gebhart/patrepeval huggingface dataset:
Data from Histone Deacetylase Inhibitors Synergize with Catalytic Inhibitors of EZH2 to Exhibit Antitumor Activity in Small Cell Carcinoma of the Ovary, Hypercalcemic Type (2023)

&lt;div&gt;Abstract&lt;p&gt;Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare but extremely lethal malignancy that mainly impacts young women. SCCOHT is characterized by a diploid genome with loss of SMARCA4 and lack of SMARCA2 expression, two mutually exclusive ATPases of the SWI/SNF chromatin-remodeling complex. We and others have identified the histone methyltransferase EZH2 as a promising therapeutic target for SCCOHT, suggesting that SCCOHT cells depend on the alternation of epigenetic pathways for survival. In this study, we found that SCCOHT cells were more sensitive to pan-HDAC inhibitors compared with other ovarian cancer lines or immortalized cell lines tested. Pan-HDAC inhibitors, such as quisinostat, reversed the expression of a group of proteins that were deregulated in SCCOHT cells due to SMARCA4 loss, leading to growth arrest, apoptosis, and differentiation &lt;i&gt;in vitro&lt;/i&gt; and suppressed tumor growth of xenografted tumors of SCCOHT cells. Moreover, combined treatment of HDAC inhibitors and EZH2 inhibitors at sublethal doses synergistically induced histone H3K27 acetylation and target gene expression, leading to rapid induction of apoptosis and growth suppression of SCCOHT cells and xenografted tumors. Therefore, our preclinical study highlighted the therapeutic potential of combined treatment of HDAC inhibitors with EZH2 catalytic inhibitors to treat SCCOHT.&lt;/p&gt;&lt;/div&gt;
Nanoimaging and Control of Molecular Vibrations through Electromagnetically Induced Scattering Reaching the Strong Coupling Regime (2018)

Optical resonators can enhance light-matter interaction, modify intrinsic molecular properties such as radiative emission rates, and create new molecule-photon hybrid quantum states. To date, corresponding implementations are based on electronic transitions in the visible spectral region with large transition dipoles yet hampered by fast femtosecond electronic dephasing. In contrast, coupling molecular vibrations with their weaker dipoles to infrared optical resonators has been less explored, despite long-lived coherences with 2 orders of magnitude longer dephasing times. Here, we achieve excitation of molecular vibrations through configurable optical interactions of a nanotip with an infrared resonant nanowire that supports tunable bright and nonradiative dark modes. The resulting antenna-vibrational coupling up to 47 ± 5 cm<sup>-1</sup> exceeds the intrinsic dephasing rate of the molecular vibration, leading to hybridization and mode splitting. We observe nanotip-induced quantum interference of vibrational excitation pathways in spectroscopic nanoimaging, which we model classically as plasmonic electromagnetically induced scattering as the phase-controlled extension of the classical analogue of electromagnetically induced transparency and absorption. Our results present a new regime of IR spectroscopy for applications of vibrational coherence from quantum computing to optical control of chemical reactions.
On the distortion of binaural localization cues using headphones (2010)

This study investigates the frequency response of different headphones in the context of their suitability to virtual binaural reproduction. Acoustic impulse responses of the combined transducer-to-eardrum coupling were measured using an Artificial Pinna/Earcanal simulator. Pairs of measurements were recorded and the time and level differences between pairs were estimated within each of the first 24 critical bands of hearing. The measurements indicate that closed type headphones can potentially produce large interaural time delays (ITD) at low frequencies which could potentially corrupt perceived source angle in virtual auditory displays.
Otimização De Amplificador De Potência Doherty Através De Computação Evolucionária E Transformada De Incerteza (2016)

Um otimizador genetico robusto baseado na transformada de incerteza e no Algoritmo Genetico de Selecao por Nao-dominacao-II e apresentado. O algoritmo proporciona reducao significativa do custo computacional se comparado com o metodo de Monte Carlo. A transformada de incerteza permite a determinacao das incertezas do desempenho do circuito a partir das incertezas dos componentes, proporcionando uma busca guiada pela robustez. Alem da economia do custo computacional apresentada, outros resultados sao as diversas opcoes de circuitos oferecidas ao projetista atraves da busca com multiplos objetivos. O amplificador de potencia Doherty foi utilizado como estudo de caso.
Modern Laboratory-Based Education for Power Electronics and Electric Machines (2005)

The study of modern energy conversion draws upon a broad range of knowledge and often requires a fair amount of experience. This suggests that laboratory instruction should be an integral component of a power electronics and electric machines curriculum. However, before a single watt can be processed in a realistic way, the student must understand not only the operation of conversion systems but also more advanced concepts such as control theory, speed and position sensing, switching signal generation, gate drive isolation, circuit layout, and other critical issues. Our approach is to use a blue-box module where these details are pre-built for convenience, but not hidden from the students inside a black box. Recent improvements to our blue-box modules are described in this paper and include a dual-MOSFET control box with independently isolated FET devices, a triple silicon controlled rectifier control box, a discretely built, high quality pulse-width modulation inverter, a small discrete brushless dc drive system, and a high-performance computer-controlled brushless dc dynamometer motor drive system. Complete details, sufficient to allow the reader to duplicate these designs, are publicly available.
Overcoming the Aging Systemic Milieu to Restore Neural Stem Cell Function (2011)

As mammals age, the rate of neurogenesis in the brain declines with a concomitant reduction in cognitive ability. Recent data suggest that plasma-borne factors are responsible for inhibition of neurogenesis. When the circulatory systems of old and young mice are connected, the old mice experience increased neurogenesis and the young mice exhibit less neurogenesis, suggesting the importance of systemic circulating factors. Chemokine CCL11/eotaxin has been identified as a factor that increases with aging. Injections of CCL11 inhibit neurogenesis in young mice, an effect likely mediated by CCR3 receptors on neural stem cells. Identification of a specific factor that plays a causative role in stem cell dysfunction in aging is consistent with data showing that transforming growth factor-β (TGF-β) inhibits satellite cell-mediated repair. Together, these data suggest that the systemic milieu plays a critical role in the aging of adult stem cells. Because adult stem cells help maintain homeostasis by providing the possibility of replacing metabolically damaged differentiated cells, aging of the systemic milieu and stem cell niches may drive functional decline during aging. The identification of a specific systemic change suggests that aging is more amenable to therapeutic modulation than work on global metabolism-derived damage and cellular senescence implies.
Cross-Reacting Antigens in Chemically Induced Sarcomas Are Fetal Determinants (1977)

Serologic cross-reactivity has been demonstrated among three MCA-induced sarcomas in C57BL/6N female mice (MCA-2, MCA-3, and MCA-12) with a microcytotoxicity assay. Serum from mice bearing MCA-3 tumor was cytotoxic to both MCA-2 and MCA-3 tumor cells at a titer of 1:8. Sequential absorptions of this serum with syngeneic embryo cells completely eliminate cytotoxicity against MCA-2 cells without affecting the cytotoxic titer against MCA-3 cells. Serum hyperimmune to the MCA-3 tumor reacted with MCA-3, MCA-2, and MCA-12 tumors. Absorption of this serum with embryo cells eliminated cytotoxicity against MCA-2 and MCA-12 cells, but was incapable of lowering the titer against MCA-3 cells below 1:40. Similarly, serum hyperimmune to MCA-2 tumor was lytic to MCA-2, MCA-3, and MCA-12 before absorption, but was lytic only to MCA-2 cells after absorption with sygeneic embryo cells. Thus, the in vitro cross-reactivity between MCA-induced sarcomas is due to a common fetal antigen(s), which is distinct from the individual tumor-specific antigens of each tumor. Since these tumors do not exhibit cross-reactivity in in vivo challenge experiments, it appears that this fetal antigen is not responsible for in vivo immune protection.
Long-term cultures of murine fetal liver retain very early B lymphoid phenotype. (1984)

Long-term cultures of murine fetal liver have been successfully established using a modification of our in vitro bone marrow culture system (14, 15). Fetal liver cells from midgestation BALB/c embryos were plated onto BAB-14 bone marrow stromal cell-adherent layers. After a 3-5 wk period, cell growth began to increase and these cells were expanded in number on fresh feeder layers. The cultured fetal liver cells were lymphoid in morphology, 5-20% cytoplasmic Ig-positive, but less than 1% surface Ig-positive. Southern blot analysis of the cultured fetal liver cells, as well as cultured bone marrow-derived B cells, demonstrated a population with germline Ig heavy chain loci, possibly representing very early B cell precursors. Abelson murine leukemia virus (A-MuLV) clonal transformants of such cultured fetal liver cells had a phenotypic distribution similar to that seen with fresh fetal liver transformants but distinct from those obtained with the transformation of either cultured or fresh bone marrow. All A-MuLV transformants isolated had rearrangements at the mu heavy chain locus of both chromosomes, irrespective of Ig production. In addition, most mu heavy chain producers had at least one rearranged kappa gene locus. These long-term fetal liver cultures provide large numbers of cells for studying events early in the B lymphocyte lineage. The cultured fetal liver cells retained phenotypic traits similar to fresh fetal liver B cells and distinctive from bone marrow cells cultured under similar conditions.
Functional downregulation of GluR2 in piriform cortex of kindled animals (2000)

We have previously shown kindling-induced downregulation of the AMPA receptor GluR2 subunit in piriform cortex, as measured by Western blotting. In the present studies, we performed whole-cell patch clamp analysis of AMPA receptor-mediated currents from kindled and control animals to determine if the downregulation observed previously had any functional significance. These experiments were done in the absence and presence of N-hydroxyphenylpropanoyl spermine (HPPS), a polyamine that blocks currents through AMPA receptors lacking GluR2. We report that AMPA receptor-mediated currents recorded from piriform cortex layer II pyramidal cells in slices from animals kindled to 10 fully generalized seizures were blocked by HPPS. In contrast, application of HPPS had no effect on current amplitude in control animals, or in animals that had not been fully kindled. Western blotting revealed that decreases in GluR2 were seen in animals that had experienced at least one fully generalized seizure, but were not observed at earlier stages of kindling development. The increased polyamine sensitivity of AMPA receptor-mediated currents in kindled animals is consistent with the hypothesis that kindling induces formation of AMPA receptors that lack GluR2 in piriform cortex pyramidal cells. It has been demonstrated that polyamine sensitivity is directly correlated with the calcium permeability of the AMPA receptor, suggesting that kindling results in the formation of AMPA receptors that are calcium-permeable. Increases in intracellular calcium through these receptors could act as a second messenger and play a role in the initiation of long-term changes that contribute to the pathogenesis of kindling-induced epilepsy.
Abstract 698: MCL1 dependent cells are sensitive to the CDK inhibitor Dinaciclib. (2013)

Abstract Dinaciclib is a potent inhibitor of cyclin dependent kinases (CDKs) 1, 2, 5, and 9 and is currently in Phase 3 for the treatment of refractory chronic lymphocytic leukemia (CLL). To further understand the mechanism of action, identify predictive biomarkers, and find additional cancer types which may benefit from dinaciclib, we evaluated cell viability following 24 hours treatment across a panel of ∼500 cells lines. Hematopoietic cell lines were on average 3-times more sensitive than solid tumor lines. In agreement with previous findings, mRNA expression of the anti-apoptotic family member BCL-xL or the ratio of MCL1-to-BCL-xL continue to be the best predictor of dinaciclib sensitivity in both hematopoietic and solid tumor cell lines. MCL1 appears to be an important target of dinaciclib particularly in MCL1 amplified cell lines. Dependence on MCL1 was established in a panel of 19 breast, NSCLC and SCLC cell lines by depletion of the protein by either dinaciclib treatment or MCL1 RNAi. The NSCLC line H23 was highly dependent on MCL1, as RNAi knockdown decreased viability to &amp;lt;20% and could be rescued by introduction of a non-targeted MCL1 expression construct. In the H23 xenograft, dinaciclib diminished MCL1 levels and induced tumor apoptosis resulting in &amp;gt;80% tumor regression. Cell lines which lacked pro-apoptotic proteins BAX / BAK or harbored a BAX mutation were insensitive to the inhibitor. Using apoptosis defective lines we demonstrate that 24 hours of dinaciclib treatment still impacted cell count by blocking cell cycle progression as measured by FACS. These data demonstrate that both cell cycle block and induction of apoptosis contribute to dinaciclib's mechanism of action. However, the observation that MCL1 and BCL-xL were top genes associated with sensitivity suggests that induction of apoptosis is the predominant mechanism of dinaciclib's anti-tumor effect and warrants further investigation of MCL1 amplification as a predictive biomarker in future clinical studies. Citation Format: Harold Hatch, Robert Booher, Samanthi Perera, Thi Nguyen, Brian Dolinski, Samer Al-Assaad, Lauren Harmonay, Alwin Schuller, Minilik Angagaw, Brian Long, Xianlu Qu, Nathan Miselis, Mark Ayers, Michael Nebozhyn, Heather Hirsch, Danielle Greenawalt, Andrey Loboda, Thorseten Graef, Ellie Im, Rebecca Blanchard, Leigh Zawel, Peter Strack. MCL1 dependent cells are sensitive to the CDK inhibitor Dinaciclib. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 698. doi:10.1158/1538-7445.AM2013-698
Influences of antigen processing on the expression of the T cell repertoire. Evidence for MHC-specific hindering structures on the products of processing. (1988)

Two lines of evidence in the current study indicate that antigen processing is a major factor, in addition to MHC binding and T cell repertoire, that determines Ir gene responsiveness and epitope immunodominance. First, immunization with synthetic peptides of myoglobin sequences revealed new reactivities that had not appeared after priming with native myoglobin. For example, B10.S mice (H-2S) immune to equine myoglobin predominantly responded to peptide 102-118, whereas there was little, if any, response to this peptide in B10.BR (H-2k) mice immunized with native equine myoglobin. However, after immunization with the 102-118 peptide, both strains responded to the peptide. After in vitro restimulation, B10.BR T cells responded as well as B10.S T cells. Similarly, some individual 102-118-specific T cell clones from mice of both haplotypes showed similar dose responses and fine specificity patterns. Thus, low responsiveness to this site is due neither to a hole in the repertoire nor to a failure to bind to the appropriate MHC molecule. An alternative explanation was suggested by the observation that, whereas B10.S T cells from peptide 102-118-immune mice responded almost as well to whole myoglobin as to the peptide, the B10.BR T cells from peptide immune mice, while responding well to peptide, were poorly stimulated by whole myoglobin. Thus, the product of natural processing of equine myoglobin probably has hindering structures in the regions flanking the core epitope 102-118 that interfere with presentation by I-Ak but not I-AS. The second line of evidence that processing of native myoglobin may influence the apparent specificity of the T cell response was obtained using the I-Ad-restricted sperm whale myoglobin 102-118-specific clone 9.27. This clone discriminated readily between whole sperm whale myoglobin and equine myoglobin, but it did not distinguish between peptides corresponding to 102-118 of the sperm whale and equine sequences. This distinction between equine peptide and native equine myoglobin could be overcome by artificial "processing" of equine myoglobin with cyanogen bromide. In both sets of experiments, F1 APCs that present the same epitope well to T cells of another haplotype failed to overcome the defect, which was therefore not due to the availability of different processed cleavage fragments in APC of different haplotypes, as would be expected if there were MHC-linked processing. Thus, the differential responses to peptides versus native molecule for both I-Ad- and I-Ak-restricted clones appeared to depend on the restricting molecule used.(ABSTRACT TRUNCATED AT 400 WORDS)
Immunization with synthetic SARS-CoV-2 S glycoprotein virus-like particles protects Macaques from infection (2021)

Abstract The SARS-CoV-2 pandemic causes an ongoing global health crisis, which requires efficient and safe vaccination programs. Here, we present synthetic SARS-CoV2 S glycoprotein-coated liposomes that resemble in size and surface structure virus-like particles. Soluble S glycoprotein trimers were stabilized by formaldehyde cross-linking and coated onto lipid vesicles (S-VLP). Immunization of cynomolgus macaques with S-VLPs induced high antibody titers and TH1 CD4+ biased T cell responses. Although antibody responses were initially dominated by RBD specificity, the third immunization boosted non-RBD antibody titers. Antibodies showed potent neutralization against the vaccine strain and the Alpha variant after two immunizations and robust neutralization of Beta and Gamma strains. Challenge of animals with SARS-CoV-2 protected all vaccinated animals by sterilizing immunity. Thus, the S-VLP approach is an efficient and safe vaccine candidate based on a proven classical approach for further development and clinical testing.
The structure of MS-3: a glyoxalase I inhibitor produced by a mushroom. (1975)

The structure of MS-3, a glyoxalase I inhibitor produced by a mushroom, was established to be 3', 4'-dihydroxymenthyl-5'-hydroxy-6'-(3-methyl-2-butenyl)-phenyl-2, 4-dihydroxy-6-methyl-benzoate.
Contribution of advanced glycosylation to the amyloidogenicity of islet amyloid polypeptide (1998)

The formation of amyloid within the islets of Langerhans is associated with the development of type II diabetes mellitus and occurs by the aggregation and insolubilization of islet amyloid polypeptide (IAPP). Recent in vitro studies suggest that amyloid formation follows a nucleation-dependent polymerization mechanism, i.e. aggregation is initiated by pre-formed aggregates or nucleation seeds. Modification of the Alzheimer's disease amyloid peptide by advanced glycosylation end products (AGEs), which form spontaneously by the non-enzymatic addition of glucose to protein amino groups, has been shown to enhance peptide aggregation in vitro. To explore the possibility that AGEs contribute to islet amyloid formation, we prepared AGE-modified IAPP (AGE-IAPP) in vitro and studied its properties by biochemical and biophysical techniques. AGE modification induced the formation of high-molecular-mass IAPP aggregates and amyloid formation was demonstrated by Congo red green-gold birefringence and by the presence of a characteristic fibrillar structure by electron microscopy. AGE-IAPP also showed an increase in cytotoxicity toward the astroglioma cell line HTB14. When added to soluble IAPP, AGE-IAPP seeds accelerated IAPP aggregation and abolished the nucleation period required for the polymerization of unseeded IAPP. Circular dichroism spectropolarimetry indicated that AGE-IAPP seeds may act as a template to stabilize the beta-sheet conformation of IAPP, thereby promoting its aggregation. Our studies demonstrate that AGE modification of IAPP results in high-molecular mass, fibrillar amyloid structures that nucleate IAPP amyloid formation and suggest a model for intra-islet amyloid deposition that may occur by the progressive advanced glycosylation of IAPP in vivo.
Bicontinuous Nanospheres from Simple Amorphous Amphiphilic Diblock Copolymers (2013)

Bicontinuous nanospheres have been observed (although rarely) from a variety of block copolymers with architectural and compositional complexity, and often in the presence of additives. Unlocking key features involved in their formation presents possibilities for bicontinuous aggregates with varied functionality and application. An attractive prospect is the ability to form them from much simpler polymeric structures derived from facile syntheses. To that end, we herein report the formation of bicontinuous aggregates from simple amorphous amphiphilic diblock copolymers of poly(ethylene oxide)-b-poly(n-butyl methacrylate), analogous to our previous report of the same from a semicrystalline comb-like block copolymer. Moreover, we demonstrate that polymorphism can be achieved by altering the relative block proportions and the nonselective cosolvent. We find that the polymeric structure is not the dominating factor in the formation of bicontinuous nanospheres but that the choice of cosolvent for the hydrophilic block appears to have greater influence on determining the end morphology.
Domino Asymmetric Ring-Opening/Cross Metathesis Reaction (2007)

The first catalytic asymmetric ring-opening/cross-metathesis for enantioselective synthesis of nitrogen heterocycles is described. Functionalized piperidines are formed in excellent yields and selectivities. A large excess of styrene is added to minimize homodimerization, and electron-deficient styrenes provide lower ee values. As one of many post-modifications described by the authors, the products can be cleaved to a styrenyl olefin in high yield and diastereoselectivity.