gebhart/patrepeval huggingface dataset:
Mammalian artificial chromosome pilot production facility: Large-scale isolation of functional satellite DNA-based artificial chromosomes (1999)

By developing new SATAC containing cell lines with fewer numbers of chromosomes in conjunction with operating a high speed flow sorter we have effectively generated an efficient production facility geared purely for the isolation of SATACs.
The Case Back on the TRAIL: Death Receptors as Markers for rhTRAIL Sensitivity (2017)

These data show the potential of this flow cytometry-based assay for the analysis of isolated tumor cells for DR membrane expression. By first determining a patient's susceptibility to rhTRAIL-based treatments, they can be more appropriately placed in rhTRAIL clinical trials and improve rhTRAIL as an anticancer therapeutic.
Minimizing the usage of hardware counters for collective communication using triggered operations (2019)

Triggered operations and counting events or counters are building blocks that can be used by communication libraries, such as MPI, to offload collective operations to the Host Fabric Interface (HFI) or Network Interface Card (NIC). Triggered operations can be used to schedule a network or arithmetic operation to occur in the future, when a trigger counter reaches a specified threshold. On completion of the operation, the value of a completion counter increases by one. With this mechanism, it is possible to create a chain of dependent operations, so that the execution of an operation is triggered when all its dependent operations have completed its execution.
White-light holographic display based on planar optics (1993)

A novel method for designing, recording, and reconstructing a planar-optics display holographic doublet, composed of two holograms on the same plate, is presented. The first hologram traps a light from a white-light source into the substrate by total internal reflection, whereas the second hologram couples out the trapped light from the plate to form the reconstructed three-dimensional image. The method is illustrated with a holographic doublet recorded at 488 nm and read out with a white-light source. A sharp image with high efficiency was reconstructed.
Time resolved contrast enhanced intracranial MRA using a single dose delivered as sequential injections and highly constrained projection reconstruction (HYPR CE) (2011)

Time-resolved contrast-enhanced magnetic resonance angiography of the brain is challenging due to the need for rapid imaging and high spatial resolution. Moreover, the significant dispersion of the intravenous contrast bolus as it passes through the heart and lungs increases the overlap between arterial and venous structures, regardless of the acquisition speed and reconstruction window. An innovative technique is presented that divides a single dose contrast into two injections. Initially a small volume of contrast material (2-3 mL) is used to acquiring time-resolved weighting images with a high frame rate (2 frames/s) during the first pass of the contrast agent. The remaining contrast material is used to obtain a high resolution whole brain contrast-enhanced (CE) magnetic resonance angiography (0.57 × 0.57 × 1 mm(3) ) that is used as the spatial constraint for Local Highly Constrained Projection Reconstruction (HYPR LR) reconstruction. After HYPR reconstruction, the final dynamic images (HYPR CE) have both high temporal and spatial resolution. Furthermore, studies of contrast kinetics demonstrate that the shorter bolus length from the reduced contrast volume used for the first injection significantly improves the arterial and venous separation.
Indolizine‐Based Donors as Organic Sensitizer Components for Dye‐Sensitized Solar Cells (2014)

Strong electron‐donating functionality is desirable for many organic donor‐π‐bridge‐acceptor (D‐π‐A) dyes. Strategies for increasing the electron‐donating strength of common nitrogen‐based donors include planarization of nitrogen substituents and the use of low resonance‐stabilized energy aromatic ring‐substituted nitrogen atoms. Organic donor motifs based on the planar nitrogen containing heterocycle indolizine are synthesized and incorporated into dye‐sensitized solar cell (DSC) sensitizers. Resonance active substitutions at several positions on indolizine in conjugation with the D‐π‐A π‐system are examined computationally and experimentally. The indolizine‐based donors are observed to contribute electron density with strengths greater than triarylamines and diarylamines, as evidenced by UV/Vis, IR absorptions, and oxidation potential measurements. Fluorescence lifetime studies in solution and on TiO 2 yield insights in understanding the performance of indolizine‐based dyes in DSC devices.
Quantitative Endovascular Angioscopy (1989)

Currently there is no available system capable of providing real-time absolute dimensional analysis of features within the field of view of conventional angioscopes. This paper describes a method which utilizes computer-based image processing equipment and novel algorithms to address this problem. By analyzing the magnification characteristics of an angioscope and analyzing any single feature from multiple angioscopic views, the cross-sectional area of the feature may be calculated. Experimental results indicate both a high accuracy and the feasibility of this approach.
New processable polyaromatic ether–keto‐sulfones curable by Diels‐Alder cycloaddition (1980)

Abstract New Processable polyaromatic ether‐keto‐sulfones were prepared from the acid chloride of bis‐ m ‐carboxyphenyl acetylene (XII), isophthaloyl chloride (XX), diphenyl ether (XVIII), and 4,4′‐diphenoxydiphenyl sulfone (XIX) in a Friedel‐Crafts‐type polymerization. These polymers were cured by Diels‐Alder cycloaddition with 1,4‐diphenyl‐1,3‐butadiene. The cured polymers showed an increase in T g and in thermal and heat stabilities. The polymers form colorless, transparent, brittle films and can be cast into a glass fiber laminate. Both meta‐and para‐substituted acid chlorides of biscarboxyphenyl‐1,3‐butadiene yielded insoluble polymers under the same conditions but form processable polymers where combined with acetylene units in the polymer chain. Polymers that contained both acetylene and butadiene units were prepared but could not be cured by an intramolecular Diels‐Alder cycloaddition reaction.
Stabilized Blue Emission from Polymer–Dielectric Nanolayer Nanocomposites (2004)

Abstract Blue‐light‐emitting polymer (polyfluorene)/dielectric nanolayer nanocomposites were prepared by the solution intercalation method and employed in an electroluminescent (EL) device. Their photoluminescence (PL) and electroluminescence characteristics demonstrates that the interruption of interchain interaction in intercalated organic/inorganic hybrid systems reduces the low‐energy emission that results from keto‐defects. By reducing the probability that the excitons initially generated on the polyfluorenes will find keto‐defects, both the color purity and the luminescence stability were improved. Furthermore, the dielectric nanolayers have an aspect ratio of about five hundred, and therefore act as efficient exciton blocking layers and barriers to oxygen diffusion, producing a dramatic increase in the device stability. A nanocomposite device with a Li:Al alloy cathode gave a quantum efficiency of 1.0 %(ph/el), which corresponds to an approximate five times enhancement compared to the neat polymer device. The nanocomposite emitting layer is considered to have a pseudo‐multiple quantum well structure.
Detection and localization of pulmonary air leaks using laser-polarized3He MRI (2000)

Pulmonary air leaks were created in the lungs of Yorkshire pigs. Dynamic, 3D MRI of laser-polarized (3)He gas was then performed using a gradient-echo pulse sequence. Coronal magnitude images of the helium distribution were acquired during gas inhalation with a voxel resolution of approximately 1.2 x 2.5 x 8 mm, and a time resolution of 5 sec. In each animal, the ventilation images reveal focal high-signal intensity within the pleural cavity at the site of the air leaks. In addition, a wedge-shaped region of increased parenchymal signal intensity was observed adjacent to the site of the air leak in one animal. (3)He MRI may prove helpful in the management of patients with pulmonary air leaks.
Coherent anti‐Stokes Raman micro‐spectroscopy using spectral focusing: theory and experiment (2009)

Abstract Coherent anti‐Stokes Raman scattering (CARS) microscopy using linearly chirped femtosecond laser pulses and spectrally and time‐integrated detection is discussed both theoretically and experimentally. By matching the linear chirp of Stokes and pump pulses, the spectral resolution is reduced to the Fourier limit of the chirped pulse duration (spectral focusing). We discuss the effect of the time‐ordering of Pump and Stokes pulses on the signal strength and selectivity, and give analytical expressions for the relevant quantities. We consider linear chirp obtained by glass elements of known group‐velocity dispersion, and analyze the limit of the spectral resolution by higher order glass dispersion. Experiments corroborating the theory are presented, using 100 fs laser pulses, SF57 glass elements, and polystyrene beads as test samples. Copyright © 2009 John Wiley & Sons, Ltd.
Process and apparatus for removing H/sub 2/S from gas streams (1983)

A gas stream containing CO/sub 2/ and H/sub 2/S is contacted with an alkanolamine in a contacting zone. The rich solution is then selectively stripped in a stripping zone to produce a gas stream containing a higher CO/sub 2/:H/sub 2/S mole ratio than the initial stream. This stream can be recycled to the alkanolamine contacting zone. The partially stripped solution can be introduced into another stripping zone to provide a third gas stream which is rich in H/sub 2/S and lean in CO/sub 2/ suitable as feed for a Claus Unit and a lean alkanolamine solution which can be recycled to the contacting zone.
Establishment of Gastrointestinal (2013)

The intestinal epithelium constitutes a system of constant and rapid renewal triggered by proliferation of intestinal stem cells (ISCs), and is an ideal system for studying cell proliferation, migration, and differentiation. Primary cell cultures have proven to be promising for unraveling the mechanisms involved in epithelium homeostasis. In 2009, Sato et al. established a long-term primary culture to generate epithelial organoids (enteroids) with crypt- and villus-like epithelial domains representing the complete census of progenitors and differentiated cells. Similarly, isolated ISCs expressing Lgr5 (leucinerich repeat-containing G protein–coupled receptor) can generate enteroids. Here, we describe methods to establish gastric, small intestinal, and colonic epithelial organoids and generate Lgr5 +ve single cell–derived epithelial organoids. We also describe the imaging techniques used to characterize those organoids. This in vitro model constitutes a powerful tool for studying stem cell biology and intestinal epithelial cell physiology throughout the digestive tract. Curr. Protoc. Mouse Biol. 3:217-240 C � 2013 by John
Disposable integrated microfluidic biochip for blood typing by plastic microinjection moulding (2006)

Blood typing is the most important test for both transfusion recipients and blood donors. In this paper, a low cost disposable blood typing integrated microfluidic biochip has been designed, fabricated and characterized. In the biochip, flow splitting microchannels, chaotic micromixers, reaction microchambers and detection microfilters are fully integrated. The loaded sample blood can be divided by 2 or 4 equal volumes through the flow splitting microchannel so that one can perform 2 or 4 blood agglutination tests in parallel. For the purpose of obtaining efficient reaction of agglutinogens on red blood cells (RBCs) and agglutinins in serum, we incorporated a serpentine laminating micromixer into the biochip, which combines two chaotic mixing mechanisms of splitting/recombination and chaotic advection. Relatively large area reaction microchambers were also introduced for the sake of keeping the mixture of the sample blood and serum during the reaction time before filtering. The gradually decreasing multi-step detection microfilters were designed in order to effectively filter the reacted agglutinated RBCs, which show the corresponding blood group. To achieve the cost-effectiveness of the microfluidic biochip for disposability, the biochip was realized by the microinjection moulding of COC (cyclic olefin copolymer) and thermal bonding of two injection moulded COC substrates in mass production with a total fabrication time of less than 20 min. Mould inserts of the biochip for the microinjection moulding were fabricated by SU-8 photolithography and the subsequent nickel electroplating process. Human blood groups of A, B and AB have been successfully determined with the naked eye, with 3 microl of the whole sample bloods, by means of the fabricated biochip within 3 min.
Expression of Maize Phospho<i>enol</i>pyruvate Carboxylase in Transgenic Tobacco (1992)

The expression of maize (Zea mays) phophoenolpyruvate carboxylase (PPC) gene constructions was studied in transgenic tobacco plants (Nicotiana tabacum). Where transcription was under the control of a maize PPC gene promoter, a low level of aberrantly large PPC transcript was detected. Analysis of this PPC transcript indicated that transcription initiation occurs upstream of the normal site. Despite the aberrant transcription initiation, expression of the PPC transcript was still light-regulated. Higher levels of maize PPC transcript of the correct size were obtained with a chimeric gene construction containing a tobacco (Nicotiana plumbaginifolia) chlorophyll a/b binding protein gene promoter. The PPC activities in the leaves of these transgenic plants were up to twofold higher than those of nontransformed plants. Two forms of PPC with different kinetic properties were identified in leaf extracts of the transgenic plants: one form with a high apparent K(m) for phosphoenolpyruvate (maize isozyme), and a second form exhibiting a low apparent K(m) (tobacco isozyme). Biochemical analyses of these plants indicated that the transgenic plants had significantly elevated levels of titratable acidity and malic acid. These biochemical differences did not produce any significant physiological changes with respect to photosynthetic rate or CO(2) compensation point.
Opiate Antagonists (1980)

Department of Medical Neurosciences, Division of Neuropsychiatry, Walter Reed Army Institute of Research, Washington, District of Columbia
Singing Voice Separation With Deep U-Net Convolutional Networks. (2017)

[TODO] Add abstract here.
Novel inflammatory biomarkers of portal pressure in compensated cirrhosis patients (2013)

A blood test for HVPG could be performed in cirrhosis patients to prevent unnecessary esophagogastroduodenoscopy.
Framework of belief condensation filtering and deterministic discrete filters (2012)

Inferring a sequence of variables from observations is a prevalent task in a multitude of applications. However, in some nonlinear or non-Gaussian scenarios, traditional techniques such as Kalman filters (KFs) and particle filters (PFs) fail to provide satisfactory performance. Moreover, there is a lack of a unifying framework for the analysis and development of different filtering techniques. In this paper, we present a general framework for filtering that allows to formulate an optimality criterium leading to the concept of belief condensation filtering (BCF). Moreover, we develop discrete BCFs that are optimal under such framework. Finally, simulation results are presented for the important filtering task that arises in ultrawide bandwidth (UWB) ranging. We show that BCF can obtain accuracies approaching the theoretical benchmark but with a smaller complexity than PFs.
A fast method for computing and correcting intensity inhomogeneities in MRI (2008)

In magnetic resonance imaging (MRI) a given tissue may have quite different intensities depending on its location in the image volume. Such intensity inhomogeneities often arise from what is usually called the bias field, and are due to radio frequency inhomogeneities, variations in the static magnetic field and the distance of the tissue to the receiving coil. We present an efficient approach to determine such inhomogeneities from a series of calibration scans, which take less than 40 seconds to acquire. This enables us to efficiently correct both T <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> and T <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> weighted images. We present the theoretical background, as well as typical results for phantom, liver, pelvic and spine images.
Seed-Initiated Anisotropic Growth of Unidirectional Armchair Graphene Nanoribbon Arrays on Germanium (2018)

It was recently discovered that the chemical vapor deposition (CVD) of CH<sub>4</sub> on Ge(001) can directly yield long, narrow, semiconducting nanoribbons of graphene with smooth armchair edges. These nanoribbons have exceptional charge transport properties compared with nanoribbons grown by other methods. However, the nanoribbons nucleate at random locations and at random times, problematically giving rise to width and bandgap polydispersity, and the mechanisms that drive the anisotropic crystal growth that produces the nanoribbons are not understood. Here, we study and engineer the seed-initiated growth of graphene nanoribbons on Ge(001). The use of seeds decouples nucleation and growth, controls where growth occurs, and allows graphene to grow with lattice orientations that do not spontaneously form without seeds. We discover that when the armchair direction (i.e., parallel to C-C bonds) of the seeds is aligned with the Ge⟨110⟩ family of directions, the growth anisotropy is maximized, resulting in the formation of nanoribbons with high-aspect ratios. In contrast, increasing misorientation from Ge⟨110⟩ yields decreasingly anisotropic crystals. Measured growth rate data are used to generate a construction analogous to a kinetic Wulff plot that quantitatively predicts the shape of graphene crystals on Ge(001). This knowledge is employed to fabricate regularly spaced, unidirectional arrays of nanoribbons and to significantly improve their uniformity. These results show that seed-initiated graphene synthesis on Ge(001) will be a viable route for creating wafer-scale arrays of narrow, semiconducting, armchair nanoribbons with rationally controlled placement and alignment for a wide range of semiconductor electronics technologies, provided that dense arrays of sub-10 nm seeds can be uniformly fabricated in the future.
Improving High-Content-Screening Assay Performance by Using Division-Arrested Cells (2005)

As cell-based assays are used more commonly in robotic high-throughput compound screening, cells themselves have become critical reagents. Thus, it has become essential to produce cell reagents with high consistency and quality. We experimented with cells division-arrested with low-level mitomycin C treatment and demonstrate that they perform with better consistency than non-division-arrested counterparts in high-content screening imaging assays. We propose that for cell-based screening, it is possible to uncouple the cell production process from the screening process. Cells can be produced en masse, treated to become irreversibly division-arrested, and cryopreserved. These "ready-to-use" reagents can be thawed, plated, and used in screening with improved consistency and convenience.
Development of a Chemoenzymatic-like and Photoswitchable Method for the Ordered Attachment of Proteins to Surfaces (2005)

Protein arrays are the best tool for the rapid analysis of a whole proteome thus helping to identify all the protein/protein interactions in a living cell and they can also be used as powerful biosensors. The objective of this proposal is to develop a new entropically activated ligation method based in the naturally occurring protein trans-splicing process. This method will be used for the generation of spatially addressable arrays of multiple protein components by standard photolithographic techniques. Key to our approach is the use of the protein trans-splicing process. This naturally occurring process will allow us to create a truly generic and highly efficient method for the covalent attachment of proteins through its C-terminus to any solid support.
Learned D-AMP: Principled Neural Network based Compressive Image\n Recovery (2017)

Compressive image recovery is a challenging problem that requires fast and\naccurate algorithms. Recently, neural networks have been applied to this\nproblem with promising results. By exploiting massively parallel GPU processing\narchitectures and oodles of training data, they can run orders of magnitude\nfaster than existing techniques. However, these methods are largely\nunprincipled black boxes that are difficult to train and often-times specific\nto a single measurement matrix.\n It was recently demonstrated that iterative sparse-signal-recovery algorithms\ncan be "unrolled" to form interpretable deep networks. Taking inspiration from\nthis work, we develop a novel neural network architecture that mimics the\nbehavior of the denoising-based approximate message passing (D-AMP) algorithm.\nWe call this new network Learned D-AMP (LDAMP).\n The LDAMP network is easy to train, can be applied to a variety of different\nmeasurement matrices, and comes with a state-evolution heuristic that\naccurately predicts its performance. Most importantly, it outperforms the\nstate-of-the-art BM3D-AMP and NLR-CS algorithms in terms of both accuracy and\nrun time. At high resolutions, and when used with sensing matrices that have\nfast implementations, LDAMP runs over $50\\times$ faster than BM3D-AMP and\nhundreds of times faster than NLR-CS.\n
TED: Teaching AI to Explain its Decisions (2018)

Artificial intelligence systems are being increasingly deployed due to their potential to increase the efficiency, scale, consistency, fairness, and accuracy of decisions. However, as many of these systems are opaque in their operation, there is a growing demand for such systems to provide explanations for their decisions. Conventional approaches to this problem attempt to expose or discover the inner workings of a machine learning model with the hope that the resulting explanations will be meaningful to the consumer. In contrast, this paper suggests a new approach to this problem. It introduces a simple, practical framework, called Teaching Explanations for Decisions (TED), that provides meaningful explanations that match the mental model of the consumer. We illustrate the generality and effectiveness of this approach with two different examples, resulting in highly accurate explanations with no loss of prediction accuracy for these two examples.