gebhart/patrepeval huggingface dataset:
Transport of Nucleoside Triphosphates into Cells by Artificial Molecular Transporters (2018)

Chemically modified nucleoside triphosphates (NTPs) are widely exploited as unnatural metabolites in chemical biology and medicinal chemistry. Because anionic NTPs do not permeate cell membranes, their corresponding neutral precursors are employed in cell-based assays. These precursors become active metabolites after enzymatic conversion, which often proceeds insufficiently. Here we show that metabolically-active NTPs can be directly transported into eukaryotic cells and bacteria by the action of designed synthetic nucleoside triphosphate transporters (SNTTs). The transporter is composed of a receptor, which forms a non-covalent complex with a triphosphate anion, and a cell-penetrating agent, which translocates the complex across the plasma membrane. NTP is then released from the complex in the intracellular milieu and accumulates in nuclei and nucleoli in high concentration. The transport of NTPs proceeds rapidly (seconds to minutes) and selectively even in the presence of other organic anions. We demonstrate that this operationally simple and efficient means of transport of fluorescently labelled NTPs into cells can be used for metabolic labeling of DNA in live cells.
Development of Compton gamma-ray sources at LLNL (2012)

Compact Compton scattering gamma-ray sources offer the potential of studying nuclear photonics with new tools. The optimization of such sources depends on the final application, but generally requires maximizing the spectral density (photons/eV) of the gamma-ray beam while simultaneously reducing the overall bandwidth on target to minimize noise. We have developed an advanced design for one such system, comprising the RF drive, photoinjector, accelerator, and electron-generating and electron-scattering laser systems. This system uses a 120 Hz, 250 pC, 2 ps, 0.35 mm mrad electron beam with 250 MeV maximum energy in an X-band accelerator scattering off a 150 mJ, 10 ps, 532 nm laser to generate 5 × 1010 photons/eV/s/Sr at 0.5 MeV with an overall bandwidth of less than 1%. The source will be able to produce photons up to energies of 2.5 MeV. We also discuss Compton scattering gamma-ray source predictions given by numerical codes.
Simultaneous recovery of phase and defocus from coherent through-focus intensity images (2021)

Phase retrieval methods have been proposed to recover phase from through-focus intensity images measured on a microscope. It requires measuring the defocus distances of intensity images, usually by a z-axis translation stage. However, it complicates the experiment, adds expense, and suffers from error in the z-stage measurement. In this paper, we propose an algorithm to recover phase from only through-focus intensity images without measuring extra parameters such as defocus, wavelength and pixel size. We formulate the phase retrieval as a least-square error optimization problem and propose an alternating update scheme to solve the nonconvex optimization problem. We validate the algorithm with simulation and experiment.
Low‐Dimensional Organic Tin Bromide Perovskites and Their Photoinduced Structural Transformation (2017)

Abstract Hybrid organic–inorganic metal halide perovskites possess exceptional structural tunability, with three‐ (3D), two‐ (2D), one‐ (1D), and zero‐dimensional (0D) structures on the molecular level all possible. While remarkable progress has been realized in perovskite research in recent years, the focus has been mainly on 3D and 2D structures, with 1D and 0D structures significantly underexplored. The synthesis and characterization of a series of low‐dimensional organic tin bromide perovskites with 1D and 0D structures is reported. Using the same organic and inorganic components, but at different ratios and reaction conditions, both 1D (C 4 N 2 H 14 )SnBr 4 and 0D (C 4 N 2 H 14 Br) 4 SnBr 6 can be prepared in high yields. Moreover, photoinduced structural transformation from 1D to 0D was investigated experimentally and theoretically in which photodissociation of 1D metal halide chains followed by structural reorganization leads to the formation of a more thermodynamically stable 0D structure.
Using Orbitrap mass spectrometry to assess the isotopic compositions of individual compounds in mixtures (2020)

The isotopic compositions of individual chemical species are routinely used by the geochemical, environmental, forensic, anthropological, chemical, and biomedical communities to elucidate the conditions, sources, and reaction pathways of the molecules in question. Mass spectrometric methods of measuring isotopic compositions of individual compounds generally require that analytes be pure to yield precise, accurate results, yet most applications examine materials that are mixtures of multiple components. Various methods of chemical purification, e.g., chromatography, are used to isolate analytes from mixtures prior to mass spectrometric analysis. However, these techniques take time and specialized instrumentation, both of which could potentially be obviated via the use of ultra-high-resolution mass spectrometry. Here we report on the use of Orbitrap™-based Fourier-transform mass spectrometry to perform isotope ratio measurements of single species within mixtures delivered to the mass spectrometer (MS) without prior chromatographic separation. We demonstrate that instrument biases (attributed here to space charge effects) within the Orbitrap mass analyzer can cause the measured 13C/12C ratio of a molecular ion in the presence of non-analyte-derived ‘contaminating’ species to spuriously decrease relative to the 13C/12C ratio measured for the same ion in a pure analyte. We observe that the decrease in 13C/12C is proportional to the relative concentrations of the additional ‘contaminating’ components. We then recommend several strategies by which this effect can be mediated such that accurate isotope ratios can be obtained.
DPLL with hybrid &#x0394;&#x03A3; phase/frequency detector (2015)

Digital phase-locked loop (PLL) with dynamic hybrid Delta-Sigma (ΔΣ) phase/frequency detector (PFD). It combines the benefits of a traditional analog charge-pump-based PLL and a modern time-to-digital converter (TDC)-based all-digital PLL, namely, infinite phase-error detection resolution and all-digital control of a digitally controlled oscillator, respectively. An Lth-order ΔΣ analog-to-digital converter (ADC) implements an (L+1)-order ΔΣ PFD via closed-loop frequency detection. Fine resolution encoding of the ΔΣ PFD output facilitates multi-bit phase/frequency error digitization. A spur-free, wide bandwidth DPLL with a hybrid 2nd-order ΔΣ PFD that is based on a 1st-order continuous-time multi-bit ΔΣ ADC is presented in this paper. Low analog implementation complexity is achieved via digital noise-shaping requantization and noise cancellation.
Temporal Lenses for Three-Dimensional Electron Pulse Compression (2015)

We propose an all-optical method of compressing electron pulses to attosecond durations and sub-micrometer dimensions using ultrafast optical pulses. Applications range from ultrafast electron imaging to coherent terahertz sources.
Neural Associative Memory with Optimal Bayesian Learning (2011)

Neural associative memories are perceptron-like single-layer networks with fast synaptic learning typically storing discrete associations between pairs of neural activity patterns. Previous work optimized the memory capacity for various models of synaptic learning: linear Hopfield-type rules, the Willshaw model employing binary synapses, or the BCPNN rule of Lansner and Ekeberg, for example. Here I show that all of these previous models are limit cases of a general optimal model where synaptic learning is determined by probabilistic Bayesian considerations. Asymptotically, for large networks and very sparse neuron activity, the Bayesian model becomes identical to an inhibitory implementation of the Willshaw and BCPNN-type models. For less sparse patterns, the Bayesian model becomes identical to Hopfield-type networks employing the covariance rule. For intermediate sparseness or finite networks, the optimal Bayesian learning rule differs from the previous models and can significantly improve memory performance. I also provide a unified analytical framework to determine memory capacity at a given output noise level that links approaches based on mutual information, Hamming distance, and signal-to-noise ratio.
Effects of molybdenum deficiency and defects in molybdate transporter MOT1 on transcript accumulation and nitrogen/sulphur metabolism in Arabidopsis thaliana (2010)

Molybdenum (Mo) is a micronutrient essential for plant growth, as several key enzymes of plant metabolic pathways contain Mo cofactor in their catalytic centres. Mo-containing oxidoreductases include nitrate reductase, sulphite oxidase, xanthine dehydrogenase, and aldehyde oxidase. These are involved in nitrate assimilation, sulphite detoxification, purine metabolism or the synthesis of abscisic acid, auxin and glucosinolates in plants. To understand the effects of Mo deficiency and a mutation in a molybdate transporter, MOT1, on nitrogen and sulphur metabolism in Arabidopsis thaliana, transcript and metabolite profiling of the mutant lacking MOT1 was conducted in the presence or absence of Mo. Transcriptome analysis revealed that Mo deficiency had impacts on genes involved in metabolisms, transport, stress responses, and signal transductions. The transcript level of a nitrate reductase NR1 was highly induced under Mo deficiency in mot1-1. The metabolite profiles were analysed further by using gas chromatography time-of-flight mass spectrometry, capillary electrophoresis time-of-flight mass spectrometry, and ultra high performance liquid chromatography. The levels of amino acids, sugars, organic acids, and purine metabolites were altered significantly in the Mo-deficient plants. These results are the first investigation of the global effect of Mo nutrition and MOT1 on plant gene expressions and metabolism.
Imaging of Shear Waves Induced by Lorentz Force in Soft Tissues (2014)

This study presents the first observation of elastic shear waves generated in soft solids using a dynamic electromagnetic field. The first and second experiments of this study showed that Lorentz force can induce a displacement in a soft phantom and that this displacement was detectable by an ultrasound scanner using speckle-tracking algorithms. For a 100 mT magnetic field and a 10 ms, 100 mA peak-to-peak electrical burst, the displacement reached a magnitude of 1 μm. In the third experiment, we showed that Lorentz force can induce shear waves in a phantom. A physical model using electromagnetic and elasticity equations was proposed. Computer simulations were in good agreement with experimental results. The shear waves induced by Lorentz force were used in the last experiment to estimate the elasticity of a swine liver sample.
Ist der Bleigleichwert zur Beurteilung der Schutzwirkung bleifreier Röntgenschutzkleidung geeignet? (2005)

Users and patients wearing lead-free x-ray-protective clothing might unknowingly be exposed to a much larger dose than generally assumed. In the future, radiation protection rating should exclusively refer to the "attenuation ratio", which is based on broad beam geometry and characterizes radiation attenuation much more precisely than the lead equivalent.
Spatially Chirped Pulses for High Aspect Ratio Micromachining by Femtosecond Laser Ablation (2010)

We demonstrate that spatially chirped femtosecond laser pulses overcome previous limitations for the machining of high-aspect ratio features with low numerical aperture beams in optically transparent materials.
Commentary (Sequist/Lynch): EGFR Inhibitors in Lung Cancer (2005)

The review by Jan Buter and Giuseppe Giaccone in this issue of ONCOLOGY is an excellent overview of the current status of the anti–epidermal growth factor receptor (EGFR) agents gefitinib (Iressa), erlotinib (Tarceva), and cetuximab (Erbitux). The authors address some of the most important issues regarding anti-EGFR agents currently in clinical development. Key among these are the importance of patient selection and drug dosage in the success and failure of various clinical trials. This article raises several very interesting questions in the development of this class of agents.
Clock: synchronizing internal relational storage with external XML documents (2002)

In many business settings, a relational database system (RDBMS) will serve as the storage manager for data from XML documents. In such a system, once the XML data is dissembled and loaded into the storage system, XML queries posed against the (virtual) XML documents are processed by translating them into SQL queries against the relational storage. However, for applications which frequently update their XML documents, we cannot afford to reload a complete, possibly large, document for each update, instead we must be able to incrementally propagate document updates to the stored XML data. We address the issue of correctly reflecting updates of external XML documents into the loaded XML data in a relational database system. We describe Clock, a framework for synchronizing the relational storage with updated XML documents by exploiting a metadata-driven technology. First, we propose a set of (DTD preserving) update primitives for XML documents. Second, based on the mapping between XML and the relational model, we describe the propagation of those update primitives. Validation of the updates ensures they will not violate the constraints specified by the DTD. We have implemented a working prototype of the Clock system using the IBM's XML4J parser JDBC 2 and Oracle 81. We report on preliminary experiments conducted using this prototype to analyze our algorithms in a document update setting.
Characterization of Anti- <i>Salmonella enterica</i> Serotype Typhi Antibody Responses in Bacteremic Bangladeshi Patients by an Immunoaffinity Proteomics-Based Technology (2010)

Salmonella enterica serotype Typhi is the cause of typhoid fever and a human-restricted pathogen. Currently available typhoid vaccines provide 50 to 90% protection for 2 to 5 years, and available practical diagnostic assays to identify individuals with typhoid fever lack sensitivity and/or specificity. Identifying immunogenic S. Typhi antigens expressed during human infection could lead to improved diagnostic assays and vaccines. Here we describe a platform immunoaffinity proteomics-based technology (IPT) that involves the use of columns charged with IgG, IgM, or IgA antibody fractions recovered from humans bacteremic with S. Typhi to capture S. Typhi proteins that were subsequently identified by mass spectrometry. This screening tool identifies immunogenic proteins recognized by antibodies from infected hosts. Using this technology and the plasma of patients with S. Typhi bacteremia in Bangladesh, we identified 57 proteins of S. Typhi, including proteins known to be immunogenic (PagC, HlyE, OmpA, and GroEL) and a number of proteins present in the human-restricted serotypes S. Typhi and S. Paratyphi A but rarely found in broader-host-range Salmonella spp. (HlyE, CdtB, PltA, and STY1364). We categorized identified proteins into a number of major groupings, including those involved in energy metabolism, protein synthesis, iron homeostasis, and biosynthetic and metabolic functions and those predicted to localize to the outer membrane. We assessed systemic and mucosal anti-HlyE responses in S. Typhi-infected patients and detected anti-HlyE responses at the time of clinical presentation in patients but not in controls. These findings could assist in the development of improved diagnostic assays.
Control of square-wave inverters in high-power hybrid active filter systems (1998)

This paper presents a new control scheme for a hybrid parallel active filter (HPAF) system intended for high-power applications-up to 100 MW nonlinear loads-to meet IEEE 519 recommended harmonic standards. The active filter inverter is realized with small-rated (1%-2% of the load rating) square-wave inverters operating at the dominant harmonic frequencies. The proposed system achieves harmonic isolation at desired dominant harmonic frequencies, such as the fifth and seventh, even in the presence of supply voltage harmonic distortions. A novel method of active filter inverter DC-bus control, as proposed here, achieves power balancing by exchanging energy at the fundamental frequency and at the dominant harmonic frequency (such as the fifth). The proposed square-wave inverter-based HPAF system provides improved filtering characteristics as compared to the conventional passive filter and is expected to be cost effective for high-power nonlinear loads compared to the conventional passive filter or other active filtering solutions. The concept of harmonic isolation at dominant harmonic frequencies by square-wave inverters with the proposed control scheme is validated by simulation results.
Molecular cloning and nucleotide sequence of a gene for alkaline celluase from Bacillus sp. KSM-635 (1990)

A gene for alkaline cellulase from the alkalophilic Bacillus sp. KSM-635 was cloned into the HindIII site of pBR322 and expressed in Escherichia coli HB101. Although the recombinant plasmid contained two HindIII inserts of 2.6 kb and 4.0 kb, the inserts were found to be contiguous in the Bacillus genome by hybridization analysis. Nucleotide sequences of a 2.4 kb region which was indispensable for the production of cellulase, and the flanking, 1.1 kb region, were determined. There was an open reading frame (ORF) of 2823 bp in the 3498 bp sequence determined, which encoded 941 amino acid residues. Two putative ribosome-binding sites and a sigma 43-type, promoter-like sequence were found upstream from an initiation codon in the ORF. The deduced amino-terminal sequence resembles the signal peptide of extracellular proteins. A region of amino acids, 249 to 568, of the deduced amino acid sequence of the cellulase from this organism is homologous with those of alkaline and neutral enzymes of other micro-organisms, but nine amino acid residues were found to be conserved only in the alkaline enzymes.
Natural Language Generation in Dialogue using Lexicalized and Delexicalized Data (2016)

Natural language generation plays a critical role in spoken dialogue systems. We present a new approach to natural language generation for task-oriented dialogue using recurrent neural networks in an encoder-decoder framework. In contrast to previous work, our model uses both lexicalized and delexicalized components i.e. slot-value pairs for dialogue acts, with slots and corresponding values aligned together. This allows our model to learn from all available data including the slot-value pairing, rather than being restricted to delexicalized slots. We show that this helps our model generate more natural sentences with better grammar. We further improve our model's performance by transferring weights learnt from a pretrained sentence auto-encoder. Human evaluation of our best-performing model indicates that it generates sentences which users find more appealing.
Mutants of Type II Heat-Labile Enterotoxin LT-IIa with Altered Ganglioside-Binding Activities and Diminished Toxicity Are Potent Mucosal Adjuvants (2006)

The structure and function LT-IIa, a type II heat-labile enterotoxin of Escherichia coli, are closely related to the structures and functions of cholera toxin and LT-I, the type I heat-labile enterotoxins of Vibrio cholerae and enterotoxigenic Escherichia coli, respectively. While LT-IIa is a potent systemic and mucosal adjuvant, recent studies demonstrated that mutant LT-IIa(T34I), which exhibits no detectable binding activity as determined by an enzyme-linked immunosorbent assay, with gangliosides GD1b, GD1a, and GM1 is a very poor adjuvant. To evaluate whether other mutant LT-IIa enterotoxins that also exhibit diminished ganglioside-binding activities have greater adjuvant activities, BALB/c mice were immunized by the intranasal route with the surface adhesin protein AgI/II of Streptococcus mutans alone or in combination with LT-IIa, LT-IIa(T14S), LT-IIa(T14I), or LT-IIa(T14D). All three mutant enterotoxins potentiated strong mucosal immune responses that were equivalent to the response promulgated by wt LT-IIa. All three mutant enterotoxins augmented the systemic immune responses that correlated with their ganglioside-binding activities. Only LT-IIa and LT-IIa(T14S), however, enhanced expression of major histocompatibility complex class II and the costimulatory molecules CD40, CD80, and CD86 on splenic dendritic cells. LT-IIa(T14I) and LT-IIa(T14D) had extremely diminished toxicities in a mouse Y1 adrenal cell bioassay and reduced abilities to induce the accumulation of intracellular cyclic AMP in a macrophage cell line.
Reconstruction of conductivity and current density images using only one component of magnetic field measurements (2003)

Magnetic resonance current density imaging (MRCDI) is to provide current density images of a subject using a magnetic resonance imaging (MRI) scanner with a current injection apparatus. The injection current generates a magnetic field that we can measure from MR phase images. We obtain internal current density images from the measured magnetic flux densities via Ampere's law. However, we must rotate the subject to acquire all of the three components of the induced magnetic flux density. This subject rotation is impractical in clinical MRI scanners when the subject is a human body. In this paper, we propose a way to eliminate the requirement of subject rotation by careful mathematical analysis of the MRCDI problem. In our new MRCDI technique, we need to measure only one component of the induced magnetic flux density and reconstruct both cross-sectional conductivity and current density images without any subject rotation.
Interactive volume rendering of thin thread structures within multivalued scientific data sets (2004)

We present a threads and halos representation for interactive volume rendering of vector-field structure and describe a number of additional components that combine to create effective visualizations of multivalued 3D scientific data. After filtering linear structures, such as flow lines, into a volume representation, we use a multilayer volume rendering approach to simultaneously display this derived volume along with other data values. We demonstrate the utility of threads and halos in clarifying depth relationships within dense renderings and we present results from two scientific applications: visualization of second-order tensor valued magnetic resonance imaging (MRI) data and simulated 3D fluid flow data. In both application areas, the interactivity of the visualizations proved to be important to the domain scientists. Finally, we describe a PC-based implementation of our framework along with domain specific transfer functions, including an exploratory data culling tool, that enable fast data exploration.
Edge emission observed in heavily boron-doped diamond films epitaxially grown on platinum (1998)

Cathodoluminescence (CL) spectra of diamond films epitaxially grown on single crystal platinum (111) have been investigated at room temperature and 89 K. It was found that the CL spectra of the heavily boron-doped (&gt;3×1020 cm−3) diamond films of more than 16 μm thickness consist only of a near-edge emission at 248±1 nm (5.00±0.02 eV), while any mid-gap emissions are absent. That result suggests that few defects are in the films. It was also found that the temperature dependence of the 248 nm band is very unique, since its intensity increases as temperature increases. The mechanism of the 248 nm band seems to involve quasi-direct transition.