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At least 253 records · Page 14Linked to original sources
PubMed2001

Minimum dataset for recording myringotomy and ventilation tube insertion.

A minimum dataset for recording of findings during myringotomy and ventilation tube insertion for cases of otitis media with effusion is presented. With increasing pressures on surgeons to audit existing practices and hence improve standards of health care, it is appropriate to produce such a set of guidelines for a surgery that is frequently performed world-wide. We believe that the data presented is not too exhaustive and can be readily incorporated into the operative notes.

Data Collection↗
PubMed1998

Virtual cystoscopy based on helical CT scan datasets: perspectives and limitations.

The purpose of the study was to simulate cystoscopy based on three-dimensional helical CT scan datasets in real-time in patients with tumours of the urinary bladder. A helical CT scan with double detector technology was carried out pre-operatively in 11 patients with histologically confirmed carcinoma of the urinary bladder and one patient with chronic cystitis. A non-enhanced scan was first performed, followed by an examination in the early phase of contrast medium enhancement. Further images were acquired after adequate filling of the bladder with contrast medium, approximately 30 min after injection. These data were transferred to a separate graphic computer workstation and reconstructed. The results were then compared with the cystoscopic and histopathological findings. All tumours of the urinary bladder identified at fibreoptic cystoscopy were shown on virtual cystoscopy. The best reconstruction results were obtained from data acquired 30 min after injection of contrast medium. The ureteric orifices were not visualized at virtual cystoscopy. These data lead us to conclude that, at present, virtual cystoscopy has not reached the quality of fibreoptic examination and remains restricted to use in specific cases, for example patients with urethral strictures.

Aged↗
PubMed2025

Alterations in ether lipid metabolism in obesity revealed by systems genomics of multi-omics datasets.

Ratios between two metabolites are sensitive indicators of metabolic changes. Lipidomic profiling studies have revealed that plasma ether lipids, a class of glycero- and glycerophospho-lipids with reported health benefits, are negatively associated with obesity. Here, we utilized lipid ratios as surrogate markers of lipid metabolism to explore the processes underlying the inverse relationship between ether lipid metabolism and obesity. Plasma lipidomics data from two independent human cohorts (n = 10,339 and n = 4,492) were integrated to assess the associations between 82 lipid ratios and obesity-related markers in males and females. Results were externally validated using mouse transcriptomics data from the Hybrid Mouse Diversity Panel (n = 152-227 across 74 strains). Genome-wide association studies using imputed genotypes from a population cohort (n = 4,492) were performed to examine the genetic architecture of the ratios. Findings showed that waist circumference (WC), body mass index, and waist-hip ratio were inversely associated with total plasmalogens relative to total phospholipids in both sexes. Ratios comprising product-substrate pairs positioned either side of enzymes involved in plasmalogen synthesis and degradation showed positive and negative associations with WC, respectively. Branched-chain fatty acids negatively correlated with WC, while omega-6 polyunsaturated fatty acids exhibited differing associations depending on their position within the pathway. Mouse transcriptomics corroborated these results. Genomics data showed strong associations between ratios containing choline-plasmalogens and single-nucleotide polymorphisms in the transmembrane protein 229B (TMEM229B) gene region. This work demonstrates the utility of lipid ratios in understanding lipid metabolism. By applying the ratios to multi-omic datasets, we identified alterations in enzymatic activity and genetic variants likely affecting ether lipid synthesis in obesity that could not have been obtained from lipidomics data alone. Additionally, we characterized a potential role for TMEM229B, offering new perspectives on ether lipid metabolism and regulation.

Humans↗
PubMed2007

Characterizing a crystal from an initial native dataset.

Methods are presented for characterizing a crystal given an initial X-ray diffraction dataset. These methods can facilitate the structure determination process and illuminate the oligomeric state and symmetry of your molecule before the crystal structure is determined. Specifically, these methods include (1) calculation of Matthews coefficient to estimate the number of molecules in the asymmetric unit; (2) calculation and interpretation of a self-rotation function to evaluate the point group symmetry of the crystallized oligomer, if contained in the crystal; (3) calculation and interpretation of a native Patterson map to evaluate the presence of noncrystallographic translational symmetry; and (4) calculation of statistics to evaluate the possibility of merohedral twinning in a crystal.

Algorithms↗
PubMed2005

A system of metadata to control the process of query, aggregating, cleaning and analysing large datasets of primary care data.

BACKGROUND: Metadata is data that describes other data or resources. It has a defined number of named elements that convey meaning. Medical data are complex to process. For example, in the Primary Care Data Quality (PCDQ) renal programme, we need to collect over 300 variables because there are so many possible causes of renal disease. These variables are not just single columns of data--all are extracted as code plus date, while others are code-date-value. Metadata has the potential to improve the reliability of processing large datasets. OBJECTIVE: To define unique and unambiguous metadata headings for clinical data and derived variables. METHOD: We defined the look-up tables we would use as a controlled vocabulary to name the core clinical concepts within the metadata. We added six other elements to describe data: (1) the study or audit name; (2) the query used to extract the data; (3) the data collection number; (4) the type of data, including specifying the units; (5) the repeat number (if the variable was extracted more than once); and (6) a processing suffix that defines how the data have been processed. RESULTS: The metadata system has enabled the development of a query library and an analysis syntax library that make data processing and analysis more efficient. Its stability means greater effort can be put into more complex data processing, and some semiautomation of processes. However, the system has had implementation problems. It has been particularly hard to stop clinicians using multiple synonyms for the same variable. CONCLUSIONS: The PCDQ metadata system provides an auditable method of data processing. It is a method that should improve the reliability, validity and efficiency of processing routinely collected clinical data. This paper sets out to demystify our data processing method and makes the PCDQ metadata system available to clinicians and data processors who might wish to adopt it.

Electronic Data Processing↗
PubMed2002

Registration of bone surfaces, extracted from CT-datasets, with 3D ultrasound.

An essential task of computer assisted surgery is the registration of preoperative image data with the coordinate system of the operating room. This can be reached by using intraoperative imaging and registrating preoperative and intraoperative datasets. For intraoperative imaging ultrasound is a powerful tool due to the lack of ionizing radiation and because of its fast, inexpensive and easy data acquisition. We propose a surface volume matching algorithm for the registration of bone surfaces and ultrasound volume data. The bone surface is estimated from the preoperative CT data by taking into account that ultrasound only shows parts of the bone surface. By our method reliable matching results are obtained. They are shown with data of the lumbar spine.

Algorithms↗
PubMed2005

A new strategy of cooperativity of biclustering and hierarchical clustering: a case of analyzing yeast genomic microarray datasets.

Hierarchical clustering is difficult to be deployed effectively in finding meaningful subtrees since genes rarely exhibit similar expression pattern across a wide range of conditions. It is also difficult to find a suitable level in cleaving a big hierarchy tree. Biclustering is a promising methodology in the field of the analysis of gene expression data of genechip. Generally it can be employed in identification of gene groups, which show a coherent expression profile across a subset of conditions. But in some cases of biclustering analysis of gene expressions, the genes in one bicluster are involved in more than one functional group, or all genes in one bicluster are involved in unknown functional groups (e.g. pattern VI and VIII in our studies). Then, how to predict the function of genes in these patterns? In the present research, we developed a new strategy of combining both of the clustering methods, hierarchical clustering and biclustering. The reserved conditions in datasets for hierarchical clustering were elicited according to the conditions in biclusters, and after hierarchical clustering, more detailed results in predicting unknown genes in certain patterns were obtained. This strategy of cooperating both of the methods during clustering procedure should be an effective guideline for functional predictions.

Cluster Analysis↗
PubMed2005

Generation of a dataset for studying ligand effect on homodimer interface.

Protein dimer interfaces (homodimer - same polypeptide and heterodimer - different polypeptide) display geometric and chemical properties that give the non-covalent assembly its stability and specificity. Therefore, it is important to understand the molecular principles of dimer interaction. Several studies on homodimer interaction are available. However, a study on the effect of ligands (i.e. non-peptide compounds) on subunit interactions is not available. Hence, we generated a dataset of 62 identical homodimer pairs (one structure determined with an interface ligand and the other without an interface ligand) and analyzed the effect of interface ligands on dimer interface. The analysis suggests that homodimer interfaces having ligands are less hydrophobic with small interface area compared to those without ligands. We also found that ligands occupying = 7% interface area have negligible effect on dimer interaction.

Binding Sites↗
PubMed1990

Establishment of national datasets for mental health and substance abuse treatment services.

Congress has recognized the importance of having complete and uniform data available from the states in order to determine the need for additional funding for services within the mental health and substance abuse service delivery system. Congress also needs data to determine the effectiveness of available services and to evaluate the typology of clients served. In order to ensure that the necessary data are available for Congress, grant funds have been allocated to many states in order to 1) implement a uniform dataset for substance abusers which will ultimately lead to a national database, and 2) promote the adoption of the Mental Health Statistics Improvement Program to allow the National Institute of Mental Health to receive uniform data upon request. Collection of the data needed by Congress will have to begin at the facility level. Therefore medical record professionals working or consulting in mental health and substance abuse facilities need to be aware of the national data sets and must be prepared for changes in data reporting requirements to their state mental health and substance abuse agencies.

Data Collection↗
PubMed2000

Birth defects and paternal occupational exposure. Hypotheses tested in a record linkage based dataset.

UNLABELLED: MAIN QUESTION: To test previously established hypotheses on associations of birth defects with paternal occupation on the basis of a Norwegian registry material. METHODS: The study comprised all births in Norway 1970 -1993 for which linkage with population censuses 1970, -80 and -90 on parents' job title could be obtained--about 1 million births (75% all births). The reference population was offspring of the group that did not belong to the actual occupation. RESULTS: Vehicle mechanics had an association with hypospadias--OR 5.19 (CI 1.31-14.24), painters had a non-significant association with spina bifida--OR 2.03 (CI 0.99-3.75) and printers with club foot--OR 1.61 (CI 0.89-2.90). Associations observed previously in off-spring of fathers in large occupational groups such as teachers, drivers, electricity related occupations, sales related occupations and agricultural workers were not confirmed in this dataset. CONCLUSIONS: The study gave further evidence of cause effect relationships in the confirmed positive associations, though without any clarification of possible mechanisms involved. Possible false negative findings might be caused by low statistical power due to small occupational groups or non-differential misclassification of exposure.

Adult↗
PubMed2002

Transmembrane topology prediction methods: a re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topologies.

We selected 10 transmembrane (TM) prediction methods (KKD, TMpred, TopPred II, DAS, TMAP, MEMSAT 2, SOSUI, PRED-TMR2, TMHMM 2.0 and HMMTOP 2.0) and re-assessed its prediction performance using a reliable dataset with 122 entries of experimentally-characterized TM topologies. Then, we improved prediction performance by a consensus prediction method. Prediction performance during re-assessment and consensus prediction were based on four attributes: (i) the number of transmembrane segments (TMSs), (ii) the number of TMSs plus TMS-position, (iii) N-tail location and (iv) TM topology. We noted that hidden Markov model-based methods dominate over other methods by individual prediction performance for all four attributes. In addition, all top-performing methods generally were model-based. Among prokaryotic sequences, HMMTOP 2.0 solely topped among other methods with prediction accuracies ranging from 64% to 86% across all attributes. However, among eukaryotic sequences, prediction performance for all the attributes was relatively poor compared with prokaryotic ones. On the other hand, our results showed that our proposed consensus prediction method significantly improved prediction performance by, at least, an additional nine percentage points particularly among prokaryotic sequences for the number of TMS (84%), number of TMS and position (80%), and TM topology attributes (74%). Although our consensus prediction method improved also the prediction performance among eukaryotic sequences, the obtained accuracies for all attributes were relatively lower than that obtained by prokaryotic counterparts particularly for TM topology.

Cell Membrane↗
PubMed1984

IUD--related uterine perforation: an epidemiologic analysis of a rare event using an international dataset.

An international dataset of 21,610 IUD insertions revealed 41 uterine perforations occurring at the time of, or subsequent to, insertion. Dat were collected on standard forms. Perforations were classified as confirmed, probable, or possible, based on the clinician's judgement and subsequent management. The uterine perforation rate was estimated as between 1.9 and 3.6/1000 insertions. 13 of the total 41 perforations were reported from 2 of 72 cooperating clinics. In 1 clinic, this center-clustering phenomenon suggested an effect of a high risk device. In the other clinic, the effect of insertor (operator) inexperience was indicated. A case-control analysis delineated previous cesarean section as a host risk factor (P0.05, McNemar's chi square). Further investigation of this association by similar case-control studies is recommended.

Age Factors↗
PubMed2003

Updated risk adjustment mortality model using the complete 1.1 dataset from the American College of Cardiology National Cardiovascular Data Registry (ACC-NCDR).

OBJECTIVES: To revise and update a risk adjustment model for in-hospital mortality following percutaneous coronary intervention (PCI) procedures using all data from the 1.1 version of the American College of Cardiology National Cardiovascular Data Registry (ACC-NCR). BACKGROUND: A model based on data received at the ACC-NCDR from 1998-2000 was previously reported. The revision of this mortality model reflects all of the data submitted using 1.1 data specifications and collected through the second quarter of 2001. The model was applied to selected high-risk subgroups from a sample of data collected during the year 2001 from version 2.0 of the NCDR. METHODS: Data on 173,743 PCI procedures collected at the ACC-NCDR between January 1, 1998 and March 31, 2001 were analyzed. A mortality model was generated as well as separate models for presentation with and without acute myocardial infarction within 24 hours. The model was used to generate predicted mortalities that were compared to observed mortalities in more current high-risk patient subgroups in the NCDR. RESULTS: The same factors that were previously found to be associated with increased risk of PCI mortality were re-verified in the current analysis. Inclusion of the complete 1.1 dataset produced some changes in the regression weights and the constant value. Excellent discrimination was achieved in the revised model (C-Index = 0.89). The model was applied to high-risk patient groups from data collected on 76,249 during the calendar year 2001 using the 2.0 NCDR data elements and definitions. These analyses showed a high level of agreement between observed mortality of each subgroup and the predicted mortality rates generated from the revised 1.1 PCI mortality model. CONCLUSIONS: Risk adjustment models for in-hospital mortality following PCI for all patients and for those with and without recent MI were regenerated using all data collected from the 1.1 data specifications of the ACC-NCDR and validated on high-risk groups from data collected during 2001 under data version 2.0 of the NCDR. These models reflect the most up-to-date analysis of mortality prediction from this large, multi-center national database.

Aged↗
PubMed2003

A colorimetric characterization of the raw digital data of the Visible Human Dataset images.

A colorimetric characterization of the all about 9 thousand Visible Human Dataset (VHD) cryosectioned color images of the male and female body is described here. Such characterization is performed keeping limited the computational time besides the high resolution of the considered VHD images. The about 27 thousand distinct histograms obtained are downloadable from the VHD Milano Mirror Site ftp server.

Algorithms↗
PubMed2003

Mining microarray datasets aided by knowledge stored in literature.

DNA microarray technology produces large amounts of data. For data mining of these datasets, background information on genes can be helpful. Unfortunately most information is stored in free text. Here, we present an approach to use this information for DNA microarray data mining.

Databases, Genetic↗