gebhart/patrepeval huggingface dataset:
Induction of Neutralizing Responses against Autologous Virus in Maternal HIV Vaccine Trials (2020)

A maternal vaccine capable of boosting neutralizing antibody (NAb) responses directed against circulating viruses in HIV-infected pregnant women could effectively decrease mother-to-child transmission of HIV. However, it is not known if an HIV envelope (Env) vaccine administered to infected pregnant women could enhance autologous virus neutralization and thereby reduce this risk of vertical HIV transmission. Here, we assessed autologous virus NAb responses in maternal plasma samples obtained from AIDS Vaccine Evaluation Group (AVEG) protocols 104 and 102, representing historical phase I safety and immunogenicity trials of recombinant HIV Env subunit vaccines administered to HIV-infected pregnant women (ClinicalTrials registration no. NCT00001041). Maternal HIV Env-specific plasma binding and neutralizing antibody responses were characterized before and after vaccination in 15 AVEG 104 (<i>n</i> = 10 vaccine recipients, <i>n</i> = 5 placebo recipients) and 2 AVEG 102 (<i>n</i> = 1 vaccine recipient, <i>n</i> = 1 placebo recipient) participants. Single-genome amplification (SGA) was used to obtain HIV <i>env</i> gene sequences of autologous maternal viruses for pseudovirus production and neutralization sensitivity testing in pre- and postvaccination plasma of HIV-infected pregnant vaccine recipients (<i>n</i> = 6 gp120, <i>n</i> = 1 gp160) and placebo recipients (<i>n</i> = 3). We detected an increase in Env subunit MN gp120-specific IgG binding in the group of vaccine recipients between the first immunization visit and the last visit at delivery (<i>P</i> = 0.027, 2-sided Wilcoxon test). While no difference was observed in the levels of autologous virus neutralization potency between groups, in both groups maternal plasma collected at delivery more effectively neutralized autologous viruses from early pregnancy than late pregnancy. Immunization strategies capable of further enhancing these autologous virus NAb responses in pregnant women will be important to block vertical transmission of HIV.<b>IMPORTANCE</b> Maternal antiretroviral therapy (ART) has effectively reduced but not eliminated the burden of mother-to-child transmission of HIV across the globe, as an estimated 160,000 children were newly infected with HIV in 2018. Thus, additional preventive strategies beyond ART will be required to close the remaining gap and end the pediatric HIV epidemic. A maternal active immunization strategy that synergizes with maternal ART could further reduce infant HIV infections. In this study, we found that two historic HIV Env vaccines did not enhance the ability of HIV-infected pregnant women to neutralize autologous viruses. Therefore, next-generation maternal HIV vaccine candidates must employ alternate approaches to achieve potent neutralizing antibody and perhaps nonneutralizing antibody responses to effectively impede vertical virus transmission. Moreover, these approaches must reflect the broad diversity of HIV strains and widespread availability of ART worldwide.
Next-generation three-dimensional full-wave electromagnetic solver hybridization for large-scale signal integrity, power integrity, and EMI modeling (2010)

This paper introduces a new methodology and conceptual framework for implementation of automated hybrid solver technology. Specifically, it addresses the challenges and approaches to automated solver hybridization, whereby a three-dimensional full-wave simulation technology may adapt automatically to geometric redundancies and significantly reduce cost while maintaining high accuracy. The proposed method is one step towards the grand goal of an adaptive error-controllable solver that embodies all aspects of 3D full-wave, 3D quasi-static, 2D solvers, and various semi-analytic and analytic approximations within a unified automated framework.
Data from CD73 Is Associated with Poor Prognosis in High-Grade Serous Ovarian Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;The cell surface nucleotidase CD73 is an immunosuppressive enzyme involved in tumor progression and metastasis. Although preclinical studies suggest that CD73 can be targeted for cancer treatment, the clinical impact of CD73 in ovarian cancer remains unclear. In this study, we investigated the prognostic value of CD73 in high-grade serous (HGS) ovarian cancer using gene and protein expression analyses. Our results demonstrate that high levels of CD73 are significantly associated with shorter disease-free survival and overall survival in patients with HGS ovarian cancer. Furthermore, high levels of CD73 expression in ovarian tumor cells abolished the good prognosis associated with intraepithelial CD8&lt;sup&gt;+&lt;/sup&gt; cells. Notably, CD73 gene expression was highest in the C1/stromal molecular subtype of HGS ovarian cancer and positively correlated with an epithelial-to-mesenchymal transition gene signature. Moreover, &lt;i&gt;in vitro&lt;/i&gt; studies revealed that CD73 and extracellular adenosine enhance ovarian tumor cell growth as well as expression of antiapoptotic BCL-2 family members. Finally, &lt;i&gt;in vivo&lt;/i&gt; coinjection of ID8 mouse ovarian tumor cells with mouse embryonic fibroblasts showed that CD73 expression in fibroblasts promotes tumor immune escape and thereby tumor growth. In conclusion, our study highlights a role for CD73 as a prognostic marker of patient survival and also as a candidate therapeutic target in HGS ovarian cancers. &lt;i&gt;Cancer Res; 75(21); 4494–503. ©2015 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Segregation of Effector Mechanisms in a Tumour‐Specific CD8<sup>+</sup> T‐Cell Clone Correlates with CD30 Expression (2001)

In this study we have analyzed CD30-antigen expression in three melanoma-directed cytotoxic T lymphocyte (CTL) clones with a T helper 0 (Th0)-like cytokine secretion profile (i.e. interleukin (IL)-4, IL-5, and interferon (IFN)-gamma). We show that all CTL clones expressed high levels of CD30 upon contact with the autologous tumour cells. One CTL clone, termed A2 with a monoclonal feature was selected for further analyses and found its CD30 expression dependent on the presence of IL-4. Functionally, a CD30-expressing A2 CTL was capable of producing higher amounts of IFN-gamma (up to 1.5-fold) and IL-4 (up to two-fold) than its CD30- counterpart. Furthermore, CD30-positive A2 CTL displayed an at least three-fold greater proliferative response to the tumour cell stimulation, contrasting with CD30- CTL. However, the antitumour cytotoxic activity of A2 CTL was not modulated by the CD30 expression. These results suggest that CD30 antigen can be inducible on a subset of tumour-directed CD8+ CTL, and that this subset of cells may have profound effector functions, such as cytokine secretion, proliferation, and cytotoxicity.
Analytical modelling and experimental verification of Fabry-Pérot resonances in multilayer sub-wavelength partially-reflecting surfaces (2010)

Transmission through stacked perforated metallic screens (2-D metallic meshes) printed on thin dielectric layers is studied at microwave frequencies using simple circuit models. The physical mechanisms of the transmission resonances are clearly explained and the most relevant parameters of the circuit are accurately determined. The results of the circuit model are tested by a proper comparison with previously obtained numerical and experimental results. The observed transmission peaks and lower/upper frequency band edges of the pass-band are explained in terms of the behaviour of a finite number of strongly coupled Fabry-Perot resonators using the circuit model.
Use of Logic Relationships to Decipher Protein Network Organization (2004)

A major focus of genome research is to decipher the networks of molecular interactions that underlie cellular function. We describe a computational approach for identifying detailed relationships between proteins on the basis of genomic data. Logic analysis of phylogenetic profiles identifies triplets of proteins whose presence or absence obey certain logic relationships. For example, protein C may be present in a genome only if proteins A and B are both present. The method reveals many previously unidentified higher order relationships. These relationships illustrate the complexities that arise in cellular networks because of branching and alternate pathways, and they also facilitate assignment of cellular functions to uncharacterized proteins.
Conformal load-bearing polymer-carbon nanotube antennas and RF front-ends (2009)

We presented a novel process for constructing high conductivity CNT surfaces. This is done by growing high density CNTs on light-weight and highly flexible polymer substrates. The proposed vertically aligned CNT printing technology can also be adapted for constructing flexible RF circuits integrated on a variety of commercial and defense related applications. Given the desirable RF and mechanical properties of polymer composites and CNTs, we expect a significant impact on multilayer integration of miniature and light-weight transceivers for future UAVs and body-worn applications.
A Cationic 1-(2-Methylpyridine)Phosphole Cymene Ruthenium Chloride Complex as an Efficient Catalyst in the Transfer Hydrogenation of Ketones (2003)

Reaction of 2,5-diphenylphospholide anion with 2-chloromethylpyridine affords the 1-(2-methylpyridine)phosphole ligand. The corresponding cationic Ru(cymene)Cl chelate complex catalyzes the hydrogen transfer process of ketones with very high TON and TOF numbers.
Design of Binary Network Codes for Multi-user Multi-way Relay Networks (2013)

We study multi-user multi-way relay networks where $N$ user nodes exchange their information through a single relay node. We use network coding in the relay to increase the throughput. Due to the limitation of complexity, we only consider the binary multi-user network coding (BMNC) in the relay. We study BMNC matrix (in GF(2)) and propose several design criteria on the BMNC matrix to improve the symbol error probability (SEP) performance. Closed-form expressions of the SEP of the system are provided. Moreover, an upper bound of the SEP is also proposed to provide further insights on system performance. Then BMNC matrices are designed to minimize the error probabilities.
A New Assay to Measure Intestinal Crypt Survival after Irradiation: Challenges and Opportunities (2020)

Radiotherapy is a critical component of many current, curative cancer treatments, yet it is accompanied by unavoidable irradiation of normal tissues. Abdominal and pelvic radiation almost always results in some dose delivered to the bowel with deleterious effects to the small and large intestines. While the likelihood of enteritis is dose dependent, there is also considerable variation between patients in both the extent of symptoms of enteritis as well as their duration. In this article, Martin and colleagues hypothesized that the radiation sensitivity of intestinal organoids could predict the sensitivity of individual patients to enteritis and have taken the first steps to develop such an assay.<i>See related article by Martin et al., p. 1219</i>.
Silicon by Sodium Reduction of Silicon Tetrafluoride (1981)

High purity silicon can be prepared from the reaction of Na with to form Si and . The is obtained from inexpensive by precipitation and decomposition of . Concentrations of B and P are each in the 0.1 ppm wt range in the product Si, separated from by aqueous leaching.
Low dark count rate and low timing jitter InGaAs/InP Single-Photon Avalanche Diode (2014)

We describe the design and characterization of a new InGaAs/InP Single-Photon Avalanche Diode (SPAD) for single-photon detection at 1.55 μm with high detection efficiency, low noise and low timing jitter. The design and fabrication have been optimized to reduce the defects (responsible for dark counts and afterpulsing). Zinc diffusion is a key step and we optimized the profile, pattern and reactor parameters to achieve uniform sensitivity in the active area, low noise and low timing jitter. The active area diameter of the device here described is 25 μm and no floating guard rings are present. It is operated in gated mode, with passive quenching, for the characterization. The dark count rate is in the order of few kilo-counts per second at 225 K and 5 V of excess bias. The photon timing resolution, measured as the full-width at half maximum of the response to a 20 ps pulsed laser, is about 90 ps, with a clean exponential tail whose time constant is about 60 ps. The photon detection efficiency is about 30% at 1550 nm. These specifications make our InGaAs/InP SPAD a good candidate for advanced time-correlated singlephoton counting applications at wavelengths up to 1700 nm.
Novel One-Beam Tracking Detection Method for Dual-Layer Blu-ray Discs (2006)

In this paper, we propose a new advanced push–pull (APP) method as a new one-beam tracking detection method suitable for a dual-layer Blu-ray disc (BD) system. This method overcomes two issues. One of them is tracking error signal (TES) offset at the boundary between recorded tracks and unrecorded tracks, and the other is TES offset caused by the stray lights from the other layer of dual-layer discs. The new APP-TES is stable at the boundary in the dual-layer BD system, because the dividing area of a far-field pattern is optimized and the detecting areas are allocated to avoid stray lights from the other layer. Its stable characteristics are confirmed experimentally.
Compartmentalization of Phosphatidylinositol 4,5-Bisphosphate Signaling Evidenced Using Targeted Phosphatases (2008)

Phosphatidylinositol 4,5-bisphosphate (PIP(2)) is a prevalent phosphoinositide in cell membranes, with important functions in cell signaling and activation. A large fraction of PIP(2) associates with the detergent-resistant membrane "raft" fraction, but the functional significance of this association remains controversial. To measure the properties of raft and nonraft PIP(2) in cell signaling, we targeted the PIP(2)-specific phosphatase Inp54p to either the raft or nonraft membrane fraction using minimal membrane anchors. Interestingly, we observed that targeting Inp54p to the nonraft fraction resulted in an enrichment of raft-associated PIP(2) and striking changes in cell morphology, including a wortmannin-sensitive increase in cell filopodia and cell spreading. In contrast, raft-targeted Inp54p depleted the raft pool of PIP(2) and produced smooth T cells void of membrane ruffling and filopodia. Furthermore, raft-targeted Inp54p inhibited capping in T cells stimulated by cross-linking the T cell receptor, but without affecting the T cell receptor-dependent Ca(2+) flux. Altogether, these results provide evidence of compartmentalization of PIP(2)-dependent signaling in cell membranes such as predicted by the membrane raft model.
Interaction corrections to two-dimensional hole transport in the<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">l</mml:mi><mml:mi mathvariant="normal">a</mml:mi><mml:mi mathvariant="normal">r</mml:mi><mml:mi mathvariant="normal">g</mml:mi><mml:mi mathvariant="normal">e</mml:mi><mml:mo>−</mml:mo><mml:mi mathvariant="normal">r</mml:mi></mml:mrow><mml:mrow><mml:mi>s</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math>limit (2003)

The metallic conductivity of dilute two-dimensional holes in a GaAs heterojunction insulated-gate field-effect transistor with extremely high mobility and large ${r}_{s}$ is found to have a linear dependence on temperature, consistent with the theory of interaction corrections in the ballistic regime. Phonon scattering contributions are negligible in the temperature range of our interest, allowing comparison between our measured data and theory without any phonon subtraction. The magnitude of the Fermi liquid interaction parameter ${F}_{0}^{\ensuremath{\sigma}}$ determined from the experiment, however, decreases with increasing ${r}_{s}$ for ${r}_{s}\ensuremath{\gtrsim}22,$ a behavior unexpected from theoretical calculations valid for small ${r}_{s}.$
Optimized Synthesis and Antimalarial Activity of 1,2‐Dioxane‐4‐carboxamides (2014)

Abstract We recently proposed 3‐methoxy‐4‐methoxycarbonyl‐1,2‐dioxanes 3 as promising scaffolds enabling access to potential antimalarial drugs. We present here an optimized two‐step synthesis of 3 characterized by high yields, simple work‐up procedures and high diastereoselectivity allowing us to readily prepare 3 on multigram scale. The versatility of the 1,2‐dioxane scaffold was demonstrated by our generation of a new family of 1,2‐dioxane‐4‐carboxamides 8a – h and the realization of their in vitro activities against chloroquine‐sensitive (D10) and chloroquine‐resistant (W2) P. falciparum strains. In particular, one of these amides ( 8e ), displayed antimalarial activity on par with the natural product lead plakortin and was 5‐fold more active than its methyl ester analogue 3 . Structure–activity relationship (SAR) analysis supported by DFT calculations revealed that, for this family of compounds, alkyl substituents at C6 dictate, in large part, the degree of antimalarial activity. This finding contrasts those previously observed for the ester series.
Short, Enantioselective Total Synthesis of Okaramine N (2003)

The first enantioselective total synthesis of a member of the okaramine family of bis-indole alkaloids, okaramine N (1), has been accomplished via intermediates 2-7, as outlined. The N-prenylated derivative of (S)-tryptophan methyl ester (2) was coupled with Fmoc-protected N-tert-prenylated tryptophan (3) to form the amide 4 in 70% yield. Pd(II)-mediated cyclization/rearrangement, a key step in the synthesis, transformed 4 into the indoloazacine 5 (44%), which was deprotected and cyclized in a single step to give the hexacyclic diketopiperazine 6 (95%). In the following novel and key sequence, 6 was transformed into 1: (1) selective ene reaction with N-methyltriazolinedione, (2) photooxidation of the remaining tert-prenylated indole subunit to provide 7, and (3) thermal retroene reaction of 7 to afford okaramine N (70% from 6).
A novel microfabrication of a self-aligned vertical comb drive on a single SOI wafer for optical MEMS applications (2004)

A novel method for fabricating a self-aligned electrostatic vertical comb drive using a single layer of a SOI wafer is introduced. The fixed combs are anchored to bimorph cantilevers made of two materials with dissimilar thermal coefficients of expansion, i.e., silicon dioxide and single crystal silicon. The cantilever, which provides the vertical offset between the fixed comb and the movable comb, is deflected by residual stress during cooling down from oxidation temperature to room temperature. In piston motion, the vertical amplitude at the resonant frequency of 3.5 kHz is 30 µm. In torsional motion, the angle of optical deflection at the resonance of 830 Hz is changed by 6.5°. The measured resonant frequencies correspond to the results from a finite element analysis within 10%. This vertical comb drive is useful for optical and biophotonic MEMS requiring out-of-plane torsional or piston motion.
Involvement of Cyclo-Oxygenase-2 in Osteoclast Formation and Bone Destruction in Bone Metastasis of Mammary Carcinoma Cell Lines (2002)

We previously reported that mouse mammary carcinoma cell lines (MMT060562 and BALB/c-MC) induced osteoclast formation through production of prostaglandin E2 (PGE2) in cocultures with mouse bone marrow cells, but the mechanism(s) of PG production remained unclear. In the present in vitro and in vivo studies, we tested the involvement of cyclo-oxygenase-2 (COX-2), an inducible rate-limiting enzyme in PG biosynthesis, in the stimulation of osteoclast formation by mouse mammary carcinoma cell lines. Addition of a selective COX-2 inhibitor, JTE-522, to cocultures of mammary carcinoma cell lines and bone marrow cells lowered PGE2 concentration in the culture media and inhibited osteoclast formation in a dose-dependent manner. Northern blotting showed a very high level of COX-2 messenger RNA (mRNA) expression in MMT060562. The mRNA expression was low in BALB/c-MC, but it increased when BALB/c-MC and bone marrow cells were cocultured. The results of immunocytochemistry for COX-2 protein in respective cultures were compatible with the results of COX-2 mRNA. In vivo, BALB/c-MC injected into the heart of Balb/c mice metastasized to bone and formed osteolytic lesions in their hindlimbs. Histological examination revealed that tumor cells had metastasized to the bone marrow cavity and destroyed the bone trabeculae. Immunohistochemistry demonstrated that bone marrow stromal cells adjacent to tumor cells expressed COX-2 protein. These findings suggest that COX-2 plays an important role in the osteolysis of bone metastasis in vivo as well as in osteoclast formation in cocultures used as an in vitro model of metastatic bone disease.
Treatment of Distillery Wastewater by the Nano‐Scale Zero‐Valent Iron and the Supported Nano‐Scale Zero‐Valent Iron (2010)

The treatment of wastewater from the distillery industry was carried out by using nano-scale- and supported nano-scale zero-valent iron at a laboratory scale and ambient temperature. Effects of dilution, pH, mixing rate, zero-valent iron dosage, and amount of support for the zero-valent iron were investigated. All parameters had a significant effect on the removal efficiency of all investigated pollutants. Increasing the number of dilutions and the nano-scale zero-valent iron dosage led to the increase of removal efficiency of pollutants. Higher removal efficiency was achieved in an acidic initial pH of wastewater. The reduction of all pollutants was limited by the kinetics of the pollutant destruction/reduction by nano-scale zero-valent iron particles at a mixing rate greater than 170 rpm. At optimum condition, greater than 95, 94, and 64% of color, chemical oxygen demand, and biochemical oxygen demand were removed, respectively, within 6 hours. Additionally, the presence of a support had a significant effect on pollutant removal.
Consistent Wiener filtering: designing generalized time-frequency masks respecting spectrogram consistency (2010)

National audience
Localization of Distant Urogenital System-, Central Nervous System-, and Endocardium-Specific Transcriptional Regulatory Elements in the GATA-3 Locus (1999)

We found previously that neither a 6-kbp promoter fragment nor even a 120-kbp yeast artificial chromosome (YAC) containing the whole GATA-3 gene was sufficient to recapitulate its full transcription pattern during embryonic development in transgenic mice. In an attempt to further identify tissue-specific regulatory elements modulating the dynamic embryonic pattern of the GATA-3 gene, we have examined the expression of two much larger (540- and 625-kbp) GATA-3 YACs in transgenic animals. A lacZ reporter gene was first inserted into both large GATA-3 YACs. The transgenic YAC patterns were then compared to those of embryos bearing the identical lacZ insertion in the chromosomal GATA-3 locus (creating GATA-3/lacZ "knock-ins"). We found that most of the YAC expression sites and tissues are directly reflective of the endogenous pattern, and detailed examination of the integrated YAC transgenes allowed the general localization of a number of very distant transcriptional regulatory elements (putative central nervous system-, endocardium-, and urogenital system-specific enhancers). Remarkably, even the 625-kbp GATA-3 YAC, containing approximately 450 kbp and 150 kbp of 5' and 3' flanking sequences, respectively, does not contain the full transcriptional regulatory potential of the endogenous locus and is clearly missing regulatory elements that confer tissue-specific expression to GATA-3 in a subset of neural crest-derived cell lineages.