gebhart/patrepeval huggingface dataset:
Cerebral expression of multiple cytokine genes in mice with lymphocytic choriomeningitis. (1994)

The simultaneous expression of multiple cytokine genes was examined within the brain and peripheral organs of euthymic and congenic athymic mice during the course of lymphocytic choriomeningitis (LCM) induced by the intracranial inoculation of LCM virus. In euthymic mice, levels of TNF-alpha, IL-1 alpha, IL-6, and IL-1 beta mRNA in the brain increased early in infection and further increased with the progression of disease; the level of IFN-gamma mRNA was expressed at high levels late in infection and correlated with the onset of clinical disease. In the peripheral organs, TNF-alpha, IL-1 alpha, and IL-1 beta gene expression predominated early and then declined late in disease. In athymic mice (which do not develop LCM), expression of TNF-alpha, IL-1 alpha, IL-6, and IL-1 beta mRNA increased progressively in brain and peripheral organs from days 3 to 6 postinfection. The levels of these transcripts were significantly lower than those in infected euthymic animals. In euthymic mice, in situ hybridization revealed IFN-gamma-, TNF-alpha-, and IL-1 alpha-expressing cells throughout the inflammatory cell infiltrates associated with areas of LCMV nucleic acid. Therefore, in mice with LCM there is simultaneous expression of multiple cytokine genes, the pattern of which is distinct for brain vs peripheral organs and for euthymic vs athymic mice. The close spatiotemporal relationship between expression of cytokine genes and evolution of disease in brain implicate cytokines are not only key coordinators of the host response but also as possible mediators of neuropathology in LCM.
Incoherent Bright Field STEM for Imaging and Tomography of Ultra-Thick TEM Cross-sections (2009)

Extended abstract of a paper presented at Microscopy and Microanalysis 2009 in Richmond, Virginia, USA, July 26 – July 30, 2009
Transition state docking: A probe for noncovalent catalysis in biological systems. Application to antibody‐catalyzed ester hydrolysis (2001)

A strategy for pinpointing favorable noncovalent interactions between transition states and active sites of biological catalysts is described. This strategy combines high-level quantum mechanical calculations of transition state geometries with an automated docking procedure using AutoDock. By applying this methodology to antibody-catalyzed hydrolyses of aryl esters (by the 48G7, CNJ206, and 17E8 families of antibodies), varying levels of catalysis are explained in terms of specific hydrogen bonding interactions between combining site residues and transition states. Although these families of antibodies were produced in separate experiments by different researchers using related but different haptens, the mechanism of transition state stabilization appears to be highly conserved. Despite being elicited in response to anionic phosphonate haptens, the best catalysts often utilize hydrogen bond acceptors to stabilize transition states. A mutant of antibody CNJ206, designed based on this observation and predicted to be a better catalyst, is proposed. In the case of antibody 48G7, affinity maturation is shown to produce a catalyst that is highly selective for one of two enantiomeric transition states from a nonselective germline precursor.
Perichondrial progenitor cells promote proliferation and chondrogenesis of mature chondrocytes (2022)

Autologous chondrocytes (C cells) are effective sources of cell therapy for engineering cartilage tissue to repair chondral defects, such as degenerative arthritis. The expansion of cells with C cell characteristics has become a major challenge due to inadequate donor sites and poor proliferation of mature C cells. The perichondrial progenitor cells (P cells) from the cambium layer of the perichondrium possessed significantly higher mesenchymal stem cell markers than C cells. In the transwell co-culture system, P cells increased the passaging capacity of C cells from P6 to P9, and the cell number increased 128 times. This system increased the percentage of Alcian blue-positive C cells from 40% in P6 to 62% in P9, contributing about 198 times more Alcian blue-positive C cells than the control group. C cells co-cultured with P cells also exhibited higher proliferation than C cells cultured with P cell-conditioned medium. Similar results were obtained in nude mice that were subcutaneously implanted with C cells, P cells or a mixture of the two cell types, in which the presence of both cells enhanced neocartilage formation <i>in vivo</i>. In aggregate, P cells enhanced the proliferation of C cells in a dose-dependent manner and prolonged the longevity of mature C cells for clinical applications.
Modelling of symmetric solid oxide cell to operate in steam electrolysis mode (2011)

International audience
Linear accelerator radiosurgery in the management of brain tumours (2000)

Radiosurgery is an increasingly popular method for treating a variety of intracranial tumours. A great deal of treatment data has been accumulated suggesting that radiosurgery may be the treatment of choice for small acoustic schwannomas. Moreover, radiosurgery promises excellent tumour control and minimal risk in the treatment of small meningiomas in risky surgical locations such as the cavernous sinus. Radiosurgery offers superior local control rates for many metastatic neoplasms and has promise as an adjuvant 'boost' technique in certain malignant gliomas. This article presents a brief description of the linear accelerator, LINAC, radiosurgical technique, followed by a review of the more common applications of stereotactic radiosurgery in the treatment of intracranial neoplastic disease.
Microwave modeling and validation in food applications (2006)

The location of the center of gravity of a rigid lens influences its on-eye centration and stability more so than does lens mass.
A Cryptographic Keys Transfer Protocol for Secure Communicating Systems (2010)

This paper describes a new key forwarding protocol for networks messages exchange which guaranties both authentication of participants and forward security. The protocol lies within the framework of a keys derivation scheme used for spanning tree-based networks messages diffusion where compromising a key in a node involves compromising all derived keys in the corresponding sub tree. A complete specification and full proof of the protocol will be subject of a longer forthcoming conjoint paper.
Identification and Quantification of a Phytotoxic Metabolite from Alternaria dauci (2020)

<i>Alternaria dauci</i> is the causal agent of <i>Alternaria</i> leaf blight (ALB) in carrot (<i>Daucus carota</i>) crops around the world. However, to date, <i>A. dauci</i> has received limited attention in its production of phytotoxic metabolites. In this investigation, the bioassay-guided isolation of the extract from liquid cultures of <i>A. dauci</i> resulted in the isolation of two metabolites identified as <i>α</i>-acetylorcinol (<b>1</b>) and <i>p</i>-hydroxybenzoic acid (<b>2</b>), based on their spectroscopic data and results from chemical correlation reactions. Testing of both metabolites in different assays showed an important phytotoxic activity for <i>p</i>-hydroxybenzoic acid (<b>2</b>) when tested in the leaf-spot assay on parsley (<i>Petroselinum crispum</i>), in the leaf infiltration assay on tobacco (<i>Nicotiana alata</i>) and marigold (<i>Tagetes erecta</i>), and in the immersion assay on parsley and parsnip (<i>Pastinaca sativa</i>) leaves. Quantification of the two metabolites in the crude extract of <i>A. dauci</i> kept at different times showed that <i>p</i>-hydroxybenzoic acid (<b>2</b>) is one of the first metabolites to be synthesized by the pathogen, suggesting that this salicylic acid derivative could play an important role in the pathogenicity of the fungus.
ChemInform Abstract: Use of Aryl Chlorides as Electrophiles in Pd‐Catalyzed Alkene Difunctionalization Reactions. (2010)

Abstract An efficient method to prepare pyrrolidines, pyrazolidines, isoxazolidines, imidazolidinones, and tetrahydrofurans is reported.
Quantifying In Vitro Growth and Metabolism Kinetics of Human Mesenchymal Stem Cells Using a Mathematical Model (2009)

Better quantitative understanding of human mesenchymal stem cells (hMSCs) metabolism is needed to identify, understand, and subsequently optimize the processes in expansion of hMSCs in vitro. For this purpose, we analyzed growth of hMSCs in vitro with a mathematical model based on the mass balances for viable cell numbers, glucose, lactate, glutamine, and glutamate. The mathematical modeling had two aims: (1) to estimate kinetic parameters of important metabolites for hMSC monolayer cultures, and (2) to quantitatively assess assumptions on growth of hMSCs. Two cell seeding densities were used to investigate growth and metabolism kinetics of MSCs from three human donors. We analyzed growth up to confluency and used metabolic assumptions described in literature. Results showed a longer initial phase, a slower growth rate, and a higher glucose, lactate, glutamine, and glutamate metabolic rates at the lower cell seeding density. Higher metabolic rates could be induced by a lower contact inhibition effect when seeding at 100 cells/cm2 than when seeding at 1000 cells/cm2. In addition, parameter estimation describing kinetics of hMSCs in culture, depending on the seeding density, showed doubling times in the order of 17-32h, specific glucose consumption in the order of 1.25 x 10(-1) to 3.77 x 10(-1) pmol/cell/h, specific lactate production in the order of 2.48 x 10(-1) to 7.67 x 10(-1)pmol/cell/h, specific glutamine production in the order of 7.04 x 10(-3) to 2.27 pmol/cell/h, and specific glutamate production in the order of 4.87 x 10(-1) to 23.4 pmol/cell/h. Lactate-to-glucose yield ratios confirmed that hMSCs use glucose via anaerobic glycolysis. In addition, glutamine and glutamate metabolic shifts were identified that could be important for understanding growth of hMSCs in vitro. This study showed that the mathematical modeling approach supports quantitative analysis of important mechanisms in proliferation of hMSCs in vitro.
Reductions of Aliphatic and Aromatic Nitriles to Primary Amines with Diisopropylaminoborane (2009)

Diisopropylaminoborane [BH(2)N(iPr)(2)] in the presence of a catalytic amount of lithium borohydride (LiBH(4)) reduces a large variety of aliphatic and aromatic nitriles in excellent yields. BH(2)N(iPr)(2) can be prepared by two methods: first by reacting diisopropylamineborane [(iPr)(2)N:BH(3)] with 1.1 equiv of n-butyllithium (n-BuLi) followed by methyl iodide (MeI), or reacting iPrN:BH(3) with 1 equiv of n-BuLi followed by trimethylsilyl chloride (TMSCl). BH(2)N(iPr)(2) prepared with MeI was found to reduce benzonitriles to the corresponding benzylamines at ambient temperatures, whereas diisopropylaminoborane prepared with TMSCl does not reduce nitriles unless a catalytic amount of a lithium ion source, such as LiBH(4) or lithium tetraphenylborate (LiBPh(4)), is added to the reaction. The reductions of benzonitriles with one or more electron-withdrawing groups on the aromatic ring generally occur much faster with higher yields. For example, 2,4-dichlorobenzonitrile was successfully reduced to 2,4-dichlorobenzylamine in 99% yield after 5 h at 25 degrees C. On the other hand, benzonitriles containing electron-donating groups on the aromatic ring require refluxing in tetrahydrofuran (THF) for complete reduction. For instance, 4-methoxybenzonitrile was successfully reduced to 4-methoxybenzylamine in 80% yield. Aliphatic nitriles can also be reduced by the BH(2)N(iPr)(2)/cat. LiBH(4) reducing system. Benzyl cyanide was reduced to phenethylamine in 83% yield. BH(2)N(iPr)(2) can also reduce nitriles in the presence of unconjugated alkenes and alkynes such as the reduction of 2-hexynenitrile to hex-5-yn-1-amine in 80% yield. Unfortunately, selective reduction of a nitrile in the presence of an aldehyde is not possible as aldehydes are reduced along with the nitrile. However, selective reduction of the nitrile group at 25 degrees C in the presence of an ester is possible as long as the nitrile group is activated by an electron-withdrawing substituent. It should be pointed out that lithium aminoborohydrides (LABs) do not reduce nitriles under ambient conditions and behave as bases with aliphatic nitriles as well as nitriles containing acidic alpha-protons. Consequently, both LABs and BH(2)N(iPr)(2) are complementary to each other and offer methods for the selective reductions of multifunctional compounds.
Field distribution of rectangular waveguides with anisotropic walls by using the modal theory (2016)

This article presents a new analytical approach to calculate very rapidely the field distribution in rectangular waveguides with anisotropic walls.
Clonality Analysis and Human Papillomavirus Infection in Squamous Metaplasia and Atypical Immature Metaplasia of Uterine Cervix (2007)

Atypical immature squamous metaplasia (ISM) of the uterine cervix often has histological features that overlap with the histological characteristics of high-grade cervical intraepithelial neoplasia. To identify the cellular basis and clinical significance of atypical immature metaplasia (AIM), 10 cases of AIM were analyzed for the clonal status, and the presence of human papillomavirus (HPV) infection. The physical status of HPV was also evaluated in HPV type 16 (HPV-16)-positive cases. Squamous metaplasias with no nuclear atypia (29 mature squamous metaplasias [SMs]) and a single case of ISM were analyzed as a control. Nine AIMs, 20 SMs, and a single case of ISM were informative for clonal analysis. Monoclonal composition of the lesion was demonstrated in 8 (89%) of 9 AIMs, but only in 2 (10%) of 21 cases of SM without atypia (AIM vs SM + ISM, 8/9 vs 2/21; P < 0.0001). High-risk HPV was detected in 6 (60%) of 10 AIMs, all were HPV-16, but only in 3 (13%) of 24 SMs with no atypia (2/23 SM and 1/1 ISM). The frequency of high-risk HPV infection was also significant between AIMs and SM with no atypia (6/10 vs 3/24; P < 0.001). Among the cases, which were informative for clonal analysis, all 5 AIMs positive for high-risk HPV were monoclonal in composition. Physical status of HPV was examined in HPV-16-positive cases. Human papillomavirus type 16 was present as a mixture of episomal form and integrated form in 4 of 6 AIMs. These observations imply that unlike SMs with no atypia, which arises as a result of reactive or inflammatory process, lesions with the histological characteristics of AIM may be indeed true precursors of cervical carcinoma.
Abstract 558: EGFR inhibition in lung adenocarcinoma upregulates cell surface expression of the placental antigen ALPP and enhances efficacy of ALPP-ADC therapy (2023)

Abstract Expression levels of placental alkaline phosphatase (ALPP) and ALPP-like 2 (ALPPL2) are relatively low in most cancer types, limiting potential benefits from ALPP or ALPPL2 targeting therapies. Enhancing their expression would be an attractive approach for targeted therapy. We have undertaken analysis of ALPP and ALPPL2 protein expression in whole cell extracts (WCE) and the surfaceome of 158 cancer cell lines and found ALPP, and to a less extent ALPPL2, to be expressed on the surface at relatively low levels across multiple cancer types. We explored various means to enhance ALPP expression in lung adenocarcinoma (LUAD) and found that induction of cancer cell quiescence via nutrient deprivation, or treatment with EGFR inhibitors, greatly enhanced ALPP surface expression. Mechanistic studies revealed that enhancement of surface ALPP expression in LUAD cells following gefitinib treatment was mediated through repression of MEK/ERK signaling and activation of the transcription factor FoxO3a, which was identified as an upstream transcriptional regulator of ALPP. Using xenograft models of LUAD, we further demonstrated that gefitinib treatment upregulates surface expression of ALPP in LUAD cells but not in normal tissues. Combination therapy with gefitinib and an ALPP antibody conjugated with Monomethylauristatin F resulted in enhanced tumor suppression compared with gefitinib alone. Our findings support a novel combination treatment modality that boosts the efficacy of ALPP-ADC directed therapy. Citation Format: Yihui Chen, Monica Hong, Hanwen Xu, Jody Vykoukal, Soyoung Park, Yining Cai, Ricardo A. León-Letelier, Fu Chung Hsiao, jennifer B. Dennison, Edwin J. Ostrin, Johannes F. Fahrmann, Hiroyuki Katayama, Samir M. Hanash. EGFR inhibition in lung adenocarcinoma upregulates cell surface expression of the placental antigen ALPP and enhances efficacy of ALPP-ADC therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 558.
Rectangular-loop slot antennas on substrate lenses for millimeter- and submillimeter-wave mixer applications (2002)

A rectangular-loop slot antenna, printed on the back surface of extended hemispherical lenses is examined as a candidate for millimeter- and submillimeter-wave integrated-circuit Schottky-diode mixers. The proposed configuration is based on coplanar waveguide (CPW) technology and incorporates a built-in integrated stub tuner (IST) to balance the geometry, help tuning the antenna and provide a DC return path for the mixing device. In order to design and optimize the antenna, a full-wave method of moments (MoM) technique has been developed for the input impedances. On the other hand, for the patterns through the lens, a geometrical-optics/diffraction theory approach is utilized. Simulation results compare well with commercially available software packages. The radiation characteristics of the proposed loop antenna, are optimized for integration with Schottky mixer diodes. The structure is well suited for implementing integrated planar mixers within the submillimeter-wave frequency spectrum.
Highly efficient silicon capacitive modulators based on a vertical oxide layer (2016)

We present two novel capacitive modulator phase shifter architectures using a vertical oxide. The first structure consists of a vertical oxide slot embedded in a silicon waveguide along the propagation direction. The second structure is based on a sub-wavelength approach, with several periodic vertical oxide layers along the propagation direction. This paper focuses on the design of the modulator devices and the simulation of their performances.
A Very Fast and Low Power Pseudo-Incrementer for Address Bus Encoder/Decoder (2006)

This paper presents a very fast yet low power pseudo incrementer structure which may be used in address bus encoders/decoders. This structure, which is based on the ripple carry incrementer, is much faster than the incrementer. Using this structure, the delay and the power of address bus encoders/decoders may be reduced considerably. Analytical and synthesis results show that the structure is faster than current incrementer circuits while its circuit area and power are much smaller than those of current fast incrementers.
Color-based visualisation of hard real-time prototyping (1992)

Experiments with color-based visualisation of hard-real time system execution with deadline scheduling discipline are reported. We have built two tools for execution of Ward&Mellor Structured Analysis for Real-Time Systems (SA/RT) specifications. A graphical animaiion tool is used for building the model, for logically validating the model, and for attaching physical attributes to the model. A hard real-time prototyper tool is used for executing and monitoring the model at real-time speeds. The computational model underlying the toolset is based on mapping SA/RT modeling elements to high level Petri nets.
Effects of X-Rays, Electron Beam, and Gamma Irradiation on Chemical and Physical Properties of EVA Multilayer Films (2022)

Gamma-ray irradiation, using the cobalt-60 isotope, is the most common radiation modality used for medical device and biopharmaceutical products sterilization. Although X-ray and electron-beam (e-beam) sterilization technologies are mature and have been in use for decades, impediments remain to switching to these sterilization modalities because of lack of data on the resulting radiation effects for the associated polymers, as well as a lack of education for manufacturers and regulators on the viability of these sterilization alternatives. For this study, the compatibility of ethylene vinyl acetate (EVA) multilayer films with different ionizing radiation sterilization (X-ray, e-beam, and gamma irradiation) is determined by measuring chemical and physical film properties using high performance liquid chromatography, differential scanning calorimetry, Fourier-Transform InfraRed spectroscopy (FTIR), surface energy measurement, and electron spin resonance techniques. The results indicate that the three irradiation modalities induce no differences in thermal properties in the investigated dose range. Gamma and X-Ray irradiations generate the same level of reactive species in the EVA multilayer film, whereas e-beam generates a reduced quantity of reactive species.
Simple and Efficient Synthesis of 2,7-Difunctionalized-1,8-Naphthyridines (2005)

The syntheses in good yields of some new difunctionalized 1,8-naphthyridines 4, 6, 8 and 9 and a novel triethylene glycol ether-linked dinaphthyridine, 10a, along with the mononaphthyridine-linked ether alcohol 10b are described. An improved and milder method for the synthesis of 2,7-diamino-1,8-naphthyridine (14) is also reported.
Transport in submicrometer buried mesotaxial cobalt silicide wires (1993)

We describe the formation of narrow (down to 130 nm) buried CoSi2 wires by implantation of Co ions through an oxide mask into a Si wafer followed by annealing. Fabrication of free-standing wires is also demonstrated. The temperature dependence of the four-terminal resistance from 4 to 600 K shows that these wires are good metals, very similar to wider layers. Measurements at high current density and temperature suggest that the wires may be robust with respect to electromigration damage.
Worst-case narrow-band interference over noisy dispersive channels (2002)

The effect of narrow-band interference (NBI) on the finite blocklength throughput of linear noisy dispersive channels is studied. Spectral characteristics (both shape and frequency location) of worst-case NBI and its associated minimum channel block throughput are derived. The performance of finite-length linear and decision feedback equalizers in the presence of worst-case NBI is presented.
CMOS active transformer current-mode phase-locked loops (2007)

This paper introduces active transformer current- mode phase-locked loops. The proposed current-mode PLLs differ from voltage-mode PLLs by replacing their RC loop filter with an active transformer loop filter to take the advantage of the large self and mutual inductances, and small silicon area of active transformers. Implemented in TSMC-0.18 mum CMOS technology, the simulation results of a 3 GHz active transformer current-mode PLL demonstrate that the PLL has the lock time 50 ns, silicon area 2800 mum <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , dc power consumption 12.2 mW, and phase noise of -81.5 dBc at 1 MHz frequency offset.
Supplementary Figures 1-7 from Suppression of the Epithelial–Mesenchymal Transition by Grainyhead-like-2 (2023)

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