gebhart/patrepeval huggingface dataset:
Hierarchical Self-Assembly of Chiral Complementary Hydrogen-Bond Networks in Water:  Reconstitution of Supramolecular Membranes (2001)

Spontaneous formation of complementary hydrogen-bond pairs and their hierarchical self-assembly (reconstitution) into chiral supramolecular membranes are achieved in water by mixing amphiphilic pairs of glutamate-derived melamine 6 and ammonium-derivatized azobenzene cyanuric acid 4. Electron microscopy is used to observe formation of helical superstructures, which are distinct from the aggregate structures observed for each of the single components in water. In addition, a spectral blue-shift and induced circular dichroism (ICD) with exciton coupling are observed for the pi-pi* absorption of the azobenzene chromophores. These observations are consistent with the reconstitution of the hydrogen-bond-mediated supramolecular membrane 6-4. Spectral titration experiments indicate the stoichiometric integration of the complementary subunits with an association constant of 1.13 x 10(5) M(-1). This value is considerably larger than those reported for the artificial hydrogen-bonding complexes in aqueous media. The remarkable reconstitution efficiency is ascribed to the hydrophobically driven self-organization of the amphiphilic, linear hydrogen-bond networks in water. Molecular structure of the complementary subunits plays an important role in the complexation process since it is restricted by the photoisomerized cis-azobenzene subunit. On the other hand, thermally regenerated trans-isomer 4 undergoes facile complexation with the counterpart 6. The present reconstitution of supramolecular membranes provides the first example of complementary hydrogen-bond-directed formation of soluble, mesoscopic supramolecular assemblies in water.
Modular verification of a non-blocking stack (2007)

This paper contributes to the development of techniques for the modular proof of programs that include concurrent algorithms. We present a proof of a non-blocking concurrent algorithm, which provides a shared stack. The inter-thread interference, which is essential to the algorithm, is confined in the proof and the specification to the modular operations, which perform push and pop on the stack. This is achieved by the mechanisms of separation logic. The effect is that inter-thread interference does not pollute specification or verification of clients of the stack.
Effect of Precovered Oxygen on the Adsorption and Decomposition of NO on Pt(110) Surface (2006)

The adsorption and decomposition of NO on clean and oxygen-precovered Pt(110) surfaces were investigated by means of thermal desorption spectroscopy, X-ray photoelectron spectroscopy, and high-resolution electron energy loss spectroscopy. At room temperature, NO molecularly adsorbs on the clean Pt(110) surface. NO adsorbing on the bridge sites dominates at low coverage whereas NO adsorbs on the terminal sites at high coverage. Some NO (mainly the bridge-bound NO) undergoes dissociation upon heating, forming N and N2O. Molecular oxygen dissociates on Pt(110) at room temperature. Precovered oxygen adatoms on Pt(110) inhibit the formation of bridge-bound NO, which results in a decrease in the desorption temperature of bridge-bound NO from the surface by 40 K. The decrease in the desorption temperature facilitates the thermal desorption of bridge-bound NO on Pt(110), and thus inhibits the dissociation reaction of NO. These results provide a reasonable surface science approach to understand the deactivation of Pt catalysts for NO decomposition under the oxygen rich atmosphere.
An Assessment of the Antioxidant and Antimicrobial Activity of Six Species of Edible Irish Seaweeds (2010)

Six species of edible Irish seaweeds; Laminaria digitata, Laminaria saccharina, Himanthalia elongata, Palmaria palmata, Chondrus crispus and Enteromorpha spirulina were screened for potential bioactivity. Extraction of secondary metabolites was carried out using different solvents to determine antioxidant and antimicrobial properties of the dried extracts. The total phenolic contents of dried methanolic extracts were significantly different (p < 0.05). H. elongata exhibited highest phenolic content at 151.3 mg GAE/g of seaweed extract and also had the highest DPPH scavenging activity (p < 0.05) with a 50% inhibition (EC50) level at 0.125μg/ml of extract. H. elongata also had the highest total tannin and total flavonoid contents (p < 0.05) of 38.34 mg CE/g and 42.5 mg QE/g, respectively. Antimicrobial activity was determined using a microtitre method which allowed detection of bacterial growth inhibition at low levels. All methanolic seaweed extracts inhibited the food spoilage and food pathogenic bacteria tested; Listeria monocytogenes, Salmonella abony, Enterococcus faecalis and Pseudomonas aeruginosa, except C. crispus extracts. It was found that dried methanolic extracts of red and green seaweeds had significantly lower antimicrobial activity than the brown species; H. elongata had the highest antimicrobial activity with up to 100% inhibition. In the studied work, the antimicrobial activity of red and green seaweed extracts significantly increased when ethanol and acetone were used as extraction solvents (p < 0.05). Inhibition of E. faecalis with C. crispus extracts increased from 39.28 to 100% when ethanol and acetone were applied as solvents.
Extraction of DNA from amniotic fluid cells for the early prenatal diagnosis of genetic disease (1991)

Ten-ml samples of amniotic fluid were taken from pregnancies being terminated at 8-14 weeks' gestation. DNA was extracted from the amniotic cells by sequential centrifugation and analysed using the polymerase chain reaction (PCR). Fifteen samples were analysed for evidence of maternal contamination using Mfd5 oligonucleotide primers for repeat polymorphisms. Ten amniotic fluid samples were tested for the Delta-F508 deletion characteristic of cystic fibrosis to demonstrate a diagnostic application for the technique. In each case, DNA extracted from fetal tissue from the same pregnancy was included in the controls. In 14 of the 15 cases tested with the Mfd5 primers, both the amniotic fluid DNA and the fetal DNA showed no evidence of contaminating DNA. In one case, neither the amniotic fluid cells nor the fetal cells yielded results. In nine of the ten cases tested with the Delta-F508 primers, the amniotic fluid cell DNA provided accurate information about the genetic status of the fetus; in the tenth, the fetal DNA failed to amplify. The results indicate that adequate DNA can be extracted from amniotic fluid from 8 weeks' gestation onward and these samples are suitable for prenatal diagnosis using PCR.
Human Major Histocompatibility Complex (MHC) Class I Molecules with Disulfide Traps Secure Disease-related Antigenic Peptides and Exclude Competitor Peptides (2008)

The ongoing discovery of disease-associated epitopes detected by CD8 T cells greatly facilitates peptide-based vaccine approaches and the construction of multimeric soluble recombinant proteins (e.g. tetramers) for isolation and enumeration of antigen-specific CD8 T cells. Related to these outcomes of epitope discovery is the recent demonstration that MHC class I/peptide complexes can be expressed as single chain trimers (SCTs) with peptide, beta(2)m and heavy chain connected by linkers to form a single polypeptide chain. Studies using clinically relevant mouse models of human disease have shown that SCTs expressed by DNA vaccination are potent stimulators of cytotoxic T lymphocytes. Their vaccine efficacy has been attributed to the fact that SCTs contain a preprocessed and preloaded peptide that is stably displayed on the cell surface. Although SCTs of HLA class I/peptide complexes have been previously reported, they have not been characterized for biochemical stability or susceptibility to exogenous peptide binding. Here we demonstrate that human SCTs remain almost exclusively intact when expressed in cells and can incorporate a disulfide trap that dramatically excludes the binding of exogenous peptides. The mechanistic and practical applications of these findings for vaccine development and T cell isolation/enumeration are discussed.
Differentiation of neuron-like cells from mouse parthenogenetic embryonic stem cells. (2013)

Parthenogenetic embryonic stem cells have pluripotent differentiation potentials, akin to fertilized embryo-derived embryonic stem cells. The aim of this study was to compare the neuronal differentiation potential of parthenogenetic and fertilized embryo-derived embryonic stem cells. Before differentiation, karyotype analysis was performed, with normal karyotypes detected in both parthenogenetic and fertilized embryo-derived embryonic stem cells. Sex chromosomes were identified as XX. Immunocytochemistry and quantitative real-time PCR detected high expression of the pluripotent gene, Oct4, at both the mRNA and protein levels, indicating pluripotent differentiation potential of the two embryonic stem cell subtypes. Embryonic stem cells were induced with retinoic acid to form embryoid bodies, and then dispersed into single cells. Single cells were differentiated in N2 differentiation medium for 9 days. Immunocytochemistry showed parthenogenetic and fertilized embryo-derived embryonic stem cells both express the neuronal cell markers nestin, βIII-tubulin and myelin basic protein. Quantitative real-time PCR found expression of neurogenesis related genes (Sox-1, Nestin, GABA, Pax6, Zic5 and Pitx1) in both types of embryonic stem cells, and Oct4 expression was significantly decreased. Nestin and Pax6 expression in parthenogenetic embryonic stem cells was significantly higher than that in fertilized embryo-derived embryonic stem cells. Thus, our experimental findings indicate that parthenogenetic embryonic stem cells have stronger neuronal differentiation potential than fertilized embryo-derived embryonic stem cells.
Reflection/transmission coefficients and azimuthal anisotropy in marine seismic studies (1991)

We introduce two methods for inferring the direction of vertical fractures from marine seismic data. First we derive the necessary reflection and transmission coefficients for an interface between a liquid and an azimuthally anisotropic solid. Next we show that multicomponent ocean bottom seismometer data from surface airgun sources along two perpendicular shot lines can be rotated into the principal directions of azimuthal anisotropy to determine the orientation of vertical fractures.
Inventory and measurement of particulates in sealed sterile containers. (1984)

Transmission holography has been used to translate the Knapp and Kushner probabilistically defined “Reject Zone” for particulate contamination in parenteral products into physical measurements. Sample containers rejected with a probability of 70% (i.e., at the lower boundary of the “Reject Zone”) in a standard paced inspection using a three diopter lens and an intense diffuse light source were investigated with holography. The containers investigated showed a major relationship between the shape of a particulate and its detectability. The net effect of magnification on the relationship between particulate size and rejection probability was also investigated.
SERS of molecules that do not adsorb on Ag surfaces: a metal–organic framework-based functionalization strategy (2014)

The potential for discriminating between analytes by their unique vibrational signature makes surface-enhanced Raman scattering (SERS) extremely interesting for chemical detection. However, for molecules that weakly adsorb to non-functionalized plasmonic materials, detection by SERS remains a key challenge. Here we present an approach to SERS-based detection where a polycrystalline metal-organic framework (MOF) film is used to recruit a range of structurally similar volatile organic compounds for detection by SERS. MOF films were grown on the surface of Ag "films-over-nanospheres" (FONs), which have previously been shown to enhance Raman signals of surface adsorbates by a factor of 10(7). Upon exposing the MOF-coated FON to benzene, toluene, nitrobenzene, or 2,6-di-tert-butylpyridine, the MOF film traps the vapors at the FON surface, allowing the unique Raman spectrum of each vapor to be recorded. By contrast, these analytes do not adsorb to a bare FON surface and thus cannot be detected by conventional SERS substrates. Pyridine was also tested as a Ag-adsorbing control analyte. Concentration dependence and time resolved measurements provide evidence for the hypothesis that the vapors are reversibly adsorbed on the surfaces of MOF nanocrystals exposed at grain boundaries. This represents a generalized approach for confining aromatic molecules through interactions with the MOF surface, which can be applied for future SERS-based sensors.
PARAGON: a new package for gate matrix layout synthesis (1990)

Gate matrix is a layout style for implementing logic in integrated MOS circuits. In this paper we discuss algorithms used in a newly developed software package called PARAGON which generates near-optimal gate matrix geometric layouts given a set of logic expressions. New features include individual sizes of transistors being taken into account at all stages of the algorithms and the use of transistor orientations to reduce the width and improve the timing performance of the gate matrix layouts. The optimisation of a gate matrix is achieved by optimising firstly its height and secondly its width. The height is optimised by the column assignment algorithm and the width is optimised by the merging, track assignment and transistor orientation algorithms. Once optimisation has been completed, a new detailed routing algorithm is performed. Although the emphasis is on the minimisation of the total area, the optimisation of the timing behaviour is also included in our algorithms.
Direct space–time characterization of the electric fields of ultrashort optical pulses (2002)

We report the complete spatiotemporal characterization of ultrashort light pulses by use of a self-referencing device based on shearing interferometry in the space and frequency domains. The apparatus combines a spatially resolved spectral shearing interferometer with a spectrally resolved spatial shearing interferometer. The electric field as a function of one transverse spatial coordinate and time is obtained from a single experimental trace by means of a direct and fast algebraic phase reconstruction algorithm. The method has been tested in several common laboratory situations.
Molecular Determinants for Assembly of G-protein-activated Inwardly Rectifying K+ Channels (1997)

Kir3.1 and Kir3.2 associate to form G-protein-activated, inwardly rectifying K+ channels. To identify regions involved in the coassembly of these subunits, truncated Kir3.1 polypeptides were coexpressed with epitope-tagged subunits in an in vitro translation system. N-terminal, C-terminal, and core region polypeptides were coimmunoprecipitated with both Kir3.2 and Kir3.1, suggesting that multiple elements distributed throughout the Kir3.1 polypeptide contribute to intersubunit binding interactions. The Kir3.2 C-terminal polypeptide coimmunoprecipitated with the Kir3.1 C-terminal polypeptide, but neither region recognized the N-terminal domain and core region of the Kir3.1 subunit. This suggests that within Kir3 channels the C-terminal domains of neighboring subunits interact. Coexpression of the truncated polypeptides with Kir3.1 and Kir3.2 in Xenopus oocytes reduced functional expression of the heteromeric channels. Constructs encoding the core region plus N-terminal and proximal C-terminal regions competed more effectively than the core region alone, which supports the contribution of all three regions to intersubunit binding interactions. Proximal and distal segments of the C-terminal domain were as effective at inhibiting functional expression as the entire C-terminal domain.
Organocatalysis in Ionic Liquids: Highly Efficient<scp>l</scp>-Proline-Catalyzed Direct Asymmetric Mannich Reactions Involving Ketone and Aldehyde Nucleophiles (2003)

Proline-catalyzed direct asymmetric Mannich reactions of N-PMP protected α-imino ethyl glyoxylate with various aldehydes and ketones in ionic liquids afforded both α- and β-amino acid derivatives with excellent yields and enantioselectivities, providing facile product isolation, catalyst recycling, and significantly improved reaction rates, ca 4- to 50-fold. Three component Mannich reactions involving other imines also worked well in ionic liquids. Significant advantages and limitations of ionic liquid solvents in this reaction have been revealed.
Collusive Bidding in the Market for Corporate Control (2000)

Part I of this article examines the historical evolution of antitrust laws, specifically as they have been applied to the market for corporate control. Part II examines the current judicial opinions advanced which reject the application of antitrust laws to the market for corporate control, including the supposed nonapplicability of antitrust laws to the sale of stock and the implied revocation of the antitrust laws by virtue of the enaction of the Williams Act. Part III addresses the inability of the Securities and Exchange Commission to regulate the market for corporate control via the Williams Act in that there is no inherent conflict between the Commission's disclosure requirements and the policy of antitrust laws. Part IV analyzes the quantitative economic effects of the diminution of competition in the market for corporate control and examine its aggregate effect on shareholders.
In-plane microneedle chip fabricated by crystalline wet etching of (110) silicon wafer (2009)

In this research, simple crystalline wet etching of (110) silicon is employed to fabricate an in-plane silicon microneedle chip, which is composed of microneedle tips, microchannels and reservoir. The required penetration forces to insert the fabricated microneedles into the skin of chicken breast flesh without failure were 70 mN (500 mum in displacement) and 250 mN (2 mm in displacement) for a single tip and five tips, respectively.
Flexural strengthening of reinforced concrete beams using prestressed, near-surface-mounted CFRP bars (2011)

This study investigates the effectiveness of using prestressed near-surface-mounted (NSM) carbon fiber-reinforced polymer (CFRP) to strengthen reinforced concrete beams. Five large-scale reinforced concrete beams were tested: one control, one strengthened with nonprestressed NSM CFRP bars, and three strengthened with NSM CFRP bars prestressed to 20%, 40%, and 60% of the ultimate strength of the CFRP. The flexural behavior of the prestressed concrete beams was compared with the nonprestressed beam and the control. Results indicate that all prestressed concrete beams failed due to rupture of the CFRP bars without any premature or debonding failure. Prestressing the embedded NSM CFRP reinforcement enhanced the overall performance of the beams by increasing the loads at cracking, yielding, and ultimate. When compared with the control beam, prestressed CFRP enhanced overall performance by decreasing crack widths and deflections, as well as delaying the formation of new cracks. In general, increasing the prestressing levels of the NSM CFRP reinforcement improved the overall flexural behavior of the beams at service and ultimate conditions, while decreasing the ductility of the beams.
Quality of Service Support for Fine-Grained Sharing on GPUs (2017)

GPUs have been widely adopted in data centers to provide acceleration services to many applications. Sharing a GPU is increasingly important for better processing throughput and energy efficiency. However, quality of service (QoS) among concurrent applications is minimally supported. Previous efforts are too coarse-grained and not scalable with increasing QoS requirements. We propose QoS mechanisms for a fine-grained form of GPU sharing. Our QoS support can provide control over the progress of kernels on a per cycle basis and the amount of thread-level parallelism of each kernel. Due to accurate resource management, our QoS support has significantly better scalability compared with previous best efforts. Evaluations show that, when the GPU is shared by three kernels, two of which have QoS goals, the proposed techniques achieve QoS goals 43.8% more often than previous techniques and have 20.5% higher throughput.
Women's interest in genetic testing for breast cancer susceptibility may be based on unrealistic expectations (2001)

We report on results of an interview study assessing women's attitudes toward and hypothetical interest in genetic susceptibility testing for breast cancer. Data are from 246 interviews with women of varying ethnicity (African American, European American, Native American, and Ashkenazi Jewish), family history of breast cancer (negative, positive, and borderline), and educational level. Semistructured interviews included questions on general health beliefs; attitudes, experiences, and concerns about breast cancer; and hypothetical interest in genetic testing. Influence of specific test characteristics was assessed with 14 Likert scales varying negative and positive predictive value, timing of disease, possible medical interventions following a positive result. Results reported include both statistical and qualitative analysis. We found that women had a high level of interest in testing which, in general, did not vary by ethnicity, level of education, or family history. Interest in testing appeared to be shaped by an exaggerated sense of vulnerability to breast cancer, limited knowledge about genetic susceptibility testing, and generally positive views about information provided through medical screening. However, study participants were most interested in a test that didn't exist (high positive predictive value followed by effective, noninvasive, preventive therapy) and least interested in the test that does exist (less than certain positive predictive value, low negative predictive value, and limited, invasive, and objectionable therapeutic options). Our data suggest that without a careful counseling process, women could easily be motivated toward interest in a test which will not lead to the disease prevention they are seeking.