gebhart/patrepeval huggingface dataset:
Multiplex Proteomic Analysis of Cells in Fine Needle Aspiration Samples: How Soon Can We Expect to Individualize Therapy by Comparing Pre- and Posttreatment Biopsies? (2014)

Individualized therapy of the future will be guided by panels of biomarkers that include proteins, nucleic acids, and metabolites. Among these analyte classes, proteins can provide direct functional information central to the disease. The added bonus is that the protein, or phosphoprotein, biomarker is the drug target itself and/or the direct readout of the signaling activity being inhibited. An example is the selection of kinase inhibitor therapy based on phosphorylated receptor tyrosine kinases, such as human epidermal growth factor receptor 2, protein kinase B, epidermal growth factor receptor, MET receptor tyrosine kinase, or cytoplasmic signaling proteins, such as mammalian target of rapamycin. Yet it has not been easy to quantitatively measure a panel of protein/phosphoprotein biomarkers in tissue biopsy samples with high precision, sensitivity, and accuracy, which are essential attributes if the data are used to select patient therapies. Addressing this challenge, Ullal et al. (1) described a new technology that uses DNA barcode labeling of antibodies for multiplex proteomic/phosphoprotein analysis of cells in a tumor fine needle aspiration (FNA).2 FNAs are challenging clinical specimens that contain relatively few cells compared to a tissue biopsy. Why is this method important, how does it compare to existing multiplexed clinical proteomic technologies, and when can we hope to see this platform routinely used in the clinical laboratory?

The author's platform (1) is divided into serial stages. In the first stage, the cells are passed through a microfluidic chamber where tumor cells are separated from host cells. Here, the cell mixture is exposed to antibodies tagged with magnetic particles. This permits the removal of contaminating immune cells or positive selection of tumor cells. In the second stage, the cancer cells are incubated with a cocktail of antibodies that are labeled with DNA “barcodes.” Each barcode is a different 70-nucleotide sequence. The DNA …
Controlling the Field‐Effect Mobility of Regioregular Polythiophene by Changing the Molecular Weight (2003)

A clear dependence of the hole mobility on molecular weight of poly(3‐hexylthiophene) in films is demonstrated. The charge carrier mobility of regioregular polythiophene is shown to increase by four orders of magnitude as the molecular weight is increased from ∼3 200 g mol –1 to 36 000 g mol –1 . These observations could explain why the mobility values obtained in different labs vary so widely and suggest that optimizing the molecular weight of conjugated polymers could lead to significant improvements in device performance.
Cyclone /spl trade/: a low-cost, high-performance FPGA (2003)

This paper describes the Altera Cyclone/spl trade/ FPGA, an architecture specifically designed for low-cost, high-volume applications. An optimized routing architecture, simplified I/O structure, and carefully selected features combine to yield a 57% die size reduction relative to a Stratix/spl trade/ device of similar logic density, with a 7% reduction in performance.
Supplementary Figures 1-3 from Untouched GMP-Ready Purified Engineered Immune Cells to Treat Cancer (2023)

&lt;p&gt;Supplementary Figures 1-3. Fig S1. Representative result of retroviral transduction with γδTCR transgene cassettes shows increased γδTCR expression with γ-T2A-δ cassette Fig S2. Fast and increased re-expression of retrovirally introduced TCR following T cell stimulation. Fig S3. Prevention of multiple myeloma growth by purified γδTCR transduced T cells in vivo.&lt;/p&gt;
<title>High-fidelity image reproduction using angular distribution of reflected spectral intensity</title> (2000)

A method to reproduce images on an object under various observation geometries is presented. In this method, a multispectral image sequence is captured with rotating the object under a point light source, where spectral distribution and the position are measured. The diffuse and specular reflection images are decomposed from the captured images based on the dichromatic reflection and the Lambertian models. The angular distribution of reflected light is obtained by the decomposed images, and the images under new observation geometry are synthesized by using light-ray rearrangement technique. In the experiments using two types of 2D objects, leather and fabric, it is confirmed that synthesized images under new illumination geometry are almost the same as the images actually captured under the new geometry.
Sequence of a new snRNA from the ciliate Tetrahymenathermophila (1992)

Journal Article Sequence of a new snRNA from the ciliate Tetrahymena thermophila Get access Henrik Ørum, Henrik Ørum Search for other works by this author on: Oxford Academic PubMed Google Scholar Henrik Nielsen, Henrik Nielsen 1Department of Biochemistry B, The Panum Institute, University of Copenhagen3 Blegdamsvej, DK-2200 Copenhagen, Denmark Search for other works by this author on: Oxford Academic PubMed Google Scholar Jan Engberg Jan Engberg Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 20, Issue 13, 11 July 1992, Page 3518, https://doi.org/10.1093/nar/20.13.3518 Published: 11 July 1992 Article history Received: 19 May 1992 Published: 11 July 1992
Enabling Safe Wireless Harbor Automation via 5G URLLC (2019)

Automated Rubber-Tyred Gantry cranes, AutoRTGs, are in many cases replacing manually operated cranes in day-to-day operations at harbor container terminals. The automated systems provide significant benefits by improving operational efficiency and predictability as well as enabling safer working environment. The crane operations are remotely controlled or automatic under supervision of the operator. The remote control, supervision and safety set extremely strict requirements for the communication between the cranes and the control room. This paper studies the potentials to use wireless, especially 4G and 5G ultra-reliable low latency communication (URLLC) link as a replacement for a cable reel of an AutoRTG. The key research question is whether these technologies can fulfil the reliability and low latency requirements for safety and remote control operations. As a research method, this paper introduces extensive lab measurements, system simulations, and a field-test trial to validate the system and communication performance. Based on our study, 5G URLLC is capable to support the studied use cases.
Transmission Kinetics and histopathology induced by European Turkey Coronavirus during experimental infection of specific pathogen free turkeys (2018)

Numerous viruses, mostly in mixed infections, have been associated worldwide with poult enteritis complex (PEC). In 2008 a coronavirus (Fr-TCoV 080385d) was isolated in France from turkey poults exhibiting clinical signs compatible with this syndrome. In the present study, the median infectious dose (ID<sub>50</sub> )<sub>,</sub> transmission kinetics and pathogenicity of Fr-TCoV were investigated in 10-day-old SPF turkeys. Results revealed a titre of 10<sup>4.88</sup> ID<sub>50</sub> /ml with 1 ID<sub>50</sub> /ml being beyond the limit of genome detection using a well-characterized qRT-PCR for avian coronaviruses. Horizontal transmission of the virus via the airborne route was not observed however, via the oro-faecal route this proved to be extremely rapid (one infectious individual infecting another every 2.5 hr) and infectious virus was excreted for at least 6 weeks in several birds. Histological examination of different zones of the intestinal tract of the Fr-TCoV-infected turkeys showed that the virus had a preference for the lower part of the intestinal tract with an abundance of viral antigen being present in epithelial cells of the ileum, caecum and bursa of Fabricius. Viral antigen was also detected in dendritic cells, monocytes and macrophages in these areas, which may indicate a potential for Fr-TCoV to replicate in antigen-presenting cells. Together these results highlight the importance of good sanitary practices in turkey farms to avoid introducing minute amounts of virus that could suffice to initiate an outbreak, and the need to consider that infected individuals may still be infectious long after a clinical episode, to avoid virus dissemination through the movements of apparently recovered birds.
Engineered Antigen-Specific T Cells Secreting Broadly Neutralizing Antibodies: Combining Innate and Adaptive Immune Response against HIV (2020)

While antiretroviral therapy (ART) can completely suppress viremia, it is not a cure for HIV. HIV persists as a latent reservoir of infected cells, able to evade host immunity and re-seed infection following cessation of ART. Two promising immunotherapeutic strategies to eliminate both productively infected cells and reactivated cells of the reservoir are the adoptive transfer of potent HIV-specific T cells and the passive administration of HIV-specific broadly neutralizing antibodies also capable of mediating antibody-dependent cellular cytotoxicity (ADCC). The simultaneous use of both as the basis of a single therapeutic has never been explored. We therefore sought to modify HIV-specific T cells from HIV-naive donors (to allow their use in the context of allotransplant, a promising platform for sterilizing cures) so they are able to secrete a broadly neutralizing antibody (bNAb) directed against the HIV envelope to elicit ADCC. We designed an antibody construct comprising bNAb 10-1074 heavy and light chains, fused to IgG3 Fc to elicit ADCC, with truncated cluster of differentiation 19 (CD19) as a selectable marker. HIV-specific T cells were expanded from HIV-naive donors by priming with antigen-presenting cells expressing overlapping HIV antigens in the presence of cytokines. T cells retained specificity against Gag, Nef, and Pol peptides (218.55 ± 300.14 interferon γ [IFNγ] spot-forming cells [SFC]/1 × 10<sup>5</sup>) following transduction (38.92 ± 25.30) with the 10-1074 antibody constructs. These cells secreted 10-1074 antibodies (139.04 ± 114.42 ng/mL). The HIV-specific T cells maintained T cell function following transduction, and the secreted 10-1074 antibody bound HIV envelope (28.13% ± 19.42%) and displayed ADCC activity (10.47% ± 4.11%). Most critically, the 10-1074 antibody-secreting HIV-specific T cells displayed superior <i>in vitro</i> suppression of HIV replication. In summary, HIV-specific T cells can be engineered to produce antibodies mediating ADCC against HIV envelope-expressing cells. This combined innate/adaptive approach allows for synergy between the two immune arms, broadens the target range of the immune therapy, and provides further insight into what defines an effective anti-HIV response.
In vitro phonophoresis: effect of ultrasound intensity and mode at high frequency on NSAIDs transport across cellulose and rabbit skin membranes. (2008)

The objective of this study was to evaluate the effect of intensity, mode, and duration of ultrasound application on the transport of three nonsteroidal anti-inflammatory drugs (NSAIDs) across cellulose membrane and rabbit-skin. Ibuprofen, piroxicam and diclofenac sodium were used as the model drugs. Studies were performed in vitro using a modified Franz diffusion assembly adapted to a therapeutic ultrasound transducer. Ultrasound had a significant and positive effect on the transport of the model NSAIDs across cellulose and rabbit skin membranes. Increasing ultrasound intensity from 0.5 to 3.0 W/cm2 led to a proportional increase in drug transport. Continuous ultrasound mode was more effective in enhancing drug transport than the pulsed mode. Diclofenac sodium had the least flux and permeability coefficient. This was attributed to its comparatively lower pKa value that renders the drug more ionizable in the buffer solution, consequently reducing its selective penetration through the membranes. This study demonstrated the therapeutic potential of ultrasound in transdermal delivery of NSAIDs and the synergistic effect of temperature and ultrasound operational parameters on drug transport.
Target infrared characteristic measurement in vacuum chamber (2019)

Orbit target IR characteristic is the basis of the IR imaging detection equipment design, the corresponding digital simulation model validation, and the application processing development, such as the target detection and tracking. In the work, an infrared measurement system for simulated space target is represented. The system can acquire the infrared characteristics of the target in the simulated space environment on the ground. In order to simulate the whole orbit environment, vacuum chamber and solar simulator are used in the work. An IR window is developed for the system. Then measurement instruments can be place outside the chamber to get the characteristic through the IR window. The work also provides a method to calibrate the IR window. The IR characteristic at the wavelength range of 3 &mu;~12 &mu;m can be obtained with the system.
Treatment patterns and burden of myelosuppression for patients with small cell lung cancer: A SEER‐medicare study (2022)

Chemotherapy remains a cornerstone of care for patients with SCLC. Slightly over half of patients completed the recommended number of cycles, underscoring the frailty of patients and aggressiveness of SCLC. HCRU associated with myelosuppression was prominent, suggesting a substantial burden on older patients with SCLC.
Front Cover: Single Laser Shot Photoinduced Phase Transition of Rubidium Manganese Hexacyanoferrate Investigated by X‐ray Diffraction (Eur. J. Inorg. Chem. 27/2019) (2019)

The Front Cover shows the ESRF synchrotron (bottom; image courtesy of ESRF/Pierre Jayet), where we studied the evolution of the crystal structure of the RbMnFe Prussian blue analogue (center) by X-ray diffraction (rings at the top). We used a single laser shot for driving a phase transition in which photoinduced charge transfer, trapped by the structural reorganization, is responsible for the change in the magnetic properties of the system. This work was performed in the frame of the IM-LED international laboratory (LIA, CNRS), JSPS, and ANR grants with a PhD funding from University Rennes 1. More information can be found in the Communication by E. Collet, R. Bertoni et al. For more on the story behind the cover research, see the Cover Profile.
Transition Metal-Catalyzed Cyclopropanation of Alkenes in Water:  Catalyst Efficiency and in Situ Generation of the Diazo Reagent (2002)

[reaction: see text] A cyclopropanation reaction involving ethyl diazoacetate and olefins proceeds with surprisingly high efficiency in aqueous media using Rh(II) carboxylates. Nishiyama's Ru(II) Py-box and Katsuki's Co(II) Salen complexes that allow for highly enantioselective cyclopropanations in organic solvents can also be applied to aqueous cyclopropanations with similar results. In situ generation of ethyl diazoacetate and cyclopropanation also proceeds efficiently. A chemoselective O-H insertion is also possible in water when hydrophobic catalysts and alcohols are used.
A Meta-Analytic Study of the Neural Systems for Auditory Processing of Lexical Tones (2017)

The neural systems of lexical tone processing have been studied for many years. However, previous findings have been mixed with regard to the hemispheric specialization for the perception of linguistic pitch patterns in native speakers of tonal language. In this study, we performed two activation likelihood estimation (ALE) meta-analyses, one on neuroimaging studies of auditory processing of lexical tones in tonal languages (17 studies), and the other on auditory processing of lexical information in non-tonal languages as a control analysis for comparison (15 studies). The lexical tone ALE analysis showed significant brain activations in bilateral inferior prefrontal regions, bilateral superior temporal regions and the right caudate, while the control ALE analysis showed significant cortical activity in the left inferior frontal gyrus and left temporo-parietal regions. However, we failed to obtain significant differences from the contrast analysis between two auditory conditions, which might be caused by the limited number of studies available for comparison. Although the current study lacks evidence to argue for a lexical tone specific activation pattern, our results provide clues and directions for future investigations on this topic, more sophisticated methods are needed to explore this question in more depth as well.
Long‐term statistical stability of industrial plants: Performance indicators and monitoring of an industrial pet plant (2013)

Abstract In the present work, usual statistical process control (SPC) definitions are reformulated to allow for long‐term analyses, giving rise to extended statistical process control (ESPC) procedures. In order to allow for implementation of the ESPC approach, t ‐ and F ‐control charts and monitoring indexes (NEPM, EPY and OEP) are designed in this work and are used to monitor the performance of a real industrial poly(ethylene terephthalate) (PET) site based on six process outputs (intrinsic viscosity, crystallinity, acetaldehyde concentration and colours a, b and L). As shown in this manuscript, ESPC tools allow for proper and systematic analysis of huge amounts of industrial data, using simple, fast and efficient statistical techniques, which can be used to improve the quality of the process operation in most industrial polymerisation plants.
Polymer-Supported Mukaiyama Reagent: A Useful Coupling Reagent for the Synthesis of Esters and Amides. (2005)

For Abstract see ChemInform Abstract in Full Text.
Broad-range, latchable reconfiguration of Bragg wavelength in optical gratings (1999)

Tunability of optical signal filters such as fiber Bragg gratings is important for high volume data communications. A magnetically tunable and latchable optical fiber Bragg grating structure has been devised, and a fine wavelength control as well as a broad-range wavelength tunability has been demonstrated. A spinodally decomposed, anisotropically elongated microstructure was induced in Fe–Cr–Co alloys to fabricate square-loop, programmable magnets. The adjustable attractive force between the magnetic poles was used to controllably strain the grating and induce a very large shift in the Bragg reflection wavelength by as much as 15 nm (which is equivalent to more than 36-channel span in a high density optical communication system). This novel approach can be useful not only for a variety of optical communication networking applications, but also for imparting latchable reconfiguration of structural periodicity and functional properties in a wide class of materials and devices.
Unicompartmental Knee Resurfacing: Enlarged Tibio-Femoral Contact Area and Reduced Contact Stress Using Novel Patient-Derived Geometries (2010)

Advances in imaging technology and computer-assisted design (CAD) have recently enabled the introduction of patient-specific knee implant designs that hold the potential to improve functional performance on the basis of patient-specific geometries, namely a patient-specific sagittal and coronal curvature, as well as enhanced bone preservation. The objective of this study was to investigate the use of a novel implant design utilizing a patient specific sagittal J-curve on the femoral component combined with a novel constant, patient-derived femoral coronal curvature and to assess tibio-femoral contact area and contact stress on a femur matched curved tibial polyethylene insert. Mean contact area and standard deviations were 81+/-5, 96+/-5 and 74+/-4 mm(2) for the heel strike, toe off and mid-stance positions, respectively. Mean contact stress and standard deviations were 23.83+/-1.39, 23.27+/-1.14 and 20.78+/-0.54 MPa for the heel strike, toe off and mid-stance positions, respectively. Standard deviations of the measurements were small, not exceeding 6-7% confirming the consistency of loading conditions across different flexion angles. The results were comparable to those reported for standard, off-the-shelf fixed-bearing implants with paired femoral and tibial geometries. These data show that a constant coronal curvature can be applied to a patient-specific implant by measuring coronal curvatures across the femoral condyle in each patient and by deriving an average curvature. This novel approach combines unique benefits of patient-specific geometry with proven design concepts for minimizing polyethylene wear.
Interleukin-10-mediated T cell apoptosis during the T helper type 2 cytokine response in murine Schistosoma mansoni parasite infection. (1997)

The pathogenesis of infection with the helminth parasite Schistosoma (S) mansoni in mice has been reported to involve a T helper (Th)1 to Th2 cytokine switch, associated with a pathogenic granulomatous response to parasite eggs and to a global defect in Th1-cell effector functions. Here we report that the Th2 cytokine response, which begins 6 weeks after infection, at the time of parasite egg laying (i) does not occur in the context of a genuine Th1 to Th2 cytokine switch, but is associated with a persistent capacity of Th1 (or Th0) cells to secrete IL-2 and IFN-gamma in response to T cell receptor (TCR) stimulation; (ii) is associated, in vitro, with spontaneous death by apoptosis of a significant fraction of the CD4 and CD8 T cells, which is greatly enhanced by TCR stimulation; and (iii) is associated, in vivo, with numerous and large clusters of apoptotic cells in the spleen and in the inflammatory infiltrates surrounding the parasite egg deposits in the liver. The in vitro addition of antibodies to the Th2 cytokine IL-10 had both a preventive effect on TCR-induced T cell apoptosis and an enhancing effect on TCR-induced T cell secretion of Th1 cytokines. Taken together, these findings suggest that the downregulation of Th1-cell-mediated effector functions in S. mansoni-infected mice may not be related to a lack of Th1 cell production, but to a process of IL-10-mediated and activation-induced premature T cell death, that include Th1 (or Th0) cells. Further identification of mechanisms involved in the regulation of T cell apoptosis has implications for the understanding of the pathogenesis of immunosuppression associated with chronic infectious diseases.
Wafer-level technology for integration of carbon nanotubes into micro-electro-mechanical systems (2016)

In this paper we present a holistic wafer-level manufacturing process for nanoscopic sensor devices based on individualized single-wall carbon nanotubes (SWCNTs) integrated in MEMS. The fabrication technology is demonstrated in detail. Moreover, a first application in form of a MEMS test stage for SWCNT strain and reliability experiments is shown.
Decentralized Probabilistic Frequency-Block Activation Control for Inter-Cell Interference Coordination and Traffic Load Balancing (2019)

We propose a decentralized probabilistic frequency-block activation control method for the cellular downlink. The aim of the proposed method is to increase the downlink system throughput within the system coverage by adaptively controlling the activation of each multiple frequency block at all base stations (BSs) to achieve inter-cell interference coordination (ICIC) and traffic load balancing effects. The proposed method does not rely on complicated inter-BS cooperation; it uses inter-BS cooperation only to share the temporal system throughput observed at the neighboring BSs. Based on the shared temporal system throughput information, each BS independently performs online activation control for the respective frequency blocks in a probabilistic manner, which autonomously achieves ICIC and load balancing effects among BSs. Computer simulation results, in which the mobility of the user terminals is taken into account, show the effectiveness of the proposed method.