gebhart/patrepeval huggingface dataset:
An Enhanced Mass Spectrometry Approach Reveals Human Embryonic Stem Cell Growth Factors in Culture (2008)

The derivation and long-term maintenance of human embryonic stem cells (hESCs) has been established in culture formats that are both dependent and independent of support (feeder) cells. However, the factors responsible for preserving the viability of hESCs in a nascent state remain unknown. We describe a mass spectrometry-based method for probing the secretome of the hESC culture microenvironment to identify potential regulating protein factors that are in low abundance. Individual samples were analyzed several times, using successive mass (m/z) and retention time-directed exclusion, without sampling the same peptide ion twice. This iterative exclusion -mass spectrometry (IE-MS) approach more than doubled protein and peptide metrics in comparison to a simple repeat analysis method on the same instrument, even after extensive sample pre-fractionation. Furthermore, implementation of the IE-MS approach was shown to enhance the performance of an older quadrupole time of flight (Q-ToF) MS. The resulting number of identified peptides approached that of a parallel repeat analysis on a newer LTQ-Orbitrap MS. The combination of the results of both instruments proved to be superior to that achieved by a single instrument in the identification of additional proteins. Using the IE-MS strategy, combined with complementary gel- and solution-based fractionation methods, the hESC culture microenvironment was extensively probed. Over 10 to 12 times more extracellular proteins were observed compared with previously published surveys. The detection of previously undetectable growth factors, present at concentrations ranging from 10(-9) to 10(-11) g/ml, highlights the depth of our profiling. The IE-MS approach provides a simple and reliable technique that greatly enhances instrument performance by increasing the effective depth of MS-based proteomic profiling. This approach should be widely applicable to any LC-MS/MS instrument platform or biological system.
Syntheses of methotrexate-hybrid compounds for target profiling of small molecules with MASPIT (2012)

We set out to synthesize alkyne-functionalized analogues of blockbuster drugs (simvastatin, propranolol and tamoxifen) and the small molecule reversine, paying close attention to SAR. These analogues were conjugated with an azide containing MTX-reagent via the Cu(I)-catalyzed Huisgen 1,3dipolar cycloaddition (CLICK chemistry). The resulting MTXconjugates are currently being evaluated in the MASPIT assay.
Visual Chatter in the Real World (2013)

When a scene is lit by a source of light, the radiance of each point in the scene can be viewed as having two components, namely, direct and global. Recently, an efficient separation method has been proposed that uses high frequency illumination patterns to measure the direct and global components of a scene. The global component could arise from not only interreflections but also subsurface scattering within translucent surfaces and volumetric scattering by participating media. In this paper, we use this method to measure the direct and global components of a variety of natural and man-made materials. The computed direct and global images provide interesting insights into the scattering properties of common real-world materials. We have also measured the two components for a 3D texture as a function of lighting direction. This experiment shows that the global component of a BTF tends vary smoothly with respect to the lighting direction compared to the direct component of the BTF. Finally, we apply the separation method to a translucent object for different imaging and illumination scales (resolutions). The results obtained show how the BSSDRF of the object gradually reduces to a BRDF as one goes from fine to coarse scale. All the measurement results reported here, as well as several others, can be viewed as high resolution images at
Face Selectivity of the Diels‐Alder Reaction of Thebaine‐Like Morphinandienes, A Computational Approach (Chemistry of Opium Alkaloids, Part XXXI) (1989)

Abstract Molecular mechanics {MMP2(85)} have been employed for the calculation of the geometry of morphinan‐6,8‐dienes. The X‐ray structure of desoxycodeine‐A, a morphinan‐5,7‐diene, and of other morphinans were well‐reproduced by the minimization program. The conformations of 4,5α‐epoxymorphinan‐6,8‐dienes and their 4‐hydroxy analogues show considerable differences, which account for the observed face selectivity in the Diels‐Alder cycloaddition.
UKRISS – Feasibility study and proof-of-concept for a shared research information reporting service based on CERIF (2012)

Poster presented at the CRIS2012 Conference.-- Full conference programme available at: http://www.cris2012.org/findByFilter.do?categoryId=1158
A microcomputed tomography guided fluorescence tomography system for small animal molecular imaging (2009)

A prototype small animal imaging system was created for coupling fluorescence tomography (FT) with x-ray microcomputed tomography (microCT). The FT system has the potential to provide synergistic information content resultant from using microCT images as prior spatial information and then allows overlay of the FT image onto the original microCT image. The FT system was designed to use single photon counting to provide maximal sensitivity measurements in a noncontact geometry. Five parallel detector locations are used, each allowing simultaneous sampling of the fluorescence and transmitted excitation signals through the tissue. The calibration and linearity range performance of the system are outlined in a series of basic performance tests and phantom studies. The ability to image protoporphyrin IX in mouse phantoms was assessed and the system is ready for in vivo use to study biological production of this endogenous marker of tumors. This multimodality imaging system will have a wide range of applications in preclinical cancer research ranging from studies of the tumor microenvironment and treatment efficacy for emerging cancer therapeutics.
The PONI optoelectronic platform (2003)

The PONI platform is designed with a keen awareness of trade-offs. The optical alignment tolerance is at the heart of the tradeoffs because it is generally the cost limiting factor that also determines the maximum performance. For example, modules designed for 50 /spl mu/m multimode optical fiber are expected to have lower package costs.
The mechanisms of plastic strain accommodation during the high strain rate collapse of corrugated Ni–Al laminate cylinders (2014)

The Thick-Walled Cylinder method was used on corrugated Ni–Al reactive laminates to examine how their mesostructures accommodate large strain, high strain rate plastic deformation and to examine the potential for intermetallic reaction initiation due to mechanical stimuli. Three main mesoscale mechanisms of large plastic strain accommodation were observed in addition to the bulk distributed uniform plastic flow: (a) the extrusion of wedge-shaped regions into the interior of the cylinder along planes of easy slip provided by angled layers, (b) the development of trans-layer shear bands in the layers with orientation close to radial and (c) the cooperative buckling of neighbouring layers perpendicular to the radius. These mesoscale mechanisms acted to block the development of periodic patterns of multiple, uniformly distributed, shear bands that have been observed in all previously examined solid homogeneous materials and granular materials. The high-strain plastic flow within the shear bands resulted in the dramatic elongation and fragmentation of Ni and Al layers. The quenched reaction between Al and Ni was observed inside these trans-layer shear bands and in a number of the interfacial extruded wedge-shaped regions. The reaction initiated in these spots did not ignite the bulk of the material, demonstrating that these mesostructured Ni-Al laminates are able to withstand high-strain, high-strain rate deformation without reaction. Numerical simulations of the explosively collapsed samples were performed using the digitized geometry of corrugated laminates and predictions of the final, deformed mesostructures agree with the observed deformation patterns.
Polarization-Independent Optical Broadband Angular Selectivity (2018)

Generalizing broadband angular selectivity to both polarizations has been a scientific challenge for a long time. Previous demonstrations of the broadband angular selectivity work only for one polarization. In this paper, we propose a method that can achieve polarization-independent optical broadband angular selectivity. Our design is based on a material system consisting of alternating one-dimensionally anisotropic photonic crystal (1D PhC) stacks and half-wave plates. 1D PhC stacks have an angular photonic band gap for p-polarized light and half-wave plates can convert s-polarized light to p-polarized light. By introducing alternating 1D PhC stacks and half-wave plates, we predict that one can achieve a central transmission angle at normal incidence and an angularly selective range of less than 30° across the whole visible spectrum.
In-Situ Synthesis of New Electrode Materials for Li-Ions Batteries using a cold FEG Environmental HRTEM (2014)

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On the possibility of the detachment of hydrogen as a result of electron capture by a Broensted center on zeolites (2009)

The structure and reactivity of the radical anion center in ZSM-5 zeolite were studied by the density functional theory method. It was shown that the interaction of the hydrogen zeolite form with adsorbed olefins and aromatic hydrocarbons could be accompanied by electron transfer from hydrocarbon molecules to the Broensted acid center with the formation of a radical anion fragment. The radical anion fragment formed is unstable, which contributes to the probability of the exothermic process (ΔE = −21 kcal/mol) of atomic hydrogen detachment with the activation energy not exceeding 10–12 kcal/mol. The atomic hydrogen split off can initiate hydrocarbon transformations, and such a radical anion center can play the role of a catalytic activity carrier on acid zeolites.
Plasma etching of Cr photomasks: optimization of process conditions and CD control (1997)

As device design rules continue to shrink, on-mask Cr structures must experience a corresponding reduction in size. Although 0.25 micrometer design rules require only 1 micrometer Cr features, the use of OPC structures, which may be needed to minimize line foreshortening and corner rounding, necessitate features to be etched into the Cr which are significantly smaller than this. This need, coupled with the demand for reduced CD bias and improved CD uniformities, requires the use of an alternate chrome etch technology. Plasma etching of Cr can be highly anisotropic, greatly reducing the etch undercut which is responsible for the CD bias typically associated with wet etching. Reactive ion etching (RIE) can provide significant enhancements in the capability of replicating micron and sub-micron features, but the Cr etch rate non-uniformity which is typical of this technique can translate into a CD non-uniformity. This is due in part to the relatively high pressure of operation (50 - 100 mTorr) which is necessary to reduce the self generated dc voltage and which, in turn, minimizes the photo resist etch rate. Recently, high density plasma sources, such as inductively coupled plasma (ICP), have become available which have the ability to operate both at low pressures and high plasma density while maintaining a low and controllable dc voltage. The low pressure operation significantly improves the etch rate uniformity and consequently the CD uniformity. By coupling this ICP plasma source with a non-contact backside photomask handling system and a true multi-station 'cluster tool.' In this study a design of experiment (DOE) is used to investigate the parameter space associated with the dry etching of Cr using an ICP source. The responses of Cr etch rate, selectivity to photo resist, CD uniformity and mean CD to target are studied, and from this an optimized parameter space is defined. Within this space the effect of overetch, dc voltage and pattern loading on the CD uniformity are also investigated. The role played by the photo resist profile in determining the Cr etch profile is also studied, and preliminary measurements are made to understand the effect of the above parameters on the mask CD bias.
Electrically controllable liquid crystal photonic bandgap fiber with dual-frequency control (2005)

We present an electrically tunable liquid crystal photonic bandgap fiber device based on a dual frequency liquid crystal with pre-tilted molecules that allows the bandgaps to be continuously tuned. The frequency dependent behavior of the liquid crystal enables active shifting of the bandgaps toward shorter or longer wavelengths. We also describe and experimentally characterize an electro-optical modulator and a birefringence controller suitable for polarization control.
ChemInform Abstract: Group Transfer Addition Reactions of Selenomalononitriles to Chiral Enol Ethers. Asymmetric Radical Addition and Selenium Transfer Reactions. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A broad-spectrum antiviral molecule, QL47, selectively inhibits eukaryotic translation (2019)

Small-molecule inhibitors of translation are critical tools to study the molecular mechanisms of protein synthesis. In this study, we sought to characterize how QL47, a host-targeted, small-molecule antiviral agent, inhibits steady-state viral protein expression. We demonstrate that this small molecule broadly inhibits both viral and host protein synthesis and targets a translation step specific to eukaryotic cells. We show that QL47 inhibits protein neosynthesis initiated by both canonical cap-driven and noncanonical initiation strategies, most likely by targeting an early step in translation elongation. Our findings thus establish QL47 as a new small-molecule inhibitor that can be utilized to probe the eukaryotic translation machinery and that can be further developed as a new therapeutic agent.
GaN MOSFETs with Large Current and Normally-off Operation (2008)

GaN is promising for high-power, high-temperature devices due to its large bandgap, high critical electric field, and high saturation velocity compared with Si and SiC. The MOSFET structure can be operated at a positive threshold voltage, namely the normally-off mode, which is preferable for power transistors in terms of fail-safe operation. In order to realize MOSFET operation, good interface quality at SiO2/GaN and low resistance in the n+-contact layer is strongly required. We have overcome these requirements by precise thermal control. Finally, we have fabricated GaN MOSFETs and have achieved more than 1 A operation in the normally-off mode at more than 250oC. The breakdown voltage was more than 1500 V.
Orthogonal luminescence lifetime encoding by intermetallic energy transfer in heterometallic rare-earth MOFs (2023)

Lifetime-encoded materials are particularly attractive as optical tags, however examples are rare and hindered in practical application by complex interrogation methods. Here, we demonstrate a design strategy towards multiplexed, lifetime-encoded tags via engineering intermetallic energy transfer in a family of heterometallic rare-earth metal-organic frameworks (MOFs). The MOFs are derived from a combination of a high-energy donor (Eu), a low-energy acceptor (Yb) and an optically inactive ion (Gd) with the 1,2,4,5 tetrakis(4-carboxyphenyl) benzene (TCPB) organic linker. Precise manipulation of the luminescence decay dynamics over a wide microsecond regime is achieved via control over metal distribution in these systems. Demonstration of this platform's relevance as a tag is attained via a dynamic double encoding method that uses the braille alphabet, and by incorporation into photocurable inks patterned on glass and interrogated via digital high-speed imaging. This study reveals true orthogonality in encoding using independently variable lifetime and composition, and highlights the utility of this design strategy, combining facile synthesis and interrogation with complex optical properties.
B/A Measurement of Clear Cell Renal Cell Carcinoma versus Healthy Kidney Tissue (2022)

The acoustic parameter of non-linearity B/A has been found capable of discriminating some types of pathological tissue from healthy tissue. The literature on the utility of B/A for cancer diagnostics is very limited, with measurements on the human breast and liver. This work expands the current research on cancer diagnostics by B/A assessment of eight slices of human clear cell renal cell carcinoma (ccRCC) from two patients and four slices of healthy kidney tissue from two healthy kidney samples. The Wilcoxon test identified the B/A distribution of malignant tissue as not significantly different from that of healthy tissue. An alternative way of defining outliers resulted in median B/A values of 8.1 for ccRCC and 6.8 for healthy tissue (p < 0.05). Acoustic attenuation at 2.1 MHz was significantly greater (p < 0.05) for ccRCC (1.7 dB/cm) than for healthy tissue (1.0 dB/cm). The observed differences in the measured values suggest that B/A and acoustic attenuation may represent potential diagnostic markers of ccRCC. More data and an improved experimental design are required to provide a definitive conclusion on the utility of B/A for cancer diagnostics.
Electrostatic Control over Optically Pumped Hot Electrons\nin Optical Gap Antennas (2020)

We investigate the influence of a\nstatic electric field on the\nincoherent nonlinear response of an unloaded electrically contacted\nnanoscale optical gap antenna. Upon excitation by a tightly focused\nnear-infrared femtosecond laser beam, a transient elevated temperature\nof the electronic distribution results in a broadband emission of\nnonlinear photoluminescence (N-PL). We demonstrate a modulation of\nthe yield at which driving photons are frequency up-converted by means\nof an external control of the electronic surface charge density. We\nshow that the electron temperature and consequently the N-PL intensity\ncan be enhanced or reduced depending on the command polarity and the\nstrength of the control static field. A modulation depth larger than\n100% is observed for activation voltages of a few volts.
Whole Body Machines: NMR Phased Array Coil Systems (2007)

The sections in this article are 1 Introduction 2 Optimum S/N for Surface Coils: Aperture Synthesis 3 NMR Phased Array Techniques: Overlapping Coils and Low-Input-Impedance Preamplifiers 4 Conventional NMR Phased Array System Architecture 5 Phased Array Image Reconstruction 6 Noise Correlations Among Surface Coils in the NMR Phased Array 7 Clinical Applications 8 Real-Time Processing 9 Biographical Sketches Related Articles
Experimental and Computational Study of Small (n = 1−16) Stoichiometric Zinc and Cadmium Chalcogenide Clusters (2006)

Zinc selenide, cadmium sulfide, and cadmium selenide clusters were produced by direct laser ablation and analyzed in a time-of-flight mass spectrometer. The positive-ion mass spectra indicated that clusters composed of six and thirteen monomer units were ultrastable in all cases. The geometries and energies of the neutral and positively charged M(n)X(n) clusters up to n = 16 were obtained computationally at the B3LYP level of theory using the SKBJ basis set for the metal atoms and the SKBJ(d,2df) basis set for the chalcogen atoms. Small neutral and positive clusters (n = 1-4) have planar geometries, neutral three-dimensional clusters have the geometry of closed-cage polyhedra, and cationic three-dimensional clusters have structures with a pair of two-coordinated atoms. Physical properties of the clusters as a function of size are reported. The relative stability of the positive stoichiometric clusters provides a thermodynamic explanation for the relative stability observed experimentally from the laser-ablation mass spectrometry.
Reconstructing Truncated Integer Variables Satisfying Linear Congruences (1988)

We propose a general polynomial time algorithm to find small integer solutions to systems of linear congruences. We use this algorithm to obtain two polynomial time algorithms for reconstructing the values of variables $x_1 , \cdots ,x_k $ when we are given some linear congruences relating them together with some bits obtained by truncating the binary expansions of the variables. The first algorithm reconstructs the variables when either the high order bits or the low order bits of the $x_i $ are known. It is essentially optimal in its use of information in the sense that it will solve most problems almost as soon as the variables become uniquely determined by their constraints. The second algorithm reconstructs the variables when an arbitrary window of consecutive bits of the variables is known. This algorithm will solve most problems when twice as much information as that necessary to uniquely determine the variables is available. Two cryptanalytic applications of the algorithms are given: predicting linear congruential generators whose outputs are truncated and breaking the simplest version of Blum’s protocol for exchanging secrets.
Variation in the expression of cell wall proteins of Staphylococcus aureus grown on solid and liquid media (1988)

To evaluate the variation in the expression of cell wall antigens between Staphylococcus aureus grown in liquid medium and solid support, bacteria were harvested from liquid chemically defined medium and chemically defined medium in a 1% agar base. Cell wall proteins were then extracted by lysostaphin in a protoplast-stabilizing medium (30% raffinose). After separation of the cell wall antigens by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blots, they were probed with chicken antiserum to an S. aureus strain grown on a solid support. For each of the 15 clinical strains analyzed, high-molecular-size bands (molecular size range, 120 to 220 kilodaltons) were either enhanced or distinctly present when compared with those from the cell wall extract of the same strain grown in liquid medium. Results of enzymatic treatment of whole staphylococci grown on solid medium suggested the proteinaceous nature and the surface location of these antigens. Limited passage studies demonstrated the ability of the staphylococci to alter these surface proteins when passaged alternately on liquid and solid media. These observations suggested the importance of the microenvironment to the expression of cell wall proteins in S. aureus. Correlations with observations in vivo may help identify the determinants of microbial pathogenicity in S. aureus.