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Differences in conformational behavior of ATA and TAT sequences in single strand DNA trimer.

The conformational behavior of single strand (ss) TAT and ATA trimers of DNA have been studied by computational chemistry tools including CICADA software interfaced with AMBER molecular mechanics and dynamics. The Single-Coordinate-Driving (SCD) method has been used in conjunction with molecular dynamics simulated annealing. It has been revealed that the conformational flexibility of each sequence differs substantially from the other one. Four common conformational families have been found for both trimers. These are: helical, reverse-stacked (base 3), half-stacked (base 3), reverse-stacked (base 1). However, the energies of conformers representing the families are different for both the studied systems. An additional conformational family, bulged, has been found for ss(ATA), while ss(TAT) has been found also in half-stacked (base 1) conformation. In general, ss(TAT) exhibits a higher number of low energy conformations while ss(ATA) shows one interesting low energy conformational interconversion between reverse-stacked (A3) family and half-stacked (A3) family. The high conformational variability of the trimers has been confirmed by flexibility analysis and by molecular dynamics simulations, which have also shown the conformational stability of single conformational families. It has been concluded that the methodology used is able to provide a very detailed picture of the conformational space of these molecules.

Computer Simulation↗

Sex discrepancy in the canal/body ratio of the cervical spine implicating the prevalence of cervical myelopathy in men.

STUDY DESIGN: A radiographic analysis of the cervical spine in healthy young adults. OBJECTIVES: To investigate the size correlations among the vertebral height, the anteroposterior diameter of the vertebral body, and the anteroposterior diameter of the spinal canal and to investigate the sex discrepancy of the canal/body ratio. SUMMARY OF BACKGROUND DATA: Narrow spinal canal, large vertebral body, and male gender have been thought to be risk factors for cervical myelopathy. However, the association among those risk factors has been seldom analyzed. METHODS: The height and the anteroposterior diameter of the vertebral body as well as the anteroposterior diameter of the spinal canal were measured on the lateral radiographs of healthy young adults (105 men and 114 women) using a distance-measuring tool of computer software. The canal/body ratio was compared between men and women. RESULTS: The height and the anteroposterior diameter of the vertebral body were both larger in males than in females throughout C3-C7, but the anteroposterior diameter of the spinal canal was similar for both sexes. The height of the vertebral body was not correlated with the spinal canal size at any measured segment in both sexes, whereas the anteroposterior diameter of the vertebral body was significantly correlated with the size of the spinal canal in males but not in females. The canal/body ratio was significantly larger in women than in men. CONCLUSIONS: A significantly small canal/body ratio in men may implicate the male prevalence of cervical myelopathy.

Adult↗

Computer simulation of the human respiratory system for educational purposes.

The main objective of this study was the development of a computer simulation system for the human respiratory system, in order to educate students of nursing. This approach was based on existing mathematical models and on our own constructed specific functions. For the development of this educational tool the appropriate software packages were used according to the special demands of this process. This system is called ReSim (Respiratory Simulation) and consists of two parts: the first part deals with pulmonary volumes and the second one represents the mechanical behavior of lungs. The target group evaluated ReSim. The outcomes of the evaluation process were positive and helped us realize the system characteristics that needed improvements. Our basic conclusion is that the extended use of such systems supports the educational process and offers new potential for learning.

Anatomy↗

Proteomics: recent applications and new technologies.

Interest in proteomics as a tool for drug development and a myriad of other applications continues to expand at a rapid rate. Proteomic analyses have recently been conducted on tissues, biofluids, subcellular components and enzymatic pathways as well as various disease and toxicological states, in both animal models and man. In addition, several recent studies have attempted to integrate proteomics data with genomics and/or metabonomics data in a systems biology approach. The translation of proteomic technology and bioinformatics tools to clinical samples, such as in the areas of disease and toxicity biomarkers, represents one of the major opportunities and challenges facing this field. An ongoing challenge in proteomics continues to be the analysis of the serum proteome due to the vast number and complexity of proteins estimated to be present in this biofluid. Aside from the removal of the most abundant proteins, a number of interesting approaches have recently been suggested that may help reduce the overall complexity of serum analysis. In keeping with the increasing interest in applications of proteomics, the tools available for proteomic analyses continue to improve and expand. For example, enhanced tools (such as software and labeling procedures) continue to be developed for the analysis of 2D gels and protein quantification. In addition, activity-based probes are now being used to tag, enrich and isolate distinct sets of proteins based on enzymatic activity. One of the most active areas of development involves microarrays. Antibody-based microarrays have recently been released as commercial products while numerous additional capture agents (e.g. aptamers) and many additional types of microarrays are being explored.

Animals↗

MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation.

BACKGROUND: The high-density oligonucleotide microarray (GeneChip) is an important tool for molecular biological research aiming at large-scale detection of small nucleotide polymorphisms in DNA and genome-wide analysis of mRNA concentrations. Local array data management solutions are instrumental for efficient processing of the results and for subsequent uploading of data and annotations to a global certified data repository at the EBI (ArrayExpress) or the NCBI (GeneOmnibus). DESCRIPTION: To facilitate and accelerate annotation of high-throughput expression profiling experiments, the Microarray Information Management and Annotation System (MIMAS) was developed. The system is fully compliant with the Minimal Information About a Microarray Experiment (MIAME) convention. MIMAS provides life scientists with a highly flexible and focused GeneChip data storage and annotation platform essential for subsequent analysis and interpretation of experimental results with clustering and mining tools. The system software can be downloaded for academic use upon request. CONCLUSION: MIMAS implements a novel concept for nation-wide GeneChip data management whereby a network of facilities is centered on one data node directly connected to the European certified public microarray data repository located at the EBI. The solution proposed may serve as a prototype approach to array data management between research institutes organized in a consortium.

Database Management Systems↗

Results of a community pharmacy-based breast cancer risk-assessment and education program.

We tested the hypothesis that an education program addressing breast cancer screening schedules and modalities coupled with a breast cancer risk assessment provided by community pharmacists can increase women's confidence in performing screening practices endorsed by the American Cancer Society (ACS). This randomized, paired, pre-post study was conducted in six community pharmacies and two health-screening fairs; subjects were 140 women over 18 years of age. The pharmacist-administered program used the Breast Cancer Risk-Assessment Tool (Gail model) software provided by the National Cancer Institute of the National Institutes of Health. In addition, pharmacists provided education and training on breast self-examination (BSE), clinical breast examination (CBE), and mammography. Adherence to ACS guidelines for monthly BSE increased from 31% to 56% (p<0.001) for all women 6 months after the program. Performance of monthly BSE by women considered at high risk for developing breast cancer increased from 20% to 60% (p<0.005). The mean number of BSEs performed over 6 months increased from 2.69 to 4.09 (p<0.001). Women's confidence performing correct BSE improved from 6.41 to 7.04 (p<0.001) on a scale of 0-10. Adherence to ACS guidelines for CBE and mammography did not reveal statistically significant improvements except for better adherence to CBE in women aged 40-49 years (81% to 97%, p<0.025). The strength of the pharmacists' intervention may not appear as manipulation of high-risk patients' behavior but as improvement of self-directed behaviors, such as BSE, across all age groups.

Adolescent↗

Electronic medical record systems as a basis for computer-based patient records.

In summation, some document imaging systems offer the capability to form what may be called electronic medical record (EMR) systems. These systems are adaptations of current paper-based record management systems into the digital environment, but they offer far more capabilities than strictly archival, historical functions. Some of the capabilities that create EMR systems will also be necessary for development of CPRs, these capabilities are listed as follows: mass storage and image management; direct capture, storage, and retrieval of digital information (native format); large volume, high-speed, client-server networks; multi-media information management; high-power, flexible database tools; workflow process software; flexible, full function security; user customizable features; and alerts and reminders. Selection and implementation of document imaging systems should, at present, be undertaken with great care to insure that the platform may be utilized to form an electronic medical record with a clear migration path to the CPR.

Database Management Systems↗

Data extraction and archiving for nursing research using a bedside clinical information system.

Institution wide use of an intensive care bedside information system creates the opportunity to make available vast amounts of clinical data to support research and quality improvement activities. Acting on this opportunity has required the development of several innovative approaches to transform this raw data into usable information. The process described herein uses commercially available software and hardware tools to extract on a daily basis, process and archive data for 7 intensive care units. Once this procedure is complete, attention is turned to using individual and combinations of data elements to build a higher level of information that more directly relates to the kinds of inquiries that help to address questions of outcome, and care quality.

Archives↗

Routine 3D treatment planning: opportunities, challenges, and hazards.

Three-dimensional (3D) treatment planning refers to the use of software and hardware tools to design and implement more accurate and conformal radiation therapy. This is a major advance in oncology that should lead to the reduction of treatment-associated morbidity and facilitate safe dose escalation for many tumor sites. This technology affords the incorporation of physiologic and anatomic information into the treatment planning process, further enhancing our ability to improve the therapeutic ratio. However, as with any new technology, care must be taken when applying it in the clinic. The introduction of 3D planning presents new challenges to existing quality assurance systems. These need to be addressed to maintain patient safety. Based on our experience with over 1,500 patients treated at Duke University, the benefits, challenges, and hazards of routine 3D treatment planning are discussed.

Dose Fractionation, Radiation↗

3D visualization and stereographic techniques for medical research and education.

While computers have been able to work with true 3D models for a long time, the same does not apply to the users in common. Over the years, a number of 3D visualization techniques have been developed to enable a scientist or a student, to see not only a flat representation of an object, but also an approximation of its Z-axis. In addition to the traditional flat image representation of a 3D object, at least four established methodologies exist: Stereo pairs. Using image analysis tools or 3D software, a set of images can be made, each representing the left and the right eye view of an object. Placed next to each other and viewed through a separator, the three dimensionality of an object can be perceived. While this is usually done on still images, tests at Mednet have shown this to work with interactively animated models as well. However, this technique requires some training and experience. Pseudo3D, such as VRML or QuickTime VR, where the interactive manipulation of a 3D model lets the user achieve a sense of the model's true proportions. While this technique works reasonably well, it is not a "true" stereographic visualization technique. Red/Green separation, i.e. "the traditional 3D image" where a red and a green representation of a model is superimposed at an angle corresponding to the viewing angle of the eyes and by using a similar set of eyeglasses, a person can create a mental 3D image. The end result does produce a sense of 3D but the effect is difficult to maintain. Alternating left/right eye systems. These systems (typified by the StereoGraphics CrystalEyes system) let the computer display a "left eye" image followed by a "right eye" image while simultaneously triggering the eyepiece to alternatively make one eye "blind". When run at 60 Hz or higher, the brain will fuse the left/right images together and the user will effectively see a 3D object. Depending on configurations, the alternating systems run at between 50 and 60 Hz, thereby creating a flickering effect, which is strenuous for prolonged use. However, all of the above have one or more drawbacks such as high costs, poor quality and localized use. A fifth system, recently released by Barco Systems, modifies the CrystalEyes system by projecting two superimposed images, using polarized light, with the wave plane of the left image at right angle to that of the right image. By using polarized glasses, each eye will see the appropriate image and true stereographic vision is achieved. While the system requires very expensive hardware, it solves some of the more important problems mentioned above, such as the capacity to use higher frame rates and the ability to display images to a large audience. Mednet has instigated a research project which uses reconstructed models from the central nervous system (human brain and basal ganglia, cortex, dendrites and dendritic spines) and peripheral nervous system (nodes of Ranvier and axoplasmic areas). The aim is to modify the models to fit the different visualization techniques mentioned above and compare a group of users perceived degree of 3D for each technique.

Adult↗

Effectively utilizing device maintenance data to optimize a medical device maintenance program.

Methods developed by the clinical engineering community and the principles outlined by ISO regulations for the application of risk management to medical devices were integrated to provide a basis for the unique optimization system implemented into the University Health Network medical device maintenance program. Device maintenance history data stored in the database is used to conduct a risk analysis and to compute predefined benchmarks to highlight groups of equipment for which the current maintenance regime is not optimal. Using a software data research tool we are able to investigate device history data and support alterations in maintenance intervals, user training, maintenance procedures, and/or device purchasing. These alterations are justified, documented, and monitored for risk in a continuous management cycle. The predicted benefits are an overall improvement in the reliability of the devices maintained, coupled with a drop in repetitive device checks that result in no measurable benefits.

Electronic Data Processing↗

Quantification of the lamina dura and dentin density in children.

This study used 150 periapical radiographs of primary mandibular molars along with an aluminum stepwedge consisting of 5 steps from 2 to 10mm which were exposed and developed under standard conditions. A Mustek (Taiwan, R.O.C.) flatbed scanner with transparency adapter was used to digitize the radiographs. A 600 dpi, 10 bit gray level scanning transparency scanning mode were used. The thickness of the lamina dura was measured with the electronic ruler whereas density of dentin was calculated using the density function of a software program (Image Tool 2.0). Dentin density of the bifuraction area was calculated as 7.42 +/- 37 mm=A1 in primary second molars and 11.02 +/- 1.37mm = A1 for permanent first molar teeth. Differences in the thickness of the lamina dura in primary posterior teeth ranged from 0.23 +/- 0.01mm to 0.42 +/- 0.01mm.

Alveolar Process↗

Terminology extraction from text to build an ontology in surgical intensive care.

In many medical fields, the maintenance of unabiguous terminologies, the comparison and aggregation of different terminologies go through the building of formal specialized clinical terminologies, the ontologies. In this paper, we describe the building of an ontology in the surgical intensive care medical domain. We considered textual reports as the main source of information and a natural language processing tool, the SYNTEX software, is used to build the ontology. We have tested the possibility for an expert to build a sizeable ontology in a reasonable time. The quality of the ontology has been evaluated according to its capacity to cover the ICD-10 terminology in the field. Examples of coding activity with the ontology are proposed and discussed.

Critical Care↗

PET/CT: panacea, redundancy, or something in between?

In the past decade, the integration of anatomic imaging and functional imaging has emerged as a new and promising diagnostic tool. Developments in software provided methods to integrate various modalities, such as PET, CT, MRI, and MR spectroscopy. The introduction of combined PET/CT scanners has boosted image fusion in this specific field and raised high expectations. Image fusion can be performed at 3 different levels: visual fusion, software fusion, and hardware fusion, each having strengths, weaknesses, and issues inherent to technique. Visual fusion is the traditional side-by-side reviewing of 2 separate modalities. Software image fusion provides evaluation of 2 modalities in 1 integrated image set. True hardware fusion of PET and CT does not exist at present. Currently, hardware fusion refers to a PET/CT scanner that consists of separate scanners, which positioned in line at a fixed distance, with projection of the PET image over the CT image. The suggested superiority of hardware fusion with these so-called hybrid PET/CT scanners over software fusion has sparked debate. Because scientific data that unequivocally show that state-of-the-art software fusion is less accurate than hardware fusion (as provided in hybrid PET/CT scanners) are unavailable, the primacy of a combined PET/CT scanner over stand-alone PET and CT is more a matter of belief than of science. Further research comparing the overall performance of PET/CT scanners with that of separate scanners with software for image fusion is much needed. The continuous development of better software for image fusion and respiratory and cardiac gating is also needed, not only for PET and CT imaging but also for fusion of PET with MRI and CT with MRI.

Artifacts↗

[Digitalizing in the orthodontic practice].

Orthodontists use several diagnostic aids for treatment planning and evaluation of treatment results. Most common are plaster casts, panoramic as well as cephalometric x-rays and often also intraoral and facial photographs. Nowadays digital alternatives are available for these diagnostic tools. Also many software programmes have been developed on subjects such as practice management and patient education. In the near future the 'paperless office' appears to become reality. In this article developments up to now are presented.

Cephalometry↗

TNEEL workshop. Interactive methods for teaching end-of-life care.

Nurse educators have identified lack of end-of-life content as a serious deficit in undergraduate nursing education. TNEEL, a new software program with tools for teaching end-of-life topics, was created to help educators overcome this problem. The authors implemented an experiential workshop to help educators learn how to use TNEEL's wide variety of educational tools. Trainers provided information about TNEEL and coached participants (N = 94) as they practiced using laptop computers to increase their familiarity and comfort in using the toolkit. Workshop participants completed pre- and posttest evaluations addressing their opinions and beliefs about using this computer tool. Findings support the workshop as an effective way to facilitate adoption of this innovative educational resource and support the development of a nation-wide training plan for TNEEL with experiential workshops.

CD-ROM↗

[Polymorphism analysis of 5' promotor region of BCR gene].

BACKGROUND & OBJECTIVE: BCR-ABL fusion gene is regarded as the molecular hallmark of chronic myelogenous leukemia (CML), and its expression is controlled by the BCR gene promoter. This study was designed to investigate the polymorphism of the promoter region of BCR gene, and its possible correlation with the disease. METHODS: A 1.13 kb fragment of BCR gene 5' promotor region was amplified and sequenced from 30 CML patients and 19 controls. Transcription factor binding sites and repeat sequences in this region were analyzed using softwares and online tools. RESULTS: Four novel single nucleotide polymorphisms (SNPs) and 3 bases different from the reference sequence were detected in the region studied. Among these 2 novel SNPs and 1 different base were located in or near several bases of binding sites. The gene frequencies of the novel SNPs had no significant difference between CML and control people. CONCLUSION: Sequence polymorphisms were found in the 5' promotor region of BCR gene, most of them being SNPs. No relativity can be validated between the SNPs and the disease. But it appears that some SNPs might have the probability of bringing influence to the transcription and expression of the gene.

Base Sequence↗

Wear of aluminum oxide antagonists by commercially available composites and compomers.

PURPOSE: To investigate the wear of aluminum oxide antagonists by 19 light curing, commercially available composites and compomers. The influence of the filler particle size of the composites, the filler particle material and the filler particle morphology was determined. METHODS: Occlusal contact wear of the antagonists was simulated in a sliding wear test. Eight antagonists and specimens of each material were tested in a pin-on-block design with oscillating sliding of an aluminum oxide antagonist (Degussit antagonist, 5 mm diameter). After 50,000 cycles the contact area was evaluated using a dedicated software (UTHSCA image tool for windows V 2.0) under a light microscope. The size of the contact area was measured. RESULTS: Three types of boundaries of the contact area could be observed: (1) Sharp boundary, (2) No sharp boundary but easy to identify, and (3) No sharp boundary and difficult to identify. The method of Pearson was used to calculate the correlation coefficients. The coefficient of determination between the ranking of the measured contact area and the ranking of the maximum particle size was r2= 0.46 (P> 0.05). Composite materials with the same particle size were ranked by their filler content (wt. %).

Aluminum Oxide↗