gebhart/patrepeval huggingface dataset:
Dietary Isothiocyanate-induced Apoptosis via Thiol Modification of DNA Topoisomerase IIα (2011)

Studies in animal models have indicated that dietary isothiocyanates (ITCs) exhibit cancer preventive activities through carcinogen detoxification-dependent and -independent mechanisms. The carcinogen detoxification-independent mechanism of cancer prevention by ITCs has been attributed at least in part to their ability to induce apoptosis of transformed (initiated) cells (e.g. through suppression of IκB kinase and nuclear factor κB as well as other proposed mechanisms). In the current studies we show that ITC-induced apoptosis of oncogene-transformed cells involves thiol modification of DNA topoisomerase II (Top2) based on the following observations. 1) siRNA-mediated knockdown of Top2α in both SV40-transformed MEFs and Ras-transformed human mammary epithelial MCF-10A cells resulted in reduced ITC sensitivity. 2) ITCs, like some anticancer drugs and cancer-preventive dietary components, were shown to induce reversible Top2α cleavage complexes in vitro. 3) ITC-induced Top2α cleavage complexes were abolished by co-incubation with excess glutathione. In addition, proteomic analysis revealed that several cysteine residues on human Top2α were covalently modified by benzyl-ITC, suggesting that ITC-induced Top2α cleavage complexes may involve cysteine modification. Interestingly, consistent with the thiol modification mechanism for Top2α cleavage complex induction, the thiol-reactive selenocysteine, but not the non-thiol-reactive selenomethionine, was shown to induce Top2α cleavage complexes. In the aggregate, our results suggest that thiol modification of Top2α may contribute to apoptosis induction in transformed cells by ITCs.
Trends in PON - fiber/wireless convergence and software-defined transmission and networking (2015)

We review recent advances in the field of passive optical networks (PONs), and discuss the future trends including fiber/wireless convergence based on mobile fronthauling, as well as software-defined access networking and transmission based on flexible modulation, detection and digital signal processing.
157-nm imaging using thick single-layer resists (2001)

During the past year the probability that 157 nm lithography will precede next generation lithographies such as EUV or EPL has increased, partly due to encouraging advances in the design of polymeric materials, which have sufficient transparency at 157 nm to serve as platforms for single layer photoresists. We have identified several fluorinated resins which can be developed in aqueous 0.26 N TMAH, have reasonable etch resistances (comparable to poly-parahydroxystyrene), and can be formulated to yield photoresists with optical absorbancies at 157 nm which are low enough to be used at thicknesses of 150-200 nm. We have imaged a number of these formulated resists at 157 nm with the Exitech microstepper at International Sematech, and the results for formulated resists with optical absorption coefficients (base 10) as low as 2.1 per micron are described.
Dendritic Cell-Dependent Inhibition of B Cell Proliferation Requires CD22 (2008)

Recent studies have shown that dendritic cells (DCs) regulate B cell functions. In this study, we report that bone marrow (BM)-derived immature DCs, but not mature DCs, can inhibit BCR-induced proliferation of B cells in a contact-dependent manner. This inhibition is overcome by treatment with BAFF and is dependent on the BCR coreceptor CD22; however, it is not dependent on expression of the CD22 glycan ligand(s) produced by ST6Gal-I sialyltransferase. We found that a second CD22 ligand (CD22L) is expressed on CD11c(+) splenic and BM-derived DCs, which does not contain ST6Gal-I-generated sialic acids and which, unlike the B cell-associated CD22L, is resistant to neuraminidase treatment and sodium metaperiodate oxidation. Examination of splenic and BM B cell subsets in CD22 and ST6Gal-I knockout mice revealed that ST6Gal-I-generated B cell CD22L plays a role in splenic B cell development, whereas the maintenance of long-lived mature BM B cells depends only on CD22 and not on alpha2,6-sialic acids produced by ST6Gal-I. We propose that the two distinct CD22L have different functions. The alpha2,6-sialic acid-containing glycoprotein is important for splenic B cell subset development, whereas the DC-associated ST6Gal-I-independent CD22L may be required for the maintenance of long-lived mature B cells in the BM.
A 678-<inline-formula> <tex-math notation="LaTeX">$\mu$ </tex-math> </inline-formula>W Frequency-Modulation-Based ADC With 104-dB Dynamic Range in 44-kHz Bandwidth (2018)

This brief presents a frequency-modulation-based analog-to-digital converter (FM ADC) that takes advantage of the coding gain resulting from bandwidth expansion in the analog domain of FM systems to achieve high dynamic range and incorporates a highly digital demodulation approach for power efficiency. The novel architecture employs a sinusoidal output voltage-controlled oscillator (VCO), a relatively low-resolution successive approximation register ADC to sample signals in the FM domain, and then a digital signal processing FM demodulator to recover high-resolution samples of the VCO's original analog input. The proposed ADC is implemented in 0.5-mm<sup>2</sup> of 65-nm CMOS; it achieves 104-dB DR, 99-dB SNR, and 71-dB SNDR in a 44-kHz bandwidth while dissipating 678 <i>μ</i>W of power. The architecture of the FM ADC leverages analog domain processing for system performance and digital domain processing for lower power. This novel approach presents a viable alternative to delta-sigma converters for high dynamic range conversion in advanced process nodes.
Ion transport in copolymers of oligo(oxyethylene) methacrylates with monomers having polar group (1992)

Abstract Copolymers of oligo(oxyethylene) methacrylates and a series of polar comonomers, i.e. acrylamide, acrylonitrile and maleic anhydride, were synthesized as media for dual‐ or single‐ion conduction, and correlation between polymer structure and properties was established through detailed studies on polymer morphology, mechanical property and the ion transport process. Polar groups in the polymer chain sequence were found to enhance matrix polarity and to retard oligoether crystallization, as well as to raise chain rigidity. Therefore, both novel dual‐ and single‐ion conduction are realized, with a simultaneous improvement in the mechanical properties of polymer materials. An investigation about the effect of matrix polarity on the ion transport process is also carried out, making use of the concepts concerning polymer segmental relaxation. Hence the enhanced matrix polarity is found to contribute to the improvement in ion conduction, mainly through its promotion of salt dissociation. However, at high temperature this facilitation is counteracted due to the “anomalous” temperature‐dependence of salt dissociation in the polymer matrix, and the higher the matrix polarity, the more drastic is the drop in carrier number with rising temperature.
Cellular Mechanisms (2018)

<strong>4.1 Inflammation</strong> Lim and co-workers found that 635-nm light irradiation at low power can lead to an anti-inflammatory effect by inhibiting prostaglandin E2 (PGE2) production and cyclo-oxygenase 1 and 2 (COX-1 and COX-2) mRNA expression. The light irradiation was able to decrease intracellular ROS, which mediates the expression of calcium-dependent phospholipase A2 (cPLA2), secretory phospholipase A2 (sPLA2), and COX-2, as well as inhibiting the release of PGE2. PGE2 synthesis is dependent on NF-&kappa;B modulation of the cellular signaling mechanism. NF-&kappa;B is found in the cytosol in its dimeric form of NF-&kappa;B/I&kappa;B (the latter is an inhibitory protein). Pro-inflammatory stimuli, such as LPS, can activate the NF-&kappa;B upstream signaling regulator I&kappa;B kinase (IKK), which is responsible for the phosphorylation and degradation of I&kappa;B. The free NF-&kappa;B is translocated to the nucleus and induces the expression of pro-inflammatory genes. Lim demonstrated that 635-nm light irradiation suppresses the release of PGE2, possibly through a mechanism related to the inhibition of the NF-&kappa;B pathway. It did not affect the phosphorylation of I&kappa;B, IKK, and NF-&kappa;B in HSP27-silenced human gingival fibroblasts (hGFs), suggesting that NF-&kappa;B modulation by 635-nm light through HSP27 is required for the down-regulation of pro-inflammatory gene expression in these fibroblasts.
In vivo, vascularized, functional, 3-dimensional cardiac tissue engineering (2004)

Birla, Ravi K. PhD; Borschel, Gregory H. MD; Dennis, Robert G. PhD; Brown, David L. MD, FACS Author Information
Membrane trafficking of the cystic fibrosis gene product, cystic fibrosis transmembrane conductance regulator, tagged with green fluorescent protein in Madin-Darby canine kidney cells. (1998)

The following grant number was omitted: National Institutes of Health Grant DK-53090 (to Dr. Dale Benos, PI).
A Rate-Splitting Strategy to Enable Joint Radar Sensing and Communication with Partial CSIT (2021)

In order to manage the increasing interference between radar and communication systems, joint radar and communication (RadCom) systems have attracted increased attention in recent years, with the studies so far considering the assumption of perfect Channel State Information at the Transmitter (CSIT). However, such an assumption is unrealistic and neglects the inevitable CSIT errors that need to be considered to fully exploit the multi-antenna processing and interference management capabilities of a joint RadCom system. In this work, a joint RadCom system is designed which marries the capabilities of a Multiple-Input Multiple-Output (MIMO) radar with Rate-Splitting Multiple Access (RSMA), a powerful down-link communications scheme based on linearly precoded Rate-Splitting (RS) to partially decode multi-user interference (MUI) and partially treat it as noise. In this way, the RadCom precoders are optimized in the presence of partial CSIT to simultaneously maximize the Average Weighted Sum-Rate (AWSR) under QoS rate constraints and minimize the RadCom Mean Squared Error (MSE) against an ideal MIMO radar beampattern. Simulation results demonstrate that RSMA provides the RadCom with more robustness, flexibility and user rate fairness compared to the baseline joint RadCom system based on Space Division Multiple Access (SDMA).
Polymer Filling of Silicon Trenches for 3-D Through Silicon vias Applications (2011)

Ring-shaped silicon trenches with a depth of 50 were filled with different spin-on dielectric (SOD) polymers. Ultimately, the polymer should serve as deep trench isolation layers, also called liners, for 3-D wafer-level packaging through silicon vias (TSVs). TSVs allow the vertical stacking and interconnection of multiple devices. 3-D packaging is an emerging technology that can be an alternative solution to scaling issues in complementary metal oxide semiconductors. SODs with different electrical, chemical, and mechanical properties were tested. The filling was conducted using spin coating, which is a readily available technology. In order to improve the filling performances, a prewetting solvent was applied prior to coating. Contact angle measurements were carried out to assess the polymer wetting properties. Without prewetting, it was observed that too high an affinity for the wafer surface was probably detrimental. With prewetting, the wetting was improved but this did not significantly modify the filling itself. The filling was rather improved due to the mechanical action of the solvent. Overall, most of the SOD could successfully fill the trenches, however, stress-related delamination could almost always be detected at the polymer/silicon interface. A stress study was carried out by finite element modeling in order to address the delamination issue. It was concluded that the level of stress is mainly governed by the cure temperature and other mechanical properties. This paper concludes with some recommendations on the choice of an SOD for filling applications.
Deep Tensor Convolution on Multicores (2016)

Deep convolutional neural networks (ConvNets) of 3-dimensional kernels allow joint modeling of spatiotemporal features. These networks have improved performance of video and volumetric image analysis, but have been limited in size due to the low memory ceiling of GPU hardware. Existing CPU implementations overcome this constraint but are impractically slow. Here we extend and optimize the faster Winograd-class of convolutional algorithms to the $N$-dimensional case and specifically for CPU hardware. First, we remove the need to manually hand-craft algorithms by exploiting the relaxed constraints and cheap sparse access of CPU memory. Second, we maximize CPU utilization and multicore scalability by transforming data matrices to be cache-aware, integer multiples of AVX vector widths. Treating 2-dimensional ConvNets as a special (and the least beneficial) case of our approach, we demonstrate a 5 to 25-fold improvement in throughput compared to previous state-of-the-art.
8.5-fm resonances in an amplified slow-light fiber Bragg grating for high-precision metrology (2020)

Fiber Bragg gratings (FBGs) with strong apodized index modulations behave like an in-line Fabry-Perot interferometer and exhibit a series of narrow resonances in the short-wavelength portion of their transmission spectrum. These resonances have proven invaluable for detecting extremely small strains (30-femtostrain/√Hz level) or temperature changes (millidegreeC/√Hz level). The sensitivity of these fiber sensors is limited by the linewidth and peak transmission of the resonance used to interrogate the sensor, which are themselves limited by the intrinsic loss of the grating. In this work, significantly narrower and stronger resonances are demonstrated by introducing a small amount of optical gain in the FBG to offset the intrinsic loss and create a resonator with a much smaller net internal loss. The fiber Bragg grating is written in an Er-doped single-mode fiber and optically pumped to provide the required gain. The device reported here is a 6.5-mm grating with an AC index modulation of 1.59×10<sup>-3</sup>. With only 30 μW of pump power absorbed by the grating (32.6 mW launched), the fundamental resonance of the FBG was observed to narrow from 737 fm in the absence of pump to a record linewidth of 8.5 fm. The measured peak transmission of the resonance improved from ~-37 dB to -0.2 dB. A new model that predicts the slow-light resonance spectrum of a slow-light grating in the presence of optical gain is presented. This model is in good quantitative agreement with the measured evolution of the resonance linewidth as the pump power and the power of the laser that probes the resonance lineshape are varied.
The Global Health Equity Clinical Immersion (HECI); An Innovation in Remote International Placements (2020)

<b>Background:</b> Each year hundreds of medical students pursue electives in resource poor settings, globally.<br/>This “rite of passage” has been criticized as “Students practising on the poor”. At Bond University in Australia we developed a new multidisciplinary clinical placement model in Kira Kira, Solomon Islands in 2013; which has now been replicated in five resource poor settings internationally. It demonstrates how students from multiple disciplines can gain a transformational personal experience and have a positive impact on the host communities.<br/><b>Summary of Work:</b> We selected five sites where students can complete a HECI – Napranam and Port Hedland-Australia; Kira Kira- Solomon Islands; Gujarat-India and Cape Town- South Africa. Partnership agreements and regular visits by academics underpin each site. Comprehensive pre-departure preparation<br/>includes a global health module, 6 hours of tutorials providing site specific cultural, epidemiological and risk management knowledge. A new model of peer to peer supervision has been developed and successfully implemented as part of the HECI. A common case-based assessment for medical students is<br/>used to compare the health care systems, observe health equity issues and identify sustainable development goals.<br/><b>Summary of Result</b>s: In 2020, sixty medical students from a cohort of 104 will complete a HECI at above sites, and thirty from Law, Urban Planning and Allied Health will complete a work integrated placement in Solomon Islands. Student evaluations demonstrate these placements as the highest rated and<br/>transformative personal experience their respective degree program. The program has achieved national recognition by winning the Australian University Award for Global Citizenship 2019; and resulted in 20 students attaining a publication.<br/><b>Discussion and Conclusions:</b> The overseas elective is an under-utilized curriculum opportunity for health professional students to gain a deep understanding of global health issues. The HECI model could be implementable by any health professional program at a range of sites. <b>Take-Home Messages</b>: The HECI program is an innovative health care clinical immersion that has delivered sustained outcomes over seven years. The program inspires young graduates to consider a future where<br/>they might choose to help those communities most in need and thus make a sustainable difference, globally.<br/>
Syk, a novel therapeutic target for PTLD, drives Epstein Barr Virus B cell lymphoma growth and survival through the PI3K/Akt pathway (141.23) (2009)

Abstract Post-transplant lymphoproliferative disorder (PTLD)-associated Epstein Barr Virus (EBV)+ B cell lymphomas are a serious, and often fatal, complication of solid organ and bone marrow transplantation. In EBV+ PTLD, latent membrane protein 2a (LMP2a), a mimic of the B cell receptor, provides a constitutive survival signal to latently infected cells. This signal is transmitted through the sequestering and activation of Lyn and Syk and subsequent activation of downstream survival pathways. We hypothesized that inhibition of Syk activity would diminish growth of EBV+ B cell lymphoma lines derived from patients with PTLD. Treatment with R406, a novel Syk inhibitor, decreased proliferation and induced apoptosis of PTLD lines. While the NFkB and p38 pathways were unaffected after PTLD lines were treated with R406, both the Akt and Erk pathways were inhibited. Akt is constitutively active in these cells, and treatment with R406 led to decreased Akt-dependent autocrine IL-10 secretion. These data indicate that Syk mediates its effects on EBV+ PTLD growth and survival through activation of the PI3K/Akt pathway. Syk inhibitors, such as R406, may serve as an effective therapeutic strategy for EBV+ PTLD.
Document similarity measures and document browsing (2011)

Managing large document databases is an important task today. Being able to automatically com- pare document layouts and classify and search documents with respect to their visual appearance proves to be desirable in many applications. We measure single page documents' similarity with respect to distance functions between three document components: background, text, and saliency. Each document component is represented as a Gaussian mixture distribution; and distances between dierent documents' components are calculated as probabilistic similarities between corresponding distributions. The similarity measure between documents is represented as a weighted sum of the components' distances. Using this document similarity measure, we propose a browsing mechanism operating on a document dataset. For these purposes, we use a hierarchical browsing environment which we call the document similarity pyramid. It allows the user to browse a large document dataset and to search for documents in the dataset that are similar to the query. The user can browse the dataset on dierent levels of the pyramid, and zoom into the documents that are of interest.
Review of formulation strategies for optimizing the morphology of polymeric bulk heterojunction organic solar cells (2014)

International audience
Estimation of the Risk of Thrombocytopenia in the Offspring of Pregnant Women with Presumed Immune Thrombocytopenic Purpura (1990)

The absence of a history of immune thrombocytopenic purpura or the presence of negative results on circulating-antibody testing in pregnant women indicates a minimal risk of severe neonatal thrombocytopenia in their offspring.
KTeXpand – a novel microfluidic device for advanced cell based cross matching (2022)

Abstract Antibody-mediated rejection after kidney transplantation is a major limitation for long-term survival of donated kidneys within the recipient allograft. With the existing HLA cross-matching test only complement activating donor specific antibodies are evaluated. Other measurements are more sensitive, but cannot assert the clinical relevance of the donor specific antibodies. Thus, novel methods that address the more complex nature of cellular interactions with serum components are needed to improve antibody-mediated rejection prediction. Recent studies suggest, that the interaction of natural killer cells of the recipient with endothelial cells of the donor is of major interest. Here we present a microfluidic cell culture device and a corresponding assay to test for the relevance of natural killer cell activated antibody-mediated rejection in vitro. Therefore, a protocol to co-cultivate both cell types and track natural killer cell activated killing within a fluorescence-based assay was established. To automate this approach, the prototype of a well plate sized microfluidic device was developed, that enables staining of the two cell types and repeatable and timedependent co-cultivation of the cells with serum. This automated approach enables further evaluation of the clinical relevance of the established assay paving the way to additional information on HLA cross-matching that helps to quickly estimate the probability of Antibody-mediated rejection and the clinical relevance of donor specific antibodies.
Oligomeric status of human cystathionine beta‐synthase modulates AdoMet binding (2016)

Cystathionine beta-synthase (CBS) plays a key role in the metabolism of sulfur-containing amino acids. CBS is a multidomain tetrameric enzyme allosterically activated by S-adenosylmethionine (AdoMet). Recent crystallographic analyses of engineered CBS lacking the loop made up of residues 516-525 revealed discrepancies in AdoMet binding compared to previous biophysical studies on a full-length CBS. Here, we show that removal of the loop 516-525 functionally eliminates the high affinity sites responsible for kinetic stabilization of the full-length enzyme and yields a dimeric AdoMet-inducible enzyme, in which kinetic stabilization is now exerted by AdoMet binding to the remaining low affinity sites.