gebhart/patrepeval huggingface dataset:
In Vivo Electrochemical Detection of Nitroglycerin‐Derived Nitric Oxide in Tumor‐Bearing Mice (2008)

Abstract The ability of an inserted electrode to detect in vivo NO in tumor was achieved by using a chemically modified Pt/Ir electrode as NO‐sensor and nitroglycerin NTG as NO donor. Enzymatically induced release of NO from NTG was tracked in the tumor, upon intra peritoneal injection of NTG. This approach allowed in vivo monitoring of the bioavailability of NO and could be applied to the in vivo study of candidate anticancer drugs acting on the NO pathways.
Astrocyte‐derived lipocalin‐2 mediates hippocampal damage and cognitive deficits in experimental models of vascular dementia (2017)

Lipocalin-2 (LCN2) has diverse functions in multiple pathophysiological conditions; however, its pathogenic role in vascular dementia (VaD) is unknown. Here, we investigated the role of LCN2 in VaD using rodent models of global cerebral ischemia and hypoperfusion with cognitive impairment and neuroinflammation. Mice subjected to transient bilateral common carotid artery occlusion (tBCCAo) for 50 min showed neuronal death and gliosis in the hippocampus at 7 days post-tBCCAo. LCN2 expression was observed predominantly in the hippocampal astrocytes, whereas its receptor was mainly detected in neurons, microglia, and astrocytes. Furthermore, Lcn2-deficient mice, compared with wild-type animals, showed significantly weaker CA1 neuronal loss, cognitive decline, white matter damage, blood-brain barrier permeability, glial activation, and proinflammatory cytokine production in the hippocampus after tBCCAo. Lcn2 deficiency also attenuated hippocampal neuronal death and cognitive decline at 30 days after unilateral common carotid artery occlusion (UCCAo). Furthermore, intracerebroventricular (i.c.v) injection of recombinant LCN2 protein elicited CA1-neuronal death and a cognitive deficit. Our studies using cultured glia and hippocampal neurons supported the decisive role of LCN2 in hippocampal neurotoxicity and microglial activation, and the role of the HIF-1α-LCN2-VEGFA axis of astrocytes in vascular injury. Additionally, plasma levels of LCN2 were significantly higher in patients with VaD than in the healthy control subjects. These results indicate that hippocampal damage and cognitive impairment are mediated by LCN2 secreted from reactive astrocytes in VaD.
Scalability upper limit estimation of silicon microring based configurable optical switches (2019)

International audience
Controlled coupling of single color centers to a photonic crystal cavity in monocrystalline diamond (2013)

Summary form only given. Deterministic coupling of a single emitter to a photonic crystal cavity is an important step towards the realization of integrated solid-state devices for quantum photonics. As single emitters, color centers in diamond, e.g. the Nitrogen-Vacancy (NV) center or the Silicon-Vacancy (SiV) center have attracted significant interest due to their extraordinary properties like long spin-coherence times or narrowband and bright single photon emission, respectively. For the realization of recent proposals like cavity-enhanced spin measurements or cavity-enhanced single photon sources, it is necessary to couple single color centers to a cavity with small mode volume and high quality factor. Photonic crystal cavities directly fabricated within a monocrystalline diamond membrane are well suited for this task, as they offer tiny mode volumes for efficient emitter-cavity coupling as well as scalable architectures for integrated photonic devices.In order to achieve controlled coupling of a color center to a photonic crystal cavity, several challenges have to be tackled, e.g. exact emitter positioning and alignment of its dipole moment with the cavity electric field as well as the ability for cavity tuning. For deterministic emitter-cavity positioning, two different routes can be pursued: In the first approach, a single emitter is localized within the diamond, its dipole orientation is determined and the cavity is subsequently structured around it. In the second approach, the cavity is fabricated first and a single color center is created within the cavity, e.g. via ion implantion or creation of vacancies. Here we present strategies to realize both methods for deterministic emitter-cavity coupling. For the first approach, we use a monocrystalline diamond film containing single SiV centers. Figure 1a) shows a fluorescence scan of a single SiV center with position markers next to it. The position markers are subsequently used to structure a photonic crystal cavity around the color center using focused ion beam milling [1]. Figures 1b) and c) show SEMimages before and after the cavity fabrication. The photonic crystal lattice constant a ≈ 283nm is chosen such that the cavity modes are red shifted with respect to the SiV emission lines. Using an oxidation tuning method, the cavity modes are tuned into resonance with the zero-phonon line at 740nm of a single SiV center (see Fig. 1d)). On resonance, we measure an intensity enhancement by a factor of 3.8 compared to the off-resonant case.
Flexible latex—polyaniline segregated network composite coating capable of measuring large strain on epoxy (2012)

International audience
Reactions of nitric oxide with tree and fungal laccase (1981)

The reactions of nitric oxide (NO) with the oxidized and reduced forms of fungal and tree laccase, as well as with tree laccase depleted in type 2 copper, are reported. The products of the reactions were determined by NMR and mass spectroscopy, whereas the oxidation states of the enzymes were monitored by EPR and optical spectroscopy. All three copper sites in fungal laccase are reduced by NO. In addition, NO forms a specific complex with the reduced type 2 copper. NO similarly reduces all of the copper sites in tree laccase, but it also oxidizes the reduced sites produced by ascorbate or NO reduction. A catalytic cycle is set up in which N2O, NO2-, and various forms of the enzyme are produced. On freezing of fully reduced tree laccase in the presence of NO, the type 1 copper becomes reoxidized. This reaction does not occur with the enzyme depleted in type 2 copper, suggesting that it involves intramolecular electron transfer from the type 1 copper to NO bound to the type 2 copper. When the half-oxidized tree laccase is formed in the presence of NO, a population of molecules exists which exhibits a type 3 EPR signal. A triplet EPR signal is also seen in the same preparation and is attributed to a population of the enzyme molecules in which NO is bound to the reduced copper of a half-oxidized type 3 copper site.
The KDK (potassium decay) experiment (2020)

Abstract Potassium-40 ( 40 K) is a background in many rare-event searches and may well play a role in interpreting results from the DAMA dark-matter search. The electron-capture decay of 40 K to the ground state of 40 Ar has never been measured and contributes an unknown amount of background. The KDK (potassium decay) collaboration will measure this branching ratio using a 40 K source, an X-ray detector, and the Modular Total Absorption Spectrometer at Oak Ridge National Laboratory.
mGluR5 and GABAA receptor‐specific parametric PET atlas construction—PET/MR data processing pipeline, validation, and application (2022)

The glutamate and γ-aminobutyric acid neuroreceptor subtypes mGluR<sub>5</sub> and GABA<sub>A</sub> are hypothesized to be involved in the development of a variety of psychiatric diseases. However, detailed information relating to their in vivo distribution is generally unavailable. Maps of such distributions could potentially aid clinical studies by providing a reference for the normal distribution of neuroreceptors and may also be useful as covariates in advanced functional magnetic resonance imaging (MR) studies. In this study, we propose a comprehensive processing pipeline for the construction of standard space, in vivo distributions of non-displaceable binding potential (BP<sub>ND</sub> ), and total distribution volume (V<sub>T</sub> ) based on simultaneously acquired bolus-infusion positron emission tomography (PET) and MR data. The pipeline was applied to [<sup>11</sup> C]ABP688-PET/MR (13 healthy male non-smokers, 26.6 ± 7.0 years) and [<sup>11</sup> C]Flumazenil-PET/MR (10 healthy males, 25.8 ± 3.0 years) data. Activity concentration templates, as well as V<sub>T</sub> and BP<sub>ND</sub> atlases of mGluR<sub>5</sub> and GABA<sub>A</sub> , were generated from these data. The maps were validated by assessing the percent error δ from warped space to native space in a selection of brain regions. We verified that the average δ<sub>ABP</sub> = 3.0 ± 1.0% and δ<sub>FMZ</sub> = 3.8 ± 1.4% were lower than the expected variabilities σ of the tracers (σ<sub>ABP</sub> = 4.0%-16.0%, σ<sub>FMZ</sub> = 3.9%-9.5%). An evaluation of PET-to-PET registrations based on the new maps showed higher registration accuracy compared to registrations based on the commonly used [<sup>15</sup> O]H<sub>2</sub> O-template distributed with SPM12. Thus, we conclude that the resulting maps can be used for further research and the proposed pipeline is a viable tool for the construction of standardized PET data distributions.
Enterobacteria-secreted particles induce production of exosome-like S1P-containing particles by intestinal epithelium to drive Th17-mediated tumorigenesis (2015)

Gut-associated inflammation plays a crucial role in the progression of colon cancer. Here, we identify a novel pathogen-host interaction that promotes gut inflammation and the development of colon cancer. We find that enteropathogenic bacteria-secreted particles (ET-BSPs) stimulate intestinal epithelium to produce IDENs (intestinal mucosa-derived exosome-like nanoparticles) containing elevated levels of sphingosine-1-phosphate, CCL20 and prostaglandin E2 (PGE2). CCL20 and PGE2 are required for the recruitment and proliferation, respectively, of Th17 cells, and these processes also involve the MyD88-mediated pathway. By influencing the recruitment and proliferation of Th17 cells in the intestine, IDENs promote colon cancer. We demonstrate the biological effect of sphingosine-1-phosphate contained in IDENs on tumour growth in spontaneous and transplanted colon cancer mouse models. These findings provide deeper insights into how host-microbe relationships are mediated by particles secreted from both bacterial and host cells.
Chemical topography analyses of silicon gates etched in HBr/Cl2/O2 and HBr/Cl2/O2/CF4 high density plasmas (2003)

We have used x-ray photoelectron spectroscopy (XPS) to analyze resist patterned silicon surfaces etched in a commercial 200 mm high density plasma etcher. After anisotropic etching using gate etching chemistries based on HBr/Cl2/O2 gas mixtures with or without CF4 addition, wafers are transferred under vacuum to perform chemical topography analysis using XPS in order to measure the element concentration on the silicon surfaces at the bottom of the trenches as well as the silicon sidewalls. Composition of the layers formed on the silicon sidewalls as a function of the plasma operating conditions is reported and discussed. The sidewall layer formation is mainly attributed to the oxidation of silicon etching by-products and the deposition of fluorocarbon species. Depending on the O2 and CF4 amount during a silicon gate main etch step, composition of the layer can be either SiOx-like or fluorocarbon rich. In all cases, the sidewall layer is transformed into a SiOx material during the subsequent fluorine free soft-landing step, as a result of the direct oxidation of silicon combined with the fluorocarbon species removal by oxygen in the plasma.
Preparation of Novel Gold Nanoparticles Modified with Thiol-Substituted Porphyrin and Their Properties (2008)

金ナノ粒子は, 生体に対する毒性が低く, 生体親和性を確保しやすい特徴をもっている。金ナノ粒子は単独では不安定なため, 安定性を確保するために生体親和性および癌細胞指向性の高いチオールポルフィリン化合物を設計・合成し, 金ナノ粒子の修飾を試みた。両者を結合させた化合物に電磁波を照射した場合, 発熱することが予測され, 有効な抗癌活性が期待できると考えた。ポルフィリン修飾型金ナノ粒子の粒子径制御では, 水素化ホウ素ナトリウム還元法およびクエン酸還元法を用い, 安定なポルフィリン修飾型金ナノ粒子を構築した。UV-visスペクトルおよび蛍光スペクトルを測定した結果, ポルフィリン修飾型金ナノ粒子の構築を確認した。また, 安定性の確認として, DLS測定を用いた擬似血中滞留試験を行った。誘電率測定により金ナノ粒子の発熱量を算出し, 調製したポルフィリン修飾型金ナノ粒子が温熱療法などにおいて有効な活性が期待できることが示唆された。
Faculty Opinions recommendation of Recycling of a regulatory protein by degradation of the RNA to which it binds. (2004)

When Bacillus subtilis is grown in the presence of excess tryptophan, transcription of the trp operon is regulated by binding of tryptophan-activated TRAP to trp leader RNA, which promotes transcription termination in the trp leader region. Transcriptome analysis of a B. subtilis strain lacking polynucleotide phosphorylase (PNPase; a 3'-to-5' exoribonuclease) revealed a striking overexpression of trp operon structural genes when the strain was grown in the presence of abundant tryptophan. Analysis of trp leader RNA in the PNPase(-) strain showed accumulation of a stable, TRAP-protected fragment of trp leader RNA. Loss of trp operon transcriptional regulation in the PNPase(-) strain was due to the inability of ribonucleases other than PNPase to degrade TRAP-bound leader RNA, resulting in the sequestration of limiting TRAP. Thus, in the case of the B. subtilis trp operon, specific ribonuclease degradation of RNA in an RNA-protein complex is required for recycling of an RNA-binding protein. Such a mechanism may be relevant to other systems in which limiting concentrations of an RNA-binding protein must keep pace with ongoing transcription. PMID: 14976255 Funding information This work was supported by: NIGMS NIH HHS, United States Grant ID: GM52840 NIGMS NIH HHS, United States Grant ID: GM48804
Fourier transform infrared spectroscopic imaging identifies early biochemical markers of tissue damage (2014)

Fourier Transform Infrared (FT-IR) spectroscopic imaging can allow for the rapid imaging of tissue biochemistry in a label-free and non-perturbing fashion. With the rapid adoption of new minimally invasive surgery (MIS) technologies over the last 20 years, adequate skill to safely and effectively use these technologies may not be achieved and risk of undue physical pressure being placed on tissues is a concern. Previous work has demonstrated that a number of histological stains can detect tissue damage, however, this process requires the initiation and progression of a signaling cascade that results in the epitope of interest being expressed. We proposed to identify the early biochemical markers associated with physical tissue damage from applied forces, thus not requiring transcriptional and translational protein synthesis as traditional immunohistochemistry does. To demonstrate that FT-IR can measure biochemical changes in tissues that have undergone physical force, we took ex-vivo lamb’s liver that had been freshly excised and applied varying levels of physical pressure (0kPa to 30kPa). Tissues were then formalin-fixed, paraffin-embedded, and sectioned on to glass for H and E staining to identify damage and on to an IR slide for FT-IR imaging. Regions of interest containing hepatocytes were identified and average FT-IR spectra were extracted from the damaged and undamaged livers. FT-IR spectra showed clear biochemical changes associated with tissue damage. In addition, chemical changes could be observed proceeding histological changes observed when using conventional staining approaches.
Fas/Apo [Apoptosis]-1 and Associated Proteins in the Differentiating Cerebral Cortex: Induction of Caspase-Dependent Cell Death and Activation of NF-κB (1999)

The developing cerebral cortex undergoes a period of substantial cell death. The present studies examine the role of the suicide receptor Fas/Apo[apoptosis]-1 in cerebral cortical development. Fas mRNA and protein are transiently expressed in subsets of cells within the developing rat cerebral cortex during the peak period of apoptosis. Fas-immunoreactive cells were localized in close proximity to Fas ligand (FasL)-expressing cells. The Fas-associated signaling protein receptor interacting protein (RIP) was expressed by some Fas-expressing cells, whereas Fas-associated death domain (FADD) was undetectable in the early postnatal cerebral cortex. FLICE-inhibitory protein (FLIP), an inhibitor of Fas activation, was also expressed in the postnatal cerebral cortex. Fas expression was more ubiquitous in embryonic cortical neuroblasts in dissociated culture compared to in situ within the developing brain, suggesting that the environmental milieu partly suppresses Fas expression at this developmental stage. Furthermore, FADD, RIP, and FLIP were also expressed by subsets of dissociated cortical neuroblasts in culture. Fas activation by ligand (FasL) or anti-Fas antibody induced caspase-dependent cell death in primary embryonic cortical neuroblast cultures. The activation of Fas was also accompanied by a rapid downregulation of Fas receptor expression, non-cell cycle-related incorporation of nucleic acids and nuclear translocation of the RelA/p65 subunit of the transcription factor NF-κB. Together, these data suggest that adult cortical cell number may be established, in part, by an active process of receptor-mediated cell suicide, initiated in situ by killer (FasL-expressing) cells and that Fas may have functions in addition to suicide in the developing brain.
Emulsion-based hydrogel phantoms for assessing boundary buildup and object detectability in photoacoustic imaging (2022)

Phantoms were designed to evaluate boundary buildup effect and object detectability. Tissue-mimicking materials simulating breast fat and parenchyma were prepared through emulsification of silicone oil, ethylene glycol and polyacrylamide hydrogel. Imaging targets were prepared by adding either India ink to the water phase or nigrosin to the oil phase. Phantom and inclusion molds were fabricated using an affordable 3D printer, yielding phantoms containing stepped-cylinder inclusions with 1-8 cm-1 optical absorption coefficients and 1-5 mm diameters. Maximum imaging depth depended on whether target boundary buildup or filled-in features were analyzed, with boundary buildup being more detectable.
Bayesian Recurrent Neural Networks (2017)

In this work we explore a straightforward variational Bayes scheme for Recurrent Neural Networks. Firstly, we show that a simple adaptation of truncated backpropagation through time can yield good quality uncertainty estimates and superior regularisation at only a small extra computational cost during training, also reducing the amount of parameters by 80\%. Secondly, we demonstrate how a novel kind of posterior approximation yields further improvements to the performance of Bayesian RNNs. We incorporate local gradient information into the approximate posterior to sharpen it around the current batch statistics. We show how this technique is not exclusive to recurrent neural networks and can be applied more widely to train Bayesian neural networks. We also empirically demonstrate how Bayesian RNNs are superior to traditional RNNs on a language modelling benchmark and an image captioning task, as well as showing how each of these methods improve our model over a variety of other schemes for training them. We also introduce a new benchmark for studying uncertainty for language models so future methods can be easily compared.
CurIAs: Current-Based IC Authentication by Exploiting Supply Current Variations (2022)

Physical unclonable functions (PUFs) have emerged as one of the most notable hardware primitives to mitigate the ever-growing global issue of counterfeiting and cloning of integrated circuits (ICs) in recent times. PUFs exploit the intrinsic manufacturing process-induced parametric variations for generating unique chip identifiers. However, most of the existing PUF implementations require complex structures or the inclusion of additional components, which incur performance and area overheads. In this work, we introduce <i>CurIAs</i> , a supply current-based novel PUF implementation to authenticate ICs and to protect them from counterfeiting attacks. It exploits the dynamic current stemming from temporal switching activities in existing on-chip structures as an entropy source to generate high-quality IC-specific digital signatures. First, we investigate the source of the entropy of this PUF, <i>i.e.</i> , the dynamic current variations in different circuit structures, with transistor-level Monte-Carlo simulations in HSPICE. Next, to evaluate its effectiveness in Silicon, we apply this approach to map LFSR (Linear Feedback Shift Register) designs into 20 FPGA chips (fabricated in TSMC 55nm process node), perform practical measurements, and generate digital signatures. These signatures show high uniqueness, robustness, uniformity, and randomness features, and the overall implementation requires modest hardware overhead ( <inline-formula><tex-math notation="LaTeX">$&lt;$</tex-math></inline-formula> 1%). We assess and substantiate the robustness of this approach at eight different operating points by varying supply voltage and temperature. Furthermore, we upscale the design to more extended LFSR sizes, and it exhibits a constant trend of performance improvement over the operating points. Through a judicious selection of challenge vectors, <i>CurIAs</i> demonstrates a high resilience against model learning attacks, with an average prediction accuracy of 50%. These intrinsic variations in supply current across ICs for varying workloads entail unique chip-specific signatures, which are extremely difficult to clone, and can be deployed effectively against IC counterfeiting issues.
On the distance distribution of duals of BCH codes (1999)

We derive upper bounds on the components of the distance distribution of duals of BCH codes. Roughly speaking, these bounds show that the distance distribution can be upper-bounded by the corresponding normal distribution. To derive the bounds we use the linear programming approach along with some estimates on the magnitude of Krawtchouk polynomials of fixed degree in a vicinity of q/2.
Experimental Evaluation of Liquid Immersed Electronics for High Density Power Converters (2023)

Advancements in power electronics, such as wide band gap semiconductors, are pushing package size reduction and higher power density through higher switching frequency operation, but continued growth requires innovation in the areas of high voltage circuit design and thermal management. High voltage component and circuit design is dictated by creepage and clearance standards for operation in ambient air. This paper presents initial experimental results utilizing an electrically insulating liquid, Cargill FR3, to provide protection against electric field breakdown in submerged electronics. This will allow for new design standards and opportunity for increasing power density and smaller footprints. Second, it is proposed that immersion in the insulating FR3 fluid will also work to improve thermal power dissipation of electronics. Preliminary results of the thermal performance of a heat-sink-free GaN inverter immersed in FR3 are included in this work.
Visually testing recursive programs in spreadsheet languages (2001)

Although there has been recent research into ways to design visual programming languages and environments, little attention has been given to systematic testing in these languages, and what work has been done does not address "power" features such as recursion. In this paper, we discuss two possible ways the "What You See Is What You Test" methodology could be extended to accommodate recursion. The approaches are presented in terms of their testing theoretic aspects and then implementation strategies and algorithms. Since the goal is to help the people using these languages, we also present an empirical study and use its results to inform our choice as to which of the two approaches to adopt.
Measuring visual field progression in the Early Manifest Glaucoma Trial (2003)

The average amount of field deterioration needed to reach EMGT visual field progression has been measured and expressed in more conventional units (i.e. a loss of about - 2dB in MD and an increase in about five highly significant points). These estimates will facilitate the clinical interpretation of the results of EMGT.