gebhart/patrepeval huggingface dataset:
Histone deacetylases 1, 6 and 8 are critical for invasion in breast cancer (2011)

Histone deacetylases (HDACs) are associated with the development and progression of cancer, but it is not known which of the HDAC isoforms play important roles in breast cancer metastasis. This study identified the specific HDAC isoforms that are necessary for invasion and/or migration in human breast cancer cell lines. MDA-MB-231 cells were significantly more invasive and expressed higher levels of matrix metalloproteinase-9 (MMP-9) compared to MCF-7 cells. We compared the expression of HDAC isoforms between MCF-7 and MDA-MB-231 cells and found greater expression of HDAC4, 6 and 8 in MDA-MB-231 cells by RT-PCR and Western blot analyses. In addition, apicidin, a histone deacetylase inhibitor, was shown to attenuate the invasion, migration and MMP-9 expression in MDA-MB-231 cells. Using specific siRNAs directed against HDAC1, 4, 6 and 8, we show that inhibition of HDAC1, 6 and 8, but not HDAC4, are responsible for invasion and MMP-9 expression in MDA-MB-231 cells. We analyzed the invasiveness of MCF-7 cells overexpressing HDAC1, 4, 6 or 8 and found that overexpression of HDAC1, 6 or 8 increased invasion and MMP-9 expression. By developing HDAC isoforms as potential biomarkers for breast cancer metastasis, the present study can be extended to developing therapies for breast cancer invasion.
Blu-ray Disc/DVD/CD Compatible Pick-up having a Single Objective Lens and SA detection Function (2003)

Postdeadline Summary: We have developed a BD/DVD/CD compatible pick-up by adding a hybrid HOE device in front of single objective lens. Statement of Significance: One solution for BD/DVD/CD compatibility in time of BD format announcement. Full text article is not available.
Antitumor activity of tripterine via cell-penetrating peptide-coated nanostructured lipid carriers in a prostate cancer model (2013)

CT-NLC noticeably enhanced antitumor activity in vitro and in vivo and showed dramatically improved cytotoxicity in normal cells in comparison with free tripterine. In summary, CT-NLC could be used as a promising drug delivery system for the treatment of prostate cancer.
Formulation and PEGylation optimization of the therapeutic PEGylated phenylalanine ammonia lyase for the treatment of phenylketonuria (2017)

Phenylketonuria (PKU) is a genetic metabolic disease in which the decrease or loss of phenylalanine hydroxylase (PAH) activity results in elevated, neurotoxic levels of phenylalanine (Phe). Due to many obstacles, PAH enzyme replacement therapy is not currently an option. Treatment of PKU with an alternative enzyme, phenylalanine ammonia lyase (PAL), was first proposed in the 1970s. However, issues regarding immunogenicity, enzyme production and mode of delivery needed to be overcome. Through the evaluation of PAL enzymes from multiple species, three potential PAL enzymes from yeast and cyanobacteria were chosen for evaluation of their therapeutic potential. The addition of polyethylene glycol (PEG, MW = 20,000), at a particular ratio to modify the protein surface, attenuated immunogenicity in an animal model of PKU. All three PEGylated PAL candidates showed efficacy in a mouse model of PKU (BTBR Pahenu2) upon subcutaneous injection. However, only PEGylated Anabaena variabilis (Av) PAL-treated mice demonstrated sustained low Phe levels with weekly injection and was the only PAL evaluated that maintained full enzymatic activity upon PEGylation. A PEGylated recombinant double mutant version of AvPAL (Cys503Ser/Cys565Ser), rAvPAL-PEG, was selected for drug development based on its positive pharmacodynamic profile and favorable expression titers. PEGylation was shown to be critical for rAvPAL-PEG efficacy as under PEGylated rAvPAL had a lower pharmacodynamic effect. rAvPAL and rAvPAL-PEG had poor stability at 4°C. L-Phe and trans-cinnamate were identified as activity stabilizing excipients. rAvPAL-PEG is currently in Phase 3 clinical trials to assess efficacy in PKU patients.
Development of a recombinant RNA technique for the construction of chimeric RNA with a long poly(C) tract (1993)

The murine cardioviruses and bovine aphthoviruses are distinguished from other (+) strand RNA viruses by their long poly(C) tract in the 5'-noncoding region. The presence of this poly(C) tract has long hampered the construction of full-length cDNA with the complete poly(C) tract, because long poly(dC-dG) homopolymer-containing plasmids are difficult to amplify in bacterial systems. To overcome this problem, we constructed a chimeric RNA by joining the poly(C) region of the viral RNA to the 5'-truncated RNA transcript of the encephalomyocarditis (EMC) virus cDNA. The non-chimeric, recombinant EMC virus with a short poly(C) tract produces recombinant progeny virus, but this is not pathogenic in vivo. On the other hand, the EMC viral RNA chimera with the complete poly(C) tract produces recombinant progeny virus that is pathogenic in vivo. This method of viral RNA construction will be invaluable for functional studies of other cardioviruses and aphthoviruses, as well as for recombinant RNA manipulations.
A Comprehensive Genetic Map of the Cattle Genome Based on 3802 Microsatellites (2004)

A microsatellite-based high-density genetic map facilitates for fine mapping of hereditary traits of interest, characterization of meiosis, and providing a foundation for physical map construction. Here, we developed a comprehensive genetic map on the basis of >880,000 genotypes across the USDA MARC cattle reference families with a potential genetic resolution of 0.8 cM at the 95% confidence level ( approximately 800 kb in the bovine genome). We incorporated 2325 microsatellites into the second-generation genetic map by linkage analysis based on sex-averaged two-point LOD scores (>3.0), of which 2293 were fine-mapped by multipoint linkage analysis. The new 3160-cM map comprised of 29 sex-averaged autosomal linkage groups and a sex-specific X-chromosome linkage group includes 3960 markers with 2389 positions, resulting in an average interval size of 1.4 cM. More than half (51%) of the total length of the map is covered with intervals of 2.0 cM or less, and the largest gap is a 10.2-cM interval on the X-linkage group. The new map should accelerate fine mapping and positional cloning of genes for genetic diseases and economically important traits in cattle, as well as related livestock species, such as sheep and goat.
ChemInform Abstract: Advances in Chemical Synthesis of Nb‐Containing Oxides (2013)

Abstract Review: 125 refs.
Estimated communication range of social sounds used by bottlenose dolphins (<i>Tursiops truncatus</i>) (2006)

Bottlenose dolphins, Tursiops truncatus, exhibit flexible associations in which the compositions of groups change frequently. We investigated the potential distances over which female dolphins and their dependent calves could remain in acoustic contact. We quantified the propagation of sounds in the frequency range of typical dolphin whistles in shallow water areas and channels of Sarasota Bay, Florida. Our results indicated that detection range was noise limited as opposed to being limited by hearing sensitivity. Sounds were attenuated to a greater extent in areas with seagrass than any other habitat. Estimates of active space of whistles showed that in seagrass shallow water areas, low-frequency whistles (7-13 kHz) with a 165 dB source level could be heard by dolphins at 487 m. In shallow areas with a mud bottom, all whistle frequency components of the same whistle could be heard by dolphins travel up to 2 km. In channels, high-frequency whistles (13-19 kHz) could be detectable potentially over a much longer distance (> 20 km). Our findings indicate that the communication range of social sounds likely exceeds the mean separation distances between females and their calves. Ecological pressures might play an important role in determining the separation distances within communication range.
Preoperative and postoperative medications used for cataract surgery (1999)

The current state of cataract surgery for the millennium may be stated as "minimally invasive techniques." This review presents recent articles on the perioperative use of antibiotics (primarily fluoroquinolones), nonsteroidal antiinflammatory drugs (Voltaren and ketorolac), and new corticosteroids (rimexolone and loteprednol etabonate). Preoperative topical application of ofloxacin or ciprofloxacin results in a satisfactory minimal inhibitory concentration for most pathogens. However, one cannot determine the actual effect of intraoperative antibiotics on acute postoperative endophthalmitis, because of its low overall incidence. Nonsteroidal antiinflammatory drugs, especially Voltaren, may offer equivalent antiinflammatory efficacy (for both postoperative inflammation and cystoid macular edema) without the typically corticosteroid-associated adverse events. Rimexolone and loteprednol etabonate, two new corticosteroids, may offer good antiinflammatory efficacy with greatly reduced risk for elevation of intraocular pressure.
Private healthcare providers: A boost for NHS productivity? (2007)

Competition from private sector providers is only one of a number of factors which are stimulating the NHS to increase productivity. Patient choice, stronger commissioning and payment by results are likely to be very strong drivers for improvement. The provision of services in the NHS of tomorrow will be largely in the hands of foundation trusts, which will need to be able to offer services that are attractive to patients and are within the care pathways set-out by commissioning primary care trusts. Fundamentally, they will need to ensure that overall their services are within the tariff price if they are to remain in business. The private healthcare sector, whether through the independent treatment centre system or as competitors for the provision of other services, will put additional pressure on NHS providers. However, private sector providers will also face the same challenges of strong commissioning and fixed tariff prices and will face productivity pressures of their own. The need to increase productivity within the NHS is widely acknowledged and some organisations are adapting process engineering from the manufacturing sector, but there is no easy solution. Increased productivity will require leadership and vision.
Material Degradation during Isothermal Aging and Thermal Cycling of Hybrid Mica Seal with Ag Interlayer under SOFC Exposure Conditions (2006)

Hybrid phlogopite mica seals with silver interlayers were evaluated in terms of material degradation in a combined isothermal aging and thermal cycling test. The hybrid mica was composed of a phlogopite mica paper sandwiched between two foils. The hybrid micas were first aged at for in a low hydrogen fuel , followed by short-term thermal cycling between and . The combined test was repeated three times for a total of aging at and 119 thermal cycles. The results of high-temperature leak rates showed very good thermal stability and thermal cycle stability with leak rates of . The hybrid mica was also tested in a high-water-content fuel and demonstrated similar leakage during the isothermal aging and the subsequent thermal cycles. Postmortem analyses showed no extensive reaction of Ag with phlogopite mica as well as the mica degradations. The issues of volatility of Ag and mica in the solid oxide fuel cell (SOFC) environments were discussed. Simple models were simulated to estimate the effect of leakage on the open-circuit voltage and the total fuel loss at various SOFC stack sizes. The results showed very minute fuel loss for the current hybrid micas and demonstrated it to be a good candidate for SOFC sealing.
Using Evolution to Learn How to Perform Interest Point Detection (2006)

The performance of high-level computer vision applications is tightly coupled with the low-level vision operations that are commonly required. Thus, it is advantageous to have low-level feature extractors that are optimal with respect to a desired performance criteria. This paper presents a novel approach that uses genetic programming as a learning framework that generates a specific type of low-level feature extractor: interest point detector. The learning process is posed as an optimization problem. The optimization criterion is designed to promote the emergence of the detectors' geometric stability under different types of image transformations and global separability between detected points. This concept is represented by the operators repeatability rate. Results prove that our approach is effective at automatically generating low-level feature extractors. This paper presents two different evolved operators: IPGP1 and IPGP2. Their performance is comparable with the Harris operator given their excellent repeatability rate. Furthermore, the learning process was able to rediscover the DET corner detector proposed by Beaudet
Elastic wave propagation and attenuation in a double-porosity dual-permeability medium (1998)

To account for large-volume low-permeability storage porosity and low-volume highpermeability fracture/crack porosity in oil and gas reservoirs, phenomenological equations for the poroelastic behavior of a double porosity medium have been formulated and the coefficients in these linear equations identified. This generalization from a single porosity model increases the number of independent inertial coefficients from three to six, the number of independent drag coefficients from three to six, and the number of independent stress-strain coefficients from three to six for an isotropic applied stress and assumed isotropy of the medium. The analysis leading to physical interpretations of the inertial and drag coefficients is relatively straightforward, whereas that for the stress-strain coefficients is more tedious. In a quasistatic analysis, the physical interpretations are based upon considerations of extremes in both spatial and temporal scales. The limit of very short times is the one most pertinent for wave propagation, and in this case both matrix porosity and fractures are expected to behave in an undrained fashion, although our analysis makes no assumptions in this regard. For the very long times more relevant to reservoir drawdown, the double porosity medium behaves as an equivalent single porosity medium. At the macroscopic spatial level, the pertinent parameters (such as the total compressibility) may be determined by appropriate field tests. At the mesoscopic scale pertinent parameters of the rock matrix can be determined directly through laboratory measurements on core, and the compressiblity can be measured for a single fracture. We show explicitly how to generalize the quasistatic results to incorporate wave propagation effects and how effects that are usually attributed to squirt flow under partially saturated conditions can be explained alternatively in terms of the double-porosity model. The result is therefore a theory that generalizes, but is completely consistent with, Biot’s theory of poroelasticity and is valid for analysis of elastic wave data from highly fractured reservoirs.
Targeting Chk1 in p53-deficient triple-negative breast cancer is therapeutically beneficial in human-in-mouse tumor models (2012)

Patients with triple-negative breast cancer (TNBC) - defined by lack of estrogen receptor and progesterone receptor expression as well as lack of human epidermal growth factor receptor 2 (HER2) amplification - have a poor prognosis. There is a need for targeted therapies to treat this condition. TNBCs frequently harbor mutations in TP53, resulting in loss of the G1 checkpoint and reliance on checkpoint kinase 1 (Chk1) to arrest cells in response to DNA damage. Previous studies have shown that inhibition of Chk1 in a p53-deficient background results in apoptosis [corrected] in response to DNA damage. We therefore tested whether inhibition of Chk1 could potentiate the cytotoxicity of the DNA damaging agent irinotecan in TNBC using xenotransplant tumor models. Tumor specimens from patients with TNBC were engrafted into humanized mammary fat pads of immunodeficient mice to create 3 independent human-in-mouse TNBC lines: 1 WT (WU-BC3) and 2 mutant for TP53 (WU-BC4 and WU-BC5). These lines were tested for their response to irinotecan and a Chk1 inhibitor (either UCN-01 or AZD7762), either as single agents or in combination. The combination therapy induced checkpoint bypass and apoptosis in WU-BC4 and WU-BC5, but not WU-BC3, tumors. Moreover, combination therapy inhibited tumor growth and prolonged survival of mice bearing the WU-BC4 line, but not the WU-BC3 line. In addition, knockdown of p53 sensitized WU-BC3 tumors to the combination therapy. These results demonstrate that p53 is a major determinant of how TNBCs respond to therapies that combine DNA damage with Chk1 inhibition.
Adjacent-track interference in dual-layer perpendicular recording (2003)

Adjacent-track interference (ATI) in a dual-layer perpendicular recording system arises during both writing and reading. During writing, the stray fields from the write head can cause side writing and side erasure. A dc-erase method using media with a low nucleation field is used to identify the extent and polarity of these fields. In media with a strong anisotropy in the soft underlayer (SUL), experimental results reveal that the fields causing ATI have a strong cross-track asymmetry due to interactions between the writing flux and the magnetization of the SUL. On readback, cross-track amplitude profiles taken at long wavelengths show a distinctive "side bump" predominantly on just one side of the track profile. This asymmetry is again found to be associated with the magnetization in the SUL. A theoretical study yields expressions for the lateral extent of the side reading and a critical bit length at which side reading becomes significant. Both of these are consistent with experimental observations. The onset of side erasure during writing is further equated with the time-dependent nucleation field of the medium. Theoretical arguments on thermal decay in the presence of external and demagnetizing field indicate that the threshold for ATI-associated side erasure is expected to follow a time dependence similar to Sharrock's formula for dynamic coercivity.
Mechanisms and Stereochemistry of Acid‐Induced Ring Opening of Optically Active 1,2‐Propene Oxides in the Gas Phase (1997)

Abstract The acid‐induced ring opening of ( S )‐(—)‐1,2‐propene oxide ( 1S ) and ( R )‐(+)‐1,2‐propene oxide ( 1R ) has been investigated in gaseous CH 4 and CH 3 F at 720 torr and in the presence of a nucleophile, NuOH (Nu = H or CH 3 ). The mechanism of the ring‐opening reaction has been assessed by modulating the composition of the gaseous mixture. Two reaction pathways are operative in the gas phase, both proceeding through complete inversion of configuration of the reaction center. A first process is detectable only in the CH 3 F/H 2 O systems and takes place within a persistent proton‐bound complex generated by interaction of the epoxide with the CH 3 OH + 2 ion, formed by methylation of H 2 O with (CH 3 ) 2 F + . Such an intracomplex ring‐opening pathway proceeds through proton transfer from the CH 3 OH + 2 ion to the epoxide followed by motion of the neutral CH 3 OH moiety around the 1‐H‐oxonia‐2‐methyl‐cyclo‐propane structure (H‐ 1R or H‐ 1S ) ( k <10 8 s ‐1 ) before attacking the ring carbons from the rear. In all the other systems with added CH 3 OH, this intracomplex pathway is preceded by a faster “ extracomplex ” pathway involving the attack of an external CH 3 OH molecule on the proton‐bound adduct. The regioselectivity of the intracomplex process is similar to that of the extracomplex pathway. Both are characterized by a slight preference for the C β center of H‐ 1 R (or H‐ 1S ) ( extra‐complex path regioselectivity: α/β = 0.72±0.05; intracomplex path regioselectivity: α/β = 0.71±0.05). The regioselectivity of H‐ 1 R (or H‐ 1S ) is substantially different from that of the 1‐Me‐oxonia‐2‐methyl‐cyclopropanes (Me‐ 1 R or Me‐ 1 S ) toward the same nucleophile NuOH (α/β = 4.1±0.35 (Nu = H); 2.28±0.16 (Nu = CH 3 )). This difference is attributed to a transition structure wherein the C α –O bond rupture increases from H‐ 1 R (or H‐ 1 S ) to Me‐ 1 R (or Me‐ 1 S ) and in passing from CH 3 OH to H 2 O. The regioand stereoselectivity of the gas‐phase acid‐induced ring opening of 1 S and 1 R are compared with those of related reactions carried out in solution.
Gluten breakdown by lactobacilli and pediococci strains isolated from sourdough (2006)

The physiological studies on gluten breakdown by LAB will contribute to the better selection of strains to produce breads with enhanced organoleptic characteristics.
Hot-electron-induced MOSFET degradation at low temperatures (1985)

The n-channel LDD MOSFET lifetime is observed to follow <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\tau=(A/I_{d})(I_{sub}/I_{d})^{-n}</tex> from 77 to 295 K when the device is stressed near the maximum I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">sub</inf> . Here I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d</inf> is the drain current and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">A</tex> is the proportionality constant. The experimental result indicates that <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</tex> is approximately 2.7 and is independent of temperature. However, the proportionality constant <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">A</tex> follows <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">A = A_{0} \exp (-E_{a}/kT)</tex> , with <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">E_{a} = 39</tex> meV. The smaller proportionality constant at low temperatures suggests that hot-electron injection (HEI) degradation is caused by the electron trapping in the oxide.
Novel Plant Immune-Priming Compounds Identified via High-Throughput Chemical Screening Target Salicylic Acid Glucosyltransferases in <i>Arabidopsis</i>   (2012)

Plant activators are compounds, such as analogs of the defense hormone salicylic acid (SA), that protect plants from pathogens by activating the plant immune system. Although some plant activators have been widely used in agriculture, the molecular mechanisms of immune induction are largely unknown. Using a newly established high-throughput screening procedure that screens for compounds that specifically potentiate pathogen-activated cell death in Arabidopsis thaliana cultured suspension cells, we identified five compounds that prime the immune response. These compounds enhanced disease resistance against pathogenic Pseudomonas bacteria in Arabidopsis plants. Pretreatments increased the accumulation of endogenous SA, but reduced its metabolite, SA-O-β-d-glucoside. Inducing compounds inhibited two SA glucosyltransferases (SAGTs) in vitro. Double knockout plants that lack both SAGTs consistently exhibited enhanced disease resistance. Our results demonstrate that manipulation of the active free SA pool via SA-inactivating enzymes can be a useful strategy for fortifying plant disease resistance and may identify useful crop protectants.