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PubMed2006

Partition function and base pairing probabilities of RNA heterodimers.

BACKGROUND: RNA has been recognized as a key player in cellular regulation in recent years. In many cases, non-coding RNAs exert their function by binding to other nucleic acids, as in the case of microRNAs and snoRNAs. The specificity of these interactions derives from the stability of inter-molecular base pairing. The accurate computational treatment of RNA-RNA binding therefore lies at the heart of target prediction algorithms. METHODS: The standard dynamic programming algorithms for computing secondary structures of linear single-stranded RNA molecules are extended to the co-folding of two interacting RNAs. RESULTS: We present a program, RNAcofold, that computes the hybridization energy and base pairing pattern of a pair of interacting RNA molecules. In contrast to earlier approaches, complex internal structures in both RNAs are fully taken into account. RNAcofold supports the calculation of the minimum energy structure and of a complete set of suboptimal structures in an energy band above the ground state. Furthermore, it provides an extension of McCaskill's partition function algorithm to compute base pairing probabilities, realistic interaction energies, and equilibrium concentrations of duplex structures.

Journal Article↗
PubMed1993

[Hypermedia software for teaching anatomy of the upper abdomen with computerized tomography and magnetic resonance].

The authors have developed a hypermedia program for creating a tutorial of CT and MR anatomy of the upper abdomen. The program was created on a Mcintosh computer, with the Supercard software: it is made up of a series of windows, each of them containing images, texts, schematic representations and sound. Moreover, each window contains buttons which are activated with the mouse and allow different kinds of function, all created by the authors to be displayed. In particular, navigation buttons allow the users to move in the program either sequentially or non-linearly, according to their needs. The possibility of obtaining information and schematic representations is given by specific buttons. There are also multiple buttons hidden in the images which, when activated, allow the name of the selected organ to be displayed. In conclusion, this program can be especially helpful since it allows different data sets to be integrated to provide the user with complete information. Moreover, the program allows learning to be controlled, that is the user to be informed on timing and methods for more effective studying.

Abdomen↗
PubMed2006

High pain ratings predict treatment failure in chronic occupational musculoskeletal disorders.

BACKGROUND: Pain intensity is one of the most widely used measures in the treatment of patients with chronic disabling occupational musculoskeletal disorders. Few studies have comprehensively investigated the relationship of pain intensity at the time of rehabilitation to objective socioeconomic outcomes at one year after treatment. This study evaluated the ability of pain intensity ratings, measured with a visual analog scale, to predict rehabilitation outcomes and to identify patients who are "at risk" for a poor outcome. METHODS: A cohort of 3106 patients with chronic disabling occupational musculoskeletal disorders in a multidisciplinary occupational tertiary rehabilitation program was divided into four groups on the basis of the pain intensity ratings (0 to 3, 4 to 5, 6 to 7, and 8 to 10) before and after rehabilitation. A structured interview to assess the socioeconomic outcomes, including work status, health-care utilization, recurrent injury, and whether there had been resolution of Workers' Compensation or third-party financial disputes, was conducted one year after rehabilitation. RESULTS: High pain intensity before rehabilitation was linearly associated with declining rates of program completion and higher rates of self-reported depression and disability after rehabilitation. Although higher pain ratings both before and after rehabilitation were associated linearly with a declining quality of socioeconomic outcomes, extremely high pain ratings (8 to 10) after rehabilitation were most predictive of poor outcomes. At the post-rehabilitation evaluation, patients with extreme pain were far more likely than those with mild pain to seek surgical treatment (risk ratio = 11.2 [95% confidence interval, 4.3, 29.5]) or to persist in seeking health care from new providers (risk ratio = 3.3 [95% confidence interval, 2.4, 4.5]). They were less likely to either return to work (risk ratio = 3.9 [95% confidence interval, 2.6, 6.0]) or to retain work (risk ratio = 4.2 [95% confidence interval, 2.9, 6.0]). They were also twice as likely to claim a new injury to the same musculoskeletal site after returning to work and to fail to settle Workers' Compensation or third-party financial disputes. CONCLUSIONS: High pain ratings before rehabilitation are associated with higher rehabilitation dropout rates. The patients with chronic disabling occupational musculoskeletal disorders who reported extreme pain after completing a full course of extended treatment (13% of 2573) were at risk for poor outcomes in terms of lost productivity, high utilization of health care, and cost-shifting of state Workers' Compensation payments to federal resources.

Adult↗
PubMed2005

Limits of multi-linear gradient optimisation in reversed-phase liquid chromatography.

The concept of limiting peak purity was applied to quantify the degree of completion of the separation capability of a chromatographic system using multi-linear gradients. The objective was to check whether the complexity of a gradient program deserves be increased to enhance resolution by inserting more linear segments, or on the contrary, no significant improvements can be expected under more complex gradients. A set of 19 isoindole derivatives of primary amino acids was selected to test the performance of isocratic, single linear and multi-linear gradients. Accurate simulated chromatograms were obtained via numerical integration of the general equation of gradient elution, using pre-established start and end conditions of the gradient program. The overall peak purity was selected as objective function. Good--although not baseline--resolution was achieved with an optimal trilinear gradient. Excellent agreement between experimental and predicted optimal chromatograms was found. With the proposed approach, a degree of completion of the separation capability of the chromatographic system of 21.2, 49.7, 81.5 and 88.5% was accomplished with optimal gradients with one, two, three and four segments, respectively. More complex gradients did not enhance the latter figure significantly. Also, multi-linear gradients gave rise to more benefits than complementary gradients.

Chromatography, Liquid↗
PubMed1995

Balancing learner control and realism with specific instructional goals: case studies in fluid balance for nursing students.

In designing instruction, there is an inherent tension between permitting learner control and focusing on specific instructional goals. This tension is particularly problematic in computer-based clinical case studies. In addition, the question of the appropriate level of realistic detail is central to case study design. More learner control and greater detail require greater complexity and interactivity, and consequently longer development time per case. They may also lead to difficulty in focusing on specific content. This program is designed to present computer-based case studies as an adjunct to classroom instruction in a specific content area, with significant compromises in realism compensated by the potential to focus on a specific set of problems and expose students to a fairly large number of "patients." The degree of learner control is necessarily limited by the program's structure, but the design attempts to allow a considerable amount of self-direction within those limits. The program's main path goes through a series of case studies illustrating a variety of fluid and electrolyte problems. These case studies are fairly simple and tightly structured: history, physical assessment, and laboratory data are presented near the beginning of each study, and learners are given predefined choices with immediate feedback at specified decision points. The case studies are designed to be completed fairly rapidly, typically no more than about thirty minutes per case. The distortion of the case study format by the obvious focus on fluid and electrolyte problems is compensated somewhat by inclusion of a number of cases with no relevant problems. Within this structured format, the program gives the learner control over a number of aspects of the learning experience. Hypertext is used hierarchically, with two levels of explanation for some central concepts and one level for material not directly relevant to the main instructional goals. Consequently, the learner controls content density to a considerable degree. Since nursing students are under pressure to absorb large amounts of clinically relevant information within a relatively short time, the availability of additional information on diagnoses, charting abbreviations, normal ranges for lab values, etc., may provide an added incentive to use the program. Though the case studies are linear with no branching, learners have several options in using them. The basic user mode involves simply going through the case studies and "solving" them: evaluating the data, identifying problems, and making basic treatment decisions. Alternatively, the learner may choose a particular problem and use the program as a "semi-tutorial." Backward movement is allowed, either to review the development of a case or to try again after an incorrect response. Accumulated information is available in an on-screen "chart" for ready reference. A "reference library" is accessible for browsing from any point in the program. Learner evaluation of the program is in progress.

Computer Simulation↗
PubMed1996

Non-linear law-like relationship between weight & height of infants & pre-school children.

A non-linear equation of the type log w - 0.008 h = a - be-kl for weight (w) and height (h) of 1177 infants and pre-school children from the Rural Health Centre area in Ballabhgarh was fitted by modified Guass-Newton Method using BMDP 03R program. On applying the non-linear model to the data of the present study it was found that the curve was a good fit in both sexes and also in all nutritional groups. The value of 'a' (the nutritional index) was almost the same in boys and girls but it was higher in case of children with normal nutrition (0.37) and lower in children with malnutrition (0.34 in Grade I, 0.32 in Grade II and 0.28 in Grades III & IV). The exponential term 'k' (index of maturation) was higher in boys compared to that of girls and higher in those with normal nutrition than with malnutrition. It was found that the rate of decay of the exponential term was slower in those with malnutrition compared to those with normal nutrition. While no difference was observed in the asymptotic value i.e., the rate at which infants reach the shape of older children, between boys and girls with normal nutrition (19 and 20 months respectively), it was delayed by 5 to 8 months in girls compared to boys with malnutrition. In the total sample, the Ehrenberg's index attained the asymptotic value at 20 months in boys and at 35 months in girls and at 27 months in the combined sample.

Body Height↗
PubMed1991

Effects of an intervention program for pregnant adolescents: educational outcomes at two years postpartum.

Examined postpartum effects of a school-based intervention program for pregnant adolescents. Interviews were conducted with 102 innercity black, low-income, school-aged mothers who had attended the program, and their academic and medical records were reviewed. For teenagers who had been poor students prior to becoming pregnant, a strong linear effect was found for duration of program attendance: with sufficient time in the program, poorer students became indistinguishable from better students in educational success. Most of the better students were educationally successful at 2 years postpartum, independent of their length of time in the program. For all students, longer durations of postnatal intervention were predictive of lower likelihood of subsequent childbearing. Numerous academic, medical, social, and demographic variables were ruled out as possible confounding factors that might have produced the positive educational outcomes for poorer students. The results suggest that adolescents who appear to have minimal academic promise prior to their pregnancy are nevertheless very responsive to school-based intervention.

Adolescent↗
PubMed1997

Comparative study of four different pharmacokinetic computer programs: case study of a factor VIII preparation.

OBJECTIVE: To compare the pharmacokinetic parameters after a single dose of a monoclonally purified factor VIII concentrate in four different computer programs for pharmacokinetic analysis. SETTING: Haemophilia unit of a tertiary care university hospital. METHODS: Ten patients with severe haemophilia A were administered a single dose of 30-50 IU kg-1 body weight. Blood samples were drawn at different times during the first 48 h after infusion of factor VIII. Plasma factor VIII activity was measured by standard one-stage clotting assay and experimental data were analysed using four computer programs: JANA, PKCALC, F8SD and PCNONLIN. The pharmacokinetic models of analysis employed in the study were both compartmental and non-compartmental. The parameters compared were half-lives (t1/2) and mean residence time (MRT), volumes of distribution (V) and clearance (CL). Values obtained for each pharmacokinetic parameter in each program for the same model were tested for differences with a multiple analysis of variance (MANOVA). Linear correlation with the equivalent parameters for each program was also performed. RESULTS: Pharmacokinetic parameters differed depending on the computer program used to analyse the same data set. There were differences of statistical significance in t1/2 and V for one-compartment and two-compartment models derived by some of the programs, but none with the non-compartmental one. CL, considered model independent, showed differences between the programs evaluated. Correlations for each parameter generated were in general good (P < 0.05). CONCLUSION: Pharmacokinetic parameters differed depending on the computer program used to analyse the same data set. The same patient data used in different computer programs will result in significantly different parameter estimations, although the non-compartmental approach is less affected by variation, and this should be taken into consideration for comparative purposes, for the development of new preparations and for the implications in patient care and therapy monitoring.

Adolescent↗
PubMed1994

Evaluation of two AIDS education programs for impoverished Latina women.

This paper evaluates and contrasts the effectiveness of two culturally sensitive AIDS education programs developed by the UCLA AIDS Nursing Network and delivered to 213 impoverished Latina homeless or drug-addicted women in Los Angeles. The Comprehensive Health Seeking and Coping Paradigm guided the program, which was implemented by specially trained Latina nurses and outreach workers. A quasi-experimental design was employed where women were randomized by site into Specialized (N = 82) and Traditional (N = 131) programs. Repeated measures ANOVAS and log-linear models were used to evaluate improvement over a two-week period for women in both groups and to identify interactions with program type. Two-week posttest analyses were also conducted to assess program effectiveness, controlling for baseline values of the measure in question, nonequivalency between groups at baseline, and selected demographic characteristics, including acculturation. Results indicated that women in both AIDS education programs improved significantly in cognitive, behavioral, and psychologic outcomes.

Acquired Immunodeficiency Syndrome↗
PubMed1994

Improved estimation of DNA fragment length from gel electrophoresis data using a graphical method.

A computer program has been developed for computing DNA fragment size from its electrophoretic mobility using a graphical method. The program uses DNA marker data and selects the semilogarithmic linear range (sl-range), i.e., the linear portion of the semilogarithmic curve (mobility vs. log of DNA fragment length). Over this range a linear interpolation is derived for calculating the size of a DNA fragment whose mobility falls in the sl-range. The program also derives a hyperbolic interpolation formula that covers the entire range for determining the size of a DNA fragment whose mobility is beyond the semilogarithmic linear range. The method described in this paper is sensitive, accurate and reliable. This program can also be used to compute protein or polypeptide size from sodium dodecyl sulfate polyacrylamide gel electrophoresis data. The DOS version of the DNASIZE program is freely available from Netserver at EMBL or from BioTechNet by EMail.

DNA↗
PubMed2006

Short-term effects of Project EX-4: a classroom-based smoking prevention and cessation intervention program.

OBJECTIVE: Researchers continue to try to develop effective teen tobacco use prevention and cessation programs. Three previous school clinic-based studies established the efficacy of Project EX for teen smoking cessation. This fourth study adapts Project EX to the classroom context. This paper reports the findings based on pretest and posttest surveys conducted immediately prior and post-intervention. METHODS: An eight-session classroom-based curriculum was developed and tested with a randomized controlled trial that involved a total of 1097 students in six program and six control continuation high schools. Program-specific knowledge and smoking measures were assessed at both the pretest and posttest surveys, and were used to evaluate the program's effect on the immediate outcomes. The immediate outcomes effects were analyzed with multi-level random coefficients models. RESULTS: Program students provided favorable process ratings of the overall program and each session. Compared with the students in the control condition, students in the program condition showed a greater change in correct knowledge responses from pretest to posttest (beta=+5.5%, p=0.0003). Students in the program condition also experienced a greater reduction in weekly smoking (beta=-6.9%, p=0.038), and intention for smoking in the next 12 months (beta=-0.21 in 5-level scale, p=0.023). CONCLUSIONS: EX-4 immediate outcome results revealed favorable student responses to the program, increases in knowledge, and decreases in smoking relative to a standard care control condition.

Adolescent↗
PubMed2000

Redasoft Plasmid 1.1: software for easy, efficient cloning and map drawing.

A computer program is described which creates circular and linear genetic maps with or without sequences, performs restriction analysis, and simulates basic molecular cloning operations. Redasoft Plasmid 1.1 is a user-friendly program for Windows 95/98/NT/2000, designed to generate high quality genetic maps for presentation and publication and to aid the molecular biologist in selecting restriction endonucleases for common molecular cloning experiments. The program incorporates an integrated web browser and can automatically generate complete, labeled maps from sequences on the Internet.

Chromosome Mapping↗
PubMed1997

Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison.

We have developed a code generating language, called Dynamite, specialised for the production and subsequent manipulation of complex dynamic programming methods for biological sequence comparison. From a relatively simple text definition file Dynamite will produce a variety of implementations of a dynamic programming method, including database searches and linear space alignments. The speed of the generated code is comparable to hand written code, and the additional flexibility has proved invaluable in designing and testing new algorithms. An innovation is a flexible labelling system, which can be used to annotate the original sequences with biological information. We illustrate the Dynamite syntax and flexibility by showing definitions for dynamic programming routines (i) to align two protein sequences under the assumption that they are both poly-topic transmembrane proteins, with the simultaneous assignment of transmembrane helices and (ii) to align protein information to genomic DNA, allowing for introns and sequencing error.

Algorithms↗
PubMed1993

Development of linear and nonlinear hand-arm vibration models using optimization and linearization techniques.

Hand-arm vibration (HAV) models serve as an effective tool to assess the vibration characteristics of the hand-tool system and to evaluate the attenuation performance of vibration isolation mechanisms. This paper describes a methodology to identify the parameters of HAV models, whether linear or nonlinear, using mechanical impedance data and a nonlinear programming based optimization technique. Three- and four-degrees-of-freedom (DOF) linear, piecewise linear and nonlinear HAV models are formulated and analyzed to yield impedance characteristics in the 5-1000 Hz frequency range. A local equivalent linearization algorithm, based upon the principle of energy similarity, is implemented to simulate the nonlinear HAV models. Optimization methods are employed to identify the model parameters, such that the magnitude and phase errors between the computed and measured impedance characteristics are minimum in the entire frequency range. The effectiveness of the proposed method is demonstrated through derivations of models that correlate with the measured X-axis impedance characteristics of the hand-arm system, proposed by ISO. The results of the study show that a linear model cannot predict the impedance characteristics in the entire frequency range, while a piecewise linear model yields an accurate estimation.

Arm↗
PubMed2004

Linear-scaling formation of Kohn-Sham Hamiltonian: application to the calculation of excitation energies and polarizabilities of large molecular systems.

We present calculations of excitation energies and polarizabilities in large molecular systems at the local-density and generalized-gradient approximation levels of density-functional theory (DFT). Our results are obtained using a linear-scaling DFT implementation in the program system DALTON for the formation of the Kohn-Sham Hamiltonian. For the Coulomb contribution, we introduce a modification of the fast multipole method to calculations over Gaussian charge distributions. It affords a simpler implementation than the original continuous fast multipole method by partitioning the electrostatic Coulomb interactions into "classical" and "nonclassical" terms which are explicitly evaluated by linear-scaling multipole techniques and a modified two-electron integral code, respectively. As an illustration of the code, we have studied the singlet and triplet excitation energies as well as the static and dynamic polarizabilities of polyethylenes, polyenes, polyynes, and graphite sheets with an emphasis on the trends observed with system size.

Journal Article↗
PubMed1980

Computer evaluation of cytostatic properties of compounds. II. In vitro studies on the activities by CY-VTP/2 program for ODRA-1204 computer.

For the second step of in vivo investigation on the basis of the NCI, NIH examination procedure of cytostatics, an evaluation program CY-VTP/2 in ALGOL-1204) of cytostatic activities was prepared for the Polish ODRA-1204 computer. The program allows: a) variety of investigation in connection with possibilities of alternative usage of examination variants; b) comparison with NIC, NIH results with an optimum for verification and unification with every program; c) to obtain precise data from a great series of compounds with additional information (inactive concentration ED0, range of ED50, activities, a degree of linear correlation; d) graphic presentation of data. Program may be useful for evaluation of other effects dependent on doses and the I-range type reactions.

Antineoplastic Agents↗
PubMed1992

Computation of dose distribution for linear radioactive sources in brachytherapy.

This paper describes a microcomputer program, written in Quick BASIC (Version 4.5), that allows the planning of radio-therapeutic doses in brachytherapy. The program allows the calculation of treatment times of prescribed doses, dose rates in selected points, as well as the computation of 2D and 3D isodose contours, of any linear source distribution. Also the volume enclosed by a chosen dose rate can be calculated. The results agree better than 1% with the results reported in the literature for discrete dose rate values, and for isodose contours.

Brachytherapy↗
PubMed1994

An algorithm and computer program for calculating the mean transit time and distribution rate parameters of generated metabolites undergoing linear tissue distribution and linear or non-linear central elimination.

A method is described for calculating the mean transit time and distribution rate parameters of a generated primary metabolite undergoing linear distribution and linear or non-linear central elimination, and of catenary metabolites with any precursor order. It is also applicable to a drug and its interconversion metabolite and does not require separate administration of the metabolite. The method allows steady-state volume of distribution and distribution clearance of a metabolite to be calculated, provided that the central volume of distribution of the metabolite is known. An algorithm and computer program to implement the proposed method are presented. The calculations require the plasma concentration versus time curves of the metabolite and its precursor. The method is applied to both published and simulated data.

Algorithms↗