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At least 721 records · Page 40Linked to original sources

PubMed2003

A novel MALDI LIFT-TOF/TOF mass spectrometer for proteomics.

A new matrix-assisted laser-desorption/ionization time-of-flight/time-of-flight mass spectrometer with the novel "LIFT" technique (MALDI LIFT-TOF/TOF MS) is described. This instrument provides high sensitivity (attomole range) for peptide mass fingerprints (PMF). It is also possible to analyze fragment ions generated by any one of three different modes of dissociation: laser-induced dissociation (LID) and high-energy collision-induced dissociation (CID) as real MS/MS techniques and in-source decay in the reflector mode of the mass analyzer (reISD) as a pseudo-MS/MS technique. Fully automated operation including spot picking from 2D gels, in-gel digestion, sample preparation on MALDI plates with hydrophilic/hydrophobic spot profiles and spectrum acquisition/processing lead to an identification rate of 66% after the PMF was obtained. The workflow control software subsequently triggered automated acquisition of multiple MS/MS spectra. This information, combined with the PMF increased the identification rate to 77%, thus providing data that allowed protein modifications and sequence errors in the protein sequence database to be detected. The quality of the MS/MS data allowed for automated de novo sequencing and protein identification based on homology searching.

Amino Acid Sequence↗

PubMed2026

An inducer-independent, single-plasmid CRISPR-Cas9 system for genome editing in Bacillus species.

Advances in molecular biology tools are essential for streamlining and accelerating genetic engineering of cells across industrial and academic applications. While CRISPR-Cas improves genome editing efficiency, current systems have limitations and are often host specific, which restricts their versatility. This study describes a versatile CRISPR-Cas9 system for genome editing in industrially relevant Bacillus species. By adapting the well-established pJOE8999 vector-based CRISPR-Cas9 genome editing system, we constructed an inducer-independent, broad-host-range genome editing system. It maintains the benefits of low toxicity to the target cell and the cloning host as well as the ease to use of a single-plasmid CRISPR-Cas9 system. We utilized the constitutive Sigma70-type promoter from the conserved veg gene of Bacillus, to develop and test the suitability of promoter variants of different strengths for Cas9 expression. Successful gene deletions in three different Bacillus species demonstrated the versatility of the modified system for this industrially important genus. This was further confirmed by the integration of a reporter gene fusion and the introduction of a single point mutation in the genome of Bacillus licheniformis. This one-step CRISPR-based transformation protocol developed in this study enables fast genome editing workflows with minimal hands-on time. KEY POINTS: • Editing and screening of promoter variants for balanced Cas9 expression in Bacillus. • Development of a versatile inducer-independent, single-plasmid CRISPR-Cas-based system. • Verification of the modified CRISPR-based system for genome editing in different Bacilli.

CRISPR-Cas Systems↗

PubMedDate not supplied

Thermoablation of liver metastases: efficacy of temporary celiac plexus block.

PURPOSE: To determine the efficacy of celiac plexus block during thermoablation of liver metastases. METHODS: Fifty-five consecutive patients underwent thermoablation therapy of liver tumors by laser-induced thermotherapy. Twenty-nine patients received a temporary celiac plexus block, 26 patients acted as control group. In both groups fentanyl and midazolam were administered intravenously upon request of the patient. The duration of the intervention, consumption of opiates, and individual pain sensations were documented. RESULTS: No complications resulting from the celiac plexus block were recorded. Celiac plexus block significantly reduced the amount of pain medication used during thermoablation therapy of liver tumors (with block, 2.45 mug fentanyl per kg body weight; without block, 3.58 mug fentanyl per kg body weight, p < 0.05; midazolam consumption was not reduced) in patients with metastases < or = 5 mm from the liver capsule. For metastases farther away from the capsule no significant differences in opiate consumption were seen. Celiac plexus block reduced the time for thermoablation significantly (178 min versus 147 min, p < 0.05) no matter how far the metastases were from the liver capsule. Average time needed to set the block was 12 min (range 9-15 min); additional costs for the block were marginal. As expected (as pain medications were given according to individual patients' needs) pain indices did not differ significantly between the two groups. CONCLUSION: In patients with liver metastases < or = 5 mm from the liver capsule, celiac plexus block reduces the amount of opiates necessary, simplifying patient monitoring. In addition celiac plexus block reduces intervention time, with positive effects on overall workflow for all patients.

Analgesics, Opioid↗

PubMed2006

[Virtual microscopy and digital pathology].

Virtual microscopy has advanced considerably and is bound to be integrated into routine diagnostics in the very near future. Its integration into existing information systems builds up digital pathology. In this review, we present details, advantages and limitations of this novel technology and describe solutions regarding its adaptation to routine workflow. The chief aim is to define an uniform data format for virtual specimens to guarantee an interoperability between different systems. In the long term, digital archives and networks will be established that will allow for a worldwide access to virtual specimens.

Humans↗

PubMed2004

IT services in a completely digitized radiological department: value and benefit of an in-house departmental IT group.

To analyze the benefit of a departmental IT group in comparison to support by hospital IT groups or system manufacturers in a completely digitized radiological department. The departmental IT group comprises a fulltime IT specialist, two student assistants and four clinical employees participating 1 day/week. For 18 months IT problems were quantified and specified according to urgency, responsibility and affected system by use of an intranet-based reporting system. For each IT service provider the performance and duration of problem solution was evaluated. In 18 months 3,234 IT problems emerged. 88.7% were solved by the departmental IT group. In 474 cases (14.7%) a solution within 2 h was required. The departmental IT group solved 35.8% within 30 min, system manufacturers needed 18 h 38 min in mean. The departmental IT group solved 90.2% of the problems within a time limit. System manufacturers met the limit in 60.1% with a mean duration of 7 days 21 h. In 6.7% of the cases, support by system manufacturers was indispensable. A considerable proportion of IT problems in completely digitized radiological departments can be solved by a departmental IT group, providing a fast and cost-efficient first-level IT support with effective prevention of major breaks in the workflow. In a small number of cases support by system manufacturers remains necessary.

Computer Communication Networks↗

PubMed2005

Flat detectors and their clinical applications.

Diagnostic and interventional flat detector X-ray systems are penetrating the market in all application segments. First introduced in radiography and mammography, they have conquered cardiac and general angiography and are getting increasing attention in fluoroscopy. Two flat detector technologies prevail. The dominating method is based on an indirect X-ray conversion process, using cesium iodide scintillators. It offers considerable advantages in radiography, angiography and fluoroscopy. The other method employs a direct converter such as selenium which is particularly suitable for mammography. Both flat detector technologies are based on amorphous silicon active pixel matrices. Flat detectors facilitate the clinical workflow in radiographic rooms, foster improved image quality and provide the potential to reduce dose. This added value is based on their large dynamic range, their high sensitivity to X-rays and the instant availability of the image. Advanced image processing is instrumental in these improvements and expand the range of conventional diagnostic methods. In angiography and fluoroscopy the transition from image intensifiers to flat detectors is facilitated by ample advantages they offer, such as distortion-free images, excellent coarse contrast, large dynamic range and high X-ray sensitivity. These characteristics and their compatibility with strong magnetic fields are the basis for improved diagnostic methods and innovative interventional applications.

Absorption↗

PubMed2001

Networks in the radiology department and the hospital.

Data networks are a basic technology with regard to an appropriate design of the information technology (IT) infrastructure for the hospital. Due to the distributed workflow within the hospital, an integrated Hospital Information System (HIS) is based mostly on a set of network applications facing specific items. Medical communication standards, i.e., HL 7, DICOM, and in the near future the migration towards XML, support the interoperability between the IT subsystems and pave the way to patient information systems with access to unified and complete electronic medical records (EMR). Furthermore, with standardized communication techniques, such as CORBAmed, an object-oriented design of Healthcare applications will be possible in the near future. The intent of this paper is to give an overview of which basic technologies are suitable for building comprehensive, flexible, and reliable hospital networks and which also meet the special demands of the radiology department.

Computer Communication Networks↗

PubMed2004

LIMaS: the JAVA-based application and database for microarray experiment tracking.

Microarrays allow monitoring of gene expression for tens of thousands of genes in parallel and are being used routinely to generate huge amounts of valuable data. Handling and analysis of such data are becoming major bottlenecks in the utilization of the technology. To enable the researcher to interpret the results postanalysis, we have developed a laboratory information management system for microarrays (LIMaS) with an n-tier Java front-end and relational database to record and manage large-scale expression data preanalysis. This system enables the laboratory to replace the paper trail with an efficient and fully customizable interface giving it the ability to adapt to any working practice, e.g., handling many resources used to form many products (chaining of resources). The ability to define sets of activities, resources, and workflows makes LIMaS MIAME-supportive.

Databases as Topic↗

PubMed2004

[Use of an electronic patient record system at the Department of Ophthalmology, Otto-von-Guericke University of Magdeburg].

BACKGROUND: The electronic or paper-based patient record is the most important documentation file. The electronic patient record has many advantages compared to a paper-based record. METHODS: An example of an electronic patient record (EPR) system accessed by several departments of the Faculty of Medicine of Magdeburg is presented. RESULTS: To guarantee faculty-wide communication with sharing of clinical pictures and findings, e.g., with the Departments of Radiology and Pathology, the system of MEDOS Inc. is used in our department. Several examination devices, for example fundus camera, slit lamp, and ultrasound, are equipped with an digital picture storage and communication system via a DICOM interface to the MEDOS system. The software AnalySIS is used as a gateway for picture transferation. The MEDOS system also supports the clinical workflow. CONCLUSIONS: The use of an electronic patient record system in ophthalmology is already possible, but still needs further tuning and improvement.

Computer Communication Networks↗

PubMed2005

Detection of putative secreted proteins in the plant-parasitic nematode Heterodera schachtii.

The beet cyst nematode Heterodera schachtii is an important pathogen worldwide, but its molecular characterization has been limited to studying individual genes of interest. We undertook a high-throughput genomic approach and drastically increased the number of available sequences for this parasite. A total of 2,662 expressed sequence tags were grouped into 1,212 clusters representing a nonredundant catalog of H. schachtii genes. Implementing a bioinformatic workflow, we identified 50 sequences coding for candidate secreted proteins. All of these contain a putative signal peptide required for entry into the secretory pathway and lack any transmembrane domain. Included are previously postulated cell-wall-degrading enzymes and other parasitism-related genes. Moreover, we provide the first report of an arabinogalactan endo-1,4-beta-galactosidase enzyme (EC 3.2.1.89) in animals. As sequence data increase at a rapid rate, developing high-throughput genomic screening is a necessity. The in silico approach described here is an effective way to identify putative secreted proteins and prioritize candidates for further studies.

Animals↗

PubMed2006

Optimal port placement and enhanced guidance in robotically assisted cardiac surgery.

BACKGROUND: Optimal port placement and enhanced guidance in robotically assisted cardiac surgery is required to improve preoperative planning and intraoperative navigation. METHODS: Offline optimal port placement is planned on a three-dimensional virtual reconstruction of the patient's computed tomography scan. Using this data, an accurate in vivo port placement can be performed, which is achieved by augmented reality techniques superimposing virtual models of the thorax and the teleoperator arms on top of the real worldview. RESULTS: A new system incorporating both port placement planning and intraoperative navigation in robotically assisted minimally invasive heart surgery was established to aid the operative workflow. A significant reduction of operation time by improved planning and intraoperative support is anticipated. CONCLUSIONS: The enhanced intraoperative orientation possibilities may lead to further decrease in operation time and have the continuing ability to improve quality.

Cardiovascular Surgical Procedures↗

PubMed2006

[Analgesia in pediatric outpatient surgery].

A number of surgical procedures for pediatric patients can be suitably performed in an outpatient setting. The advantages are impressive: reduced costs, lower rate of infection, avoidance of hospitalization with the inherent psychological stress, and timely return of the patients to their familiar home environment. An essential feature of the quality of outpatient surgery is the efficacy of the perioperative pain therapy for which a multimodal approach has proven to be very effective: workflow tailored to children's needs, ambiance appropriate for children, and pharmacological analgesia. In the preliminary counseling session it is imperative that parents and children receive detailed information on procedures (role playing, modeling). Associated unpleasant factors prior to induction of anesthesia should be avoided. The primary element of pharmacological analgesia is regional anesthesia; additional options are paracetamol, nonsteroidal antirheumatic agents (be aware of the highest dosages!), and opioids. When opioids are employed, care should be taken that monitoring standards in the recovery room are not lowered and include pulsoxymetry. Because of the clearly elevated rate of postoperative nausea and vomiting related to perioperative administration of opioids, the lower dosage level should be chosen. This article presents concepts of perioperative analgesia.

Adolescent↗

PubMed2006

The HUPO Brain Proteome Project--no need to hurry?

The HUPO Brain Proteome Project (HUPO BPP) is dedicated to the analysis of the brain proteome and has initiated two pilot studies in order to elaborate a standardised system for data collection and reprocessing. Samples of mouse brains (different developmental stages) and human brain tissue (biopsy and post-mortem samples) were shipped to different laboratories in Europe, Asia and the US that were invited to identify as many proteins as possible using their own approaches. In addition, a centralised data reprocessing strategy has been elaborated in an iterative way to generate highly reliable lists of identified proteins. This consortium could be a good example for a standardized proteomics workflow.

Animals↗

PubMed2006

Reverse genetics for proteomics: from proteomic discovery to scientific content.

Proteomic strategies generally result in rather descriptive outcomes. Although proteomic patterns may lead to understanding of cellular function or failure, they do not provide insights into cellular mechanisms of normal physiology or molecular mechanisms of disease. The integration of single events or patterns into complex biological processes and signaling networks must be functionally validated by studying these processes in a dynamic physiological context. Effective methodologies, applied at the level of intact cells and model organisms that monitor their function, topology and interaction of proteins are necessary and essential. Reverse genetic strategies can greatly advance the understanding of patterns identified through proteomic analysis. RNAi as an accessible method for routine functional analysis of cells and whole model organisms represents a quantum leap in revolutionizing reverse genetics. This paper aims at describing an integrated workflow linking proteome-based discovery to molecular analysis of single genes and proteins by RNAi, potentially contributing to the advanced understanding of molecular mechanisms in neurodegenerative disease, including Parkinson's disease.

Animals↗

PubMed2026

A python based automated computational framework to classify and comparative genomics analysis of the global diversity of chili leaf curl virus (ChiLCV) strains to understand virus host interactions.

Chili leaf curl virus (ChiLCV) is a Begomovirus chillicapsici that is one of the most devastating viruses impacted on the production of chili in the world, especially in South Asia. In the present study, we combined high-throughput computational genomics with experimental analysis of global diversity. A workflow was created using automated Python scripts to download, curate and process ChiLCV genomes from public database. About 410 complete ChiLCV genomes download from public databases. Using a phylogenetic approach, these isolates were subdivided into 34 strains, belonging to 10 major clades, showing significant genetic diversity. Geographic analysis revealed that Pakistan (207 isolates) and India (148 isolates) were the main sources of ChiLCV diversity and the remainder of the isolates were from Oman, Bangladesh, Iran, Saudi Arabia and Sri Lanka. Recombination was observed as a major evolutionary force as more than twenty recombination events were detected. Analysis of cis-regulatory elements showed a complex structure of the viral promoter, including multiple binding sites for transcription factors, hormone-response elements, light-responsive elements, and stress-responsive elements, indicating a high number of interactions between viral regulatory elements and host signaling pathways. Pangenome analysis showed the presence of a highly dynamic open pangenome made up of strain-specific orthologous groups (species-specific orthogroups). Experimental inoculation of chili plants was also carried out to assess the biological effects of infection, along with phytochemical, FTIR, HPLC, and qPCR analyses.

Begomovirus↗

PubMed2006

Models for guideline representation.

Despite the great emphasis that the medical community has dedicated to clinical practice guidelines in the last few decades, it has become clear that it is difficult to adequately distribute texts (paper-based guidelines) and for them to be used by final users. The reasons for this are manifold: the large number of guidelines delivered each year, their necessary updates on the face of new scientific evidence, the text is not always free from ambiguities, etc. When these problems became evident, the medical informatics community hypothesised that more formal electronic versions would increase the probability of the effective diffusion of guidelines and also physicians' compliance to them. This claim was based on a few hypotheses: one is that formal models, such as flowcharts or other graphical metaphors, provide a more friendly and immediate way of reading a guideline, thus improving learning and absorbing of the guideline content (e. g. using formal models as educational/simulation tools); another hypothesis is that formal models allow easier guideline integration with the daily clinical workflow, raising the possibility of building real-time decision support systems, which again should improve physicians' compliance. This paper focuses on the issues that must be taken into account when modelling guidelines to ensure their effective implementation in real-world computerised environments.

Computer Simulation↗

PubMed2006

Stroke Active Guideline Evaluation (STAGE) project.

In 2005 the American Stroke Association's task force on the development of stroke systems established that providers and policymakers at the local, state and national levels can make significant contributions to reducing the devastating effects of stroke by working to promote coordinated systems that improve patient care. In the last few years in North America and Canada several quality stroke registers have been implemented with the aim of improving the processes of care by the diffusion and implementation of national guidelines and by the identification and correction of critical points of stroke care provided in the hospitals participating in the register. The Italian guidelines for stroke, SPREAD, have been developed with the aim of generating a tool applicable to the Italian clinical setting, able to promote the planning and linking of the assistant interventions between the different phases of the stroke care process, from the hyper-acute to the rehabilitation phase, and from primary to secondary prevention in order to harmonise and streamline the actions of the various health-care providers involved in the different phases of the diagnostic and therapeutic path of patients with stroke. The primary end-point of the Stroke Active Guideline Evaluation (STAGE) project, founded by the Italian Ministry of Health in 2003, is the diffusion, implementation and validation of the Italian Guideline for Stroke, SPREAD, in 15 acute care and 3 rehabilitative institutions across Italy. Secondary end-points are the evaluation of impact of the implementation of a workflow management in the processes of care and the identification of a national, streamlined diagnostic and therapeutic path for ischaemic stroke patients. An existing electronic patient record (EPR) has been shared with the referents of the Centres participating in the study and adapted to SPREAD's indicators. This EPR has been augmented with the decision support system. The STAGE project represents the first Italian effort in this direction. A lot of work has to be done before this goal will be achieved, but as Albert Einstein said "Imagination is more important than intelligence".

Database Management Systems↗

PubMed2005

Lack of effect of shorter turnaround time of microbiological procedures on clinical outcomes: a randomised controlled trial among hospitalised patients in the Netherlands.

Shortening the turnaround time of microbiological procedures was associated with an improved clinical outcome in two studies performed in the USA. To study the clinical impact of a shortened turnaround time in a northwest European setting in which an automated system was used for bacterial identification and susceptibility testing, a single-blind, prospective, randomised controlled trial was conducted in a hospital in the Netherlands. All hospitalised patients with a bacterial infection confirmed by culture were randomly assigned to a control (conventional) group or an intervention (rapid) group. Overnight methods were used for identification and susceptibility testing in the control group, while the Vitek 2 system (bioMerieux, Marcy l'Etoile, France) was used in the rapid group. In each of three consecutive study periods, accelerating factors were added progressively to the laboratory workflow of the rapid group to increase same-day reporting, whereas methods remained identical in the conventional group. The turnaround time of the microbiological cycle using the Vitek 2 system as compared to conventional methods was studied and the clinical impact of a shortened turnaround time assessed in terms of mortality, morbidity, and cost. For the rapid groups, the turnaround time was significantly shorter for oral reporting of final susceptibility results in all three study periods and for reporting on paper in the third study period. There was no significant difference between groups in any of the clinical impact variables. Vitek 2 results were available for reporting significantly earlier as compared to conventional testing. For the overall patient group in our hospital setting, however, this had no clinical impact.

Aged↗