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Search Results: 1 - 10 of 45286 matches for " Michael Snyder "
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Relationship of nine constants  [PDF]
Michael Snyder
Natural Science (NS) , 2013, DOI: 10.4236/ns.2013.59117
Abstract:

Through the process of trial and error, four unitless equations made up of nine constants have been found with exact answers. The related constants are the Speed of Light [1], the Planck constant [2], Wien’s displacement constant [3], Avogadro’s number [4], the universal Gravity constant [5], the Ampere constant [6], the Faraday constant [7], the Gas constant [8] and Apery’s constant [9].

RNA polymerase II stalling: loading at the start prepares genes for a sprint
Jia Wu, Michael Snyder
Genome Biology , 2008, DOI: 10.1186/gb-2008-9-5-220
Abstract: The recruitment of RNA polymerase II (Pol II) to the promoter has been generally believed to be the rate-limiting step in gene activation [1]. However, a series of discoveries made since the mid-1980s, combined with recent genome-wide studies, suggest that many developmental and inducible Drosophila and mammalian genes, prior to their expression, contain Pol II bound predominantly in their promoter proximal regions in a 'stalled' state [1-8]. Activation of the stalled polymerase is thought to be responsible for the expression of these genes [1].Distinct sets of accessory factors are associated with Pol II stalling and its escape from stalling, acting either by direct interaction with Pol II, or by manipulating the chromatin environment - for example, by affecting histone modifications by histone methyltransferases (HMTs) or histone acetyltransferases (HATs) [1]. Proteins associated with Pol II stalling include the DRB sensitivity-inducing factor (DSIF) and the negative elongation factor (NELF) [9,10], whereas proteins such as the positive transcription-elongation factor-b (P-TEFb) complex, and the general transcription factors TFIIS and TFIIF contribute to escape from stalling [11,12]. These latter proteins enable Pol II to begin transcription elongation on induction by heat shock, for example. Thus, all the factors mentioned above may serve as a stalling checkpoint to poise genes for prompt expression.Although initial studies revealed that Pol II stalling is present on several genes, it has recently been found that Pol II stalling is more common than previously thought [13-16]. Technologies such as ChIP-chip (chromatin immunoprecipitation in combination with genomic DNA microarrays) allow transcriptional regulation to be examined genome wide [17,18]. Through the ENCODE (Encyclopedia of DNA Elements) project [19], in which 1% of the human genome has been extensively analyzed, and through genomic studies in Drosophila, human embryonic stem cells (hESCs) and other hum
Photonic Dipole Contours of Ferrofluid Hele-Shaw Cell
Michael Snyder,Jonathan Frederick
Physics , 2008,
Abstract: This investigation describes and demonstrates a novel technique for the visualization of magnetic fields. Two ferrofluid Hele-Shaw cells have been constructed to facilitate the imaging of magnetic field lines. We deduce that magnetically induced photonic band gap arrays similar to electrostatic liquid crystal operation are responsible for the photographed images and seek to mathematically prove the images are of dipole nature. A simple way of explaining this work is to think of the old magnetic iron filling experiments; but now each iron filling is a molecule floating in a liquid. Each molecule has the freedom to act as an independent lens that can be aligned by an external magnetic field. Because each lens directs light, the external field can be analyzed by following the light paths captured in the photographs.
Left Atrial Appendage Occlusion Device: Evaluation of Surgical Implant Success and in Vivo Corrosion Performance  [PDF]
Jonathan Snyder, Amy M. Engel, Kevin C. White, Noah Budiansky, J. Michael Smith
Surgical Science (SS) , 2012, DOI: 10.4236/ss.2012.31005
Abstract: Objective: The purpose of this study was to compare the in vivo corrosion resistance of the implanted titanium, nitinol annular occlusion device to a control device, i.e. an implantable device containing nitinol, approved by the FDA and currently on the market. Methods: The annular occlusion device is a self-closing, implantable clip. Three canines underwent placement of devices on the left and right atrial appendages. Two Vnus U-clips were secured to either atrium. On post-operative day 95, animals underwent en-bloc cardiac resection via the previous left thoracotomy incision. The annular occlusion device and U-clips were dissected free from the atria. The polyester fabric and tissue ingrowth were removed from the devices and were sent for corrosion analysis. Results: Gross examination of resected hearts of two canines revealed no abnormalities. The compressed endocardial surfaces were completely fused and the appendages fully necrosed. All devices were located and harvested. The annular occlusion device clips and Medtronic Vnus U-clips were evaluated using scanning electron microscopy. Both low and high magnification examination of the nitinol springs and the site of insertion of the nitinol springs into the titanium tubes in the annular occlusion device showed no evidence of localized corrosion. In no case was any evidence of general or localized corrosion found in the form of metallic oxidation. Conclusion: The annular occlusion device provides safe and reliable exclusion of the left atrial ap-pendage without evidence of general or localized corrosion over the 95-day exposure period in canines and may therefore provide a reasonable therapeutic option for stroke risk reduction in patients with atrial fibrillation.
ProCAT: a data analysis approach for protein microarrays
Xiaowei Zhu, Mark Gerstein, Michael Snyder
Genome Biology , 2006, DOI: 10.1186/gb-2006-7-11-r110
Abstract: DNA microarray technologies have proven to be extremely valuable for probing biological processes by measuring mRNA expression profiles. However, studies at the protein level have the potential to provide more direct information since most genes function through their protein products. Traditional investigations focus on individual proteins in a system and then combine such individual analyses to provide a more global perspective. Recently, technologies to analyze proteins in a high throughput and unbiased fashion have become feasible [1]. One particular powerful technology is protein microarrays, which contain a high density of proteins and allow a systematic probing of biochemical activities [2,3].There are two types of protein microarrays [3]. A 'functional protein microarray' contains a set of proteins individually produced and positioned in an addressable format on a microarray surface. Functional protein microarrays are useful for identifying binding activities or targets of modification enzymes. The first version of a proteome microarray was reported in 2001 and contained 5,800 yeast proteins with amino-terminal glutathione S-transferase (GST) tags printed on the array [4]. A second version of yeast protein microarrays was generated recently and contained 5,600 proteins with carboxy-terminal 6His-HA-ZZ domain tags [5]. Proteins from both collections were overexpressed, purified and spotted onto the protein microarrays. Global proteome studies were performed on these chips to understand various biological mechanisms. For example, 87 yeast kinases were examined for their substrates using yeast protein microarrays and over 4,200 in vitro substrates representing 1,325 unique proteins were identified [6]. Compared with the approximately 150 known in vivo kinase-substrate interactions, this global study served as an important first step for dissecting yeast signaling networks. In addition to searching for kinase substrates, proteome chips can be probed with labeled
Eosinophilic and neutrophilic leukemoid reaction in a woman with spindle cell sarcoma: a case report
Michael C Snyder, Carl B Lauter
Journal of Medical Case Reports , 2010, DOI: 10.1186/1752-1947-4-335
Abstract: A 41-year-old African American woman presented with an enlarging, painful mass in her right knee area. Four years previously, she had had a mass similar to this diagnosed as an osteosarcoma, and had undergone a radical resection and hinge-knee replacement. Before the surgery, she was treated with neoadjuvant docetaxel and gemcitabine. A biopsy was taken from the recurrent mass, and histological examination revealed high-grade soft-tissue sarcoma. The patient received no further treatment. Complete blood counts revealed a white blood cell (WBC) count of 13.6 to 17.9 × 109/L, with neutrophils being 8.2 to 10.9 × 109/L and eosinophils 1.8 to 1.9 × 109/L. At readmission six months later, WBC was 126.7 × 109/L, with neutrophils being 57.02 × 109/L and eosinophils 60.82 × 109/L. The eosinophils peaked at 77.79 × 109/L two days later. Evaluations for allergies, infection, and autoimmune mechanisms were negative. Bone marrow revealed increased eosinophils without blasts. After resection, blood counts abruptly decreased to the normal range. Pathology confirmed high-grade spindle cell sarcoma. Approximately one year after resection, the patient was readmitted with metastatic disease to her lungs. During this presentation, her eosinophil and neutrophil count was again increased. WBC was 107.8 × 109/L, with eosinophil count of 47.43 × 109/L and neutrophil count of 44.10 × 109/L. Interleukin-5 was normal, and granulocyte–macrophage colony-stimulating factor (GM-CSF) was elevated at 208.8 (normal < 4.8).In our case, the patient had eosinophilia and neutrophilia associated with a spindle cell sarcoma, possibly representing a paraneoplastic syndrome secondary to GM-CSF. There were no signs of infectious, allergic, or autoimmune causes for the eosinophilia or neutrophilia. Even though the occurrence of eosinophilia and neutrophilia with malignancy is rare, patients who have either condition without an apparent cause should be checked for malignancy.Eosinophilia can be a manifestatio
Shot noise in an electron waveguide square root of NOT gate
Linda E. Reichl,Michael G. Snyder
Physics , 2006, DOI: 10.1103/PhysRevA.74.012318
Abstract: We present a calculation of the shot noise in a ballistic electron waveguide square root of NOT gate. A general expression for the shot noise in the leads connected to these types of gates is shown. We then parameterize an S-matrix which qualitatively describes the action of a square root of NOT gate previously found through numerical methods for GaAs/Al_xGa_{1-x}As based waveguides systems. Using this S-matrix, the shot noise in a single output lead and across two output leads is calculated. We find that the measurement of the shot noise across two output leads allows for the determination of the fidelity of the gate itself.
Coulomb entangler and entanglement testing network for waveguide qubits
Linda E. Reichl,Michael G. Snyder
Physics , 2005, DOI: 10.1103/PhysRevA.72.032330
Abstract: We present a small network for the testing of the entanglement of two ballistic electron waveguide qubits. The network produces different output conditional on the presence or absence of entanglement. The structure of the network allows for the determination of successful entanglement operations through the measurement of the output of a single qubit. We also present a simple model of a dynamic coulomb-like interaction and use it to describe some characteristics of a proposed scheme for the entanglement of qubits in ballistic electron waveguides.
A High-Resolution Whole-Genome Map of Key Chromatin Modifications in the Adult Drosophila melanogaster
Hang Yin,Sarah Sweeney,Debasish Raha,Michael Snyder,Haifan Lin
PLOS Genetics , 2011, DOI: 10.1371/journal.pgen.1002380
Abstract: Epigenetic research has been focused on cell-type-specific regulation; less is known about common features of epigenetic programming shared by diverse cell types within an organism. Here, we report a modified method for chromatin immunoprecipitation and deep sequencing (ChIP–Seq) and its use to construct a high-resolution map of the Drosophila melanogaster key histone marks, heterochromatin protein 1a (HP1a) and RNA polymerase II (polII). These factors are mapped at 50-bp resolution genome-wide and at 5-bp resolution for regulatory sequences of genes, which reveals fundamental features of chromatin modification landscape shared by major adult Drosophila cell types: the enrichment of both heterochromatic and euchromatic marks in transposons and repetitive sequences, the accumulation of HP1a at transcription start sites with stalled polII, the signatures of histone code and polII level/position around the transcriptional start sites that predict both the mRNA level and functionality of genes, and the enrichment of elongating polII within exons at splicing junctions. These features, likely conserved among diverse epigenomes, reveal general strategies for chromatin modifications.
Molecular Mechanisms of Ethanol-Induced Pathogenesis Revealed by RNA-Sequencing
Laura Camarena,Vincent Bruno,Ghia Euskirchen,Sebastian Poggio,Michael Snyder
PLOS Pathogens , 2010, DOI: 10.1371/journal.ppat.1000834
Abstract: Acinetobacter baumannii is a common pathogen whose recent resistance to drugs has emerged as a major health problem. Ethanol has been found to increase the virulence of A. baumannii in Dictyostelium discoideum and Caenorhabditis elegans models of infection. To better understand the causes of this effect, we examined the transcriptional profile of A. baumannii grown in the presence or absence of ethanol using RNA-Seq. Using the Illumina/Solexa platform, a total of 43,453,960 reads (35 nt) were obtained, of which 3,596,474 mapped uniquely to the genome. Our analysis revealed that ethanol induces the expression of 49 genes that belong to different functional categories. A strong induction was observed for genes encoding metabolic enzymes, indicating that ethanol is efficiently assimilated. In addition, we detected the induction of genes encoding stress proteins, including upsA, hsp90, groEL and lon as well as permeases, efflux pumps and a secreted phospholipase C. In stationary phase, ethanol strongly induced several genes involved with iron assimilation and a high-affinity phosphate transport system, indicating that A. baumannii makes a better use of the iron and phosphate resources in the medium when ethanol is used as a carbon source. To evaluate the role of phospholipase C (Plc1) in virulence, we generated and analyzed a deletion mutant for plc1. This strain exhibits a modest, but reproducible, reduction in the cytotoxic effect caused by A. baumannii on epithelial cells, suggesting that phospholipase C is important for virulence. Overall, our results indicate the power of applying RNA-Seq to identify key modulators of bacterial pathogenesis. We suggest that the effect of ethanol on the virulence of A. baumannii is multifactorial and includes a general stress response and other specific components such as phospholipase C.
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