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Search Results: 1 - 10 of 28098 matches for " Steve Lee "
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A derivation of the master equation from path entropy maximization
Julian Lee,Steve Pressé
Physics , 2012, DOI: 10.1063/1.4743955
Abstract: The master equation and, more generally, Markov processes are routinely used as models for stochastic processes. They are often justified on the basis of randomization and coarse-graining assumptions. Here instead, we derive n-th order Markov processes and the master equation as unique solutions to an inverse problem. In particular, we find that when the constraints are not enough to uniquely determine the stochastic model, the n-th order Markov process emerges as the unique maximum entropy solution to this otherwise under-determined problem. This gives a rigorous alternative for justifying such models while providing a systematic recipe for generalizing widely accepted stochastic models usually assumed to follow from first principles.
Effect of Thermal Treatment of the Hydroxyapatite Powders on the Micropore and Microstructure of Porous Biphasic Calcium Phosphate Composite Granules  [PDF]
David S. H. Lee, Yuni Pai, Steve Chang
Journal of Biomaterials and Nanobiotechnology (JBNB) , 2013, DOI: 10.4236/jbnb.2013.42015

The effect of thermal treatment of the hydroxyapatite powders on the micropore structure of porous biphasic calcium phosphate (BCP) granules was examined. The porous BCP granules could be attained through mixing and sintering/fracturing thermally treated 60 wt% hydroxyapatite powders and calcined 40 wt% β-tricalcium phosphate powders. The observed Scanning electron microscopy (SEM) morphologies showed that the density of micropores (0.1 - 2.0 μm) including interconnected micropores of the porous BCP granules mixed with hydroxyapatite powders thermally treated at 900°C was significantly improved and the composite particles of porous BCP granules were homogeneously mixed and distributed. This result indicates that the particles of hydroxyapatite powders that have a tendency to agglomerate at a room temperature were well isolated and dispersed through thermal treatment processing before mixing with calcined β-tricalcium phosphate powders. The microstructural characterizations such as phase purity and composition of porous BCP granules were performed and verified by X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FT-IR) analysis.

Subcutaneous Trastuzumab (Herceptin®): A UK Time and Motion Study in Comparison with Intravenous Formulation for the Treatment of Patients with HER2-Positive Early Breast Cancer  [PDF]
Russell Burcombe, Steve Chan, Richard Simcock, Kunal Samanta, Fran Percival, Peter Barrett-Lee
Advances in Breast Cancer Research (ABCR) , 2013, DOI: 10.4236/abcr.2013.24022

Aim: Firstly, to quantify active healthcare professional (HCP) time and costs associated with subcutaneous (SC) administration of trastuzumab (Herceptin?) compared with the standard intravenous infusion (IV) in the treatment of patients with HER2-positive early breast cancer within the adjuvant PrefHer trial setting; secondly, to measure patient time in the care unit and patient infusion chair time for both routes of administration. Methods: A UK multi-centre prospective, observational Time and Motion study was conducted alongside the PrefHer trial (ClinicalTrials.gov id: NCT01401166). Trained observers measured the duration of each SC and IV related task that HCPs undertook and recorded patient time in the chemotherapy unit and infusion chair. The type and quantity of medical consumables used with each route of administration were also collected. Twenty-four patient episodes were recorded (12 SC, 12 IV). Mean total administration time was calculated as the mean sum of task times, both for IV and SC formulations. The mean cost of each route of administration was calculated as the mean cost of HCP time plus the mean cost of consumables used. HCP time was costed using Personal Social Services Research Unit. Consumables were costed using hospital pharmacy data and online sources. Results: Mean active HCP time for IV administration was 92.6 minutes compared with 24.6 minutes for SC administration. The mean cost for IV preparation and administration was £144.96 (£132.05 of HCP time and £12.92 of consumables) versus £33.15 (£31.99 of HCP time and £1.17 of consumables) for SC administration. Mean time spent in the care unit and in the infusion chair was 94.5 minutes and 75 minutes respectively for IV, and 30.3 minutes and 19.8 minutes for SC. SC administration of trastuzumab could translate to a time saving of 68 minutes (versus IV) with a total cost saving of £111.81 per

Phenotypic Variability in a Family with Aicardi-Goutières Syndrome Due to the Common A177T RNASEH2B Mutation  [PDF]
Victoria Tüngler, Franziska Schmidt, Steve Hieronimus, Claudio Reyes-Velasco, Min Ae Lee-Kirsch
Case Reports in Clinical Medicine (CRCM) , 2014, DOI: 10.4236/crcm.2014.33037

Aicardi-Goutières syndrome (AGS) is a rare inflammatory encephalopathy mimicking in utero acquired viral infection. Cardinal findings comprise leukodystrophy, basal ganglia calcifications and cerebral atrophy along with cerebrospinal fluid lymphocytosis and elevated interferon-α. In the majority of cases AGS is inherited as an autosomal recessive trait and caused by mutations in six genes including RNASEH2A, RNASEH2B, RNASEH2C, TREX1, SAMHD1 and ADAR1, all of which encode enzymes acting on nucleic acid species. Most patients present with first neurological signs in early infancy and experience severe global developmental delay. Here, we report on the unusual divergent phenotype of two siblings who both carry the most frequent AGS causing p.A177T (c.529G > A) RNASEH2B mutation in the homozygous state. While one sibling showed a typical AGS presentation with early onset and severe statomotor and mental impairment, the older sibling was intellectually completely normal. She was only diagnosed because of mild spasticity of the legs and serological signs of autoimmunity. These findings highlight the phenotypic

Bayesian Classification and Feature Selection from Finite Data Sets
Frans Coetzee,Steve Lawrence,C. Lee Giles
Computer Science , 2013,
Abstract: Feature selection aims to select the smallest subset of features for a specified level of performance. The optimal achievable classification performance on a feature subset is summarized by its Receiver Operating Curve (ROC). When infinite data is available, the Neyman- Pearson (NP) design procedure provides the most efficient way of obtaining this curve. In practice the design procedure is applied to density estimates from finite data sets. We perform a detailed statistical analysis of the resulting error propagation on finite alphabets. We show that the estimated performance curve (EPC) produced by the design procedure is arbitrarily accurate given sufficient data, independent of the size of the feature set. However, the underlying likelihood ranking procedure is highly sensitive to errors that reduces the probability that the EPC is in fact the ROC. In the worst case, guaranteeing that the EPC is equal to the ROC may require data sizes exponential in the size of the feature set. These results imply that in theory the NP design approach may only be valid for characterizing relatively small feature subsets, even when the performance of any given classifier can be estimated very accurately. We discuss the practical limitations for on-line methods that ensures that the NP procedure operates in a statistically valid region.
The Dark Side of Micro-Task Marketplaces: Characterizing Fiverr and Automatically Detecting Crowdturfing
Kyumin Lee,Steve Webb,Hancheng Ge
Computer Science , 2014,
Abstract: As human computation on crowdsourcing systems has become popular and powerful for performing tasks, malicious users have started misusing these systems by posting malicious tasks, propagating manipulated contents, and targeting popular web services such as online social networks and search engines. Recently, these malicious users moved to Fiverr, a fast-growing micro-task marketplace, where workers can post crowdturfing tasks (i.e., astroturfing campaigns run by crowd workers) and malicious customers can purchase those tasks for only $5. In this paper, we present a comprehensive analysis of Fiverr. First, we identify the most popular types of crowdturfing tasks found in this marketplace and conduct case studies for these crowdturfing tasks. Then, we build crowdturfing task detection classifiers to filter these tasks and prevent them from becoming active in the marketplace. Our experimental results show that the proposed classification approach effectively detects crowdturfing tasks, achieving 97.35% accuracy. Finally, we analyze the real world impact of crowdturfing tasks by purchasing active Fiverr tasks and quantifying their impact on a target site. As part of this analysis, we show that current security systems inadequately detect crowdsourced manipulation, which confirms the necessity of our proposed crowdturfing task detection approach.
α2 Integrin-Dependent Suppression of Pancreatic Adenocarcinoma Cell Invasion Involves Ectodomain Regulation of Kallikrein-Related Peptidase-5
Chia-Yao Lee,David Marzan,Grace Lin,Steve Goodison,Steve Silletti
Journal of Oncology , 2011, DOI: 10.1155/2011/365651
Abstract: Previous reports demonstrate that the α2-integrin (α2) mediates pancreatic ductal adenocarcinoma (PDAC) cell interactions with collagens. We found that while well-differentiated cells use α2 exclusively to adhere and migrate on collagenI, poorly differentiated PDAC cells demonstrate reduced reliance on, or complete loss of, α2. Since well-differentiated PDAC lines exhibit reduced in vitro invasion and α2-blockade suppressed invasion of well-differentiated lines exclusively, we hypothesized that α2 may suppress the malignant phenotype in PDAC. Accordingly, ectopic expression of α2 retarded in vitro invasion and maintenance on collagenI exacerbated this effect. Affymetrix profiling revealed that kallikrein-related peptidase-5 (KLK5) was specifically upregulated by α2, and reduced α2 and KLK5 expression was observed in poorly differentiated PDAC cells in situ. Accordingly, well-differentiated PDAC lines express KLK5, and KLK5 blockade increased the invasion of KLK5-positive lines. The α2-cytoplasmic domain was dispensable for these effects, demonstrating that the α2-ectodomain and KLK5 coordinately regulate a less invasive phenotype in PDAC. 1. Introduction Pancreatic ductal adenocarcinoma (PDAC) has one of the highest mortality rates of all cancers; although it accounts for only 2% of new cancer cases each year in the United States, it is the fourth leading cause of cancer mortality [1]. Despite this, the biology of PDAC remains poorly understood. Mutations associated with PDAC initiation have allowed the development of a timeline of PDAC etiology [2]; however, factors contributing to the progression of the disease are less well defined. PDAC is associated with prominent desmoplasia, which is characterized by significant deposition of collagen I, II, and IV [3]. The collagen-binding α2-integrin (α2) is expressed by both normal pancreatic ductal epithelium and PDAC in situ [4, 5], and previous studies have implicated the α2β1 integrin as the primary collagen receptor in PDAC cells [6]. However, immunohistochemical studies have failed to demonstrate a consistent pattern of α2 expression in PDAC in situ [3–5, 7, 8], complicating the determination of α2’s role in PDAC etiology and/or progression. Importantly, while well-differentiated, poorly metastatic PDAC cells demonstrate α2-dependent responses to collagenI, poorly differentiated and highly metastatic MIAPaCa2 cells lack collagenI interactions altogether [6]. Moreover, α2 is associated with maintenance of tissue architecture and cellular differentiation in other epithelial tissues [9]. Indeed, while
AGORA: Assembly Guided by Optical Restriction Alignment
Lin Henry C,Goldstein Steve,Mendelowitz Lee,Zhou Shiguo
BMC Bioinformatics , 2012, DOI: 10.1186/1471-2105-13-189
Abstract: Background Genome assembly is difficult due to repeated sequences within the genome, which create ambiguities and cause the final assembly to be broken up into many separate sequences (contigs). Long range linking information, such as mate-pairs or mapping data, is necessary to help assembly software resolve repeats, thereby leading to a more complete reconstruction of genomes. Prior work has used optical maps for validating assemblies and scaffolding contigs, after an initial assembly has been produced. However, optical maps have not previously been used within the genome assembly process. Here, we use optical map information within the popular de Bruijn graph assembly paradigm to eliminate paths in the de Bruijn graph which are not consistent with the optical map and help determine the correct reconstruction of the genome. Results We developed a new algorithm called AGORA: Assembly Guided by Optical Restriction Alignment. AGORA is the first algorithm to use optical map information directly within the de Bruijn graph framework to help produce an accurate assembly of a genome that is consistent with the optical map information provided. Our simulations on bacterial genomes show that AGORA is effective at producing assemblies closely matching the reference sequences. Additionally, we show that noise in the optical map can have a strong impact on the final assembly quality for some complex genomes, and we also measure how various characteristics of the starting de Bruijn graph may impact the quality of the final assembly. Lastly, we show that a proper choice of restriction enzyme for the optical map may substantially improve the quality of the final assembly. Conclusions Our work shows that optical maps can be used effectively to assemble genomes within the de Bruijn graph assembly framework. Our experiments also provide insights into the characteristics of the mapping data that most affect the performance of our algorithm, indicating the potential benefit of more accurate optical mapping technologies, such as nano-coding.
Muscular Recovery of Hip Flexors and Extensors after Two-incision Total Hip Arthroplasty
Shih-Wei Chou,Steve WN Ueng,Mel S. Lee
Chang Gung Medical Journal , 2008,
Abstract: Background: The influence of two-incision total hip arthroplasty on muscular function hasnot been reported. We hypothesized that recovery could be different for thehip flexors and extensors because an intermuscular interval was used in theflexors but a trans-muscular approach was used for the extensors.Methods: Two-incision total hip arthroplasties were performed in 10 patients (8 menand 2 women) with a mean age of 47.2 years (range, 27 to 63 years). Muscletorques were measured prospectively in the 10 patients using a cybexdynamometer preoperatively, 6 weeks postoperatively, and at the latest follow-up.Results: It was found that muscle torque improved from 0.51 (preoperative) to 0.68Ft-Lbs/Lbs 6 weeks postoperatively. (p = 0.007) However, this improvementwas contributed by the flexors but not the extensors. In contrast to the flexors,the torques of the extensors significantly decreased to 86%, 78%, and63% at the angular velocity of 60°/min, 90°/min, and 180°/min, respectively,6 weeks postoperatively. At the most recent follow-up (average 40 ± 2months), differences could not be found in either the flexors or the extensorscompared with the unaffected side.Conclusion: The causes for the delayed recovery of hip extensor muscles could be relatedto surgical techniques that traverse the muscle during femoral canal preparationand stem implantation. This study suggests that the two-incision techniquecan be further refined in view of the muscular function.
Reply to C. Tsallis' Comment on our "Nonadditive Entropies Yield Probability Distributions with Biases not Warranted by the Data"
Steve Pressé,Kingshuk Ghosh,Julian Lee,Ken A. Dill
Physics , 2015,
Abstract: We reply to Tsallis' Comment on our "Nonadditive Entropies Yield Probability Distributions with Biases not Warranted by the Data" which first appeared in PRL.
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