gebhart/patrepeval huggingface dataset:
Myeloablative Temozolomide Enhances CD8+ T-Cell Responses to Vaccine and Is Required for Efficacy against Brain Tumors in Mice (2013)

Temozolomide (TMZ) is an alkylating agent shown to prolong survival in patients with high grade glioma and is routinely used to treat melanoma brain metastases. A prominent side effect of TMZ is induction of profound lymphopenia, which some suggest may be incompatible with immunotherapy. Conversely, it has been proposed that recovery from chemotherapy-induced lymphopenia may actually be exploited to potentiate T-cell responses. Here, we report the first demonstration of TMZ as an immune host-conditioning regimen in an experimental model of brain tumor and examine its impact on antitumor efficacy of a well-characterized peptide vaccine. Our results show that high-dose, myeloablative (MA) TMZ resulted in markedly reduced CD4(+), CD8(+) T-cell and CD4(+)Foxp3(+) TReg counts. Adoptive transfer of naïve CD8(+) T cells and vaccination in this setting led to an approximately 70-fold expansion of antigen-specific CD8(+) T cells over controls. Ex vivo analysis of effector functions revealed significantly enhanced levels of pro-inflammatory cytokine secretion from mice receiving MA TMZ when compared to those treated with a lower lymphodepletive, non-myeloablative (NMA) dose. Importantly, MA TMZ, but not NMA TMZ was uniquely associated with an elevation of endogenous IL-2 serum levels, which we also show was required for optimal T-cell expansion. Accordingly, in a murine model of established intracerebral tumor, vaccination-induced immunity in the setting of MA TMZ-but not lymphodepletive, NMA TMZ-led to significantly prolonged survival. Overall, these results may be used to leverage the side-effects of a clinically-approved chemotherapy and should be considered in future study design of immune-based treatments for brain tumors.
Visible near-infrared (VNIR) reflectance hyperspectral imagery for identifying aflatoxin-contaminated corn kernels (2015)

<abstract> <b>Abstract.</b> Aflatoxin contamination can be found in various agricultural commodities. Because of their toxic and carcinogenic properties, both pre-harvest and post-harvest strategies have been developed. In this study, visible near-infrared (VNIR) reflectance hyperspectral imaging was employed as a post-harvest strategy to identify aflatoxin-contaminated corn kernels rapidly and non-invasively. Corn ears in the field were inoculated with toxigenic Aspergillus flavus spores at early dough stage to artificially create aflatoxin contamination. Kernels were removed from the inoculated corn ears and scanned using the hyperspectral imagery on the germ side. Subsequently, chemical analyses were performed to determine aflatoxin concentration for each kernel. For all kernel samples, mean spectra were extracted and compressed using principal component analysis. Both the threshold values of 20 ppb and 100 ppb were applied separately to designate each sample as contaminated or healthy. The algorithm of decision trees was then employed to classify contaminated and healthy samples based on the extracted PCs. The best overall accuracy was 90.00% from the test sets for both 20 ppb based and 100 ppb based classification. Since the gradient of the slope of the reflectance curve ranging from 700 to 800 nm increased as the aflatoxin contamination level of samples increased, the band ratio image of 800 nm to 700 nm was calculated on one hyperspectral image to identify contaminated kernels. The overall identification rate was 80%. Though this accuracy was lower than that using mean spectra analysis, the two band ratio analysis was simpler with less computation time and a lower cost.
Cytotoxic and apoptotic effects of ceranib-2 offering potential for a new antineoplastic agent in the treatment of cancer cells (2014)

Fibrocarcinomas are malignant tumours that originate in mesenchymal cells. The tumours typically form in the presence of connective tissue and are of key consideration when assessing research priorities for future healthcare management. Ceramidase inhibitors, such as ceranib-2, have demonstrated capacity to interfere with cellular DNA functionality, initiating apoptosis in many cancer cell lines. The enzyme ceramidase can regulate cellular levels of sphingosine and sphingosine-1-phosphate by controlling hydrolysis of ceramide. The present study investigates the antigrowth effects of ceranib-2 on mouse embryonic fibroblast cells (NIH/3T3 normal cell line) and rat embryonic fibroblast cells (5RP7 cancer cell line). Research was conducted using colorimetric 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay, confocal microscopy, and transmission electron microscopy. The results indicate that in vitro fibrocarcinomas have the potential to undergo apoptotic death when influenced by the antigrowth behaviour of ceranib-2. This is true even of cells exposed only to minimal doses of ceranib-2. Indicators of apoptotic death, specifically presentation of a pyknotic nucleus, were observed by confocal micrographs in treated cells double-stained with acridine orange and Alexa Fluor-488 Phalloidin. It is theorised that ceranib-2 will function in accordance with the antiproliferative activity of other acid ceramidases, ultimately resulting in the molecule&amp;apos;s classification as a new antitumour agent.
Curvilinear capacitive micromachined ultrasonic transducer (CMUT) array fabricated using a reverse process (2008)

This paper presents the manufacturing of a flexible 192-elements curvilinear CMUT array developed using our patented reverse fabrication process. In this process the silicon nitride CMUT membranes are surface micromachined over a silicon substrate such that the non-radiating surface of the transducer corresponds to the last layer deposited, while the radiating membranes are uncovered by completely etching the silicon substrate. Before the removal of the silicon substrate a flexible backing material is poured and cured on the non-radiating surface, and after the removal another layer of flexible suited material is applied to cover the membranes. At the end of the process the large 24-mm by 6-mm CMUT die with a total thickness of just 6.5 mum, embedded in the flexible backing and coating layers, was bent to a radius of curvature of less than 10 mm in an azimuth direction, showing great flexibility. The functionality of the device wire-bonded to a flex printed circuit and mounted on a curved backing with a radius of curvature of 25 mm was demonstrated by means of electrical impedance tests and pulse-echo measurements in water. The tested elements showed a pulse-echo center frequency of about 11.0 MHz with a fractional bandwidth of at least 100%, with no apparent performance degradation resulting from curving the array.
Cyclic association rules (2002)

We study the problem of discovering association rules that display regular cyclic variation over time. For example, if we compute association rules over monthly sales data, we may observe seasonal variation where certain rules are true at approximately the same month each year. Similarly, association rules can also display regular hourly, daily, weekly, etc., variation that is cyclical in nature. We demonstrate that existing methods cannot be naively extended to solve this problem of cyclic association rules. We then present two new algorithms for discovering such rules. The first one, which we call the sequential algorithm, treats association rules and cycles more or less independently. By studying the interaction between association rules and time, we devise a new technique called cycle pruning, which reduces the amount of time needed to find cyclic association rules. The second algorithm, which we call the interleaved algorithm, uses cycle pruning and other optimization techniques for discovering cyclic association rules. We demonstrate the effectiveness of the interleaved algorithm through a series of experiments. These experiments show that the interleaved algorithm can yield significant performance benefits when compared to the sequential algorithm. Performance improvements range from 5% to several hundred percent.
Active Fixturing for Mesoscale Manufacturing Systems: Fixel Design Alternatives (2008)

This paper presents an investigation of fixel design alternatives for active (dynamic) fixturing to be incorporated into mesoscale manufacturing systems. Using simple compliant mechanisms and components (e.g., monolithic four-bar mechanisms and/or cantilever beams), fixels exhibiting mechanically adjustable stiffness characteristics are achievable. Manually or automating the stiffness adjustments, these fixels provide a functionality for enabling greater control of the dynamic response of the workpiece due to vibrations and variation in contact forces at the tool-workpiece-fixture interface. To quantify the fixel functionality and its dynamic range, this paper presents the theoretical models of the stiffness characteristics expressed as a function of each fixel design’s mechanical variables. Upon establishing a common stiffness range for the different fixel designs, a metric is formed based on the sensitivity of stiffness expressed as a function of slenderness ratio and an operation range, bounded by a maximum possible stiffness value shared by all fixture models. Using this metric, results are generated to delineate the advantages and disadvantages of each design and their potential impact on fixturing and material handling in the creation of micron features on micro and macro parts.
A comparative study of branched and linear mannitol-based amphiphiles on membrane protein stability (2018)

The study of membrane proteins is extremely challenging, mainly because of the incompatibility of the hydrophobic surfaces of membrane proteins with an aqueous medium. Detergents are essential agents used to maintain membrane protein stability in non-native environments. However, conventional detergents fail to stabilize the native structures of many membrane proteins. Development of new amphipathic agents with enhanced efficacy for membrane protein stabilization is necessary to address this important problem. We have designed and synthesized linear and branched mannitol-based amphiphiles (MNAs), and comparative studies showed that most of the branched MNAs had advantages over the linear agents in terms of membrane protein stability. In addition, a couple of the new MNAs displayed favorable behaviors compared to n-dodecyl-β-d-maltoside and the previously developed MNAs in maintaining the native protein structures, indicating potential utility of these new agents in membrane protein study.
Compact characterization of liquid absorption and emission spectra using linear variable filters integrated with a CMOS imaging camera (2016)

A compact analysis platform for detecting liquid absorption and emission spectra using a set of optical linear variable filters atop a CMOS image sensor is presented. The working spectral range of the analysis platform can be extended without a reduction in spectral resolution by utilizing multiple linear variable filters with different wavelength ranges on the same CMOS sensor. With optical setup reconfiguration, its capability to measure both absorption and fluorescence emission is demonstrated. Quantitative detection of fluorescence emission down to 0.28 nM for quantum dot dispersions and 32 ng/mL for near-infrared dyes has been demonstrated on a single platform over a wide spectral range, as well as an absorption-based water quality test, showing the versatility of the system across liquid solutions for different emission and absorption bands. Comparison with a commercially available portable spectrometer and an optical spectrum analyzer shows our system has an improved signal-to-noise ratio and acceptable spectral resolution for discrimination of emission spectra, and characterization of colored liquid's absorption characteristics generated by common biomolecular assays. This simple, compact, and versatile analysis platform demonstrates a path towards an integrated optical device that can be utilized for a wide variety of applications in point-of-use testing and point-of-care diagnostics.
Characterisation of Macrophage Inflammatory Protein‐5/Human CC Cytokine‐2, A Member of the Macrophage‐Inflammatory‐Protein Family of Chemokines (1997)

A human monocyte-activating CC chemokine has been identified based on sequences in an expressed sequence tag (EST) cDNA database. The protein shows highest sequence identity to the macrophage inflammatory protein (MIP) group of chemokines, particularly MIP-3 (76.7%) and MIP-1alpha (75.4%), and has been named MIP-5. Model building confirms that the protein has a similar three dimensional structure to other chemokines, but has an additional third disulphide bond. Northern blot analysis and reverse-transcriptase PCR show that the mRNA for MIP-5 is expressed at a high levels in liver, intestine and in lung leukocytes. MIP-5 induces chemotaxis of human monocytes, T-lymphocytes and, to a lesser degree, eosinophils at nanomolar concentrations; it has no effect on neutrophil migration. In receptor-binding assays, MIP-5 shows IC50 values of 12 nM for competition with 125I-MIP-1alpha for binding to CC-chemokine receptor (CCR)1, and 2.5 nM for competition with 125I-MCP-3 for binding to CCR3. It shows no ability to compete with ligand for binding to the two interleukin (IL)-8 receptors (CXC-chemokine receptors 1 and 2) or to CCR2, CCR4 or CCR5. Consistent with this binding data, MIP-5 was only able to induce calcium fluxes in CHO cells stably transfected with CCR1 or CCR3.
Effect of EGFRvIII-targeted vaccine (CDX-110) on immune response and TTP when given with simultaneous standard and continuous temozolomide in patients with GBM (2008)

2011 Background: Conventional therapies for GBM fail to target tumor cells exclusively. Immunologic targeting of tumor- specific gene mutations may allow more precise eradication of neoplastic cells. The epidermal growth factor receptor variant III (EGFRvIII) is a consistent and immunogenic mutation that is not expressed in any normal tissues, but is widely expressed in GBMs and other neoplasms making it an attractive target for active immunotherapy. Methods: A phase II multicenter clinical trial was undertaken to assess the immunogenicity and efficacy of an EGFRvIII-specific peptide vaccine in patients with newly-diagnosed, EGFRvIII+ GBM in combination with simultaneous standard or continuous temozolomide (TMZ). After resection and radiation/TMZ (75 mg/m2/d), consecutive cohorts received subsequent monthly cycles of 200 mg/m2 (N=13) or continuous 100 mg/m2 (N=8) TMZ simultaneous with intradermal vaccinations with an EGFRvIII-specific peptide (PEPvIII) conjugated to keyhole limpet hemocyanin (KLH) until tumor progression or death. Results: 21 patients were enrolled. There was one allergic reaction, but no other SAEs. There were no significant differences in vaccine immunogenicity (p>0.999; binomial proportions), PFS (p=0.7979; log-rank), or OS (p=0.7728; log-rank) between TMZ regimens. Although TMZ induced grade II lymphopenia in 53.8% of patients, the co-administration of TMZ with the EGFRvIII vaccine (CDX-110) results in strong sustained immune responses to EGFRvIII in 100% (95%CI: 0.72, 1.00) of evaluated patients. Median PFS was 16.6 months (95%CI: 9.1, 22.7). Median survival has not been reached. The survival of the vaccinated patients is better than a matched historical control group (14.3 months; 95%CI: 13.0, 16.2) (p<0.0001; log-rank) and a subgroup treated with TMZ (15.2; 95%CI: 13.9, 20.5) (p=0.0078) and is also equivalent to the results seen in patients vaccinated without simultaneous temozolomide (p=0.4108; log-rank). Conclusions: CDX-110 peptide vaccination with standard of care temozolomide in patients with GBM appears very promising and is under investigation in a phase III, randomized clinical trial. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Celldex Therapeutics Celldex Therapeutics Celldex Therapeutics Celldex Therapeutics
Three-dimensional circuit integration based on self-synchronized RF-interconnect using capacitive coupling (2004)

A self-synchronized RF-interconnect (SSRFI), based on capacitive coupling and peak signal detection, is presented. In this SSRFI, small coupling capacitor (60fF) is used to interconnect vertical active layers in 3-Dimensional IC. The demonstrated SSRFI system, including both transmitter and receiver, has been designed, fabricated and verified in UMC 0.18 /spl mu/m CMOS with a PRBS data rate of 3Gbit/s, a BER of 1.2/spl times/10/sup -10/ and a rms jitter of 1.28ps. The core circuit burns 4mW from a 1.8V supply and occupies 0.02mm/sup 2/ chip area.
Corrosion characteristics of the wrought Ni‐Cr‐Mo alloys (2005)

Abstract This paper concerns the wrought, nickel‐chromium‐molybdenum (Ni‐Cr‐Mo) alloys, a family of materials with a long history of use in the chemical process industries. Their attributes include resistance to the halogen acids and resistance to pitting, crevice attack, and stress corrosion cracking in hot, halide salt solutions. The purpose of this paper is to characterize the performance of the Ni‐Cr‐Mo alloys in several key chemicals, using iso‐corrosion diagrams. These indicate the expected corrosion rates over wide ranges of concentration and temperature. Furthermore, the differences between individual Ni‐Cr‐Mo alloys, and their behavior relative to the stainless steels are defined. The data indicate benefits of both a high chromium content and a copper addition, as used in Hastelloy® C‐2000® alloy.
Optimization of the pre-pumping NO/ClO2 chemistry in a purely chemical HCl laser (1977)

The laser output at 3.8 micrometers from a purely chemical HCl laser was used to obtain information about the pre-pumping chemistry of the NO/ClO2 system. The reaction of chemically produced chlorine atoms with hydrogen iodide was the laser pumping reaction. Successful laser operation was confirmed using three different kinetic or chemical modes. These modes are distinguishable by whether the chlorine enters the optical (laser) region directly in the form of chlorine atoms, ClO radicals or parent ClO2 molecules. A comparison of experimental results for the latter two modes, using computer simulation results for the time evolution HCl, showed that the main features of the coupling of the pumping reaction to the pre-pumping chemistry are understood. (Author)
Accurate low-power CMOS autozeroed comparator (1992)

A low-power CMOS autozeroed comparator suitable for high-frequency A/D convertors is discussed. The use of a source follower in the autozeroed inverter stage allows the circuit to provide an optimum tradeoff between speed, gain and power dissipation. Relationships are given that relate the time response, both in the autozeroing and comparating phase, to the circuit parameters. An experimental prototype, fabricated with a 2μm CMOS process, is also presented.
Statistical Method Based Waveform Optimization in Collocated MIMO Radar Systems (2023)

Multiple-input multiple-output (MIMO) radar has acquired considerable attention as it offers an additional degree of freedom which results in performance gains when contrasted with the regular single antenna element radar system. Waveform optimization in MIMO radar is essential as it can offer tremendous improvements in target detection which are quantified in terms of reductions in the symbol error rate and improvements in target detection probability. In this work, we foster a strategy for the optimization of transmitter and receiver waveform in a collocated MIMO radar by only considering the second order statistics, thus relaxing the information of the instantaneous target states. Our contributions are primarily two-fold. First, we find a closed-form expression of the outage probability of an unknown target under clutter environment. For this prospect, we model the signal-to-interference-plus-noise ratio in a canonical quadratic structure, and then utilize the modern residue theory approach to characterize the distribution function. Secondly, we propose constrained and unconstrained optimization problems for the reduction in outage probability using algorithmic techniques such as interior-point, sequential-quadratic programming, and the active-set method for the optimization of the transmitter and receiver waveform. We also provide simulated re-enactments to validate our hypothetical deductions.
Single-shot phase-shifting digital holography (2013)

Single-shot three-dimensional biological imaging has broad applications in basic and clinical research as well as clinical use. We propose a three-dimensional imaging system that can be configured in transmission, reflection or fluorescence modes. This system is capable of recording/measuring the amplitude, phase and polarization of an optical wavefront in a single shot and reconstructing numerically objects with three-dimensional volumetric information. Built upon the principle of digital holography (DH), the proposed system uses a reference beam to interfere with the light field under investigation and digitally records/measures the in-phase and quadrature interference patterns. Single-shot in-phase and quadrature interference pattern recording is made possible by incorporating technologies widely used in coherent optical communication. Specifically, a free-space optical 90° hybrid is employed to measure the complex (real and imaginary) optical field from transmission through, reflection from or fluorescence of biological samples. We have constructed a single-shot phase-shifting digital holography system and experimentally demonstrated its operation for the first time.
Wavelength-resonant enhanced gain/absorption structure for standing-wave optoelectronic devices and its application to surface-emitting semiconductor lasers (1988)

A novel design for optoelectronic devices which utilize interaction between electromagnetic standing wave and carrier population is described. The structure consists of quantum well layers spaced at one half the wavelength of a particular optical transition in quantum wells. In such periodic medium, the gain (or absorption) for a selected wavelength determined by the periodicity is enhanced by a factor of two compared to uniform medium. The design has been implemented experimentally by growing a surface-emitting semiconductor laser structure in GaAs/AlGaAs system and have demonstrated lasing with the shortest gain medium length (320 nm) ever reported for a semiconductor laser. 7 refs., 4 figs.
Stained-glass visualization for highly condensed video summaries (2005)

This work presents a method for creating highly condensed video summaries called stained-glass visualizations. These are especially suitable for small displays on mobile devices. A morphological grouping technique is described for finding 3D regions of high activity or motion from a video embedded in x-y-t space. These regions determine areas in the keyframes, which can be subsumed in a more general geometric framework of germs and supports: germs are the areas of interest, and supports give the context. Algorithms for packing and laying out the germs are provided. Gaps between the germs are filled using a Voronoi-based method. Irregular shapes emerge, and the result looks like stained glass.
Transformation with <i>katG</i> restores isoniazid‐sensitivity in <i>Mycobacterium tuberculosis</i> isolates resistant to a range of drug concentrations (1993)

Isoniazid-resistant isolates of Mycobacterium tuberculosis were transformed with a plasmid vector carrying the functional catalase-peroxidase (katG) gene. Expression of katG restored full drug susceptibility in isolates initially resistant to concentrations ranging from 3.2 to > 50 micrograms ml-1. Transformation with the corresponding katG gene from Escherichia coli resulted in low-level expression of catalase and peroxidase activities and conferred partial isoniazid sensitivity.