gebhart/patrepeval huggingface dataset:
Comparative Molecular Analysis of Primary Central Nervous System Lymphomas and Matched Vitreoretinal Lymphomas by Vitreous Liquid Biopsy (2021)

Primary Central Nervous System Lymphoma (PCNSL) is a lymphoid malignancy of the brain that occurs in ~1500 patients per year in the US. PCNSL can spread to the vitreous and retina, where it is known as vitreoretinal lymphoma (VRL). While confirmatory testing for diagnosis is dependent on invasive brain tissue or cerebrospinal fluid sampling, the ability to access the vitreous as a proximal biofluid for liquid biopsy to diagnose PCNSL is an attractive prospect given ease of access and minimization of risks and complications from other biopsy strategies. However, the extent to which VRL, previously considered genetically identical to PCNSL, resembles PCNSL in the same individual with respect to genetic alterations, diagnostic strategies, and precision-medicine based approaches has hitherto not been explored. Furthermore, the degree of intra-patient tumor genomic heterogeneity between the brain and vitreous sites has not been studied. In this work, we report on targeted DNA next-generation sequencing (NGS) of matched brain and vitreous samples in two patients who each harbored VRL and PCSNL. Our strategy showed enhanced sensitivity for molecular diagnosis confirmation over current clinically used vitreous liquid biopsy methods. We observed a clonal relationship between the eye and brain samples in both patients, which carried clonal <i>CDKN2A</i> deep deletions, a highly recurrent alteration in VRL patients, as well as <i>MYD88</i> p.L265P activating mutation in one patient. Several subclonal alterations, however, in the genes <i>SETD2</i>, <i>BRCA2</i>, <i>TERT</i>, and broad chromosomal regions showed heterogeneity between the brain and the eyes, between the two eyes, and among different regions of the PCNSL brain lesion. Taken together, our data show that NGS of vitreous liquid biopsies in PCNSL patients with VRL highlights shared and distinct genetic alterations that suggest a common origin for these lymphomas, but with additional site-specific alterations. Liquid biopsy of VRL accurately replicates the findings for PCNSL truncal (tumor-initiating) genomic alterations; it can also nominate precision medicine interventions and shows intra-patient heterogeneity in subclonal alterations. To the best of our knowledge, this study represents the first interrogation of genetic underpinnings of PCNSL with matched VRL samples. Our findings support continued investigation into the utility of vitreous liquid biopsy in precision diagnosis and treatment of PCNSL/VRL.
Modeling Polymer Processes (2017)

No AccessUnderstanding Polymer ProcessingOct 2017Modeling Polymer ProcessesTim A. OsswaldTim A. OsswaldSearch for more papers by this authorhttps://doi.org/10.3139/9781569906484.010SectionsAboutPDF ToolsAdd to FavoritesDownload CitationTrack CitationsCopy LTI LinkPDF key 'share (en)' returned an object instead of string.FacebookTwitterEmailLinkedIn previous chapternext chapter FiguresReferencesRelatedDetails 2017Pages: 259-357Print ISBN: 978-1-56990-647-7eISBN: 978-1-56990-648-4 Copyright & Permissions© 2017 Carl Hanser Verlag GmbH & Co. KGPDF downloadLoading ...
Selective etch of poly(methyl methacrylate) in block copolymer based on control of ion energy and design of gas chemistry for directed self assembly lithography (2014)

The selective etching of poly(methyl methacrylate) (PMMA) in a block copolymer was studied with a focus on the material structures of polystyrene (PS) and PMMA. Based on our predictions, we investigated the effect of ion bombardment and designed a carbon-containing gas plasma to improve selectivity. The etching characteristics of the carbon-containing gas plasma on the polymers were examined. Highly selective etching of PMMA to PS was achieved using the carbon-containing gas plasma. The carbon species in the plasma increased with increasing carbon-containing gas ratio and suppressed the PS etch rate drastically. The CO plasma process was successfully applied to a dry development process for directed-self assembly lithography.
BET Inhibitors Suppress ALDH Activity by Targeting ALDH1A1 Super-Enhancer in Ovarian Cancer (2016)

The emergence of tumor cells with certain stem-like characteristics, such as high aldehyde dehydrogenase (ALDH) activity due to ALDH1A1 expression, contributes to chemotherapy resistance and tumor relapse. However, clinically applicable inhibitors of ALDH activity have not been reported. There is evidence to suggest that epigenetic regulation of stem-related genes contributes to chemotherapy efficacy. Here, we show that bromodomain and extraterminal (BET) inhibitors suppress ALDH activity by abrogating BRD4-mediated ALDH1A1 expression through a super-enhancer element and its associated enhancer RNA. The clinically applicable small-molecule BET inhibitor JQ1 suppressed the outgrowth of cisplatin-treated ovarian cancer cells both in vitro and in vivo Combination of JQ1 and cisplatin improved the survival of ovarian cancer-bearing mice in an orthotopic model. These phenotypes correlate with inhibition of ALDH1A1 expression through a super-enhancer element and other stem-related genes in promoter regions bound by BRD4. Thus, targeting the BET protein BRD4 using clinically applicable small-molecule inhibitors, such as JQ1, is a promising strategy for targeting ALDH activity in epithelial ovarian cancer. Cancer Res; 76(21); 6320-30. ©2016 AACR.
ChemInform Abstract: Olefin Metathesis for Chemical Biology (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Femtosecond Single-Shot Imaging of Nanoscale Ferromagnetic Order inCo/PdMultilayers Using Resonant X-Ray Holography (2012)

We present the first single-shot images of ferromagnetic, nanoscale spin order taken with femtosecond x-ray pulses. X-ray-induced electron and spin dynamics can be outrun with pulses shorter than 80 fs in the investigated fluence regime, and no permanent aftereffects in the samples are observed below a fluence of 25 mJ/cm(2). Employing resonant spatially muliplexed x-ray holography results in a low imaging threshold of 5 mJ/cm(2). Our results open new ways to combine ultrafast laser spectroscopy with sequential snapshot imaging on a single sample, generating a movie of excited state dynamics.
A TSH-CREB1-microRNA Loop Is Required for Thyroid Cell Growth (2011)

MicroRNA (miRNA or miR) are an important class of regulators that participate in such biological functions as development, cell proliferation, differentiation, and apoptosis. The aim of this study was to elucidate the role of miRNA in cell proliferation using a unique cell system, namely thyroid cells that require thyrotropin for their growth. Here, we report the identification of a set of five specific miRNA (miR-1, miR-28-A, miR-290-5p, miR-296-3p, and miR-297a), whose down-regulation by thyrotropin is required for thyroid cell growth. In fact, overexpression of these miRNA negatively affects cell growth. We show that three of these miRNA target cAMP-responsive element binding protein (CREB)1, a thyrotropin-activated transcription factor, and that CREB1 binds the regulatory regions of the down-regulated miRNA. Hence, these data indicate that a synergistic loop involving thyrotropin, CREB1, and miRNA is required for thyroid cell proliferation.
New chromophores from click chemistry for two-photon absorption and tuneable photoluminescence (2005)

New multipolar derivatives built from triazole moieties that combine full transparency and strong TPA in the visible region as well as fully tuneable fluorescence have been designed; such chromophores open a new route for optical limiting.
SmartID: a highly accurate physics-based isotope attribution algorithm (2010)

The spectral post-processing algorithm Advanced Synthetically Enhanced Detector Resolution Algorithm (ASEDRA (patent pending)) has shown to be a powerful tool for deconvolving full energy peaks from scintillation spectrometeracquired gamma-ray spectra, effectively improving obtainable data-synthesized energy resolutions by a factor of four to six times over what is rendered from the detector. An isotope attribution algorithm, SmartID, was developed to augment ASEDRA in order to improve radionuclide identification accuracy. SmartID utilizes a novel, physics-based method of importance weighting the ASEDRA-identified peaks and the emissions of a candidate isotope. This methodology enhances the screening of potential false peaks and prevents isotope mismatches. As a final step, SmartID assigns a physical matching attribution score to each possible isotope match to reflect goodness-of-fit. A test suite of 105 gammaray spectra acquired with a 2"&times;2" NaI:Tl spectrometer under varying shielding conditions and various single and multisource configurations were recorded for testing the accuracy of ASEDRA+SmartID. The sources utilized in the tests included <sup>133</sup>Ba, <sup>109</sup>Cd, <sup>57</sup>Co, <sup>60</sup>Co, <sup>137</sup>Cs, <sup>152</sup>Eu, <sup>54</sup>Mn, <sup>22</sup>Na, <sup>232</sup>Th, natural uranium rods and a PuBe source. Shielding configurations varied widely, ranging from none to more than 2.5cm Pb. Overall, SmartID proved to be more than 95% accurate in attributing the correct isotope(s) to the spectra.
Proceedings of the ACM SIGMETRICS joint international conference on Measurement and modeling of computer systems (2011)

Welcome to San Jose, to ACM's Federated Computing Research Conference (FCRC), and to SIGMETRICS 2011! We are proud to carry on the SIGMETRICS tradition of presenting highquality, innovative research on the measurement and modeling of computer systems. The program includes papers on a wide variety of topics, including resource allocation, multicore processing, network protocols, failure analysis, power management and network characterization, using a wide variety of techniques, including mathematical analysis, simulation, emulation, prototype experimentation, observation of real systems, and combinations thereof.

SIGMETRICS 2011 received 177 submissions, from which 26 papers were accepted, for an acceptance rate of 15%. Additionally, 20 submissions were selected to appear as posters, leading to a combined paper and poster acceptance rate of 26%. Each paper received at least three reviews from PC members. Over 90% of papers received four or more reviews. Overall, program committee and external reviewers provided a total of 756 reviews.

The review process was conducted online using the HotCRP conference management software over a period of two months. The program committee meeting, held at Columbia University in New York, NY, in January 2011, was attended in person by 36 of the 57 PC members, and virtually by another four members. During the review, deliberation, and decision process, we emphasized novelty and excitement: papers that took risks and were controversial were viewed more favorably than solid papers that provided limited new insights and took limited risks. As a result, we expect the program to generate active discussion.
ChemInform Abstract: Toward Chemical Libraries of Annonaceous Acetogenins. Total Synthesis of Trilobacin. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
N1-methyl-pseudouridine in mRNA enhances translation through eIF2α-dependent and independent mechanisms by increasing ribosome density (2017)

Certain chemical modifications confer increased stability and low immunogenicity to in vitro transcribed mRNAs, thereby facilitating expression of therapeutically important proteins. Here, we demonstrate that N1-methyl-pseudouridine (N1mΨ) outperforms several other nucleoside modifications and their combinations in terms of translation capacity. Through extensive analysis of various modified transcripts in cell-free translation systems, we deconvolute the different components of the effect on protein expression independent of mRNA stability mechanisms. We show that in addition to turning off the immune/eIF2α phosphorylation-dependent inhibition of translation, the incorporated N1mΨ nucleotides dramatically alter the dynamics of the translation process by increasing ribosome pausing and density on the mRNA. Our results indicate that the increased ribosome loading of modified mRNAs renders them more permissive for initiation by favoring either ribosome recycling on the same mRNA or de novo ribosome recruitment.
Energy-delay complexity of asychronous circuits (2002)

In this thesis, a circuit-level theory of energy-delay complexity is developed for asynchronous circuits. The energy-delay efficiency of a circuit is characterized using the metric Et^n , where E is the energy consumed by the computation, t is the delay of the computation, and n is a positive number that reflects a chosen trade-off between
energy and delay. Based on theoretical and experimental evidence, it is argued that for a circuit optimized for minimal Et^n, the consumed energy is independent, in first
approximation, of the types of gates (NAND, NOR, etc.) used by the circuit and is solely dependent on n and the total amount of wiring capacitance switched during computation. Conversely, the circuit speed is independent, in first approximation, of the wiring capacitance and depends only on n and the types of gates used.

The complexity model allows us to compare the energy-delay efficiency of two circuits implementing the same computation. On the other hand, the complexity model itself does not say much about the actual transistor sizes that achieve the optimum. For this reason, the problem of transistor sizing of circuits optimized for Et^n is investigated, as well. A set of analytical formulas that closely approximate the optimal transistor sizes are explored. An efficient iteration procedure that can further
improve the original analytical solution is then studied. Based on these results, a novel transistor-sizing algorithm for energy-delay efficiency is introduced.

It is shown that the Et^n metric for the energy-delay efficiency index n ≥ 0 characterizes any optimal trade-off between the energy and the delay of a computation. For
example, any problem of minimizing the energy of a system for a given target delay can be restated as minimizing Et^n for a certain n. The notion of minimum-energy function is developed and applied to the parallel and sequential composition of circuits in general and, in particular, to circuits optimized through transistor sizing and
voltage scaling. Bounds on the energy and delay of the optimized circuits are computed, and necessary and sufficient conditions are given under which these bounds are
reached. Necessary and sufficient conditions are also given under which components of a design can be optimized independently so as to yield a global optimum when
composed. Through these applications, the utility of the minimum-energy function is demonstrated. The use of this minimum-energy function yields practical insight into
ways of improving the overall energy-delay efficiency of circuits.
Boron Nitride Nanotubes for Optical Fiber Chemical Sensing Applications (2020)

Boron nitride nanotubes (BNNTs) are 1-D hollow fibrous nanomaterials. They are thermally stable up to 800 °C in open air and up to 1000 °C in a pure chlorine atmosphere, are electrically insulating, and possess superlative mechanical properties. Since the BNNT assembly is highly porous and easily penetrated by liquids and gases, BNNT thin film coated on optical fiber can be used as a novel sensing medium with enhanced sensitivity and selectivity. In this letter, uniform BNNT films have been successfully coated on optical fibers and tapered optical fibers (TOFs). A BNNT-coated TOF sensor has been developed for various liquids and gases sensing applications. We demonstrated experimentally that the BNNT-coated TOF can be used as a level sensor for liquids, even for those with refractive indices smaller than that of silica such as the organic solvents like acetone, hexane, tetrahydrofuran, ethyl ether, and dimethylformamide. As to gas sensing, HCl was selectively detected with enhanced sensitivity due to its high polarity and good affinity to the OH/NH2 functionalized BNNTs. The BNNT-coated optical fiber sensors can be potentially used at high temperatures and in some harsh environments.
Prospectively gated cardiac CT (2007)

Future cardiac CT protocols will utilize large area detectors with whole heart scans performed within one heartbeat. For such scans, accurate prospective ECG gating is essential to capture the heart at the correct phase. This report addresses one of the main factors affecting the prospective gating accuracy: the ability to predict the cardiac phase from the ECG signal. Two different scanning methods with equal average dose utilization along with 6 different prediction algorithms are compared and evaluated on 245 patient ECG signals. In general, all the algorithms performed comparably while, perhaps surprisingly, the best scan method was to rescan the patient as necessary as opposed to elongating a single scan.
Optimal Structure of a Plasmonic Chip for Sensitive Bio-Detection with the Grating-Coupled Surface Plasmon-Field Enhanced Fluorescence (GC-SPF) (2017)

Surface plasmon field-enhanced fluorescence (SPF) has been one of the powerful tools for biosensors and bioimaging. A wavelength-scale periodic structure coated with a thin metal film is called a plasmonic chip, and it can provide SPF. SPF of Cy5-streptavidin (Cy5-SA) was measured on a biotinylated plasmonic chip with a grating of 480 nm-pitch. The optimal structure of a plasmonic sensor-chip was designed for improving detection sensitivity. The silver film thickness dependence of the SPF intensity was measured under the irradiation of the top panel of a sensor chip. Furthermore, the dependence of the SPF intensity on the distance from the metal surface was also investigated. The optimal structure for the largest fluorescence enhancement factor was 150 nm-thick silver and 10 nm-thick SiO₂ layers due to the enhanced electric field (excitation field), the surface plasmon coupled emission (SPCE), and the interference effect with reflected light. The largest enhancement factor was found to be 170-fold. Furthermore, not only the largest fluorescence intensity but also stable lower background noise were found to be essential for higher-sensitive detection.
A Mesh-based Robust Topology Discovery Algorithm for Hybrid Wireless Networks (2002)

Wireless networks in home, office and sensor applications consist of nodes with low mobility. Most of these networks have at least a few powerful machines additionally connected by a wireline network. Topology information of the wireless network at these powerful nodes can be used to control transmission power, avoid congestion, compute routing tables, discover resources, and to gather data. In this paper we propose an algorithm for topology discovery in wireless networks with slow moving nodes and present various performance characteristics of this algorithm. The proposed algorithm discovers all links and nodes in a stable wireless network and has an excellent message complexity: the algorithm has an optimal message complexity in a stable network and the overhead degrades slowly with increasing mobility of the nodes.
Effect of UV Crosslinking on Transport Properties of CO2 and N2 Through Poly(Imide-siloxane) Segmented Copolymer (2014)

Crosslinkable segmented random copolymers are made by synthesizing a polyimide in the presence of bisaminopropyl dimethylsiloxane (PDMS) oligomers. The polyimide segments of these materials are composed of two different dianhydrides, 2,2'-bis-(3,4-dicarboxyphenyl) hexafluoropropane dianhydride (6FDA), and 3,3',4,4'- benzophenone tetracarboxylic dianhydride (BTDA) with the base diamine, 2,4,6-trimethyl-1,3-phenylenediamine (DAM). Upon irradiation with UV light, the ketone group in BTDA can form radicals that crosslink with adjacent benzylic methyl groups on DAM. Thermal analysis reveals that siloxane-containing polyimide copolymer films are phase segregated, composed of a polyimide-rich continuous phase and dispersed PDMS phase. CO2 and N2 gas permeabilities of uncrosslinked and crosslinked samples were measured to investigate the effect of UV crosslinking on permeability and permselectivity. Incorporation of PDMS did not significantly change the transport properties of the membranes. Densification occurred as a result of UV crosslinking, which enhanced the size-sieving capability of the poly(imide-siloxane) segmented copolymer membrane.
Fusing Bird View LIDAR Point Cloud and Front View Camera Image for Deep Object Detection (2017)

We propose a new method for fusing a LIDAR point cloud and camera-captured images in the deep convolutional neural network (CNN). The proposed method constructs a new layer called non-homogeneous pooling layer to transform features between bird view map and front view map. The sparse LIDAR point cloud is used to construct the mapping between the two maps. The pooling layer allows efficient fusion of the bird view and front view features at any stage of the network. This is favorable for the 3D-object detection using camera-LIDAR fusion in autonomous driving scenarios. A corresponding deep CNN is designed and tested on the KITTI bird view object detection dataset, which produces 3D bounding boxes from the bird view map. The fusion method shows particular benefit for detection of pedestrians in the bird view compared to other fusion-based object detection networks.
Reliability, solderability and electrical performance of high density ultra thin capacitors based on carbon nanofibers (2021)

This paper investigates the suitability of the Carbon Nano-Fiber Metal-Insulator-Metal (CNF-MIM) capacitor for integration in future miniaturized electronics. The CNF-MIM has previously shown electrical properties suitable for use in a variety of applications such as digital electronics. The CNF-MIM capacitors are subjected to high ambient temperature and constant voltage bias environments over long periods of time to assess their long-term durability. The devices are also subjected to standard surface-mount solder reflow procedure to investigate the compatibility with industry-standard assembly techniques. The capacitors are characterized in both DC and RF and are shown to be robust against degradation in these scenarios. Finally, ultra-thin CNF-MIM capacitors are manufactured, showing that the established technology can be further shrunk for further miniaturization and future applications.
An Unsupervised Adaptation Approach to Leveraging Feedback Loop Data by Using i-Vector for Data Clustering and Selection (2014)

We present a study of using unsupervised adaptation approaches to improve speech recognition accuracy of a deployed speech service by leveraging large-scale untranscribed speech data collected from a feedback loop (FBL). For a regular user with lots of adaptation utterances, conventional CMLLR-based adaptation can be used for personalization directly. For a casual user with a few adaptation utterances, we propose to use CMLLR-based adaptation by augmenting his / her adaptation utterances with utterances acoustically close to the user, which are selected from the FBL data by an i-vector based approach. For a new user, we propose to perform a CMLLR-based recognition of an unknown utterance by selecting a set of CMLLR transforms from the most similar cluster, which are pre-trained by using the utterances from the corresponding cluster generated by an i-vector based utterance clustering method from the FBL data. The effectiveness of the above approaches are confirmed by our experiments on a short message dictation task on smart phones.