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Find video protocols related to scientific articles indexed in Pubmed.
Are endosomal trafficking parameters better targets for improving mAb pharmacokinetics than FcRn binding affinity?
Mol. Immunol.
PUBLISHED: 05-09-2013
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F.W.R. Brambell deduced the existence of a protective receptor for IgG, the neonatal Fc receptor (FcRn), long before its discovery in the early to mid-1990s. With the coincident, explosive development of IgG-based drugs, FcRn became a popular target for tuning the pharmacokinetics of monoclonal antibodies (mAbs). One aspect of Brambells initial observation, however, that is seldom discussed since the discovery of the receptor, is the compliance in the mechanism that Brambell observed (saturating at 10s-100s of ?M concentration), vs. the comparative stiffness of the receptor kinetics (saturating in the nM range for most species). Although some studies reported that increasing the already very high Fc-FcRn affinity at pH 6.0 further improved mAb half-life, in fact the results were mixed, with later studies increasingly implicating non-FcRn-dependent mechanisms as determinants of mAb pharmacokinetics. Mathematical modelling of the FcRn system has also indicated that the processes determining the pharmacokinetics of mAbs have more nuances than had at first been hypothesised. We propose, in keeping with the latest modelling and experimental evidence reviewed here, that the dynamics of endosomal sorting and trafficking have important roles in the compliant salvage mechanism that Brambell first observed nearly 50 years ago, and therefore also in the pharmacokinetics of mAbs. These ideas lead to many open questions regarding the endosomal trafficking of both FcRn and mAbs and also to what properties of a mAb can be altered to achieve an improvement in pharmacokinetics.
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Pharmacokinetics, pharmacodynamics and physiologically-based pharmacokinetic modelling of monoclonal antibodies.
Clin Pharmacokinet
PUBLISHED: 01-10-2013
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Development of monoclonal antibodies (mAbs) and their functional derivatives represents a growing segment of the development pipeline in the pharmaceutical industry. More than 25 mAbs and derivatives have been approved for a variety of therapeutic applications. In addition, around 500 mAbs and derivatives are currently in different stages of development. mAbs are considered to be large molecule therapeutics (in general, they are 2-3 orders of magnitude larger than small chemical molecule therapeutics), but they are not just big chemicals. These compounds demonstrate much more complex pharmacokinetic and pharmacodynamic behaviour than small molecules. Because of their large size and relatively poor membrane permeability and instability in the conditions of the gastrointestinal tract, parenteral administration is the most usual route of administration. The rate and extent of mAb distribution is very slow and depends on extravasation in tissue, distribution within the particular tissue, and degradation. Elimination primarily happens via catabolism to peptides and amino acids. Although not definitive, work has been published to define the human tissues mainly involved in the elimination of mAbs, and it seems that many cells throughout the body are involved. mAbs can be targeted against many soluble or membrane-bound targets, thus these compounds may act by a variety of mechanisms to achieve their pharmacological effect. mAbs targeting soluble antigen generally exhibit linear elimination, whereas those targeting membrane-bound antigen often exhibit non-linear elimination, mainly due to target-mediated drug disposition (TMDD). The high-affinity interaction of mAbs and their derivatives with the pharmacological target can often result in non-linear pharmacokinetics. Because of species differences (particularly due to differences in target affinity and abundance) in the pharmacokinetics and pharmacodynamics of mAbs, pharmacokinetic/pharmacodynamic modelling of mAbs has been used routinely to expedite the development of mAbs and their derivatives and has been utilized to help in the selection of appropriate dose regimens. Although modelling approaches have helped to explain variability in both pharmacokinetic and pharmacodynamic properties of these drugs, there is a clear need for more complex models to improve understanding of pharmacokinetic processes and pharmacodynamic interactions of mAbs with the immune system. There are different approaches applied to physiologically based pharmacokinetic (PBPK) modelling of mAbs and important differences between the models developed. Some key additional features that need to be accounted for in PBPK models of mAbs are neonatal Fc receptor (FcRn; an important salvage mechanism for antibodies) binding, TMDD and lymph flow. Several models have been described incorporating some or all of these features and the use of PBPK models are expected to expand over the next few years.
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Multiscale analysis of heart rate variability in non-stationary environments.
Front Physiol
PUBLISHED: 01-01-2013
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Heart rate variability (HRV) is highly non-stationary, even if no perturbing influences can be identified during the recording of the data. The non-stationarity becomes more profound when HRV data are measured in intrinsically non-stationary environments, such as social stress. In general, HRV data measured in such situations are more difficult to analyze than those measured in constant environments. In this paper, we analyze HRV data measured during a social stress test using two multiscale approaches, the adaptive fractal analysis (AFA) and scale-dependent Lyapunov exponent (SDLE), for the purpose of uncovering differences in HRV between chronic fatigue syndrome (CFS) patients and their matched-controls. CFS is a debilitating, heterogeneous illness with no known biomarker. HRV has shown some promise recently as a non-invasive measure of subtle physiological disturbances and trauma that are otherwise difficult to assess. If the HRV in persons with CFS are significantly different from their healthy controls, then certain cardiac irregularities may constitute good candidate biomarkers for CFS. Our multiscale analyses show that there are notable differences in HRV between CFS and their matched controls before a social stress test, but these differences seem to diminish during the test. These analyses illustrate that the two employed multiscale approaches could be useful for the analysis of HRV measured in various environments, both stationary and non-stationary.
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Randomization modeling to ascertain clustering patterns of human papillomavirus types detected in cervicovaginal samples in the United States.
PLoS ONE
PUBLISHED: 01-01-2013
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Detection of multiple human papillomavirus (HPV) types in the genital tract is common. Associations among HPV types may impact HPV vaccination modeling and type replacement. The objectives were to determine the distribution of concurrent HPV type infections in cervicovaginal samples and examine type-specific associations. We analyzed HPV genotyping results from 32,245 cervicovaginal specimens collected from women aged 11 to 83 years in the United States from 2001 through 2011. Statistical power was enhanced by combining 6 separate studies. Expected concurrent infection frequencies from a series of permutation models, each with increasing fidelity to the real data, were compared with the observed data. Statistics were computed based on the distributional properties of the randomized data. Concurrent detection occurred more than expected with 0 or ?3 HPV types and less than expected with 1 and 2 types. Some women bear a disproportionate burden of the HPV type prevalence. Type associations were observed that exceeded multiple hypothesis corrected significance. Multiple HPV types were detected more frequently than expected by chance and associations among particular HPV types were detected. However vaccine-targeted types were not specifically affected, supporting the expectation that current bivalent/quadrivalent HPV vaccination will not result in type replacement with other high-risk types.
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Entropies of negative incomes, Pareto-distributed loss, and financial crises.
PLoS ONE
PUBLISHED: 08-06-2011
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Health monitoring of world economy is an important issue, especially in a time of profound economic difficulty world-wide. The most important aspect of health monitoring is to accurately predict economic downturns. To gain insights into how economic crises develop, we present two metrics, positive and negative income entropy and distribution analysis, to analyze the collective "spatial" and temporal dynamics of companies in nine sectors of the world economy over a 19 year period from 1990-2008. These metrics provide accurate predictive skill with a very low false-positive rate in predicting downturns. The new metrics also provide evidence of phase transition-like behavior prior to the onset of recessions. Such a transition occurs when negative pretax incomes prior to or during economic recessions transition from a thin-tailed exponential distribution to the higher entropy Pareto distribution, and develop even heavier tails than those of the positive pretax incomes. These features propagate from the crisis initiating sector of the economy to other sectors.
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Functional genomics of serotonin receptor 2A (HTR2A): interaction of polymorphism, methylation, expression and disease association.
Neuromolecular Med.
PUBLISHED: 06-07-2010
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Serotonergic neurotransmission plays a key role in the pathophysiology of neuropsychiatric illnesses. The functional significance of a promoter polymorphism, -1438G/A (rs6311), in one of the major genes of this system (serotonin receptor 2A, HTR2A) remains poorly understood in the context of epigenetic factors, transcription factors and endocrine influences. We used functional and structural equation modeling (SEM) approaches to assess the contributions of the polymorphism (rs6311), DNA methylation and clinical variables to HTR2A expression in chronic fatigue syndrome (CFS) subjects from a population-based study. HTR2A was up-regulated in CFS through allele-specific expression modulated by transcription factors at critical sites in its promoter: an E47 binding site at position -1,438, (created by the A-allele of rs6311 polymorphism), a glucocorticoid receptor (GR) binding site encompassing a CpG at position -1,420, and Sp1 binding at CpG methylation site -1,224. Methylation at -1,420 was strongly correlated with methylation at -1,439, a CpG site that is dependent upon the G-allele of rs6311 at position -1,438. SEM revealed a strong negative interaction between E47 and GR binding (in conjunction with cortisol level) on HTR2A expression. This study suggests that the promoter polymorphism (rs6311) can affect both transcription factor binding and promoter methylation, and this along with an individuals stress response can impact the rate of HTR2A transcription in a genotype and methylation-dependent manner. This study can serve as an example for deciphering the molecular determinants of transcriptional regulation of major genes of medical importance by integrating functional genomics and SEM approaches. Confirmation in an independent study population is required.
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Quadratic variance models for adaptively preprocessing SELDI-TOF mass spectrometry data.
BMC Bioinformatics
PUBLISHED: 04-12-2010
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Surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI) is a proteomics tool for biomarker discovery and other high throughput applications. Previous studies have identified various areas for improvement in preprocessing algorithms used for protein peak detection. Bottom-up approaches to preprocessing that emphasize modeling SELDI data acquisition are promising avenues of research to find the needed improvements in reproducibility.
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Benchmarking currently available SELDI-TOF MS preprocessing techniques.
Proteomics
PUBLISHED: 03-19-2009
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SELDI protein profiling experiments can be used as a first step in studying the pathogenesis of various diseases such as cancer. There are a plethora of software packages available for doing the preprocessing of SELDI data, each with many options and written from different signal processing perspectives, offering many researchers choices they may not have the background or desire to make. Moreover, several studies have shown that mistakes in the preprocessing of the data can bias the biological interpretation of the study. For this reason, we conduct a large scale evaluation of available signal processing techniques to establish which are most effective. We use data generated from a standard, published simulation engine so that "truth" is known. We select the top algorithms by considering two logical performance metrics, and give our recommendations for research directions that are likely to be most promising. There is considerable opportunity for future contributions improving the signal processing of SELDI spectra.
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Sensitive and specific peak detection for SELDI-TOF mass spectrometry using a wavelet/neural-network based approach.
PLoS ONE
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SELDI-TOF mass spectrometers compact size and automated, high throughput design have been attractive to clinical researchers, and the platform has seen steady-use in biomarker studies. Despite new algorithms and preprocessing pipelines that have been developed to address reproducibility issues, visual inspection of the results of SELDI spectra preprocessing by the best algorithms still shows miscalled peaks and systematic sources of error. This suggests that there continues to be problems with SELDI preprocessing. In this work, we study the preprocessing of SELDI in detail and introduce improvements. While many algorithms, including the vendor supplied software, can identify peak clusters of specific mass (or m/z) in groups of spectra with high specificity and low false discover rate (FDR), the algorithms tend to underperform estimating the exact prevalence and intensity of peaks in those clusters. Thus group differences that at first appear very strong are shown, after careful and laborious hand inspection of the spectra, to be less than significant. Here we introduce a wavelet/neural network based algorithm which mimics what a team of expert, human users would call for peaks in each of several hundred spectra in a typical SELDI clinical study. The wavelet denoising part of the algorithm optimally smoothes the signal in each spectrum according to an improved suite of signal processing algorithms previously reported (the LibSELDI toolbox under development). The neural network part of the algorithm combines those results with the raw signal and a training dataset of expertly called peaks, to call peaks in a test set of spectra with approximately 95% accuracy. The new method was applied to data collected from a study of cervical mucus for the early detection of cervical cancer in HPV infected women. The method shows promise in addressing the ongoing SELDI reproducibility issues.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.