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At least 217 records · Page 12Linked to original sources
PubMed2001

Neural-network analysis of the vibrational spectra of N-acetyl L-alanyl N'-methyl amide conformational states.

Density-functional theory (DFT) calculations utilizing the Becke 3LYP hybrid functional have been carried out for N-acetyl L-alanine N'-methylamide and examined with respect to the effect of water on the structure, the vibrational frequencies, vibrational absorption (VA), vibrational circular dichroism (VCD), Raman spectra, and Raman optical activity (ROA) intensities. The large changes due to hydration in the structures, and the relative stability of the conformer, reflected in the VA, VCD, Raman spectra, and ROA spectra observed experimentally, are reproduced by the DFT calculations. A neural network has been constructed for reproducing the inverse scattering data (we infer the structural coordinates from spectroscopic data) that the DFT method could produce. The purpose of the network has also been to generate the large set of conformational states associated with each set of spectroscopic data for a given conformer of the molecule by interpolation. Finally the neural network performances are used to monitor a sensitivity analysis of the importance of secondary structures and the influence of the solvent. The neural network is shown to be good in distinguishing the different conformers of the small alanine peptide, especially in the gas phase.

Alanine↗
PubMed2002

Increasing social capital via local networks: analysis in the context of a surgical practice.

The relationship between social capital (support, trust, patient awareness, and increased practice revenue) and local networks (university hospital) in communities has received little attention. The development of computer-based communication networks (social networks) has added a new dimension to the argument, posing the question of whether local networks can (re-)create social capital in local communities. This relationship is examined through a review of the literature on local networks and social capital and a surgeon's practice management from 1990 to 2001 with respect to repair of pectus chest deformities. With respect to pectus repair there was a consistent but small number of new referrals (15-20 new patients/year), lack of patient awareness (eight to 12 self-referred patients/year), and modest practice revenue. Since the inception of an Internet website (social network) dedicated to pectus repair in 1996 there has been increased social participation (n = 630 hits/year to the website); facilitation of spread of information through E-mail messages (n = 430 messages/year); and a greater participation of groups such as women, minorities, adults, and those with disability (n = 120 patients/year). The dissemination of information via the local network has also allowed an "outward movement" with increased participation by interconnecting communities (n = 698,300 global Internet participants based on statistical ratios). We conclude that local networks have enhanced social networks providing new grounds for the development of relationships based on choice and shared interest.

Adult↗
PubMed1999

Neural network analysis of preoperative variables and outcome in epilepsy surgery.

OBJECT: Because appropriate patient selection is essential for achieving successful outcomes after epilepsy surgery, the need for more robust methods of predicting postoperative seizure control has been created. Standard multivariate techniques have been only 75 to 80% accurate in this regard. Recent use of artificial intelligence techniques, including neural networks, for analyzing multivariate clinical data has been successful in predicting medical outcome. METHODS: The authors applied neural network techniques to 80 consecutive patients undergoing epilepsy surgery in whom data on demographic, seizure, operative, and clinical variables to predict postoperative seizures were collected. Neural networks could be used to predict postoperative seizures in up to 98% of cases. Student's t-tests or chi-square analysis performed on individual variables revealed that only the preoperative medication index was significantly different (p = 0.02) between the two outcome groups. Six different combinations of input variables were used to train the networks. Neural network accuracies differed in their ability to predict seizures: using all data (96%); all data minus electroencephalography concordance and operative side (93%); all data except intra- or postoperative variables such as tissue pathological category (98%); all data excluding pathological category, intelligence quotient (IQ) data, and Wada results (84%); only demographics and tissue pathological category (65%); and only IQ data (63%). CONCLUSIONS: Analysis of the results reveals that several networks that are trained with the usual accepted variables characterizing the typical evaluation of epilepsy patients can predict postoperative seizures with greater than 95% accuracy.

Anticonvulsants↗
PubMed2003

Metabolic flux and metabolic network analysis of Penicillium chrysogenum using 2D [13C, 1H] COSY NMR measurements and cumulative bondomer simulation.

At present two alternative methods are available for analyzing the fluxes in a metabolic network: (1) combining measurements of net conversion rates with a set of metabolite balances including the cofactor balances, or (2) leaving out the cofactor balances and fitting the resulting free fluxes to measured (13)C-labeling data. In this study these two approaches are applied to the fluxes in the glycolysis and pentose phosphate pathway of Penicillium chrysogenum growing on either ammonia or nitrate as the nitrogen source, which is expected to give different pentose phosphate pathway fluxes. The presented flux analyses are based on extensive sets of 2D [(13)C, (1)H] COSY data. A new concept is applied for simulation of this type of (13)C-labeling data: cumulative bondomer modeling. The outcomes of the (13)C-labeling based flux analysis substantially differ from those of the pure metabolite balancing approach. The fluxes that are determined using (13)C-labeling data are shown to be highly dependent on the chosen metabolic network. Extending the traditional nonoxidative pentose phosphate pathway with additional transketolase and transaldolase reactions, extending the glycolysis with a fructose 6-phosphate aldolase/dihydroxyacetone kinase reaction sequence or adding a phosphoenolpyruvate carboxykinase reaction to the model considerably improves the fit of the measured and the simulated NMR data. The results obtained using the extended version of the nonoxidative pentose phosphate pathway model show that the transketolase and transaldolase reactions need not be assumed reversible to get a good fit of the (13)C-labeling data. Strict statistical testing of the outcomes of (13)C-labeling based flux analysis using realistic measurement errors is demonstrated to be of prime importance for verifying the assumed metabolic model.

Ammonia↗
PubMed2006

Network analysis of the protein chain tertiary structures of heterocomplexes.

In this paper, the tertiary structures of protein chains of heterocomplexes were mapped to 2D networks; based on the mapping approach, statistical properties of these networks were systematically studied. Firstly, our experimental results confirmed that the networks derived from protein structures possess small-world properties. Secondly, an interesting relationship between network average degree and the network size was discovered, which was quantified as an empirical function enabling us to estimate the number of residue contacts of the protein chains accurately. Thirdly, by analyzing the average clustering coefficient for nodes having the same degree in the network, it was found that the architectures of the networks and protein structures analyzed are hierarchically organized. Finally, network motifs were detected in the networks which are believed to determine the family or superfamily the networks belong to. The study of protein structures with the new perspective might shed some light on understanding the underlying laws of evolution, function and structures of proteins, and therefore would be complementary to other currently existing methods.

Models, Molecular↗
PubMed2002

Estimation of pulmonary arterial pressure by a neural network analysis using features based on time-frequency representations of the second heart sound.

The objective of the study was to develop a non-invasive method for the estimation of pulmonary arterial pressure (PAP) using a neural network (NN) and features extracted from the second heart sound (S2). To obtain the information required to train and test the NN, an animal model of pulmonary hypertension (PHT) was developed, and nine pigs were investigated. During the experiments, the electrocardiogram, phonocardiogram and PAP were recorded. Subsequently, between 15 and 50 S2 heart sounds were isolated for each PAP stage and for each animal studied. A Coiflet wavelet decomposition and a pseudo smoothed Wigner-Ville distribution were used to extract features from the S2 sounds and train a one-hidden-layer NN using two-thirds of the data. The NN performance was tested on the remaining one-third of the data. NN estimates of the systolic and mean PAPs were obtained for each S2 and then ensemble averaged over the 15-50 S2 sounds selected for each PAP stage. The standard errors between the mean and systolic PAPs estimated by the NN and those measured with a catheter were 6.0 mmHg and 8.4 mmHg, respectively, and the correlation coefficients were 0.89 and 0.86, respectively. The classification accuracy, using 23 mmHg mean PAP and 30 mmHg systolic PAP thresholds between normal PAP and PHT, was 97% and 91%, respectively.

Animals↗
PubMed2026

Examining early-phase symptom trajectories in interpersonal psychotherapy versus antidepressant medication for adults with depression: A dynamic time warp network analysis.

BACKGROUND: Depression is characterized by substantial symptom heterogeneity, which is often concealed when examining total severity scores. Analyzing symptom-level change can improve our understanding of treatment effects and recovery processes. This study, therefore, examined dynamic symptom networks during early-phase interpersonal psychotherapy (IPT) and selective serotonin reuptake inhibitor (SSRI) antidepressant treatment, assessing patterns of symptom change across as well as differences between treatments. METHODS: Using weekly item-level Hamilton Depression Rating Scale (HAM-D) data from a randomized clinical trial comparing IPT and SSRIs for adults with depression, this preregistered study examined symptom trajectories in the first six weeks of treatment with Dynamic Time Warping (DTW). RESULTS: Depressive symptom trajectories and DTW-based symptom networks were largely similar for IPT and SSRI. In both conditions, changes in somatic symptoms of anxiety and middle insomnia tended to precede improvements in depressed mood. CONCLUSIONS: Early symptom change may occur outside the core affective domain, underscoring the importance of monitoring symptoms broadly. Symptom-level patterns may reflect patients' stage of recovery and provide clinically relevant information beyond total severity scores. The absence of differences in improvement patterns between IPT and SSRI suggest few indications for treatment selection based on baseline symptom profiles. Future research should replicate and extend these findings to subsequent treatment phases using more frequent assessments and a broader range of interventions.

Humans↗
PubMed2002

Quantification of human brain metabolites from in vivo 1H NMR magnitude spectra using automated artificial neural network analysis.

Long echo time (TE=270 ms) in vivo proton NMR spectra resembling human brain metabolite patterns were simulated for lineshape fitting (LF) and quantitative artificial neural network (ANN) analyses. A set of experimental in vivo 1H NMR spectra were first analyzed by the LF method to match the signal-to-noise ratios and linewidths of simulated spectra to those in the experimental data. The performance of constructed ANNs was compared for the peak area determinations of choline-containing compounds (Cho), total creatine (Cr), and N-acetyl aspartate (NAA) signals using both manually phase-corrected and magnitude spectra as inputs. The peak area data from ANN and LF analyses for simulated spectra yielded high correlation coefficients demonstrating that the peak areas quantified with ANN gave similar results as LF analysis. Thus, a fully automated ANN method based on magnitude spectra has demonstrated potential for quantification of in vivo metabolites from long echo time spectroscopic imaging.

Aspartic Acid↗
PubMed1996

Introduction of a new laboratory test: an econometric approach with the use of neural network analysis.

We designed a simulation model for the assessment of the financial risks involved when a new diagnostic test is introduced in the laboratory. The model is based on a neural network consisting of ten neurons and assumes that input entities can have assigned appropriate uncertainty. Simulations are done on a 1-day interval basis. Risk analysis completes the model and the financial effects are evaluated for a selected time period. The basic output of the simulation consists of total expenses and income during the simulation time, net present value of the project at the end of simulation, total number of control samples during simulation, total number of patients evaluated and total number of used kits.

Chemistry, Clinical↗
PubMed1988

Network analysis of an arterial tree.

The arterial tree of a Sprague-Dawley rat was casted and carefully mapped with the aim of comparing its network characteristics with those suggested by the classical model of an arterial tree. It is shown that if the tree is to be measured accurately, the concept of 'whole vessels' on which the classical model is based must be abandoned since such vessels do not actually exist in the network, nor can they be accurately defined. The concept of 'vessel segments' is proposed instead and its use is demonstrated. A total of 1313 vessel segments in the arterial tree of the rat are mapped and divided into well defined 'levels'. The length and diameter of each segment are measured and the distribution and averages of these at different levels are presented as indicators of the branching characteristics of the tree.

Animals↗
PubMed2002

Functional connectivity in the resting brain: a network analysis of the default mode hypothesis.

Functional imaging studies have shown that certain brain regions, including posterior cingulate cortex (PCC) and ventral anterior cingulate cortex (vACC), consistently show greater activity during resting states than during cognitive tasks. This finding led to the hypothesis that these regions constitute a network supporting a default mode of brain function. In this study, we investigate three questions pertaining to this hypothesis: Does such a resting-state network exist in the human brain? Is it modulated during simple sensory processing? How is it modulated during cognitive processing? To address these questions, we defined PCC and vACC regions that showed decreased activity during a cognitive (working memory) task, then examined their functional connectivity during rest. PCC was strongly coupled with vACC and several other brain regions implicated in the default mode network. Next, we examined the functional connectivity of PCC and vACC during a visual processing task and show that the resultant connectivity maps are virtually identical to those obtained during rest. Last, we defined three lateral prefrontal regions showing increased activity during the cognitive task and examined their resting-state connectivity. We report significant inverse correlations among all three lateral prefrontal regions and PCC, suggesting a mechanism for attenuation of default mode network activity during cognitive processing. This study constitutes, to our knowledge, the first resting-state connectivity analysis of the default mode and provides the most compelling evidence to date for the existence of a cohesive default mode network. Our findings also provide insight into how this network is modulated by task demands and what functions it might subserve.

Adult↗
PubMed2001

Neural network analysis in predicting 2-year survival in elderly people: a new statistical-mathematical approach.

We designed this study to test the usefulness of artificial neural networks (ANN) in assessing 2-year survival in elderly persons, and to understand the net's logical functioning, thus determining the relative importance of the single biological and clinical variables which influence survival. ANN are statistical-mathematical tools able to determine the existence of a correlation between series of data and, once 'trained', to predict output data given input data. Although ANN have been applied in various areas of medical research, they have only very recently been applied in geriatrics (Cacciafesta et al., 2000. Arch. Gerontol. Geriatr. 31 (in press)). We built up an ANN to investigate how 17 clinical variables relating to a sample of 159 elderly people affect survival, and the possibility of predicting 2-year survival or non-survival for each single subject. When tested on a sample of 20 elderly people, the trained network gave the correct answer in 85% of the cases. We then extracted the mathematical function that the net used for calculating the output (survival) for each set of input data (clinical variables). Using this formula, we investigated how some clinical variables influence 2-year survival: we found that a low serum cholesterol level is an unfavourable characteristic in relation to survival. We conclude-despite the fact that the sample studied was relatively small-that ANN are useful in predicting 2-year survival in elderly people. The mathematical function we obtained from the net seems useful in determining the relative importance of single variables related to survival.

Journal Article↗
PubMed2003

Process mapping as a tool for home health network analysis.

Process mapping is a qualitative tool that allows service providers, policy makers, researchers, and other concerned stakeholders to get a "bird's eye view" of a home health care organizational network or a very focused, in-depth view of a component of such a network. It can be used to share knowledge about community resources directed at the older population, identify gaps in resource availability and access, and promote on-going collaborative interactions that encourage systemic policy reassessment and programmatic refinement. This article is a methodological description of process mapping, which explores its utility as a practice and research tool, illustrates its use in describing service-providing networks, and discusses some of the issues that are key to successfully using this methodology.

Community Health Planning↗
PubMed1999

Neural network analysis of the volumetric capnogram to detect pulmonary embolism.

BACKGROUND: Pulmonary embolism (PE) produces ventilation/perfusion mismatch that may be manifested in various variables of the volume-based capnogram (VBC). We hypothesized that a neural network (NN) system could detect changes in VBC variables that reflect the presence of a PE. METHODS: A commercial VBC system was used to record multiple respiratory variables from consecutive expiratory breaths. Data from 12 subjects (n = 6 PE+ and n = 6 PE-) were used as input to a fully connected back-propagating NN for model development. The derived model was tested in a prospective, observational study at an urban teaching hospital. Volumetric capnograms were then collected on 53 test subjects: 30 subjects with PE confirmed by pulmonary angiography or diagnostic scintillation lung scan, and 23 subjects without PE based on pulmonary angiography. The derived NN model was applied to VBC data from the test population. RESULTS: Seventeen VBC variables were used by the derived NN model to generate a numeric probability of PE. When the derived NN model was applied to VBC data from the 53 test subjects, PE was detected with a sensitivity of 100% (95% CI = 89% to 100%) and a specificity of 48% (95% CI = 27% to 69%). The likelihood ratio positive [LR(+)] for the VBC-NN test was 1.82 and the LR (-) was 0.1. CONCLUSION: This study demonstrates the feasibility of developing a rapid, noninvasive breath test for diagnosing PE using volumetric capnography and NN analysis.

Angiography↗
PubMed2003

Determination of the composition of light thin films with artificial neural network analysis of Rutherford backscattering experiments.

AlO(x)N(y) ultrathin films are used as insulating layers in advanced microelectronic devices. Structural characterization of these films is often done by the Rutherford backscattering (RBS) analysis. The RBS analysis of these oxinitrides is a difficult task since the relevant signals of the spectrum are washed out by the large substrate background and a considerable time is required for an analyst to characterize the sample. In this work we developed specialized artificial neural networks that are able to perform a fast and efficient analysis of the data. The results are in good agreement with traditional methods.

Journal Article↗
PubMed2003

A metabolic network analysis & NMR experiment design tool with user interface-driven model construction for depth-first search analysis.

A Windows program for metabolic engineering analysis and experimental design has been developed. A graphical user interface enables the pictorial, "on-screen" construction of a metabolic network. Once a model is composed, balance equations are automatically generated. Model construction, modification and information exchange between different users is thus considerably simplified. For a given model, the program can then be used to predict all the extreme point flux distributions that optimize an objective function while satisfying balances and constraints by using a depth-first search strategy. One can also find the minimum reaction set that satisfies different conditions. Based on the identified flux distributions or linear combinations, the user can simulate the NMR and GC/MS spectra of selected signal molecules. Alternately, spectra vectorization allows for the automated optimization of labeling experiments that are intended to distinguish between different, yet plausible flux extreme point distributions. The example provided entails predicting the flux distributions associated with deleting pyruvate kinase and designing 13C NMR experiments that can maximally discriminate between the flux distributions.

Computer Simulation↗
PubMed2003

Neural network analysis of lymphoma microarray data: prognosis and diagnosis near-perfect.

BACKGROUND: Microarray chips are being rapidly deployed as a major tool in genomic research. To date most of the analysis of the enormous amount of information provided on these chips has relied on clustering techniques and other standard statistical procedures. These methods, particularly with regard to cancer patient prognosis, have generally been inadequate in providing the reduced gene subsets required for perfect classification. RESULTS: Networks trained on microarray data from DLBCL lymphoma patients have, for the first time, been able to predict the long-term survival of individual patients with 100% accuracy. Other networks were able to distinguish DLBCL lymphoma donors from other donors, including donors with other lymphomas, with 99% accuracy. Differentiating the trained network can narrow the gene profile to less than three dozen genes for each classification. CONCLUSIONS: Here we show that artificial neural networks are a superior tool for digesting microarray data both with regard to making distinctions based on the data and with regard to providing very specific reference as to which genes were most important in making the correct distinction in each case.

Algorithms↗