gebhart/patrepeval huggingface dataset:
Smart Vaults: Thermally-Responsive Protein Nanocapsules (2012)

Synthetic modification of a recombinant protein cage called a vault with stimuli-responsive smart polymers provides access to a new class of biohybrid materials; the polymer nanocapsules retain the structure of the protein cage and exhibit the responsive nature of the polymer. Vaults are naturally occurring ubiquitous ribonucleoprotein particles 41 × 41 × 72.5 nm composed of a protein shell enclosing multiple copies of two proteins and multiple copies of one or more small untranslated RNAs. Recombinant vaults are structurally identical but lack the vault content. Poly(N-isopropylacrylamide) (pNIPAAm), a polymer responsive to heat, was conjugated to recombinant vaults that were composed of ~78 copies of the major vault protein (MVP) modified to contain a cysteine rich region at the N-terminus (CP-MVP). The polymer was synthesized using reversible addition-fragmentation chain transfer (RAFT) polymerization to have a dansyl group at the alpha end and modified to have a thiol-reactive pyridyl disulfide at the omega end, which readily coupled to CP-MVP vaults. The resulting vault nanocapsules underwent reversible aggregation upon heating above the lower critical solution temperature (LCST) of the polymer as determined by electron microscopy (EM), dynamic light scattering experiments, and UV-vis turbidity analysis. The vault structure remained entirely intact throughout the phase transition; suggesting its use in a myriad of biomedical and biotechnology applications.
Wave Field Simulation with the Functional Transformation Method (2006)

The functional transformation method (FTM) provides a frequency domain based analytic solution of arbitrary linear partial differential equation. For wave field simulations however, its application was so far restricted to simple geometries as the FTM involves a search for the eigenmodes of the model. Recently so called block based modeling algorithms were introduced, that follow a divide-and-conquer approach. A complex geometry is split into several simple elementary blocks. These blocks are solved and discretized separately, while their connection is realized in the discrete system during run-time. In this paper a 2D wave field simulation program based on block based modeling is demonstrated. Elementary block models are solved with the FTM and can be connected together to create complex 2D geometries. The complete system benefits from the advantages of the FTM (e.g. dispersion-free simulations), while the complexity of the geometry fits the needs of typical CAD drawings
A Murine Homologue of the Drosophila brainiac Gene Shows Homology to Glycosyltransferases and Is Required for Preimplantation Development of the Mouse (2001)

The neurogenic gene brainiac was first isolated in Drosophila melanogaster, where it interacts genetically with members of the Notch signaling cascade. We have isolated a murine homologue of the Drosophila brainiac gene and delineated its highly specific expression pattern during development and adult life. We find particularly strong expression in the developing central nervous system, in the developing retina, and in the adult hippocampus. Targeted deletion of mouse Brainiac 1 expression leads to embryonic lethality prior to implantation. Null embryos can be recovered as blastocysts but do not appear to implant, indicating that mouse Brainiac 1, likely a glycosyltransferase, is crucial for very early development of the mouse embryo.
Gold Nanoelectrode Arrays and their Evaluation by Impedance Spectroscopy and Cyclic Voltammetry (2010)

A sol-gel strategy is developed to fabricate highly regular Au nanoelectrode arrays (NEAs) consisting of a nanoperforated ultrathin membrane of ZrO(2), which exhibits a well-ordered array of pores (65+/-5) nm in diameter with a mean center-to-center distance of (110+/-10) nm, on a polycrystalline gold surface. The structural properties are investigated by field-emission scanning electron microscopy (FE-SEM), while grazing incidence small-angle X-ray scattering (GISAXS) is used to assess the thickness homogeneity and the period of the array of electrodes. In addition, cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) are carried out to describe quantitatively the accessibility, electrochemical behavior, and diffusion processes of the gold NEA. A model applying parameters obtained from FE-SEM, CV, and EIS analyses is proposed to simulate the experimental results. A fairly good agreement between the experimental and the simulated data is obtained, thus allowing the deconvolution of the different diffusion regimes at the NEA.
Comprehensive gene expression profiles reveal pathways related to the pathogenesis of chronic obstructive pulmonary disease (2004)

To better understand the molecular basis of chronic obstructive pulmonary disease (COPD), we used serial analysis of gene expression (SAGE) and microarray analysis to compare the gene expression patterns of lung tissues from COPD and control smokers. A total of 59,343 tags corresponding to 26,502 transcripts were sequenced in SAGE analyses. A total of 327 genes were differentially expressed (1.5-fold up- or down-regulated). Microarray analysis using the same RNA source detected 261 transcripts that were differentially expressed to a significant degree between GOLD-2 and GOLD-0 smokers. We confirmed the altered expression of a select number of genes by using real-time quantitative RT-PCR. These genes encode for transcription factors (EGR1 and FOS), growth factors or related proteins (CTGF, CYR61, CX3CL1, TGFB1, and PDGFRA), and extracellular matrix protein (COL1A1). Immunofluorescence studies on the same lung specimens localized the expression of Egr-1, CTGF, and Cyr61 to alveolar epithelial cells, airway epithelial cells, and stromal and inflammatory cells of GOLD-2 smokers. Cigarette smoke extract induced Egr-1 protein expression and increased Egr-1 DNA-binding activity in human lung fibroblast cells. Cytomix (tumor necrosis factor α, IL-1β, and IFN-γ) treatment showed that the activity of matrix metalloproteinase-2 (MMP-2) was increased in lung fibroblasts from EGR1 control (+/+) mice but not detected in that of EGR1 null (-/-) mice, whereas MMP-9 was regulated by EGR1 in a reverse manner. Our study represents the first comprehensive analysis of gene expression on GOLD-2 versus GOLD-0 smokers and reveals previously unreported candidate genes that may serve as potential molecular targets in COPD.
Crystal structures of mercury(II) chloride and bromide addition complexes of carbonylchlorobis(triphenylphosphine)iridium(I) (1976)

The crystal structures of the oxidative-addition products of trans-[IrCl(CO)(PPh3)2] with HgCl2 and HgBr2 have been determined by X-ray diffraction. The structure of [IrCl2(HgCl)(CO)(PPh3)2] was refined by least squares to R 0.059 (3 430 observed reflections). Crystals are monoclinic, space group P21/n, a= 15.805(2), b= 21.734(3), c= 10.537(1)Å, β= 92.13(2)°, Z= 4. The two chlorines bonded to the pseudo-octahedral iridium are mutually cis[Ir-Cl, 2.453(5), 2.401 (4)Å]. while the two PPh3 ligands are trans[Ir–;P, 2.387(4), 2.378(4)Å], with the HgCl group trans to the Ir–Cl bond [Ir–Hg, 2.570(1)Å]. The mercury atom lies close to a centre of symmetry and Ir–Hg–Cl is slightly perturbed from linearity by interaction of Hg with the chlorine of its inversion image [Hg–Cl, 2.366(5), Hg ⋯ Cl′, 3.148(5)Å; Ir–Hg–Cl, 172.2(1)°]. The structure of the isomorphous [IrBrCl(HgBr)(CO)(PPh3)2][a= 16.021(7), b= 21.788(6), c= 10.568(4)Å, β= 93.11(3)°] indicates that the oxidative-addition reaction is predominantly trans in this instance: the partial bromine occupancy of the equatorial chlorine site is ca. 0.15; R was 0.072 for 3 810 observed reflections.
Mucosal Imprinting of Vaccine-Induced CD8 + T Cells Is Crucial to Inhibit the Growth of Mucosal Tumors (2013)

Although many human cancers are located in mucosal sites, most cancer vaccines are tested against subcutaneous tumors in preclinical models. We therefore wondered whether mucosa-specific homing instructions to the immune system might influence mucosal tumor outgrowth. We showed that the growth of orthotopic head and neck or lung cancers was inhibited when a cancer vaccine was delivered by the intranasal mucosal route but not the intramuscular route. This antitumor effect was dependent on CD8⁺ T cells. Indeed, only intranasal vaccination elicited mucosal-specific CD8⁺ T cells expressing the mucosal integrin CD49a. Blockade of CD49a decreased intratumoral CD8⁺ T cell infiltration and the efficacy of cancer vaccine on mucosal tumor. We then showed that after intranasal vaccination, dendritic cells from lung parenchyma, but not those from spleen, induced the expression of CD49a on cocultured specific CD8⁺ T cells. Tumor-infiltrating lymphocytes from human mucosal lung cancer also expressed CD49a, which supports the relevance and possible extrapolation of these results in humans. We thus identified a link between the route of vaccination and the induction of a mucosal homing program on induced CD8⁺ T cells that controlled their trafficking. Immunization route directly affected the efficacy of the cancer vaccine to control mucosal tumors.
Theorem: General Intelligence Entails Creativity, Assuming $$\ldots $$ (2014)

There appears to be considerable evidence against the claim that general intelligence entails creativity. For example, with this claim unpacked as the proposition that any general-intelligent agent must be creative, the field of AI declares the claim to be false. To see this, we need but note that the dominant and encyclopedic AI textbook [16] defines an intelligent agent as one that computes a mapping from its percepts to its actions. The range of potential mappings explored in this volume is non-trivial, ranging from simple arithmetic functions to functions that leverage declarative knowledge, and beyond. But never is creativity discussed in connection with any of these functions; indeed creativity is nowhere discussed in the book, period; nor for that matter is any synonym (e.g., ‘innovative’) discussed. In short, as far as this highly influential and comprehensive volume is concerned, general-intelligent agents needn’t be creative.
Data for "Single-Shot Readout of a Superconducting Qubit Using a Thermal Detector" (2023)

Data and code used to generate the plots in the publication "Single-Shot Readout of a Superconducting Qubit Using a Thermal Detector".
Automated maintenance of embryonic stem cell cultures (2006)

Embryonic stem cell (ESC) technology provides attractive perspectives for generating unlimited numbers of somatic cells for disease modeling and compound screening. A key prerequisite for these industrial applications are standardized and automated systems suitable for stem cell processing. Here we demonstrate that mouse and human ESC propagated by automated culture maintain their mean specific growth rates, their capacity for multi-germlayer differentiation, and the expression of the pluripotency-associated markers SSEA-1/Oct-4 and Tra-1-60/Tra-1-81/Oct-4, respectively. The feasibility of ESC culture automation may greatly facilitate the use of this versatile cell source for a variety of biomedical applications.
Near-field optical spectroscopy of localized excitons in strained CdSe quantum dots (1996)

Control of the growth dynamics during the epitaxy of coherently strained ZnSe/CdSe quantum structures results in a varied interfacial texture that broadly defines two qualitatively different regimes for exciton localization. An island growth mode produces quantum dot regions in which the lateral confinement of excitons is directly revealed through the observation of resolution-limited (full width at half maximum of 0.8 meV) emission peaks in near-field photoluminescence spectra. By contrast, layer-by-layer growth produces potential fluctuations at length scales small compared to the exciton diameter, so that the localization of excitons is driven by a random interfacial potential with a smooth density of states.
Handwriting Reconstruction for a Camera Pen Using Random Dot Patterns (2010)

This paper proposes a new method of handwriting reconstruction using a camera pen. We print random dot patterns on the document background to enable retrieval of both the current document and the pen position on this document. Dot arrangements are stored in a hash table using Locally Likely Arrangement Hashing. For retrieval, they are extracted from the camera image and matched to the corresponding points in the hash table. We were able to achieve high retrieval accuracy (81.1~100.0%), given a sufficient amount of visible dots. Using a two-step homography approximation, an accurate image of handwriting can be reconstructed. By using knowledge about document context and a client-server architecture, our method allows real-time processing on ordinary hardware.
Pressure Study of a Hexatic B and Crystal B Phase (1982)

Abstract Pressure temperature phase diagrams of two compounds exhibiting smectic B phases are presented. In one compound, the smectic B phase is liquid (no long range positional correlations) and is called a hexatic B phase, whereas in the other the smectic B phase is crystalline in nature. “Transition bars”, which are often observed at a smectic A to crystal B transition are observed above 1.5 kbar (and not below) in the former compound and the smectic A phase appears quite piezo-resistant. In contrast, for the latter compound, the smectic A phase disappears above 1.94 kbars. These results suggest that the two smectic phases are stabilized by different forces and we suggest a model.
Abelson murine leukemia virus mutants deficient in kinase activity and lymphoid cell transformation (1980)

Abelson murine leukemia virus transforms both lymphoid cells and fibroblasts in vitro and induces a unique type of thymus-dependent lymphoma in vivo. Four fibroblast-transforming strains of Abelson murine leukemia virus were identified, based on the sizes of the Abelson murine leukemia virus-specific phosphoproteins produced by these isolates. Two of these strains, the standard P120- and the P160-producing viruses, transformed lymphoid cells efficiently in vitro and induced Abelson disease in vivo. Two other strains, which synthesized small Abelson murine leukemia virus-specific proteins with molecular weights of 90,000 (P90) and 100,000 (P100), transformed lymphoid cells very poorly both in vitro and in vivo. The reduced oncogenic potentials of these isolates were correlated with a high level of synthesis of fairly unstable P90 and P100. In addition, neither P90 nor P100 functional efficiently in protein kinase assays. The correlation of abnormal metabolism and deficient protein kinase activity with the reduced oncogenic potentials of these virus strains supported a direct role for these proteins and the kinase activity in transformation. Furthermore, these results suggested that the requirements for lymphoid cell transformation and fibroblast transformation are different.
Implementation of the Quantum Fourier Transform (2001)

A quantum Fourier transform (QFT) has been implemented on a three qubit nuclear magnetic resonance (NMR) quantum computer to extract the periodicity of an input state. Implementation of a QFT provides a first step towards the realization of Shor's factoring and other quantum algorithms. The experimental implementation of the QFT on a periodic state is presented along with a quantitative measure of its efficiency measured through state tomography. Experimentally realizing the QFT is a clear demonstration of the ability of NMR to control quantum systems.
Liquid−Liquid Equilibria of Selected Dibasic Ester + Water + Solvent Ternary Systems (1996)

Experimental liquid−liquid equilibria for various dibasic ester + solvent + water systems were obtained at 297 K. These systems are suggested as possible substitutes in applications where chlorocarbons and aromatic hydrocarbons are used. The dibasic esters can also be used as novel solvents in separation techniques.
Magnetic resonance imaging ( MRI )‐guided transurethral ultrasound therapy of the prostate: a preclinical study with radiological and pathological correlation using customised MRI ‐based moulds (2013)

MRI-guided transurethral US therapy enabled safe and targeted ablations of prescribed lesions in a preclinical canine prostate model. Ablation volumes were reliably predicted by intra- and post-procedural imaging. Clinical studies are needed to confirm the feasibility, safety, oncological control, and functional outcomes of this therapy in patients in whom focal therapy is indicated.
Industrial talks (2011)

These industrial talks discuss the following: GPU revolutionized graphics; impacted parallel computing; mainstream developer parallelism; high level programming environment and accelerated computing.
Supplementary Figure 1 from Inhibitors of Deacetylases Suppress Oncogenic KIT Signaling, Acetylate HSP90, and Induce Apoptosis in Gastrointestinal Stromal Tumors (2023)

Supplementary Figure 1 from Inhibitors of Deacetylases Suppress Oncogenic KIT Signaling, Acetylate HSP90, and Induce Apoptosis in Gastrointestinal Stromal Tumors
A dispersion engineering enabled broadband optical metamaterial filter (2013)

In this paper, we show that the optical metamaterial dispersion can be controllably tailored to produce an ultrathin, broadband filter with a flat transmission band and near-constant in-band group delay in the 3 ∼ 3.5 µm midwave infrared window. It is achieved by strategically incorporating deep-subwavelength nano-notches into a fishnet structure. The deep-subwavelength inclusions, which have critical dimensions of less than 1/15 ± 1/100 of the shortest design wavelength, can perturb the mode patterns and strength of the unmodified fishnet nanostructure resonances, thereby shaping the dispersion in the effective medium properties to meet the specific design metrics. The designed free-standing optical metamaterial filter was fabricated and characterized, showing strong agreement between measured and simulated results. This powerful design approach will dramatically expand the opportunities to create new and practical broadband metamaterial-enabled optical devices and components.
The Cramér-Rao Bound for Estimating a Sparse Parameter Vector (2010)

The goal of this contribution is to characterize the best achievable mean-squared error (MSE) in estimating a sparse deterministic parameter from measurements corrupted by Gaussian noise. To this end, an appropriate definition of bias in the sparse setting is developed, and the constrained Cramer-Rao bound (CRB) is obtained. This bound is shown to equal the CRB of an estimator with knowledge of the support set, for almost all feasible parameter values. Consequently, in the unbiased case, our bound is identical to the MSE of the oracle estimator. Combined with the fact that the CRB is achieved at high signal-to-noise ratios signal-to-noise ratio (SNRs) by the maximum likelihood technique, our result provides a new interpretation for the common practice of using the oracle estimator as a gold standard against which practical approaches are compared.
A system to impose prescribed homogenous strains on cultured cells (2001)

There is presently significant interest in cellular responses to physical forces, and numerous devices have been developed to apply stretch to cultured cells. Many of the early devices were limited by the heterogeneity of deformation of cells in different locations and by the high degree of anisotropy at a particular location. We have therefore developed a system to impose cyclic, large-strain, homogeneous stretch on a multiwell surface-treated silicone elastomer substrate plated with pulmonary epithelial cells. The pneumatically driven mechanism consists of four plates each with a clamp to fix one edge of the cruciform elastomer substrate. Four linear bearings set at predetermined angles between the plates ensure a constant ratio of principal strains throughout the stretch cycle. We present the design of the device and membrane shape, the surface modifications of the membrane to promote cell adhesion, predicted and experimental measurements of the strain field, and new data using cultured airway epithelial cells. We present for the first time the relationship between the magnitude of cyclic mechanical strain and the extent of wound closure and cell spreading.
Heart failure with normal LVEF in BIOSTAT-CHF (2022)

Only 3.6% of patients with HF had a sex-adjusted normal LVEF. Despite the sex-adjusted cut-offs they were more frequently female with less ischemic heart disease, higher cardiac output and better clinical outcomes.
Electrospray mass spectrometry and UV/visible spectrophotometry studies of aluminum(III)-flavonoid complexes (1998)

Aluminum(III) complexes formed by the isoflavone biochanin-A and the flavones kaempeferol and quercetin in CH3OH, CH3CN, i-C3H7OH, and the mixed solvents CH3CN/CH3OH (1/1 v/v), CH3CN/H2O (1/1 v/v) CH3CN/CH2Cl2 (1/1 v/v) and CH3CN/i-C3H7OH (1/1 v/v), were investigated by means of electrospray mass spectrometry (ES-MS) and UV/visible absorbance spectrophotometry. Electrospray mass spectra of solutions that were indicated by their UV/visible spectra to have formed an Al-flavonoid complex displayed singly-charged ions corresponding in m/z to the 1:2, dimeric complex, viz., [AlL2]+, L=(flavonoid-H+)-. Lesser abundant singly-charged ions corresponding in m/z to [AlR(L)]+, where R=H-, HO- or CH3O- were also sometimes observed. Formation of the 1:2 complex was favored in CH3OH relative to all other solvent systems investigated. The relative amounts of complexed and free flavonoid in solution, as estimated by the appearance of the UV/visible spectra, correlated well with the abundance ratio of the 1:2, Al-flavonoid dimer to the protonated flavonoid (indicative of free flavonoid) observed in the ES mass spectrum of the same solution. © 1998 John Wiley & Sons, Ltd.
Method for HPRF radar measurement with phase shift keying (2015)

This paper presents a method of concurrently measuring range and Doppler frequency of at least one target. The transmitted signal consists of two pulse sequences intertwined on a pulse to pulse basis and having the same pulse repetition frequency PRF and transmit frequency RF. The pulses of the first pulse sequence have a linearly increasing phase value with a fixed phase difference Φ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1n</sub> from pulse to pulse and those of the second sequence have a linearly increasing phase with a fixed phase difference Φ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2n</sub> from pulse to pulse with Φ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1n</sub> ≠ Φ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2n</sub> . Each pulse sequence of the two base-band signals is processed separately and transformed into the frequency domain using FFT processing. In both transformed sequences, pairs of spectral lines are sought which cross a threshold and which have a Doppler frequency shift Δf = PRF(Φ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2n</sub> - Φ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1n</sub> )/2π between the sequences. The target Doppler frequency can be calculated from the FFT Doppler bin position, taking into account the increasing phase. Target range can be calculated from the phase difference between the two spectral lines.