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  • 2018 Users Meeting

    On May 15th,speakers from all areas of research will present at CHESS. Followed by an X-Ray Emission Spectroscopic Methods workshop on the 16th 17th.

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  • CHESS-U

    The CHESS-U upgrade requires the construction and installation in CESR of a large number (~100) of new magnets.

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  • Next Generation of Scientists

    CHESS teaches hundreds of students per year in x-ray science. See what makes our lab on Cornell campus a training ground for the next generation of synchrotron scientists.

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  • The Beautiful World of X-Rays

    Analyzing pigments in medieval illuminated manuscript pages at CHESS is opening up some new areas of research bridging the arts and sciences.

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  • Understanding Stress in Materials

    The InSitu group at CHESS measures modeling activity for the development of structural materials and applications. See how Caterpillar validates their engineering models.

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  • Economic Impact Through CHESS-U Upgrade

    This NYS funded project is creating more than just jobs in research, it is sparking advanced manufacturing across the region.

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  • Truly Bright Light

    CHESS is a high-intensity x-ray source which provides users state-of-the-art synchrotron radiation for research in physics, chemistry, biology, and environmental and materials sciences.

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Cell Ranger 1.2 and later support libraries generated by the Chromium Single Cell 3′ v1 and v2 reagent kits, whereas Cell Ranger 1.1 and earlier do not support v2 libraries. Support for 5′ reagents is new in Cell Ranger 2.1.

The Cell Ranger workflow starts with demultiplexing the raw base call (BCL) files for each flowcell directory. 10x recommends using cellranger mkfastq as described in free nike font mac c
. However, it is possible to get compatible FASTQ files other ways, such as by starting with a public dataset which provides them, or using nike air max 1 leather white gumba
. In that case, you would skip mkfastq and begin with nike free run 5 6pm shoes
. Please see the nike air max zero us 1000
page for specific guidelines on which arguments to use for your scenario.

The subsequent steps vary depending on how many samples, libraries, and flowcells you have. We will describe them in order of increasing complexity:

This is the most basic case. You have a single biological sample, which was prepared into a single library, and then sequenced on a single flowcell. Assuming the FASTQs have been generated with cellranger mkfastq , you just need to run cellranger count as described in nike free 40 flyknit pure platinum womens
.

If you have a library which was sequenced across multiple flowcells (e.g. to increase sequencing saturation), you can pool the reads from both sequencing runs. Follow the steps in mens nike air jordan flight
to combine them in a single cellranger count run.

This comprises two scenarios.

If you prepared multiple libraries from the same sample (technical replicates, for example), then each one should be run through a separate instance of cellranger count . Once those are completed, you can perform a combined analysis using cellranger aggr , as described in air jordan 6 black infrared 2014 uk football
. (This is illustrated in the figure).

If you prepared multiple libraries from the same sample and want to pool them and analyze the combined data as a single sample, then you will need to use the nike shoes air force 2015 lt
to treat the multiple libraries as coming from a single sample. (This is not illustrated in the figure).

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Array-CGH

Mature B-cell neoplasms arise in B-cells that have entered germinal centers within lymph nodes as part of the immune response. They display great heterogeneity at the clinical, pathologic, and genetic levels and represent 6-7% and 5-6% of all new estimated cancer cases and deaths respectively in the US in 2009. They are the fifth most common neoplasm in both males and females, and of the 103,960 estimated new cases in 2009, 20,860 comprise diffuse large B-cell lymphoma (DLBCL), 20,580 multiple myeloma (MM), 15,490 chronic lymphocytic leukemia /small lymphocytic lymphoma (CLL/SLL), 14,900 follicular lymphoma (FL), 8,510 Hodgkin’s lymphoma (HL), 6,000 marginal zone lymphomas (MZL) (including the three subtypes: extranodal marginal zone of mucosa-associated lymphoid tissue [MALT], nodal marginal zone, and splenic marginal zone), and 3,730 mantle cell lymphomas (MCL), as the major subtypes. With the exclusion of HL, 32,520 deaths are expected in 2009 in the US as a result of these neoplasms.

Diagnosis of these neoplasms relies mostly on the pathologic examination of biopsy material, be it either of an incisional or excisional biopsy of a suspect lymph node, a fine needle aspirate of a suspect lymph node (as yet to be considered adequate for initial diagnosis, unless it is the only safe option), or a bone marrow aspirate. Unlike other cancers, rarely are other biopsy/surgical procedures performed prior to the initiation of treatment, thus limiting the amount of tissue available for diagnostic and prognostic purposes. CGI has optimized the utility of array-CGH so that it can be routinely applied to the study of a range of specimen types including formalin-fixed paraffin-embedded (FFPE) specimens, often the only specimen available for analysis.

CGI has designed an oligonucleotide-based array (MatBA®) for the detection of gains and losses in mature B-cell neoplasms for utilization within a clinical laboratory.

For CLL/SLL, it’s primary value is in routine prognostication, and as an assay, has been approved in the CGI Diagnostic Laboratory by both CLIA and New York State. In this disease where approximately 50% patients have an aggressive course and 50% can live for many years without requiring treatment, robust prognostication is highly desirable. Together with IGHV mutation status, theMatBA®-CLL Array-CGH test provides important genetic-based information to guide clinical management of this disease.

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I am interested in understanding how cancer cells ‘switch off’ the normal immune response in acute myeloid leukaemia with the aim of developing novel immunotherapeutic strategies.

I am currently developing several research projects:

I started work in the Haemato-Oncology department in the Barts Cancer Institute in October 2011 as part of John Gribben’s cancer immunotherapy group. I developed my research interests as an MRC Clinical Training Fellow in the group between 2005 and 2009 when I investigated T cells in acute myeloid leukaemia. I gained experience in immunomagnetic cell separation, flow cytometry, gene expression profiling and confocal microscopy of the immune synapse.

I developed a technique for separating T cells from the peripheral blood of patients presenting with AML that was published in the Journal of Immunological Methods in 2009 and my data characterising T cell defects in AML was published in Blood in the same year. I left Barts in 2009 to complete my clinical haematology training which included a year spent at the Hammersmith Hospital as a stem cell transplant coordinator. During this time, I gained valuable experience in the organisation as well as inpatient and outpatient management of patients undergoing allogeneic stem cell transplantation.

I now plan to develop as an independent researcher taking forward my basic science research examining T cell function in haematologic malignancy to investigate new immunotherapeutic strategies in AML.

Peripheral blood T cells in acute myeloid leukemia (AML) patients at diagnosis have abnormal phenotype and genotype and form defective immune synapses with AML blasts. Le Dieu R, Taussig D, Ramsay AG, Mitter R, Lee AM, Lister TA, Gribben JG. Blood 2009 Oct; 114 (18): 3909-16 PMID: nike air max 1 ultra moire og red bottoms

Array-based DNA methylation profiling in follicular lymphoma. O’Riain C, O’Shea DM, Yang Y, Le Dieu R, Gribben JG, Summers K, Yeboah-Afari J, Bhaw-Rosen L, Fleischmann C, Mein CA, Crook T, Smith P, Kelly G, Rosenwald A, Ott G, Campo E, Rimsza LM, Smeland EB, Chan WC, John son N, Gascoyne RD, Reimer S, Braziel RM, Wright GW, Staudt LM, Lister TA, Fitzgibbon J. Leukemia 2009 Oct; 23 (10): 1858-66 PMID: bmx freestyle bike sizing chart

Negative immunomagnetic selection of T cells from peripheral blood of presentation AML specimens. Le Dieu R, Taussig D, Lister TA, Gribben JG. Journal of Immunological Methods 2009 Aug ; 348 (1-2): 95-100 PMID: nike air max sneakers defect

The AMI (Apparatus for Meridian Identification)works by monitoring the electrical conductivity and capacity at specific acupoints at the tip of fingers and toes (called Sei point, or Jing/Well points). After years of research, Dr. Motoyama was able to show that there is a close correlation between the electrical conductivity of meridians and the flow of Ki (or Chi) in the meridians. The basic research Dr. Motoyama did to support his claim about the AMI can be found in his book “ Measurement of Ki Energy Diagnoses Treatment: Treatment Principle of Oriental Medicine from an Electrophysiological Viewpoints” published by Human Science Press in 1977. Please see below (Dr. Motoyama’s Findings using the AMI)for the pages from this book.

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The AMI measures the electrical conductivity, capacitance, and polarization of skin tissue and fluids; it uses these to evaluate the tissue condition and the functioning of the acupuncture meridians and their corresponding internal organs.

The AMI data tells you:

● The condition of the meridians and the functioning of their corresponding internal organs – lung, large intestine, heart, small intestine, spleen, liver, stomach, urinary bladder, kidney and gall bladder; ● Whether your Ki energy is excessive or deficient ; ● An objective analysis of your autonomic nervous system; ● The effects of acupuncture, meditation, and exercise through continuous monitoring of the autonomic nervous system and Ki energy; ● Chakra type, meaning which chakra is most active/inactive. The data cannot measure the amount of energy in the chakra quantitatively but can indicate which one is activated at the moment.

Extracts from “Measurements of Ki Energy, Diagnosis, Treatments” (1997) by HiroshiMotoyama, Ph.D., Ph.D., Tokyo, Japan, Human Science Press

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Data Obtained Using the AMI

1) Explanation of Measured Wave Form (BP, IQ, TC, AP)

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BP is a Parameter Reflecting Meridian Function. Evidence suggests that the Dermal Connective Tissue is the Physical Location of the Acupuncture Meridian

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