Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “data reproducibility”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

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

Development of the ReaxFF reactive force field for describing transition metal catalyzed reactions, with application to the initial stages of the catalytic formation of carbon nanotubes.

With the aim of developing a computationally inexpensive method for modeling the high-temperature reaction dynamics of transition metal catalyzed reactions we have developed a ReaxFF reactive force field in which the parameters are fitted to a substantial quantum mechanics (QM) training set, containing full reaction pathways for relevant reactions. In this paper we apply this approach to reactions involving carbon materials plus Co, Ni, and Cu atoms. We find that ReaxFF reproduces the QM reaction data with good accuracy while also reproducing the binding characteristics of Co, Ni, and Cu atoms to hydrocarbon fragments. To demonstrate the applicability of ReaxFF we performed high-temperature (1500 K) molecular dynamics simulations on a nonbranched all-carbon feedstock in the presence and absence of Co, Ni, and Cu atoms. We find that the presence of Co and Ni leads to substantial amounts of branched carbon atoms, leading eventually to the formation of carbon-nanotube-like species. In contrast, we find that under the same simulation conditions Cu leads to very little branching and leads to products with no nanotube character. In the absence of metals no branching is observed at all. These results suggest that Ni and Co catalyze the production of nanotube-like species whereas Cu does not. This is in excellent agreement with experimental observations, demonstrating that ReaxFF can provide a useful and computational tractable tool for studying the dynamics of transition metal catalytic chemistry.

Catalysis↗

Prediction of bacterial protein-compound interactions with only positive samples.

MOTIVATION: Prediction of Compound-Protein Interactions (CPI) in bacteria is crucial to advance various pharmaceutical and chemical engineering fields, including biocatalysis, drug discovery, and industrial processing. However, current CPI models cannot be applied for bacterial CPI prediction due to the lack of curated negative interaction samples. RESULTS: We propose a novel Positive-Unlabeled (PU) learning framework, named BIN-PU, to address this limitation. BIN-PU generates pseudo positive and negative labels from known positive interaction data, enabling effective training of deep learning models for CPI prediction. We also propose a weighted positive loss function that weights to truly positive samples. We have validated BIN-PU coupled with multiple CPI backbone models, comparing the performance with the existing PU models using bacterial cytochrome P450 (CYP) data. Extensive experiments demonstrate the superiority of BIN-PU over the benchmark models in predicting CPIs with only truly positive samples. Furthermore, we have validated BIN-PU on additional bacterial proteins obtained from literature review, human CYP datasets, and uncurated data for its reproducibility. We have also validated the CPI prediction for the uncurated CYP data with biological and biophysical experiments. BIN-PU represents a significant advancement in CPI prediction for bacterial proteins, opening new possibilities for improving predictive models in related biological interaction tasks. AVAILABILITY AND IMPLEMENTATION: The source code and data are available at https://github.com/datax-lab/CYP.

Bacterial Proteins↗

Quality improvement through teleradiology: opportunities and challenges.

Teleradiology is rapidly establishing its presence as an effective solution to the problem of provision of radiological services in remote locations. Although significant effort has been put into the development and establishment of quality assurance (QA) processes required for the implementation and conduct of this new technology, little attention has been given to the possible use of teleradiology in enhancing quality and safety of radiological practice, and as an alternative to conventional quality improvement (QI) initiatives. This paper critically evaluates teleradiology from the point of view of its potential use in QA/QI and considers its possible advantages as well as limitations. Considering the unique features of teleradiology such as remote access that can be simultaneous at multiple sites, rapid transfer of information and computerized data storage as well as good reproducibility and reliability of data, the authors argue that teleradiology represents an ideal tool which can not only be equivalent to other methods of QA in radiology but in some instances may be superior to them.

Humans↗

Reproducibility of ambulatory blood pressure monitoring.

OBJECTIVE: To investigate whether blood pressure monitoring is reproducible. DESIGN: Reproducibility of ambulatory blood pressure monitoring data was assessed by means of traditional and relatively new statistical methods, namely correlation coefficients, regression analysis and agreement analysis. METHODS: Ninety-one normotensive and hypertensive, uncomplicated outpatients underwent monitoring twice (mean interval 241 days). Data were analysed for reproducibility, correlation, difference and adaptation. Analyses were performed to verify the reproducibilities of the diagnosis of hypertension and of the treatment assessment. RESULTS: Ambulatory blood pressure monitoring is highly reproducible in terms of traditional statistics, but not in terms of the agreement analysis (error as high as 18 mmHg), although it performs better than does office sphygmomanometry (error as high as 38 mmHg). Reproducibility is acceptable in normotensive subjects and in patients who respond to treatment, but untreated hypertensives and those who do not respond to treatment show a worse ratio. CONCLUSION: The reproducibility of ambulatory blood pressure monitoring requires improvement. We do not know how many repeated measurements we need before diagnosing hypertension. Spontaneous variability of blood pressure interferes with blood pressure reproducibility. Diagnosis and treatment assessment in hypertension must take into account poor reproducibility.

Journal Article↗

The intima: development and monoclonal responses to injury.

Most current concepts of the biology of atherosclerosis and restenosis are highly hypothetical, based on studies of the growth properties of medial smooth muscle cells. These cells are clearly different in many ways from intimal smooth muscle cells. Indeed, in a recent compilation of the literature, we found approximately 80 genes that show constitutive differences in expression levels between intimal versus medial smooth muscle cells [122]. An important example of the possible importance of the intimal cell may be the still poorly-understood mechanism in restenosis. If this process is not due to simple neointimal formation, it may well be the result of the remodeling properties of pre-existing intimal cells. Perhaps, like fibroblasts in skin, intimal cells respond to injury by forming and then contracting a scar. Unfortunately, the literature contains little evidence on the properties of intimal or plaque smooth muscle in any species except the rat. In part, this lack of cell culture data on human plaque smooth muscle cells reflects the short replicative life span of these cells. This phenomenon may reflect the high apoptotic rate of these cells; indeed, recent in vivo studies show extensive apoptosis in the plaque smooth muscle cells in tissue sections as well [123-125]. Finally, while the observation of monoclonality has been neglected in recent reviews, those data have been reproduced several times, including recently in this laboratory (Murry et al., unpublished data). Any competent hypothesis of atherosclerosis must account for monoclonality. As noted above, it is possible that monoclonality of the intima is a normal part of development of the intima. This is a critical hypothesis, since the alternatives, i.e., existence of a proliferative subset or benign transformation of plaque smooth muscle cells both imply unique properties of the plaque smooth muscle cell that would become prime targets in understanding the ontogeny of this most important vascular disease.

Animals↗

What time is the "biologic zero hour" of circadian variability?

Most ambulatory blood pressure monitoring (ABPM) studies have used a mechanical clock as the reference time, but there is no biologic background for assuming that midnight by the mechanical clock is zero hour by the biologic clock. The aim of this study was to determine the biologic zero hour as the zero reference time by evaluating the circadian rhythm of blood pressure, heart rate, and activity. Twenty healthy medical students (18 men, 2 women, mean age 26 years old) were recruited and blood pressure, heart rate, and physical activity were monitored simultaneously by an ABPM device every 30 min for 48 h. Four concepts of zero time were selected in this study and analyzed regarding biologic zero hour: 24:00 by the mechanical clock (clock time); the time of awakening, based on a diary (diary time); the time of a sudden increment in physical activity in the morning (activity time); and the middle of the total sleeping time, based on the diary (midsleeping time). The awakening time is a better individual index than the mechanical clock, and the midsleeping time as the zero reference point is better than the awakening time. We assessed the reproducibility of the data regarding the circadian troughs between the first and second day. The reproducibility of the day-to-day variation of the blood pressure and heart rate was poor. The reproducibility of physical activity was fairly good, but the magnitude of activity was small. A 48-h monitoring profile is superior to a 24-h monitoring period.

Adult↗

Quantitation of articular cartilage using magnetic resonance imaging and three-dimensional reconstruction.

A quadrature knee coil was used in conjunction with a magnetic resonance imaging scanner for quantitation of test phantom volumes, ex vivo bovine cartilage thickness, and in vivo human articular cartilage volumes. Optimal magnetic resonance parameters were obtained by testing a series of spin-echo and gradient-echo pulse sequences to determine the sequence that provided the highest resolution of articular cartilage and best defined the cartilage interfaces with synovial fluid and subchondral bone. Extensive testing revealed that two sequences were required to define articular cartilage accurately: a spoiled gradient-echo sequence and a steady state free-precession sequence. Three-dimensional reconstruction and statistical analyses of test phantoms and of bovine and human cartilage images were performed. Differences between actual phantom volumes and three-dimensional measurements demonstrated that, as magnetic resonance slice thickness was increased, the measurement variability also increased (coefficient of variation ranging from 1.7 +/- 1.3% for 1.0 mm slice thickness to 22.7 +/- 1.9% for 3.0 mm slice thickness). When the phantom volume was greater than 1,800 mm3, the intraobserver, interobserver and interscan accuracies were greater than 97, 98, and 96%, respectively. This high degree of reproducibility pertained for the data on in vivo human cartilage data also. For experienced observers, the intraobserver and interobserver reproducibility were greater than 98 and 97%, respectively. The interscan reproducibility was greater than 98%. These data demonstrate that improved magnetic resonance pulse sequencing, in conjunction with three-dimensional reconstruction and measurement techniques, can accurately and reproducibly measure the volume of articular cartilage. Clinical application of this approach offers the potential for early diagnosis of osteoarthritis and for serial, noninvasive assessment of changes in articular cartilage volume in response to therapeutic modalities.

Adult↗

Correction of logistic regression relative risk estimates and confidence intervals for random within-person measurement error.

Frequently, covariates used in a logistic regression are measured with error. The authors previously described the correction of logistic regression relative risk estimates for measurement error in one or more covariates when a "gold standard" is available for exposure assessment. For some exposures (e.g., serum cholesterol), no gold standard exists, and one must assess measurement error via a reproducibility substudy. In this paper, the authors present measurement error methods for logistic regression when there is error (possibly correlated) in one or more covariates and one has data from both a main study and a reproducibility substudy. Confidence intervals from this procedure reflect error in parameter estimates from both studies. These methods are applied to the Framingham Heart Study, where the 10-year incidence of coronary heart disease is related to several coronary risk factors among 1,731 men disease-free at examination 4. Reproducibility data are obtained from the subgroup of 1,346 men seen at examinations 2 and 3. Estimated odds ratios comparing extreme quintiles for risk factors with substantial error were increased after correction for measurement error (serum cholesterol, 2.2 vs. 2.9; serum glucose, 1.3 vs. 1.5; systolic blood pressure, 2.8 vs. 3.8), but were generally decreased or unchanged for risk factors with little or no error (body mass index, 1.6 vs. 1.6; age 65-69 years vs. 35-44 years, 4.3 vs. 3.8; smoking, 1.7 vs. 1.7).

Adult↗

Optimized normalization for antibody microarrays and application to serum-protein profiling.

The measurements of coordinated patterns of protein abundance using antibody microarrays could be used to gain insight into disease biology and to probe the use of combinations of proteins for disease classification. The correct use and interpretation of antibody microarray data requires proper normalization of the data, which has not yet been systematically studied. Therefore we undertook a study to determine the optimal normalization of data from antibody microarray profiling of proteins in human serum specimens. Forty-three serum samples collected from patients with pancreatic cancer and from control subjects were probed in triplicate on microarrays containing 48 different antibodies, using a direct labeling, two-color comparative fluorescence detection format. Seven different normalization methods representing major classes of normalization for antibody microarray data were compared by their effects on reproducibility, accuracy, and trends in the data set. Normalization with ELISA-determined concentrations of IgM resulted in the most accurate, reproducible, and reliable data. The other normalization methods were deficient in at least one of the criteria. Multiparametric classification of the samples based on the combined measurement of seven of the proteins demonstrated the potential for increased classification accuracy compared with the use of individual measurements. This study establishes reliable normalization for antibody microarray data, criteria for assessing normalization performance, and the capability of antibody microarrays for serum-protein profiling and multiparametric sample classification.

Adenocarcinoma↗

Terahertz Spectroscopy of the Amidogen Radical, NH2.

The rotational spectrum of the NH2 radical in its &Xtilde;2B1 ground vibronic state was investigated between 614 and 1003 GHz. One hundred fifty-nine newly observed lines (188 hyperfine components) of six rotational transitions with 0 </= N </= 5 and 0 </= Ka </= 4 were used in the final, global fit of field-free data for the (000) vibrational state. Recent results from Fourier transform far-infrared (FT-FIR), and millimeter- and submillimeter-wave spectroscopy, as well as microwave optical double resonance (MODR) and recent FIR laser sideband data, were also used in the fit. A large set of spectroscopic constants reproduces the input data within experimental uncertainties and permits the precise prediction of low-N, low-Ka transitions of interest for the astrophysical community. In particular, the astrophysically important 111-000 transition of ortho NH2 was observed near 952.57 and 959.50 GHz. Copyright 1999 Academic Press.

Journal Article↗

Reliability of data obtained by radionuclide angiocardiography in follow-up studies with special reference to intra- and interobserver variations.

The reproducibility of the data obtained by radionuclide angiocardiography was studied in terms of the intra- and intervariations of three technicians. Three parameters were chosen: the left ventricular ejection fraction (LVEF), the 1/3 filling fraction (1/3FF), and the ratio of the time from end systole to the point of peak filling rate against the entire diastolic period (TRPFR). First, each technician studied an independent consecutive series of 40 patients for the initial analysis. The original data of each patient, composed of 26 frames for one beat, were stored on an optical disc for the intra- and intervariation studies. In this study, analysis of the volume curve was performed by using both 3rd order and 4th order Fourier series. The region of interest (ROI) for the left ventricle, which was set for the initial analysis, was recorded by Polaroid photography to be used as a reference for the later analyses for the variation studies. The least variation was noted in the LVEF not only for the intravariation study but also for the intervariation study, no matter which order of the Fourier series was used. However, the 3rd order Fourier series seemed to give better curve fitting to avoid fluctuation of the diastolic parameters. The results indicate that we can expect more steady and reliable information from LVEF than from the diastolic parameters, even when various technicians perform the follow-up study of a particular patient.

Angiocardiography↗

Substance abuse vulnerability loci: converging genome scanning data.

Classical genetic studies suggest strong complex genetic contributions to a predisposition to abuse multiple addictive substances. Until recently, there were no reproducible genome scanning data identifying chromosomal positions likely to contain allelic variants that predispose the carrier to illegal substance addiction. Nominal results of linkage-based genome scanning studies for ethanol and nicotine addictions failed to display much agreement. Our recent data from association-based genome scans for illegal addictions, and reanalyses of previous results now provide a substantial body of converging results. The 15 reproducible chromosomal loci identified here are good candidates to harbor allelic variants that alter human substance abuse vulnerabilities. We discuss several approaches to identifying the specific gene variants that underlie these convergent association and linkage observations, and the impact that these convergent observations should have on understanding important human addictive disorders.

Chromosome Mapping↗

pmultiqc: An Open-Source, Lightweight, and Metadata-Oriented QC Reporting Library for MS Proteomics.

The increasing scale and complexity of proteomics data demand robust, scalable, and interpretable quality control (QC) frameworks to ensure data reliability and reproducibility. Here, we present pmultiqc, an open-source Python package that standardizes and generates web-based QC reports across multiple proteomics data analysis platforms. Built on top of the widely adopted MultiQC framework, pmultiqc offers specialized modules tailored to mass spectrometry workflows, with full initial support for quantms, DIA-NN, MaxQuant/MaxDIA, FragPipe, and mzIdentML/mzML-based pipelines. The package computes a wide range of QC metrics, including raw intensity distributions, identification rates, retention time consistency, and missing value patterns, and presents them in interactive, publication-ready reports. By leveraging sample metadata in the Sample and Data Relationship Format format, pmultiqc enables metadata-aware QC and introduces, for the first time in proteomics, QC reports and metrics guided by standardized sample metadata. Its modular architecture allows easy extension to new workflows and formats. Alongside comprehensive documentation and examples for running pmultiqc locally or integrated into existing workflows, we offer a cloud-based service that enables users to generate QC reports from their own data or public PRIDE datasets.

Proteomics↗

Structure of aqueous glucose solutions as determined by neutron diffraction with isotopic substitution experiments and molecular dynamics calculations.

Neutron diffraction with isotopic substitution (NDIS) experiments and molecular dynamics (MD) simulations have been used to examine the structuring of solvent around d-glucose in aqueous solution. As expected, no significant tendency for glucose molecules to aggregate was found in either the experiments or the simulation. To the extent that solute pairing does occur as the result of the high concentration, it was found to take place through hydroxyl-hydroxyl hydrogen bonds, in competition with water molecules for the same hydrogen-bonding sites. A detailed analysis of the hydrogen-bonding patterns occurring in the simulations found that the sugar hydroxyl groups are more efficient hydrogen bond donors than acceptors. From the comparison of the MD and NDIS data, it was found that while the modeling generally does a satisfactory job in reproducing the experimental data the force fields may produce sugar rings that are too rigid and thus may require future revisions.

Computer Simulation↗

Structure determination of a novel protein by sulfur SAD using chromium radiation in combination with a new crystal-mounting method.

A novel and easy crystal-mounting technique was developed for the sulfur SAD method using Cr Kalpha radiation (2.29 A). Using this technique, the cryo-buffer and cryoloop around the protein crystal can be removed before data collection in order to eliminate their X-ray absorption. The superiority and reproducibility of the data sets with this mounting technique were demonstrated using tetragonal hen egg-white lysozyme crystals. The structure of a novel protein, PH1109, from Pyrococcus horikoshii OT3 was solved using this technique. At the wavelength of Cr Kalpha radiation, the anomalous signal |DeltaF|/|F| of PH1109 is expected to be 1.72% as this protein of 144 residues includes four methionines and two cysteines. Sulfur SAD phasing was performed using SHELXD and SHELXE. In the case of the data set obtained using this novel crystal-mounting technique, 54.9% of all residues were built with side chains automatically by RESOLVE. On the other hand, only 16.0% were built with side chains for the data set collected using the standard cryoloop. These results indicated that this crystal-mounting technique was superior to the standard loop-mounting method for the measurement of small anomalous differences at longer wavelength and yielded better results in sulfur-substructure solution and initial phasing. The present study demonstrates that the sulfur SAD method with a chromium source becomes enhanced and more practical for macromolecular structure determination using the new crystal-mounting technique.

Absorption↗

Analysis of functional coupling: mitochondrial creatine kinase and adenine nucleotide translocase.

The mechanism of functional coupling between mitochondrial creatine kinase (MiCK) and adenine nucleotide translocase (ANT) in isolated heart mitochondria is analyzed. Two alternative mechanisms are studied: 1), dynamic compartmentation of ATP and ADP, which assumes the differences in concentrations of the substrates between intermembrane space and surrounding solution due to some diffusion restriction and 2), direct transfer of the substrates between MiCK and ANT. The mathematical models based on these possible mechanisms were composed and simulation results were compared with the available experimental data. The first model, based on a dynamic compartmentation mechanism, was not sufficient to reproduce the measured values of apparent dissociation constants of MiCK reaction coupled to oxidative phosphorylation. The second model, which assumes the direct transfer of substrates between MiCK and ANT, is shown to be in good agreement with experiments--i.e., the second model reproduced the measured constants and the estimated ADP flux, entering mitochondria after the MiCK reaction. This model is thermodynamically consistent, utilizing the free energy profiles of reactions. The analysis revealed the minimal changes in the free energy profile of the MiCK-ANT interaction required to reproduce the experimental data. A possible free energy profile of the coupled MiCK-ANT system is presented.

Adenosine Diphosphate↗

Value of repeated measures of nerve conduction and quantitative sensory testing in a diabetic neuropathy trial.

Conduct of a large, multicenter trial of the aldose reductase inhibitor zenarestat provided data on the reproducibility of multiple electrophysiologic (nerve conduction studies, NCS) and quantitative sensory (QST) tests. Baseline and 12-month electrophysiologic data from approximately 1100 patients at multiple centers were available for analysis. Intersite variability contributed minimally to overall test variance. All NCS tests were highly reproducible. Cool thermal and vibration QST thresholds, as measured by CASE IV instrumentation, were also highly reproducible. Intersubject variance accounted for the majority of variance for all parameters measured. Repeating NCS and QST measures decreased sample sizes needed to show statistical significance. Consideration of these observations, particularly with regard to QST, should aid in the design of future clinical trials investigating neuropathy.

Adolescent↗