gebhart/patrepeval huggingface dataset:
Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment (2021)

The prognosis of early breast cancer (BC) relies on cell autonomous and immune parameters. The impact of the intestinal microbiome on clinical outcome has not yet been evaluated. Shotgun metagenomics was used to determine the composition of the fecal microbiota in 121 specimens from 76 early BC patients, 45 of whom were paired before and after chemotherapy. These patients were enrolled in the CANTO prospective study designed to record the side effects associated with the clinical management of BC. We analyzed associations between baseline or post-chemotherapy fecal microbiota and plasma metabolomics with BC prognosis, as well as with therapy-induced side effects. We examined the clinical relevance of these findings in immunocompetent mice colonized with BC patient microbiota that were subsequently challenged with histo-compatible mouse BC and chemotherapy. We conclude that specific gut commensals that are overabundant in BC patients compared with healthy individuals negatively impact BC prognosis, are modulated by chemotherapy, and may influence weight gain and neurological side effects of BC therapies. These findings obtained in adjuvant and neoadjuvant settings warrant prospective validation.
IFNγ production in peripheral blood of early Lyme disease patients to hLFAαL (aa326-345) (2002)

IFNgamma was produced in response to stimulation with peptide hLFAalphaL (aa326-345) in peripheral blood of 58% of patients with early Lyme disease without signs of arthritis, as well as in peripheral blood of 20% of healthy individuals, but not in response to stimulation with the homologous OspAB31 (aa164-183) peptide (p < 0.05). Our results suggest that reactivity to the hLFA1 peptide in peripheral blood may be the result of T cell degeneracy.
Engineered Upconversion Nanoparticles for Resolving Protein Interactions inside Living Cells (2016)

Upconversion nanoparticles (UCNPs) convert near-infrared into visible light at much lower excitation densities than those used in classic two-photon absorption microscopy. Here, we engineered <50 nm UCNPs for application as efficient lanthanide resonance energy transfer (LRET) donors inside living cells. By optimizing the dopant concentrations and the core-shell structure for higher excitation densities, we observed enhanced UCNP emission as well as strongly increased sensitized acceptor fluorescence. For the application of these UCNPs in complex biological environments, we developed a biocompatible surface coating functionalized with a nanobody recognizing green fluorescent protein (GFP). Thus, rapid and specific targeting to GFP-tagged fusion proteins in the mitochondrial outer membrane and detection of protein interactions by LRET in living cells was achieved.
MeV‐energy probe SIMS imaging of major components in washed and fractured animal cells (2010)

Abstract Molecular images of pretreated animal cells were measured by secondary ion mass spectrometry (SIMS) with MeV‐energy ion beam. SIMS analysis was performed for cell surfaces washed with buffers not only at high vacuum, but also at several tens Pa by using an orthogonal acceleration time of flight mass spectrometer (oaTOFMS) system. Moreover, molecular images of major components from washed and freeze fractured cells were obtained using MeV‐energy probe SIMS. Copyright © 2010 John Wiley &amp; Sons, Ltd.
The Role of Portable Air Purifiers and Effective Ventilation in Improving Indoor Air Quality in University Classrooms (2022)

In this study we investigated the effectiveness of air purifiers and in-line filters in ventilation systems working simultaneously inside various classrooms at the University of Southern California (USC) main campus. We conducted real-time measurements of particle mass (PM), particle number (PN), and carbon dioxide (CO<sub>2</sub>) concentrations in nine classrooms from September 2021 to January 2022. The measurement campaign was carried out with different configurations of the purifier (i.e., different flow rates) while the ventilation system was continuously working. Our results showed that the ventilation systems in the classrooms were adequate in providing sufficient outdoor air to dilute indoor CO<sub>2</sub> concentrations due to the high air exchange rates (2.63-8.63 h<sup>-1</sup>). The particle penetration coefficients (P) of the investigated classrooms were very low for PM (<0.2) and PN (<0.1), with the exception of one classroom, corroborating the effectiveness of in-line filters in the ventilation systems. Additionally, the results showed that the efficiency of the air purifier exceeded 95% in capturing ultrafine and coarse particles and ranged between 82-88% for particles in the accumulation range (0.3-2 µm). The findings of this study underline the effectiveness of air purifiers and ventilation systems equipped with efficient in-line filters in substantially reducing indoor air pollution.
Antitumor Efficacy of 34.5ENVE: A Transcriptionally Retargeted and “Vstat120”-expressing Oncolytic Virus (2011)

Here, we describe the construction and testing of a novel herpes simplex virus type 1 (HSV-1) derived oncolytic virus (OV): 34.5ENVE (viral ICP34.5 Expressed by Nestin promotor and Vstat120 Expressing), for the treatment of cancer. This virus showed significant glioma-specific killing and antiangiogenic effects in vitro and in vivo. Treatment of subcutaneous and intracranial glioma-bearing mice with 34.5ENVE showed a significant increase in median survival of mice in four different glioma models. Histology and dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) revealed reduced microvessel density (MVD) and increased tumoral necrosis in 34.5ENVE-treated tumor tissue compared to control OV-treated tumor tissue. Collectively, these results describe the construction, efficacy, and impact on tumor microenvironment of a transcriptionally driven OV armed with Vstat120 gene expression. These preclinical results will facilitate future clinical testing of 34.5ENVE.
The identification and purification of the heterotrimeric GTP-binding protein from squid (<i>Loligo forbesi</i>) photoreceptors (1991)

The principal GTP-binding protein (G-protein) from squid (Loligo forbesi) photoreceptor membranes has been identified by amino acid sequencing. The heterotrimeric protein was purified by detergent solubilization and ion-exchange chromatography. The amino acid sequence of the G-protein alpha-subunit (G-alpha) indicates that this subunit is closely related to the recently characterized Gq subgroup, whereas the G-gamma subunit varies widely in sequence from other homologues.
Synthesis and Antitumor Activity of 1- -4-Selenoarabinofuranosyl cytosine (4'-Seleno-ara-C) (2008)

4-Seleno analogue of 1-beta-arabinofuranosyl cytosine (ara-C) was synthesized via 4'-selenouridine as a key intermediate, which was easily prepared from D-ribose. The arabino configuration was achieved by chemoselective ring opening of the 2,2'-anhydro-4'-selenouridine. The synthesized 4'-seleno-ara-C showed potent antitumor activity (IC(50) = 1.5 microM) against stomach cancer cells (SNU638).
The Near Field Effect in Transmitter Design for Incoherent Millimeter-Wave Imaging (2021)

The use of incoherent signal illumination is seeing increasing interest for millimeter-wave imaging applications, due to the fact that the transmitters and receivers need not be synchronized in such systems. Furthermore, exact knowledge of the transmit waveforms and the resultant radiation pattern is not required either, so long as the spatiotemporal radiation pattern is sufficiently uncorrelated. Designing the transmit systems to ensure such spatio-temporal properties is not always straight-forward, especially when a small number of transmitters is used, since the image plane is typically in the near-field of the array. In this paper, we discuss the connection between the near field and spatiotemporal incoherence for illuminating signals in incoherent millimeter-wave imaging.
Static and dynamic power system load emulation in converter-based reconfigurable power grid emulator (2014)

A hardware test-bed platform emulating multiple-area power system scenario dynamics has been established aiming at multiple time-scale emulations. In order to mimic real power flow situation in the system, the load emulators have to behave like real ones in both its static and dynamic characteristics. A constant-impedance, constant-current, and constant-power (ZIP) model has been used for static load type, while a three-phase induction motor model has been built to represent dynamic load types. In this paper, ways of modeling ZIP and induction motor loads and the performance of each load emulator are discussed. A comparison between simulation and experimental results are shown as well for the validation of the emulator behavior.
Vaccines That Reduce Viral Shedding Do Not Prevent Transmission of H1N1 Pandemic 2009 Swine Influenza A Virus Infection to Unvaccinated Pigs (2020)

Swine influenza A virus (swIAV) infection causes substantial economic loss and disease burden in humans and animals. The 2009 pandemic H1N1 (pH1N1) influenza A virus is now endemic in both populations. In this study, we evaluated the efficacy of different vaccines in reducing nasal shedding in pigs following pH1N1 virus challenge. We also assessed transmission from immunized and challenged pigs to naive, directly in-contact pigs. Pigs were immunized with either adjuvanted, whole inactivated virus (WIV) vaccines or virus-vectored (ChAdOx1 and MVA) vaccines expressing either the homologous or heterologous influenza A virus hemagglutinin (HA) glycoprotein, as well as an influenza virus pseudotype (S-FLU) vaccine expressing heterologous HA. Only two vaccines containing homologous HA, which also induced high hemagglutination inhibitory antibody titers, significantly reduced virus shedding in challenged animals. Nevertheless, virus transmission from challenged to naive, in-contact animals occurred in all groups, although it was delayed in groups of vaccinated animals with reduced virus shedding.<b>IMPORTANCE</b> This study was designed to determine whether vaccination of pigs with conventional WIV or virus-vectored vaccines reduces pH1N1 swine influenza A virus shedding following challenge and can prevent transmission to naive in-contact animals. Even when viral shedding was significantly reduced following challenge, infection was transmissible to susceptible cohoused recipients. This knowledge is important to inform disease surveillance and control strategies and to determine the vaccine coverage required in a population, thereby defining disease moderation or herd protection. WIV or virus-vectored vaccines homologous to the challenge strain significantly reduced virus shedding from directly infected pigs, but vaccination did not completely prevent transmission to cohoused naive pigs.
Phosphorylation of Janus kinase 1 (JAK1) by AMP-activated protein kinase (AMPK) links energy sensing to anti-inflammatory signaling (2016)

Adenosine 5'-monophosphate-activated protein kinase (AMPK) is a pivotal regulator of metabolism at cellular and organismal levels. AMPK also suppresses inflammation. We found that pharmacological activation of AMPK rapidly inhibited the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) pathway in various cells. In vitro kinase assays revealed that AMPK directly phosphorylated two residues (Ser<sup>515</sup> and Ser<sup>518</sup>) within the Src homology 2 domain of JAK1. Activation of AMPK enhanced the interaction between JAK1 and 14-3-3 proteins in cultured vascular endothelial cells and fibroblasts, an effect that required the presence of Ser<sup>515</sup> and Ser<sup>518</sup> and was abolished in cells lacking AMPK catalytic subunits. Mutation of Ser<sup>515</sup> and Ser<sup>518</sup> abolished AMPK-mediated inhibition of JAK-STAT signaling stimulated by either the sIL-6Rα/IL-6 complex or the expression of a constitutively active V658F-mutant JAK1 in human fibrosarcoma cells. Clinically used AMPK activators metformin and salicylate enhanced the inhibitory phosphorylation of endogenous JAK1 and inhibited STAT3 phosphorylation in primary vascular endothelial cells. Therefore, our findings reveal a mechanism by which JAK1 function and inflammatory signaling may be suppressed in response to metabolic stress and provide a mechanistic rationale for the investigation of AMPK activators in a range of diseases associated with enhanced activation of the JAK-STAT pathway.
Cost comparison of 1&amp;#x002B;1 path protection schemes: A case for coding (2012)

Communication networks have to provide a high level of resilience in order to ensure sufficient Quality of Service for mission-critical services. Currently, dedicated 1+1 path protection is implemented in backbone networks to provide the necessary resilience. On the other hand, there are several possible realization strategies for 1+1 path protection functionality (1PPF), utilizing both diversity- and network coding. In this paper we consider the cost aspects of the different realization strategies. We evaluate the cost of providing 1PPF both analytically and empirically in realistic network topologies. Our results show that both diversity and network coding can provide 1PPF with reduced cost compared to traditional 1+1 path protection, even in case of short paths and strict coding restrictions. Specifically, the network coding scheme could be used as a cost-efficient and potentially all-optical realization of 1PPF.
Localization and Neurochemical Aspects of Serotonin in the Gut (2020)

The ability of the enteric nervous system to mediate reflex activity, even when isolated from the brain and spinal cord, is the physiological characteristic that most strikingly distinguishes the intrinsic innervation of the gut from that of any other peripheral organ. Recent experiments in which vagal efferent terminals were identified with an anterograde tracer support the idea that many enteric neurons do not receive a central nervous system innervation, although there are many vagal motor terminals in the gut, especially in the stomach. Enteric neurons project out of the gut to innervate pancreatic ganglia, the ganglionated plexus of the gallbladder, and prevertebral sympathetic ganglia. Surprisingly, the crest-derived emigres that colonize the bowel are not committed to develop specifically as enteric neurons or glia, either at the time they depart from the crest or even after they have completed their migration and arrived in the gut.
Network Science Experimentation Vision (2015)

Abstract : The success of military operations has been shown to depend upon the capabilities and performance of a heterogeneous collection of interdependent networks. This report outlines and discusses an experimentation vision that identifies and organizes a set of research activities and the experimentation ecosystem necessary to improve our understanding of these multi-genre composite networks.
Brief Announcement: Towards Reduced Instruction Sets for Synchronization (2017)

Contrary to common belief, a recent work by Ellen, Gelashvili, Shavit, and Zhu has shown that computability does not require multicore architectures to support "strong" synchronization instructions like compare-and-swap, as opposed to combinations of "weaker" instructions like decrement and multiply. However, this is the status quo, and in turn, most efficient concurrent data-structures heavily rely on compare-and-swap (e.g. for swinging pointers). We show that this need not be the case, by designing and implementing a concurrent linearizable Log data-structure (also known as a History object), supporting two operations: append(item), which appends the item to the log, and get-log(), which returns the appended items so far, in order. Readers are wait-free and writers are lock-free, hence this data-structure can be used in a lock-free universal construction to implement any concurrent object with a given sequential specification. Our implementation uses atomic read, xor, decrement, and fetch-and-increment instructions supported on X86 architectures, and provides similar performance to a compare-and-swap-based solution on today's hardware. This raises a fundamental question about minimal set of synchronization instructions that the architectures have to support.
Modelling and experimental validation of internal short‐circuit fault in salient‐pole synchronous machines using numerical gap function including stator and rotor core saturation (2013)

In this study, the winding function method is modified and used to calculate the machine inductances in two different cases, namely, a healthy case and a short‐circuited stator winding case. For the first time, a numerical air‐gap function is used in addition to a model of the air gap of salient‐pole machines which considers the stator slot effects. The modified winding function (MWF) method introduced here is more precise when compared with previous methods. This MWF enables one to compute the air‐gap function more accurately. Also a mathematical model that allows taking stator and rotor core saturation into account in both healthy and faulty conditions is presented in this study. Stator and rotor winding currents in healthy and faulty condition, obtained from experimental results, are compared with simulation results to verify the accuracy of the proposed method.
Leitfaden für die Praxis - Unklar erhöhte Transaminasen und die klinische Bedeutung der nichtalkoholischen Fettleber (2004)

Die Fettleber - ein häufiger Zufallsbefund bei einer bildgebenden Untersuchung - ist mit einer Prävalenz von etwa 20 % die häufigste pathologische Leberveränderung in der westlichen Welt. Ihr pathologischer Charakter ist jedoch noch nicht definitiv geklärt. Zur Entzündung der Fettleber kommt es nach heutigem Verständnis, wenn ihre Schädigung durch hepatotrope Noxen wie zum Beispiel Medikamente, Alkohol, bakterielle Toxine aus der Darmflora, Hyperglykämie oder Hyperlipidämie eine hypothetische Toleranzschwelle der Leber übersteigen („Double-hit-Hypothese”). Bevor die Diagnose jedoch endgültig festgestellt werden kann, müssen andere Lebererkrankungen differenzialdiagnostisch ausgeschlossen werden. Bestätigt sich die Diagnose „Steatohepatitis”, müssen zur ursächlichen individuellen Therapie die häufig multifaktoriellen Ursachen der Erkrankung abgeklärt werden (z.B. Diabetes: Insulinsensitizer, optimierte Insulintherapie; Adipositas: kalorienreduzierte Diät). Unabhängig von der Pathogenese werden zusätzlich häufig Ursodeoxycholsäure, Betain, Vitamin E und Gemfibrozil eingesetzt - obwohl die Effizienz dieser Therapiestrategien nicht oder noch nicht ausreichend durch evidenzbasierte Studien belegt ist.
The effect of partial pressure of carbon dioxide on anorthite dissolution. (1999)

The dissolution experiment of anorthite was carried out under different partial pressures of CO2 (PCO2) to understand the role of weathering of Ca and Mg silicates in the removal of CO2 from the atmosphere in the Precambrian. A newly-developed apparatus can control PCO2 in a mineral-water reaction vessel and vary PCO2 and temperatures from 10−3.5 (the present atmospheric level, PAL) to 5.0 atm and from 40 to 150°C, respectively. The experiments were carried out at 150°C and pH 4.56, varying PCO2 from 10−3.5 to 1.2 atm. The dissolution rate of anorthite under high PCO2 (=1.2 atm) is faster than that under PAL by about 4 times. Calcium and Si dissolve congruently from anorthite under PAL, whereas a Ca/Si ratio in solution is lower under high PCO2. Our results suggest that the weathering rates and processes in the Archean are different from the present ones, and that the amount of Ca flux into the Archean ocean is less than that predicted assuming congruent dissolution of anorthite.
Development of microLIPS (Luciferase Immunoprecipitation Systems): a novel microfluidic assay for rapid serum antibody detection (2012)

There is considerable interest in the development of rapid, point-of-care antibody detection for the diagnosis of infectious and auto-immune diseases. In this paper, we present work on the development of a self-contained microfluidic format for the Luciferase Immunoprecipitation Systems (LIPS) assay. Whereas the majority of immunoassays for antigen-specific antibodies employ either bacteria- or yeast-expressed proteins and require the use of secondary antibodies, the LIPS technique uses a fusion protein comprised of a Renilla luciferase reporter and the antigen of interest produced via mammalian cell culture, ensuring the addition of mammalian post-translational modifications. Patient serum is mixed with the fusion protein and passed over immobilized Protein A/G; after washing, the only remaining luciferase-tagged antigens are those retained by specific antibodies. These can be quantitatively measured using chemiluminescence upon the introduction of coelenterazine. The assay has been successfully employed for a wide variety of diseases in a microwell format. We report on a recent demonstration of rapid HSV-2 diagnosis with the LIPS assay in a microfluidic format, using one microliter of serum and obtaining results in under ten minutes. We will also discuss recent progress on two fronts, both aimed at the deployment of this technology in the field: first, simplifying assay operation through the automation of flow control using power-free means; and second, efforts to increase signal levels, primarily through strategies to increase antibody binding capacity, in order to move towards portable battery powered electronics.
Distribution of m6A in mRNA and its Possible Biological Role (1986)

Methylation of cellular and viral mRNA is a common post-transcriptional event whose function is not well understood. Although a role for 5′ terminal methylated cap structures in translation and mRNA stability has been demonstrated (Both et al., 1975), the function of internal methylation of specific adenine residues, to form N6-methyladenosine (m6A), is not clear. It has been suggested that m6A serves some nuclear role in precursor processing and/or transport (Camper et al., 1984) although m6A is not universally found in eukaryotic messages (Perry and Scherrer, 1975; Surrey and Nemer, 1976). The postulated nuclear role for m6A correlates positively with its presence in viral RNAs which spend a portion of their replicative cycle within the nucleus. Internal m6As are found in both cellular and viral mRNAs within the consensus sequence, AG m6AC, (Dimock and Stoltzfus, 1979; Wei et al., 1976) and it has been suggested that these residues may be involved in mRNA precursor splicing (Aloni et al., 1979; Canaani et al., 1979; Chen-Kiang et al ; 1979).
Integrated control, diagnosis and reconfiguration of a heat exchanger (1998)

Heat exchangers play an important role in chemical and process industries. In order to improve reliability and control performance, intelligent concepts for control, supervision and reconfiguration are necessary. In the paper, an approach is presented which integrates model-based adaptive control and reconfiguration based on fault detection/diagnosis applied to a heat exchanger plant. The adaptive controller and the fault detection scheme are based on a fuzzy model of the process (Takagi-Sugeno type). The fault diagnosis is performed using a self-organizing fuzzy structure.
Vertical GaN Power Electronics - Opportunities and Challenges (invited). (2021)

Abstract not provided.
On the security of OCDM-based encryption against key-search attacks (2009)

Monte-Carlo simulations of the effectiveness of key-search attacks on OCDM-based encryption reveal that proper code scrambling can result in codes that obscure one another and are resilient against iteratively improving an attacker's key guesses.
Pf HRP2 and Pf LDH antigen detection for monitoring the efficacy of artemisinin-based combination therapy (ACT) in the treatment of uncomplicated falciparum malaria (2009)

Although both RDTs are as sensitive as microscopy in detecting true malaria cases, the PfHRP2 RDT had very low specificity during follow-up until day 28. On the other hand, the PfLDH test could be used to detect failures and, therefore, to assess anti-malarial efficacy.