gebhart/patrepeval huggingface dataset:
Defect detection in silicon by optical beam-induced reflectance (1986)

Microstructural flaws near the surface of a silicon wafer generally impair the successful manufacture of integrated circuits. Detrimental defects such as stacking faults, dislocations, and metallic precipitates are often 1-2 µ m in size. In the semiconductor industry, these defects are usually revealed by destructive chemical etching procedures. The scientific community has explored several schemes for detecting defects in silicon. Most systems excite a sample with a beam of electrons or photons and then monitor phenomena such as electrical conductivity, microwave absorption, acoustic or thermal-wave scattering, inductive coupling, or surface photovoltage. No system appears to be capable of detecting 1- µ m sized defects in silicon via a completely nondestructive measurement. We have developed an electrooptical system based on a pump-probe laser arrangement to satisfy these requirements. The system excites a wafer surface with a focused visible pumping laser. Holes and electrons generated by the pump alter the optical constants of silicon in the infrared. A second laser then probes the infrared reflectance of the photoexcited area. Electrically active defects consume the photoexcited carriers and reduce the magnitude of the optically induced change in infrared reflectance from levels observed in a nondefective crystal. Stress-induced changes in mobility can also lead to defect contrast.
Trivalent PROTACs Enhance Protein Degradation Through Cooperativity and Avidity (2020)

<p><b>Bivalent small-molecule degraders, or proteolysis targeting chimeras (PROTACs), work by simultaneously binding a target protein and E3 ubiquitin ligase to produce a ternary complex. To drive target ubiquitination and degradation at low catalytic concentrations, degraders must form appropriately positioned complexes of sufficient stability, aided by intra-complex interactions. We hypothesized these molecular recognition features could be enhanced by increasing binding valency. Here we present trivalent PROTACs as a strategy to boost protein degradation. Our design for a trivalent PROTAC consisted of two BET bromodomain inhibitors and an E3 ligase ligand, each separately tethered via a branched linker. In screening, we identified SIM1, a VHL-based PROTAC, as a highly potent BET degrader, capable of low picomolar degradation for all family members, with preference for BRD2. In functional comparison studies to bivalent PROTACs or inhibitors, SIM1 showed more sustained anti-cancer activity across numerous therapeutically relevant cell lines. Biophysical, biochemical, and cellular mechanistic studies showed SIM1 induces conformational changes upon binding to the BET protein to simultaneously engage with high avidity both its bromodomains in a cis intramolecular fashion. The resulting 1:1:1 complex showed positive cooperativity, high stability and prolonged cellular residence time. We provide proof-of-concept for augmenting the binding valency of proximity-induced modalities as a strategy to leverage both cooperativity and avidity within the ternary complex to advance functional outcomes.</b></p>
The mechanism of alkylamine-stabilized copper fine particles towards improving the electrical conductivity of copper films at low sintering temperature (2015)

A facile oxidation process was demonstrated, for the first time, and it can facilitate particle sintering by generating nanostructures.
Candida albicans fibrinogen binding mannoprotein: expression in clinical strains and immunogenicity in patients with candidiasis. (1998)

A 58 kDa cell wall-associated fibrinogen binding mannoprotein (mp58), previously characterized by our group in a Candida albicans laboratory strain (ATCC 26555), was found to be also present in the cell wall of clinical isolates of this fungus. Most strains examined appear to have functional mp58 species, as detected by their ability to bind fibrinogen. Western immunoblot analysis, with a monovalent polyclonal antibody generated against the mp58 species from strain ATCC 26555, revealed differences in recognition patterns depending on the strain tested and the culture conditions used. Serum samples from normal and Candida infected individuals were examined for the presence of antibodies against mp58 by Western immunoblotting. None of the sera from control individuals and patients suffering from superficial candidiasis contained antibodies against mp58. However, positive reactivity with this antigen and other cell wall constituents was detected for all sera from patients with confirmed systemic candidiasis. Together, these results suggest that mp58 could play an active role during infection and may be useful as a specific antigenic marker for candidiasis.
Isolation and Characterization of a Tomato Acid Phosphatase Complementary DNA Associated with Nematode Resistance (1991)

The tomato (Lycopersicon esculentum) acid phosphatase-1 (Apase-1(1), EC 3.1.3.2) isozyme variant, genetically linked to the root-knot nematode resistance locus (Mi) on chromosome 6, has been purified by a rapid procedure from tomato cell suspension cultures. Peptide fragments of the purified enzyme were generated from trypsin and Lys-C endoprotease digests and separated by reverse-phase high-performance liquid chromatography. Amino acid sequences derived from the purified peptide fragments represented >50% of the total amino acid content of the protein and enabled the construction of degenerate oligonucleotide probes that were used to screen a tomato cell culture complementary DNA library. Clones corresponding to full-length coding sequences for Apase-1 have been isolated and sequenced. Southern blot analysis of DNA isolated from a number of tomato cultivars shows that the Apase-1(1) gene (aps1) is present at one copy per genome and that genotypes containing the aps1(1) allele have restriction fragment length polymorphisms that distinguish them from cultivars having the aps1(+) allele. Segregation analysis demonstrates that the restriction fragment length polymorphisms are associated with the aps1 locus. Tomato Apase-1(1) is also found to have significant homology at the amino acid sequence level to a class of vegetative storage proteins characterized in soybean.
Natural and experimental infection of white spot syndrome virus (WSSV) in benthic larvae of mud crab Scylla serrata (2000)

White spot syndrome virus (WSSV), the causative agent of white spot syndrome in shrimp, has a wide host range which extends to crabs, copepods and other arthropods. In this study, benthic larvae of the mud crab Scylla serrata were captured from Taiwan's coastal waters and screened for the presence of WSSV by polymerase chain reaction (PCR) and in situ hybridization. WSSV was detected in around 60% of the larvae, and this prevalence rate remained fairly constant when the captured larvae were subsequently maintained in an aerated system in the laboratory. WSSV-free larvae obtained from a hatchery were challenged by immersion in a WSSV inoculum. Fifteen days after challenge, cumulative mortality in the experimental group reached 43% compared to 20% in the control group. PCR detection of WSSV in both moribund and surviving specimens clearly implicated the virus as the cause of death in most cases. Histological and in situ hybridization data confirmed that WSSV tissue tropism in Scylla serrata crab larvae is similar to that found in shrimp.
A Hardware-Independent Colour Calibration Technique (2007)

Most colour‐normal human observers have no difficulty to adjust a coloured light such that it appears neither red nor green, or such that it appears neither yellow nor blue. Moreover, it has been shown that these hue judgements are not significantly influenced by language or age and individual differences in colour sensitivity are not reflected in the unique‐hue settings. Here we show how we can use the invariance of these unique‐hue judgements to develop a colour calibration technique for display devices, which eliminates the need for an external calibration standard or a measurement device. 1
Ten-channel optical transmitter module for sub-system interconnection operating at λ=1.3 μm up to 12.5 Gbit/s (1999)

Parallel optical interconnection devices feature wide bandwidth, low loss and cross-talk, small size and weight along with low power consumption and cost. They appear particularly suitable to replace the electrical interconnections wherever high connection density and transmission capacity are required (e.g., in board-, cabinet-, and building interconnections). We report on a 10-channel parallel optical transmitter module with a 12.5 Gbit/s total bit-rate. The module includes a commercial 10-channel Fabry-Perot laser array chip) emitting at /spl lambda/=1.3 /spl mu/m, coupled to a standard 50/125 /spl mu/m multimode fiber ribbon, and a silicon CMOS laser driver IC. The IC allows low power consumption even at the high bit-rate achieved, and therefore requires only a passive thermal management, contributing to lower the costs. The output optical power of both logicall 0 and 1 levels can be adjusted externally. The module operates up to 1.25 Gbit/s/ch, exhibiting at a bit error ratio (BER) better than 10/sup -14/. With a power budget of more than 10 dB and a power consumption of 130 mW per channel. An interconnection distance in excess of 1200 m has been demonstrated, with a residual power margin of 4 dB without BER degradation. In this way our transmitter gives interconnection distances in excess of 500 m, not attainable with the shorter wavelengths given by surface emitters, and permits low power dissipation (low threshold light source and CMOS circuits) and low cost fabrication. Such characteristics make the module interesting for applications in which medium-long distances are involved and high bit-rates required, but reduced power consumption and dimensions are mandatory, as for interconnections between submodules in the large switching nodes of new generation.
3D High-Resolution Imaging Using Separated Wavefields (2013)

Conventional wave equation migration extrapolates upcoming boundary data generated from primary reflections to image the subsurface. In marine seismic data processing, sea surface related multiples are a major challenge. Particularly, when the water bottom is shallow, short period multiples are difficult to deal with. Acquisition footprint of seismic imaging is another issue for shallow water bottom geology, where the primary reflections do not have the complete illumination coverage to the shallow targets, including the water bottom. In this paper, we review a method of separated wavefield imaging using sea surface related multiples. We present a data processing work flow of separated wavefield imaging including up and down-going wavefield separation using dual-sensor data, wave equation migration of wavefield extrapolation and imaging condition, and a post processing step of amplitude balancing. A shallow water example from Asia-Pacific is tested, where the separated wavefield imaging generates remarkable high resolution 3D images. The separated wavefield image has greater area of subsurface illumination, which mitigates the strong acquisition footprint. The method and results can be useful to reduce well drilling geohazards.
Phase-locking of a two-mode THz quantum cascade laser (2006)

We studied the phase locking and spectral linewidth of a 2.7 THz quantum cascade laser by mixing its two lateral lasing modes using a superconducting bolometer mixer.
Twin-image elimination experiments for three-dimensional images in optical scanning holography (2000)

Twin-image elimination in the context of optical scanning holography has recently been proposed. The proposed technique involves simultaneously acquiring sine and cosine Fresnel holograms. A complex hologram is then formed by complex addition of the holograms, and twin-image rejection is predicted by computer simulations. An experimental verification of the technique by optical acquisition of the two holograms and subsequent reconstruction of the complex hologram digitally is reported. Three-dimensional image reconstruction without twin-image noise is demonstrated.
Development and Application of Surfactant-Based Systems for Treatment of Wells Drilled with OBM (2001)

Wells drilled with oil-based muds can suffer from severe damage which decreases their overall productivity. During drilling, mud solid parts tend to form an external and internal filtercake along well bore through filtration, while liquid part (filtrate) tends to leak off into the formation. Clean-up process is then necessary to restore the productive zone to a nearnatural state before production. Chemical treatment is often used to break external cake and to wash-off damage zone around well bore, so that formation recovers its fluid transfer properties (water, oil).This paper focuses on the development and application of surfactant-based systems for treatment of wells drilled with oil-based muds. Aqueous based systems are widely used in such cases to effect significant production increases, but they create an additional damage which may even block oil production. A promising issue would be to use a surfactant-based system in a non-pollutant organic base to limit in situ formation of emulsion and water saturation around the well bore.Though, our research methodology aims to select an organic-based surfactant system able to break the cake formed by filtration of a given oil-based mud system. The demulsifying formulation should be able to bother interface surfactants stabilizing effect to allow water droplets coalescence inside the cake. Through breaking emulsion inside the cake, surfactants may decrease cake cohesion and bore adherence. Careful choice may help preventing the system composed of filtrate, reservoir fluids and treatment fluid from forming a stable emulsion inside the porous medium, which could block oil production. Laboratory data are presented showing the relative effects of the organic phase surfactant system and of a conventional commercial treatment on cake destruction and productivity recovering. Results are held by a precise experimental methodology combining Differential Scanning Calorimetry and Cryomicroscopy. Both techniques characterize emulsion stability and destabilization as a function of wellbore parameters (contact time, overbalance pressure...).
Overview: Structure-Activity Relationships of Prostaglandin Analogues as Ocular Hypotensive Agents (1993)

(1993). Overview: Structure-Activity Relationships of Prostaglandin Analogues as Ocular Hypotensive Agents. Current Opinion on Therapeutic Patents: Vol. 3, No. 6, pp. 781-795.
In operando Detection of Three-Way Catalyst Aging by a Microwave-Based Method: Initial Studies (2015)

Initial studies on aging detection of three way catalysts with a microwave cavity perturbation method were conducted. Two physico-chemical effects correlate with the aging state. At high temperatures, the resonance frequencies for oxidized catalysts (λ = 1.02) are not influenced by aging, but are significantly affected by aging in the reduced case (λ = 0.98). The catalyst aging state can therefore potentially be inferred from the resonance frequency differences between reduced and oxidized states or from the resonance frequency amplitudes during lambda oscillations. Secondly, adsorbed water at low temperatures strongly affects the resonance frequencies. Light-off experiment studies showed that the resonance frequency depends on the aging state at temperatures below the oxygen storage light-off. These differences were attributed to different water sorption capabilities of differently aged samples due to a surface area decrease with proceeding aging. In addition to the aging state, the water content in the feed gas and the temperature affect the amount of adsorbed water, leading to different integral electrical material properties of the catalyst and changing the resonance properties of the catalyst-filled canning. The classical aging-related properties of the catalyst (oxygen storage capacity, oxygen storage light-off, surface area), agreed very well with data obtained by the microwave-based method.
Novel Pyridinium Derivatives as Inhibitors for Acetylcholinesterase (1995)

The carbamate 1-(methyl-3-(N,N-dimethylcarbamoyloxy)-2-pyridylmethylene)-4 -(4-phenyl) diazinecarboxamide chloride (MHP 133) is the parent for a new class of pyridinium salts which inhibit acetylcholinesterase (AChE) in vitro as well as in vivo. Fourteen new derivatives of MHP 133 have been synthesized with the intention of improving their hydrophobicity while maintaining their propensity to inhibit acetylcholinesterase. Upon prolonged incubation with AChE, the pyridinium salts exhibit progressive time-dependent inhibition according to first order kinetics with kobs/[I] values ranging from 3 to 345 M-1s-1. The enzyme did not regain any activity after prolonged incubation with the inhibitors (1 day). The partition coefficients for each inhibitor were evaluated in octanol/water in order to determine their hydrophobic character as hydrophobicity is a key prerequisite for crossing the blood brain barrier.
Construct design for efficient, effective and high‐throughput gene silencing in plants (2001)

Post-transcriptional silencing of plant genes using anti-sense or co-suppression constructs usually results in only a modest proportion of silenced individuals. Recent work has demonstrated the potential for constructs encoding self-complementary 'hairpin' RNA (hpRNA) to efficiently silence genes. In this study we examine design rules for efficient gene silencing, in terms of both the proportion of independent transgenic plants showing silencing, and the degree of silencing. Using hpRNA constructs containing sense/anti-sense arms ranging from 98 to 853 nt gave efficient silencing in a wide range of plant species, and inclusion of an intron in these constructs had a consistently enhancing effect. Intron-containing constructs (ihpRNA) generally gave 90-100% of independent transgenic plants showing silencing. The degree of silencing with these constructs was much greater than that obtained using either co-suppression or anti-sense constructs. We have made a generic vector, pHANNIBAL, that allows a simple, single PCR product from a gene of interest to be easily converted into a highly effective ihpRNA silencing construct. We have also created a high-throughput vector, pHELLSGATE, that should facilitate the cloning of gene libraries or large numbers of defined genes, such as those in EST collections, using an in vitro recombinase system. This system may facilitate the large-scale determination and discovery of plant gene functions in the same way as RNAi is being used to examine gene function in Caenorhabditis elegans.
Low-temperature coal desulfurization (1977)

Economical, low-temperature chlorinolysis converts sulfur to water-soluble sulfates. Sulfates are removed by washing. Subsequent steps dry coal and remove chlorine. Chlorine and solvents can be reused.
Toxin A–Predominant Pathogenic Clostridioides difficile: A Novel Clinical Phenotype (2019)

We report the discovery of clinical pathogenic C. difficile strains that produce high levels of toxin A but minimal or no toxin B. This pattern of toxin production is not rare (>5% of isolates) and is consistently observed in vitro and in vivo in humans and mice. Our study highlights the significance of toxin A in human CDI pathogenesis and has important implications for CDI diagnosis, treatment, and vaccine development.
The Enzymology of Castor Oil Biosynthesis (2007)

The castor plant Ricinus communis L., Euphorbiaceae produces seeds containing a unique oil. Castor oil is the only commodity vegetable oil that contains significant amounts of hydroxy fatty acid. This fatty acid is ricinoleic acid (12-hydroxy oleic acid) (Fig. 1) and it comprises up to 90% of the total fatty acid (FA) content of castor oil. Due to the physical and chemical properties imparted by the mid-chain hydroxy group, the oil has many important industrial uses. However, due to the presence of the toxic protein ricin and hyperallergenic 2S albumins, the production of castor oil is problematic. One logical approach to solving the biohazard problem presented by castor meal is to produce ricinoleate in plants lacking these noxious components. Several researchers have attempted to produce a ricinoleate oil by transgenic expression of the oleoyl-12-hydroxylase, the enzyme that is responsible for ricinoleate biosynthesis. This approach of introducing a single gene to engineer a novel oil composition was pioneered by the Calgene company the in order to develop laurate canola (Voelker et al. 1992). Expression of the cDNA that encodes the oleoyl-12-hydroxylase (or FAH, for fatty acyl hydroxylase), resulted in the accumulation of a low level of hydroxy fatty acids in tobacco and Arabidopsis (Broun and Somerville 1997). These results suggested that the FAH gene by itself is not sufficient to produce high levels of ricinoleate in plants other than castor (McKeon and Lin 2002). An in vitro system using microsomes isolated from developing castor seed endosperm provided an effective means for following fatty acid hydroxylation and castor oil biosynthesis (McKeon et al. 1997; Lin et al. 1998a). Using metabolic profiling tools for analyzing lipid biosynthetic products (Lin et al. 1998a, 2002), the analysis of radiolabeled products from fatty acids incubated in the microsomal system enabled identification of several enzyme activities that give castor its unique ability to produce a high ricinoleate oil (McKeon and Lin 2002). Based on these studies, the preferential incorporation of ricinoleate into triacylglycerol (TG) led us to identify the final step in oil biosynthesis (Fig. 2) as a key step in maintaining high ricinoleate content while minimizing oleate incorporation into the TG fraction. Table 1 shows that the microsomes incorporate ricinoleate preferentially by a factor of 6-fold. The diacylglycerol acyltransferase (DGAT) is a transmembrane enzyme that catalyzes the acylation of diacylglycerol (DG) to TG, using acylCoA as the source for the final acyl group. This step has long been considered to be a rate limiting step in oil biosynthesis, and considerable evidence has accumulated to indicate that altered DGAT activity levels dramatically affect the yield of oil (He et al. 2004). AcylCoA synthetases (ACS) produce the acyl-donor
Tuneable broadband optical parametric oscillator pumped by an Yb:KLu(WO<inf>4</inf>)<inf>2</inf> thin-disk laser oscillator (2011)

In this work, we present a broadband OPO, for the first time based on a broadband zero-dispersion setup. The novel OPO is pumped by a home built frequency-doubled Yb:KLu(WO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> ) <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> thin-disk laser oscillator delivering 23 W of average output power. After the SHG of the infrared 500 fs-pulses to the OPO-pump wavelength of 516 nm, more than 13.5 W of green pump power are available for pumping the BBO crystal within the OPO.
GM-CSF in the Lung Protects against Lethal Influenza Infection (2011)

GM-CSF confers resistance to influenza by enhancing innate immune mechanisms that depend on alveolar macrophages. Pulmonary delivery of this cytokine has the potential to reduce the morbidity and mortality due to influenza virus.