Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Program Efficiency”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 379 records · Page 21Linked to original sources
PubMed1996

Empirical free energy as a target function in docking and design: application to HIV-1 protease inhibitors.

Structure-based drug design requires the development of efficient computer programs for exploring the structural compatibility of various flexible ligands with a given receptor. While various algorithms are available for finding docked conformations, selecting a target function that can reliably score the conformations remains a serious problem. We show that the use of an empirical free energy evaluation method, originally developed to characterize protein-protein interactions, can substantially improve the efficacy of search algorithms. In addition to the molecular mechanics interaction energy, the function takes account of solvation and side chain conformational entropy, while remaining simple enough to replace the incomplete target functions used in many drug docking and design procedures. The free energy function is used here in conjunction with a simple site mapping-fragment assembly algorithm, for docking the MVT-101 non-peptide inhibitor to HIV-1 protease. In particular, we predict the bound structure with an all atom RMSD of 1.21 A, compared to 1.69 A using an energy target function, and also accurately predict the free energy shifts obtained with a series of five trimeric hydroxyethylene isostere analogs.

Algorithms↗
PubMed1990

Flexible protein sequence patterns. A sensitive method to detect weak structural similarities.

The concept of a flexible protein sequence pattern is defined. In contrast to conventional pattern matching, template or sequence alignment methods, flexible patterns allow residue patterns typical of a complete protein fold to be developed in terms of residue positions (elements), separated by gaps of defined range. An efficient dynamic programming algorithm is presented to enable the best alignment(s) of a pattern with a sequence to be identified. The flexible pattern method is evaluated in detail by reference to the globin protein family, and by comparison to alignment techniques that exploit single sequence, multiple sequence and secondary structural information. A flexible pattern derived from seven globins aligned on structural criteria successfully discriminates all 345 globins from non-globins in the Protein Identification Resource database. Furthermore, a pattern that uses helical regions from just human alpha-haemoglobin identified 337 globins compared to 318 for the best non-pattern global alignment method. Patterns derived from successively fewer, yet more highly conserved positions in a structural alignment of seven globins show that as few as 38 residue positions (25 buried hydrophobic, 4 exposed and 9 others) may be used to uniquely identify the globin fold. The study suggests that flexible patterns gain discriminating power both by discarding regions known to vary within the protein family, and by defining gaps within specific ranges. Flexible patterns therefore provide a convenient and powerful bridge between regular expression pattern matching techniques and more conventional local and global sequence comparison algorithms.

Amino Acid Sequence↗
PubMed1989

Computer assisted treatment planning for 125I ophthalmic plaque radiotherapy.

This paper describes a computer program for planning the treatment of ocular tumors with 125I plaques. The program permits the input of the tumor configuration into a model eye and facilitates the viewing of the relative geometry of the tumor and various eye structures in different perspectives. Custom-designed 125I plaques can be localized onto the globe, and dose distributions can be calculated and superimposed on the eye structures in any plane or on the inner eye surface. The program allows efficient evaluation of the plaque design in terms of radiation dose distribution relative to the tumor and critical structures.

Brachytherapy↗
PubMed1993

High-performance liquid chromatographic separation of biogenic polyamines using 2-(1-pyrenyl)ethyl chloroformate as a new fluorogenic derivatizing reagent.

The application of a new fluorogenic pre-column derivatizing reagent, 2-(1-pyrenyl)ethyl chloroformate (PEOC), is reported for the separation and detection of biogenic polyamines using column liquid chromatography. The development of the method included the optimization of excitation and emission wavelengths, efficient gradient programming, derivatization temperature, time, and pH. Minimum detection limits, linear ranges, reproducibility, and recovery from analyzed samples were determined. The procedure was applied to hydrolyzed serum samples taken from healthy individuals and cancer patients. Separation of PEOC-derivatized polyamines from the serum hydrolysis by-products was successful and detection limits were more favorable than those previously reported for 9-fluorenyl-methyl chloroformate-derivatized polyamines.

Biogenic Amines↗
PubMed2006

In vivo, in vitro and ex vivo models to assess pulmonary absorption and disposition of inhaled therapeutics for systemic delivery.

Despite the interest in systemic delivery of therapeutic molecules including macromolecular proteins and peptides via the lung, the accurate assessment of their pulmonary biopharmaceutics is a challenging experimental task. This article reviews in vivo, in vitro and ex vivo models currently available for studying lung absorption and disposition for inhaled therapeutic molecules. The general methodologies are discussed with recent advances, current challenges and perspectives, especially in the context of their use in systemic pulmonary delivery research. In vivo approaches in small rodents continue to be the mainstay of assessment by virtue of the acquisition of direct pharmacokinetic data, more meaningful when attention is given to reproducible dosing and control of lung-regional distribution through use of more sophisticated lung-dosing methods, such as forced instillation, microspray, nebulization and aerosol puff. A variety of in vitro lung epithelial cell lines models and primary cultured alveolar epithelial (AE) cells when grown to monolayer status offer new opportunity to clarify the more detailed kinetics and mechanisms of transepithelial drug transport. While continuous cell lines, Calu-3 and 16HBE14o-, show potential, primary cultured AE cell models from rat and human origins may be of greater use, by virtue of their universally tight intercellular junctions that discriminate the transport kinetics of different therapeutic entities. Nevertheless, the relevance of using these reconstructed barriers to represent complex disposition of intact lung may still be debatable. Meanwhile, the intermediate ex vivo model of the isolated perfused lung (IPL) appears to resolve deficiencies of these in vivo and in vitro models. While controlling lung-regional distributions, the preparation alongside a novel kinetic modeling analysis enables separate determinations of kinetic descriptors for lung absorption and non-absorptive clearances, i.e., mucociliary clearance, phagocytosis and/or metabolism. This ex vivo model has been shown to be kinetically predictive of in vivo, with respect to macromolecular disposition, despite limitations concerning short viable periods of 2-3 h and likely absence of tracheobronchial circulation. Given the advantages and disadvantages of each model, scientists must make appropriate selection and timely exploitation of the best model at each stage of the research and development program, affording efficient progress toward clinical trials for future inhaled therapeutic entities for systemic delivery.

Absorption↗
PubMed2005

Movement preparation is affected by tissue damage in multiple sclerosis: evidence from EEG event-related desynchronization.

OBJECTIVE: To investigate the impact of brain tissue damage in Multiple Sclerosis (MS) on the efficiency of programming of voluntary movement, assessed using event-related desynchronization of the EEG. METHODS: The onset latency of mu ERD (percent desyncronization of the mu rhythm preceding movement onset) to hand movement was studied in 34 MS patients. ERD onset was compared with normative data and correlated with T1 and T2 total lesion volume (TLV) at magnetic resonance imaging (MRI). RESULTS: ERD onset latency was significantly correlated with T1-TLV (r = 0.53, P = 0.001) and T2 lesion load (r = 0.5, P = 0.003), even after correcting for disability. Patients with higher T1-TLV had significantly delayed ERD onset compared with normal subjects and with patients with lower T1-TLV; patients with higher T2-TLV had significantly delayed ERD compared with normal subjects only. ERD onset latency was not correlated to clinical disability. CONCLUSIONS: Our finding of delayed ERD onset in patients with more severe measures of brain damage, independently from clinical disability, suggests that functional cortico-cortical and cortico-subcortical connections underlying the expression of ERD during programming of voluntary movement are disrupted by the MS related pathological process. Further, studies are needed to evaluate the role of specific anatomical cortico-subcortical circuits in determining this abnormality. SIGNIFICANCE: The extent of brain lesion load in multiple sclerosis affects cortical changes related to motor preparation, detected by analysis of onset latency of event-related desynchronization (ERD) of the mu rhythm to self-paced movement.

Adult↗
PubMed2005

Revisiting community-based distribution programs: are they still needed?

Community-based distribution (CBD) programs are the optimum way of reaching people in rural areas of developing countries where conventional methods of delivery do not exist or fail. This paper reviews findings and experiences from over 30 years of efforts to implement CBD of family planning methods around the world. Although research suggests that community-based service delivery can contribute to contraceptive use, the magnitude of impact is often in doubt or its existence is questionable when compared to alternative family planning delivery services. After the review of more than 30 years of CBD work, we found that these programs are still needed to meet the needs for contraception in rural communities and isolated city neighborhoods in developing countries. Integration with other health outreach programs, effective management, keeping training of agents brief and letting them distribute contraceptives and keeping all or part of the profits instead of paying them salaries are some of the strategies that can make CBD programs more efficient.

Contraception↗
PubMed2006

Validity and reliability of a new in vivo ankle stiffness measurement device.

This investigation was designed to test the validity and reliability of a new measure of inversion/eversion ankle stiffness on a unique medial/lateral swaying cradle device utilizing a test/retest with comparison to a known standard. Ankle stiffness is essential to maintaining joint stability. Most ankle injuries occur via an inversion mechanism. To date, very little information is available regarding stiffness of the evertor muscles in the prevention of excessive inversion joint rotation. Transient oscillation data representing inversion/eversion stiffness was obtained in a bipedal weight-bearing stance with an upright posture. Using commercially available springs with stiffness of 4.80N/cm the measured value recorded by the cradle was 4.87N/cm. Mean active stiffness values of the ankle were 35.70Nm/cm (SD 9.45). The trial-to-trial reliability ICC (2,1) coefficient was 0.96 with an SEM of 2.05Nm/rad, and the day-to-day reliability ICC (2,k) coefficient was 0.93 and an SEM of 3.00Nm/rad. The results demonstrate that inversion/eversion ankle stiffness measures on this device are a valid, repeatable and consistent measure. This is relevant because the ability to accurately quantify inversion/eversion ankle stiffness will improve our understanding of biomechanical stability and factors that influence it. It will also enable identification of ankle injury risk factors that will lead to more efficient rehabilitation programs and injury prevention strategies.

Adult↗
PubMed2006

[Evolution of nosocomial infection prevalence in an Algeria university hospital (2001 to 2005)].

OBJECTIVE: A program against nosocomial infections was implemented in 2001 in the university hospital of Blida. A yearly survey of nosocomial infection (NI) prevalence was carried out from 2001 to 2005 to evaluate this program's impact. The aim of these surveys was to evaluate the rate of NI prevalence. PATIENTS AND METHODS: All patients hospitalized for more than 48 h in acute care units were included. The study was designed as a one-day prevalence survey. For each patient, risk factors and presence of active nosocomial infections during the study day were recorded on a standardized form. Centers of Disease Control definitions criteria were used to identify nosocomial infections. Prevalence and frequency of risk factors were compared between the five yearly surveys. RESULTS: A total of 1,362 patients were included in the five surveys. From 2001 to 2005, the prevalence of nosocomial infections and infected patients decreased respectively from 9.8 to 4%, and from 9.5 to 4% (P<0.001). In contrast, the frequency of risk factors, except for the frequency of patients with ASA score>or=3, did not significantly vary. The prevalence of surgical site infection very significantly decreased from 11.9 to 2.5%. The proportion of microbiological diagnoses was 61.6%. Gram-negative bacilli were predominant (77.2%). CONCLUSION: These results show a decrease in the prevalence of nosocomial infections and suggest that the hospital program was efficient.

Adult↗
PubMed2004

Genetically programmed B lymphocytes are highly efficient in inducing anti-virus protective immunity mediated by central memory CD8 T cells.

The hallmarks of specific T cell immunity include proliferative expansion, acquisition of effector function and memory T cell formation. Here, we used priming with B lymphocytes transgenic for the dominant epitope (NP366-374) of the influenza virus nucleoprotein, to study the characteristics of the CD8 T cell memory response in C57Bl/6 mice and elucidate which subset of CD8 T cells memory mediates protection from disease. We found that (i) the size of the memory CTL response is independent of the priming dose and is similar to that induced by the live virus, (ii) priming with a low dose (3 x 10(2)cells/inoculum) of transgenic B lymphocytes confers a protective memory CTL response, and (iii) protection from disease is mediated by central memory (T(CM)) CD8 T cells.

Animals↗
PubMed2003

Molecular characterization of two genotypes of mumps virus circulated in Korea during 1998-2001.

Sequence analyses of the entire small hydrophobic (SH) and hemagglutinin-neuraminidase (HN) genes of mumps viruses circulated in Korea from 1998 to 2001 showed that these isolates were grouped into two genotypes, H and I. While genotype I was predominant throughout the country during this period, genotype H was found in the restricted region, 1999. The nucleotide and deduced amino acid sequences of Korean isolates showed the type-specific changes including the signature motif at positions 28-30 in the SH gene and the neutralizing epitopes in the HN gene. Particularly, Asian strains including Korean isolates and European strains differed from 2.3 to 3.8% at the nucleotide sequence level in the SH gene although they belonged to the same genotype H. Furthermore, none of Korean isolates were genetically related to the vaccine strains used in Korea. The results provide important information to understand the epidemiology of mumps infection and to facilitate the development of more efficient vaccine program in Korea.

Amino Acid Motifs↗
PubMedDate not supplied

[Efficiency of a gambling prevention program for youths: results from the pilot study].

UNLABELLED: A meta-analysis of North American studies indicates that the prevalence rate of pathological gambling varies between 4.4% and 7.4% among adolescents. Pathological gambling is thus not a phenomenon that suddenly appears once youths reach an adult age. On the contrary, significant contact with gambling occurs in childhood adolescence. For this reason, it is important to develop an effective gambling prevention program that will reduce the risk that youths will develop gambling problems. The information promoted in the prevention program our research team created and evaluated here teaches youths to recognize the traps of gambling activities, while enabling them to make an informed decision as to their eventual participation in those activities. The program is based on knowledge and recognition of key indices that can be easily identified as warning signs of a loss of control. It is predicted that youths who participate in this prevention program will improve their knowledge of gambling activities and will develop a more realistic attitude towards those activities than youths from a control group. The experimental group's problem-solving skills are also expected to improve. An experimental design (pre-test, post-test and follow-ups with control group) was used to evaluate the program's effectiveness. Overall, 1193 youths participated in this study. The prevention program involves three 60-minute meetings. The objectives of these meetings are the following: (meeting #1) improve youths' knowledge of gambling activities and help them acquire a more realistic attitude towards these activities; (meeting #2) teach a structured problem-solving approach to resist to peer-pressure; (meeting #3) inform youths of the consequences that may be associated with abusive participation in gambling and teach them to recognize warning signs of a loss of control over gambling habits. DEPENDENT VARIABLES: (a) knowledge of and attitudes towards gambling and gambling activities; (b) problem-solving skills; (c) frequency of participation in gambling activities; (d) discussion with relatives, friends and teachers regarding gambling activities and attention paid towards gambling habits among close friends and family. Participation in the gambling prevention program significantly improves youths' knowledge of the real probabilities of winning and the pitfalls included in gambling activities and favours the development of a more realistic attitude towards these activities. However, the participation in the prevention program does not help to improve their problem-solving skills. Nonetheless, it leads more youths to talk about gambling with their parents and teachers, and enables them to be more aware of the gambling habits of their friends and family. Finally, note that it was impossible to verify any decrease in gambling habits as the majority of participants (62%) were non or very occasional gamblers. However, no iatrogenic effect was observed on the frequency of participation in gambling activities. Aside the positive impact of the program on the attitudes and knowledge of students, participation in the preventive sessions contributed to create a dialogue with adults and increased youths' interest in the gambling habits of their friends and family. These discussions enabled the youths to validate the information they received during class, to consolidate what they learned during the prevention sessions, and favour the dissemination of this knowledge beyond the scope of the academic environment. The results obtained regarding youths' attitudes and knowledge demonstrate that attitude modification takes place progressively. However, once well assimilated, these new attitudes seem to take hold in a fairly durable way. On the other hand, acquisition of knowledge seems to take place immediately after the theoretical concepts are taught. Yet, they slightly decreased before stabilising a few months later. This suggests that assimilation of new knowledge may be optimized by the addition of an intervention session a couple of months after the end of the intervention. Even if it was impossible to verify any decrease in participants' gambling habits, it is possible to think that the impact of participation in the gambling prevention program could be observable and measurable within a few years. However, only a long-term follow-up study would make it possible to assess whether participation in the program does indeed contribute to decreasing gambling habits and the number of youths who regularly participate in gambling activities. Despite the non-significant results observed for problem-solving skills, it seems nonetheless important to include this component, which benefits from great theoretical support, especially within the framework of prevention programs targeting youths. However, the teaching method must be changed in order to maximize the intervention's effectiveness. Despite some methodological limitations observed during the evaluation of this program, the results obtained clearly demonstrate that participation in the prevention program significantly improves youths' attitudes and knowledge regarding gambling activities. The teaching of accurate knowledge and realistic attitudes towards gambling should help youths to recognize the cognitive traps inherent to gambling activities and thus contribute, over the long run, to decrease the number of youths with gambling problems.

Adolescent↗
PubMed2002

Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot.

A hairpin-type messenger RNA pseudoknot from pea enation mosaic virus RNA1 (PEMV-1) regulates the efficiency of programmed -1 ribosomal frameshifting. The solution structure and 15N relaxation rates reveal that the PEMV-1 pseudoknot is a compact-folded structure composed almost entirely of RNA triple helix. A three nucleotide reverse turn in loop 1 positions a protonated cytidine, C(10), in the correct orientation to form an A((n-1)).C(+).G-C(n) major groove base quadruple, like that found in the beet western yellows virus pseudoknot and the hepatitis delta virus ribozyme, despite distinct structural contexts. A novel loop 2-loop 1 A.U Hoogsteen base-pair stacks on the C(10)(+).G(28) base-pair of the A(12).C(10)(+).G(28)-C(13) quadruple and forms a wedge between the pseudoknot stems stabilizing a bent and over-rotated global conformation. Substitution of key nucleotides that stabilize the unique conformation of the PEMV-1 pseudoknot greatly reduces ribosomal frameshifting efficacy.

Base Pairing↗
PubMed2003

A long HBV transcript encoding pX is inefficiently exported from the nucleus.

The longest hepatitis B virus transcript is a 3.9-kb mRNA whose function remained unclear. In this study, we wished to identify the translation products and physiological role of this viral transcript. This transcript initiates from the X promoter region ignoring the inefficient and noncanonical viral polyadenylation signal at the first round of transcription. However, an HBV mutant with canonical polyadenylation signal continues, though with lower efficiency, to program the synthesis of this long transcript, indicating that the deviated HBV polyadenylation signal is important but not essential to enable transcription of the 3.9-kb species. The 3.9-kb RNA contains two times the X open reading frame (ORF). The X ORF at the 5'-end is positioned upstream of the CORE gene. By generating an HBV DNA mutant in which the X and Core ORFs are fused, we demonstrated the production of a 40-kDa X-Core fusion protein that must be encoded by the 3.9-kb transcript. Mutagenesis studies revealed that the production of this protein depends on the 5' X ORF ATG, suggesting that the 3.9-kb RNA is active in translation of the X ORF. Based on these features, the 3.9-kb transcript was designated lxRNA for long X RNA. Unlike other HBV transcripts, lxRNA harbors two copies of PRE, the posttranscriptional regulatory element that controls the nuclear export of HBV mRNAs. Unexpectedly, despite the presence of PRE sequences, RNA fractionation analysis revealed that lxRNA barely accumulates in the cytoplasm, suggesting that nuclear export of lxRNA is poor. Collectively, our data suggest that two distinct HBV mRNA species encode pX and that the HBV transcripts are differentially regulated at the level of nuclear export.

Active Transport, Cell Nucleus↗
PubMed1985

An intraocular lens power calculator for the IBM PC and PCjr computers using input variable selection.

A BASIC program to calculate intraocular lens power and refractive errors using previously derived equations is presented. The program was written for the IBM PC and PCjr computers with an emphasis on clinical usefulness. Program features include a comparison of refractive and axial length predictions of secondary implant power and velocity compensation for axial length measurements made on aphakic patients. Equation specification by input variable selection and automatic averaging of keratometer readings make the program highly efficient.

Computers↗
PubMed1987

The efficiency of different combined treatment programs (combination chemotherapy-radiotherapy) used for stage I-II Hodgkin's disease.

This study presents the analysis of results obtained in 237 Hodgkin's disease patients, stages I and II, treated with combined modality therapy. The overall and disease-free survival rates at 5 years were 96.6 and 85.2%, respectively. The study has demonstrated the superiority of the following treatment program: one cycle of combination chemotherapy + radiation therapy + 5 cycles of combination chemotherapy. It has been found possible to reduce the number of radiation fields in combined modality therapy: for patients with stage IA-IIA lymphocyte predominant or nodular sclerosing Hodgkin's disease it was sufficient only to treat clinically involved sites. Short- and long-term consequences of combined modality therapy have been analysed.

Adult↗
PubMed2003

[Risk factors related with eating disorders in a community of adolescents].

OBJECTIVE: To detect risk factors related with eating disorders. DESIGN: Descriptive, cross-sectional study. SETTING: 5 secondary schools in the Virgen de Rocío health area in Seville, Spain. PARTICIPANTS: 789 students enrolled in the first and second years of compulsory secondary school, and their families. MAIN MEASURES. Body mass index, risk behaviors related with food and exercise, influence of the mass media on models of desirable body types, and family climate. Data were obtained with three validated questionnaires: the Eating Attitudes Test (EAT-40), the CIMEC-26, and the Family Environment Scale (FES). RESULTS: In 6.9% of the participants, BMI was between 15 and 17, reflecting slight malnutrition. On the EAT scale, 68 participants (8.8%) had scores that were indicative of illness or risk of illness, and 25 (3.3%) could be diagnosed as having eating behavior disorder according to DSM-IV criteria. According to the CIMEC questionnaire, 104 participants (13.5%) were found to be significantly vulnerable to media pressures, and 85 (11.1%) were considered highly vulnerable. Parents' comments on eating behavior were related with the results on the EAT-40 CIMEC questionnaires (P=.01). No statistically significant relationship was found between family climate scores and the scores on the EAT-40 or CIMEC questionnaires. Students in rural or suburban area schools scored higher on the EAT-40 (P=.04) and CIMEC (P=.01) than students in urban or city center schools. CONCLUSION: The identification of persons considered at risk will allow us to use primary prevention programs more efficiently.

Adolescent↗