assumed strong enough to break friction so that localized slip takes place along the interface. The present problem is indeed a non‐linear boundary value problem since the mixed boundary conditions involve unknown intervals (the slip and stick zones). In order to determine the intervals, an iterative technique is developed. As an example, we consider the scattering of a circular cylinder embedded in an infinite solid. The numerical results of the interface traction and relative slip velocity are presented. Copyright © 2003 John Wiley & Sons, Ltd.
Numerical performance of preconditioning techniques for the solution of complex sparse linear systems
Authors: Mazzia Annamaria , Pini Giorgio 
Published: December 2002

AbstractPreconditioning techniques based on ILU decomposition, on Frobenius norm minimization and on factorized sparse approximate inverse are considered. These algorithms are applied with conjugate gradient‐type methods, namely Bi‐CGSTAB, QMR and TFQMR for the solution of complex, large, sparse linear systems. The results of numerical experiments in scalar environment with matrices arising from transport in porous media, quantum chemistry, structural dynamics and electromagnetism are analysed. The preconditioner that appears most significant in parallel environment (based on factorized sparse approximate inverse) is then employed on a Cray T3E supercomputer. The experimental results show the satisfactory parallel performance of the proposed algorithm. Copyright © 2003 John Wiley & Sons, Ltd.
A convergent and universally bounded interpolation scheme for the treatment of advection
Authors: Alves M. A. , Oliveira P. J. , Pinho F. T. 
Published: December 2002

AbstractA high resolution scheme with improved iterative convergence properties was devised by incorporating total‐variation diminishing constraints, appropriate for unsteady problems, into an implicit time‐marching method used for steady flow problems. The new scheme, referred to as Convergent and Universally Bounded Interpolation Scheme for the Treatment of Advection (CUBISTA), has similar accuracy to the well‐known SMART scheme, both being formally third‐order accurate on uniform meshes for smooth flows. Three demonstration problems are considered: (1) advection of three scalar profiles, a step, a sine‐squared, and a semi‐ellipse; (2) Newtonian flow over a backward‐facing step; and (3) viscoelastic flow through a planar contraction and around a cylinder. For the case of the viscoelastic flows, in which the high resolution schemes are also used to represent the advective terms in the constitutive equation, it is shown that only the new scheme is able to provide a converged solution to the prescribed tolerance. Copyright © 2003 John Wiley & Sons, Ltd.
Uranium and thorium isotopes in the rivers of the Amazonian basin: hydrology and weathering processes
Authors: Marques Aguinaldo N. , Al‐Gharib Iyad , Bernat Michel , Fernex François 
Published: December 2002

AbstractTwo expeditions (October 1989 and May 1992) were carried out to two points of the main Amazon River channel and four tributaries. The Solimões and Madeira rivers, taking their origin in the Andes, are whitewater rivers. The Negro River is a typical acid, blackwater river. The Trombetas River flows through bauxite‐rich areas, and is characterized by low concentrations of dissolved humic substances. The 238U, 234U, 232Th and 230Th activities were recorded from dissolved, suspended particulate phases and river bank sediments. The latter were analysed for their 226Ra, 228Ra and 210Pb contents, and also subjected to leaching with 0·2 M hydroxylamine–hydrochloride solution to determine the concentrations of radionuclides bound to amorphous Fe hydroxides and Mn oxides and hydroxides.The dissolved U average concentration in the Amazon system is ten times lower than the mean world river concentration. The uranium concentration observed at Óbidos in the lower Amazon (0·095 µg L−1), where the U content in the river bank sediments and suspended matter is lowest, suggests U release from the solid phase during river transport. About 485 t of U are transported annually to the Amazon delta area in dissolved form, and 1943 t bound to suspended particulate matter.Total U and Th concentrations in the river bank sediments ranged from 1·59 to 7·14 µg g−1 and from 6·74 to 32 µg g−1, respectively. The highest concentrations were observed in the Trombetas River. The proportion extracted by means of the hydroxylamine solution (HL) was relatively high for U in the Trombetas river bank sediment (31%) and for Th in the Solimões sediment (30%).According to the alpha recoil effects, the 234U/238U activity ratios of the Andean river waters and downstream Amazon water (Óbidos) were >1, but were <1 in the Negro River (at Manaus). The activity ratios of dissolved U correlate with pH and also with the U activity ratios in the river bank sediment hydroxylamine extracts. As expected, the 234U/238U activity ratios in river bank sediments were <1 in the Andean rivers and in the downstream Amazon, but they were >1 in the Trombetas and Negro rivers. Such ratios probably result from the binding of dissolved uranium to solid sediment.The 228Th/232Th ratios of river bank sediments were close to unity (except for the Negro River, where it is lower), suggesting no significant Th exchanges between the river water and the sediment. The 226Ra/232Th activity ratios were <1, and the 226Ra/228Ra activity ratios generally were significantly higher than the activity ratios of their respective parents. This perhaps is the result of easier leaching of the 226Ra parent, 230Th, from solid material (owing to the alpha recoil effect) than of the 228Ra parent.Uranium and thorium isotopes were used as tools to evaluate the chemical weathering rate of rocks in the Amazon system, which was estimated to be 2·7 cm 1000 year−1 s−1. Copyright © 2002 John Wiley & Sons, Ltd.
Slope–area relationships and sediment dynamics in two alpine streams
Authors: Fontana Giancarlo Dalla , Marchi Lorenzo 
Published: December 2002

AbstractThe paper focuses on the channel network of alpine basins, attempting to interpret channel reaches in terms of response to erosion and deposition processes. Two basins in the Dolomites (north‐eastern Italy) were considered: the Rio Cordon (5 km2) and the upper Boite River (163 km2). The channel network was extracted from raster‐type digital elevation models (DEM) using a slope–area threshold criterion. A contribution area index (CAI), which combines drainage area, A, and local slope, S (CAI = A0·5S), was used to identify channel heads. The channel network extracted from the DEM was then analysed to recognize cells showing a value of CAI lower than the threshold adopted for channel initiation. Contiguous cells with low values of CAI define channel reaches with low transport efficiency. Field surveys carried out for some selected cases showed a good agreement between prevailing sediment deposition predicted by the analysis of the channel network and observed channel morphological features. Sediment sources mapped in two study basins were also analysed in relation to the location of channels with high potential for sediment deposition: this made it possible to classify the potential role of different types of sediment sources with regard to basin sediment yield. Topographic characteristics of the channel network, expressed by CAI, were compared with a classification of channel morphology in the Rio Cordon. It was found that cells with low values of CAI frequently occur in the riffle–pool reaches, whereas the percentage significantly decreases in step–pool and bedrock channels. Copyright © 2003 John Wiley & Sons, Ltd.
Calculation of NMR chemical shifts for taxol and α‐pinene within the generalized gradient approximation
Authors: Bouř Petr 
Published: December 2002

AbstractSimulations of the nuclear magnetic shielding within the generalized gradient approximation (GGA) for α‐pinene and taxol were carried out to assess the performance of the method for bigger molecules. The localized orbital/local origin gauge (LORG) formalism and the modified “0.05” Becke's three‐parameter exchange functional and the gradient‐corrected functional of Lee, Yang, and Paar (B3LYP) proposed recently by Wilson and others was used. A modest dependence of the results on the basis set size was observed. For the current implementation, the uncoupled calculations were up to 47 times faster than the usual coupled‐perturbed (CP)–gauge‐invariant atomic orbital (GIAO) method and provided similar accuracy. Reproducing both the absolute as the relative chemical shifts the GGA/LORG procedure can thus be used as a faster alternative to the coupled techniques. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Geometric and electronic structure of zwitterionic push–pull polyenes for nonlinear optics
Authors: Geskin V. M. , Bredas J. L. 
Published: December 2002

AbstractWe present a study of the chemical structure of highly polar push–pull conjugated molecules of interest for nonlinear optics, in which purely inductive ammonium/borate substituents, R3N+/BR, are attached to a trans‐polyene chain of variable length either directly or via phenyl groups. The performance of ab initio Hartree–Fock and Møller–Plesset second order (MP2) methods is compared with that of the hybrid density functional theory (DFT) and semiempirical (AM1) Hartree–Fock and configuration interaction methods. Taking into account electron correlation at the MP2 level is important to obtain reliable molecular geometries; the hybrid DFT (BH and HLYP functional) results are found to be in close agreement with the MP2 results. Some geometries obtained with the semiempirical methods are in qualitative disagreement with the MP2/6‐31G results. A chemical rationalization of the optimized structures and the nature of the substituent effect is proposed. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Density functional study of the redox processes in subphthalocyanines
Authors: Ferro V. R. , Poveda L. A. , Claessens C. G. , González‐Jonte R. H. , García de la Vega J. M. 
Published: December 2002

AbstractA theoretical investigation on the redox processes in the subphthalocyanines (SubPcs) was performed. Singly and doubly oxidative and reductive transformations were considered. The full geometry optimization of the participating molecules showed that the cone shape arrangement of the SubPc is preserved in their ionic derivatives even when two electrons are either donated or subtracted from the molecule. The biggest geometric changes under electron exchange processes were calculated for the BCl bond distance. The electronic density distribution over all the products remains almost invariable with respect to the neutral molecule. Our calculations on the neutral and charged SubPcs demonstrated that they behave as conjugated systems, their electronic parameters being correlatively altered by the redox electron exchange. Further, the electronic state of the macrocycle atoms also depends on an intense electronic flow among the macrocyclic skeleton and the surrounding (axial chlorine and peripheral hydrogen) atoms that is associated with the redox process. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Theoretical studies of isomerization barriers of 2‐pentoxy radical and its products
Authors: Lin Ching‐Yeh , Ho Jia‐Jen 
Published: December 2002

AbstractThis article deals with the calculation of isomerization reaction of 2‐pentoxy radical via its possible processes to form the stable products by density functional theory. We studied the intramolecular hydrogen transfers from the five carbon positions to the oxygen atom of 2‐pentoxy and then followed by successive transfers from the unstable hydroxy radical to the final stable one. There are five paths of hydrogen transfer discussed, which include the transition structures of pseudo three‐, four‐, five‐, and six‐membered rings. The results indicated that the rate constant of the process via six‐membered ring transition state calculated at the B3LYP/6‐311++G** level was close to the experimental value and it had the lowest calculated energy barrier among all, 8.63 kcal/mol. We also studied the isomerization barriers of the first‐stage product to form the most stable conformation via possible paths. The calculated lowest barrier was 18.41 kcal/mol via a five‐membered ring process. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Reactivity descriptors applied to the study of cobalt porphyrin and their aza derivatives
Authors: Cárdenas‐Jirón Gloria I. 
Published: December 2002

AbstractA theoretical study at the density functional level of theory (ROB3LYP/3‐21G*) of the reactivity of cobalt porphyrin (CoP) and their aza derivatives (CoP(xN)) by using global and local indexes is presented. First, vertical ionization potentials and electronic affinities are calculated to determine global reactivity descriptors such as the chemical potential (μ), molecular hardness (η), and electrophilicity (ω). In general, it is found that η and ω increase with the inclusion of aza‐N atoms in the cobalt porphyrin. The cobalt condensed Fukui function (f) and cobalt condensed electrostatic potential (EPCo) for the set of CoP(xN) are also determined. We obtained that f decreases with the increase of aza‐N atoms, which indicates that a minimum Fukui function is preferred for hard–hard interactions, in agreement with previous results (Cárdenas‐Jirón, G. J. J Phys Chem A 2002, 106, 3202). Results obtained for EPCo indicates that the increase of aza‐N atoms leads to a more electrophilic site for the cobalt atom that is also stated at a global level through the results of ω, which are referred to the molecule as a whole. It is concluded that global and local descriptors are complementary in this reactivity study and both give enough information to rationalize the effect of the inclusion of aza‐N atoms in the porphyrin upon the reactivity. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Work Attitudes, Employment Barriers, and Mental Health Symptoms in a Sample of Rural Welfare Recipients
Authors: Taylor Lorraine C. 
Published: December 2002

AbstractMost of the extant research on welfare reform has neglected to consider the experiences of families in rural settings. Fifty women receiving welfare for their dependent children in a rural community were interviewed about their work experiences and aspirations, barriers to employment and service use, as well as mental health and social support. The findings indicate that the majority of participants were connected to the labor force and expressed positive attitudes about work. Barriers to employment (lack of available jobs, child care) and service use (transportation, inconvenient office hours) were endorsed. Perceived social support was negatively related to depression symptoms and positively related to self‐efficacy and self‐esteem. The importance of understanding the life experiences of welfare recipients in different contexts is discussed.
Determinants of Social Support Among Low‐Income Mothers: A Longitudinal Analysis
Authors: Green Beth L. , Rodgers Angela 
Published: December 2002

AbstractThis study examined the reciprocal relationships between perceived mastery, stress, and three functional areas of social support: tangible support, informational support, and belongingness support. Data were collected during two face‐to‐face interviews with a sample of low‐income, primarily African‐American mothers, conducted approximately 1 year apart. Consistent with predictions, initial levels of mastery predicted higher subsequent levels of instrumental social supports (tangible and advice support), but were unrelated to belonging support. Conversely, initial levels of tangible support were predictive of later mastery. Perceived stress did not account for any additional variance in subsequent support, although initial levels of belonging support only did predict reduced stress at Time 2. Results suggest that successful attempts to garner instrumental supports is an important contributor to individuals' sense of self‐efficacy, at the same time, self‐efficacy leads to more successful use of existing social support systems. These findings point to the importance of having both available tangible support networks as well as close emotional supports for low‐income parents. The importance of using longitudinal, multidimensional analyses to better understand the social support process is discussed.
Understanding Dignity in the Lives of Homeless Persons
Authors: Miller Alison B. , Keys Christopher B. 
Published: December 2002

AbstractThe current investigation is a planned, systematic study of dignity as critical to understanding the experience of homelessness and improving services and programs for the homeless. Specifically, we conducted a thematic content analysis of interviews with 24 homeless men and women to identify their perception of specific environmental events that validate and invalidate dignity. In addition, we explored the impact that these events have on homeless persons. Eight types of events were identified that sustain dignity such as being cared for by staff and having resources available to meet basic needs. Eight types of events were found that undermine dignity, such as being yelled at or insulted by staff persons and having staff use rules in an excessive and arbitrary way. Two outcomes followed the sustenance of dignity including increased self‐worth and motivation to exit homelessness. Three outcomes followed the undermining of dignity including anger, depression, and feelings of worthlessness. The results suggest that dignity is an important variable to consider in understanding the experience of homelessness. Policies and programs that support validating the dignity of homeless persons are encouraged.
Correlates of Employment Among Welfare Recipients: Do Psychological Characteristics and Attitudes Matter?
Authors: Kalil Ariel , Schweingruber Heidi A. , Seefeldt Kristin S. 
Published: December 2002

AbstractThis study examines whether and how a wide range of potential barriers to work,including psychological characteristics and attitudes, are associated with current employment in a recent sample of welfare recipients in Michigan (N = 672). Psychological factors include measures of depressive symptoms, work attitudes, and perceived risks associated with leaving welfare. Over and above demographic, economic, and contextual factors, positive psychological characteristics and attitudes were found to be moderately associated with currently being employed. Implications for welfare‐to‐work programs and policy are discussed.