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PubMed2001

Deep brain stimulation for chronic pain: results of two multicenter trials and a structured review.

OBJECTIVES: A U.S. Food and Drug Administration ruling required clinical trials to evaluate the safety and efficacy of deep brain stimulation devices, thereby limiting treatment to the investigational setting. INTRODUCTION: As an investigator in two clinical trials of deep brain stimulation, I sought to determine why pain remained an unapproved indication despite regulatory approval of the same device for tremor. METHODS: The results of two multicenter trials of deep brain stimulation for pain were analyzed, and the pertinent literature was reviewed using published guidelines for the evaluation of clinical trial reports. RESULTS: The first-generation Model 3380 lead trial enrolled 196 patients; the current Model 3387 trial enrolled 50 patients. Prospectively defined criteria for success included at least half of patients reporting >/=50% pain relief at 1 year. Manufacture of the Model 3380 lead was discontinued, and the 3387 trial closed early because of slow enrollment, high attrition, and low efficacy. When results were analyzed according to the study plan, neither trial was successful. Consequently, deep brain stimulation has not been approved for pain control by the U.S. Food and Drug Administration. CONCLUSIONS: Deep brain stimulation has not been shown to produce effective long-term pain relief. Future studies of motor cortex stimulation and similar therapies will require appropriate control groups and accepted methods of data collection and analysis to support claims that predictable and reliable analgesic effects are produced in humans.

Journal Article↗
PubMed2002

Child-rearing practices of primary caregivers of HIV-infected children: An integrative review of the literature.

The number of human immunodeficiency virus (HIV)-infected children has increased because of the HIV and acquired immunodeficiency syndrome epidemic. Yet little is known about the child-rearing practices of these children's primary caregivers. The purpose of this article is to describe what is known about the child-rearing practices of primary caregivers of HIV-infected children. The review covers a 10-year period from 1990 to 2000. Three electronic bibliographic databases (MEDLINE, CINAHL, and AIDSLINE) were explored. Key words used were HIV-positive children, caregivers, and child-rearing. A total of 50 papers were examined. Using the Matrix Method, each paper was evaluated according to five frames of reference: journal, purpose, sample, method, and findings. Content analysis was used to identity salient themes. Themes that emerged were: caregiver, child, and interactions or child-rearing practices. These findings affirm the parent-child interaction model generated by Kathryn E. Barnard and support this framework as a tool for investigating the relationships between these children and their caregivers.

Adaptation, Psychological↗
PubMedDate not supplied

[Accuracy of fluoroscopically navigated drilling procedures at the hip].

AIM: Many orthopaedic procedures require an accurate drilling in bone. The outcome is frequently dependent on the geometric accuracy of this surgical step. The precision of such a procedure can be improved with the help of fluoroscopic navigation. Reliability, accuracy and benefit of this new method for the patient, as well as for the surgical staff, need to be analysed. METHOD: In a standardised in vitro trial, the drilling of a 5 mm spherical lesion implanted in an artificial femoral head was performed using a navigated drill-guide and a navigated drill. In groups A and B, the distance of the tip of the drill to the center of the lesion was analysed in a 3D CT-generated model and in macroscopic cross section. Additionally, in group B the actual direction of the drill canal was measured. RESULTS: The mean distance in group A was measured to be 1 mm, with all results ranging between 0 and 2.5 mm. In group B the planned direction of the canal was reproduced with a deviation of 0 degrees to 7 degrees, the target only being missed by a mean distance of 2.5 mm and a maximum of 3.5 mm. Compared to the macroscopic and 3D-CT findings, the correlation of the data calculated by the navigation system was accurate up to a difference of 4 degrees or 2 mm. CONCLUSION: The fluoroscopically assisted freehand navigation used during the drilling of bone led to a high accuracy of three-dimensional tip placement while reducing radiation exposure to a minimum. It represents a promising and efficient application for a variety of procedures in orthopaedic surgery.

Artifacts↗
PubMed2006

Numerical study of the steady state fluctuation relations far from equilibrium.

A thermostatted dynamical model with five degrees of freedom is used to test the fluctuation relation of Evans and Searles (Omega-FR) and that of Gallavotti and Cohen (Lambda-FR). In the absence of an external driving field, the model generates a time-independent ergodic equilibrium state with two conjugate pairs of Lyapunov exponents. Each conjugate pair sums to zero. The fluctuation relations are tested numerically both near and far from equilibrium. As expected from previous work, near equilibrium the Omega-FR is verified by the simulation data while the Lambda-FR is not confirmed by the data. Far from equilibrium where a positive exponent in one of these conjugate pairs becomes negative, we test a conjecture regarding the Lambda-FR [Bonetto et al., Physica D 105, 226 (1997); Giuliani et al., J. Stat. Phys. 119, 909 (2005)]. It was conjectured that when the number of nontrivial Lyapunov exponents that are positive becomes less than the number of such negative exponents, then the form of the Lambda-FR needs to be corrected. We show that there is no evidence for this conjecture in the empirical data. In fact, when the correction factor differs from unity, the corrected form of Lambda-FR is less accurate than the uncorrected Lambda-FR. Also as the field increases the uncorrected Lambda-FR appears to be satisfied with increasing accuracy. The reason for this observation is likely to be that as the field increases, the argument of the Lambda-FR more and more accurately approximates the argument of the Omega-FR. Since the Omega-FR works for arbitrary field strengths, the uncorrected Lambda-FR appears to become ever more accurate as the field increases. The final piece of evidence against the conjecture is that when the smallest positive exponent changes sign, the conjecture predicts a discontinuous change in the "correction factor" for Lambda-FR. We see no evidence for a discontinuity at this field strength.

Journal Article↗
PubMed2002

Winners don't take all: Characterizing the competition for links on the web.

As a whole, the World Wide Web displays a striking "rich get richer" behavior, with a relatively small number of sites receiving a disproportionately large share of hyperlink references and traffic. However, hidden in this skewed global distribution, we discover a qualitatively different and considerably less biased link distribution among subcategories of pages-for example, among all university homepages or all newspaper homepages. Although the connectivity distribution over the entire web is close to a pure power law, we find that the distribution within specific categories is typically unimodal on a log scale, with the location of the mode, and thus the extent of the rich get richer phenomenon, varying across different categories. Similar distributions occur in many other naturally occurring networks, including research paper citations, movie actor collaborations, and United States power grid connections. A simple generative model, incorporating a mixture of preferential and uniform attachment, quantifies the degree to which the rich nodes grow richer, and how new (and poorly connected) nodes can compete. The model accurately accounts for the true connectivity distributions of category-specific web pages, the web as a whole, and other social networks.

Journal Article↗
PubMed2002

A small-molecule inhibitor of the ribonucleolytic activity of human angiogenin that possesses antitumor activity.

The results of previous preclinical and clinical studies have identified angiogenin (ANG) as a potentially important target for anticancer therapy. Here we report the design and implementation of a high-throughput screening assay to identify small molecules that bind to the ribonucleolytic active site of ANG, which is critically involved in the induction of angiogenesis by this protein. Screening of 18,310 compounds from the National Cancer Institute (NCI) Diversity Set and ChemBridge DIVERSet yielded 15 hits that inhibit the enzymatic activity of ANG with K(i) values <100 microM. One of these, NCI compound 65828 [8-amino-5-(4'-hydroxybiphenyl-4-ylazo)naphthalene-2-sulfonate; K(i) = 81 microM], was selected for more detailed studies. Minor changes in ANG or ligand structure markedly reduced potency, demonstrating that inhibition reflects active-site rather than nonspecific binding; these observations are consistent with a computationally generated model of the ANG.65828 complex. Local treatment with modest doses of 65828 significantly delayed the formation of s.c. tumors from two distinct human cancer cell types in athymic mice. ANG is the likely target involved because (i) a 65828 analogue with much lower potency against the enzymatic activity of ANG failed to exert any antitumor effect, (ii) tumors from 65828-treated mice had fewer interior blood vessels than those from control mice, and (iii) 65828 appears to have no direct effect on the tumor cells. Our findings provide considerable support for the targeting of the enzymatic active site of ANG as a strategy for developing new anticancer drugs.

Amino Acid Substitution↗
PubMed1992

Similarity between fluorescein-specific T-cell receptor and antibody in chemical details of antigen recognition.

A computer-generated model of the single-chain variable V alpha V beta fragment of the RFL3.8 T-cell receptor (TCR) specific for fluorescein served as a starting point for mutagenesis aimed at identification of its antigen-contacting residues. Selected backbone segments of the model representing regions of prominent sequence similarity between antibodies and TCRs were least-squares superimposed onto the corresponding segments of the crystallographically resolved 4-4-20 antibody complexed with its antigen, fluorescein. The superimposition placed the antibody-bound fluorescein molecule close to a cavity on the surface of the TCR model formed by the complementarity-determining region (CDR) loops. Some of the TCR cavity forming loops displayed sequence motifs related to canonical CDR loops previously found in antibodies. Six putative amino acid contacts were identified and single-chain TCRs with mutations at each of these positions were expressed in Escherichia coli, purified, refolded, and assayed for fluorescein binding. Five of the six mutations resulted in a loss of detectable binding. These RFL3.8 antigen combining site residues are distributed among the beta 3, alpha 1, and alpha 2 CDR loops and show striking chemical similarity to the known fluorescein contact residues on 4-4-20. Thus, antibodies and TCRs are similar both in their overall architecture and in the chemical details of specific antigen recognition.

Amino Acid Sequence↗
PubMed1997

Targeting RNA decay with 2',5' oligoadenylate-antisense in respiratory syncytial virus-infected cells.

Treatment of human cells with 2',5' oligoadenylate covalently linked to antisense (2-5A-antisense) results in the selective cleavage of targeted RNA species by 2-5A-dependent RNase L. Here we show that 2-5A-antisense containing stabilizing modifications at both termini are effective in suppressing the replication of respiratory syncytial virus (RSV) in human tracheal epithelial cells. The affinity of 2-5A-antisense for different regions in the RSV M2 and L mRNAs was predicted from a computer-generated model of the RNA secondary structure. The most potent 2-5A-antisense molecule caused a highly effective, dose-dependent suppression of RSV yields when added to previously infected cells. In contrast, control oligonucleotides, including an inactive dimeric form of 2-5A linked to antisense, 2-5A linked to a randomized sequence of nucleotides, and antisense molecules lacking 2-5A, had minimal effects on virus replication. The specificity of this approach was shown by reverse transcriptase-coupled PCR analysis of RSV M2, P, and N mRNA and of cellular glyceraldehyde-3-phosphate dehydrogenase mRNA. The RSV M2 mRNA amounts were depleted after treating RSV-infected cells with 2-5A-antisense targeted to this mRNA, whereas the amounts of the other RNA species were unchanged. These studies demonstrate that 2',5' oligoadenylate covalently linked to antisense (2-5A-antisense) can effectively suppress RSV replication by directing the cellular RNase L to selectively degrade an essential viral mRNA.

Adenine Nucleotides↗
PubMed1995

Immunoadsorption of hepatic vesicles carrying newly synthesized dipeptidyl peptidase IV and polymeric IgA receptor.

Hepatocytes must transport newly synthesized apical membrane proteins from the basolateral to the apical plasma membrane. Our earlier morphological study showed that the apical proteins share a late (subapical) part of the transcytotic pathway with the well characterized polymeric immunoglobulin A receptor (Barr, V. A., and Hubbard, A. L. (1993) Gastroenterology 105, 554-571). Starting with crude microsomes from the livers of [35S]methionine-labeled rats, we sequentially immunoadsorbed first vesicles containing the endocytic asialoglycoprotein receptor and then (from the depleted supernatant) vesicles containing the polymeric IgA receptor. Biochemical characterization indicated that early basolateral and late endosomes were present in the first population but not in the second. Neither Golgi-, apical plasma membrane (PM)-, nor basolateral PM-derived vesicles were significant contaminants of either population. Both vesicle populations contained 35S-labeled receptor and 35S-labeled-dipeptidyl peptidase IV. Importantly, the elevated relative specific activity of the dipeptidyl peptidase (% of 35S-labeled/% immunoblotted) in the second population indicated that these vesicles must transport newly synthesized dipeptidyl peptidase IV. A distinct kind of vesicle was immunoadsorbed from a "carrier-vesicle fraction"; surprisingly, these vesicles contained little 35S-receptor and virtually no dipeptidyl peptidase IV. These results, together with previous kinetic data from in vivo experiments, are consistent with a computer-generated model predicting that newly synthesized dipeptidyl peptidase IV is delivered to basolateral endosomes, which also contain newly synthesized polymeric immunoglobulin A receptor. The two proteins are then transcytosed together to the subapical region.

Animals↗
PubMed1997

Interactions between conserved residues in transmembrane helices 1, 2, and 7 of the thyrotropin-releasing hormone receptor.

The roles of conserved residues in transmembrane helices (TMs) of G protein-coupled receptors have not been well established. A computer-generated model of the thyrotropin-releasing hormone receptor (TRH-R) indicated that conserved Asp-71 (TM-2) could interact with conserved asparagines 316 (TM-7) and 43 (TM-1). To test this model, we constructed mutant TRH-Rs containing polar or alanine substitutions of these residues. The maximal activities of N43A and N316A TRH-Rs were diminished, whereas D71A (Perlman, J. H., Nussenzveig, D. R., Osman, R., and Gershengorn, M. C. (1992) J. Biol. Chem. 267, 24413-24417) and N43A/N316A TRH-Rs were inactive. Computer models of D71A and N43A/N316A TRH-Rs show similar changes from native TRH-R in their TM bundle conformations. The inactivity and the similarity of the computer models of D71A and N43A/N316A TRH-Rs are consistent with the idea that Asp-71 bridges Asn-43 and Asn-316 and suggest that activity is critically dependent on these interactions. The conservation of these residues suggests these specific interactions involving TMs 1, 2, and 7 may be structurally important for all members of the rhodopsin/beta-adrenergic receptor subfamily of G protein-coupled receptors.

Amino Acid Sequence↗
PubMed2002

Oxygen affinity of hemoglobin regulates O2 consumption, metabolism, and physical activity.

The oxygen affinity of hemoglobin is critical for gas exchange in the lung and O(2) delivery in peripheral tissues. In the present study, we generated model mice that carry low affinity hemoglobin with the Titusville mutation in the alpha-globin gene or Presbyterian mutation in the beta-globin gene. The mutant mice showed increased O(2) consumption and CO(2) production in tissue metabolism, suggesting enhanced O(2) delivery by mutant Hbs. The histology of muscle showed a phenotypical conversion from a fast glycolytic to fast oxidative type. Surprisingly, mutant mice spontaneously ran twice as far as controls despite mild anemia. The oxygen affinity of hemoglobin may control the basal level of erythropoiesis, tissue O(2) consumption, physical activity, and behavior in mice.

Animals↗
PubMed2003

Use of artificial neural networks to estimate production variables of broilers breeders in the production phase.

1. Although the poultry industry uses state-of-the-art equipment and up-to-date services, in Brazil it generally makes decisions involving all its production variables based on purely subjective criteria. This paper reports the use of artificial neural networks to estimate performance in production birds belonging to a South Brazilian poultry farm. 2. Recorded data from 22 broiler production breeder flocks were obtained, from April, 1998 to December, 1999, which corresponded to 689 data lines of weekly recordings. 3. These data were processed by artificial neural networks using the software NeuroShell 2 version 4.0 (Ward Systems Group). The artificial neural network models generated were compared and selected based on their largest determination coefficient (R2), lowest Mean Squared Error (MSE), as well as on a uniform scatter in the residual plots. The authors conclude that it is possible to explain the performance variables of production birds, with the use of artificial neural networks. 4. The method allows the decisions made by the technical staff to be based on objective, scientific criteria, allows simulations of the consequences related to these decisions, and reports the contribution of each variable to the variables under study.

Animal Feed↗
PubMed1992

Groove width and depth of B-DNA structures depend on local variation in slide.

The groove widths of DNA helix, especially minor groove width, are generally believed to be important for recognition of DNA by various types of ligands. It has been postulated earlier that large negative propeller twist, in the AT rich regions compresses the minor groove of duplex DNA. A systematic study has now been carried out by generating models with different values of local doublet and intra-basepair parameters and calculating their minor groove widths. It is found that several local doublet parameters affect the minor groove width but it depends most strongly on the local step parameters roll and slide when each parameter is considered individually. However, a detailed analysis of the various local parameters within the B-DNA family of crystal structures indicates that propeller twist and slide are most strongly correlated with the observed values of minor groove width. The groove depth is also strongly correlated with slide. Thus the local base sequence dependent variations in slide can modify both the groove width and depth and consequently determine the ligand binding properties of DNA.

Base Sequence↗
PubMedDate not supplied

Loss of cannabinoid CB(1) receptors in the basal ganglia in the late akinetic phase of rats with experimental Huntington's disease.

We have recently examined the status of the endocannabinoid transmission in the basal ganglia in Huntington's disease (HD) using a rat model generated by bilateral intrastriatal injections of 3-nitropropionic acid (3-NP). In these previous studies, we focused on the early phase of hyperactivity that occurs 1-2 weeks after the lesion, comparable to early grades of the human disease, while in the present study, we wanted to explore the late akinetic phase observed 3-4 weeks after the lesion (similar to advanced grades). First, we confirmed that 3-NP-lesioned rats exhibited a marked akinesia tested at 4 weeks post-lesion. We observed a marked reduction in ambulatory and exploratory activities and a trend towards a decrease in stereotypies, paralleled by a strong increase in the time spent in inactivity. There was also a profound reduction in GABA contents and glutamic acid decarboxylase activity, particularly in the caudate-putamen and the globus pallidus. Dopamine and DOPAC contents, as well as the activity of tyrosine hydroxylase, were also reduced, particularly in the caudate-putamen. mRNA levels for neuronal-specific enolase, proenkephalin and substance P were also dramatically reduced in the caudate-putamen, thus indicating a death of both the direct (striatonigral) and the indirect (striatopallidal) GABAergic projection pathways, which corresponded with a marked loss of CB(1) receptor-mRNA levels observed in both parts, lateral and medial, of the caudate-putamen. However, losses of CB(1) receptor binding were confined to the globus pallidus and the caudate-putamen, whereas there were no changes in the substantia nigra and the entopeduncular nucleus. Finally, we failed to reduce the marked akinesia found in these animals by administering SR141716A, a selective antagonist of CB(1) receptors, which had exhibited hyperlocomotor effects in previous studies with naive animals. In summary, behavioral and biochemical changes observed in rats intrastriatally lesioned with 3- NP were compatible with a profound degeneration of striatal efferent GABAergic neurons, similar to those occurring in advances stages of the human disease. As expected, a loss of CB(1) receptors was evident in the basal ganglia of these rats during the late akinetic stage of the disease. Further studies should demonstrate whether these receptors might be a target for a new therapy in HD, a disease with a poor pharmacological outcome.

Journal Article↗
PubMed2006

New probabilistic network models and algorithms for oncogenesis.

Chromosomal aberrations in solid tumors appear in complex patterns. It is important to understand how these patterns develop, the dynamics of the process, the temporal or even causal order between aberrations, and the involved pathways. Here we present network models for chromosomal aberrations and algorithms for training models based on observed data. Our models are generative probabilistic models that can be used to study dynamical aspects of chromosomal evolution in cancer cells. They are well suited for a graphical representation that conveys the pathways found in a dataset. By allowing only pairwise dependencies and partition aberrations into modules, in which all aberrations are restricted to have the same dependencies, we reduce the number of parameters so that datasets sizes relevant to cancer applications can be handled. We apply our framework to a dataset of colorectal cancer tumor karyotypes. The obtained model explains the data significantly better than a model where independence between the aberrations is assumed. In fact, the obtained model performs very well with respect to several measures of goodness of fit and is, with respect to repetition of the training, more or less unique.

Algorithms↗
PubMed2005

Clinical assessment of near-infrared spectroscopy for noninvasive diabetes screening.

BACKGROUND: Current diabetes screening techniques comprise the fasting plasma glucose (FPG) and oral glucose tolerance tests. Both tests demand patient compliance, and neither test has ideal performance. Near-infrared (NIR) spectroscopy is a noninvasive means of interrogating characteristics of a sample and is evaluated as a novel screening method for type 2 diabetes. METHODS: One hundred fifty-four patients with and without type 2 diabetes were recruited. Their forearm skin was measured with the NIR spectroscopic system, and a capillary blood glucose measurement was also taken. Sixty-six patients returned for a second visit at a later date. A multivariate model, generated from a separate training study, was employed to produce a quantitative risk marker of disease for each NIR spectrum. Sensitivity and specificity (the probabilities that the NIR method will correctly identify a subject as having diabetes or as not having diabetes, respectively) were calculated. As the NIR method produces a continuous rather than categorical classification, various thresholds were evaluated to give several sensitivity and specificity pairs. Test reproducibility was also determined. RESULTS: At a false-positive rate of 70%, the NIR test had a sensitivity of 77.7%, which is comparable to the 77.3% sensitivity for the FPG test as reported for the Third National Health and Nutrition Examination Survey (NHANES III) study. The reproducibility of the NIR test was also similar to the FPG test (inter-day agreement rates of 84.2% and 79.2%, respectively). CONCLUSIONS: A noninvasive NIR spectroscopic measurement of the volar forearm was shown to have comparable performance characteristics with the FPG test. The source of the spectroscopic signal is still uncertain and is the subject of ongoing research.

Adult↗
PubMed2003

Markovian negentropies in bioinformatics. 1. A picture of footprints after the interaction of the HIV-1 Psi-RNA packaging region with drugs.

MOTIVATION: Many experts worldwide have highlighted the potential of RNA molecules as drug targets for the chemotherapeutic treatment of a range of diseases. In particular, the molecular pockets of RNA in the HIV-1 packaging region have been postulated as promising sites for antiviral action. The discovery of simpler methods to accurately represent drug-RNA interactions could therefore become an interesting and rapid way to generate models that are complementary to docking-based systems. RESULTS: The entropies of a vibrational Markov chain have been introduced here as physically meaningful descriptors for the local drug-nucleic acid complexes. A study of the interaction of the antibiotic Paromomycin with the packaging region of the RNA present in type-1 HIV has been carried out as an illustrative example of this approach. A linear discriminant function gave rise to excellent discrimination among 80.13% of interacting/non-interacting sites. More specifically, the model classified 36/45 nucleotides (80.0%) that interacted with paromomycin and, in addition, 85/106 (80.2%) footprinted (non-interacting) sites from the RNA viral sequence were recognized. The model showed a high Matthews' regression coefficient (C = 0.64). The Jackknife method was also used to assess the stability and predictability of the model by leaving out adenines, C, G, or U. Matthews' coefficients and overall accuracies for these approaches were between 0.55 and 0.68 and 75.8 and 82.7, respectively. On the other hand, a linear regression model predicted the local binding affinity constants between a specific nucleotide and the aforementioned antibiotic (R2 = 0.83,Q2 = 0.825). These kinds of models may play an important role either in the discovery of new anti-HIV compounds or in the elucidation of their mode of action. AVAILABILITY: On request from the corresponding author (humbertogd@cbq.uclv.edu.cu or humbertogd@navegalia.com).

Binding Sites↗
PubMed2004

Mismatch string kernels for discriminative protein classification.

MOTIVATION: Classification of proteins sequences into functional and structural families based on sequence homology is a central problem in computational biology. Discriminative supervised machine learning approaches provide good performance, but simplicity and computational efficiency of training and prediction are also important concerns. RESULTS: We introduce a class of string kernels, called mismatch kernels, for use with support vector machines (SVMs) in a discriminative approach to the problem of protein classification and remote homology detection. These kernels measure sequence similarity based on shared occurrences of fixed-length patterns in the data, allowing for mutations between patterns. Thus, the kernels provide a biologically well-motivated way to compare protein sequences without relying on family-based generative models such as hidden Markov models. We compute the kernels efficiently using a mismatch tree data structure, allowing us to calculate the contributions of all patterns occurring in the data in one pass while traversing the tree. When used with an SVM, the kernels enable fast prediction on test sequences. We report experiments on two benchmark SCOP datasets, where we show that the mismatch kernel used with an SVM classifier performs competitively with state-of-the-art methods for homology detection, particularly when very few training examples are available. Examination of the highest-weighted patterns learned by the SVM classifier recovers biologically important motifs in protein families and superfamilies.

Algorithms↗