gebhart/patrepeval huggingface dataset:
Use of MCSS to Design Small Targeted Libraries:  Application to Picornavirus Ligands (2001)

Computational methods were used to design structure-based combinatorial libraries of antipicornaviral capsid-binding ligands. The multiple copy simultaneous search (MCSS) program was employed to calculate functionality maps for many diverse functional groups for both the poliovirus and rhinovirus capsid structures in the region of the known drug binding pocket. Based on the results of the MCSS calculations, small combinatorial libraries consisting of 10s or 100s of three-monomer compounds were designed and synthesized. Ligand binding was demonstrated by a noncell-based mass spectrometric assay, a functional immuno-precipitation assay, and crystallographic analysis of the complexes of the virus with two of the candidate ligands. The P1/Mahoney poliovirus strain was used in the experimental studies. A comparison showed that the MCSS calculations had correctly identified the observed binding site for all three monomer units in one ligand and for two out of three in the other ligand. The correct central monomer position in the second ligand was reproduced in calculations in which the several key residues lining the pocket were allowed to move. This study validates the computational methodology. It also illustrates that subtle changes in protein structure can lead to differences in docking results and points to the importance of including target flexibility, as well as ligand flexibility, in the design process.
Lexical Chaining for Measuring Discourse Coherence Quality in Test-taker Essays (2014)

This paper presents an investigation of lexical chaining (Morris and Hirst, 1991) for measuring discourse coherence quality in test-taker essays. We hypothesize that attributes of lexical chains, as well as interactions between lexical chains and explicit discourse elements, can be harnessed for representing coherence. Our experiments reveal that performance achieved by our new lexical chain features is better than that of previous discourse features used for this task, and that the best system performance is achieved when combining lexical chaining features with complementary discourse features, such as those provided by a discourse parser based on rhetorical structure theory, and features that reflect errors in grammar, word usage, and mechanics.
Water Management at the Cathode of a Planar Air-Breathing Fuel Cell with an Electroosmotic Pump (2006)

Water management is a significant challenge in portable fuel cells and particularly in fuel cells with air-breathing cathodes. Liquid water condensation and accumulation at the cathode surface is unavoidable in a passive design operated over a wide range of ambient and load conditions. Excessive flooding of the open cathode can lead to a dramatic reduction of fuel cell power. We report a novel water management design based on a hydrophilic and electrically conductive wick in conjunction with an electroosmotic (EO) pump. A prototype air- breathing fuel cell with the proposed water management design successfully functioned under severe flooding conditions, including ambient temperature 10ºC and relative humidity 80 %, for up to 6 h without any observable cathode flooding or loss of performance.
Image-based object editing (2004)

We examine the problem of editing complex 3D objects. We convert the problem of editing a 3D object of arbitrary size and surface properties to a problem of editing a 2D image. We allow the user to specify edits in both geometry and surface properties from any view and at any resolution they find convenient, regardless of the interactive rendering capability of their computer. We use specially-constrained shape from shading algorithms to convert a shaded image specified by the user into a 3D geometry.
7-Arylidenenaltrexones as Selective δ<sub>1</sub> Opioid Receptor Antagonists (1998)

A series of 7-arylidinenaltrexones (2a-m) related to the prototypical delta1-selective antagonist, 7-benzylidenenaltrexone 1 (BNTX), have been synthesized in an effort to develop more selective ligands. Testing in smooth muscle preparations revealed that members of the series exhibited varying degrees of selectively for delta receptors, with the o-methoxy (2e) and o-chloro (2j) congeners being most potent and most selective (Ke approximately 0.8 nm). Evaluation of 1, 2e, and 2f sc in mice using the tail-flick procedure indicated that they are selective delta1 opioid receptor antagonists in the lower dose range. At high doses these ligands, including BNTX, exhibited decreased delta1 selectivity due to increases in the ED50 ratios of [D-Ser2,Leu5]enkephalin-Thr6 and morphine. It is concluded that 2e and 2f possess in vivo selectivity similar to that of BNTX, but are less potent as delta1 antagonists.
The antichlamydial, antiviral, and antiproliferative activities of human gamma interferon are dependent on the integrity of the C terminus of the interferon molecule (1987)

The effects of recombinant human gamma interferon (rHuIFN-gamma; two identical monomers of 140 residues in length) and of two re-engineered C-terminal variants, rHuIFN-gamma Tetra-Ser (residues 129 to 132 replaced by serine) and rHuIFN-gamma 125 (two identical monomers of 125 residues each with the last 14 residues plus an additional alanine from the C terminus deleted), were compared in terms of several in vitro biological activities. By using three different human cell lines (HeLa 229, HEp-2, and A549), the interferons were tested for their ability to inhibit: (i) growth of Chlamydia trachomatis; (ii) replication of encephalomyocarditis virus; and (iii) cell growth. rHuIFN-gamma restricted the growth of chlamydiae to 50% of the non-IFN-treated control at concentrations ranging from 0.01 to 0.05 ng/ml, depending on the cell type assayed. One of the modified proteins, rHuIFN-gamma Tetra-Ser, also decreased the growth of chlamydiae, but it required a concentration of approximately 0.5 ng/ml to produce 50% inhibition. rHuIFN-gamma 125 had the lowest antichlamydial activity of the three IFN-gamma variants tested; concentrations of 1 to 20 ng/ml were needed to reduce the growth of C. trachomatis to 50% of that of the control. The relative antiviral and antiproliferative activities of the three IFN-gamma preparations paralleled their antichlamydial activities in these three cell lines. The antiencephalomyocarditis virus activities of rHuIFN-gamma Tetra-Ser and rHuIFN-gamma 125 were reduced by approximately 10-fold and 10(2)- to 10(3)-fold, respectively, compared with the antiviral activity of rHuIFN-gamma. Proliferation of the three cell lines was restricted to approximately 50% of the control with 0.5 to 10 ng of rHuIFN-gamma per ml. Inhibition of cell growth by rHuIFN-gamma Tetra-Ser was significant only at concentrations equal to or greater than 30 ng/ml, and the rHuIFN-gamma 125 variant did not significantly decrease the growth of any of the three cell lines at the concentrations tested. These results suggest that the C-terminal portion of rHuIFN-gamma is critical for maintaining the conformation necessary for inducing the antichlamydial, antiviral, and antiproliferative activities of the molecule.
Two-Dimensional Surface-Emitting Arrays Of GaAs/AlGaAs Diode Lasers (1989)

Three approaches to fabricating two-dimensional surface-emitting GaAs/AlGaAs diode laser arrays are discussed: a hybrid approach in which linear arrays of edge-emitting lasers with cleaved end facets are mounted on microchanneled Si heatsinks with integral 45° deflecting mirrors, a monolithic approach in which edge-emitting lasers are fabricated with deflecting mirrors adjacent to both end facets of each laser, and a monolithic approach in which horizontal-cavity lasers are fabricated with intracavity 45° deflecting mirrors. In both monolithic approaches, all the laser facets and deflecting mirrors are fabricated by ion-beam-assisted etching.
Algorithms for automated oximetry along the retinal vascular tree from dual-wavelength fundus images (2005)

We present an automated method to perform accurate, rapid, and objective measurement of the blood oxygen saturation over each segment of the retinal vascular hierarchy from dual-wavelength fundus images. Its speed and automation (2 s per entire image versus 20 s per segment for manual methods) enables detailed level-by-level measurements over wider areas. An automated tracing algorithm is used to estimate vessel centerlines, thickness, directions, and locations of landmarks such as bifurcations and crossover points. The hierarchical structure of the vascular network is recovered from the trace fragments and landmarks by a novel algorithm. Optical densities (OD) are measured from vascular segments using the minimum reflected intensities inside and outside the vessel. The OD ratio (ODR=OD600/OD570) bears an inverse relationship to systemic HbO2 saturation (SO2). The sensitivity for detecting saturation change when breathing air versus pure oxygen was calculated from the measurements made on six subjects and was found to be 0.0226 ODR units, which is in good agreement with previous manual measurements by the dual-wavelength technique, indicating the validity of the automation. A fully automated system for retinal vessel oximetry would prove useful to achieve early assessments of risk for progression of disease conditions associated with oxygen utilization.
THIN-FILM THICKNESS MEASUREMENTS WITH THERMAL WAVES (1983)

We have combined a new laser beam deflection technique using high frequency thermal waves with a three-dimensional depth-profiling theoretical model to measure the thickness of opaque and transparent films. Thickness sensitivities of ±2% over the range 500Å - 25,000Å have been obtained for Al and SiO2 films on Si substrates.
Miniature thermoacoustic cryocooler driven by a vertical comb-drive (2003)

In this paper, we propose a novel miniature MEMS based thermoacoustic cryo-cooler for thermal management of cryogenic electronic devices. The basic idea is to exploit a new way to realize a highly-reliable miniature cryo-cooler, which would allow integration of a cryogenic cooling system directly into a cryogenic electronic device. A vertical comb-drive is proposed as the means to provide an acoustic source through a driving plate to a resonant tube. By exciting a standing wave within the resonant tube, a temperature difference develops across the stack in the tube, thereby enabling heat exchange between two heat exchangers. The use of gray scale technology to fabricate tapered resonant tube provides a way to improve the efficiency of the cooling system, compared with a simple cylinder configuration. Furthermore, a tapered tube leads to extremely strong standing waves with relatively pure waveforms and reduces possible harmonics. The working principle of this device is described here. The fabrication of this device is considered, which is compatible with current MEMS fabrication technology. Finally, the theoretical analysis of key components of this cryo-cooler is presented.
Evolution of B-cell malignancy: pre-B-cell leukemia resulting from MYC activation in a B-cell neoplasm with a rearranged BCL2 gene. (1988)

We have analyzed the molecular genetics of the breakpoints involved in the t(8;14) and t(14;18) translocations of an acute pre-B-cell leukemia from a patient with a history of follicular lymphoma. In this patient's leukemic cells, the breakpoint of the t(14;18) translocation occurred in the major breakpoint-cluster region of the BCL2 gene and became linked to the JH4 joining-region gene segment of the immunoglobulin heavy-chain locus on the 14q+ chromosome as previously observed in follicular lymphoma. An N region and heptamer and nonamer signal sequences indicated that this translocation occurred as a mistake in VH-DH-JH joining (where VH and DH are the variable and diversity segments). In the t(8;14) translocation, the breakpoint was located immediately 5' of the first exon of the MYC protooncogene, which was juxtaposed with the C gamma 2 constant gene segment of the second 14q+ chromosome. The finding of repeated sequences typical of switch regions suggested that this translocation occurred during heavy-chain isotype switching, resulting in progression to pre-B-cell leukemia with both the t(8;14) and the t(14;18) translocations. The terminal deoxynucleotidyltransferase-positive phenotype of the patient's leukemic cells further suggests that the pre-B-cell leukemia was derived from a pre-B cell carrying a t(14;18) translocation in the original follicular lymphoma. The polymerase chain reaction method was then used to identify cancer cells in the bone marrow of the patient.
Autoantibodies to MUC1 glycopeptides cannot be used as a screening assay for early detection of breast, ovarian, lung or pancreatic cancer (2013)

This robust, validated study shows autoantibodies to MUC1 peptide or glycopeptides cannot be used for breast, ovarian, lung or pancreatic cancer screening. This has significant implications for research on the use of MUC1 in cancer detection.
Concatenation of Space-Time Coding and FEC for Few-Mode Fiber Systems (2017)

Space-division multiplexing (SDM) is becoming essential to increase the capacity of future optical communication systems. Propagating modes through multimode fibers are affected by a non-unitary crosstalk known as mode dependent loss (MDL), that requires either optical or digital signal processing solutions to be reduced. Space-time (ST) coding designed and used for wireless communications was proved to be efficient to reduce polarization-dependent loss in PolMux systems and MDL in SDM systems. In this letter, we study a complete transmission scheme, including forward error correction (FEC) and ST coding. FEC is used to protect the transmission from errors, but in the presence of MDL, system's performance is reduced. We show by simulations and error probability derivation that coding gain summation is obtained, which makes both codes essential for the next generation of optical transmission systems.
Modular Synthesis of Peptide-Based Single- and Multimodal Targeted Molecular Imaging Agents (2021)

A practical, modular synthesis of targeted molecular imaging agents (TMIAs) containing near-infrared dyes for optical molecular imaging (OMI) or chelated metals for magnetic resonance imaging (MRI) and single-photon emission correlation tomography (SPECT) or positron emission tomography (PET) has been developed. In the method, imaging modules are formed early in the synthesis by attaching imaging agents to the side chain of protected lysines. These modules may be assembled to provide a given set of single- or dual-modal imaging agents, which may be conjugated in the last steps of the synthesis under mild conditions to linkers and targeting groups. A key discovery was the ability of a metal such as gadolinium, useful in MRI, to serve as a protecting group for the chelator, 1,4,7,10-tetraazacyclododecane-1,4,7,10-<i>tetraacetic acid (</i>DOTA). It was further discovered that two lanthanide metals, La and Ce, can double as protecting groups and placeholder metals, which may be transmetalated under mild conditions by metals used for PET in the final step. The modular method enabled the synthesis of discrete targeted probes with two of the same or different dyes, two same or different metals, or mixtures of dyes and metals. The approach was exemplified by the synthesis of single- or dual-modal imaging modules for MRI-OMI, PET-OMI, and PET-MRI, followed by conjugation to the integrin-seeking peptide, c(RGDyK). For Gd modules, their efficacy for MRI was verified by measuring the NMR spin-lattice relaxivity. To validate functional imaging of TMIAs, dual-modal agents containing Cy5.5 were shown to target A549 cancer cells by confocal fluorescence microscopy.
Preparation of Unique 1-D Nanoparticle Superstructures and Tailoring their Structural Features (2010)

Designed peptide conjugate molecules are used to simultaneously direct both the synthesis and assembly of gold nanoparticles into various complex 1-D nanoparticle superstructures. We show how synthetic conditions, including reaction time and temperature, can be varied to carefully control the structure of the gold nanoparticle assembly and also the size and density of the nanoparticles within the assembly. We also demonstrate that particle capping agents such as citrate and adenosine triphosphate can be used to adjust the metrics of double-helical gold nanoparticle assemblies, in particular interhelical distances and particle size.
PD34-07 A NOVEL MICROFLUIDIC DEVICE TO IMPROVE SPERM SEARCHING IN MICRODISSECTION TESE SAMPLES (2019)

CONCLUSIONS: In this novel comparison of fertility outcomes between men with CF and CBAVD, those with CF had lower sperm quality with MESA, were more likely to require rescue TESE, and experienced a lower fertilization rate with ICSI compared with CBAVD patients. In addition to causing OA, homozygous CFTR mutations, particularly homozygous delta F508 mutations, also significantly impair spermatogenesis and sperm function.
Post-beamforming second-order Volterra filter for pulse-echo ultrasonic imaging (2003)

We present a new algorithm for deriving a second-order Volterra filter (SVF) capable of separating linear and quadratic components from echo signals. Images based on the quadratic components are shown to provide contrast enhancement between tissue and ultrasound contrast agents (UCAs) without loss in spatial resolution. It is also shown that the quadratic images preserve the low scattering regions due to their high dynamic range when compared with standard B-mode or harmonic images. A robust algorithm for deriving the filter has been developed and tested on real-time imaging data from contrast and tissue-mimicking media. Illustrative examples from image targets containing contrast agent and tissue-mimicking media are presented and discussed. Quantitative assessment of the contrast enhancement is performed on both the RF data and the envelope-detected log-compressed image data. It is shown that the quadratic images offer levels of enhancement comparable or exceeding those from harmonic filters while maintaining the visibility of low scattering regions of the image.
Recent advances in olefin polymerization (1996)

Abstract Various metallocenes were tested for syndiotactic polymerization of propylene. Reduction in the amount of costly methylalumoxane (MAO) or replacement with the other components was accomplished. Small modifications in the metallocene ligands brought about remarkable differences in the resulting catalysts concerning their storage stability, H 2 response as well as stereo‐specificity. Syndiotactic polypropylene (SPP) in the melt state behaves very differently compared to isotactic polypropylene (IPP). The notion that these polymers have different distributions of molecular entanglements are pursued, and verified for the first time. Excellent dispersibility of other olefin polymers in SPP matrix contributed to improve the usefulness of SPP.
Quantitation of intracellular [Na<sup>+</sup>] in vivo by using TmDOTP<sup>5−</sup> as an NMR shift reagent and extracellular marker (1998)

A method is presented to measure the absolute concentration of intracellular Na+ ([Na+]i) in vivo by using interleaved 23Na- and 31P-nuclear magnetic resonance (NMR) spectroscopy and TmDOTP5- as shift reagent and chemical marker of tissue extracellular space (ECS). The technique was used to determine [Na+]i and relative ECS in livers of control rats (21 +/- 3 and 0.11 +/- 0.02 mM, respectively) and in rats exposed to carbon tetrachloride (103 +/- 29 and 0.23 +/- 0.03 mM, respectively). The NMR measurements were confirmed independently on excised tissue samples by using atomic absorption spectroscopy. The results confirm that TmDOTP5- can be used as a combined cation shift reagent and ECS marker, thereby allowing quantitation of [Na+]i in vivo by NMR.
CORRELATION BETWEEN THE PROPERTIES OF POLYMERS AND OF POLYMER-MODIFIED BITUMENS (1996)

Polymeric modifiers are more and more used to improve asphalt performance. The applicability to polymer modified bitumens (PMBs) of the tests usually carried out on bitumens is now questioned: test standardisation and a wide agreement on the required specifications is necessary. In the present work, the properties of a number of polymers commonly proposed for PMBs were studied in order to suggest a way to select the polymer suitable for the required application; the prediction of the performance in the final application would allow to by-pass the tests on PMBs and asphalt mixtures. Rheological and mechanical tests were performed both on raw materials and on PMBs containing 5% polymer. Tensile DMTA, hardness, tensile properties and tension set test were carried out on polymers; the tendency of the polymers to absorb aromatic oil was also determined in order to simulate their swelling in the PMBs. Rheometer dynamic tests, R&B, penetration and elastic recovery were carried out on PMBs. Rheometer dynamic parameters, R&B, penetration, and elastic recovery were measured on the bitumen. Good correlation between polymer properties and PMB performance was found, supporting the hypothesis that mechanical and rheological properties of PMBs depend more on type and characteristics of the polymer (monomer type, molecular weight, crystallinity, etc) rather than on the composition of the bitumen. (A) For the covering abstract see IRRD 885061.
G-DOC: A Systems Medicine Platform for Personalized Oncology (2011)

Currently, cancer therapy remains limited by a "one-size-fits-all" approach, whereby treatment decisions are based mainly on the clinical stage of disease, yet fail to reference the individual's underlying biology and its role driving malignancy. Identifying better personalized therapies for cancer treatment is hindered by the lack of high-quality "omics" data of sufficient size to produce meaningful results and the ability to integrate biomedical data from disparate technologies. Resolving these issues will help translation of therapies from research to clinic by helping clinicians develop patient-specific treatments based on the unique signatures of patient's tumor. Here we describe the Georgetown Database of Cancer (G-DOC), a Web platform that enables basic and clinical research by integrating patient characteristics and clinical outcome data with a variety of high-throughput research data in a unified environment. While several rich data repositories for high-dimensional research data exist in the public domain, most focus on a single-data type and do not support integration across multiple technologies. Currently, G-DOC contains data from more than 2500 breast cancer patients and 800 gastrointestinal cancer patients, G-DOC includes a broad collection of bioinformatics and systems biology tools for analysis and visualization of four major "omics" types: DNA, mRNA, microRNA, and metabolites. We believe that G-DOC will help facilitate systems medicine by providing identification of trends and patterns in integrated data sets and hence facilitate the use of better targeted therapies for cancer. A set of representative usage scenarios is provided to highlight the technical capabilities of this resource.
Synchronizing Light Pulses With Video Camera (1993)

Interface circuit triggers laser or other external source of light to flash in proper frame and field (at proper time) for video recording and playback in pause mode. Also increases speed of electronic shutter (if any) during affected frame to reduce visibility of background illumination relative to that of laser illumination.