SEARCH · Search PubMed

Results for “Dynamic Programming”

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.

SourceResearch connectionFrom yearThrough year

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

At least 1,513 records · Page 84Linked to original sources

PubMed2006

Interaction between the HIV-1 protein Vpr and the adenine nucleotide translocator.

The HIV-1 protein Vpr circulates in the serum of seropositive individuals and in the cerebrospinal fluid of AIDS patients with neurological disorders. Vpr triggers apoptosis of numerous cell types after extracellular addition, vpr gene transfer or in the context of viral infection. Moreover, in vivo, transgenic mice over-expressing Vpr have enhanced T lymphocytes apoptosis. In previous studies, we suggested that the Vpr apoptotic activities were because of its binding to the adenine nucleotide translocator (ANT), a mitochondrial ATP/ADP antiporter. To specify this interaction, fragments of both proteins were synthesized and used in biochemical and biophysical experiments. We demonstrate here that in vitro, the (27-51) and (71-82) Vpr peptides bind to a region encompassing the first ANT intermembrane space loop and part of its second and third transmembrane helices. Computational analysis using a docking program associated to dynamic simulations enabled us to construct a three-dimensional model of the Vpr-ANT complex. In this model, the N-terminus of Vpr plunges in the ANT cavity whereas the Vpr C-terminal extremity is located at the surface of the ANT allowing possible interactions with a third partner. These results could be used to design molecules acting as pro-apoptotic Vpr analogs or as apoptosis inhibitors preventing the Vpr-ANT interaction.

Animals↗

PubMed2000

Spatial expression of Hox cluster genes in the ontogeny of a sea urchin.

The Hox cluster of the sea urchin Strongylocentrous purpuratus contains ten genes in a 500 kb span of the genome. Only two of these genes are expressed during embryogenesis, while all of eight genes tested are expressed during development of the adult body plan in the larval stage. We report the spatial expression during larval development of the five 'posterior' genes of the cluster: SpHox7, SpHox8, SpHox9/10, SpHox11/13a and SpHox11/13b. The five genes exhibit a dynamic, largely mesodermal program of expression. Only SpHox7 displays extensive expression within the pentameral rudiment itself. A spatially sequential and colinear arrangement of expression domains is found in the somatocoels, the paired posterior mesodermal structures that will become the adult perivisceral coeloms. No such sequential expression pattern is observed in endodermal, epidermal or neural tissues of either the larva or the presumptive juvenile sea urchin. The spatial expression patterns of the Hox genes illuminate the evolutionary process by which the pentameral echinoderm body plan emerged from a bilateral ancestor.

Animals↗

PubMed2005

Directed migration of positively selected thymocytes visualized in real time.

Development of many vertebrate tissues involves long-range cell migrations. In most cases, these migrations have been inferred from analysis of single time points and the migration process has not been directly observed and quantitated in real time. In the mammalian adult thymus, immature CD4+ CD8+ double-positive (DP) thymocytes are found in the outer cortex, whereas after T cell antigen receptor (TCR) repertoire selection, CD4+ CD8- and CD4- CD8+ single-positive (SP) thymocytes are found in the central medulla. Here we have used two-photon laser-scanning microscopy and quantitative analysis of four-dimensional cell migration data to investigate the movement of thymocytes through the cortex in real time within intact thymic lobes. We show that prior to positive selection, cortical thymocytes exhibit random walk migration. In contrast, positive selection is correlated with the appearance of a thymocyte population displaying rapid, directed migration toward the medulla. These studies provide our first glimpse into the dynamics of developmentally programmed, long-range cell migration in the mammalian thymus.

Animals↗

PubMed2004

[Evaluation of students and teachers concerning the "Vital Signs" software].

This article had for objective to get students' and teacher's opinions about "Vital Signals" software. The investigation was developed in the Nursing Department of the Federal University of Ceará. The sample population was a total of 6 students and 3 teachers, who were submitted to an interview after using the software. The interviews generated 10 categories, which were separated in two themes: Features which stimulated the use of the "Vital Signals" software; and software educationally correct. The results showed that the teachers valued the correction of the content, while the students focused more on the dynamics of the program.

Education, Nursing↗

PubMed2006

Connecting: perceptions of becoming a faculty mentor.

The school of nursing faculty at a liberal arts university created an innovative group-mentoring course to support students' progression through the undergraduate nursing program. The foundation of the mentoring program is the dynamic relationship between novice and expert. Students are enrolled in this one-hour course for each of their four semesters in the upper division nursing curriculum. Group membership (faculty and students) is consistent throughout this time. The mentoring course requires faculty to lead a process-oriented group. Faculty are confident in teaching courses that are content-driven but have struggled with the unstructured nature of facilitating a process-oriented group. Therefore, the role of group mentor has been identified by faculty as very challenging.The purpose of this study was to explore faculty members' perceptions of assuming the role of a group mentor. Eight subjects participated in audio-taped interviews guided by open-ended questions. Four themes emerged including uncertainty, evolution, mutuality, and milieu.

Curriculum↗

PubMed2000

Computational fluid dynamics as a method for assessing fume cupboard performance.

A commercially available computational fluid dynamic (CFD) software program, specific for HVAC systems, was used to study the performance of an aerodynamic fume cupboard. The numerical results showed good qualitative agreement with physical measurements giving confidence in the CFD model to simulate and predict overall fume cupboard performance. However, there were some quantitative differences specifically around 'aerodynamic' features that could not be accurately simulated by the software code. The CFD model was clearly able to demonstrate differences in performance between good and bad cupboard designs, and show the importance of using rear baffles and lipfoils. It also showed the importance of good design features when a 'worker' was standing against the front edge or when there were draughts in front of the aperture. The computer model was used to simulate the gas tracer containment test method described in BS 7258 (1994) [Laboratory Fume Cupboards], and had a much greater sensitivity than the recommended physical measuring instruments. The results given in this paper demonstrate the potential for using a commercially available software package for the optimisation of fume cupboard design and testing. It also indicates the economy of using CFD compared with building a prototype and testing a model.

Air Pollution, Indoor↗

PubMed2000

Numerical simulation of a child restraint system in an aircraft crash-test.

Studies conducted at the FAA Civil Aeromedical Institute have shown that when used in aircraft, automotive child restraint devices do not always provide the level of safety desired. Various factors that contribute to poor performance, such as seat belt anchor location, cushion stiffness, and child restraint device design features, were evaluated by a dynamic impact test program. To efficiently continue the research, a computer model was developed using MADYMO. Results of two of the impact tests were used to validate the model. Both test configurations utilized a typical commercial transport airplane passenger seat and a popular automotive child restraint device. These tests were considered representative of the extremes of child restraint device and occupant kinematics due to variance in seat belt anchor location. Details are presented of the test parameters and geometry, as well as cushion and restraint system properties. Test and modelling results for these two impact conditions are summarized and compared. Parametric studies were then conducted that used the model to investigate the effect of cushion stiffness, belt anchor spacing, and initial belt tension.

Accidents, Aviation↗

PubMed2001

Rational procedure for 3D-QSAR analysis using TRNOE experiments and computational methods: application to thermolysin inhibitors.

The success or failure of 3D QSAR, particularly CoMFA, is most strongly dependent, especially for flexible compounds, on the conformation of the molecule used in the analysis, and on the orientation of the molecule relative to the other molecules in 3D space (i.e., alignment). The present study suggests a rational procedure for the estimation of binding conformation that uses the transferred nuclear Overhauser effect (TRNOE) experiment in combination with conformational analysis using CAMDAS (Conformational Analyzer with Molecular Dynamics And Sampling) program that is developed in our laboratory. In the next step the TRNOE-obtained conformation can be used as a reference template in order to obtain alignment of other ligands, that have a common binding site. In this step we used the SUPERPOSE program created in our laboratory, in order to estimate the binding conformation of other compounds, and to simultaneously obtain the alignment of compounds for CoMFA. The resulting CoMFA models could be expected to closely reproduce the interaction mode with protein represented by the reported X-ray results. In order to confirm the validity of our procedure described above, we show its application in obtaining CoMFA models of thermolysin inhibitors. We obtained twenty CoMFA models, and that with the highest q2 value (q2 = 0.701) was found to provide an interaction mode very similar to that represented by the X-ray results.

Molecular Conformation↗

PubMedDate not supplied

Combined instabilities of the knee.

A knee with a combination of instabilities in very difficult to restore to a completely stable condition. The ligamentous structure of the knee is a functional unit. Laxity in any of the planes of the knee motion can produce increased stretching and stress to the structures, which help to provide stability in the other planes. Since it is almost impossible to restore the knee to the pre-injury state, residual laxity in different planes of motion is going to produce increasing stress to the other components, which may have been restored to a greater degree of stability. This emphasizes the importance of a good muscular rehabilitation program and a dynamic component to knee reconstructive procedures to protect against this eventuality. Passive laxity, if present, should not be taken as a sign of failure of the procedure. Often the patient's assessment of his functional capabilities have improved after the reconstructive procedures.

Casts, Surgical↗

PubMed1994

Detection of the new tuberculosis: ocular examination as a diagnostic imperative.

BACKGROUND: Until recently, tuberculosis in the U.S. had been considered a public health concern of the past, largely conquered by therapy devised in the 1950s. However, in the past several years, the incidence of tuberculosis has increased steeply and unexpectedly, owing to a conspiracy of new factors. These include: the epidemic of acquired immune deficiency, the emergence of drug-resistant strains, the confinement of susceptibles in crowded shelters, and the premature demolition of public health programs. METHODS: A dynamic interplay exists between the tubercle bacillus and the declining immune system in AIDS patients. Because of this, many atypical, clinical presentations of tuberculosis have emerged. RESULTS: The detection of ocular manifestations of tuberculosis has thus assumed increased importance. It can allow not only for an earlier diagnosis of TB, but an earlier diagnosis of AIDS, preventing spread of both diseases within the population. CONCLUSIONS: Evaluation of ocular signs of tuberculosis should now be a diagnostic imperative.

AIDS-Related Opportunistic Infections↗

PubMed1997

Constitution and solution conformation of the antibiotic mersacidin determined by NMR and molecular dynamics.

The solution structure of the tetracyclic lantibiotic mersacidin in methanol (CD3OH) has been determined by NMR followed by distance bound driven dynamics and subsequent restrained molecular dynamics simulations combined with an iterative relaxation matrix approach and alternatively by a simulated annealing protocol. The molecular dynamics simulations were performed with the AMBER program system and with the INSIGHT program package. The distance bound driven dynamics calculation was conducted using a modified version of the DISGEO II program. The interproton distance restraints were derived from jump symmetrized rotating-frame Overhauser enhancement and exchange (JS-ROESY) spectra, which yield optimum sensitivity for medium-sized molecules like mersacidin. The connectivities via the sulfide bridges were unambiguously confirmed by heteronuclear NMR techniques (heteronuclear single quantum coherence and heteronuclear multiple bond correlation methods). Due to the tetracyclic structure, mersacidin exhibits a rather rigid globular shape, which neither belongs to the duramycin nor to the nisin structure type lantibiotics. The resulting structures for the simulated annealing protocol of restrained and subsequent free molecular dynamics were compared and found to be very similar.

Amino Acid Sequence↗

PubMed2002

Fold prediction of helical proteins using torsion angle dynamics and predicted restraints.

We describe a procedure for predicting the tertiary folds of alpha-helical proteins from their primary sequences. The central component of the procedure is a method for predicting interhelical contacts that is based on a helix-packing model. Instead of predicting the individual contacts, our method attempts to identify the entire patch of contacts that involve residues regularly spaced in the sequences. We use this component to glue together two powerful existing methods: a secondary structure prediction program, whose output serves as the input to the contact prediction algorithm, and the tortion angle dynamics program, which uses the predicted tertiary contacts and secondary structural states to assemble three-dimensional structures. In the final step, the procedure uses the initial set of simulated structures to refine the predicted contacts for a new round of structure calculation. When tested against 24 small to medium-sized proteins representing a wide range of helical folds, the completely automated procedure is able to generate native-like models within a limited number of trials consistently.

Algorithms↗

PubMed2004

[Effects of training on static and dynamic balance in elderly subjects who have had a fall or not].

OBJECTIVE: To evaluate the effects of a physical training program on static and dynamic balance during single and dual task conditions in elderly subjects who have had a fall or not. PATIENTS: Two groups, comprising a total of 33 elderly subjects, were trained: 16 who had a fall were 69.2 +/- 5.0 years old and 17 who had not had a fall were 67.3 +/- 3.8 years. METHODS: All subjects underwent an unipedal test with eyes open and eyes closed, followed by gait assessment during single and dual motor task conditions, before and after a physical training program. RESULTS: All subjects showed a significant decrease, by six times for subjects who had fallen and four times by those who had not, in the number of touch-downs in the unipedal test with eyes open (P < 0.05), and by 2.5 and 2 times, respectively, with eyes closed (P < 0.05) after the training program. All subjects showed a significant increase in speed (P < 0.05), cadence (P < 0.05) and stride length (P < 0.05) and a significant decrease in the single support time (P < 0.05) and stride time (P < 0.05) in gait assessment during single and dual task conditions after the training program. During the training program, no subjects fell. CONCLUSION: The physical training program improved static balance and quality of gait in elderly subjects who had had a fall and those who had not, which could contribute to minimizing and/or retarding the effects of aging and maintaining physical independence.

Accidental Falls↗

PubMed2005

Multisite protein modification and intramolecular signaling.

Post-translational modification is a major mechanism by which protein function is regulated in eukaryotes. Instead of single-site action, many proteins such as histones, p53, RNA polymerase II, tubulin, Cdc25C and tyrosine kinases are modified at multiple sites by modifications like phosphorylation, acetylation, methylation, ubiquitination, sumoylation and citrullination. Multisite modification on a protein constitutes a complex regulatory program that resembles a dynamic 'molecular barcode' and transduces molecular information to and from signaling pathways. This program imparts effects through 'loss-of-function' and 'gain-of-function' mechanisms. Among the latter, covalent modifications specifically recruit a diverse array of modules, including the SH2 domain, 14-3-3, WW domain, Polo box, BRCT repeat, bromodomain, chromodomain, Tudor domain and motifs binding to ubiquitin and other protein modifiers. Such recruitments are often modulated by modifications occurred at neighboring and distant sites. Multisite modification thus coordinates intermolecular and intramolecular signaling for the qualitative and quantitative control of protein function in vivo.

Acetylation↗

PubMed2005

Issues and challenges in international doctoral education in nursing.

Education is a driving force in improving the health and welfare of communities globally. Doctoral education of nurses has been identified as a critical factor for provision of leadership in practice, scholarship, research, policy and education. Since the genesis of doctoral education in nursing in the USA in the 1930s, this movement has burgeoned to over 273 doctoral programs in over 30 countries globally. The present article seeks to identify the issues and challenges in nursing doctoral education globally, and those encountered by doctoral program graduates in meeting the challenges of contemporary health care systems. Information was derived from a comprehensive literature review. Electronic databases and the Internet, using the Google search engine, were searched using the key words "doctoral education"; "nursing"; "International Network for Doctoral Education in Nursing"; "global health"; "international research collaboration". Doctoral education has been a critical force in developing nurse leaders in education, management, policy and research domains. An absence of consensus in terminology and of accurate minimum data sets precludes comparison and debate across programs. The complexity and dynamism of contemporary globalized communities render significant challenges in the conduct of doctoral programs. Addressing funding issues and faculty shortages are key issues for doctoral programs, especially those in developing countries, to achieve an identity uniquely their own. These challenges can also afford considerable opportunities for discussion, debate and the formulation of innovative and collaborative solutions to advance nursing knowledge and scholarship. In spite of discrete differences between countries and regions, the similarities in the issues facing the development of doctoral programs internationally are more striking than the differences. The harnessing of a global collective to address these issues will likely serve to not only forge the future viability of doctoral education of nurses but to improve the health and well-being of communities. This paper proposes international collaborative strategies to address a number of the challenges identified.

Cooperative Behavior↗

PubMed1999

Integrating Application Programs for Bioinformatics Using a Web Browser.

We have constructed a general framework for integrating application programs with control through a local Web browser. This method is based on a simple inter-process message function from an external process to application programs. Commands to a target program are prepared in a script file, which is parsed by a message dispatcher program. When it is used as a helper application to a Web browser, these messages will be sent from the browser by clicking a hyper-link in a Web document. Our framework also supports pluggable extension-modules for application programs by means of dynamic linking. A prototype system is implemented on our molecular structure-viewer program, MOSBY. It successfully featured a function to load an extension-module required for the docking study of molecular fragments from a Web page. Our simple framework facilitates the concise configuration of Web softwares without complicated knowledge on network computation and security issues. It is also applicable for a wide range of network computations processing private data using a Web browser.

Journal Article↗

PubMedDate not supplied

Computer simulation of plasma insulin and glucose dynamics after subcutaneous insulin injection.

We developed a computer program for the simulation of plasma insulin and glucose dynamics after subcutaneous injection of insulin. The program incorporates a pharmacokinetic model to calculate the time courses of plasma insulin for various combinations of popular preparations (regular, NPH, lente, and ultralente). With the use of a pharmacodynamic model describing the dependence of glucose dynamics on plasma insulin and glucose levels, the program can predict the expected time course of plasma glucose in response to a change in carbohydrate intake, insulin dose, timing, or regimen. A set of typical parameters has been obtained by analysis of data from the literature. The results of several computer simulations are presented showing the effect on a 24-h insulin and glucose profile of systematically changing insulin regimen, dose, timing of meals, or timing of preprandial insulin administration. The program can be used to explore on a theoretical basis the impact of various factors associated with glycemic control in insulin-dependent diabetes mellitus. As an educational tool, the program provides a realistic environment for demonstration of the combined or isolated effects of insulin and diet on glycemia.

Absorption↗

PubMed2003

QM/MM calculations of kinetic isotope effects in the chorismate mutase active site.

Kinetic isotope effects have been computed for the Claisen rearrangement of chorismate to prephenate in aqueous solution and in the active site of chorismate mutase from B. subtilus. These included primary 13C and 18O and secondary 3H effects for substitutions at the bond-making and bond-breaking positions. The initial structures of the putative stationary points on the potential energy surface, required for the calculations of isotope effects using the CAMVIB/CAMISO programs, have been selected from hybrid QM/MM molecular dynamical simulations using the DYNAMO program. Refinement of the reactant complex and transition-state structures has been carried out by means of AM1/CHARMM24/TIP3P calculations using the GRACE program, with full gradient relaxation of the position of > 5200 atoms for the enzymic simulations, and with a box containing 711 water molecules for the corresponding reaction in aqueous solution. Comparison of these results, and of gas phase calculations, with experimental data has shown that the chemical rearrangement is largely rate-determining for the enzyme mechanism. Inclusion of the chorismate conformational pre-equilibrium step in the modelled kinetic scheme leads to better agreement between recent experimental data and theoretical predictions. These results provide new information on an important enzymatic transformation, and the key factors responsible for the kinetics of its molecular mechanism are clarified. Treatment of the enzyme and/or solvent environment by means of a large and flexible model is absolutely essential for prediction of kinetic isotope effects.

Bacillus subtilis↗