gebhart/patrepeval huggingface dataset:
Data from Mutated <i>BCR-ABL</i> Generates Immunogenic T-cell Epitopes in CML Patients (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Characterization of an approach to identify leukemia neoantigens arising in the context of drug resistance.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We assessed whether leukemia neoantigens could be generated from drug-resistant mutations in &lt;i&gt;BCR-ABL&lt;/i&gt; after imatinib relapse in patients with chronic myelogenous leukemia (CML).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; We computationally predicted that approximately 70 peptides derived from 26 &lt;i&gt;BCR-ABL&lt;/i&gt; mutations would bind eight common alleles of MHC class I (IC&lt;sub&gt;50&lt;/sub&gt; &lt; 1,000 nmol/L). Seven of nine imatinib-resistant CML patients were predicted to generate at least 1 peptide that binds autologous HLA alleles. We predicted and confirmed that an E255K mutation-derived peptide would bind HLA-A3 with high affinity (IC&lt;sub&gt;50&lt;/sub&gt; = 28 nmol/L), and showed that this peptide is endogenously processed and presented. Polyfunctional E255K-specific CD8+ T cells were detected in two imatinib-resistant HLA-A3+ CML patients concurrent with an effective anti-CML response to further therapy.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Our &lt;i&gt;in vitro&lt;/i&gt; studies support the hypothesis that leukemia-driven genetic alterations are targeted by the immune system in association with a clinical response, and suggest the possibility of immunizing relapsed patients with CML against newly acquired tumor neoantigens. &lt;i&gt;Clin Cancer Res; 18(20); 5761–72. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Electron transfer chemistry of metalloporphyrins and related metal complexes (2000)

Recent advances in the electron transfer chemistry of metalloporphyrins and related metal complexes are reviewed briefly by focusing not only on the electron transfer processes but also on the subsequent chemical processes associated with electron transfer processes of metalloporphyrins and related metal complexes with macrocyclic ligands.
The Physical Principles of Magneto-optical Recording (1995)

This book covers the physics of magneto-optical recording, beginning with first principles, and working through to contemporary state-of-the-art topics. The first half of the book teaches the theory of diffraction using an original unified approach. It also covers the optics of multilayers, polarization optics, noise in photodetection, and thermal aspects. The second half of the book describes the basics of magnetism and magnetic materials, magneto-static field calculations, domains and domain walls, the mean-field theory, magnetization dynamics, the theory of coercivity, and the process of thermomagnetic recording. Numerous examples based on real-world problems encountered in the engineering design of magneto-optical media and systems will give the reader valuable insights into the science and technology of optical recording. In addition, there are extensive problem sets at the end of each chapter.
Table S1 from RNA Editing in Pathogenesis of Cancer (2023)

&lt;p&gt;Levels of global A&gt;I RNA editing in cancer&lt;/p&gt;
ChemInform Abstract: HETEROCYCLIC QUINONOID CHROMOPHORIC SYSTEMS: PART I. THIATHIOPHTHENES AND ANALOGS AS DYES (1979)

Abstract Umsetzung des Anthrachinons (I) mit Natriumsulfid in DMF führt zum grünen Trithiapentalen (II).
Relation between Fish Habitat and the Periodicity of Incremental Lines in the Fossil Otoliths (2020)

There are few research reports on the relationship between fish habitats and the periodicity of the fishes’ incremental lines of otolith fossils. The present study examines this relationship through histological and analytical studies on otolith fossils from Nobori Formation, Pliocene, Japan. The specimens were observed and analyzed using light microscopy, polarizing microscopy, Miniscopy, Scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS) analysis, electron probe X-ray microanalyzer (EPMA), Raman spectroscopy, and XRD. The otolith crystals were aragonite according to XRD and Raman analysis. The incremental lines contained C, O, and Ca, with Si as a trace element. In the layer between the incremental lines, Si was not detected. The circadian incremental lines were unclear and irregularly observed in both Lobianchia gemellarii and Diaphus gigas. Their behavioral pattern included a diurnal vertical movement. By comparison, for Cetonurus noboriensis, Ventrifossa sp., Sebastes scythropus, and Congriscus megastomus, the circadian incremental lines were evident. The habitat of the fishes that live exclusively on the continental slope is kept constant, and the circadian incremental lines are formed regularly. However, for fishes that spend the day in the deep sea and ascend to the shallow sea at night, the ecosystem, such as seawater temperature and pressure, fluctuates, and the circadian incremental lines become unclear and irregular. The period of the circadian incremental lines of otolith may vary due to differences in the ecosystems.
A CS1 maze lab, using joysticks and MIPPETs (1999)

We are designing a number of programming projects which utilize input/output devices, such as joysticks or a homebrewed board we call a MIPPET (Module for Input/Output Programming Projects Enhancing Teaching). These projects have been used or will be used in the closed labs of our CS1 course (taught in C++). The goal of these projects is to enhance student comprehension (by teaching objects with "real" objects) and student motivation (by providing "fun" projects). This paper focuses on an early project, where the student's program provides support for a human solving a maze.
The architecture of hydroxy‐functionalized aPS‐b‐random copolymer‐b‐PE via one‐pot strategy combining living free radical polymerization with coordination polymerization (2011)

Abstract The copolymerization of styrene with ethylene was promoted by CpTiCl 3 /BDGE/Zn/MAO catalyst system combining free radical polymerization with coordination polymerization via sequential monomer addition strategy in one‐pot. The effect of polymerization conditions such as temperature, time, ethylene pressure, and Al/Ti molar ratio on the polymerization performance was investigated. The hydroxy‐functionalized aPS‐b‐random copolymer‐b‐PE triblock copolymer was obtained by solvent extraction and determined by GPC, DSC, WAXD, and 13 C‐NMR. The DSC result indicated that the aPS‐b‐random copolymer‐b‐PE had a T g at 87°C and a T m at 119°C which attributed to the T g of aPS segment and the T m of PE segment, respectively. The microstructure of the hydroxy‐functionalized aPS‐b‐random copolymer‐b‐PE was further confirmed by WAXD, 13 C‐NMR, and 1 H‐NMR analysis; and these results demonstrated that the obtained block copolymer consisted of aPS segment, S ‐E random copolymer segment, and crystalline PE segment. The connection polymerization of the hydroxy‐functionalized aPS with random copolymer‐b‐PE was revealed by GPC results. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Leukocyte count and risk of thrombosis in patients undergoing haematopoietic stem cell transplantation or intensive chemotherapy (2010)

Elevated white blood cell count has recently been established as an independent risk factor for thromboembolic events in patients with myeloproliferative syndromes. Thrombotic events occur frequently in patients with haematological malignancies undergoing intensive cytoreductive treatment. We evaluated retrospectively the association of leukocyte counts and thrombosis in three cohorts of 100 patients each undergoing autologous or allogeneic haematopoietic stem cell transplantation or chemotherapy, respectively. A total of 26 thromboembolic events were recorded, 10 in recipients of allogeneic transplants, five in autografted patients, and 11 in the chemotherapy group. Fifteen events were central venous catheter related. Non-catheter related thrombotic events were pulmonary embolism (N=5), hepatic veno-occlusive disease (N=2), deep-vein thrombosis (N=1), stroke (N=1), ovarian vein thrombosis (N=1), and left ventricular thrombosis (N=1). Hazard rates showed two peaks, a first during cytoreduction in all groups, and a second after engraftment in transplanted patients. Time-dependent multivariable Cox analysis confirmed an association of leukocytosis with development of thrombosis (hazard ratio for leukocyte count > 11G/l: 9.73, 95% confidence interval 1.98-47.9, p=0.005). The risk associated with leukocytosis was independent from C-reactive protein level. Thrombocyte count and type of treatment (allogeneic vs. autologous transplantation vs. chemotherapy) had no significant influence on thrombosis development. In three cohorts of patients undergoing intensive cytoreductive treatment for haematological malignancy, leukocyte count was strongly associated with development of thrombotic complications.
On failure detection algorithms in overlay networks (2005)

One of the key reasons overlay networks are seen as an excellent platform for large scale distributed systems is their resilience in the presence of node failures. This resilience rely on accurate and timely detection of node failures. Despite the prevalent use of keep-alive algorithms in overlay networks to detect node failures, their tradeoffs and the circumstances in which they might best he suited is not well understood. In this paper, we study how the design of various keep-alive approaches affect their performance in node failure detection time, probability of false positive, control overhead, and packet loss rate via analysis, simulation, and implementation. We find that among the class of keep-alive algorithms that share information, the maintenance of backpointer state substantially improves detection time and packet loss rate. The improvement in detection time between baseline and sharing algorithms becomes more pronounced as the size of neighbor set increases. Finally, sharing of information allows a network to tolerate a higher churn rate than baseline.
An investigation into the effect of magnetic domains in cobalt on an electron beam (1957)

Abstract The effect on an electron beam of the leakage field due to the magnetic domains in an unmagnetized crystal of hexagonal cobalt has been investigated. A conventional electron-diffraction camera was used, the primary beam being limited by a small movable aperture and the deflexions observed on a photographic plate. Both the hexagonal and prism faces were examined. Magnetic effects were found (a) on the primary beam, (b) on the diffraction pattern, (c) on the shadow edge of the diffraction pattern, and (d) on the shadow photograph of the crystal produced by diffuse scattering from the edge of the aperture. These effects are analyzed in terms of the fields produced by the magnetic domains; measurements are made of the size of the domains and of the magnitude of the leakage field at the surface and its varia­tion with the distance from the surface.
Lipophilicity and serotonin agonist activity in a series of 4-substituted mescaline analogs (1977)

Replacement of the 4-methoxy of mescaline with higher alkyl homologues or with bromine led to increased activity at serotonin receptors in a sheep umbilical artery preparation. This activity appears correlated with lipophilicity, as measured by 1-octanol-water partition coefficients, but drops off when the 4-substituent is about five atoms in length. It is suggested that 3,4,5-trisubhe 2,4,5-substitution pattern.
An electronically switchable leaky wave antenna (2000)

We report an electronically switchable dielectric leaky wave antenna. The main beam angle can be electronically steered using p-i-n diodes. The diodes are used as switches to control the radiation from two sets of gratings with different periods, thereby switching the main beam angle. Beam steering is achieved at a single fixed frequency; no frequency sweeping is necessary. A microwave prototype demonstrates a 35/spl deg/ change in beam direction at 3.5 GHz. Measured antenna patterns agree with theoretical predictions. This approach should be scalable to millimeter-wave frequencies using diodes monolithically integrated on a semiconductor waveguide.
Synthèse d’images infrarouges sans calcul préalable du champ de température (2019)

National audience
Model‐based image reconstruction for four‐dimensional PET (2006)

Positron emission tonography (PET) is useful in diagnosis and radiation treatment planning for a variety of cancers. For patients with cancers in thoracic or upper abdominal region, the respiratory motion produces large distortions in the tumor shape and size, affecting the accuracy in both diagnosis and treatment. Four-dimensional (4D) (gated) PET aims to reduce the motion artifacts and to provide accurate measurement of the tumor volume and the tracer concentration. A major issue in 4D PET is the lack of statistics. Since the collected photons are divided into several frames in the 4D PET scan, the quality of each reconstructed frame degrades as the number of frames increases. The increased noise in each frame heavily degrades the quantitative accuracy of the PET imaging. In this work, we propose a method to enhance the performance of 4D PET by developing a new technique of 4D PET reconstruction with incorporation of an organ motion model derived from 4D-CT images. The method is based on the well-known maximum-likelihood expectation-maximization (ML-EM) algorithm. During the processes of forward- and backward-projection in the ML-EM iterations, all projection data acquired at different phases are combined together to update the emission map with the aid of deformable model, the statistics is therefore greatly improved. The proposed algorithm was first evaluated with computer simulations using a mathematical dynamic phantom. Experiment with a moving physical phantom was then carried out to demonstrate the accuracy of the proposed method and the increase of signal-to-noise ratio over three-dimensional PET. Finally, the 4D PET reconstruction was applied to a patient case.
Clinico-pathological correlations in 127 patients in 11 large pedigrees, segregating one of three heterozygous mutations in the COL4A3/ COL4A4 genes associated with familial haematuria and significant late progression to proteinuria and chronic kidney disease from focal segmental glomerulosclerosis (2009)

Our data confirm for the first time a definite association of heterozygous COL4A3/COL4A4 mutations with familial microscopic haematuria, thin basement membrane nephropathy and the late development of familial proteinuria, CRF, and ESRD, due to FSGS, indicating that the term 'benign familial haematuria' is a misnomer, at least in this cohort. A strong hypothesis for a causal relationship between these mutations and FSGS is also made. Benign familial haematuria may not be so benign as commonly thought.
PHYSICAL STABILITY OF SUSPENSIONS (1985)

Considerations, en particulier, sur les problemes de mouillage et de dispersion, de sedimentation en relation avec la rheologie et de prevention de prise en masse
INFLUENCE OF AGGREGATE CHEMISTRY ON THE ADSORPTION AND DESORPTION OF ASPHALT (1992)

Asphalt-aggregate interactions were investigated by evaluating the adsorption and desorption of aged and unaged asphalts on four aggregates: limestone, greywacke, gravel, and basalt. The aggregate composition and surface chemistry had a greater effect on the adsorption and desorption characteristics of the asphalt-aggregate pair than the properties of the asphalt did. Adsorption and desorption isotherms were fitted to the Langmiur model and yielded predicted monolayer amounts, equilibrium constants for adsorption, and Gibbs free energy of adsorption. The Gibbs free energies were evaluated in terms of the principles of soil mechanics, which showed that water in the voids can be drawn to the asphalt-aggregate interface at relative humidities of 99% or above. Estimates of minimum tensile strength ratios were determined from Gibbs free energies and the extrapolated measured enthalpy values. The presence of water at the interface reduces the Gibbs free energy values between the asphalt and aggregate, thereby reducing the tensile strength and resistance to debonding fracture.
Surface Plasmon Resonance Assays of DNA-Protein Interactions (2009)

Assaying sequence-specific DNA-protein complex formation in vitro often involves the use of specific labelling or modification of the components of the complex to provide unique signals that can be used to assess the affinity of the interaction. Surface plasmon resonance (SPR) spectroscopy is an optical technique that can be used without radio- or other labelling of the components of a complex provided that one of the partners can be immobilised to a solid support. For DNA oligonucleotides this can easily be achieved by the incorporation of a biotin end label, but proteins can also be immobilised if they carry conventional tags for affinity purification, such as GST or polyhistidine extensions. The SPR effect relies on changes in the refractive index of solutions adjacent to the immobilised surface and is extremely sensitive. The continuous flow systems developed by BIAcore AB (now GE Healthcare Biosciences AB) permit real-time recording of the binding and dissociation of analyte species to the immobilised ligand, resulting in both rapid stoichiometric kinetic, affinity, and thermodynamic measurements. These assays can be carried out with complex mixtures of analytes, providing a powerful addition to the techniques available to probe such interactions. We illustrate the use of such assays here using the example of the E. coli methionine repressor, MetJ, which is also described in Chapters "Filter-Binding Assays" and "Ethylation Interference Footprinting of DNA-Protein Complexes."
Association between Intraoperative Hypotension and Hypertension and 30-day Postoperative Mortality in Noncardiac Surgery (2015)

Intraoperative hypotension, but not hypertension, is associated with increased 30-day operative mortality.
Coupled Contour and Thickness Shear Vibrations (1960)

In this paper, Cauchy's [l] two-dimensional equations of coupled flexural and extensional vibrations of thin crystal plates are extended to the next hi&er order of approximation so as to accommodate the frequencies of the two lowest thickness-shear modes. The equations obtained are also extensions of previous equations [2] in which flexure and the same thickness-shear defomations were taken into account but coupling with contour modes was omitted. The coupled equations of higher order are dedwed fmm the three-dimensional equations of linear elasticity by a procedure based on Cauchy's series expansion and IUrchhoff's [3] variational methods. A system of five, secondorder, displacement-equations of motion is obtained, along with theorems of orthogoaality and uniqueness of solution. Comparison of the appropriate solution of the equations with Ekstein's [4] solution of the three-dimensional equations, for an infinite plate, reveals close agreement between the two frequency spectra, over the extended range of frequencies, for all five branches of the approximate equations. Solutions of the five equations are exhibited for rotated Y-cut rectangular quartz plates under various edge-conditions. One of these is a solution, found previously by another method [5], for contour modes, of rectangular plates with all edges free, not coupled with flexure.
Urban object reconstruction using airborne laser elevation image and aerial image (2002)

Creating three-dimensional (3-D) models of real urban objects is an important goal in a wide variety of applications. This paper describes a method that utilizes airborne laser elevation images and aerial images for the 3-D reconstruction of urban objects. Our modeling approach uses the vertical geometric pattern analysis of elevation images. These patterns correspond to object contours and, thus, enable the extraction of the object. In addition, to provide realistic textured details, textures are cut from aerial images and mapped onto 3-D models. Our texture-mapping approach can avoid geometry mismatching and enable the automatic registration to determine the most reliable correspondence between projected outlines of 3-D models and contours of real objects shown in aerial images. Edge pairs, which are matched with projected outlines, are detected from aerial images. In order to minimize mismatching, we apply the voting technique based on the generalized Hough transform. Experimental results show that 3-D reconstruction of urban objects is generally successful.
Disentanglement of protease substrate repertoires (2008)

Identification of protease substrates and detailed characterization of processed sites are essential for understanding the biological function of proteases. Because of inherent complexity reasons, this however remains a formidable analytical challenge, illustrated by the fact that the majority of the more than 500 human proteases are uncharacterized to date. Recently, in addition to conventional genetic and biochemical approaches, diverse quantitative peptide-centric proteomics approaches, some of which selectively recover N-terminal peptides, have emerged. These latter proteomic technologies in particular allow the identification of natural protease substrates and delineation of cleavage sites in a complex, natural background of thousands of different proteins. We here review current biochemical, genetic and proteomic methods for global analysis of substrates of proteases and discuss selected applications.
Luminescent Ceramics for Phosphor Converted LEDs (2010)

Abstract not Available.
The paraventricular nucleus of the hypothalamus – a potential target for integrative treatment of autonomic dysfunction (2008)

This review highlights data showing that individual afferent inputs (subfornical organ), signaling molecules (orexins, adiponectin), and interneurons (glutamate/GABA), all have the potential to influence (and thus coordinate) multiple PVN output pathways. We also highlight recent studies showing that modifications in this integrated circuitry may play significant roles in the pathology of diseases such as congestive heart failure and hypertension.
Subviral Dense Bodies of Human Cytomegalovirus Enhance Interferon-Beta Responses in Infected Cells and Impair Progeny Production (2023)

(1) Background: Infection with human cytomegalovirus (HCMV) leads to the production and release of subviral particles, termed Dense Bodies (DB). They are enclosed by a membrane resembling the viral envelope. This membrane mediates the entrance of DBs into cells in a way that is comparable to virus infection. HCMV attachment and entry trigger the induction of interferon synthesis and secretion, and the subsequent expression of interferon-regulated genes (IRGs) that might inhibit replication of the virus. Recently, we demonstrated that DBs induce a robust interferon response in the absence of infection. Little is known thus far, including how DBs influence HCMV infection and virus-host interaction. (2) Methods: Purified DBs were used to study the impact on virus replication and on the innate defense mechanisms of the cell. (3) Results: The incubation of cells with DBs at the time of infection had little effect on viral genome replication. Preincubation of DBs, however, led to a marked reduction in viral release from infected cells. These cells showed an enhancement of the cytopathic effect, associated with a moderate increase in early apoptosis. Despite virus-induced mechanisms to limit the interferon response, the induction of interferon-regulated genes (IRGs) was upregulated by DB treatment. (4) Conclusions: DBs sensitize cells against viral infection, comparable to the effects of interferons. The activities of these particles need to be considered when studying viral-host interaction.