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Search Results: 1 - 10 of 300754 matches for " J. Kenneth Wickiser "
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Similar Pathogen Targets in Arabidopsis thaliana and Homo sapiens Protein Networks
Paulo Shakarian, J. Kenneth Wickiser
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0045154
Abstract: We study the behavior of pathogens on host protein networks for humans and Arabidopsis - noting striking similarities. Specifically, we preform -shell decomposition analysis on these networks - which groups the proteins into various “shells” based on network structure. We observe that shells with a higher average degree are more highly targeted (with a power-law relationship) and that highly targeted nodes lie in shells closer to the inner-core of the network. Additionally, we also note that the inner core of the network is significantly under-targeted. We show that these core proteins may have a role in intra-cellular communication and hypothesize that they are less attacked to ensure survival of the host. This may explain why certain high-degree proteins are not significantly attacked.
Single Institution Experience with Tru-Cut Renal Mass Biopsy for Diagnosing WilmsTumor
Nicholas G. Cost,Candace F. Granberg,Bruce J. Schlomer,Jonathan E. Wickiser
Urology Journal , 2013,
Abstract: PURPOSE: To evaluate the efficacy of needle biopsy for diagnosing Wilmstumor (WT) before chemotherapy. MATERIALS AND METHODS:We reviewed our institutional experience with Tru-Cut biopsy of pediatric renal masses in patients who subsequently underwent nephrectomy. We compared biopsy pathology with nephrectomy specimens to determine if biopsy accurately predicted final pathology. RESULTS: Seven children underwent Tru-Cut renal mass biopsy followed by surgical resection. In 4 patients, the final biopsy pathology was definitively read as WT and in 3 subjects, the pathology was read as WT versus hyperplastic nephrogenic rest. In all 7 patients, the nephrectomy pathology confirmed a diagnosis of WT. There were no complications after biopsy, and no patients have had local or regional recurrence.CONCLUSION: In our experience, pre-therapy Tru-Cut biopsy safely provides an adequate specimen for pathologic review in diagnosing WT.
Delayed Lumbar Artery Laceration and Symptomatic Retroperitoneal Hemorrhage Following IVC Filter Placement  [PDF]
Jennifer P. Montgomery, Kenneth J. Kolbeck
Open Journal of Radiology (OJRad) , 2015, DOI: 10.4236/ojrad.2015.54029
Abstract: Inferior vena cava filters are placed in selected patients to protect against potentially fatal pulmonary embolism. Generally, filter placement is regarded as a safe procedure although rare complications may arise. Recurrent thromboembolic events are the most common complications assoiated with inferior vena cava filters; however, there are multiple reports of filter fracture, migration, embolization, penetration and perforation. The aim of this report is to illustrate a serious potential complication of inferior vena cava filters. We report a rare case of symptomatic retroperitoneal hemorrhage occurring 3 weeks after filter placement treated successfully with selective arterial embolization of a lumbar artery laceration. This case serves to highlight the importance of retrieving filters when they are no longer beneficial.
Validating HeartSmart® against the Cardiopulmonary Bypass Machine  [PDF]
Kenneth J. Warring-Davies, Martin J. Bland
Surgical Science (SS) , 2012, DOI: 10.4236/ss.2012.31004
Abstract: Purpose: To assess the utility of HeartSmart?, a new method that uses empirical physiological formulae to estimate hemodynamic variables, in estimating cardiac index during open heart surgery when compared with the cardiopulmonary bypass machine. Methods: This was a prospective, blinded study of patients undergoing elective cardiac bypass surgery. We monitored and compared the flow rates provided by the cardiopulmonary bypass machine (roller pump) with estimates derived from the empirical physiological formulae embedded in the HeartSmart? monitor in 32 patients. Cardiac index values were compared at the start of cardiopulmonary bypass, during re-warming, and at the end of cardiopulmonary bypass. Results: A total of 256 paired sets of measurements were suitable for comparison. The mean of the differences or bias (95% limits of agreement) was 0.09 l/min/m2 and the limits of agreement –0.86 to 1.05 l/min/m2. The mean difference of the sets of 256 measurements was 585.5 l/min/m for the pump and 575.0 l/min/m2 for the empirical physiological formulae—a difference of 5% l/min/m2. The range of flow rates for the pump was 1.2 to 2.85 l/min/m2; for the empirical physiological formulae, the range was 1.2 to 3.0 l/min/m2. Conclusion: The cardiac index estimates derived from the empirical physiological formulae in the HeartSmart? software are in good agreement with pump cardiac output rates. These results suggest that HeartSmart? measurements are sufficiently accurate for assessing hemodynamic variables in many groups of patients.
Developing an Evolutionary Algorithm to Search for an Optimal Multi-Mother Wavelet Packets Combination  [PDF]
Ohad Bar Siman Tov, J. David Schaffer, Kenneth J. McLeod
Journal of Biomedical Science and Engineering (JBiSE) , 2015, DOI: 10.4236/jbise.2015.87043
Abstract: The wavelet transform is a popular analysis tool for non-stationary data, but in many cases, the choice of the mother wavelet and basis set remains uncertain, particularly when dealing with physiological data. Furthermore, the possibility exists for combining information from numerous mother wavelets so as to exploit different features from the data. However, the combinatorics become daunting given the large number of basis sets that can be utilized. Recent work in evolutionary computation has produced a subset selection genetic algorithm specifically aimed at the discovery of small, high-performance, subsets from among a large pool of candidates. Our aim was to apply this algorithm to the task of locating subsets of packets from multiple mother wavelet decompositions to estimate cardiac output from chest wall motions while avoiding the computational cost of full signal reconstruction. We present experiments which show how a continuous assessment metric can be extracted from the wavelets coefficients, but the dual-objective nature of the algorithm (high accuracy with small feature sets) imposes a need to restrict the sensitivity of the continuous accuracy metric in order to achieve the small subset size desired. A possibly subtle tradeoff seems to be needed to meet the dual objectives.
Thrombosis after Travel
Kenneth J Rothman
PLOS Medicine , 2006, DOI: 10.1371/journal.pmed.0030300
Strand bias structure in mouse DNA gives a glimpse of how chromatin structure affects gene expression
Kenneth J Evans
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-16
Abstract: The mouse genome is shown to have a segmented structure defined by strand bias. Transcription is known to cause a strand bias and numerous analyses are presented to show that the strand bias in question is not caused by transcription. However, these strand bias segments influence the position of genes and their unspliced length. The position of genes within the strand bias structure affects the probability that a gene is switched on and its expression level. Transcription has a highly directional flow within this structure and the peak volume of transcription is around 20 kb from the A-rich/T-rich segment boundary on the T-rich side, directed away from the boundary. The A-rich/T-rich boundaries are SATB1 binding regions, whereas the T-rich/A-rich boundary regions are not.The direct cause of the strand bias structure may be DNA replication. The strand bias segments represent a further biological feature, the chromatin structure, which in turn influences the ease of transcription.Because of the Watson-Crick structure of DNA – A paired with T and C with G – the number of As must equal the number of Ts when the bases on both strands are counted. Although this equality does not have to be true for a single strand, Chargaff's second law refers to the equality of A/T and C/G bases on a single strand [1] and broadly speaking eukaryote genomes are free of intrastrand bias [2].Early work on strand bias analysed prokaryote and viral genomes where strand biases have been observed and associated with origins of replication: the leading strand is found to be G-rich and T-rich, with the G-C bias often being found to be more consistent than the A-T bias [3-6].Strand bias has been discovered at transcription start sites in plants and fungi [7], animals [8,9], and splice sites [10]. Strand bias has been found for long regions of DNA around actual and putative origins of replication [11]. An analysis of nearby divergent genes concluded that both replication and transcription effects w
Genomic DNA from animals shows contrasting strand bias in large and small subsequences
Kenneth J Evans
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-43
Abstract: For a typical mammal, for example mouse or human, there is a small strand bias throughout the genomic DNA: there is a correlation between (G - C) and (A - T) on the same strand, (that is between the difference in the number of guanine and cytosine bases and the difference in the number of adenine and thymine bases). For small subsequences – up to 1 kb – this correlation is weak but positive; but for large windows – around 50 kb to 2 Mb – the correlation is strong and negative. This effect is largely independent of GC%. Transcribed and untranscribed regions give similar correlations both for small and large subsequences, but there is a difference in these regions for intermediate sized subsequences. An analysis of the human genome showed that position within the isochore structure did not affect these correlations. An analysis of available genomes of different species shows that this contrast between large and small windows is a general feature of mammals and birds. Further down the evolutionary tree, other organisms show a similar but smaller effect. Except for the nematode, all the animals analysed showed at least a small effect.The correlations on the large scale may be explained by DNA replication. Transcription may be a modifier of these effects but is not the fundamental cause. These results cast light on how DNA mutations affect the genome over evolutionary time. At least for vertebrates, there is a broad relationship between body temperature and the size of the correlation. The genome of mammals and birds has a structure marked by strand bias segments.Because of the Watson-Crick structure of DNA – A paired with T and C with G – it is necessary that the number of As must equal the number of Ts when the bases on both strands are counted. Although, this equality does not have to be true for a single strand, Chargaff's second law refers to the equality of A/T and C/G bases on a single strand [1] and broadly speaking eukaryote genomes are free of intrastrand bias
Most transcription factor binding sites are in a few mosaic classes of the human genome
Kenneth J Evans
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-286
Abstract: We find that the human genome may be described by 19 pairs of mosaic classes, each defined by its base frequencies, (or more precisely by the frequencies of doublets), so that typically a run of 10 to 100 bases belongs to the same class. Most experimentally verified binding sites are in the same four pairs of classes. In our sample of seventeen transcription factors — taken from different families of transcription factors — the average proportion of sites in this subset of classes was 75%, with values for individual factors ranging from 48% to 98%. By contrast these same classes contain only 26% of the bases of the genome and only 31% of occurrences of the motifs of these factors — that is places where one might expect the factors to bind. These results are not a consequence of the class composition in promoter regions.This method of analysis will help to find transcription factor binding sites and assist with the problem of false positives. These results also imply a profound difference between the mosaic classes.The DNA sequence has no landmarks to guide the search for transcription factor binding sites: these binding sites may be near the transcription start site but may also be far from it [1,2]. Many papers have examined how these sites might be found computationally [3]. Some methods use a comparison between orthologous regions of different species [4], often treating the problem as one of multiple alignment [5,6]. Other algorithms use a collection of subsequences containing a binding site (for example the promoter regions of coregulated genes or subsequences derived from ChIp-chip experiments) to deduce the form or motif of the binding site which is then used to identify sites in other sequences — reviews of these methods are given in [7,8]. These methods include Weeder [9], MEME [10], ANN-SPEC [11], MORPH [12] and GLAM [13]. Some authors have proposed a statistical test to decide whether a region of DNA is a regulatory region: two methods [14,15] tested on f
McKenzie,Kenneth J.;
Revista de Economía Institucional , 1999,
Abstract: this survey article provides a microeconomic perspective of institutional design and public policy, focusing on the way the relations between voters, politicians and bureaucrats produce efficients outcomes in public policy. it points out the relevance of information and monitoring costs, competition and the structural features of institutions in the search of efficient results, and the way social scientists explain the failures of the political and burocratic markets.
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