PubMed Health⌕ Search

Biomedical subjects

I Reuter

Publications and source records attributed to I Reuter.

At least 19 recordsLinked to original sources
PubMed2003

MATCH: A tool for searching transcription factor binding sites in DNA sequences.

Match is a weight matrix-based tool for searching putative transcription factor binding sites in DNA sequences. Match is closely interconnected and distributed together with the TRANSFAC database. In particular, Match uses the matrix library collected in TRANSFAC and therefore provides the possibility to search for a great variety of different transcription factor binding sites. Several sets of optimised matrix cut-off values are built in the system to provide a variety of search modes of different stringency. The user may construct and save his/her specific user profiles which are selected subsets of matrices including default or user-defined cut-off values. Furthermore a number of tissue-specific profiles are provided that were compiled by the TRANSFAC team. A public version of the Match tool is available at: http://www.gene-regulation.com/pub/programs.html#match. The same program with a different web interface can be found at http://compel.bionet.nsc.ru/Match/Match.html. An advanced version of the tool called Match Professional is available at http://www.biobase.de.

Algorithms↗
PubMed2003

TRANSFAC: transcriptional regulation, from patterns to profiles.

The TRANSFAC database on eukaryotic transcriptional regulation, comprising data on transcription factors, their target genes and regulatory binding sites, has been extended and further developed, both in number of entries and in the scope and structure of the collected data. Structured fields for expression patterns have been introduced for transcription factors from human and mouse, using the CYTOMER database on anatomical structures and developmental stages. The functionality of Match, a tool for matrix-based search of transcription factor binding sites, has been enhanced. For instance, the program now comes along with a number of tissue-(or state-)specific profiles and new profiles can be created and modified with Match Profiler. The GENE table was extended and gained in importance, containing amongst others links to LocusLink, RefSeq and OMIM now. Further, (direct) links between factor and target gene on one hand and between gene and encoded factor on the other hand were introduced. The TRANSFAC public release is available at http://www.gene-regulation.com. For yeast an additional release including the latest data was made available separately as TRANSFAC Saccharomyces Module (TSM) at http://transfac.gbf.de. For CYTOMER free download versions are available at http://www.biobase.de:8080/index.html.

Animals↗
PubMed2002

Evaluation of sequence motifs found in scaffold/matrix-attached regions (S/MARs).

Based on the contents of the database S/MARt DB, the most comprehensive data collection of scaffold/matrix-attached regions (S/MARs) publicly available thus far, we initiated a systematic evaluation of the stored data. By analyzing the 245 S/MAR sequences presently described in this database, we found that the S/MARs contained in this collection are generally AT-rich, with certain significant exceptions. Comparative analyses showed that most of the AT-rich motifs which were found to be enriched in S/MARs are also enriched in randomized S/MAR sequences of the same AT content. Some sequence patterns previously suggested to be characteristic for S/MARs were also investigated, among them potential binding sites for homeodomain transcription factors. Even though hexanucleotides containing the core motif of homeodomain factors were frequently observed in S/MARs, only a few potential binding sites for these factors were found enriched when compared with regulatory regions or exon sequences. All our analyses indicated that, on average, the observed frequency of motifs in S/MAR elements is largely influenced by the AT content. Our results can serve as a guideline for further improvements in the definition of S/MARs, which are now believed to constitute the functional coordinate system for genomic regulatory regions.

AT Rich Sequence↗
PubMed2000

TRANSFAC: an integrated system for gene expression regulation.

TRANSFAC is a database on transcription factors, their genomic binding sites and DNA-binding profiles (http://transfac.gbf.de/TRANSFAC/). Its content has been enhanced, in particular by information about training sequences used for the construction of nucleotide matrices as well as by data on plant sites and factors. Moreover, TRANSFAC has been extended by two new modules: PathoDB provides data on pathologically relevant mutations in regulatory regions and transcription factor genes, whereas S/MARt DB compiles features of scaffold/matrix attached regions (S/MARs) and the proteins binding to them. Additionally, the databases TRANSPATH, about signal transduction, and CYTOMER, about organs and cell types, have been extended and are increasingly integrated with the TRANSFAC data sources.

Database Management Systems↗
PubMed2000

The effect of exercise on pharmacokinetics and pharmacodynamics of levodopa.

The aim of our study was to evaluate the influence of low-intensity exercise on levodopa absorption and levodopa motor effect. We studied the pharmacokinetics and pharmacodynamics of levodopa under resting conditions and under a workload of 50 watts for 2 hours on a cycle ergometer in 12 parkinsonian patients with predictable fluctuations of motor disability. The patients attended the hospital on both days in a provoked off state. After a baseline assessment of motor disability using the Columbia University rating scale (CURS scale) and a blood test for measurement of the baseline levodopa concentration in the plasma, 100 mg levodopa and 25 mg benserazide were administered as a single dose orally. Blood samples for measurement of the levodopa concentration in the plasma were taken, and motor assessments were conducted at 15-minute intervals for 240 minutes and at 30-minute intervals from 240 to 360 minutes. All patients were able to perform the exercise program. The baseline Columbia University rating scale score did not differ significantly between both days. The mean levodopa concentration in plasma at half-maximal motor effect tended to be higher during exercise and indicated that the patients needed a higher levodopa concentration in plasma to achieve the half-maximal motor effect. The maximal levodopa concentration in plasma tended to be higher with exercise. Both trends did not reach statistical significance. In summary, there was not a negative or a positive net effect of exercise on pharmacokinetics and pharmacodynamics of levodopa. However, there were two counteracting trends: a trend toward better levodopa absorption and a trend toward a deteriorated concentration-effect correlation.

Administration, Oral↗
PubMed2000

Prospective study on the reproducibility of cephalometric landmarks on conventional and digital lateral headfilms.

The introduction of digital X-ray techniques offered a variety of new possibilities for digital image enhancement and exposure reduction. In order to compare the reproducibility of cephalometric landmarks on conventional and digital lateral headfilms 100 digital and 100 conventional lateral headfilms of patients attending our clinic were randomly selected. The digital cephalograms were obtained using storage phosphor plates in standard X-ray cassettes. All X-rays had been taken at 77 kV. For the digital images the mAs settings for conventional images minus 4 mAs were used. Two orthodontists traced each X-ray twice (21 reference points) at an interval of at least 1 week. The tracings were superimposed and the distances between the tracings of identical reference points were registered. The average reproducibility of cephalometric landmarks was significantly higher on the digitally obtained images, despite a reduction of radiation exposure of 23.7% in the digital images.

Cephalometry↗
PubMed2000

A clinical evaluation of some factors affecting image quality in panoramic radiography.

AIM: To evaluate the suitability of panoramic radiographs obtained with two different machines for clinical use. MATERIAL AND METHODS: Three observers assessed 111 pairs of panoramic radiographs taken with the Scanora (Soredex, Orion Corp., Helsinki, Finland) programme 001, and the Orthophos Plus (Sirona, Bensheim, Germany), programme P1 respectively, for visualisation of seven anatomical structures on each side, on a 5-point scale where 1 = very good. The median values were computed and a descriptive analysis performed. Interrater and intrarater agreement were expressed as weighted kappa. RESULTS: The median values of both Scanora and Orthophos radiographs were the same, scoring 2. The intra- and inter-observer agreement was generally poor and similar for both machines. CONCLUSIONS: The two panoramic machines were both given good ratings for evaluation of anatomical structures. The differences were very small and suggest that both machines are suitable for clinical use.

Alveolar Process↗
PubMed2000

Late onset levodopa responsive Huntington's disease with minimal chorea masquerading as Parkinson plus syndrome.

Huntington's disease is characterised by hyperkinetic movements, mainly chorea, cognitive dysfunction, and psychiatric abnormalities. Non-dopa responsive parkinsonism occurs in the later stages of choreic disease or as the predominant feature of juvenile patients (Westphal variant). Late onset Huntington's disease presenting as levodopa responsive parkinsonism is rare. A series of four patients with late onset Huntington's disease presenting as levodopa responsive parkinsonism and cardiovascular dysautonomia, initially misdiagnosed as multiple system atrophy (MSA) in three patients, is reported. Levodopa treatment did not unmask significant chorea. These cases suggest the presence of a distinct phenotypic variant of Huntington's disease to be added to the differential diagnosis of other akinetic rigid syndromes.

Aged↗
PubMed1999

Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms.

TRANSFAC is a database on transcription factors, their genomic binding sites and DNA-binding profiles. In addition to being updated and extended by new features, it has been complemented now by a series of additional database modules. Among them, modules which provide data about signal transduction pathways (TRANSPATH) or about cell types/organs/developmental stages (CYTOMER) are available as well as an updated version of the previously described COMPEL database. The databases are available on the WWW at http://transfac.gbf.de/

Animals↗
PubMed1999

Exercise test in Parkinson's disease.

UNLABELLED: In this study we assessed cardiovascular performance and metabolic response after an exercise test in Parkinsonian patients (PD patients). METHODS: 15 PD patients (10 male, 5 female; mean age:63 +/- 6.17 y; mean weight: 72.2 +/- 9.5 kg) and 15 sex, age (mean: 63.8 +/- 5.38 y), and weight-(mean: 72.2 +/- 8.69 kg) matched controls performed an exercise test using a cycle ergometer and a ramp protocol. All patients and control subjects underwent a heart rate variability test prior to the exercise test. At rest and at the end of each interval blood pressure (BP) and capillary lactate samples were taken. Heart rate was monitored continuously. RESULTS: The heart rate variability tests were abnormal in Parkinson's patients. All patients and control subjects achieved an intensity level of 75 watts, 12/15 PD patients managed 100 watts, and 7/15 PD patients managed 150 watts. 12/15 control subjects performed at an intensity level of 125 Watts and 9/15 at an intensity level of 150 Watts. There was no statistically significant difference in heart rate increase but there was a tendency to lower lactate levels at high intensity levels in PD patients. PD patients had a statistically lower systolic BP at 75, 100, 125, and 150 watts. CONCLUSION: We did not find striking differences in cardiovascular adaptation to physical work in PD patients and we propose, therefore, that it should be possible to improve cardiovascular endurance in PD patients. Previously, reports have suggested respiratory chain impairment in Parkinson's disease and poor endurance performance. However, our results do not support a clinically relevant impairment of the respiratory chain.

Blood Pressure↗
PubMed1999

Triple images on panoramic radiographs.

OBJECTIVE: To explain the formation of triple images on panoramic radiographs. METHODS: A metal test object was placed in defined positions in relation to movement path of a panoramic X-ray beam. RESULTS: The test object was portrayed once, twice or three times with varying degrees of distortion depending on its location. Triple images were formed when the test object was located in a specific diamond-shaped area distal to the path of the rotation centre of the X-ray beam. CONCLUSIONS: The formation of triple images on panoramic radiographs can be explained on the basis of known projection geometry.

Artifacts↗
PubMed1999

Reproducible X-ray projection geometry in edentulous patients.

OBJECTIVE: To evaluate a novel fixation system for reproducible radiography in edentulous patients. METHODS: A conventional extra-oral fixation system was modified with a filmholder and adjustable scales. For measuring reproducibility and angulation errors two rods and two balls were fixed on the alveolar crests of the maxilla and the mandible and angular variations were measured. One hundred radiographs of a conventional phantom were taken by one of the authors and by ten dental students. The angular disparity was calculated and intra- and interoperator precision determined. RESULTS: The average time taken to assemble the fixation system was 4 min. The 95% confidence interval for precision of the single operator was less than 2.5 degrees in both the maxilla and mandible. The 95% confidence interval for precision of the ten students was less than 2.2 degrees for the maxilla and 2.7 degrees for the mandible. There was no significant difference (P>0.05) in interoperator precision. CONCLUSION: The novel extra-oral fixation system appears to be a potential means of obtaining reproducible radiographs of edentulous patients.

Humans↗
PubMed1999

Therapeutic value of exercise training in Parkinson's disease.

PURPOSE: The objective of this study was to investigate the influence of an intensive exercise training on motor disability, mood, and subjective well-being in parkinsonian patients. METHODS: The study was designed as an open long-term pilot trial over 20 wk. Sixteen slightly to moderately affected idiopathic parkinsonian patients (PD) were included. An intensive standardized exercise training was performed twice weekly over 14 wk in all patients. Evaluations were performed before the start of the study (exam. 1), after 7 wk (exam 2), 14 wk (exam 3), and 20 wk (exam 4/long-term effect). The test battery included: 1) basic motor test (BMT) [test for muscle strength, flexibility, and coordination]; 2) Unified Parkinson's Disease Rating Scale (UPDRS) and Columbia University Rating Scale (CURS) for PD-specific motor disability; and 3) registration of psychometric data by Mini Mental State (MMS) for dementia and the Adjective Mood Questionnaire of Zeersen (AMQZ) and Sickness Impact Profile (SIP) for subjective well-being. RESULTS: UPDRS sigma score (P < 0.0001), CURS sigma score (P < 0.0001) and BMT 2 score (P < 0.0001) improved significantly by exercise training. Six weeks after termination of the training program, the majority of the patients had lost only minor components of their regained motor skills. There was no significant change in cognitive function during the study. The results of open interviews referring to subjective well-being were confirmed by the AMQZ and SIP. As an unexpected side effect, dyskinesias seemed to be better controlled. CONCLUSION: Motor disability as well as mood and subjective well-being can be clearly improved by intensive sports activities in early to medium stage PD patients. A sustained ongoing benefit outlasting the active training period for at least 6 wk can be achieved but the exact duration of this benefit is open.

Affect↗
PubMed1999

Nocturnal subcutaneous apomorphine infusion in Parkinson's disease and restless legs syndrome.

OBJECTIVES: Nocturnal disabilities leading to fragmented sleep arising from parkinsonian off period related complications are common, under-reported and are difficult to treat. In this study, we evaluate the use of nocturnal continuous subcutaneous overnight apomorphine infusion in Parkinson's disease and restless legs syndrome. METHODS: Six parkinsonian patients and 2 patients with restless legs syndrome with nocturnal disabilities refractory to conventional oral therapy were assessed using a sleep diary while on standard treatment and during nocturnal apomorphine infusion. Three patients agreed to assessments during placebo infusion with normal saline. RESULTS: Apomorphine led to a dramatic reduction of nocturnal awakenings, nocturnal off periods, pain, dystonia and nocturia in parkinsonian patients. In patients with restless legs syndrome, apomorphine reduced nocturnal discomfort, reduced leg movements and improved pain and spasm scores significantly. Placebo infusion reproduced pain, nocturnal spasms and sleep disruption. CONCLUSION: This study suggests that overnight apomorphine infusion may be effective in overcoming refractory nocturnal disabilities in selected patients with Parkinson's disease and restless legs syndrome.

Adult↗
PubMed1998

Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL.

TRANSFAC, TRRD (Transcription Regulatory Region Database) and COMPEL are databases which store information about transcriptional regulation in eukaryotic cells. The three databases provide distinct views on the components involved in transcription: transcription factors and their binding sites and binding profiles (TRANSFAC), the regulatory hierarchy of whole genes (TRRD), and the structural and functional properties of composite elements (COMPEL). The quantitative and qualitative changes of all three databases and connected programs are described. The databases are accessible via WWW:http://transfac.gbf.de/TRANSFAC orhttp://www.bionet.nsc.ru/TRRD

Animals↗