Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Packaging”

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 1,351 records · Page 75Linked to original sources
PubMed1994

GREEN: a program package for docking studies in rational drug design.

A program package, GREEN, has been developed that enables docking studies between ligand molecules and a protein molecule. Based on the structure of the protein molecule, the physical and chemical environment of the ligand-binding site is expressed as three-dimensional grid-point data. The grid-point data are used for the real-time evaluation of the protein-ligand interaction energy, as well as for the graphical representation of the binding-site environment. The interactive docking operation is facilitated by various built-in functions, such as energy minimization, energy contribution analysis and logging of the manipulation trajectory. Interactive modeling functions are incorporated for designing new ligand molecules while considering the binding-site environment and the protein-ligand interaction. As an example of the application of GREEN, a docking study is presented on the complex between trypsin and a synthetic trypsin inhibitor. The program package will be useful for rational drug design, based on the 3D structure of the target protein.

Algorithms↗
PubMed1990

The cis-acting DNA sequences required in vivo for bacteriophage Mu helper-mediated transposition and packaging.

The 37,000 bp double-stranded DNA genome of bacteriophage Mu behaves as a plaque-forming transposable element of Escherichia coli. We have defined the cis-acting DNA sequences required in vivo for transposition and packaging of the viral genome by monitoring the transposition and maturation of Mu DNA-containing pSC101 and pBR322 plasmids with an induced helper Mu prophage to provide the trans-acting functions. We found that nucleotides 1 to 54 of the Mu left end define an essential domain for transposition, and that sequences between nucleotides 126 and 203, and between 203 and 1,699, define two auxiliary domains that stimulate transposition in vivo. At the right extremity, the essential sequences for transposition require not more than the first 62 base pairs (bp), although the presence of sequences between 63 and 117 bp from the right end increases the transposition frequency about 15-fold in our system. Finally, we have delineated the pac recognition site for DNA maturation to nucleotides 32 to 54 of the Mu left end which reside inside of the first transposase binding site (L1) located between nucleotides 1-30. Thus, the transposase binding site and packaging domains of bacteriophage Mu DNA can be separated into two well-defined regions which do not appear to overlap.

Bacteriophage mu↗
PubMed1987

Upper limit for DNA packaging by Bacillus subtilis bacteriophage phi 105: isolation of phage deletion mutants by induction of oversized prophages.

We have determined the upper size limit for DNA packaging in Bacillus subtilis bacteriophage phi 105 by examining the plaque-forming and transducing capabilities of lysates made from strains containing prophages of various sizes. The upper size limit for efficient packaging of the phage genome appears to be about 40.2 kb, which is about 1 kb larger than the wild-type genome. This places an upper limit of about 5 kb on the size of insertions that can be accommodated in phi 105 transfection cloning vectors, such as phi 105J27. Induction of prophages that exceed that upper limit, followed by selection for plaque formation or transduction, provides a powerful means of isolating phage deletion mutants. A comparison of the location of each deletion with the resultant phenotype has enabled us to identify non-essential regions of the phage genome, and regions that are required for tail biosynthesis and for host cell lysis.

Bacillus subtilis↗
PubMed1988

Molecular analysis of the packaging signal in bacteriophage CP-T1 of Vibrio cholerae.

We have previously identified a unique site, pac, from which packaging of precursor concatameric viral DNA into proheads starts during the maturation process of bacteriophage CP-T1. The direction of this packaging was determined from restriction enzyme cleavage patterns of CP-T1 DNA. A restriction enzyme generated fragment containing pac was cloned and the surrounding DNA region sequenced. Analysis of the nucleotide sequence revealed numerous repeat regions related to the consensus sequence PuagttGAT.AAT.aa.t. Within the sequenced region an open reading frame encoding a 12260 Mr protein was also identified. This protein appears to share homology with the binding domains of known DNA binding proteins and may represent a putative Pac terminase possessing the specific endonuclease activity required for cleavage at the pac site. Minicell analysis of deletion derivatives of the pac-containing clone revealed a protein of approximately 12,900 Mr encoded within this same region, confirming that this Pac protein is phage encoded.

Amino Acid Sequence↗
PubMed1984

pac sites are indispensable for in vivo packaging of DNA by phage P22.

F' pro+ plasmids were selected and used as donors to prepare P22 transducing phages. Two types of result were observed. pro+ from type I donors cannot be packaged by wild-type P22 to yield transducing particles unless a prophage pac site is introduced into the plasmid. Transposon Tn10 also allows initiation of packaging. pro+ from type II plasmids can be transduced with the same efficiency as pro+ DNA on the chromosome, indicating that a chromosomal pac site was included when the F' pro+ was excised from the Hfr strain. The usefulness of type I plasmids as a test substrate for pac signals is discussed.

Chromosome Deletion↗
PubMed1989

A generalized laboratory software package--a prototype approach.

A prototyped model of a generalized table-driven software package for laboratory testing and results registration is presented. The need to computerize dozens of laboratories performing hundreds of tests, called for a radical approach which would enable the quick addition of new laboratories to the system, as well as ease of maintenance. The generalized laboratory software package (GLAB) relies on a set of data tables, maintained by users, and a menu controlled environment interfacing GLAB with the rest of the hospital's systems.

Clinical Laboratory Information Systems↗
PubMed1982

Dielectric relaxation studies of ionic processes in lysolecithin-packaged gramicidin channels.

Dielectric permitivities have been determined for suspensions of lysolecithin packaged malonyl gramicidin channels over the frequency range of 5 kHz to 900 MHz and under conditions of approximately equimolar concentrations (approximately 10mM) of channels and salts. The salts were lithium chloride, sodium chloride and thallium acetate. A relaxation process unique to the thallium acetate-channel system was observed which on analysis gave rise to a relaxation time at 25 degrees of 120 msec. The permitivity data, as well as a comparison of binding constants, indicate that the relaxation process results from TI+ being bound within the channel and more specifically from an intrachannel ion translocation with a rate constant of approximately 4 x 10(6) sec-1 and with an energy of activation of less than 6.7 kcal/mole. These data compare favorably with data from conductance studies on planar bilayers and with ion and carbon-13 nuclear magnetic studies on the lysolecithin packaged malonyl gramicidin channels which combine to indicate that the relaxation process is due to the jump of the thallium ion across a central barrier.

Circular Dichroism↗
PubMed1980

Demonstration of a software package for the reconstruction of the dynamically changing structure of the human heart from cone beam x-ray projections.

The Dynamic Spatial Reconstructor (DSR) is a device constructed at the Biodynamics Research Unit of the Mayo Clinic for (among other things) the visualization of the beating heart inside the intact thorax. The device consists of 28 rotating X-ray sources arranged on a circular arc at 6 degrees intervals (total span 162 degrees) and a matching set of 28 imaging systems. The whole thorax of the patient is projected onto the two-dimensional screen of the imaging systems by cone beams of X rays from the sources. All of the X-ray sources are switched on and off within a total period of 10 milliseconds. The Medical Image Processing Group at the State University of New York at Buffalo has developed a software package for the design and evaluation of algorithms to be used by the DSR. In this paper we illustrate the operation of the package and a particular algorithm for the reconstruction of the dynamically changing structure of the heart from data collected by the DSR.

Computers↗
PubMed1984

Development of a friendly, self-teaching, interactive statistical package for analysis of clinical research data. The BRIGHT STAT-PACK.

We have developed a new statistical analysis package for use by the clinical investigator, the clinician, and the laboratory researcher. This package attempts to implement the following philosophy: The programs should be essentially self-teaching, friendly, and forgiving; the programs should educate the user regarding the underlying theory, assumptions, and interpretation of the statistical methods involved; the programs should automatically test relevant assumptions and warn the user when these assumptions appear to have been violated; the programs should make recommendations about the availability of alternative statistical methods and automatically perform such analyses when indicated; the programs should interpret the results; and the programs should mimic, insofar as possible, the logic used in a routine, elementary statistical consultation. Several programs have been developed, extensively tested, and used.

Computer-Assisted Instruction↗
PubMed2001

Java-based graphical user interface for the MRUI quantitation package.

This article describes the Java-based version of the magnetic resonance user interface (MRUI) quantitation package. This package allows MR spectroscopists to easily perform time-domain analysis of in vivo MR spectroscopy data. We show that the Java programming language is very well suited for developing highly interactive graphical software applications such as the MRUI software. We have also established that MR quantitation algorithms, programmed in other languages, can easily be embedded into the Java-based MRUI by using the Java native interface (JNI). This new graphical user interface (GUI) has been conceived for the processing of large data sets and uses prior knowledge data-bases to make interactive quantitation algorithms more userfriendly.

Algorithms↗
PubMed2001

Bioactivities of culture supernatants from retroviral packaging cells carrying the mouse Fas ligand gene.

The bioactivities of culture supernatants from retroviral packaging cells carrying the mouse Fas ligand (mFasL) gene was investigated. FasLcDNA was cloned into PLXIN with an internal ribosome entry site to link two cistrons through gene recombination technology, PLXIN and the recombinant vector PLFIN were separately transfected into PA317 retrovirus packing cell line by lipofectamine 2000, and the resistant clones were selected with G418 selective medium. The integration of genome DNA was assayed by genomic DNA PCR. NIH3T3 cells were transduced by the culture supernatants from PA317 carrying the mFasLcDNA gene, and were selected with G418 selective medium, so as to select the PLFIN-PA317 clone capable of producing higher titer of supernatants. The levels of mFasL protein on NIH3T3 cells membrane were assayed by flow cytometry (FCM). The biological activity of mFasL on NIH3T3 cells membrane was investigated by the inducing apoptosis of Fas+ Yac-1 cells co-cultured with NIH3T3 cells expressing Fas ligand. To explore the direct mFasL cytotoxicity of culture supernatants from retroviral packaging cells carrying the mFasL gene, the culture supernatants from PLFIN-PA317 and PLXIN-PA317 were separately co-cultured with Yac-1 cells in parallel. The recombinant PLFIN was successfully constructed. The highest titer of supernatants from twelve resistant clones was 8.5 x 10(5) colony-forming-unit (CFU)/ml. The NIH3T3 cells transfected by above supernatants had a higher level of mFasL (53.81 +/- 6.9%), and significantly induced the apoptosis of Fas+ Yac-1 cells (56.78 +/- 4.5%), as both were cocultured for 5 h at 1:1 ratio, whereas it is 7.08 +/- 3.4% in control group (P < 0.01). Supernatant from PLFIN-PA317 could also directly induce the apoptosis of Yac-1 within 5 h of incubation. Thus, the culture supernatants from PLFIN-PA317 possessed both infectivity and cytotoxicity of mFasL.

3T3 Cells↗
PubMed2006

Hexameric molecular motors: P4 packaging ATPase unravels the mechanism.

Genome packaging into an empty capsid is an essential step in the assembly of many complex viruses. In double-stranded RNA (dsRNA) bacteriophages of the Cystoviridae family this step is performed by a hexameric helicase P4 which is one of the simplest packaging motors found in nature. Biochemical and structural studies of P4 proteins have led to a surprising finding that these proteins bear mechanistic and structural similarities to a variety of the pervasive RecA/F1-ATPase-like motors that are involved in diverse biological functions. This review describes the role of P4 proteins in assembly, transcription and replication of dsRNA bacteriophages as it has emerged over the past decade while focusing on the most recent structural studies. The P4 mechanism is compared with the models proposed for the related hexameric motors.

Adenosine Triphosphatases↗
PubMed2006

A package of interventions to reduce school dropout in public schools in a developing country. A feasibility study.

OBJECTIVE: School dropout rates are staggeringly high in developing countries, even for elementary school children. This study aims to assess the feasibility and initial efficacy of a package of interventions tailored to reduce school dropout in public schools in an urban city in Brazil. METHOD: Two public schools with similar high rates of dropout in elementary grades were selected. In one of them, a package of universal preventive interventions was implemented during a school year, including two workshops with teachers, five informative letters to parents, three meetings with parents at school, a telephone helpline at school, and a 1-day cognitive intervention. For children who stayed ten consecutive days out of school without reason, mental health assessment and referral to mental health services in the community were offered. In the second school, no intervention was implemented. RESULTS: After this 1-year intervention, there were significant differences between the two schools in rates of both dropout (P < 0.001) and absenteeism in the last trimester (P < 0.05; effect size = 0.64). In the intervention school, 18 (45%) youths returned to school after intervention among the 40 at-risk students. Moderate engagement of school staff was the main logistic problem. CONCLUSIONS: Our findings suggest that programs combining universal primary preventive strategies and interventions focused on at-risk students can be implemented and useful in developing countries to reduce school dropout.

Adolescent↗
PubMed2005

Use of 3D imaging in CT of the acute trauma patient: impact of a PACS-based software package.

To evaluate the impact of a picture archiving and communication systems (PACS)-based software package on the requests for 3D reconstructions of multidetector CT (MDCT) data sets in the emergency radiology of a level 1 trauma center, we reviewed the number and type of physician requests for 3D reconstructions of MDCT data sets for patients admitted after sustaining multiple trauma, during a 12-month period (January 2003-December 2003). During the first 5 months of the study, 3D reconstructions were performed in dedicated workstations located separately from the emergency radiology CT interpretation area. During the last 7 months of the study, reconstructions were performed online by the attending radiologist or resident on duty, using a software package directly incorporated into the PACS workstations. The mean monthly number of 3D reconstructions requested during the two time periods was compared using Student's t test. The monthly mean +/- SD of 3D reconstructions performed before and after 3D software incorporation into the PACS was 34+/-7 (95% CI, 10-58) and 132+/-31 (95% CI, 111-153), respectively. This difference was statistically significant (p<0.0001). In the multiple trauma patient, implementation of PACS-integrated software increases utilization of 3D reconstructions of MDCT data sets.

Emergency Service, Hospital↗
PubMed1981

Poison Prevention Packaging Act, 1970: A human factors standard.

This paper, the first of two, gives an account of legislation and regulations made in the USA requiring hazardous pharmaceutical and other household products to be packaged in child-resistant containers. Human factors test procedures and standards, in terms of which child-resistance is defined, are described. An account is given of those hazardous substances which regulations in the USA require should be packed in child-resistant containers. The paper concludes with a description of the effects of the regulations and of child-resistant containers in reducing mortality and morbidity associated with the ingestion of poisonous substances, particularly aspirin, in the USA. The second paper will briefly describe the effects of legislation made in England and Wales requiring certain pharmaceutical products to be packaged in child-resistant containers. It will also give an account of experiments, carried out in England and Sweden, describing the difficulties and inconvenience which the elderly and disabled experience when they attempt to use such containers.

Journal Article↗
PubMed1991

Intervention package for treating sleep disorders in a four-year-old girl.

The study describes an intervention package for the treatment of sleep disorders in a 4-year-old girl, using a multiple-baseline design. The subject's sleep disorders included several undesirable habits: never going to sleep in her own bed; waking up several times during the night, screaming and shouting for hours; and entering her parents' bed and insisting on staying there. The intervention package was carried out with the parents, the child, and her sister. It was based on the disconnection of the contingencies between behavior and outcome; rewards; praise; and time-out. The whole process was terminated in 8 weeks, and maintenance levels were assessed via follow-up after three and six months.

Behavior Therapy↗
PubMed1979

A data analysis microcomputer package (DAMP) for biomedical signals.

The advent of cheap, powerful microcomputer systems makes the analysis of data via sophisticated techniques available to the personnel who are non-specialists in computing systems. The DAMP package described here is intended for use on personal computers and has therefore been written in BASIC for portability. The analysis techniques are powerful, comprising algorithms to perform sample-data generation, plotting displays, digital data filtering, auto-correlation functions, fast Fourier transforms and autoregressive modelling. The last technique contains a number of options including the display of z-plane plots, frequency response of the model, residual plotting and auto-correlation of the residuals. Illustrative results are shown from psychological mood data and rat locomotor activity. The package is designed both to instruct a user in the techniques of spectral analysis, and also to provide a range of methods for investigating time and frequency behaviour of biomedical data.

Biomedical Engineering↗
PubMedDate not supplied

NEUREC - a program package for 3D-reconstruction from serial sections using a microcomputer.

A software package is described to reconstruct three-dimensional pictures in true perspective from a series of parallel sections using a low-cost computer system (Apple II plus). Data sampling via a graphic tablet and graphical output on the monitor screen or a digital plotter are assigned to different programs under control of a menu program. The number of data representing the object under study is unlimited. Originally written in BASIC, the programs were translated to machine language. As an application of the package, reconstructions of an identified large interneuron of the locust brain are presented.

Animals↗