gebhart/patrepeval huggingface dataset:
Epstein-Barr Virus Latent Gene Expression in Primary Effusion Lymphomas Containing Kaposi's Sarcoma–Associated Herpesvirus/Human Herpesvirus-8 (1997)

Primary effusion (body cavity-based) lymphoma (PEL) is a recently recognized subtype of malignant lymphoma that exhibits distinctive clinical and biological features, most notably its usual infection with the Kaposi's sarcoma-associated herpesvirus (KSHV). The vast majority of cases also contain Epstein-Barr virus (EBV). This dual viral infection is the first example of a consistent dual herpesviral infection in a human neoplasm and provides a unique model to study viral interactions. We analyzed the pattern of EBV latent gene expression to determine the pathogenic role of this agent in PELs. We examined five PELs coinfected with EBV and KSHV by reverse transcription-polymerase chain reaction (RT-PCR), in situ hybridization, and immunohistochemistry. EBER1 mRNA, a consistent marker of viral latency, was positive in all PEL cases, although at lower levels than in the non-PEL controls due to EBER1 expression by only a variable subset of lymphoma cells. Qp-initiated mRNA, encoding only EBNA1 and characteristic of latencies I and II, was positive in all PEL cases. Wp- and Cp-initiated mRNAs, encoding all EBNAs and characteristic of latency III, were negative in all cases. LMP1 mRNA, expressed in latencies II and III, was present in three cases of PEL, although at very low levels that were not detectable at the protein level by immunohistochemistry. Low levels of LMP2A mRNA were detected in all cases. BZLF1, an early-intermediate lytic phase marker, was weakly positive in four cases, suggesting a productive viral infection in a very small proportion of cells, which was confirmed by ZEBRA antigen expression. Therefore, PELs exhibit a restricted latency pattern, with expression of EBNA1 in all cases, and low LMP1 and LMP2A levels.
Abstract 974: Alternative polyadenylation of androgen receptor variants in castration-resistant prostate cancer (2018)

Abstract The androgen receptor (AR), which is activated by androgens, functions in the normal prostate as a master transcriptional regulator. Accordingly, prostate cancer (PCa) presents as an androgen- and AR-dependent disease. Inhibition of AR transcriptional activity with androgen-deprivation therapy (ADT) is effective for patients with locally advanced and metastatic disease. All ADT suppresses AR via interference with its ligand binding domain (LBD)-dependent transcriptional activity. However, development of therapy resistance and transition to castration-resistant prostate cancer (CRPC) represents a major clinical challenge. CRPC circumvents ADT by expressing constitutively active AR variants (AR-Vs) that lack the LBD. Therapies targeting constitutively active AR variants are not currently available. To address this problem, we investigated the mechanisms underlying AR-V expression in CRPC. One particular AR-V, called AR-V7, consists of contiguously spliced exons 1, 2, 3, and a cryptic exon, CE3, and has been shown to be associated with clinical resistance to second-generation AR inhibitors abiraterone and enzalutamide. We noted that CE3 contains a consensus hexameric AAUAAA polyadenylation signal (PAS). We hypothesized that intronic polyadenylation promotes AR-V7 expression in CRPC. To test this, we developed a morpholino that sterically blocked the CE3 PAS to prevent splicing of AR-V7. We have demonstrated that the PAS in CE3 controls expression of AR-V7, as well as a broad array of AR variants arising by splicing of adjacent cryptic exons that use the shared CE3 PAS. Furthermore, our data demonstrate that the cleavage and polyadenylation complex (CPSF complex) is enriched in primary PCa tumors relative to normal tissues. We have also demonstrated that CPSF1, a member of the CPSF complex, controls expression of AR-Vs relative to full length AR and plays a global role in the determination of mRNA isoform length in prostate cancer cells. Collectively, these findings reveal alterations in the cellular machinery governing mRNA cleavage and polyadenylation in prostate cancer, and identify specific opportunities for therapeutic intervention. Citation Format: Jamie L. Van Etten, Michael Nyquist, Yingming Li, Rebecca LaRue, Yeung Ho, Rendong Yang, Daniel F. Voytas, Christine Henzler, Scott M. Dehm. Alternative polyadenylation of androgen receptor variants in castration-resistant prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 974.
Selective modulation of two human monocyte Fc receptors for IgG by immobilized immune complexes. (1988)

Two types of IgG FcR, FcRI and FcRII, are constitutively expressed by human monocytes. FcRI (identified by mAb 32.2) binds human (h) IgG, FcRII (identified by mAb IV.3) has a low affinity for hIgG but interacts strongly with murine (m) IgG1. These receptors can be assayed by using indicator E sensitized by hIgG (EA-hIgG) or mIgG1 (EA-mIgG1), respectively. We further characterized these two FcR by modulation studies by using substrate-immobilized immune complexes containing rabbit IgG, goat IgG, or one of the mouse Ig classes or subclasses. After incubating monocytes in microtiter wells containing such immune complexes, binding of the two types of indicator red cells on the apical surface of the monocytes was quantitated using a photometric assay employing the pseudoperoxidase activity of E. No effect on the binding of sensitized E was observed after incubation of monocytes with immune complexes containing mouse IgE, IgA, or IgM, or F(ab')2 fragments of rabbit IgG. High concentrations of immune complexes containing IgG of mouse, rabbit, or goat, however, were able to induce a decrease in binding of both types of sensitized E, suggestive of modulation of both FcRI and FcRII. At lower concentrations of immune complexes, more selective patterns of modulation emerged. Under these conditions, immune complexes containing mIgG1 or mIgG2b, or, surprisingly, goat IgG induced a selective decrease in the binding of EA-mIgG1 (FcRII modulation), while immune complexes containing mIgG2a or rabbit IgG mainly affected the binding of EA-hIgG (FcRI modulation). By using anti-FcR mAb IV.3, it was confirmed that FcRII was modulated from the apical surface of monocytes after incubation on immune complex coated substrates. Selectivity of FcR-modulation was demonstrated by showing that under these conditions binding of anti-C receptor mAb, and several other anti-monocyte mAb did not decrease.
Acoustic wave spectroscopy inside a reverberant media with moving scatterers (2002)

In this work, we present an original method in order to measure static and dynamic parameters of moving scatterers confined inside a strong reverberant cavity. In such media, wave propagation is very complex due to multiple scattering and multiple reflections. In a previous article (de Rosny et al., J. Acoust. Soc. Am. (2001)], we have shown that the number or the elastic cross section of moving scatterers, like a school of fish in an aquarium, are deduced from the pressure field averaged over different and independent positions of the scatterers cloud. In this talk, we present an extension of this work which also takes into account the scatterer’s dynamics, e.g., mean speed. Basically, the idea is to relate the correlation of the pressure field to the scatterer’s motion. A DAWS-like (Diffusive Acoustic Wave Spectroscopy) theory based on a statistical approach of this system is presented. The theory is compared with experimental data obtained with scatterers whose motion and elastic cross section are known. Finally this method is applied in order to survey the dynamic behavior of a school of fish inside an aquarium under some environmental modifications as luminosity or temperature.
The Alpha–Bet(a) of Glucose Pyrolysis: Computational and Experimental Investigations of 5-Hydroxymethylfurfural and Levoglucosan Formation Reveal Implications for Cellulose Pyrolysis (2014)

As biomass pyrolysis is a promising technology for producing renewable fuels, mechanistic descriptions of biomass thermal decomposition are of increasing interest. While previous studies have demonstrated that glucose is a key primary intermediate and have elucidated many important elementary mechanisms in its pyrolysis, key questions remain. For example, there are several proposed mechanisms for evolution of an important product and platform chemical, 5-hydroxymethylfurfural (5-HMF), but evaluation with different methodologies has hindered comparison. We evaluated a host of elementary mechanisms using a consistent quantum mechanics (QM) level of theory and reveal a mechanistic understanding of this important pyrolysis pathway. We also describe a novel route as a target for catalyst design, as it holds the promise of a more selective pathway to 5-HMF from glucose. We further demonstrate the effect of conformational and structural isomerization on dehydration reactivity. Additionally, we combined QM and experimental studies to address the question of whether only the reactions of β-d-glucose, the cellulose monomer, are relevant to biomass pyrolysis, or if α-d-glucose needs to be considered in mechanistic models of glucose and cellulose pyrolysis. QM calculations show notable differences in elementary mechanisms between the anomers, especially in levoglucosan formation, which provide a means for evaluating experimental yields of α-d-glucose and β-d-glucose pyrolysis. The combined data indicate that both anomers are accessible under pyrolysis conditions. The kinetic and mechanistic discoveries in this work will aid catalyst design and mechanistic modeling to advance renewable fuels from nonfood biomass.
Neue Ansätze zur Empfindlichkeitssteigerung in der biomolekularen NMR‐Spektroskopie (2015)

Abstract Im Frühling 2013 versammelten sich NMR‐Spektroskopiker am Weizmann‐Institut in Israel, um neue Ansätze zur Verbesserung der Empfindlichkeit von NMR‐Experimenten zu diskutieren, besonders im Hinblick auf Experimente an biomolekularen Systemen. Der vorliegende Aufsatz ist von vielen Autoren mit unterschiedlichem fachlichem Hintergrund verfasst worden; er beschreibt den Stand der Forschung auf diesem Gebiet, wie er im Rahmen des Treffens diskutiert wurde. Es werden Ansätze für Ultra‐Hochfeld‐NMR‐Spektroskopie, für neuartige Techniken der NMR‐Detektion, für Prinzipien und Methoden der Kernhyperpolarisation, aber auch für neue Probenpräparationsmethoden diskutiert. Diese Ansätze verbessern die Empfindlichkeit von NMR‐Experimenten im Festkörper und in Lösung, sind voneinander unabhängig und können sich in ihren Auswirkungen multiplizieren. Auch wenn in allen genannten Bereichen bereits substanzielle Verbesserungen erzielt wurden, ist doch noch eine weite Strecke zu überwinden, um an die Empfindlichkeiten von optischen und elektronischen Spektroskopien heranzureichen. Diese Probleme und erste Lösungsansätze werden ebenfalls diskutiert.
ChemInform Abstract: Biosynthetic Studies on the Fungal Secondary Metabolites CP‐225,917 and CP‐263,114. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Multi-Wavelength Optical Fiber Refractive Index Profiling by Spatially Resolved Fourier Transform Spectroscopy (2009)

A non-destructive technique to measure an optical fiber's refractive index profile with sub-¿m spatial resolution over a wavelength range spanning more than one octave (from 480 to 1040 nm) in a single measurement is described. Data showing the variation of refractive index with wavelength for several fiber types is presented.
The concept of PICaboo: from individual building blocks to complex photonic integrated circuits for future access and metro networks (2022)

Abstract The immense growth of data traffic that traverses modern networks, calls for immediate solutions to tackle the challenges that arise in terms of speed, capacity, cost and energy efficiency. This manuscript outlines the key technological aspects of the PICaboo project, that aims to develop novel building blocks and photonic integrated circuits for the next generation of optical metro and access networks enhanced with optical signal processing functionalities exploiting the generic foundry model approach.
Protease resistance of infectious prions is suppressed by removal of a single atom in the cellular prion protein (2017)

Resistance to proteolytic digestion has long been considered a defining trait of prions in tissues of organisms suffering from transmissible spongiform encephalopathies. Detection of proteinase K-resistant prion protein (PrP Sc ) still represents the diagnostic gold standard for prion diseases in humans, sheep and cattle. However, it has become increasingly apparent that the accumulation of PrP Sc does not always accompany prion infections: high titers of prion infectivity can be reached also in the absence of protease resistant PrP Sc . Here, we describe a structural basis for the phenomenon of protease-sensitive prion infectivity. We studied the effect on proteinase K (PK) resistance of the amino acid substitution Y169F, which removes a single oxygen atom from the 2-2 loop of the cellular prion protein (PrP C ). When infected with RML or the 263K strain of prions, transgenic mice lacking wildtype (wt) PrP C but expressing MoPrP 169F generated prion infectivity at levels comparable to wt mice. The newly generated MoPrP 169F prions were biologically indistinguishable from those recovered from prion-infected wt mice, and elicited similar pathologies in vivo. Surprisingly, MoPrP 169F prions showed greatly reduced PK resistance and density gradient analyses showed a significant reduction in high-density aggregates. Passage of MoPrP 169F prions into mice expressing wt MoPrP led to full recovery of protease resistance, indicating that no strain shift had taken place. We conclude that a subtle structural variation in the 2-2 loop of PrP C affects the sensitivity of PrP Sc to protease but does not impact prion replication and infectivity. With these findings a specific structural feature of PrP C can be linked to a physicochemical property of the corresponding PrP Sc .
Neurostimulation and functional brain imaging (2000)

Recent advancements in functional neuroimaging have furthered our understanding of the normal and pathological brain. These non-invasive imaging modalities have allowed us to study the human brain in vivo. Concurrently, the revival of neurostimulation in the treatment of pain, movement disorders, and epilepsy has allowed the synergistic combination of these two technologies. Several studies focusing on the use of functional imaging in patients with implanted neurostimulation devices are reviewed. The anticipated roles of these two disciplines are discussed.
sim2real: Cardiac MR Image Simulation-to-Real Translation via Unsupervised GANs (2022)

There has been considerable interest in the MR physics-based simulation of a database of virtual cardiac MR images for the development of deep-learning analysis networks. However, the employment of such a database is limited or shows suboptimal performance due to the realism gap, missing textures, and the simplified appearance of simulated images. In this work we 1) provide image simulation on virtual XCAT subjects with varying anatomies, and 2) propose sim2real translation network to improve image realism. Our usability experiments suggest that sim2real data exhibits a good potential to augment training data and boost the performance of a segmentation algorithm.
Magnetic levitation-based electromagnetic energy harvesting: a semi-analytical non-linear model for energy transduction (2016)

Magnetic levitation has been used to implement low-cost and maintenance-free electromagnetic energy harvesting. The ability of levitation-based harvesting systems to operate autonomously for long periods of time makes them well-suited for self-powering a broad range of technologies. In this paper, a combined theoretical and experimental study is presented of a harvester configuration that utilizes the motion of a levitated hard-magnetic element to generate electrical power. A semi-analytical, non-linear model is introduced that enables accurate and efficient analysis of energy transduction. The model predicts the transient and steady-state response of the harvester a function of its motion (amplitude and frequency) and load impedance. Very good agreement is obtained between simulation and experiment with energy errors lower than 14.15% (mean absolute percentage error of 6.02%) and cross-correlations higher than 86%. The model provides unique insight into fundamental mechanisms of energy transduction and enables the geometric optimization of harvesters prior to fabrication and the rational design of intelligent energy harvesters.
Functional characterization of BbCRASP‐2, a distinct outer membrane protein of Borrelia burgdorferi that binds host complement regulators factor H and FHL‐1 (2006)

Borrelia burgdorferi, the aetiological agent of Lyme disease, employs sophisticated means to survive in diverse mammalian hosts. Recent studies demonstrated that acquisition of complement regulators factor H and factor H-like protein-1 (FHL-1) allows spirochetes to resist complement-mediated killing. Serum-resistant B. burgdorferi express up to five distinct complement regulator-acquiring surface proteins (CRASPs) that bind factor H and/or FHL-1. In this study we have identified and characterized one of those B. burgdorferi proteins, named BbCRASP-2. BbCRASP-2 is distinct from the four previously identified factor H/FHL-1-binding CRASPs of B. burgdorferi strains. The single copy of the gene encoding BbCRASP-2, cspZ, is located on the linear plasmid lp28-3. BbCRASP-2 is highly divergent from the factor H/FHL-1-binding protein BbCRASP-1 and from members of the factor H-binding Erp (OspE/F-related) protein family. Peptide mapping analysis revealed that the factor H/FHL-1 binding site is discontinuous and it was found that C-terminal truncations abrogate factor H and FHL-1 binding. The predominant BbCRASP-2 binding site of both host complement regulators was mapped to the short consensus repeat 7 (SCR 7). Factor H and FHL-1 bound to BbCRASP-2 maintain cofactor activity for factor I-mediated C3b inactivation and accelerate the decay of the C3 convertase. Expression of BbCRASP-2 in serum-sensitive B. burgdorferi mutant B313 increased resistance to complement-mediated lysis. The characterization of BbCRASP-2 now provides a complete picture of the three diverse complement regulator-binding protein families of B. burgdorferi yielding new insights into the pathogenesis of Lyme disease.
Future research directions for accessible social media (2020)

Social media platforms are deeply ingrained in society, and they offer many different spaces for people to engage with others. Unfortunately, accessibility barriers prevent people with disabilities from fully participating in these spaces. Social media users commonly post inaccessible media, including videos without captions (which are important for people who are Deaf or Hard of Hearing) and images without alternative text (descriptions read aloud by screen readers for people who are blind). Users with motor impairments must find workarounds to deal with the complex user interfaces of these platforms, and users with cognitive disabilities may face barriers to composing and sharing information. We invited accessibility researchers, industry practitioners, and end-users with disabilities to come together at the Computer-Supported Cooperative Work conference (CSCW 2019) to discuss challenges and solutions for improving social media accessibility. Over the course of a day that included two panels and breakout sessions, the workshop attendees outlined four critical future research directions to progress on the path to accessible social media: tooling to support disabled people authoring content, developing more accessible formats/tools for new forms of interaction (e.g, Augmented and Mixed Reality), using communities to distribute accessibility labor, and ensuring machine learning systems are built on representative datasets for disability use-cases.
A lentiviral vector expressing a dendritic cell-targeting multimer induces mucosal anti-mycobacterial CD4+ T-cell immunity (2022)

Most viral vectors, including the potently immunogenic lentiviral vectors (LVs), only poorly direct antigens to the MHC-II endosomal pathway and elicit CD4<sup>+</sup> T cells. We developed a new generation of LVs encoding antigen-bearing monomers of collectins substituted at their C-terminal domain with the CD40 ligand ectodomain to target and activate antigen-presenting cells. Host cells transduced with such optimized LVs secreted soluble collectin-antigen polymers with the potential to be endocytosed in vivo and reach the MHC-II pathway. In the murine tuberculosis model, such LVs induced efficient MHC-II antigenic presentation and triggered both CD8<sup>+</sup> and CD4<sup>+</sup> T cells at the systemic and mucosal levels. They also conferred a significant booster effect, consistent with the importance of CD4<sup>+</sup> T cells for protection against Mycobacterium tuberculosis. Given the pivotal role of CD4<sup>+</sup> T cells in orchestrating innate and adaptive immunity, this strategy could have a broad range of applications in the vaccinology field.
Effects of Molecular Weight of PVA on the Adsorption and Dispersibility of Silica Microspheres in Aqueous Media (1996)

Aqueous solutions of PVA with their average degree of polymerization(dp)500 and 2240 were prepared, to which 0.9 μm uniform silica microspheres were dispersed. The amount of PVA adsorbed was larger on the molar basis with smaller dp, but indifferent on the weight basis. This indicates the different molecular configuration of adsorbed PVA with different dp. Maximum adsorption was observed at the isoelectric point of silica, i.e., around pH 3, and decreased with increasing pH. A good dispersion on the floc basis was accomplished at pH 3 with PVA concentration above 0.2wt%, irrespective of dp. At pH 11, appreciable coagulation began above 1.0wt% for dp 2240 and 2.0wt% for dp 500. The PVA concentration dependence of the effective solid volume fraction, estimated from steady shear measurement is similar to that of the Bingham yield value for the suspension at pH 3. The concentration dependence was smaller at pH 11. Small but appreciable coagulation was observed at pH 11 under optical microscope with increasing PVA concentration, which is reflected on the Bingham yield value but not on the effective solid volume fraction. This, together with the value of the average occupation of PVA per unit surface are of silica, indicates that the flocculation at pH 11 is due to coacervation mechanism.
Homologous NRPS‐like Gene Clusters Mediate Redundant Small‐Molecule Biosynthesis in Aspergillus flavus (2012)

Biosynthetic crosstalk: Most gene clusters in fungi are orphans with no known associated metabolites. NMR-based comparative metabolomics was used to identify the products of two highly homologous orphan clusters in Aspergillus flavus. The two clusters encode partially redundant biosynthetic pathways that produce overlapping sets of novel fungal alkaloids, feature NRPS-like genes with unusual functions, and regulate fungal development. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.