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PubMed2006

An integrated proteomic workflow for two-dimensional differential gel electrophoresis and robotic spot picking.

New technologies have advanced the field of proteomics, and a number of companies have developed innovative platforms to drive this research. However, significant challenges are often encountered when trying to integrate complementary technologies from multiple manufacturers. We have developed a software and hardware solution to integrate the Ettan two-dimensional difference gel electrophoresis (2-D DIGE) system (GE Healthcare) with the Investigator ProPic spot picking robot (Genomic Solutions). We have analyzed protein sample preparations from bacterial and mammalian sources to demonstrate a new workflow with increased throughput for gel-based proteomics.

Electrophoresis, Gel, Two-Dimensional↗

PubMed1997

An automatic approach to the analysis, quantitation and review of perfusion and function from myocardial perfusion SPECT images.

UNLABELLED: We have developed a software suite that automatically selects, analyses, quantitates and displays all the key image data in a myocardial perfusion SPECT study. METHODS: The files automatically selected (upon specification of the patient name) are rest and stress projections, rest and stress short axis and gated short axis files, and all 'snapshot' files. The projection data sets are presented in cine mode for evaluation of patient motion, while the lung/heart ratio at rest and stress is calculated from regions of interest (ROIs) that are automatically derived and overlayed on the LAO 45 images. Left ventricular (LV) cavity volumes at rest and stress are calculated from the short axis data sets, and the related transient ischemic dilation (TID) ratio derived and displayed. Quantitative measurements of global (ejection fraction) and regional function parameters are performed from the gated short axis dataset. All algorithms use the C++, X-Windows and OSF-Motif standards. The overall suite executes in less than 1 minute on a SunSPARC5 with 32 Mb of RAM and no proprietary hardware. RESULTS: The software was validated on 144 patients (118 rest 201T1/post-stress 99mTc-sestamibi, 18 post-stress 99mTC-sestamibi, 8 rest 201Tl) acquired on a 90 degrees dual detector (ADAC Vertex, 91 patients) and a triple detector camera (Picker Prism 3000, 53 patients). Overall, the individual algorithms for the analysis of projection, short axis and gated short axis images were successful in 622/660 (94.2%) of the images. In 80.5% of the patients (73/91 + 43/53) all algorithms executed successfully, without significant difference in success rates for 201Tl versus 99mTc-sestamibi images. CONCLUSION: Our automated approach to myocardial perfusion SPECT analysis and review is highly successful, intrinsically reproducible, and can produce time and cost savings while improving accuracy in a clinical or teleradiology-type environment.

Algorithms↗

PubMed2003

SkinChip, a new tool for investigating the skin surface in vivo.

BACKGROUND/AIMS: Non-invasive methods used for characterizing skin micro-relief and skin surface hydration were developed in the 1980s. Although they allowed some progress in the knowledge of skin properties, they are not completely satisfactory in many aspects. Today, new technologies are emerging that may address such issues. METHODS: We adapted the technology produced by the ST Microelectronics Company for sensing fingerprint for the measurement of skin surface properties. Accordingly, we developed acquisition software for obtaining routinely the distribution of skin surface capacitance along different body sites. Image analysis softwares were also processed for collecting both the main orientations of the micro-relief lines and their density. The average value of skin capacitance is also obtained. RESULTS: The images allow a highly precise observation of the skin topography that can be easily quantified in terms of line density and line orientation. The mean gray levels of the images appear much closely correlated to the Corneometer values. CONCLUSION: This new device appears to be a very convenient way for characterizing the properties of the skin surface. With regard to hydration, it usefully provides both the average value and the hydration chart of the investigated skin zones.

Face↗

PubMed1993

Interrupted time-series analysis with brief single-subject data.

Assessing change with short time-series data is difficult because visual inference is unreliable with such data, and current statistical procedures cannot control Type I error because they underestimate positive autocorrelation. This article describes these problems and shows how they can be solved with a new interrupted time-series analysis procedure (ITSACORR) that uses a more accurate estimate of autocorrelation. Monte Carlo analyses show that, with short series, ITSACORR provides better control of Type I error than all previous procedures and has acceptable power. Clinical examples also show that ITSACORR is easy to use and functions well with real data.

Adolescent↗

PubMed1999

Genome-wide mapping with biallelic markers in Arabidopsis thaliana.

Single-nucleotide polymorphisms, as well as small insertions and deletions (here referred to collectively as simple nucleotide polymorphisms, or SNPs), comprise the largest set of sequence variants in most organisms. Positional cloning based on SNPs may accelerate the identification of human disease traits and a range of biologically informative mutations. The recent application of high-density oligonucleotide arrays to allele identification has made it feasible to genotype thousands of biallelic SNPs in a single experiment. It has yet to be established, however, whether SNP detection using oligonucleotide arrays can be used to accelerate the mapping of traits in diploid genomes. The cruciferous weed Arabidopsis thaliana is an attractive model system for the construction and use of biallelic SNP maps. Although important biological processes ranging from fertilization and cell fate determination to disease resistance have been modelled in A. thaliana, identifying mutations in this organism has been impeded by the lack of a high-density genetic map consisting of easily genotyped DNA markers. We report here the construction of a biallelic genetic map in A. thaliana with a resolution of 3.5 cM and its use in mapping Eds16, a gene involved in the defence response to the fungal pathogen Erysiphe orontii. Mapping of this trait involved the high-throughput generation of meiotic maps of F2 individuals using high-density oligonucleotide probe array-based genotyping. We developed a software package called InterMap and used it to automatically delimit Eds16 to a 7-cM interval on chromosome 1. These results are the first demonstration of biallelic mapping in diploid genomes and establish means for generalizing SNP-based maps to virtually any genetic organism.

Arabidopsis↗

PubMed2000

Facial and dental changes in adolescents and their clinical implications.

Assessment and Prediction of Dentofacial growth are perhaps the most essential, yet to a great extent the most subjective, aspects of clinical orthodontics. Although the percentage of adult patients has increased in recent years, the majority of treatment is still directed toward pre-adolescent and adolescent patients. These individuals are undergoing significant growth changes in their occlusions, facial skeletons, and profiles. The purpose of this paper is to review pertinent longitudinal facial growth data and some of the methods used to predict facial growth. The clinical implications of the available information is also discussed. The ability to forecast or predict growth lies at the very heart of contemporary clinical orthodontics. The orthodontist in formulating a treatment plan relies largely upon subjective criteria in conceiving the outcome of treatment. This intuitive perception is necessary, but the overall approach should be based on the available scientific information. There are several components to be dealt with in the prediction of craniofacial changes: the direction, the magnitude, the timing, the rate of change, and the effects of treatment. Orthodontists, in general, are well informed regarding the effects of orthodontic treatment on the patient, but are not yet able to accurately predict the direction, timing, and magnitude of the facial changes that occur with growth in any single individual.

Adolescent↗

PubMed1996

Characteristics of fasting and fed myoelectric activity in rat small intestine: evaluation by computer analysis.

Evaluation of gastrointestinal myoelectric activity has been limited by the assessment techniques and the complexity of the recorded myoelectric signal. Commonly, myoelectric activity is evaluated as motor patterns, which only gives a semiquantitative measure of myoelectric events within the bowel wall. Using myoelectric recordings from the proximal small intestine in rats, a computerized system for acquisition, storage, display and calculation of characteristics for the myoelectric activity was developed. The software was tested in myoelectric recordings from nine rats in fasting and fed states. All migrating myoelectric complexes (MMCs) during fasting and fed myoelectric patterns were recognized in both digital and analog recordings. Reproduction of myoelectric recordings by the computerized system was indistinguishable from that of the analog system. Employing an appropriate cut-off trigger level and a high sampling frequency, spike potentials were recorded in the proximal jejunum with 0.4 (0.3-0.5) spikes 10 s-1 during phase 1 of MMC, 19.5 (15.1-23.9) (P < 0.001) during phase 2, and 103.8 (97.2-110.5) (P < 0.001) during phase 3. In fasted state, MMCs were most frequent in the proximal jejunum whereas fewer were found in the duodenum and distal jejunum. To achieve stable values for MMC cycle length at least four MMCs had to be calculated. After feeding in phase 1, the myoelectric activity increased to 23.8 (13.6-33.9) spikes 10 s-1 (P < 0.001), whereafter the spiking activity decreased over a period of 2 h until a fasting motor pattern was resumed. It is concluded that computerized technology enables evaluation not only of myoelectric patterns, but also of spiking activity per time unit, i.e. the intensity of myoelectric activity in the gut.

Amplifiers, Electronic↗

PubMed1995

From intelligence to evidence-based healthcare: a purchasing odyssey.

Since the appearance of the NHS Executive's guidance document, Purchasing Intelligence (1991), efforts have been concentrated on the development of 'purchasing intelligence facilities' staffed, in the main, by health librarians. However, the concept of 'intelligence' has a wider dimension that impacts upon the whole culture of an organization. The authors examine purchasing organizations against popular theories of organizational development. The characteristics of Handy's Task culture, with Athena as its patron, may be observed in many authorities. Using the results of two surveys, conducted in March 1995, they identify some key information management issues involving structure, tasks, technology and people. Skills in information 'transformation' must be acquired by all staff in purchasing authorities. The intelligence officer must become a modern-day Odysseus if the intelligence facility is to 'survive and thrive'.

Computer Communication Networks↗

PubMed2001

Free cytosolic Ca2+ recordings from myenteric neurones in multilayer intestinal preparations.

The ability to simultaneously monitor different myenteric neurones in a multilayer preparation may enhance our understanding of the enteric nervous system. Longitudinal muscle myenteric plexus preparations were mounted in recording chambers with a coverslip base and loaded with Indo-1-AM. cytosolic Ca2+ concentration ([Ca2+]i); changes were recorded at room temperature with a confocal microscope. In addition to mechanical (pressure-ring) and pharmacological (nifedipine) reduction of muscle contractions, purpose-designed software was developed to reposition regions of interest and avoid artefacts. Confocal scanning permitted optical selection of single cell layers. High K+ depolarization, used to distinguish between excitable and nonexcitable cells, caused a synchronous [Ca2+]i rise in 84.3% of the ganglion cells. Acetylcholine, substance P and serotonin (all at 10(-5) mol L(-1)) induced transient [Ca2+]i changes in subpopulations of myenteric neurones (45.1%, 42.9 and 21.9%, respectively). In addition to immediate responses to agonists, delayed [Ca2+]i changes were also recorded, suggesting the presence of both directly activated and synaptically driven neurones. Functionally identified neurones and other cells in close apposition to the ganglia (interstitial cells of Cajal) could also be studied. This study demonstrates the potential of optical Ca2+ recordings to monitor spread of activity in myenteric neurones and to study their interaction with non-neuronal targets.

Acetylcholine↗

PubMed2003

Concept and realization of a multimedia program for veterinary physiology.

A multimedia program, a non-linear system which supplements the traditional, linear way of learning (e.g. with a text book), was developed. Non-linear systems allow the direct use of information in a free sequence. A problem of these systems is the danger that the reader becomes lost in detail. Therefore, a program was constructed which tries to combine the properties of linear and non-linear teaching systems. Student groups were continuously involved during all stages of the project. The program is organized in several levels. These are: (1) choice of chapters; (2) table of contents of one chapter; (3) summary; (4) text and (5) pictures, animations, simulations and video sequences. The program can be used in different ways. In the linear mode, the reader selects via action words different levels of the program. The user can read either only on the level of the summaries or on detailed information (text, pictures, simulations and videos). In the non-linear mode the user jumps via menu items or buttons to selected pictures, simulations or a searched term. In this way, more than 3500 screen pages are integrated into a multimedia program for veterinary physiology. The program is written in TOOLBOOK, and can be used on a personal computer with Windows 95 or higher.

Animal Population Groups↗

PubMed2004

A web application to manage a database for liquid nitrogen tanks.

Summary We have developed a software, Cell Database, for archiving records about cells stored in liquid nitrogen tanks. Once installed on a web server, the database is accessed through a standard web browser. This user-friendly and self-explanatory application is independent of computer platform and periodic upgrades of a commercial software. Our web application allows import of data from other database programs and adaptation to different tank formats, types of samples, and archiving needs.

Cells↗

PubMed2000

Networking of three dimensional sonography volume data.

Three-dimensioned (3D) sonography enables the examiner to store, instead of copies from single B-scan planes, a volume consisting of 300 scan planes. The volume is displayed on a monitor in form of three orthogonal planes--longitudinal, axial and coronal. Translation and rotation facilitates anatomical orientation and provides any arbitrary plane within the volume to generate organ optimized scan planes. Different algorithms allow the extraction of different information such as surface, or bone structures by maximum mode, or fluid filled structures, such as vessels by the minimum mode. The volume may contain as well color information of vessels. The digitized information is stored on a magnetic optical disc. This allows virtual scanning in absence of the patient under the same conditions as the volume was primarily stored. The volume size is dependent on different, examiner-controlled settings. A volume may need a storage capacity between 2 and 16 MB of 8-bit gray level information. As such huge data sets are unsuitable for network transfer, data compression is of paramount interest. 100 stored volumes were submitted to JPEG, MPEG, and biorthogonal wavelet compression. The original and compressed volumes were randomly shown on two monitors. In case of noticeable image degradation, information on the location of the original and compressed volume and the ratio of compression was read. Numerical values for proving compression fidelity as pixel error calculation and computation of square root error have been unsuitable for evaluating image degradation. The best results in recognizing image degradation were achieved by image experts. The experts disagreed on the ratio where image degradation became visible in only 4% of the volumes. Wavelet compression ratios of 20:1 or 30:1 could be performed without discernible information reduction. The effect of volume compression is reflected both in the reduction of transfer time and in storage capacity. Transmission time for a volume of 6 MB using a normal telephone with a data flow of 56 kB/s was reduced from 14 min to 28 s at a compression rate of 30:1. Compression reduced storage requirements from 6 MB uncompressed to 200 kB at a compression rate of 30:1. This successful compression opens new possibilities of intra- and extra-hospital and global information for 3D sonography. The key to this communication is not only volume compression, but also the fact that the 3D examination can be simulated on any PC by the developed 3D software. PACS teleradiology using digitized radiographs transmitted over standard telephone lines. Systems in combination with the management systems of HIS and RIS are available for archiving, retrieval of images and reports and for local and global communication. This form of tele-medicine will have an impact on cost reduction in hospitals, reduction of transport costs. On this fundament worldwide education and multi-center studies becomes possible.

Algorithms↗

PubMed2001

[Automated image analysis of lateral roentgen images of the spine using anatomic models].

PURPOSE: Development of a software for fully automated image analysis of lateral lumbar spine X-rays. MATERIAL AND METHOD: Using the concept of active shape models, we developed a software that produces a form model of the lumbar spine from lateral lumbar spine radiographs and runs an automated image segmentation. This model is able to detect lumbar vertebrae automatically after the filtering of digitized X-ray images. The model was trained with 20 lateral lumbar spine radiographs with no pathological findings before we evaluated the software with 30 further X-ray images which were sorted by image quality ranging from one (best) to three (worst). There were 10 images for each quality. RESULTS: Image recognition strongly depended on image quality. In group one 52 and in group two 51 out of 60 vertebral bodies including the sacrum were recognized, but in group three only 18 vertebral bodies were properly identified. CONCLUSION: Fully automated and reliable recognition of vertebral bodies from lateral spine radiographs using the concept of active shape models is possible. The precision of this technique is limited by the superposition of different structures. Further improvements are necessary. Therefore standardized image quality and enlargement of the training data set are required.

Humans↗

PubMed2005

[Endolaryngeal distance measurement by laser light projection--from the idea to clinical application].

INTRODUCTION: In clinical and scientific examinations with rigid and flexible endoscopes quantitative morphometric measurements of intralaryngeal structures have been difficult whereas qualitative laryngoscopic examinations are routine procedures. MATERIAL AND METHODS: The development of a two-point light projection method for endolaryngeal morphometry in its different phases is described. The way from a first prototype for endolaryngeal morphometry that works with a prism technique to the latest, most modern prototype, which works with a double reflecting mirror is shown. RESULTS: In combination with a newly developed PC software the latest prototype for two-point laser-light projection enables an accuracy of 95 % to 99 % in the measurement of intralaryngeal distances. The contrast of the laser beams to the mucous membrane of the larynx could be optimized by the use of green--instead of red--laser light. CONCLUSION: Morphological measurements within the larynx are now possible for clinical and scientific questions. Former limitations in quantitative morphometric examinations will be reduced.

Equipment Design↗

PubMed2005

[Topographical anatomy of the female pelvis in ultrasound].

AIM: Achieving a high quality gynaecological ultrasound examination requires thorough knowledge of topographic anatomy. To date, there are no guidelines for a standardised course of the examination. The goal of the study was to define exact planes by means of cross-sectional anatomy and then to standardise the gynaecological ultrasound examination with the transabdominal, introital and transvaginal technique. METHOD: We developed a software tool based on IDL (Interactive Data Language) for the female data set of the Visible Human Project which generates free determinable planes in the volume. The organs of the female pelvis were divided into landmark- and target structures according to the ultrasonic visibility and the variability of the position, shape and structure. From this, a course for the gynaecological ultrasound examination was created and verified on 65 patients each with an inconspicuous ultrasound finding. In addition, the average duration of the examination was determined. RESULTS: The landmark structures could be demonstrated in all patients. Five planes were defined for each technique, and the course of the whole examination with 15 exact planes was described. The average duration of the examination was 4.5 minutes. CONCLUSION: As of now, the digitally reconstructed anatomical illustrations have achieved the best image resolution and quality regardless of the position of the plane in the examination volume. The standardised course of the gynaecological ultrasound examination can serve as a basis for the improvement of training quality and the evaluation of a general gynaecological ultrasound screening.

Female↗

PubMed1996

[3-D visualization of thoracic tumors from MR images].

AIM: In cooperation with the thoracic surgery department 3-D visualizations of tumors were generated to support the surgeons in preoperative planning. As opposed to 3-D reconstructions of CT data, those representations based on MRI images remain an exception. In this paper different methods of three dimensional visualization of lung tumors are presented and compared to each other. DESIGN: These methods are 1. contour based surface models, 2. threshold based surface models and 3. rendered scenes of segmented volume data with transparent, color-coded display. RESULTS: Combinations of all three methods in one single image are possible as well with the software we developed. Furthermore, cut planes through the original data can be integrated into the 3-D scene. The segmentation of anatomical objects is performed either manually or automatically with various procedures. CONCLUSIONS: Adequate possibilities of manipulation and archiving allow a fast handling and processing even of large data sets. The calculated volumes of the anatomical objects can be used for quantitative studies. Arbitrary views of the three dimensional reconstructions can be generated within a few seconds. Even animation can easily be calculated and displayed with 30 frames/second.

Adult↗

PubMed1998

Predicting amino acid sequences of the antibody human VH chains from its first several residues.

A new method for classification of Ig sequences is suggested. The defining characteristic of a class is presence of particular residues at several class-determining positions. Sequences within a class follow the same amino acid pattern, i.e., residues at identical positions are, in an overwhelming majority of sequences of that class, identical or chemically related. Thus, once the class of a sequence is determined, one can predict the residue(s) at almost any position in the sequence. In this paper, results of analysis of 1,172 human heavy chains are presented. It was shown that a sequence can be assigned to one of six classes depending on which residues are found at its positions 1, 3, 5, 6, 7, 9, 10, 12, and 13. It is important to note that it is possible to achieve same six-class classification of the human heavy chains on the basis of a different set of positions found not at the beginning but near the end of the sequence (around position 80). For every class, an amino acid pattern of an entire sequence (complementarity determining regions excepting) has been determined. Our approach allowed us to reconstruct the incomplete human heavy chains in which residues at certain positions at the beginning or end of the chain are known. We developed a software tool for analysis, classification, and prediction of residues in sequences of the Ig family.

Algorithms↗

PubMed2005

Improved classification of mass spectrometry database search results using newer machine learning approaches.

Manual analysis of mass spectrometry data is a current bottleneck in high throughput proteomics. In particular, the need to manually validate the results of mass spectrometry database searching algorithms can be prohibitively time-consuming. Development of software tools that attempt to quantify the confidence in the assignment of a protein or peptide identity to a mass spectrum is an area of active interest. We sought to extend work in this area by investigating the potential of recent machine learning algorithms to improve the accuracy of these approaches and as a flexible framework for accommodating new data features. Specifically we demonstrated the ability of boosting and random forest approaches to improve the discrimination of true hits from false positive identifications in the results of mass spectrometry database search engines compared with thresholding and other machine learning approaches. We accommodated additional attributes obtainable from database search results, including a factor addressing proton mobility. Performance was evaluated using publically available electrospray data and a new collection of MALDI data generated from purified human reference proteins.

Amino Acid Sequence↗