gebhart/patrepeval huggingface dataset:
Antigenic expression and spontaneous immune responses support the use of a selected peptide set from the IMA950 glioblastoma vaccine for immunotherapy of grade II and III glioma (2017)

Gliomas are lethal brain tumors that resist standard therapeutic approaches. Immunotherapy is a promising alternative strategy mostly developed in the context of glioblastoma. However, there is a need for implementing immunotherapy for grade II/III gliomas, as these are the most common CNS tumors in young adults with a high propensity for recurrence, making them lethal despite current treatments. We recently identified HLA-A2-restricted tumor-associated antigens by peptide elution from glioblastoma and formulated a multipeptide vaccine (IMA950) evaluated in phase I/II clinical trials with promising results. Here, we investigated expression of the IMA950 antigens in patients with grade II/III astrocytoma, oligodendroglioma or ependymoma, at the mRNA, protein and peptide levels. We report that the BCAN, CSPG4, IGF2BP3, PTPRZ1 and TNC proteins are significantly over-expressed at the mRNA (n = 159) and protein (n = 36) levels in grade II/III glioma patients as compared to non-tumor samples (IGF2BP3 being absent from oligodendroglioma). Most importantly, we detected spontaneous antigen-specific T cell responses to one or more of the IMA950 antigens in 100% and 71% of grade II and grade III patients, respectively (27 patients tested). These patients displayed T cell responses of better quality (higher frequency, broader epitope targeting) than patients with glioblastoma. Detection of spontaneous T cell responses to the IMA950 antigens shows that these antigens are relevant for tumor targeting, which will be best achieved by combination with CD4 epitopes such as the IDH1R132H peptide. Altogether, we provide the rationale for using a selective set of IMA950 peptides for vaccination of patients with grade II/III glioma.
PARP6 is a Regulator of Hippocampal Dendritic Morphogenesis (2016)

Mono-ADP-ribosylation (MARylation) of mammalian proteins was first described as a post-translational modification catalyzed by bacterial toxins. It is now known that endogenous MARylation occurs in mammalian cells and is catalyzed by 11 members of the poly-ADP-ribose polymerase (PARP) family of proteins (17 in humans). The physiological roles of these PARPs remain largely unknown. Here we demonstrate that PARP6, a neuronally enriched PARP that catalyzes MARylation, regulates hippocampal dendrite morphogenesis, a process that is critical for proper neural circuit formation during development. Knockdown of PARP6 significantly decreased dendritic complexity in embryonic rat hippocampal neurons in culture and in vivo. Expression of wild-type PARP6 increased dendritic complexity; conversely, expression of a catalytically inactive PARP6 mutant, or a cysteine-rich domain deletion mutant that has significantly reduced catalytic activity, decreased dendritic complexity. The identification of PARP6 as a regulator of dendrite morphogenesis supports a role for MARylation in neurons during development.
Tissue Bioavailability of Tart Cherry Anthocyanins (2015)

The therapeutic effects of tart cherry anthocyanins cannot be understood without analysis of their tissue distribution,metabolism, and excretion. The definition of bioavailability simply refers to the proportion of known compound that is absorbed and metabolised in an organism. Tissue uptake of anthocyanins may depend on their chemical structure, as influenced by the nature of the attached sugar moiety, and also, by the structure of the aglycone. The parent phytochemicals contain functional groups (e.g., a hydroxyl group) that often undergo conjugation reactions with endogenous compounds to yield more polar and water‐soluble compounds. The latter are usually ideal substrates for active transport out of cells, tissues, and organs with eventual excretion from the body. The sugar conjugates of anthocyanins may also have an effect on the bioavailability of bioactive phytochemicals. Consequently, it is not only important to know how much of a bioactive metabolite is present in tart cherry; but it is even more important to know how much of that present is bioavailable. In the present study, we show that intake of tart cherry is associated with anthocyanin appearance in several tissues of healthy rats. This information affects hypotheses of the molecular mechanisms of bioactive compounds at target sites and how they vary among tissues. While the current work focuses on anthocyanin tissue bioavailability, results may be impacted by the complex polypharmacy of bioavailable tart cherry phytochemicals and their varied sugar moieties that affect absorption, distribution, metabolism, and excretion. Acknowledgements: This study was supported by an unrestricted grant provided by The Cherry Marketing Institute, MI, USA.
Ray Contribution Masks for Structure Adaptive Sinogram Filtering (2012)

The patient dose in computed tomography (CT) imaging is linked to measurement noise. Various noise-reduction techniques have been developed that adapt structure preserving filters like anisotropic diffusion or bilateral filters to CT noise properties. We introduce a structure adaptive sinogram (SAS) filter that incorporates the specific properties of the CT measurement process. It uses a point-based forward projector to generate a local structure representation called ray contribution mask (RCM). The similarities between neighboring RCMs are used in an enhanced variant of the bilateral filtering concept, where the photometric similarity is replaced with the structural similarity. We evaluate the performance in four different scenarios: The robustness against reconstruction artifacts is demonstrated by a scan of a high-resolution-phantom. Without changing the modulation transfer function (MTF) nor introducing artifacts, the SAS filter reduces the noise level by 13.6%. The image sharpness and noise reduction capabilities are visually assessed on in vivo patient scans and quantitatively evaluated on a simulated phantom. Unlike a standard bilateral filter, the SAS filter preserves edge information and high-frequency components of organ textures well. It shows a homogeneous noise reduction behavior throughout the whole frequency range. The last scenario uses a simulated edge phantom to estimate the filter MTF for various contrasts: the noise reduction for the simple edge phantom exceeds 80%. For low contrasts at 55 Hounsfield units (HU), the mid-frequency range is slightly attenuated, at higher contrasts of approximately 100 HU and above, the MTF is fully preserved.
Outgassing Properties of Micro-ark Oxidized Aluminum Alloys (2007)

Micro-arc oxidation (MAO) is an anodizing technique applied to valve metals. With MAO, a crystalline aluminum oxide layer can be grown on aluminum alloys. This paper examines MAO as a surface treatment for metals for vacuum use. A 17.6 μm-thick MAO layer was grown on an A5052 aluminum alloy surface employing 50 Hz AC and a maximum of 450 V. This oxide layer contained α-alumina and γ-alumina crystalline aluminum oxide, and actually consisted of two distinct layers: first, a dense layer about 500 nm thick directly on the substrate, and, second, a 17 μm-thick layer on the dense layer which included numerous voids, each about 10 μm in size. Neither layer had the fine pores - 20-30 nm-structures - exhibited by alumite film. The outgassing rate of a MAO-treated A5052 sample after 10 hours of evacuation was 1.0×10-5 Pa•m3•s-1•m-2, i.e., 1/30 that of alumite with sulfuric acid. The most dominant gas species was water. The MAO sample's corrosion resistance to hydrochloric acid was the same as that of an alumite sample.
Deacetoxycephalosporin C from Streptomyces and fungi (1974)

R. Nagarajan, L. D. Boeck, R. L. Hamill, C. E. Higgens and K. S. Yang, J. Chem. Soc., Chem. Commun., 1974, 321 DOI: 10.1039/C39740000321
Optimal waveform design for UWB radios (2006)

With transmit power spectra strictly limited by regulatory spectral masks, the emerging ultra-wideband (UWB) communication systems call for judicious pulse shape design in order to achieve optimal spectrum utilization, spectral mask compatibility, and coexistence with other wireless services. Meanwhile, orthogonal pulse sets are often desired in order to apply high-rate multidimensional modulation and (carrier-free) orthogonal frequency-division multiple access. Motivated by these considerations, we suggest a digital finite impulse response (FIR) filter approach to synthesizing UWB pulses and propose filter design techniques by which optimal waveforms that satisfy the spectral mask can be efficiently obtained. For single pulse design, we develop a convex formulation for the design of the FIR filter coefficients that maximize the spectrum utilization efficiency in terms of both the bandwidth and power allowed by the spectral mask. For orthogonal pulse design, a sequential strategy is derived to formulate the overall pulse design problem as a set of convex subproblems, which are then solved in a sequential manner to yield a set of mutually orthogonal pulses. Our design techniques not only provide waveforms with high spectrum utilization and guaranteed spectral mask compliance but also permit simple modifications that can accommodate several other system objectives.
Modeling of a Heat Pump Cycle. (1992)

In order to simulate the behavior of heat pumps, theoretical models of heat exchangers and compressors are developed. The distribution of refrigerant flow rate between two paths in the heat exchangers can be satisfactorily simulated. Unbalanced distribution of the refrigerant flow rate among multiple paths frequently occurs in the condenser in contrast with in the evaporator. This different feature is ascribed to the different orders of magnitude of frictional and gravitational components of pressure drop in the condenser and the evaporator. The new compressor model requires neither the polytropic exponent nor the volumetric efficiency. The present models can estimate the mass of refrigerant existing in the heat exchangers and the compressor.
Blocking lnterleukin-1 in Disease (1993)

Numerous studies implicate a role for cytokines in the pathogenesis of disease. These are primarily derived from experiments in which cytokines are injected into experimental animals and disease activity is monitored. Other studies measure elevated cytokines in either animals or humans during the development of disease. Although cytokines are thought to play a role in the outcome of various diseases, only a few have been directly implicated as mediators of the pathogenic mechanisms of illness and death of the host. Recent studies using specific cytokine antagonism have shed considerable light on which cytokines appear to be playing a critical role.
Formation of an Aza‐nickelacycle by Reaction of an Imine and an Alkyne with Nickel(0): Oxidative Cyclization, Insertion, and Reductive Elimination (2007)

Cyclisieren, Addieren, Reduzieren: Die oxidative Cyclisierung eines Imins und eines Alkins mit einem Nickel(0)-Zentrum und die anschließende Insertion eines zweiten Alkins führen zu einem siebengliedrigen Azanickelacyclus, der durch reduktive Eliminierung ein 1,2-Dihydropyridin bildet (siehe Schema). Der sequenzielle Prozess wurde zu einer einstufigen nickelkatalysierten [2+2+2]-Cycloaddition von zwei Alkinen mit einem Imin weiterentwickelt.
Analysis of Gas Diffusion Layer and Flow Field Design using Neutron Radiography (2006)

A carbon cloth gas diffusion layer (GDL) displays better performance than a carbon paper GDL under humidified conditions. A straight flow field displays better performance than a serpentine flow field. To investigate these phenomena, neutron radiography was used to compare the amount of liquid water that accumulated in test fuel cells. It was found that a larger amount of water accumulated in a carbon cloth GDL than in a carbon paper GDL. From the standpoint of cell performance, the carbon cloth GDL was less influenced by the accumulated water than the carbon paper GDL. It is assumed that the broader pore distribution of a carbon cloth GDL creates oxygen diffusion paths even if water accumulates in the GDL. With a serpentine flow field, water accumulated in the corner and the gas bypassed the flow field. These phenomena are the main causes of performance deterioration with a serpentine flow field.
ChemInform Abstract: Intramolecular Simmons—Smith Cyclopropanation. Studies into the Reactivity of Alkyl‐Substituted Zinc Carbenoids, Effect of Directing Groups and Synthesis of Bicyclo[n.1.0]alkanes. (2010)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Short-lag spatial coherence weighted minimum variance beamformer for plane-wave images (2016)

The minimum variance (MV) beamformer is an adaptive beamforming technique that can convey enhancements in resolution and contrast and that can be applied to various ultrasonic sequences, including plane-wave imaging. Despite its improvements, it is still susceptible to clutter. The present work uses the short-lag spatial coherence (SLSC) value as a weighting factor in order to improve over conventional MV beamformed images. The proposed SLSC weighted MV beamformer (SLSCw-MV) coherently compounds the different emissions of a plane wave sequence in order to synthesize a tight transmission focus and then computes the SLSC value of signal. This SLSC value is used as a weigthing factor for the beamformed value obtained from the application of the frequency-domain version of the MV beamformer. The proposed method is tested on the 75 plane-wave dataset of the 2016 International Ultrasonics Symposium (IUS) beamforming challenge. Results on simulated and experimental data reveal that SLSCw-MV can convey improvements of 7%-55% in lateral resolution and of 2.5%-13% in contrast with respect to conventional delay-and-sum coherent plane-wave images.
The Startup Problem in Fault-Tolerant Time-Triggered Communication (2006)

Fault-tolerant time-triggered communication relies on the synchronization of local clocks. The startup problem is the problem of reaching a sufficient degree of synchronization after power-on of the system. The complexity of this problem naturally depends on the system assumptions. The system assumptions in this paper were compiled from cooperation with partners in the automotive and aeronautic industry. We present a general startup strategy for safety-critical systems that discusses the solution to the startup problem from an abstract point of view. From this abstract view we derive and analyze a new startup algorithm that is used in a TTP/C research derivative protocol (LTTP). We also analyze the FlexRay startup algorithm and discuss its behavior in presence of simple failures. The analyses were done by exhaustive fault simulation using the SAL model checker. While LTTP was found to tolerate the arbitrary failure of one node, the FlexRay startup shows to be vulnerable to simple failure modes
Testing "untestable" faults in three-state circuits (2002)

High-performance, complex CMOS designs such as microprocessors continue to gain performance by the use of "non-conventional" circuits such as tri-state, ratio or precharged logic. Such circuits are also used in noncomplementary or DC-redundant structures. While such design styles are not really new, their widespread use in very large, complex circuits (e.g., microprocessors) make "conventional" fault modeling and test generation ineffective. This paper describes test generation techniques to handle such circuits without affecting their performance or area. These techniques exploit circuit particularities of noncomplementary CMOS design in fault modeling, use automatic learning of useful relations about nodes in the design, and innovative test vector generation. On several designs ranging up to 2.5 million gates, the combined application of these methods increased test coverage from 50% to 100% while decreasing CPU time by orders of magnitude.
The Effects of Incident Photon Energy on the Time-Dependent Voltage Response of Lead Halide Perovskites (2019)

Tuning the halide composition in semiconductor perovskite materials is relevant for light-emitting and absorbing applications, as it significantly affects the dynamics of both the optical and electrical properties. Yet, a precise understanding of how the halide species influence the electrical behavior of the perovskite remains vague and speculative. In this work, we elucidate the transient voltage of two pure-halide perovskite film compositions (CH3NH3PbBr3 and CH3NH3PbI3) to directly compare the role of the halide in ionic species migration. We capture the photovoltage rise and residual voltage relaxation upon switching the illumination ON and subsequently OFF using Kelvin-probe force microscopy. We discover a unique and unforeseen wavelength-dependent voltage decay for CH3NH3PbBr3. Here, high-energy photons induce a more than 1 order of magnitude slower voltage decline toward equilibrium (i.e., dark conditions) than low-energy photons. Conversely, we find that the CH3NH3PbI3 perovskite composition has a wavelength-independent decay rate. The difference in electrical response occurs primarily because of the halide composition, as ion migration rates are reduced with higher Br content. The results detailed here yield new experimental insights about ion/defect activation energies in different perovskite films and devices, underlining a new parameter, photon energy (wavelength), which must be considered when assessing the fundamental photophysics within these materials.
Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.) (2010)

The cucumber genome is rich in microsatellites; AT and AAG are the most abundant repeat motifs in genomic and EST sequences of cucumber, respectively. Considering all the species investigated, some commonalities were noted, especially within the monocot and dicot groups, although the distribution of motifs and the frequency of certain repeats were characteristic of the species examined. The large number of SSR markers developed from this study should be a significant contribution to the cucurbit research community.
The clinical syndrome of specific antibody deficiency in children (2006)

Specific antibody deficiency (SAD) is an immune deficiency which has been reported in adults and children with recurrent respiratory tract infections; however, the clinical features of SAD are not well described. This study evaluated formally the clinical syndrome of SAD, by comparing the clinical features of children with SAD and those of children with recurrent infection but normal immune function tests. SAD was defined as an adequate IgG antibody response to less than 50% of 12 pneumococcal serotypes tested following 23-valent unconjugated pneumococcal immunization. An adequate IgG antibody response was defined as a post-immunization titre of >or= 1.3 microg/ml or >or= four times the preimmunization value. Seventy-four children with recurrent infection were evaluated where immune deficiencies other than SAD had been excluded. Eleven (14.9%) of these children had SAD. Clinical features differed between the group with SAD and the group with normal antibody responses. A history of otitis media, particularly in association with chronic otorrhoea was associated with SAD [relative risk (RR) of SAD in those with chronic otorrhoea 4.64 (P = 0.02)]. SAD was associated with allergic disease, particularly allergic rhinitis [RR of SAD in those with allergic rhinitis 3.77 (P = 0.04)]. These two clinical associations of SAD were independent in this study [RR of chronic otorrhoea in those with allergic rhinitis 0.85 (P = 0.28)]. SAD was not an age-related phenomenon in this population. SAD has a distinct clinical phenotype, presenting as recurrent infection associated with chronic otorrhoea and/or allergic disease, and the condition should be sought in children with these features.
A genomic screen for activators of the antioxidant response element (2007)

The antioxidant response element (ARE) is a cis-acting regulatory enhancer element found in the 5' flanking region of many phase II detoxification enzymes. Up-regulation of ARE-dependent target genes is known to have neuroprotective effects; yet, the mechanism of activation is largely unknown. By screening an arrayed collection of approximately 15,000 full-length expression cDNAs in the human neuroblastoma cell line IMR-32 with an ARE-luciferase reporter, we have identified several cDNAs not previously associated with ARE activation. A subset of cDNAs, encoding sequestosome 1 (SQSTM1) and dipeptidylpeptidase 3 (DPP3), activated the ARE in primary mouse-derived cortical neurons. Overexpression of SQSTM1 and DPP3 in IMR-32 cells stimulated NF-E2-related factor 2 (NRF2) nuclear translocation and led to increased levels of NAD(P)H:quinone oxidoreductase 1, a protein which is transcriptionally regulated by the ARE. When transfected into IMR-32 neuroblastoma cells that were depleted of transcription factor NRF2 by RNA interference, SQSTM1 and DPP3 were unable to activate the ARE or induce NAD(P)H:quinone oxidoreductase 1 expression, indicating that the ARE activation upon ectopic expression of these cDNAs is mediated by NRF2. Studies with pharmacological inhibitors indicated that 1-phosphatidylinositol 3-kinase and protein kinase C signaling are essential for activity. Overexpression of these cDNAs conferred partial resistance to hydrogen peroxide or rotenone-induced toxicity, consistent with the induction of antioxidant and phase II detoxification enzymes, which can protect from oxidative stress. This work and other such studies may provide mechanisms for activating the ARE in the absence of general oxidative stress and a yet-unexploited therapeutic approach to degenerative diseases and aging.
ChemInform Abstract: Nucleoside Phosphitylation Using Ionic Liquid Stabilized Phosphorodiamidites and Mechanochemstry. (2013)

Abstract The purification is conducted by filtration.
48.1: A Novel Method for Image Contrast Enhancement in TFT‐LCDs: Dynamic Gamma Control (DGC) (2003)

Abstract This paper describes a novel method for image contrast enhancement by controlling gamma curve in AMLCD. The key idea is to automatically manipulate gamma voltage in accordance with the image data distribution. This method is applied to 17″ SXGA LCD monitor module. The contrast ratio and the brightness are enhanced by about 3 times and 1.7 times, respectively, by using the proposed method.