gebhart/patrepeval huggingface dataset:
Contribution of B Cells to Autoimmune Pathogenesis (2005)

This chapter contains sections titled: Introduction Autoimmunity and Immune Deficiency Basic Mechanisms Providing Diversity to the B Cell Receptor Ig V Gene Usage by B Cells of Healthy Individuals Potential Abnormalities in Molecular Mechanisms Underlying IgV Gene Usage in Systemic Autoimmune Diseases Lack of Molecular Differences in V(D)J Recombination in Patients with Systemic Autoimmune Diseases Receptor Editing/Revision and Autoimmunity Selective Influences Shaping the Ig V Gene Repertoire in Autoimmune Diseases IgV Gene Usage by Autoantibodies Role of Somatic Hypermutation in Generating Autoantibodies Disturbed Homeostasis of Peripheral B Cells in Autoimmune Diseases Signal Transduction Pathways in B Cells B Cell Function Results from Balanced Agonistic and Antagonistic Signals Altered B Cell Longevity can Lead to Autoimmunity Altered B Cell Activation can Lead to Autoimmunity Inhibitory Receptors of B Cells Inhibitory Receptor Pathways and Autoimmunity B Cell Abnormalities Leading to Rheumatoid Arthritis Activated B Cells may Bridge the Innate and Adaptive Immune System “Humoral Imprinting” in Rheumatoid Arthritis Indications of Enhanced B Cell Activity in RA T Cell Independent B Cell Activation Depleting anti-B Cell Therapy as a Novel Therapeutic Strategy
Outage minimization and optimal power control for the fading relay channel (2005)

In this work, we show that in the wireless relay network, a tremendous savings in energy can be achieved by having side information at the transmitters and by employing power control. We present efficient protocols and the corresponding optimal power control policies that approach the universal lower bound on the outage probability of the block fading relay channel. Each of the proposed protocols have their own utility for specific channel conditions. However, a hybrid protocol between two known coding schemes is the best scheme for all channel conditions and is sufficient to approach the lower bound on outage probability. Unlike the single link channel, we show that exploiting the knowledge of the channel at the transmitters can significantly lower the outage even if the transmit powers at the source and relay have to be kept constant. In this case, it is also demonstrated that the lower bound on outage is closely followed by the outage probability of the hybrid protocol. Our results reveal that exploiting the right network protocol in conjunction with power control result in orders of magnitude savings in power over direct transmission for a target performance level.
Measurement of the isolated prompt photon cross section in<i>p</i>¯<i>p</i>collisions at √<i>s</i>=1.8 TeV (1992)

We present a measurement of the cross section for production of isolated prompt photons in p\ifmmode\bar\else\textasciimacron\fi{}p collisions at \ensuremath{\surd}s =1.8 TeV. The cross section, measured as a function of transverse momentum (${\mathit{P}}_{\mathit{T}}$), agrees qualitatively with QCD calculations but has a steeper slope at low ${\mathit{P}}_{\mathit{T}}$.
Supplementary Table 4 from A High-Throughput Panel for Identifying Clinically Relevant Mutation Profiles in Melanoma (2023)

&lt;p&gt;PDF file - 210K, Results of matching/ duplicate samples.&lt;/p&gt;
Indistinguishability of independent single photons (2009)

The indistinguishability of independent single photons is presented by decomposing the single photon pulse into the mixed state of different transform-limited pulses. The entanglement between single photons and outer environment or other photons induces the distribution of the center frequencies of those transform-limited pulses and makes photons distinguishable. Only the single photons with the same transform-limited form are indistinguishable. In details, the indistinguishability of single photons from the solid-state quantum emitter and spontaneous parametric down-conversion is examined with two-photon Hong-Ou-Mandel interferometer. Moreover, experimental methods to enhance the indistinguishability are discussed, where the usage of spectral filter is highlighted.
Quantifying electronic charge trap states and the effect of imprint on ferroelectric poly(vinylidene fluoride-trifluoroethylene) thin films (2010)

Poly(vinylidene fluoride-trifluoroethylene) [P(VDF-TrFE)] thin films have been extensively studied for their ferroelectric properties and are a promising material for sensing and memory applications. Imprint, the time-dependent resistance to polarization reversal, is a key material property that limits applications and is poorly understood. We have used a fast ramp rate thermally stimulated current (FR-TSC) technique to investigate the proposed link between imprint time and filling of charge trap states, and to characterize these traps in an appropriate time-frame. Thin films of P(VDF-TrFE) on oxidized Si substrates were characterized following controlled initialization, fatigue, polarization, and imprint. Traps were allowed to fill during room temperature imprint for times from 1 to 104 s. Remaining unfilled traps were subsequently filled and quantified by FR-TSC temperature cycling from 20 to 100 °C at 1 K/s. Results confirm that charge trap filling occurs both with time, under isothermal conditions, as well as with increasing temperature. The rate of charge accumulation induced by FR-TSC exhibits the same logarithmic dependence with time as the experimentally measured imprint voltage; this strongly suggests a direct link between these trapped charges and the imprint field. Furthermore, measurements of the switching speed in post FR-TSC films were found to be independent of the imprint time, confirming that thermal cycling brought all samples to a common final state. These results provide further understanding of the polarization dynamics and materials interactions affecting the ferroelectric properties of P(VDF-TrFE).
A NEUROSURGEON'S GUIDE TO STEM CELLS, CANCER STEM CELLS, AND BRAIN TUMOR STEM CELLS (2009)

Stem cells and their potential applications have become the forefront of scientific, political, and ethical discourse. Whereas stem cells were long accepted as units of development and evolution, it is now becoming increasingly clear that they are also units of oncogenesis. Although the field of stem cell biology is expanding at an astounding rate, the data attained are not readily translatable for the physicians who may eventually deliver these tools to patients. Herein, we provide a brief review of stem cell and cancer stem cell biology and highlight the scientific and clinical implications of recent findings regarding the presence of cancer-forming stem cells in brain tumors.
Highly strained channel with low-resistivity carbon-doped source/drain formed by cascade C<sub>7</sub>H<i><sub>x</sub></i>implantation followed by rapid solid-phase epitaxy and laser annealing for n-channel metal–oxide–semiconductor field-effect transistor (2015)

We show the systematical investigation results of the effects of the implanted ion dose of P or As under various solid-phase epitaxy (SPE) conditions on the local stress in channel regions in metal–oxide–semiconductor field-effect transistor (MOSFET) structures, and on sheet resistance and strain in carbon-doped source/drain (Si:C-S/D) layers. P or As substitution is in conflict with C substitution in Si:C layers during SPE. Furthermore, the amount of P incorporated instead of C into the Si lattice site is larger than that of As incorporated instead of C. Therefore, low-resistivity Si:C layers with low stress in the case of using P and high-resistivity Si:C layers with high stress in the case of using As are formed by single-step C7Hx implantation with rapid thermal annealing and nonmelt laser annealing, respectively. As a countermeasure, we demonstrate that cascade C7Hx implantation to control the C profiles in Si:C layers is effective for achieving high-strain channels and low-resistivity Si:C-S/D layers. Control of C profiles is a key technology for state-of-the-art complementary MOS devices with Si:C-S/D.
Thermal instability control by four wave mixing in optical microcavities (2017)

Summary form only given. The interplay between ultrafast and slow nonlinearities, like Kerr and thermo-optical nonlinearities, is well-known for generating bistability, self-pulsing and chaotic regimes in optical microcavities. These effects have been observed in different kinds of devices, such as doped silica glass optical microcavities with high refractive index [1], and numerical models have been investigated to provide a description of such dynamics, e.g. in semiconductor nanocavities [2-3]. Specifically, self-pulsing can be explored to generate all-optical stochastic sources, and it has been recently demonstrated with opto-mechanical nonlinearities [4]. In this framework, all-optical control of multistable or self-pulsing regions is highly desirable and it is usually achieved with an additional control signal.
WE‐DE‐BRA‐05: Monte Carlo Simulation of a Novel Multi‐Layer MV Imager (2016)

Purpose: To develop and validate a Monte Carlo (MC) model of a novel multi‐layer imager (MLI) for megavolt (MV) energy beams. The MC model will enable performance optimization of the MLI design for clinical applications including patient setup verification, tumor tracking and MVCBCT. Methods: The MLI is composed of four layers of converter, scintillator and light detector, each layer similar to the current clinical AS1200 detector (Varian Medical Systems, Inc). The MLI model was constructed using the Geant4 Application for Tomographic Emission (GATE v7.1) and includes interactions for x‐ray photons, charged particles and optical photons. Computational experiments were performed to assess Modulation Transfer Function (MTF), Detective Quantum Efficiency (DQE) and Noise Power Spectrum normalized by photon fluence and average detector signal (qNNPS). Results were compared with experimental measurements. The current work incorporates, in one model, the complete chain of events occurring in the imager; i.e. starting from x‐ray interaction to charged particle transport and energy deposition to subsequent generation, interactions and detection of optical photons. Results: There is good agreement between measured and simulated MTF, qNNPS and DQE values. Normalized root mean squared error (NRMSE) between measured and simulated values over all four layers was 2.18%, 2.43% and 6.05% for MTF, qNNPS and DQE respectively. The relative difference between simulated and measured values for qNNPS(0) was 1.68% and 1.57% for DQE(0). Current results were obtained using a 6MV Varian Truebeam™ spectrum. Conclusion: A comprehensive Monte Carlo model of the MLI prototype was developed to allow optimization of detector components. The model was assessed in terms of imaging performance using standard metrics (i.e. MTF, qNNPS, DQE). Good agreement was found between simulated and measured values. The model will be used to assess alternative detector constructions to facilitate advanced clinical imaging applications including MV‐CBCT and tumor tracking. The project was supported, partially, by a grant from Varian Medical Systems, Inc., and Award No. R01CA188446‐01 from the National Cancer Institute. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Cancer Institute or the National Institutes of Health.
Oxidative stress at low levels can induce clustered DNA lesions leading to NHEJ mediated mutations (2020)

DNA damage and mutations induced by oxidative stress are associated with various different human pathologies including cancer. The facts that most human tumors are characterized by large genome rearrangements and glutathione depletion in mice results in deletions in DNA suggest that reactive oxygen species (ROS) may cause gene and chromosome mutations through DNA double strand breaks (DSBs). However, the generation of DSBs at low levels of ROS is still controversial. In the present study, we show that H2O2 at biologically-relevant levels causes a marked increase in oxidative clustered DNA lesions (OCDLs) with a significant elevation of replication-independent DSBs. Although it is frequently reported that OCDLs are fingerprint of high-energy IR, our results indicate for the first time that H2O2, even at low levels, can also cause OCDLs leading to DSBs specifically in G1 cells. Furthermore, a reverse genetic approach revealed a significant contribution of the non-homologous end joining (NHEJ) pathway in H2O2-induced DNA repair & mutagenesis. This genomic instability induced by low levels of ROS may be involved in spontaneous mutagenesis and the etiology of a wide variety of human diseases like chronic inflammation-related disorders, carcinogenesis, neuro-degeneration and aging.
Non-invasive and continuous monitoring of the sol–gel phase transition of supramolecular gels using a fast (open-ended coaxial) microwave sensor (2015)

An open coaxial re-entrant microwave sensor has been used for the non-invasive and continuous monitoring of the sol-gel transition of physical gels characterized by different gelation mechanisms, solvents, compositions, and stabilities. Comparison of measurements by differential scanning calorimetry allowed the identification of the phase transition by a change in the dielectric properties of the material over time.
Tim1 and Tim3 are not essential for experimental allergic asthma (2011)

Thus, Tim1 and Tim3 are not essential for the induction of the type-2 response in lung allergy. This is contrary to what was proposed in a number of other studies using neutralizing and activating antibodies and questions the clinical relevance of Tim1 and Tim3 for novel allergy therapies.
Metabolism of Tenofovir and Didanosine in Quiescent or Stimulated Human Peripheral Blood Mononuclear Cells (2003)

There is no significant interaction between tenofovir and didanosine in human PBMCs as determined by the extent of formation of the phosphorylated anabolites. This suggests that adjusting didanosine dosage, when given with tenofovir, to achieve similar didanosine plasma concentrations, may be sufficient to accommodate the systemic drug interaction.
Mutations in<i>GPR143/OA1</i>and<i>ABCA4</i>Inform Interpretations of Short-Wavelength and Near-Infrared Fundus Autofluorescence (2018)

These studies corroborate RPE melanin as the major source of NIR-AF but also indicate that bisretinoid lipofuscin, when present at sufficient concentrations, contributes to the NIR-AF signal. Ocular melanin attenuates the SW-AF signal.
MicroRNA-135a Modulates Hepatitis C Virus Genome Replication through Downregulation of Host Antiviral Factors (2018)

Cellular microRNAs (miRNAs) have been shown to modulate HCV infection via directly acting on the viral genome or indirectly through targeting the virus-associated host factors. Recently we generated a comprehensive map of HCV-miRNA interactions through genome-wide miRNA functional screens and transcriptomics analyses. Many previously unappreciated cellular miRNAs were identified to be involved in HCV infection, including miR-135a, a human cancer-related miRNA. In the present study, we investigated the role of miR-135a in regulating HCV life cycle and showed that it preferentially enhances viral genome replication. Bioinformatics-based integrative analyses and subsequent functional assays revealed three antiviral host factors, including receptor interacting serine/threonine kinase 2 (RIPK2), myeloid differentiation primary response 88 (MYD88), and C-X-C motif chemokine ligand 12 (CXCL12), as bona fide targets of miR-135a. These genes have been shown to inhibit HCV infection at the RNA replication stage. Our data demonstrated that repression of key host restriction factors mediated the proviral effect of miR-135a on HCV propagation. In addition, miR-135a hepatic abundance is upregulated by HCV infection in both cultured hepatocytes and human liver, likely mediating a more favorable environment for viral replication and possibly contributing to HCV-induced liver malignancy. These results provide novel insights into HCV-host interactions and unveil molecular pathways linking miRNA biology to HCV pathogenesis.
Public Readiness to Adopt Solar Energy – Responses of Some Finnish Citizens (2018)

Although most of the Finns are positive toward solar energy, they have long been stumbled to adopt and hesitated to rely on it due to its traditional weak images and mostly unfavourable weather conditions. However, in solar energy, Finland is already credited to award-winning innovation, demonstration projects, business models, and so on. Additionally, decreased price and the availability of some incentives have got the public attraction. In such contexts, the prospects of solar energy in the country in terms of public readiness to invest and adopt, have induced this study to undertake. Results driven by this qualitative study through some semi-structured interviews have shown a trend of escalating social acceptance rate of solar energy among Finns. However, they were seemed to be still entangled with some misconceptions, lack of well-exposed information, good numbers of visible success stories, etc. This study has also included some recommendations and future research directions.
Mapping of Major Carrot Color Genes an Expression of Carotenoid Biosynthetic Genes (2004)

While the carotenoid biosynthetic pathway has been studied several horticultural and agronomic crops, very little information exists for this conserved pathway in carrot, a primary source of dietary carotenoids. Though orange carrots are the most familiar color to Western consumers, yellow, red, and white carrots also exist and have been historically important. Modern carrot breeders are showing renewed interest in these unusual color phenotypes. Beta- and alpha-carotene are the primary pigments in orange carrot roots. Yellow carrots accumulate xanthophylls (oxygenated carotenes), red carrots accumulate lycopene (the precursor to alpha- and beta-carotene), and white carrots accumulate no detectable pigments. Differences between these phenotypes are usually monogenic or oligogenic. Our research has focused on identifying putative genes for carotenoid biosynthetic enzymes in the carrot genome, mapping them, and examining expression patterns in various tissues and carrot root pigment phenotypes. We are using this information to create a carrot pigment biosynthesis function map incorporating biosynthetic enzymes, major carrot color genes, and gene expression information.
Supplementary Figure 5 from Oncogenic MUC1-C Promotes Tamoxifen Resistance in Human Breast Cancer (2023)

&lt;p&gt;PDF file - 622K, BT474/MUC1shRNA (A) and MCF-7/vector (B) cells were treated with fixed IC50 ratios of (i) GO-203 alone on days 0, 1, 2, 3 and 4, (ii) tamoxifen alone on days 0, 2 and 4 and (iii) the GO-203/tamoxifen combination. For tamoxifen-resistant BT-474/CshRNA and MCF-7/MUC1-C cells, tamoxifen was used at the half-maximal inhibitory concentrations obtained for the tamoxifen-sensitive BT-474/MUC1shRNA and MCF-7/vector cells, respectively. The multiple effect-level isobologram analyses are shown for the ED50 (X), ED75 (+) and ED90 (⊗) values.&lt;/p&gt;
Tone in the Nugunu verb phrase (1991)

https://www.sil.org/resources/archives/47918
<i>Leishmania donovani</i> infection enhances macrophage viability in the absence of exogenous growth factor (1994)

Bone marrow-derived macrophages rapidly die in the absence of macrophage growth factor (M-CSF). However, as demonstrated here, bone marrow-derived macrophages infected with Leishmania donovani exhibit increased viability in the absence of exogenous growth factor. Forty-eight hours after inoculation with promastigotes or amastigotes, infected cell cultures contained 180 and 95% more cells, respectively, than control cultures. This effect was specific to Leishmania infection, as uptake of latex beads or avirulent promastigotes by macrophages did not enhance cell viability. L. donovani-infected macrophages also displayed increased phagocytic capacity, as compared with control macrophages and macrophages grown continuously in M-CSF-containing medium. Supernatants collected from infected cells elaborated a factor(s) that enhanced macrophage viability but did not stimulate macrophage DNA synthesis. This activity of L. donovani-infected cell-conditioned medium could be abrogated by preincubation of macrophages with cycloheximide before inoculation with the parasite, implying that macrophage protein synthesis is required for the elaboration of this factor(s).
Metabolomic and transcriptomic signatures of influenza vaccine response in healthy young and older adults (2022)

Seasonal influenza causes mild to severe respiratory infections and significant morbidity, especially in older adults. Transcriptomic analysis in populations across multiple flu seasons has provided insights into the molecular determinants of vaccine response. Still, the metabolic changes that underlie the immune response to influenza vaccination remain poorly characterized. We performed untargeted metabolomics to analyze plasma metabolites in a cohort of younger and older subjects before and after influenza vaccination to identify vaccine-induced molecular signatures. Metabolomic and transcriptomic data were combined to define networks of gene and metabolic signatures indicative of high and low antibody response in these individuals. We observed age-related differences in metabolic baselines and signatures of antibody response to influenza vaccination and the abundance of α-linolenic and linoleic acids, sterol esters, fatty-acylcarnitines, and triacylglycerol metabolism. We identified a metabolomic signature associated with age-dependent vaccine response, finding increased tryptophan and decreased polyunsaturated fatty acids (PUFAs) in young high responders (HRs), while fatty acid synthesis and cholesteryl esters accumulated in older HRs. Integrated metabolomic and transcriptomic analysis shows that depletion of PUFAs, which are building blocks for prostaglandins and other lipid immunomodulators, in young HR subjects at Day 28 is related to a robust immune response to influenza vaccination. Increased glycerophospholipid levels were associated with an inflammatory response in older HRs to flu vaccination. This multi-omics approach uncovered age-related molecular markers associated with influenza vaccine response and provides insight into vaccine-induced metabolic responses that may help guide development of more effective influenza vaccines.
ChemInform Abstract: CONSTRUCTION OF INDOLIZIDINE AND QUINOLIZIDINE RING SYSTEMS BY AN INTRAMOLECULAR 1‐AZA‐1,3‐DIENE DIELS‐ALDER REACTION. SYNTHESIS OF (.+‐.)‐EPILUPININE (1985)

Abstract Die aus dem Amin (I) und den Säurechloriden (II) zugänglichen Amide (III) und (IV) werden über (V) durch Wittig‐Reaktion mit (VI) in die ungesättigten Ester (VII) übergefuhrt, deren in situ hergestellte O‐Silyl‐amid‐Derivate in einer intramolekularcn Diels‐ Alder‐Reaktion zu den Indolizidinen (VIII) und (IX) (als Nebenprodukte) cyclisiert werden.