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At least 1,045 records · Page 58Linked to original sources
PubMed2004

Survival after surgery or therapeutic catheterisation for congenital heart disease in children in the United Kingdom: analysis of the central cardiac audit database for 2000-1.

OBJECTIVES: To analyse simple national statistics and survival data collected in the central cardiac audit database after treatment for congenital heart disease and to provide long term comparative statistics for each contributing centre. DESIGN: Prospective, longitudinal, observational, national cohort survival study. SETTING: UK central cardiac audit database. MAIN OUTCOME MEASURES: Survival at 30 days and one year after treatment in the year April 2000-March 2001, assessed by using both volunteered life status and independently validated life status through the Office for National Statistics, using the patient's unique NHS number, or the general register offices of Scotland and Northern Ireland. Institutional results following a group of six benchmark operations and three benchmark catheterisation procedures. RESULTS: Since April 2000 data have been received from all 13 UK tertiary centres performing cardiac surgery or therapeutic cardiac catheterisation in children with congenital heart disease. Altogether 3666 surgical procedures and 1828 therapeutic catheterisations were performed. Central tracking of mortality identified 469 deaths, 194 occurring within 30 days and 275 later. Forty two of the 194 deaths within 30 days were detected by central tracking but not by volunteered data. For surgery overall, survival at 30 days was 94.9%, falling to 91.2% at one year; this effect was most marked for infants. For therapeutic catheterisation survival at 30 days was 99.1%, falling to 98.1% at one year. Survival of individual centres or individual operators did not differ from the national average after benchmark procedures. CONCLUSIONS: Independent data validation is essential for accurate survival analysis. One year survival gives a more realistic view of outcome than traditional perioperative mortality. Currently no detectable difference exists in survival between any of the 13 UK tertiary congenital heart disease centres, but confidence intervals for small centres are wide, limiting our power to detect underperformance from analysis of a single year's data. Appropriately resourced, focused national audit is capable of accurate data collection on which nationwide, long term quality control can be based.

Cardiac Catheterization↗
PubMed2006

A real-time quantitative PCR detection method specific to widestrike transgenic cotton (event 281-24-236/3006-210-23).

In compliance with global regulations on transgenic crops, a real-time quantitative PCR method specific to Widestrike transgenic cotton (event 281-24-236/3006-210-23, OECD Unique Identifier DAS-24236-5/DAS-21023-5) was established on the basis of the DNA sequences in the junction between the transgene insert and cotton genome. The optimized method consists of a DNA extraction method for cotton seeds and three PCR systems corresponding to a cotton-specific endogenous reference DNA sequence SAH7 (Sinapis Arabidopsis Homolog 7) and specific detection of event 281-24-236 and event 3006-210-23. The method performance including specificity, sensitivity, accuracy, and precision was determined at a dynamic range of Widestrike DNA levels from 0.04% to 5.0%. The limits of detection (LOD) and quantification (LOQ) were < or =0.04% and < or =0.09%, respectively, at 100 ng of DNA sample per reaction. The quantification results using either the event 281-24-236 or 3006-210-23 system were consistent, and the relative deviation from the expected (true) value was in the range of +/-25%. The robustness of the method was demonstrated by a series of tests with deviations from the optimized assay parameters such as annealing temperature, extension time, PCR instrument, interlaboratory transferability, etc. All the measurements from these tests met the criteria set by EU JRC-CRL (European Commission Joint Research Centre-Community Reference Lab). This real-time quantitative PCR method is accurate and robust, and is recommended as a global benchmark method for the detection and quantification of Widestrike cotton. The method including description, protocol, and performance results is available on the JRC-CRL website (http://gmo-crl.jrc.it/statusofdoss.htm).

DNA, Plant↗
PubMed2001

Basecalling with LifeTrace.

A pivotal step in electrophoresis sequencing is the conversion of the raw, continuous chromatogram data into the actual sequence of discrete nucleotides, a process referred to as basecalling. We describe a novel algorithm for basecalling implemented in the program LifeTrace. Like Phred, currently the most widely used basecalling software program, LifeTrace takes processed trace data as input. It was designed to be tolerant to variable peak spacing by means of an improved peak-detection algorithm that emphasizes local chromatogram information over global properties. LifeTrace is shown to generate high-quality basecalls and reliable quality scores. It proved particularly effective when applied to MegaBACE capillary sequencing machines. In a benchmark test of 8372 dye-primer MegaBACE chromatograms, LifeTrace generated 17% fewer substitution errors, 16% fewer insertion/deletion errors, and 2.4% more aligned bases to the finished sequence than did Phred. For two sets totaling 6624 dye-terminator chromatograms, the performance improvement was 15% fewer substitution errors, 10% fewer insertion/deletion errors, and 2.1% more aligned bases. The processing time required by LifeTrace is comparable to that of Phred. The predicted quality scores were in line with observed quality scores, permitting direct use for quality clipping and in silico single nucleotide polymorphism (SNP) detection. Furthermore, we introduce a new type of quality score associated with every basecall: the gap-quality. It estimates the probability of a deletion error between the current and the following basecall. This additional quality score improves detection of single basepair deletions when used for locating potential basecalling errors during the alignment. We also describe a new protocol for benchmarking that we believe better discerns basecaller performance differences than methods previously published.

Algorithms↗
PubMed2002

Physiological variables at lactate threshold under-represent cycling time-trial intensity.

BACKGROUND: The importance of lactate threshold (LT) as a determinant of performance in endurance sports has been established. In addition, it has been shown that during running and selected other endurance competitions, athletes perform at a velocity and VO2 slightly above LT for the duration of the event. Prior work indicates however, that this may not be true during a cycling time-trial (TT). This investigation sought to compare physiological variables during a 20-k TT with those corresponding to the athlete's LT. METHODS: Thirteen male cyclists (22.7+/-0.8 yrs; 180.6+/-8.0 cm; 77.1+/-10.0 kg; 8.3+/-2.5% fat; 4.9+/-2.2 l x min(-1), VO2max) participated in the study. Subjects performed a graded protocol starting at 150 Watts (W) to determine LT (2 mmol x L(-1) above baseline) which consisted of 20 W increases every 4-min. Following an 8 min-recovery, subjects cycled at the wattage corresponding to LT-20 W for 1 min and then workload increased 20 W every minute until volitional exhaustion to determine VO2max x On a separate occasion a self-paced, 20-k TT was completed. RESULTS: Mean values of blood lactate, HR and % HRmax, VO2 and % VO2max, and power output throughout the 20-k TT were greater (p<0.01) than those at LT. During the TT these cyclists performed at an intensity well above LT (blood lactate=252.0+/-0.1%, HR=9.4+/-0.03%, %HRmax=9.2+/-0.15%, VO2=26.5+/-0.7%, %VO2max=17.2+/-0.08% and power out-put=14.8+/-0.14% above LT) for over 30 min. CONCLUSIONS: Therefore, while LT may be highly correlated to performance, it may not be representative of race pace for a cycling TT, and may be questionable as a benchmark used to prescribe training intensity for competitive TT-cycling.

Adult↗
PubMed2025

Prediction of local convergent shifts in evolutionary rates with phyloConverge.

MOTIVATION: Convergence analysis can characterize genetic elements underlying morphological adaptations. However, its performance on regulatory elements is limited due to their modular composition of transcription factor motifs, which have rapid turnover and experience different evolutionary pressures. RESULTS: We introduce phyloConverge, a phylogenetic method that performs scalable, fine-grained local convergence analysis of genomic elements at flexible length scales. Using a benchmarking case of convergent subterranean mammal adaptation, phyloConverge identifies rate-accelerated conserved noncoding elements (CNEs) with high specificity and statistical robustness relative to competing methods. From CNE-level scoring, we detect the convergent regression of entire CNE units and highlight the contrast that subterranean-associated coding region regression is highly specific to ocular functions, whereas regulatory element regression is enriched for accompanying neuronal phenotypes and other developmental processes. From transcription factor motif-level scoring, we dissect elements into subregions with uneven convergence signals and demonstrate the modular adaptation of CNEs with high functional specificity. Finally, we demonstrate phyloConverge's scalability to perform high-resolution convergence analysis genome-wide. AVAILABILITY AND IMPLEMENTATION: phyloConverge is available at https://github.com/ECSaputra/phyloConverge.

Evolution, Molecular↗
PubMed2001

LiveBench-1: continuous benchmarking of protein structure prediction servers.

We present a novel, continuous approach aimed at the large-scale assessment of the performance of available fold-recognition servers. Six popular servers were investigated: PDB-Blast, FFAS, T98-lib, GenTHREADER, 3D-PSSM, and INBGU. The assessment was conducted using as prediction targets a large number of selected protein structures released from October 1999 to April 2000. A target was selected if its sequence showed no significant similarity to any of the proteins previously available in the structural database. Overall, the servers were able to produce structurally similar models for one-half of the targets, but significantly accurate sequence-structure alignments were produced for only one-third of the targets. We further classified the targets into two sets: easy and hard. We found that all servers were able to find the correct answer for the vast majority of the easy targets if a structurally similar fold was present in the server's fold libraries. However, among the hard targets--where standard methods such as PSI-BLAST fail--the most sensitive fold-recognition servers were able to produce similar models for only 40% of the cases, half of which had a significantly accurate sequence-structure alignment. Among the hard targets, the presence of updated libraries appeared to be less critical for the ranking. An "ideally combined consensus" prediction, where the results of all servers are considered, would increase the percentage of correct assignments by 50%. Each server had a number of cases with a correct assignment, where the assignments of all the other servers were wrong. This emphasizes the benefits of considering more than one server in difficult prediction tasks. The LiveBench program (http://BioInfo.PL/LiveBench) is being continued, and all interested developers are cordially invited to join.

Computer Simulation↗
PubMed1997

Do aligned sequences share the same fold?

Sequence comparison remains a powerful tool to assess the structural relatedness of two proteins. To develop a sensitive sequence-based procedure for fold recognition, we performed an exhaustive global alignment (with zero end gap penalties) between sequences of protein domains with known three-dimensional folds. The subset of 1.3 million alignments between sequences of structurally unrelated domains was used to derive a set of analytical functions that represent the probability of structural significance for any sequence alignment at a given sequence identity, sequence similarity and alignment score. Analysis of overlap between structurally significant and insignificant alignments shows that sequence identity and sequence similarity measures are poor indicators of structural relatedness in the "twilight zone", while the alignment score allows much better discrimination between alignments of structurally related and unrelated sequences for a wide variety of alignment settings. A fold recognition benchmark was used to compare eight different substitution matrices with eight sets of gap penalties. The best performing matrices were Gonnet and Blosum50 with normalized gap penalties of 2.4/0.15 and 2.0/0.15, respectively, while the positive matrices were the worst performers. The derived functions and parameters can be used for fold recognition via a multilink chain of probability weighted pairwise sequence alignments.

Databases as Topic↗
PubMed2005

[Quality control in imaging standards for stroke diagnosis].

Hospitals in "Rhineland-Palatinate" and "Saarland" as well as in other German states are using benchmarking in quality control and to improve diagnostic procedures and treatment in stroke. The goal is a continuous learning process in which participants improve their performance by comparing themselves to the highest quality care. CCT/MRI procedures are an important tool in stroke therapy and prophylaxis. Structural quality was good in all 39 participating hospitals. The best evidence-based indicator in quality control of CCT/MRI procedures is the process quality in performing these procedures within 3 h after stroke onset. Process quality was better in hospitals that cared for many stroke patients than in those with fewer cases. The latter hospitals also had less clinical and diagnostic competence. Benchmarking in quality control was successful because over the years improvement in stroke management was obvious in the participating hospitals.

Appointments and Schedules↗
PubMed2006

Density functional computations of 99Ru chemical shifts: relativistic effects, influence of the density functional, and study of solvent effects on fac-[Ru(CO)3I3]-.

Solvent effects on the 99Ru NMR chemical shift of the complex fac-[Ru(CO)3I3]- are investigated computationally using density functional theory. Further, benchmark calculations of the 99Ru shift for a set of ten Ru complexes have been performed in order to calibrate the computational model and to determine the importance of relativistic effects on the 99Ru nuclear magnetic shielding and on the chemical shift. A computational model for fac-[Ru(CO)3I3]- that includes both explicit solvent molecules and a continuum model is shown to yield the best agreement with experiment. Relativistic corrections are shown to be of minor importance for determining 99Ru chemical shifts. On the other hand, the nature of the density functional is of importance. In agreement with literature data for ligand trends of 99Ru chemical shifts, the chemical shift range for different solvents is also best reproduced by a hybrid functional.

Journal Article↗
PubMed2001

A statistical model for the evaluation of barrier contraceptive efficacy.

This paper describes an approach for the analysis of barrier contraceptive efficacy trials that accounts for timing frequency of intercourse and compliance. We allow exposure variables to vary for each act of intercourse and we control for timing of each act through a specific parametric function of the day of the act relative to the last day of the follicular phase of the cycle. The model can be used to examine the level of protection provided by a barrier versus no contraceptive method even when no control group of non-users is studied, as long as there are acts with no barrier use during the fertile window. We present results of a simulation study which examines performance of estimators and power under a variety of scenarios, including situations where an accurate benchmark for ovulation day is not available. As compared to the survival analysis approach commonly used in this setting, simulation results show that the new approach yields considerable gains in power to detect differences between the efficacy of contraceptive methods. An application to data from the FemCap versus diaphragm trial show results consistent with previous findings suggesting superiority of the diaphragm but also provides new evidence of the per act protection provided by both methods.

Biometry↗
PubMed1990

A CPU benchmark for protein crystallographic refinement.

The CPU time required to complete a cycle of restrained least-squares refinement of a protein structure from X-ray crystallographic data using the FORTRAN codes PROTIN and PROLSQ are reported for 48 different processors, ranging from single-user workstations to supercomputers. Sequential, vector, VLIW, multiprocessor, and RISC hardware architectures are compared using both a small and a large protein structure. Representative compile times for each hardware type are also given, and the improvement in run-time when coding for a specific hardware architecture considered. The benchmarks involve scalar integer and vector floating point arithmetic and are representative of the calculations performed in many scientific disciplines.

Computers↗
PubMed2005

SPINEVOLUTION: a powerful tool for the simulation of solid and liquid state NMR experiments.

Exact numerical simulations of NMR experiments are often required for the development of new techniques and for the extraction of structural and dynamic information from the spectra. Simulations of solid-state magic angle spinning (MAS) experiments can be particularly demanding both computationally and in terms of the programming required to carry them out, even if special simulation software is used. We recently developed a number of approaches that dramatically improve the efficiency and allow a high degree of automation of these computations. In the present paper, we describe SPINEVOLUTION, a highly optimized computer program that implements the new methodology. The algorithms used in the program will be described separately. Although particularly efficient for the simulation of experiments with complex pulse sequences and multi-spin systems in solids, SPINEVOLUTION is a versatile and easy to use tool for the simulation and optimization of virtually any NMR experiment. The performance of SPINEVOLUTION was compared with that of another recently developed NMR simulation package, SIMPSON. Benchmarked on a series of examples, SPINEVOLUTION was consistently found to be orders of magnitude faster. At the time of publication, the program is available gratis for non-commercial use.

Algorithms↗
PubMed1999

Technical validation of low-cost videoconferencing systems applied in orthopaedic teleconsulting services.

Investigation on the applicability of low-cost videoconferencing (VC) for health care services is becoming a real need. Reduced resources drive the administrators to evaluate inexpensive solutions for telemedicine. Considering this scenario, this work is a preliminary step to validate, from a technical point of view, if low-cost VC systems could be suitable for orthopaedic teleconsulting services. For this purpose, four different videoconferencing systems were tested. Each VC system was composed of a computer and a VC device installed in. VC devices were chosen among the most popular and distributed products (made by Intel, PictureTel and Aethra). The Telemedicine Benchmark, a specific tool defined by the authors, was applied to measure the overall systems performances in terms of time delays during basic rate ISDN connections (128 Kbit/s). Results showed that it is possible to apply low-cost videoconferencing systems for orthopaedic teleconsulting services. Most of the systems provided acceptable performance for medical image visualization and real time joint working. Further developments are recommendable to enhance the VC software tools capabilities and to improve software-user interface. reserved.

Costs and Cost Analysis↗
PubMed2001

Measuring and improving patients' and families' perceptions of care in a system of pediatric hospitals.

BACKGROUND: Shriners Hospitals for Children (SHC) is a network of 22 pediatric specialty hospitals that provide medical care free of charge to children up to 18 years of age and that serve as referral centers for children with complex orthopedic and burn problems. In 1998 the SHC system began using The Picker Institute's Patient and Family Perception of Care inpatient survey throughout its hospitals. SYSTEMWIDE IMPLEMENTATION: A broad-based implementation plan was developed to promote acceptance of the perception of care topic and provide education on performance improvement. In 1999 a work group was formed to prioritize areas for improvement, survey benchmark hospitals, and identify best practices in benchmark hospitals. This work group first focused on the dimensions of Partnership Between Families and Clinicians and Information and Education to the Child. In May 1999 the work group began the task of identifying best practices in these two priority dimensions from the SHC benchmark hospitals. Surveys were submitted to those hospitals, asking what they perceived as being the reasons they scored well in those areas. The results of these surveys were used to identify key practices in these benchmark hospitals that are of significant importance in patient and family perceptions of quality care. NEXT STEPS: The challenge is to facilitate cross-facility interactions to understand and adopt best practices. Focus groups will be conducted to further delineate the dimensions with higher problem scores. The SHC system plans to expand the patient surveys to outpatients, to allow for the evaluation of the full complement of hospital patients.

Burn Units↗
PubMed2003

Intensity-based statistical scorer for tandem mass spectrometry.

We describe a new statistical scorer for tandem mass spectrometry. The scorer is based on the probability that fragments with given chemical properties create measured intensity levels in the experimental spectrum. The scorer's parameters are computed using a fully automated procedure. Benchmarking the new scorer on a large set of experimental spectra, we show that it performs significantly better than the widely used cross-correlation scoring algorithm of Eng et al. (Eng, J. K; McKormack, A. L.; Yates, J. R. J. Am. Soc. Mass Spectrom. 1994, 5, 976-989.).

Mass Spectrometry↗
PubMed2006

Multilevel and density functional electronic structure calculations of proton affinities and gas-phase basicities involved in biological phosphoryl transfer.

Five multilevel model chemistries (CBS-QB3, G3B3, G3MP2B3, MCG3/3, and MC-QCISD/3) and seven hybrid density functional methods (PBE0, B1B95, B3LYP, MPW1KCIS, PBE1KCIS, and MPW1B95) have been applied to the calculation of gas-phase basicity and proton affinity values for a series of 17 molecules relevant to the study of biological phosphoryl transfer. In addition, W1 calculations were performed on a subset of molecules. The accuracy of the methods was assessed and the nature of systematic errors was explored, leading to the introduction of a set of effective bond enthalpy and entropy correction terms. The multicoefficient correlation methods (MCG3/3 and MC-QCISD), with inclusion of specific zero-point scale factors, slightly outperform the other multilevel methods tested (CBS-QB3, G3B3, and G3MP2B3), with significantly less computational cost, and in the case of MC-QCISD, slightly less severe scaling. Four density functional methods, PBE1KCIS, MPW1B95, PBE0, and B1B95 perform nearly as well as the multilevel methods. These results provide an important set of benchmarks relevant to biological phosphoryl transfer reactions.

Electrons↗