116 research outputs found
SAGE: Sequential Attribute Generator for Analyzing Glioblastomas using Limited Dataset
While deep learning approaches have shown remarkable performance in many
imaging tasks, most of these methods rely on availability of large quantities
of data. Medical image data, however, is scarce and fragmented. Generative
Adversarial Networks (GANs) have recently been very effective in handling such
datasets by generating more data. If the datasets are very small, however, GANs
cannot learn the data distribution properly, resulting in less diverse or
low-quality results. One such limited dataset is that for the concurrent gain
of 19 and 20 chromosomes (19/20 co-gain), a mutation with positive prognostic
value in Glioblastomas (GBM). In this paper, we detect imaging biomarkers for
the mutation to streamline the extensive and invasive prognosis pipeline. Since
this mutation is relatively rare, i.e. small dataset, we propose a novel
generative framework - the Sequential Attribute GEnerator (SAGE), that
generates detailed tumor imaging features while learning from a limited
dataset. Experiments show that not only does SAGE generate high quality tumors
when compared to standard Deep Convolutional GAN (DC-GAN) and Wasserstein GAN
with Gradient Penalty (WGAN-GP), it also captures the imaging biomarkers
accurately
Minimally invasive determination of mRNA concentration in single living bacteria
Fluorescence correlation spectroscopy (FCS) has permitted the characterization of high concentrations of noncoding RNAs in a single living bacterium. Here, we extend the use of FCS to low concentrations of coding RNAs in single living cells. We genetically fuse a red fluorescent protein (RFP) gene and two binding sites for an RNA-binding protein, whose translated product is the RFP protein alone. Using this construct, we determine in single cells both the absolute [mRNA] concentration and the associated [RFP] expressed from an inducible plasmid. We find that the FCS method allows us to reliably monitor in real-time [mRNA] down to ∼40 nM (i.e. approximately two transcripts per volume of detection). To validate these measurements, we show that [mRNA] is proportional to the associated expression of the RFP protein. This FCS-based technique establishes a framework for minimally invasive measurements of mRNA concentration in individual living bacteria
MRI Imaging Characteristics of Glioblastoma with Concurrent Gain of Chromosomes 19 and 20
Glioblastoma (GBM) is the most common and deadly primary brain tumor in adults. Some of the genetic variations identified thus far, such as IDH mutation and MGMT promotor methylation, have implications for survival and response to therapy. A recent analysis of long-term GBM survivors showed that concurrent gain of chromosomes 19 and 20 (19/20 co-gain) is a positive prognostic factor that is independent of IDH mutation status. In this study, we retrospectively identified 18 patients with 19/20 co-gain and compared their imaging features to a control cohort without 19/20 co-gain. Imaging features such as tumor location, size, pial invasion, and ependymal extension were examined manually. When compared without further genetic subclassification, both groups showed similar imaging features except for rates of pial invasion. When each group was subclassified by MGMT promotor methylation status however, the two groups showed different imaging features in a number of additional ways including tumor location, size, and ependymal extension. Our results indicate that different permutations of various genetic mutations that coexist in GBM may interact in unpredictable ways to affect imaging appearance, and that imaging prognostication may be better approached in the context of the global genomic profile rather than individual genetic alterations
High-resolution, long-term characterization of bacterial motility using optical tweezers
We present a single-cell motility assay, which allows the quantification of bacterial swimming in a well-controlled environment, for durations of up to an hour and with a temporal resolution higher than the flagellar rotation rates of ~100 Hz. The assay is based on an instrument combining optical tweezers, light and fluorescence microscopy, and a microfluidic chamber. Using this device we characterized the long-term statistics of the run-tumble time series in individual Escherichia coli cells. We also quantified higher-order features of bacterial swimming, such as changes in velocity and reversals of swimming direction
Search for heavy resonances in the W/Z-tagged dijet mass spectrum in pp collisions at 7 TeV
A search has been made for massive resonances decaying into a quark and a vector boson, qW or qZ, or a pair of vector bosons, WW, WZ, or ZZ, where each vector boson decays to hadronic final states. This search is based on a data sample corresponding to an integrated luminosity of 5.0 fb 121 of proton\u2013proton collisions collected in the CMS experiment at the LHC in 2011 at a center-of-mass energy of 7 TeV. For sufficiently heavy resonances the decay products of each vector boson are merged into a single jet, and the event effectively has a dijet topology. The background from QCD dijet events is reduced using recently developed techniques that resolve jet substructure. A 95% CL lower limit is set on the mass of excited quark resonances decaying into qW (qZ) at 2.38 TeV (2.15 TeV) and upper limits are set on the cross section for resonances decaying to qW, qZ, WW, WZ, or ZZ final states
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