gebhart/patrepeval huggingface dataset:
Computer-aided prognosis of ER+ breast cancer histopathology and correlating survival outcome with Oncotype DX assay (2009)

The current gold standard for predicting disease survival and outcome for lymph node-negative, estrogen receptor-positive breast cancer (LN-, ER+ BC) patients is via the gene-expression based assay, Oncotype DX. In this paper, we present a novel computer-aided prognosis (CAP) scheme that employs quantitatively derived image information to predict patient outcome analogous to the Oncotype DX Recurrence Score (RS), with high RS implying poor outcome and vice versa. While digital pathology has made tissue specimens amenable to computer-aided diagnosis (CAD) for disease detection, our CAP scheme is the first of its kind for predicting disease outcome and patient survival. Since cancer grade is known to be correlated to disease outcome, low grade implying good outcome and vice versa, our CAP scheme captures quantitative image features that are reflective of BC grade. Our scheme involves first semi-automatically detecting BC nuclei via an Expectation Maximization driven algorithm. Using the nuclear centroids, two graphs (Delaunay Triangulation and Minimum Spanning Tree) are constructed and a total of 12 features are extracted from each image. A non-linear dimensionality reduction scheme, Graph Embedding, projects the image-derived features into a low-dimensional space, and a Support Vector Machine classifies the BC images in the reduced dimensional space. On a cohort of 37 samples, and for 100 trials of 3-fold randomized cross-validation, the SVM yielded a mean accuracy of 84.15% in distinguishing samples with low and high RS and 84.12% in distinguishing low and high grade BC. The projection of the high-dimensional image feature data to a 1D line for all BC samples via GE shows a clear separation between, low, intermediate, and high BC grades, which in turn shows high correlation with low, medium, and high RS. The results suggest that our image-based CAP scheme might provide a cheaper alternative to Oncotype DX in predicting BC outcome.
An information theorectic model for physical uncloneable functions (2004)

A "physical uncloneable function" (PUF) is a function that is realized by a physical system, such that the function is easy to evaluate but the physical system is hard to characterize. PUFs were introduced as a cost-effective way of generating secure keys for cryptographic purposes. A PUF is a physical system designed such that it interacts in a complicated way with stimuli (challenges) and leads to unique but unpredictable responses. A PUF is similar to a keyed hash function. The key is the physical system consisting of many "random" components.
Thermomechanical Analysis of Soft-Tissue Thermotherapy (2003)

Soft-tissue thermotherapy based on sub-ablative heating of collagenous tissues finds wide-spread application in medicine such as tissue welding, thermokeratoplasty, skin resurfacing, elimination of discogenic pain in the spine and treatment of joint instability. In this paper, heat-induced thermomechanical response characteristics of collagenous tissues are quantified by means of in vitro experimentation with a representative model tissue (New Zealand white rabbit patellar tendon). Three distinct heat-induced thermomechanical response regimes (defined by the rate of deformation and the variation of material properties) are identified. Arrhenius damage integral representation of collagenous tissue thermal history is shown to be adequate in establishing the master response curves for quantification of thermomechanical response for modeling purposes. The trade-off between the improved kinematical stability and compromised mechanical stability of the heated collagenous tissue is shown to be the major challenge hindering the success of subablative thermotherapies.
Direct Water Removal in Gas Diffusion Layer of Proton Exchange Membrane Fuel Cells by a Flexible Electroosmotic Pump (2006)

An electroosmotic pump is a non-mechanical pump that can remove water by applied electric field. A flexible electroosmotic (EO) pump was directly attached to a gas diffusion layer (GDL) on the cathode side of a miniature proton exchange membrane fuel cell (PEMFC). The operation of EO pump improved the voltage-current response of a PEMFC. Especially, the increase of limiting current was observed. We assume the reduced flooding in GDL was achieved by the operation of EO pump. Further investigation with AC impedance spectroscopy support the assumption as the reduced mass transport resistance was observed.
Low power mode in cloud storage systems (2009)

We consider large scale, distributed storage systems with a redundancy mechanism; cloud storage being a prime example. We investigate how such systems can reduce their power consumption during low-utilization time intervals by operating in a low-power mode. In a low power mode, a subset of the disks or nodes are powered down, yet we ask that each data item remains accessible in the system; this is called full coverage. The objective is to incorporate this option into an existing system rather than redesign the system. When doing so, it is crucial that the low power option should not affect the performance or other important characteristics of the system during full-power (normal) operation. This work is a comprehensive study of what can or cannot be achieved with respect to full coverage low power modes. The paper addresses this question for generic distributed storage systems (where the key component under investigation is the placement function of the system) as well as for specific popular system designs in the realm of storing data in the cloud. Our observations and techniques are instrumental for a wide spectrum of systems, ranging from distributed storage systems for the enterprise to cloud data services. In the cloud environment where low cost is imperative, the effects of such savings are magnified by the large scale.
Co-learning of Word Representations and Morpheme Representations (2014)

The techniques of using neural networks to learn distributed word representations (i.e., word embeddings) have been used to solve a variety of natural language processing tasks. The re-cently proposed methods, such as CBOW and Skip-gram, have demonstrated their effectiveness in learning word embeddings based on context information such that the obtained word embed-dings can capture both semantic and syntactic relationships between words. However, it is quite challenging to produce high-quality word representations for rare or unknown words due to their insufficient context information. In this paper, we propose to leverage morphological knowledge to address this problem. Particularly, we introduce the morphological knowledge as both ad-ditional input representation and auxiliary supervision to the neural network framework. As a result, beyond word representations, the proposed neural network model will produce morpheme representations, which can be further employed to infer the representations of rare or unknown words based on their morphological structure. Experiments on an analogical reasoning task and several word similarity tasks have demonstrated the effectiveness of our method in producing high-quality words embeddings compared with the state-of-the-art methods. 1
High-density, high performance data storage via volume holography (2003)

Summary form only given. It has long been known that volume holography allows multiple pages of data to be stored in the same volume, therefore allowing densities exceeding the diffraction limit for 2-dimensional optical storage. The attraction, is storage of individual Mbit data pages addressed by changing either the angle, wave-length, or phase code of the reference beams, resulting in the rapid parallel storage and retrieval of digital data. Although this technology has been proposed since the 1970's it has failed to achieve viability. Our team has made great strides toward resolving the key problems with the technology. First, a new series of methods for recording multiplexed holograms has been developed. These techniques can be implemented with an uncomplicated mechanical geometry, individual holograms are addressed by a simple translation of the media. In addition, for one particular technique, phase correlation multiplexing is reported.
Heterogeneous Spacecraft Networks: Performance analysis for low-cost Earth Observation missions (2014)

Heterogeneous Spacecraft Networks (HSNs) are network environments in which spacecraft from different missions and institutions can communicate with each other at low cost and with low impact on overall system resources. The Mission Design Center (MDC) at NASA Ames Research Center has been studying solutions for low cost multi-spacecraft systems for a number of years. One may now build on the idea to interconnect clusters of spacecraft with each other to have them act as mobile nodes belonging to the same collaborative mission. Recent progress in small satellite technology is significant, and one of the advantages of small satellites lies precisely in the large quantity of spacecraft that can be produced at accessible costs. It follows naturally that small satellites are an interesting candidate platform for development and demonstration of the HSN concept. This paper is the second in a series of three companion papers. The general concept of operations for HSNs in LEO and a number of future applications are proposed in the first paper [6], while enabling technology such as devices and lower layer protocols are discussed in paper three [7]. In this paper, we pick up the scenario of a low-cost and multi-institutional network of Earth Observation (EO) missions in LEO and conduct network performance analysis using the AGI System Tool Kit (STK) and the open-source Network Simulator (NS-3). A multi-spacecraft network consolidates the individual capabilities of each spacecraft from different institutions by combining benefits of both frequent revisit and concentrated observation. Complementary and correlated data could be collected simultaneously from a large set of distributed spacecraft utilizing HSN capability. In this specific configuration, communication distance between spacecraft, related delays and error rate are the major factors in network performance. Also, average duration of communication opportunities between spacecraft is usually very limited. Thus, it is important to simulate orbital dynamics, link margins, and protocols simultaneously to analyze network performances. In this paper, we compare some existing protocols to obtain a measure for the practical performance of the candidate network. We focus on best-effort data delivery, an approach necessitated by the severe constraints on communications resulting from low-cost and low system resource small spacecraft. In the application layer, we show that packet size and data rate of a source node also affect overall performance of the network. We present the resulting figures of merit from our simulations. The paper concludes with a summary of the simulation results.
[Characterization of helical coil microwave antenna for interstitial hyperthermia]. (1988)

Implantable microwave antennas for interstitial hyperthermia have been constructed by using a fine wire helical coil extension of the coax feedline inner conductor. The effects of the variable coil length the winding density, and the antenna insertion depth in the tissue on the heating patterns from a single antenna were characterized in phantom models. Results indicated that the helical coil microwave antenna provided localized heat at depth near the antenna tip, and the heating patterns were easily modified by minor changes in the coil length, winding density, and altering the separation gap. The characteristics of the helical coil microwave antenna may increase its potential application to cases of interstitial hyperthermia.
Generation of Recombinant Arenavirus for Vaccine Development in FDA-Approved Vero Cells (2013)

The development and implementation of arenavirus reverse genetics represents a significant breakthrough in the arenavirus field. The use of cell-based arenavirus minigenome systems together with the ability to generate recombinant infectious arenaviruses with predetermined mutations in their genomes has facilitated the investigation of the contribution of viral determinants to the different steps of the arenavirus life cycle, as well as virus-host interactions and mechanisms of arenavirus pathogenesis. In addition, the development of trisegmented arenaviruses has permitted the use of the arenavirus genome to express additional foreign genes of interest, thus opening the possibility of arenavirus-based vaccine vector applications. Likewise, the development of single-cycle infectious arenaviruses capable of expressing reporter genes provides a new experimental tool to improve the safety of research involving highly pathogenic human arenaviruses. The generation of recombinant arenaviruses using plasmid-based reverse genetics techniques has so far relied on the use of rodent cell lines, which poses some barriers for the development of Food and Drug Administration (FDA)-licensed vaccine or vaccine vectors. To overcome this obstacle, we describe here the efficient generation of recombinant arenaviruses in FDA-approved Vero cells.
Abstract B039: Peptide-MHC-directed expansion of multifunctional antigen-responsive T-cells (2019)

Abstract Functional properties and antigen specificity of expanded T-cells are crucial for the efficacy of adoptive cell transfer-based therapies in cancer. Most current strategies involve nonspecific expansion of bulk tumor-infiltrating lymphocytes, often providing growth preference to co-infiltrated virus specific T-cells and driving an exhausted phenotype of the expanded T-cell product.A potential way to resolve this challenge, is the use of artificial antigen-presenting scaffolds providing both an antigen specific stimulation through peptide-MHC interaction and additional the required co-stimulatory and growth signals through associated stimulatory molecules and cytokines. We have designed such antigen-presenting scaffolds; build on a dextran-polysaccharide, carrying both peptide-MHC and relevant stimulatory molecules. The artificial antigen-presenting scaffolds interacts specifically with T-cells based on recognition of the peptide-MHC molecule and effectively expand and functionally stimulate specific T-cells in a peptide-MHC-directed fashion, while leaving all other T-cell specificities untouched. Results from in vitro experiments have showed that antigen specific CD8 T-cells stimulated with these artificial antigen-presenting scaffolds express a less differentiated phenotype and low PD-1 expression, associated with high proliferation potential and enhanced antitumor effect in vivo. Furthermore, this expansion strategy provides a high frequency of multifunctional antigen specific CD8 T-cells expressing IFN-γ, TNF-α, and CD107a upon target recognition and provide improved cancer cell killing over IL2-driven expansion of tumor-infiltrating lymphocytes. Furthermore, the current strategy allows for simultaneous expansion of numerous different T-cell populations, required to generate T-cell products with broad recognition profiles based on the personal cancer-antigen and mutational profile. All of these characteristics are of significant importance for in vivo tumor cell killing following adoptive transfer of expanded T-cell products. Thus, the present strategy represents an optimized method for expansion of cancer-restricted T-cells for adoptive cell therapy. Citation Format: Vibeke Mindahl Rafa, Mona Bodenhöfer, Amalie Kai Bentzen, Tripti Tamhane, Marco Donia, Inge Marie Stentoft Svane, Søren Nyboe Jakobsen, Christian Schmess, Sine Reker Hadrup. Peptide-MHC-directed expansion of multifunctional antigen-responsive T-cells [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B039.
Diaphragm unit of a condenser microphone, a method of fabricating the same, and a condenser microphone (1992)

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Extraction of Message Sequence Charts from Narrative History Text (2019)

Girish Palshikar, Sachin Pawar, Sangameshwar Patil, Swapnil Hingmire, Nitin Ramrakhiyani, Harsimran Bedi, Pushpak Bhattacharyya, Vasudeva Varma. Proceedings of the First Workshop on Narrative Understanding. 2019.
CD8+ T cells suppress human immunodeficiency virus replication by inhibiting viral transcription. (1995)

CD8+ cells from human immunodeficiency virus (HIV)-infected individuals suppress HIV replication in cultured CD4+ cells by a noncytolytic mechanism that involves a secreted CD8(+)-cell antiviral factor (CAF). The results of this study suggest that CD8+ cells, as well as CAF, arrest HIV replication at the level of viral transcription. Culturing naturally infected CD4+ cells actively producing HIV with autologous CD8+ cells or a 50% dilution of culture fluids from these cells results in a > 80% reduction in the number of cells expressing HIV antigens and RNA. This effect was observed within 2 days after exposure to CD8+ cells but required 6 days in the presence of CAF-containing culture fluids to reach the same extent of HIV suppression. Northern blot analysis of CD4+ cell extracts revealed that all viral RNA species (unspliced and single and double spliced) were reduced in quantity to a similar extent. CAF-containing culture fluids also had a direct inhibitory effect on HIV long terminal repeat (LTR)-driven transcription in HIV-infected 1G5 cells carrying an LTR-luciferase construct. Suppression of basal levels of LTR-driven transcription was not detected. Thus, the results suggest that the noncytolytic CD8+ cell antiviral activity observed in HIV infection exerts its effects, at least in part, by specifically interrupting HIV transcription. These findings could help in developing therapies for HIV infection.
Rate Equation Analysis of <italic>Q</italic>-Modulated Strongly Injection-Locked Whistle-Geometry Ring Lasers (2015)

In a monolithically integrated strongly injection-locked whistle-geometry semiconductor ring laser, modulating the photon lifetime or the optical losses in the cavity can lead to higher modulation bandwidth and complete elimination of low-frequency roll-off, which is commonly observed during the current modulation of injection-locked semiconductor lasers. Rate equation analysis is performed to show that modulating the photon-lifetime is significantly more advantageous than the conventional injection-current modulation. Different schemes to achieve photon-lifetime or optical-loss modulation in a strongly injection-locked whistle-geometry ring laser are discussed.
20dB-enhanced coupling to slot photonic crystal waveguide based on multimode interference (2008)

We experimentally demonstrate a novel slot photonic crystal waveguide for guiding light with low group velocity in a 100-nm-wide low-index region. The unique optical property and structural features of the slotted photonic crystals best match the requirements for active material-based silicon devices. We integrate the novel photonic crystal waveguide with a multimode interference-based coupling structure and measure a 20dB efficiency enhancement compared with direct coupling configuration. The measured transmission spectra are in good agreement with simulated band diagram.
Accelerated Chemical Reactions and Organic Synthesis in Leidenfrost Droplets (2016)

Abstract Leidenfrost levitated droplets can be used to accelerate chemical reactions in processes that appear similar to reaction acceleration in charged microdroplets produced by electrospray ionization. Reaction acceleration in Leidenfrost droplets is demonstrated for a base‐catalyzed Claisen–Schmidt condensation, hydrazone formation from precharged and neutral ketones, and for the Katritzky pyrylium into pyridinium conversion under various reaction conditions. Comparisons with bulk reactions gave intermediate acceleration factors (2–50). By keeping the volume of the Leidenfrost droplets constant, it was shown that interfacial effects contribute to acceleration; this was confirmed by decreased reaction rates in the presence of a surfactant. The ability to multiplex Leidenfrost microreactors, to extract product into an immiscible solvent during reaction, and to use Leidenfrost droplets as reaction vessels to synthesize milligram quantities of product is also demonstrated.
Fabrication and properties of rare‐earth‐doped optical fiber using barium as an alternate codopant (2016)

Barium has been established as an alternate codopant other than conventional aluminum or phosphorous for fabrication of rare‐earth‐ (RE) doped optical fiber through modified chemical vapor deposition (MCVD) coupled with solution doping technique. Different optical and material characterization results of our fabricated fibers indicate potential application as amplifier and laser. The amplifier performance of Er‐doped fiber and lasing as well as photo darkening (PD) experiment of Yb‐doped fiber doped with BaO is presented where Ba serves as an alternate candidate for enhancement of RE solubility in silica glass.
Generation and characterization of transgene-free human induced pluripotent stem cells and conversion to putative clinical-grade status (2013)

For the first time, these studies provide a proof-of-principle for the generation of fully characterized transgene-free human iPSCs and, in light of the limited availability of current good manufacturing practice cellular manufacturing facilities, highlight an attractive potential mechanism for converting research-grade cell lines into putatively clinical-grade biologics for personalized cellular therapeutics.
Identification of cDNA clones expressing immunodiagnostic antigens from Trichinella spiralis (1987)

A cDNA expression library was built in lambda gt11 phage using poly A mRNA isolated from Trichinella spiralis muscle stage larvae. This library was screened with rabbit antibodies to parasite excretory-secretory (ES) products and greater than 180 clones were isolated. Thirteen clones producing highly immunogenic protein antigens were plaque purified and rescreened with pig antisera to T.spiralis, Trichuris suis or Ascaris suum to identify clones producing epitopes specific to T.spiralis ES products, only. Two clones, TsAc-2 and TsAc-8, which displayed strong interactions with pig antisera to T. spiralis were lysogenized in E. coli Y1089 and the protein extracted. Western blots of the crude fusion proteins revealed molecular weights of 133 kD and 129 kD, respectively. Northern blot analysis of total RNA with TSP labelled cDNA:lambda gt11 probes indicated single RNA transcripts for each clone with molecular sizes corresponding to 800-850 nucleotides. dscDNA inserts were estimated by southern blot analysis to be 500 bp and 340 bp, respectively, with no cross-hybridization observed between the cloned sequences. Dot blots using pig sera to screen crude fusion protein preparations, total bacterial protein (negative controls) and crude worm extract or ES products from T.spiralis, T.suis and A.suum (positive controls) corroborated the specificity and sensitivitymore » of these clones as potential diagnostic antigens for swine trichinellosis.« less