gebhart/patrepeval huggingface dataset:
The Effects of ONO thickness on Memory Characteristics in Nano-scale Charge Trapping Devices (2007)

In the use of single/few electrons in distributed storage for nonvolatile, low power and fast memories, providing statistical reproducibility at the nanoscale is a key challenge since relative variance has a radic <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</i> dependence and we are working with limited number of storage sites. We have used defects at interfaces of dielectrics to evaluate this reproducibility and evaluate the performance of memories. These experiments show that nearly 100 electrons can be stored at 30 nm dimensions, sufficient for reproducibility, and that a minimum of tunneling oxide thickness is required to assure reliable retention characteristics. Different tunneling oxide thicknesses and the effect of low doped drain (LDD) process is investigated to draw these conclusions.
Quantum dots coordinated with conjugated organic ligands: new nanomaterials with novel photophysics (2007)

Abstract CdSe quantum dots functionalized with oligo-(phenylene vinylene) (OPV) ligands (CdSe-OPV nanostructures) represent a new class of composite nanomaterials with significantly modified photophysics relative to bulk blends or isolated components. Single-molecule spectroscopy on these species have revealed novel photophysics such as enhanced energy transfer, spectral stability, and strongly modified excited state lifetimes and blinking statistics. Here, we review the role of ligands in quantum dot applications and summarize some of our recent efforts probing energy and charge transfer in hybrid CdSe-OPV composite nanostructures.
Electrochemistry Characteristic of Carbon Steel under Biofilm and Sulfide Film (2001)

Wire Beam Electrode (WBE) made of Q235 carbon steel was applied to study the heterogeneous corrosion beneath biofilm formed by Sulfate Reducing Bacteria (SRB) in culture and sulfide film in solution with 1% NaCl and 300 mg/L S 2- . The potential,galvanic density mapping,as well as polarization curve and Electrochemical Impedance Spectrum (EIS) were measured to predict the localized corrosion under biofilm and sulfide film.As a result,the mapping showed the potential fluctuation on the WBE surface decreased over time due to the conductivity of the biofilm and sulfide film.Therefore,the potential mapping could not be a criterion of localized corrosion under biofilm.Instead,the current mapping could give a good prediction to the MIC.The sulfide film could inhibit corrosion of carbon steel.However,the biofilm accelerate the corrosion.Polarization resistance R p increased over time in the Na 2S solution if lack of O 2.In addition,the biofilm capacity moved up to a very large level (～10 5 μF/cm 2)in shape of Sigmoid with its polarization resistance decreasing exponentially when SRB grew.
Wellbore-Stability Predictions by Use of a Modified Lade Criterion (1999)

Summary The two most commonly used rock failure criteria in wellbore stability analyses are the Mohr–Coulomb criterion and the Drucker–Prager criterion. Neither of these is compatible with three-dimensional rock strength measurements that have explored the influence of the intermediate principal stress. This paper presents a modified Lade criterion which has the following desirable qualities: 1. it correctly describes the influence of the intermediate stress on rock strength, and therefore on wellbore stability, 2. it can be rearranged to give a closed-form solution for critical mud weight, for any wellbore orientation, and 3. only two rock strength parameters are required, such as cohesion and friction angle. The modified Lade criterion predicts critical mud weight values that are less conservative than those predicted by the Mohr–Coulomb criterion yet are not as unconservative as those predicted by the Drucker–Prager criterion. It also reveals that the required increase in mud weight when going from low hole angle to high hole angle is not as great as predicted by either the Mohr–Coulomb or Drucker–Prager criteria.
The "chemoinvasion assay": a tool to study tumor and endothelial cell invasion of basement membranes (2004)

Several genetic and epigenetic factors, both in the cell and in the host, contribute to the progression of tumors towards metastases. The escape of cancer cells from a primary, localized tumor to distant organs transforms a relatively curable pathology to an almost untreatable one. Metastatic lesions are often resistant to cancer therapy because of the progressive phenotypic changes that they have undergone. In this article we will give a bird's eye view on the features of metastatic cells and potential therapeutic targets. In particular, the invasion of basement membranes represents a fundamental step for cell dispersion. Over seventeen years ago we established the Matrigel "chemoinvasion" assay, a useful tool for studying the mechanisms involved in tumor and endothelial cell invasion of basement membranes and for the screening of anti-invasive agents. We will describe the assay and review some of the major results it enabled to obtain.
Evaluation and Comparison of the Electrostatic Dust Print Lifter and the Electrostatic Detection Apparatus2 on the Development of Footwear Impressions on Paper* (2006)

The Electrostatic Dust Print Lifter (EDPL) and the Electrostatic Detection Apparatus(2) (ESDA(2)) were compared to determine if both processes could be used to develop footwear impressions of the same or similar quality and in what order they should be used to develop the highest quality footwear impression. The sensitivity of each technique was also evaluated. The quality of the footwear impressions developed was determined by comparing 25 individual characteristics present on the known shoe to the footwear impressions developed using each technique. The footwear impressions were made by stepping on paper placed over several different surfaces, which included: linoleum, industrial Berber carpet, nylon carpet placed over a (3/8)-in. pad, ceramic tile, cardboard, 1-in. foam, 4-in. foam, cement, asphalt, grass, and mulch. Each of the papers placed on these surfaces was developed using the EDPL before the ESDA(2) and vice versa. The sensitivity test for the ESDA(2) was conducted by processing 10 sheets of stacked paper that were stepped on with the known shoe, beginning with the top sheet. The sensitivity test for the EDPL was conducted by processing 10 sheets of paper stepped on with the known shoe in succession. This study determined the footwear impressions developed using the EDPL were of better comparative value than impressions developed with the ESDA(2). On average, 72.4% of the individual characteristics from the known impression were identified on images developed when the EDPL was used first compared with an average of 38.9% when the ESDA(2) was used first. Therefore, if only one technique is used, the EDPL should be chosen. The sensitivity test determined the ESDA(2) develops high-quality footwear impressions on only the top sheet of paper. No footwear impressions were developed on any sheets under the top sheet of paper. The sensitivity test also determined the EDPL results increase in quality as the amount of dust residue decreases on the surface.
Designing isoform-specific peptide disruptors of protein kinase A localization (2003)

A kinase-anchoring proteins (AKAPs) coordinate cAMP-mediated signaling by binding and localizing cAMP-dependent protein kinase (PKA), using an amphipathic helical docking motif. Peptide disruptors of PKA localization that mimic this helix have been used successfully to assess the involvement of PKA in specific signaling pathways. However, these peptides were developed as disruptors for the type II regulatory subunit (RII) even though both RI and RII isoforms can bind to AKAPs and have discrete functions. To evaluate the effects of each localized isoform, we designed peptides that specifically bind to either RI or RII. Using a peptide array, we have defined the minimal binding sequence of dual specific-AKAP 2 (d-AKAP2), which binds tightly to both RI and RII. Side-chain requirements for affinity and isoform specificity were evaluated by using a peptide substitution array where each position along the A kinase binding domain of d-AKAP2 was substituted by the other 19 l-amino acids. This array comprises 513 single-site substitution analogs of the d-AKAP2 sequence. Peptides containing single and multiple mutations were evaluated in a quantitative fluorescence binding assay and a cell-based colocalization assay. This strategy has allowed us to design peptides with high affinity (K(D) = 1-2 nM) and high specificity for RIalpha versus RIIalpha. These isoform-specific peptides will be invaluable tools to evaluate functional differences between localized RI and RII PKA and are RIalpha-specific disruptors. This array-based analysis also provides a foundation for biophysical analysis of this docking motif.
Realizing the performance potential of the virtual interface architecture (1999)

The Virtual Interface (VI) Architecture provides protected userlevel communication with high delivered bandwidth and low permessage latency, particularly for small messages. The VI Architecture attempts to reduce latency by eliminating user/kernel transitions on routine data transfers and by allowing direct use of user memory for network buffering. This results in significantly lower latencies than those achieved by network protocols such as TCP/IP and UDP. In this paper we examine the low-level performance of two VI implementations, one implemented in hardware, the other implemented in device driver software. Using a set of low-level benchmarks, we measure bandwidth, latency, and processor utilization as a function of message size for the GigaNet CLAN and Tandem ServerNet VI implementations. We report that both VI implementations offer significant performance advantage relative to the corresponding UDP implementation on the same hardware. We also investigate the problems associated with delivering this performance to distributed applications running on clustered multiprocessor workstations. Using an existing MPI library implemented using UDP as a baseline, we explore several performance and implementation issues that arise when adapting this library to use VI instead of UDP. Among these issues are memory registration costs, polling vs. blocking, reliability of delivery, and memory-to-memory copying. By eliminating explicit acknowledgements, reducing memory-tomemory copying, and choosing the most appropriate synchronization primitives, we reduced the message latency seen by user applications by an average of 55% across all message sizes. We also identify several areas that offer the potential for further performance enhancement.
Human complement proteins D, C2, and B. Active site mapping with peptide thioester substrates. (1987)

The specificity and reactivity of complement serine proteases D, B, Bb, C2, and C2a were determined using a series of peptide thioester substrates. The rates of thioester hydrolysis were measured using assay mixtures containing the thiol reagent 4,4'-dithiodipyridine at pH 7.5. Each substrate contained a P1 arginine residue, and the effect of various groups and amino acids in the P2, P3, P4, and P5 positions was determined using kcat/Km values to compare reactivities. Among peptide thioesters corresponding to the activation site sequence in B, dipeptide thioesters containing a P2 lysine residue were the best substrates for D. Extending the chain to include a P3 or P4 amino acid resulted in loss of activity, and neither the tripeptide nor the tetrapeptide containing the cleavage sequence of B was hydrolyzed. Overall, D cleaved fewer substrates and was 2-3 orders of magnitude less reactive than C1s against some thioester substrates. C2 and fragment C2a had comparable reactivities and hydrolyzed peptides containing Leu-Ala-Arg and Leu-Gly-Arg, which have the same sequence as the cleavage sites of C3 and C5, respectively. The best substrates for C2 and C2a were Z-Gly-Leu-Ala-Arg-SBzl and Z-Leu-Gly-Leu-Ala-Arg-SBzl, respectively, where Bzl is benzyl. B was the least reactive among these complement enzymes. The best substrate for B was Z-Lys-Arg-SBzl with a kcat/Km value of 1370 M-1 s-1. The catalytic fragment of B, Bb, had higher activity toward these peptide thioester substrates. The best substrate for Bb was Z-Gly-Leu-Ala-Arg-SBzl with a kcat/Km similar to C2a and 10 times higher than the value for B. Both C2a and Bb were considerably more reactive against C3-like than C5-like substrates. Bovine trypsin hydrolyzed thioester substrates with kcat/Km approximately 10(3) higher than the complement enzymes. These thioester substrates for D, B, and C2 should be quite useful in kinetic and active site studies of the purified enzymes.
Propene Polymerization with Catalyst Mixtures Containing Different ansa-Zirconocenes:  Chain Transfer to Alkylaluminum Cocatalysts and Formation of Stereoblock Polymers (2000)

Substantial transfer of growing polypropyl chains to methylalumoxane and trimethylaluminum occurs with the highly substituted, isospecific zirconocene catalyst Me2Si(2-Me-4-tBu-C5H2)2ZrCl2/MAO, while little if any such chain transfer is observed for the more open isospecific catalyst Me2Si(2-MeInd)2ZrCl2/MAO, for aspecific H4C2(Flu)2ZrCl2/MAO, and for syndiospecific Ph2C(Cp)FluZrCl2/MAO. Propene polymerization with MAO-activated mixtures of Me2Si(2-MeInd)2ZrCl2 and H4C2(Flu)2ZrCl2 gives completely separable mixtures of the isotactic and atactic polymers characteristic for each of the individual catalysts. MAO-activated mixtures of Me2Si(2-Me-4-tBu-C5H2)2ZrCl2 and H4C2(Flu)2ZrCl2, however, give polypropene mixtures that contain, besides isotactic and atactic polymers, polymer fractions in which isotactic and atactic polypropene chain segments are inseparably linked. While clear evidence for isotactic−syndiotactic stereoblock formation was not obtained, some polymeryl exchange between isospecific and syndiospecific catalyst sites in MAO-activated mixtures of Me2Si(2-Me-4-tBu-C5H2)2ZrCl2 and Ph2C(Cp)FluZrCl2 is indicated by increased stereoerror frequencies in some fractions of the polymer product mixture obtained by temperature-rising elution fractionation. Structural prerequisites for an efficient transfer of growing polymer chains between different types of catalyst centers are discussed.
Programmed cell death of dendritic cells in immune regulation (2010)

Programmed cell death is essential for the maintenance of lymphocyte homeostasis and immune tolerance. Dendritic cells (DCs), the most efficient antigen-presenting cells, represent a small cell population in the immune system. However, DCs play major roles in the regulation of both innate and adaptive immune responses. Programmed cell death in DCs is essential for regulating DC homeostasis and consequently, the scope of immune responses. Interestingly, different DC subsets show varied turnover rates in vivo. The conventional DCs are relatively short-lived in most lymphoid organs, while plasmacytoid DCs are long-lived cells. Mitochondrion-dependent programmed cell death plays an important role in regulating spontaneous DC turnover. Antigen-specific T cells are also capable of killing DCs, thereby providing a mechanism for negative feedback regulation of immune responses. It has been shown that a surplus of DCs due to defects in programmed cell death leads to overactivation of lymphocytes and the onset of autoimmunity. Studying programmed cell death in DCs will shed light on the roles for DC turnover in the regulation of the duration and magnitude of immune responses in vivo and in the maintenance of immune tolerance.
Raspberry-like Metamolecules Exhibiting Strong Magnetic Resonances (2015)

We report a synthetic approach to produce raspberry-like plasmonic nanostructures with unusually strong magnetic resonances, termed raspberry-like metamolecules (raspberry-MMs). The synthesis based on the surfactant-assisted templated seed-growth method allows for the simultaneous one-step synthesis and assembly of well-insulated gold nanoparticles. The aromatic surfactant used for the syntheses forms a thin protective layer around the nanoparticles, preventing them from touching each other and making it possible to pack discrete nanoparticles at close distances in a single cluster. The resulting isotropic gold nanoparticle clusters (i.e., raspberry-MMs) exhibit unusually broad extinction spectra in the visible and near-IR region. Finite-difference time-domain (FDTD) modeling showed that the raspberry-MMs support strong magnetic resonances that contribute significantly to the broadband spectra. The strong magnetic scattering was also verified by far-field scattering measurements, which show that in the near-IR region the magnetic dipole resonance can be even stronger than the electric dipole resonance in these raspberry-MMs. Structural parameters such as the size and the number of gold nanoparticles composing raspberry-MMs can be readily tuned in our synthetic method. A series of syntheses with varying structure parameters, along with FDTD modeling and mode analyses of corresponding model structures, showed that the close packing of a large number of metal nanoparticles in raspberry-MMs is responsible for the unusually strong magnetic resonances observed here.
Optimized paired‐sgRNA/Cas9 cloning and expression cassette triggers high‐efficiency multiplex genome editing in kiwifruit (2018)

Kiwifruit is an important fruit crop; however, technologies for its functional genomic and molecular improvement are limited. The clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system has been successfully applied to genetic improvement in many crops, but its editing capability is variable depending on the different combinations of the synthetic guide RNA (sgRNA) and Cas9 protein expression devices. Optimizing conditions for its use within a particular species is therefore needed to achieve highly efficient genome editing. In this study, we developed a new cloning strategy for generating paired-sgRNA/Cas9 vectors containing four sgRNAs targeting the kiwifruit phytoene desaturase gene (AcPDS). Comparing to the previous method of paired-sgRNA cloning, our strategy only requires the synthesis of two gRNA-containing primers which largely reduces the cost. We further compared efficiencies of paired-sgRNA/Cas9 vectors containing different sgRNA expression devices, including both the polycistronic tRNA-sgRNA cassette (PTG) and the traditional CRISPR expression cassette. We found the mutagenesis frequency of the PTG/Cas9 system was 10-fold higher than that of the CRISPR/Cas9 system, coinciding with the relative expressions of sgRNAs in two different expression cassettes. In particular, we identified large chromosomal fragment deletions induced by the paired-sgRNAs of the PTG/Cas9 system. Finally, as expected, we found both systems can successfully induce the albino phenotype of kiwifruit plantlets regenerated from the G418-resistance callus lines. We conclude that the PTG/Cas9 system is a more powerful system than the traditional CRISPR/Cas9 system for kiwifruit genome editing, which provides valuable clues for optimizing CRISPR/Cas9 editing system in other plants.
Molecular Packing Parameter and Surfactant Self-Assembly:  The Neglected Role of the Surfactant Tail (2001)

The concept of molecular packing parameter is widely invoked in the literature to explain, rationalize and even predict molecular self-assembly in surfactant solutions. The molecular packing parameter is defined as vo/aelo, where vo is the surfactant tail volume, lo is the tail length, and ae is the equilibrium area per molecule at the aggregate surface. A particular value of the molecular packing parameter can be translated via simple geometrical relations into specific shape and size of the equilibrium aggregate. This is the predictive application of the concept of molecular packing parameter, as discussed in the literature. In calculating the packing parameter, the dominant notion in the literature is that the surfactant headgroup determines the surface area per molecule of equilibrium aggregates ae. It follows that, given a headgroup, the molecular packing parameter vo/aelo is fixed, because the volume-to-length ratio (vo/lo) of the tail is a constant independent of the tail length for common surfactants. Therefore, in this view, the surfactant tail has no role in determining the size and shape of equilibrium aggregates. We show that this is contrary to fact, by focusing on the neglected role of the surfactant tail. Illustrative calculations are presented in this paper to demonstrate that the surfactant tail does also control equilibrium aggregate structures. It is shown that the role of the tail can be either explicit via modification of the area ae and thus of the packing parameter, or implicit via other means, without modifying ae or the packing parameter.
Fowlicidin‐3 is an α‐helical cationic host defense peptide with potent antibacterial and lipopolysaccharide‐neutralizing activities (2006)

Cathelicidins are an important family of cationic host defense peptides in vertebrates with both antimicrobial and immunomodulatory activities. Fowlicidin-1 and fowlicidin-2 are two newly identified chicken cathelicidins with potent antibacterial activities. Here we report structural and functional characterization of the putatively mature form of the third chicken cathelicidin, fowlicidin-3, for exploration of its therapeutic potential. NMR spectroscopy revealed that fowlicidin-3 comprises 27 amino-acid residues and adopts a predominantly alpha-helical structure extending from residue 9 to 25 with a slight kink induced by a glycine at position 17. It is highly potent against a broad range of Gram-negative and Gram-positive bacteria in vitro, including antibiotic-resistant strains, with minimum inhibitory concentrations in the range 1-2 microM. It kills bacteria quickly, permeabilizing cytoplasmic membranes immediately on coming into contact with them. Unlike many other host defense peptides with antimicrobial activities that are diminished by serum or salt, fowlicidin-3 retains bacteria-killing activities in the presence of 50% serum or physiological concentrations of salt. Furthermore, it is capable of suppressing lipopolysaccharide-induced expression of proinflammatory genes in mouse macrophage RAW264.7 cells, with nearly complete blockage at 10 microM. Fowlicidin-3 appears to be an excellent candidate for future development as a novel antimicrobial and antisepsis agent, particularly against antibiotic-resistant pathogens.
A Low-Bandgap Semiconducting Polymer for Photovoltaic Devices and Infrared Emitting Diodes (2002)

A novel low-bandgap conjugated polymer (PTPTB, Eg = ∼ 1.6 eV), consisting of alternating electron-rich N-dodecyl-2,5-bis(2′-thienyl)pyrrole (TPT) and electron-deficient 2,1,3-benzothiadiazole (B) units, is introduced for thin-film optoelectronic devices working in the near infrared (NIR). Bulk heterojunction photovoltaic cells from solid-state composite films of PTPTB with the soluble fullerene derivative [6,6]-phenyl C61 butyric acid methyl ester (PCBM) as an active layer shows promising power conversion efficiencies up to 1 % under AM1.5 illumination. Furthermore, electroluminescent devices (light-emitting diodes) from thin films of pristine PTPTB show near infrared emission peaking at 800 nm with a turn on voltage below 4 V. The electroluminescence can be significantly enhanced by sensitization of this material with a wide bandgap material such as the poly(p-phenylene vinylene) derivative MDMO-PPV.