gebhart/patrepeval huggingface dataset:
Enhancement of critical current density in MgB <sub>2</sub> bulk superconductor by Ti doping (2002)

We studied the Ti doping effect on the superconducting properties and microstructure of sintered MgB2 bulk polycrystals. Using Ti as a sintering assistant, we have fabricated MgB2 bulk materials consisting of fine 10 nm scale particles and achieved a high Jc of 1MA/cm2 in self-field and 3 x 105 A/cm2 in 1T at 20 K. The large enhancement of Jc is explained by the excellent connection between grains and the high density of pinning centers served by both grain boundaries and MgO nanoparticles.
Monitoring cerebral venous blood oxygenation in neonates with a medical-grade optoacoustic system (2015)

Premature, very-low-birth-weight (VLBW; ≤1500 g) and low-birth-weight (LBW; 1500-2499 g) infants are at increased risk for severe neurological disability. 25-50% of the 63,000 VLBW infants born annually in the USA have major longterm cognitive or neurobehavioral deficits in which cerebral hypoxia plays an important role. At present, no technology is capable of noninvasive, accurate monitoring of cerebral oxygenation in newborns. We proposed to use an optoacoustic technique for noninvasive cerebral hypoxia monitoring by probing the superior sagittal sinus (SSS). Recently, we developed and built a medical grade, multi-wavelength, near-infrared optoacoustic system suitable for neonatal applications. We designed and built an adjustable patient interface for neonates with VLBW, LBW, and normal weight (NBW) that provides single or continuous measurements of the SSS blood oxygenation in both the reflection and transmission modes. We performed pilot clinical tests of the system in VLBW, LBW, and NBW hemodynamically stable infants admitted to the neonatal intensive care unit. The system was capable of detecting SSS signals through the open anterior and posterior fontanelles and through the skull and allowed for monitoring of the SSS blood oxygenation in both modes. To the best of our knowledge this paper reports for the first time detection of optoacoustic signals from human cerebral blood vessels in both the transmission mode and the reflection mode. Analysis of the signals allows for noninvasive measurement of cerebral venous blood oxygenation in newborns in both modes. The transmission mode can be used for accurate measurement of the total hemoglobin concentration as well. The method and system proposed in this study can be used for optoacoustic human brain imaging, tomography, and mapping.
The First General Enantioselective Catalytic Diels−Alder Reaction with Simple α,β-Unsaturated Ketones (2002)

The first general approach to enantioselective catalysis of the Diels-Alder reaction with simple ketone dienophiles has been accomplished. The use of iminium catalysis has enabled enantioselective access to a fundamental Diels-Alder reaction variant that has previously been unavailable using chiral Lewis acid catalysis. A new chiral amine catalyst has been developed that allows a variety of monodentate cyclic and acyclic ketones to successfully participate in enantioselective [4 + 2] cycloadditions. A wide spectrum of cyclic and acyclic diene substrates can also be accommodated in this new organocatalytic transformation. A computational model is provided that is in accord with the sense of enantioinduction observed for all reactions conducted during the course of this study.
Select human anthrax protective antigen (PA) epitope-specific antibodies provide protection from lethal toxin challenge in vitro and in vivo (129.16) (2009)

Abstract The release of Bacillus anthracis spores can cause significant morbidity and mortality and an effective vaccine as well as directed immunotherapeutics are needed. The currently licensed vaccine requires six primary vaccinations, annual boosters, and has been associated with serious adverse events. Thus there is increasing interest in developing an improved vaccination strategy which can generate lasting protective immunity with reduced vaccinations. This study seeks to identify the major humoral targets of B. anthracis that provide protection. To this end, plasma was obtained from two hundred vaccinated individuals and thirty unvaccinated controls. Ninety-five percent of all vaccinated individuals had anti-protective antigen antibodies and these antibodies correlated with in vitro protection against lethal toxin. Utilizing overlapping decapeptides, we identified common antigenic regions within those individuals with high toxin neutralizing activity. Epitope-specific antibodies directed against three of these regions were isolated and were able to mediate protection in vitro and in a mouse model of in vivo lethal toxin challenge. Identification of common, protective, peptide-specific humoral immune responses provide key information for further immunotherapeutic and vaccine development. NIAID: 5U19AI062629
Active-site residue, domain and module swaps in modular polyketide synthases (2003)

Sequence comparisons of multiple acyltransferase (AT) domains from modular polyketide synthases (PKSs) have highlighted a correlation between a short sequence motif and the nature of the extender unit selected. When this motif was specifically altered in the bimodular model PKS DEBS1-TE of Saccharopolyspora erythraea, the products included triketide lactones in which acetate extension units had been incorporated instead of propionate units at the predicted positions. We also describe a cassette system for convenient construction of hybrid modular PKSs based on the tylosin PKS in Streptomyces fradiae and demonstrate its use in domain and module swaps.
Cytotoxicity of release products from magnetic nanocomposites in targeted drug delivery (2011)

The efficacy of chemotherapy can be significantly improved if the therapeutic agent remains localized at the afflicted area and released at controlled rates. Such a targeted drug delivery can be achieved using magnetic nanocomposite (MNC), which incorporates drug and magnetic nanoparticles in biodegradable polymer microspheres. Reported here are results from an in vitro study on drug release rate and cytotoxicity of other release products from MNC. The model system contains an anti-cancer chemotherapy agent 5-flurouracil (5-FU) and (Co(0.5)Zn(0.5))Fe(2)O(4) in poly(lactic-co-glycolic acid) (PLGA) matrix produced by an oil/oil emulsion technique. Cell proliferation data indicate a sustained release of 5-FU for mouse macrophage cell eradication, whereas other microsphere components of magnetic nanoparticles and PLGA have little cytotoxic effects.
Frequent downregulation and loss of WWOX gene expression in human hepatocellular carcinoma (2004)

The WWOX (WW-domain containing oxidoreductase) is a candidate tumour suppressor gene spanning the same chromosome region, 16q23, as the second most common fragile site (FS), FRA16D. Deletions detected by comparative genomic hybridisation (CGH) and loss of heterozygosity at microsatellite markers on chromosome 16q are common in many human cancers including hepatocellular carcinoma (HCC). The development of human HCC is closely associated with exposure to oncogenic viruses and chemical carcinogens, agents known to frequently target common FS. We examined the status of WWOX genomic DNA, RNA and protein in 18 cell lines derived from human HCC and found recurrent alterations of the gene. Loss of DNA copy-number confined to band 16q23 was detected by CGH in several cell lines. Although homozygous deletions of the WWOX gene were not detected, WWOX mRNA expression was absent or lower in 60% of cell lines. The occurrence of aberrant WWOX reverse transcription-PCR products with deletion of exons 6-8 correlated significantly with altered WWOX expression. All of the cell lines showing mRNA downregulation had a decreased or undetectable level of WWOX protein as demonstrated by Western blotting with antibody to WWOX. Furthermore, 13 out of the 18 cell lines expressed decreased levels or no WWOX protein when compared with normal liver. These results show that WWOX gene is frequently altered in HCC and raise the possibility that this gene is implicated in hepatocarcinogenesis.
Differences in Stability among the Human Apolipoprotein E Isoforms Determined by the Amino-Terminal Domain (2000)

Denaturation by guanidine-HCl, urea, or heating was performed on the common isoforms of human apolipoprotein (apo) E (apoE2, apoE3, and apoE4) and their 22-kDa and 10-kDa fragments in order to investigate the effects of the cysteine/arginine interchanges at residues 112 and 158. Previous physical characterization of apoE3 established that apoE contains two domains, the 10-kDa carboxyl-terminal and 22-kDa amino-terminal domains, which unfold independently and exhibit large differences in stability. However, the physical properties of apoE2, apoE3, and apoE4 have not been compared before. Analysis by circular dichroism showed that the different isoforms have identical alpha-helical contents and guanidine-HCl denaturation confirmed that the two domains unfold independently in all three isoforms. However, guanidine-HCl, urea, and thermal denaturation showed differences in stability among the 22-kDa amino-terminal fragments of the apoE isoforms (apoE4 < apoE3 < apoE2). Furthermore, guanidine-HCl denaturation monitored by circular dichroism and fluorescence suggested the presence of a folding intermediate in apoE, most prominently in apoE4. Thus, these studies reveal that the major isoforms of apoE, which are associated with different pathological consequences, exhibit significant differences in stability.
Estimating randomness using seismic disorder (2014)

Abstract The new seismic disorder attribute quantitatively describes the degree of randomness embedded in 3D poststack seismic data. We compute seismic disorder using a filter operation that removes simple structures including constant values, constant slopes, and steps in axial directions. We define the power of the filtered data as the seismic disorder attribute, which approximately represents data randomness. Seismic data irregularities are caused by a variety of reasons, including random reflection, diffraction, near-surface variations, and acquisition noise. Consequently, the spatial distribution of the seismic disorder attribute may help hydrocarbon exploration in several ways, including identifying geologic features such as fracture zones, gas chimneys, and terminated unconformities; indicating the signal-to-noise ratio to assess data quality; and providing a confidence index for reservoir simulation and engineering projects. We present three case studies and a comparison to other noise-estimation methods.
Visual analytics for neuroscience-inspired dynamic architectures (2014)

We introduce a visual analytics tool for neuroscience-inspired dynamic architectures (NIDA), a network type that has been previously shown to perform well on control, anomaly detection, and classification tasks. NIDA networks are a type of spiking neural network, a non-traditional network type that captures dynamics throughout the network. We demonstrate the utility of our visualization tool in exploring and understanding the structure and activity of NIDA networks. Finally, we describe several extensions to the visual analytics tool that will further aid in the development and improvement of NIDA networks and their associated design method.
1,1-Bisphosphonate Squalene Synthase Inhibitors: Interplay Between the Isoprenoid Subunit and the Diphosphate Surrogate (1995)

Inhibitors of squalene synthase have the potential to be superior cholesterol-lowering agents. We previously disclosed that lipophilic 1,1-bisphosphonates I are potent squalene synthase inhibitors and orally active cholesterol-lowering agents in animal models (Ciosek, C. P., Jr.; et al. J. Biol. Chem. 1993, 268, 24832-24837). In this paper, we describe modifications to the bisphosphonate moiety, in an attempt to reduce the number of acidic functions contained in these inhibitors. Replacing one of the acidic groups with a methyl (II, R2 = CH3) results in potent inhibitors when paired with a close mimic of the naturally occurring farnesyl moiety (R1 = farnesylethyl) but not when paired with the shorter isoprene surrogates (R1 = geranylethyl or 4-biphenylpropyl). In contrast, all three corresponding bisphosphonates I are potent squalene synthase inhibitors. Inhibitory potency is recovered with the shorter isoprene surrogates when R2 is CH2OH or CH2OCH3. It is proposed that these R2 groups serve as hydrogen bond acceptors with the active site of the enzyme. The properties of these compounds as cholesterol biosynthesis inhibitors in rats are described, and synthetic routes to these and related compounds are detailed.
Optical time-division multiplexed transmission system experiment at 8 Gbit/s (1987)

We describe the design and performance of an experimental two-channel optical time-division multiplexed fibre transmission system operating at a wavelength of 1.3 μm and a bit rate of 8 Gbit/s. Transmission over 8 km of single-mode fibre with low crosstalk and transmission error rates as low as 10−10 is demonstrated.
Recent advances in flexible low power cholesteric LCDs (2006)

Bistable reflective cholesteric displays are a liquid crystal display technology developed to fill a market need for very low power displays. Their unique look, high reflectivity, bistability, and simple structure make them an ideal flat panel display choice for handheld or other portable devices where small lightweight batteries with long lifetimes are important. Applications ranging from low resolution large signs to ultra high resolution electronic books can utilize cholesteric displays to not only benefit from the numerous features, but also create enabling features that other flat panel display technologies cannot. Flexible displays are the focus of attention of numerous research groups and corporations worldwide. Cholesteric displays have been demonstrated to be highly amenable to flexible substrates. This paper will review recent advances in flexible cholesteric displays including both phase separation and emulsification approaches to encapsulation. Both approaches provide unique benefits to various aspects of manufacturability, processes, flexibility, and conformability.
Integrated On-Line System for DNA Sequencing by Capillary Electrophoresis:  From Template to Called Bases (1997)

An integrated on-line prototype for coupling a microreactor to capillary electrophoresis for DNA sequencing has been demonstrated. A dye-labeled terminator cycle-sequencing reaction is performed in a fused-silica capillary. Subsequently, the sequencing ladder is directly injected into a size-exclusion chromatographic column operated at ∼95 °C for purification. On-line injection to a capillary for electrophoresis is accomplished at a junction set at ∼70 °C. High temperature at the purification column and injection junction prevents the renaturation of DNA fragments during on-line transfer without affecting the separation. The high solubility of DNA in and the relatively low ionic strength of 1× TE buffer permit both effective purification and electrokinetic injection of the DNA sample. The system is compatible with highly efficient separations by a replaceable poly(ethylene oxide) polymer solution in uncoated capillary tubes. Future automation and adaptation to a multiple-capillary array system should allow high-speed, high-throughput DNA sequencing from templates to called bases in one step.
Deterministic, analytically complete measurement of polarization-dependent transmission through optical devices (1992)

Polarization dependence of the loss or gain of an optical device has been difficult to measure in a consistent and reproducible manner because it has been necessary to search for the extrema of transmission over a two-dimensional polarization space. It is shown that the global variation of the transmission through any linear, time-invariant optical device, over all states of polarization, can be found in a strictly deterministic, analytically complete manner by measuring the polarization responses to only three input polarizations. A series of fast, automated measurements of two test devices yielded standard deviations of 0.017 and 0.033 dB and agreement with manual measurements.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Correction: Nanoscale structure and superhydrophobicity of sp<sup>2</sup>-bonded boron nitride aerogels (2015)

Correction for ‘Nanoscale structure and superhydrophobicity of sp2-bonded boron nitride aerogels’ by Thang Pham et al., Nanoscale, 2015, 7, 10449–10458.
Extraction of orthogonal incident state of polarization spectra using Mueller matrix approach (2006)

Novel algorithms based upon Mueller matrix terms are presented herein, which allow the recovery of the spectra associated with incident transverse electrical (<i>TE</i>) and transverse magnetic (<i>TM</i>) orthogonal states of polarization. These, in turn, give more insight into polarization-dependent frequency shifts and other performance-related parameters of interest. This elegant patent-pending solution entails little computational efforts and can significantly improved the testing capacity and capabilities of component designers and contract manufacturers.
Complementary heterostructure insulated gate field effect transistors (HIGFETs) (1985)

Both n-channel and p-channel high mobility (Al,Ga)As/GaAs heterostructure insulated gate field effect transistors (HIGFETs) have been fabricated for the first time on the same planar wafer surface using MBE and a self-aligned gate by ion implantation process. Enhancement-mode (E-mode) n-channel HIGFETs have demonstrated extrinsic transconductances of 385 mS/mm at 77 K and 218 mS/mm at room temperature. E-mode p-channel HIGFETs have demonstrated extrinsic transconductances of 59 mS/mm at 77 K and 28 mS/mm at room temperature. These are the highest transconductance values ever reported for a p-channel FET device. The hole field effect mobility was deduced from 3-µm gate length p-channel HIGFETs to be 1,300 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /Vs and 500 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /Vs at 77 K and room temperature, respectively. The HIGFET approach appears to be very promising for the development of a new generation of high speed, low power complementary circuits.
Fractionation of heparin by chromatography on a tissue plasminogen activator-Sepharose column. (1990)

Heparin stimulates the activity of tissue plasminogen activator (t-PA) and binds to t-PA. To study this interaction, a complex between t-PA and N-acetylated heparin was formed and then linked to Sepharose. This procedure selectively links the t-PA to the column because the acetylated heparin has no free amino groups. The procedure also protects the heparin-binding site(s) on the enzyme during coupling to the matrix. The t-PA column separates heparin into two fractions, one with low affinity for t-PA and one with high affinity. Both fractions of heparin effectively accelerate inactivation of thrombin by antithrombin III. However, the fractions differ in their ability to stimulate t-PA: the low-affinity heparin has no effect on the activity of t-PA, whereas the high-affinity heparin enhances this activity. These heparin fractions will be useful in characterizing the biochemical basis and physiological consequences of the heparin--t-PA interaction.
Development of the mist flow process. Final report (1981)

The Mist Flow Ocean Thermal Energy Process is a practical method for exploiting the ocean temperature difference without using heat exchangers or large vapor turbines. Warm ocean surface water is sprayed upward into the bottom of an evacuated vertical duct. Vapor flashes from the sprayed water droplets and drags them upward as it proceeds to the top of the duct. There the vapor is condensed by cold water obtained from the depths. The validity of the concept has been demonstrated in a set of experiments conducted in a 4-meter tall transparent test column of 23 x 36 cm cross section. The coupling between the vapor and the droplets remained strong as energy equivalent to over 60 meters of lift was transferred from the vapor to the water droplets.
Prospective estimation of organ dose in CT under tube current modulation (2015)

This study developed a quantitative model to predict organ dose for clinical chest and abdominopelvic scans. Such information may aid in the design of optimized CT protocols in relation to a targeted level of image quality.
Role of eIF5A in TNF-α–Mediated Apoptosis of Lamina Cribrosa Cells (2004)

TNF-alpha, in synergy with camptothecin, induces apoptosis in human LC cells. eIF5A is upregulated by LC cells in response to TNF-alpha, and siRNAs against eIF5A protect LC cells from apoptosis. Thus, eIF5A appears to be a novel proapoptotic protein in the TNF pathway and a possible target for treatment of glaucoma.
PEREGRINE: An all-particle Monte Carlo code for radiation therapy (1994)

The goal of radiation therapy is to deliver a lethal dose to the tumor while minimizing the dose to normal tissues. To carry out this task, it is critical to calculate correctly the distribution of dose delivered. Monte Carlo transport methods have the potential to provide more accurate prediction of dose distributions than currently-used methods. PEREGRINE is a new Monte Carlo transport code developed at Lawrence Livermore National Laboratory for the specific purpose of modeling the effects of radiation therapy. PEREGRINE transports neutrons, photons, electrons, positrons, and heavy charged-particles, including protons, deuterons, tritons, helium-3, and alpha particles. This paper describes the PEREGRINE transport code and some preliminary results for clinically relevant materials and radiation sources.
DDIS-17. DEVELOPMENT OF BRAIN-PENETRANT EGFR INHIBITORS FOR CNS MALIGNANCIES (2019)

Abstract The epidermal growth factor receptor (EGFR) is altered in nearly 60% of glioblastoma (GBM) tumors, however, EGFR tyrosine kinase inhibitors (TKIs) have failed to improve outcomes for patients with GBM. This can be attributed to the inability of clinically available EGFR TKIs (e.g., erlotinib, gefitinib, lapatinib, afatinib, cetuximab) to effectively cross the blood-brain-barrier (BBB) and reach adequate pharmacological levels for a tumor response. Herein, we performed a structure-activity relationship (SAR) to obtain EGFR TKIs with both high brain penetrance and potency against EGFR-activated GBM cells. From over 80 novel compounds synthesized, our lead EGFR TKI—JCN068—exhibited exceptional BBB penetration (350% brain to plasma) while also having optimal ADME properties (60% oral bioavailability, ~5 hr half-life, >100 µg/mL solubility, etc). Moreover, JCN068 demonstrated picomolar potency against purified EGFR kinase, 1000-fold selectivity for EGFR relative to other kinases, and nanomolar activity against EGFR-altered, GBM patient-derived cells in culture. Importantly, JCN068 demonstrated superior efficacy—with negligible toxicity—compared to clinically available small molecule EGFR TKIs (erlotinib and lapatinib) against multiple EGFR-altered patient-derived orthotopic GBM xenografts. Due to these excellent drug-like properties, JCN068 is currently progressing towards clinical development for EGFR-activated GBM patients.