gebhart/patrepeval huggingface dataset:
Immune Targeting of the Phosphoproteome in Lymphoma and Leukemia. (2007)

Abstract CD8+ T cells have been identified as potent effectors of the adaptive anti-tumor immune response. So far, only a small number of tumor antigens have been objectively linked to the oncogenic processes. Alteration in phosphorylation status of cellular proteins is a hallmark of malignant transformation and a proven important therapeutic target. Phosphorylated antigens thus represent attractive targets for immunotherapeutic development based on the hypothesis that immune escape through mutation may be more difficult without compromising the malignant phenotype. Using a mass spectrometry approach phosphopeptide display was analyzed in CLL, AML, ALL, hairy cell leukemia and mantle cell lymphoma samples and compared against normal tissue. 109 or more primary tumor cells from HLA-A*0201+ or HLA-B*0702+ patients were lysed and peptides extracted from the surface HLA molecules and phosphopeptides isolated using in-line immobilized metal ion affinity chromatography and analyzed using tandem mass spectrometry using previously established methodology (Zarling A.L. et al PNAS 2006). 55 HLA-B*0702 phosphopeptides and 12 HLA-A*0201 phosphopeptides have been characterized. Many of these phosphopeptides are derived from phosphoproteins known to function in signaling cascades implicated in neoplastic transformation including MAP kinase pathway signaling proteins, c-Myc, NFAT and Bcl-11 with many representing novel phosphorylation sites. Peptide binding assays reveal IC50 binding affinities ranging between 4 and 300nM within the immunogenic range for the subset of phosphopeptides investigated. To investigated the mechanism of binding X-ray crystallography was performed in combination of peptide binding assays. Six HLA-phosphopeptide structures were resolved and demonstrate upward facing phosphate moiety directly interacting with HLA alpha helix residues yet with potential for direct recognition by the TCR. Peptide binding data support contributions from phosphate group in binding to the HLA in some but not all phosphopeptides tested and these data support a novel non-canonical binding mechanism for phosphopeptides complexed with HLA-A*0201. We have used mice transgenic for HLA-A*0201 and HLA-B*0702 to demonstrate in vivo immunogenicity of a subset of these peptides in a dendritic cell-based vaccination model. T cells generated differentially recognized phosphopeptides over non-phosphopeptide counterparts. Phosphopeptide-specific primary T cell lines were also generated ex-vivo from healthy lab donors which bound HLA-phosphopeptide tetramers and recognized HLA-matched primary tumor samples. In summary this work characterizes phosphopeptides that are differentially presented on primary leukemia and lymphoma samples by class I MHC molecules. These post-translationally modified peptide antigens represent distinct antigenic determinants which may overcome barriers of immune tolerance and autoimmunity inherent with other tumor antigens. These phosphopeptides therefore represent attractive novel candidates for future cancer immunotherapy.
Detection of anisotropy in the Cosmic Microwave Background at horizon and sub-horizon scales with the BOOMERanG experiment (2000)

BOOMERanG has recently resolved structures on the last scattering surface at redshift $\sim$ 1100 with high signal to noise ratio. We review the technical advances which made this possible, and we focus on the current results for maps and power spectra, with special attention to the determination of the total mass-energy density in the Universe and of other cosmological parameters.
Dimensional Analysis in Heat Transfer (1999)

Technical Briefs Dimensional Analysis in Heat Transfer T. M. Dalton, T. M. Dalton PEI Technologies, Thermofluids Research Centre, Department of Mechanical and Aeronautical Engineering, University of Limerick, Limerick, Ireland Search for other works by this author on: This Site PubMed Google Scholar M. R. D. Davies M. R. D. Davies PEI Technologies, Thermofluids Research Centre, Department of Mechanical and Aeronautical Engineering, University of Limerick, Limerick, Ireland Search for other works by this author on: This Site PubMed Google Scholar Author and Article Information T. M. Dalton PEI Technologies, Thermofluids Research Centre, Department of Mechanical and Aeronautical Engineering, University of Limerick, Limerick, Ireland M. R. D. Davies PEI Technologies, Thermofluids Research Centre, Department of Mechanical and Aeronautical Engineering, University of Limerick, Limerick, Ireland J. Heat Transfer. May 1999, 121(2): 471-473 (3 pages) https://doi.org/10.1115/1.2826002 Published Online: May 1, 1999 Article history Received: March 6, 1998 Revised: January 1, 1999 Online: December 5, 2007
Theory of quantum-circuit refrigeration by photon-assisted electron tunneling (2017)

We focus on a recently experimentally realized scenario of normal-metal--insulator--superconductor tunnel junctions coupled to a superconducting resonator. We develop a first-principles theory to describe the effect of photon-assisted electron tunneling on the quantum state of the resonator. Our results are in very good quantitative agreement with the previous experiments on refrigeration and heating of the resonator using the photon-assisted tunneling, thus providing a stringent verification of the developed theory. Importantly, our results provide simple analytical estimates of the voltage-tunable coupling strength and temperature of the thermal reservoir formed by the photon-assisted tunneling. Consequently, they are used to introduce optimization principles for initialization of quantum devices using such a quantum-circuit refrigerator. Thanks to the first-principles nature of our approach, extension of the theory to the full spectrum of quantum electric devices seems plausible.
Teaching electromagnetic field theory using differential forms (1997)

The calculus of differential forms has significant advantages over traditional methods as a tool for teaching electromagnetic (EM) field theory. First, films clarify the relationship between field intensity and flux density, by providing distinct mathematical and graphical representations for the two types of fields. Second, Ampere's and Faraday's laws obtain graphical representations that are as intuitive as the representation of Gauss's law. Third, the vector Stokes theorem and the divergence theorem become special cases of a single relationship that is easier for the student to remember, apply, and visualize than their vector formulations. Fourth, computational simplifications result from the use of forms: derivatives are easier to employ in curvilinear coordinates, integration becomes more straightforward, and families of vector identities are replaced by algebraic rules. In this paper, EM theory and the calculus of differential forms are developed in parallel, from an elementary, conceptually oriented point of view using simple examples and intuitive motivations. We conclude that because of the power of the calculus of differential forms in conveying the fundamental concepts of EM theory, it provides an attractive and viable alternative to the use of vector analysis in teaching electromagnetic field theory.
Biomimetic synthesis and tensile properties of nanostructured high volume fraction hydroxyapatite and chitosan biocomposite films (2009)

Chitosan–Hydroxyapatite (HA) nanostructured composite films have been prepared by solvent casting their hybrid suspensions. The synthesis of suspensions involves mediating the crystallization of HA by introducing chitosan solution into the reaction mixture. Both formaldehyde-treated chitosan and untreated chitosan solutions were used to study the effect of formaldehyde on chitosan–HA interactions and subsequent effective load transfer in biocomposites. The nanostructure and phase purity of HA (mildly carbonated HA) in the films were verified using SEM, XRD and FTIR. Tensile testing of the films showed significant increases in both the Young's modulus (E) and ultimate tensile strength (UTS) with HA content, reaching up to 17.3 GPa and 222 MPa, respectively, for films containing 66 wt.% (or 47 vol.%) HA in formaldehyde-treated chitosan films. In comparison to untreated chitosan composite films (<40 wt.% HA), formaldehyde-treated chitosan composite films resulted in higher E and UTS values, despite the observation of similar dispersion levels of HA particles. It is argued that apart from the uniform dispersion of HA particles in the chitosan matrix, the chemical binding between the constituents in the formaldehyde-treated chitosan composite films played a major role in the observed high tensile properties.
Depression of Intraocular Pressure Following Inactivation of Connexin43 in the Nonpigmented Epithelium of the Ciliary Body (2009)

Cx43 expression in the nonpigmented epithelium of the ciliary body contributes to the formation of gap junctions with the cells of the pigmented epithelium. These gap junctions play a critical role in maintaining the physical integrity of the ciliary body epithelium. Although the partial loss of Cx43 from the nonpigmented epithelium was correlated with a measurable drop in intraocular pressure, possible changes in Cx43 in the aqueous outflow pathway may provide an additional contribution to the observed phenotype.
Homing and Self-Renewal of Hematopoietic Stem Cells (2000)

I. INTRODUCTION Hematopoietic stem cell (HSC) transplantation has been shown to be a lifesaving procedure for a variety of malignant and hereditary diseases. The success of transplantation, both allogeneic and autologous, hinges on the abilities of the HSC to ‘‘home’’ to the bone marrow. Once homed in the appropriate microenvironment, the HSCs proliferate and make sequential decisions to self-renew as well as to produce progenitors that ultimately give rise to the mature blood cells. Hence homing to the marrow on the one hand and the dual abilities of self-renewal and differentiation on the other represent unique properties of HSCs.
Note on Equivalence Between Recurrent Neural Network Time Series Models and Variational Bayesian Models (2015)

We observe that the standard log likelihood training objective for a Recurrent Neural Network (RNN) model of time series data is equivalent to a variational Bayesian training objective, given the proper choice of generative and inference models. This perspective may motivate extensions to both RNNs and variational Bayesian models. We propose one such extension, where multiple particles are used for the hidden state of an RNN, allowing a natural representation of uncertainty or multimodality.
Modification of Lipid Composition by Genetic Engineering in Oleaginous Marine Microorganism, Thraustochytrid (2010)

This chapter contains sections titled: Introduction Materials and methods Results and discussion References
Angular needle tracker and stabilizer for image-guided interventions (2020)

The accuracy was comparable with some commercially available solutions. The novel and low-cost needle tracking device may find a role as part of a real-time precision approach to both planning and implementation of image-guided therapies.
Disproportionate left atrial myopathy in heart failure with preserved ejection fraction among participants of the PROMIS-HFpEF study (2021)

Abstract Impaired left atrial (LA) function in heart failure with preserved ejection fraction (HFpEF) is associated with adverse outcomes. A subgroup of HFpEF may have LA myopathy out of proportion to left ventricular (LV) dysfunction; therefore, we sought to characterize HFpEF patients with disproportionate LA myopathy. In the prospective, multicenter, Prevalence of Microvascular Dysfunction in HFpEF study, we defined disproportionate LA myopathy based on degree of LA reservoir strain abnormality in relation to LV myopathy (LV global longitudinal strain [GLS]) by calculating the residuals from a linear regression of LA reservoir strain and LV GLS. We evaluated associations of disproportionate LA myopathy with hemodynamics and performed a plasma proteomic analysis to identify proteins associated with disproportionate LA myopathy; proteins were validated in an independent sample. Disproportionate LA myopathy correlated with better LV diastolic function but was associated with lower stroke volume reserve after passive leg raise independent of atrial fibrillation (AF). Additionally, disproportionate LA myopathy was associated with higher pulmonary artery systolic pressure, higher pulmonary vascular resistance, and lower coronary flow reserve. Of 248 proteins, we identified and validated 5 proteins (involved in cardiomyocyte stretch, extracellular matrix remodeling, and inflammation) that were associated with disproportionate LA myopathy independent of AF. In HFpEF, LA myopathy may exist out of proportion to LV myopathy. Disproportionate LA myopathy is a distinct HFpEF subtype associated with worse hemodynamics and a distinct proteomic signature, independent of AF.
A Chimeric Ligand Approach Leading to Potent Antiprion Active Acridine Derivatives:  Design, Synthesis, and Biological Investigations (2006)

Human transmissible neurodegenerations including Creutzfeldt-Jakob disease are unique, since they are caused by prions, an infectious agent that replicates without nucleic acids but instead by inducing conversion of a host-resident normal prion protein to a misfolded conformational isoform. For pharmacotherapy of these unusual diseases, tricyclic heterocyclic compounds such as quinacrine have been considered, but with ambiguous success in vivo, so far. On the basis of the synergistic antiprion effects of quinacrine and iminodibenzyl derivatives, we introduce a novel class of potential pharmaceuticals representing structural chimeras of quinacrine and imipramine analogues. We describe the chemical synthesis and bioassays of a focused library of these compounds. The most potent target compound 2a revealed an EC(50) value of 20 nM determined with a cell model of prion disease, thus substantially improving the antiprion efficacy of quinacrine.
Similarities between Transplantation Antigens on Methylcholanthrene‐Induced Sarcomas and T‐Cell Regulatory Molecules (1983)

Successful interaction among T-cell subsets requires, among other things, homology at certain genetic loci that code for cellular interaction molecules (CIM). One such interaction, the induction of an acceptor-cell population by an Ly-1 T-suppressor-inducer cell, is controlled by genes that map to the variable region of the immunoglobulin heavy chain (Igh) complex. If the suppressor-induced cells (or their cell-free products) do not share Igh-V polymorphisms with their acceptor cells, the induction event fails to take place. Recently, structural genes of a transplantation antigen on the methylcholanthrene-induced sarcoma Meth A were mapped to the same region of chromosome 12 as the Igh gene complex. We tested whether there was any relationship between the Meth A transplantation antigen and T-cell regulatory molecules by using antisera against the Meth A antigen to block this particular Igh-linked T-T interaction. We found that isoantisera against a large number of methylcholanthrene-induced sarcomas tested were capable of blocking the induction of T-suppressor cells so long as the inducer and acceptor cells bore the Igha polymorphism. Further, we found a structural gene on MC-induced tumors that could absorb out this activity, and the structural gene for this antigen is coded for the same region as the Igh gene loci. The antisera binds to the I-J+ portion of a T-cell regulatory molecule Ly-1 TsiF, the portion of the molecule that has no specificity for antigen and imparts the Igh-linked genetic restriction. The implications of these findings for both oncology and immunology were discussed.
Compact and small size antenna for an UHF RFID tag placed over a metallic thing (2017)

We report in this paper the design of a compact and small size patch antenna for a RFID tag in American UHF band. The size of the proposed antenna is 91 × 36 × 6.34 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> . The antenna presents good performances. A good matching of -22 dB and a high gain of 4.7 dBi are achieved at the resonant frequency (918 MHz). The proposed antenna is well adapted for a compact and small size RFID tag placed over a metallic thing.
Ultrabroadband infrared nanospectroscopic imaging (2014)

Characterizing and ultimately controlling the heterogeneity underlying biomolecular functions, quantum behavior of complex matter, photonic materials, or catalysis requires large-scale spectroscopic imaging with simultaneous specificity to structure, phase, and chemical composition at nanometer spatial resolution. However, as with any ultrahigh spatial resolution microscopy technique, the associated demand for an increase in both spatial and spectral bandwidth often leads to a decrease in desired sensitivity. We overcome this limitation in infrared vibrational scattering-scanning probe near-field optical microscopy using synchrotron midinfrared radiation. Tip-enhanced localized light-matter interaction is induced by low-noise, broadband, and spatially coherent synchrotron light of high spectral irradiance, and the near-field signal is sensitively detected using heterodyne interferometric amplification. We achieve sub-40-nm spatially resolved, molecular, and phonon vibrational spectroscopic imaging, with rapid spectral acquisition, spanning the full midinfrared (700-5,000 cm(-1)) with few cm(-1) spectral resolution. We demonstrate the performance of synchrotron infrared nanospectroscopy on semiconductor, biomineral, and protein nanostructures, providing vibrational chemical imaging with subzeptomole sensitivity.
Design clues from functional constraints and broadly neutralizing antibodies (2006)

Two strategies have been proposed for the rationale design of vaccine immunogens that elicit broadly neutralizing antibodies against HIV-1. One strategy involves exploiting functional constraints, focusing on regions of the envelope where function requires conservation and exposure. This strategy has lead to the identification of coreceptor-binding-site antibodies as well as antibodies reactive with the site of T-20 binding. One drawback of this strategy, however, is the limited potency of the antibodies thus far identified. A second strategy involves the characterization of rare broadly neutralizing antibodies such as 2G12, 2F5, 4E10 and b12. Unfortunately, strains of virus resistant to these antibodies evolve with relative ease. We used X-ray crystallography to define functional constraints related to binding of the CD4 receptor and found that the site of initial CD4 contact on gp120 is the epitope for the broadly neutralizing antibody, b12. Functional analysis allowed us to transcend the particulars of b12 binding to focus on the conserved site of initial CD4 contact. The results suggest that a combination of functional analysis and potent antibody characterization may provide design clues necessary to create immunogens capable of eliciting potent broadly neutralizing antibodies.
Fabrication of a Patterned Ferromagnetic Thin Film with an Si3N4 Membrane Mask. (2001)

Spin-polarized scanning tunneling microscopy (SP-STM) is a promising technique for atomically resolved surface magnetic structure imaging. Since SP-STM is a surface-sensitive technique, the sample to be observed, such as a magnetic nanostructure, is required to have a well-defined clean surface. The magnetic sample preparation technique presented in this paper makes it easy to fabricate magnetic nanostructures in a vacuum. An Si3N4 membrane with submicron holes was used as a shadow mask for thin-film deposition. Conventional silicone processes were employed to make the Si3N4 membrane, and the shadow mask holes were formed on it using focused ion beam etching. The usability of this shadow mask was demonstrated by forming Co thin-film nanostructures on an Si substrate through the mask. The nanostructures were characterized by atomic force microscopy and magnetic force microscopy.
Probabilistic Interval-Valued Computation: Toward a Practical Surrogate for Statistics Inside CAD Tools (2008)

Interval methods offer a general fine-grain strategy for modeling correlated range uncertainties in numerical algorithms. We present a new improved interval algebra that extends the classical affine form to a more rigorous statistical foundation. Range uncertainties now take the form of confidence intervals. In place of pessimistic interval bounds, we minimize the probability of numerical "escape"; this can tighten interval bounds by an order of magnitude while yielding 10-100 times speedups over Monte Carlo. The formulation relies on the following three critical ideas: liberating the affine model from the assumption of symmetric intervals; a unifying optimization formulation; and a concrete probabilistic model. We refer to these as probabilistic intervals for brevity. Our goal is to understand where we might use these as a surrogate for expensive explicit statistical computations. Results from sparse matrices and graph delay algorithms demonstrate the utility of the approach and the remaining challenges.
Influence of shell parameters on response of polymer-shelled microbubbles to high-frequency ultrasound (2011)

Polymer-shelled ultrasound contrast agents (UCAs) can undergo a “compression only” behavior leading to shell rupture and nonlinear response of the released gas bubbles when ultrasonically excited below 10 MHz. This study investigated if polymer-shelled UCAs exhibited a similar behavior when excited at frequencies above 10 MHz. Accordingly, two experiments were performed: one examined the compression-induced rupture of UCA shells by subjecting them to static overpressure, and the other investigated subharmonic components in the backscattered signal produced by individual UCAs sonicated with 20-MHz tonebursts. Four varieties of polylactide-shelled UCAs, each with a distinct shell-thickness-to-radius ratio (STRR), were employed; the STRRs were 7.5, 40, 65, and 100 nm/μm. Different UCA types exhibited distinctly different rupture thresholds that were linearly related to their STRR, but uncorrelated with UCA size. The subharmonic response of these polymer-shelled UCAs did not exhibit a strong correlation with UCA-rupture pressures and, consequently, their STRRs. Although the Philips UCAs had greater STRRs in comparison to Point UCAs and were more resilient, they produced significantly greater subharmonic activity than the Point UCAs. The results of this two-part study indicated that the polymer-shelled UCAs may not adhere to the rupture-based mechanism of subharmonic generation when excited at 20 MHz.
Neurturin-Deficient Mice Develop Dry Eye and Keratoconjunctivitis Sicca (2003)

Neurturin-deficient mice show phenotypic changes and ocular surface inflammation that mimic human keratoconjunctivitis sicca. This model supports the importance of a functional ocular surface-central nervous system-lacrimal gland sensory-autonomic neural network in maintaining ocular surface health and homeostasis.