gebhart/patrepeval huggingface dataset:
The Interdependence of Frequency Variation and Harmonic Content, and the Problem of Constant-Frequency Oscillators (1933)

The investigations of the frequency variations in oscillating systems with negative nonlinear resistance were based until now on the fundamental differential equation of the simple oscillatory circuit. This method, although very exact, is not always sufficiently simple and even not always possible, especially if it concerns more complicated schemes. The symbolic calculus, although very simple in use, if applied to the nonlinear systems, gives only approximate results. The following paper represents the operation of nonlinear systems from a different point of view. Here the symbolic calculus has been used throughout in a complete and exact manner, by employing it for the fundamental frequency as well as for all harmonic frequencies which appear in the system. This could be done owing to the investigation of the negative resistance operation from the energy point of view. It was taken into consideration, that in the negative resistance characteristics i = f(v), i must be the univocal function of v, and therefore the area described by the instantaneous point of work during one cycle of the fundamental oscillation must be zero or, ⨖ idv = 0. On the other hand i and v can be considered, with regard to the external circuit connected to the negative resistance, as the sum of harmonic currents and voltages. In this way we obtain the formulas which allow the interdependence of the frequency variation and the content of harmonics to be determined.
Heterologous RNA Encapsidated in Pariacoto Virus-Like Particles Forms a Dodecahedral Cage Similar to Genomic RNA in Wild-Type Virions (2004)

The genome of some icosahedral RNA viruses plays an essential role in capsid assembly and structure. In T=3 particles of the nodavirus Pariacoto virus (PaV), a remarkable 35% of the single-stranded RNA genome is icosahedrally ordered. This ordered RNA can be visualized at high resolution by X-ray crystallography as a dodecahedral cage consisting of 30 24-nucleotide A-form RNA duplex segments that each underlie a twofold icosahedral axis of the virus particle and interact extensively with the basic N-terminal region of 60 subunits of the capsid protein. To examine whether the PaV genome is a specific determinant of the RNA structure, we produced virus-like particles (VLPs) by expressing the wild-type capsid protein open reading frame from a recombinant baculovirus. VLPs produced by this system encapsidated similar total amounts of RNA as authentic virus particles, but only about 6% of this RNA was PaV specific, the rest being of cellular or baculovirus origin. Examination of the VLPs by electron cryomicroscopy and image reconstruction at 15.4-A resolution showed that the encapsidated RNA formed a dodecahedral cage similar to that of wild-type particles. These results demonstrate that the specific nucleotide sequence of the PaV genome is not required to form the dodecahedral cage of ordered RNA.
Microglial Receptor for Advanced Glycation End Product-Dependent Signal Pathway Drives β-Amyloid-Induced Synaptic Depression and Long-Term Depression Impairment in Entorhinal Cortex (2010)

Overproduction of beta-amyloid (Abeta) is a pathologic feature of Alzheimer's disease, leading to cognitive impairment. Here, we investigated the impact of cell-specific receptor for advanced glycation end products (RAGE) on Abeta-induced entorhinal cortex (EC) synaptic dysfunction. We found both a transient depression of basal synaptic transmission and inhibition of long-term depression (LTD) after the application of Abeta in EC slices. Synaptic depression and LTD impairment induced by Abeta were rescued by functional suppression of RAGE. Remarkably, the rescue was only observed in slices from mice expressing a defective form of RAGE targeted to microglia, but not in slices from mice expressing defective RAGE targeted to neurons. Moreover, we found that the inflammatory cytokine IL-1beta (interleukin-1beta) and stress-activated kinases [p38 MAPK (p38 mitogen-activated protein kinase) and JNK (c-Jun N-terminal kinase)] were significantly altered and involved in RAGE signaling pathways depending on RAGE expression in neuron or microglia. These findings suggest a prominent role of microglial RAGE signaling in Abeta-induced EC synaptic dysfunction.
EAX: A Conventional Authenticated-Encryption Mode. (2003)

We propose a block-cipher mode of operation, EAX, for authenticated-encryption with associateddata (AEAD). Given a nonce N , a message M , and a header H, the mode protects the privacy of M and the authenticity of both M and H. Strings N, M, H E {0, 1} are arbitrary, and the mode uses 2→M/n∈ + →H/n∈ + →N/n∈ block-cipher calls when these strings are nonempty and n is the block length of the underlying block cipher. Among EAX’s characteristics are that it is on-line (the length of a message isn’t needed to begin processing it) and a fixed header can be pre-processed, effectively removing the per-message cost of binding it to the ciphertext. EAX is obtained by instantiating a simple genericcomposition method, EAX2, and then collapsing its two keys into one. EAX is provably secure under a standard complexity-theoretic assumption. EAX is an alternative to CCM [19], and is likewise patent-free.
Design of a Tumor-Homing Cell-Penetrating Peptide (2007)

Chemotherapy is often limited by toxicity to normal cells. Therefore, an ideal anticancer drug should discriminate between normal tissue and tumors. This would require a target receptor molecule mostly present in tumors. The cyclic peptide cCPGPEGAGC (PEGA) is a homing peptide that has previously been shown to accumulate in breast tumor tissue in mice. PEGA peptide does not cross the plasma membrane per se; however, when attached to the cell-penetrating peptide pVEC, the conjugate is taken up by different breast cancer cells in vitro. Additionally, the homing capacity of the PEGA- pVEC is conserved in vivo, where the conjugate mainly accumulates in blood vessels in breast tumor tissue and, consequently is taken up. Furthermore, we show that the efficacy of the anticancer drug, chlorambucil, is increased more than 4 times when the drug is conjugated to the PEGA- pVEC chimeric peptide. These data demonstrate that combining a homing sequence with a cell-penetrating sequence yields a peptide that combines the desirable properties of the parent peptides. Such peptides may be useful in diagnostics and delivery of therapeutic agents to an intracellular location in a specific tumor target tissue.
Targeting p53 as a general tumor antigen. (1995)

A major barrier to the design of immunotherapeutics and vaccines for cancer is the idiosyncratic nature of many tumor antigens and the possibility that T cells may be tolerant of broadly distributed antigens. We have devised an experimental strategy that exploits species differences in protein sequences to circumvent tolerance of high-affinity T cells. HLA transgenic mice were used to obtain cytotoxic T lymphocytes specific for peptides from the human p53 tumor-suppressor molecule presented in association with HLA-A2.1. Although such p53-specific cytotoxic T cells did not recognize nontransformed human cells, they were able to lyse a wide variety of human tumor cells lines, thus confirming the existence of broadly distributed determinants that may serve as targets for immunotherapy.
Carcinoembryonic Antigen as a Target to Induce Anti-Tumor Immune Responses (2004)

Identification of relevant targets for cancer therapy is a major goal in cancer research. In this field, the identification of tumor antigens has opened the possibility of inducing specific anti-tumor immune responses. Among these antigens, carcinoembryonic antigen (CEA) is especially relevant because CEA is expressed in a wide variety of adenocarcinomas such as colon, rectum, pancreas, gastric, breast, etc. The present review focuses on different strategies to induce anti-CEA immune responses. In a first group of strategies, the antigen is administered using viral and bacterial vectors expressing CEA, dendritic cells loaded with CEA protein, or dendritic cells transfected with DNA or RNA expressing CEA. A second group of strategies is based on immunizations with antigenic peptide determinants from CEA, rather than with immunogens containing the whole protein. This has been possible due to the identification of different peptide determinants from CEA, which when presented by MHC class I molecules, are recognized by T cytotoxic lymphocytes. More recently, due to the importance of CD4(+) T cells in the induction of immune responses, T helper peptides presented by MHC class II molecules have also been identified. To overcome the poor immunogenicity of CEA-derived peptide determinants, a common feature of self-antigens, their sequence has been modified to improve binding to MHC molecules or recognition by T cell receptors. Finally, in order to enhance immunization efficacy, some of these strategies have combined the administration of immunogens and cytokines or co-stimulatory molecules. Some of the immunization protocols developed are being tested in clinical trials with promising results. Thus, CEA may prove to be a valuable target antigen for the therapy of a high number of malignancies.
Interaction of Eukaryotic Initiation Factor 5A with the Human Immunodeficiency Virus Type 1 Rev Response Element RNA and U6 snRNA Requires Deoxyhypusine or Hypusine Modification (1997)

Hypusine formation on the eukaryotic initiation factor 5A (eIF-5A) precursor represents a unique posttranslational modification that is ubiquitously present in eukaryotic cells and archaebacteria. Specific inhibition of deoxyhypusine synthase leads to growth arrest and cell death. The precise cellular function of eIF-5A and the physiological significance of hypusine modification are not clear. Although the methionyl-puromycin synthesis has been suggested to be the functional assay for eIF-5A activity in vitro, the role of eIF-5A in protein synthesis has not been established. Recent studies have suggested that eIF-5A may be the cellular target of the human immunodeficiency virus type 1 Rev and human T cell leukemia virus type 1 Rex proteins. Motif analysis suggested that eIF-5A resembles a bimodular RNA-binding protein in that it contains a stretch of basic amino acids clustered at the N-terminal region and a leucine-rich stretch at the C-terminal region. Using Rev target RNA, RRE, as a model, we tested the hypothesis that eIF-5A may be an RNA-binding protein. We found that both deoxyhypusine and hypusine-containing eIF-5A can bind to the 252-nt RRE RNA, as determined by a gel mobility shift assay. In contrast, the unmodified eIF-5A precursor cannot. Deoxyhypusine-containing eIF-5A, but not its precursor, could also cause supershift of the Rev stem-loop IIB RRE complex. Preliminary studies also indicated that eIF-5A can bind to RNA such as U6 snRNA and that deoxyhypusine modification appears to be required for the binding. The ability of eIF-5A to directly interact with RNA suggests that deoxyhypusine formation of eIF-5A may be related to its role in RNA processing and protein synthesis. Our study also suggests the possibility of using a gel mobility shift assay for eIF-5A-RNA binding as a functional assay for deoxyhypusine and hypusine formation.
Fast template matching for intra prediction (2017)

Intra prediction is an important step in video coding, where spatial redundancy is exploited for coding efficiency. The state-of-the-art H.265/High Efficiency Video Coding (HEVC) standard provides 35 intra prediction modes including 33 angular modes and a DC as well as a Planar mode. Although these intra prediction methods are quite efficient, there is still room for improvements, especially when complex image structures are involved. Template matching was proposed previously for H.264/Advanced Video Coding (AVC) with up to 11% BD-rate gain. However substantial decoder complexity increase from the implied search algorithm makes it less attractive for practical applications. In this paper, we propose a fast template matching intra mode for HEVC. The proposed mode is scalable in the sense of providing different trade-offs between decoder complexity and BD-rate gains. For a specific choice of parameters, fast template matching mode can achieve an average BD-rate gain of 1.15% with a maximum BD-rate gain of up to 4.6% at a 33% increase in decoder run-time. Overall, fast template matching can provide the same coding gain as conventional template matching approaches, but with significantly less decoder complexity.
Interferometric surface mapping with variable sensitivity (1978)

In the photolithographic process, presently employed for the production of integrated circuits, sets of correlated masks are used for exposing the photoresist on silicon wafers. Various sets of masks which are printed in different printing tools must be aligned correctly with respect to the structures produced on the wafer in previous process steps. Even when perfect alignment is considered, displacements and distortions of the printed wafer patterns occur. They are caused by imperfections of the printing tools or/and wafer deformations resulting from high temperature processes. Since the electrical properties of the final integrated circuits and therefore the manufacturing yield depend to a great extent on the precision at which such patterns are superimposed, simple and fast overlay measurements and flatness measurements as well are very important in IC-manufacturing. A simple optical interference method for flatness measurements will be described which can be used under manufacturing conditions. This method permits testing of surface height variations by nearly grazing light incidence by absence of a physical reference plane. It can be applied to polished surfaces and rough surfaces as well.
Simultaneous detection of mRNA and protein stem cell markers in live cells (2009)

Molecular beacons have the potential to provide a powerful tool for highly specific detection and isolation of stem cells, including cancer stem cells and induced pluripotent stem (iPS) cells without disturbing cell physiology. It is advantageous to perform simultaneous detection of intracellular (mRNA) and cell-surface (protein) stem cell markers in flow cytometric analysis, which may lead to high detection sensitivity and efficiency.
Identification and Molecular Characterization of the RNA Polymerase-Binding Motif of Infectious Bursal Disease Virus Inner Capsid Protein VP3 (2003)

Infectious bursal disease virus (IBDV), a member of the Birnaviridae family, is the causative agent of one of the most important infectious poultry diseases. Major aspects of the molecular biology of IBDV, such as assembly and replication, are as yet poorly understood. We have previously shown that encapsidation of the putative virus-encoded RNA-dependent RNA polymerase VP1 is mediated by its interaction with the inner capsid protein VP3. Here, we report the characterization of the VP1-VP3 interaction. RNase A treatment of VP1- and VP3-containing extracts does not affect the formation of VP1-VP3 complexes, indicating that formation of the complex requires the establishment of protein-protein interactions. The use of a set of VP3 deletion mutants allowed the mapping of the VP1 binding motif of VP3 within a highly charged 16-amino-acid stretch on the C terminus of VP3. This region of VP3 is sufficient to confer VP1 binding activity when fused to an unrelated protein. Furthermore, a peptide corresponding to the VP1 binding region of VP3 specifically inhibits the formation of VP1-VP3 complexes. The presence of Trojan peptides containing the VP1 binding motif in IBDV-infected cells specifically reduces infective virus production, thus showing that formation of VP1-VP3 complexes plays a critical role in IBDV replication.
Evaluation of Polymethine Dyes as Potential Probes for Near Infrared Fluorescence Imaging of Tumors: Part - 1 (2013)

Near-infrared (NIR) organic dyes have become important for many biomedical applications, including in vivo optical imaging. Conjugation of NIR fluorescent dyes to photosensitizing molecules (photosensitizers) holds strong potential for NIR fluorescence image guided photodynamic therapy (PDT) of cancer. Therefore, we were interested in investigating the photophysical properties, in vivo tumor-affinity and fluorescence imaging potential of a series of heterocyclic polymethine dyes, which could then be conjugated to certain PDT agents. For our present study, we selected a series of symmetrical polymethine dyes containing a variety of bis-N-substituted indole or benzindole moieties linked by linear conjugation with and without a fused substituted cyclohexene ring. The N-alkyl side chain at the C-terminal position was functionalized with sulfonic, carboxylic acid, methyl ester or hydroxyl groups. Although, among the parent cyanine dyes investigated, the commercially available, cyanine dye IR783 (3) (bis-indole-N-butylsulfonate)-polymethine dye with a cyclic chloro-cyclohexene moiety showed best fluorescence-imaging ability, based on its spectral properties (λAbs=782 nm, λFl=810 nm, ε = 261,000 M(-1)cm(-1), ΦFl≈0.08) and tumor affinity. In addition to 3, parent dyes IR820 and Cypate (6) were also selected and subjected to further modifications by introducing desired functional groups, which could enable further conjugation of the cyanine dyes to an effective photosensitizer HPPH developed in our laboratory. The synthesis and biological studies (tumor-imaging and PDT) of the resulting bifunctional conjugates are discussed in succeeding paper (Part-2 of this study).
Transgenic Nicotiana debneyii expressing viral coat protein are resistant to potato virus S infection (1990)

The coat protein gene from potato virus S (PVS) was introduced into Nicotiana debneyii by leaf disc transformation using Agrobacterium tumefaciens. Transgenic plants expressing the viral coat protein were highly resistant to subsequent infection by the ME strain of PVS as indicated by an absence of symptom development and a lack of accumulation of virus in both the inoculated and upper leaves. As in reported experiments with plants expressing potato virus X coat protein, plants expressing PVS coat protein were also protected from inoculation with PVS RNA. These results provide further evidence that coat protein-mediated protection for these two groups of viruses, which share similar genome organizations, may involve inhibition of some early event in infection other than or in addition to virus uncoating.
Transforming growth factor beta2 promotes glucose carbon incorporation into nucleic acid ribose through the nonoxidative pentose cycle in lung epithelial carcinoma cells. (2000)

The invasive transformation of A-459 lung epithelial carcinoma cells has been linked to the autocrine regulation of malignant phenotypic changes by transforming growth factor beta (TGF-beta). Here we demonstrate, using stable 13C glucose isotopes, that the transformed phenotype is characterized by decreased CO2 production via direct glucose oxidation but increased nucleic acid ribose synthesis through the nonoxidative reactions of the pentose cycle. Increased nucleic acid synthesis through the nonoxidative pentose cycle imparts the metabolic adaptation of nontransformed cells to the invasive phenotype that potentially explains the fundamental metabolic disturbance in tumor cells: highly increased nucleic acid synthesis despite hypoxia and decreased glucose oxidation.
A Simplified Superior Floating-Body/Gate DRAM Cell (2009)

The basic concept of a simplified and easily manufacturable version of the two-transistor floating-body/gate DRAM cell (FBGC) is proposed and demonstrated via simulation and fabrication/experiment. Converting the charge-storage transistor (T1) to a gated diode enables easy and direct connection of its body to the gate of the sensing transistor in conventional planar SOI CMOS and in FinFET technologies, and also reduces the cell size. Numerical simulations show that the new cell can yield a much better signal margin and dissipate much less power than the one-transistor floating-body DRAM cells currently being assessed. A FinFET-based prototype of the new cell provides experimental corroboration of these features.
Complement-dependent Proinflammatory Properties of the Alzheimer's Disease β-Peptide (1998)

Large numbers of neuritic plaques (NP), largely composed of a fibrillar insoluble form of the beta-amyloid peptide (Abeta), are found in the hippocampus and neocortex of Alzheimer's disease (AD) patients in association with damaged neuronal processes, increased numbers of activated astrocytes and microglia, and several proteins including the components of the proinflammatory complement system. These studies address the hypothesis that the activated complement system mediates the cellular changes that surround fibrillar Abeta deposits in NP. We report that Abeta peptides directly and independently activate the alternative complement pathway as well as the classical complement pathway; trigger the formation of covalent, ester-linked complexes of Abeta with activation products of the third complement component (C3); generate the cytokine-like C5a complement-activation fragment; and mediate formation of the proinflammatory C5b-9 membrane attack complex, in functionally active form able to insert into and permeabilize the membrane of neuronal precursor cells. These findings provide inflammation-based mechanisms to account for the presence of complement components in NP in association with damaged neurons and increased numbers of activated glial cells, and they have potential implications for the therapy of AD.
Parametric resonance in tunable superconducting cavities (2013)

We develop a theory of parametric resonance in tunable superconducting cavities. The nonlinearity introduced by the superconducting quantum interference device (SQUID) attached to the cavity and damping due to connection of the cavity to a transmission line are taken into consideration. We study in detail the nonlinear classical dynamics of the cavity field below and above the parametric threshold for the degenerate parametric resonance, featuring regimes of multistability and parametric radiation. We investigate the phase-sensitive amplification of external signals on resonance, as well as amplification of detuned signals, and relate the amplifier performance to that of linear parametric amplifiers. We also discuss applications of the device for dispersive qubit readout. Beyond the classical response of the cavity, we investigate small quantum fluctuations around the amplified classical signals. We evaluate the noise power spectrum both for the internal field in the cavity and the output field. Other quantum-statistical properties of the noise are addressed such as squeezing spectra, second-order coherence, and two-mode entanglement.
Oxidative stress and nitration in neurodegeneration: Cause, effect, or association? (2003)

Nonstandard abbreviations used: amyotrophic lateral sclerosis (ALS); manganese superoxide dismutase (Mn-SOD); Cu/Zn superoxide dismutase (Cu/Zn-SOD); hypochlorous acid (HOCl); nitric oxide synthase (NOS); 1-methyl-4-phenyl-1,2,3,6tetrahydropyridine (MPTP); copper chaperone for Cu/Zn superoxide dismutase (CCS).