gebhart/patrepeval huggingface dataset:
Application of Free-Energy Decomposition to Determine the Relative Stability of <i>R</i> and <i>S</i> Oligodeoxyribonucleotide Methylphosphonates (1991)

The stereoselective stability of oligodeoxyribonucleotide methylphosphonates is examined using free-energy computer simulations. These modified phosphate linkages have the potential to be important antisense therapeutics that can be targeted on specific sequences of single- and double-stranded DNA, as well as crucial RNA messages. The stability of hybrid duplexes that contain these modified linkages is known experimentally to depend on the configuration of the chiral phosphonate center. Free-energy decomposition calculations were performed on three DNA oligomers to determine the origin of the structural interactions and physical properties that influence the relative stability of R and S methylphosphonate diastereomers. The strategy applied used free-energy decomposition methods to evaluate the free-energy contributions from selected groups. The results indicated that only three groups have a steric effect on the stability: the C2' and C3' substituents on the S diastereomer (5' side) and the C5' substituents on the R diastereomer (3' side). The balance considerably favors the R configuration in all the isomers studied and is not sequence dependent. The electrostatic effects were much more variable and were shown to be dependent on the conformation of duplex. The solvent interactions, however, were consistent and contributed favorably to the stability of the R over the S diastereomer. This favorable solvation energy for the R diastereomer was surprising (since the methyl group is more solvent exposed in this configuration) and was further supported by ab initio and associated free-energy calculations. This study concludes that oligonucleotides containing R-methylphosphonate linkages will normally form more stable duplexes than the corresponding S diastereomer irrespective of sequence, but also points that conformational changes may allow for a reversal in stability.
Cooperative effects of <i>INK4a</i> and <i>ras</i> in melanoma susceptibility in vivo (1997)

The familial melanoma gene (INK4a/MTS1/CDKN2) encodes potent tumor suppressor activity. Although mice null for the ink4a homolog develop a cancer-prone condition, a pathogenetic link to melanoma susceptibility has yet to be established. Here we report that mice with melanocyte-specific expression of activated H-rasG12V on an ink4a-deficient background develop spontaneous cutaneous melanomas after a short latency and with high penetrance. Consistent loss of the wild-type ink4a allele was observed in tumors arising in ink4a heterozygous transgenic mice. No homozygous deletion of the neighboring ink4b gene was detected. Moreover, as in human melanomas, the p53 gene remained in a wild-type configuration with no observed mutation or allelic loss. These results show that loss of ink4a and activation of Ras can cooperate to accelerate the development of melanoma and provide the first in vivo experimental evidence for a causal relationship between ink4a deficiency and the pathogenesis of melanoma. In addition, this mouse model affords a system in which to identify and analyze pathways involved in tumor progression against the backdrop of genetic alterations encountered in human melanomas.
Head, neck, and brain tumor embolization guidelines (2012)

Peri-operative embolization of vascular head, neck, and brain tumors is an effective and safe adjuvant to surgical resection. Major complications reported in the literature are rare when these procedures are performed by operators with appropriate training and knowledge of the relevant vascular and surgical anatomy. These standards may help to standardize reporting and publication in future studies.
A Statistical Framework for Estimation of Full-Chip Leakage-Power Distribution Under Parameter Variations (2007)

This paper presents a novel framework for accurate estimation of key statistical parameters of the subthreshold-and gate-leakage distributions of a chip under parameter variations while considering both within-die and die-to-die variabilities in process (P), temperature (T), and supply voltage (V). For the first time, temperature variations and, more importantly, electrothermal couplings between junction (substrate or die) temperature and leakage power have been accounted for in a full-chip leakage estimation methodology. In the proposed framework, instead of exact leakage distribution profile, its statistically important parameters, such as nominal value and spread, are computed. Initially, at the transistor level, a quantitative analysis of the relative sensitivities of device leakage components to P-T-V variations is performed to extract a transistor-level variation model. It is shown that the proposed statistical model, as compared to others in the literature, shows better agreement with BSIM <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> model-based simulations. It is also demonstrated that failing to account for temperature variations and electrothermal couplings can result in significant inaccuracy in chip-level leakage estimation. Furthermore, the full-chip leakage-power distribution is used to estimate the leakage-constrained yield under the impact of variations. The calculations show that yield is significantly lowered due to the within-die and die-to-die process and temperature variations. Subsequently, the proposed framework is applied in the leakage estimation of complex logic circuits with a consideration of spatial correlations of process parameters and transistor stacking effects.
New Verification Methods for Low-Frequency Susceptibility Testing (2020)

The MIL-STD-461 CS101 test is one of the essential low-frequency conducted susceptibility tests for military and aerospace equipment. The CS101 test firstly requires a calibration process performed using a 0.5 Ω resistor to verify functionality of the test equipment and to establish a maximum drive power. The test stage follows the calibration using the verified test equipment. Observation is required during the CS101 calibration and test stages to detect the sinusoidal quality of the injected signal into the EUT. The standard supports the use of a frequency domain measurement receiver which limits verification of the sinusoidal waveform characteristics. This issue arises for AC-powered devices even if an oscilloscope is used instead of the frequency domain measurement receiver. As a solution, in this research, we evaluated using quick 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> and 3 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rd</sup> harmonic measurements of each test frequency during the calibration and test stages. If the 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> and 3 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rd</sup> harmonic levels are high for the test frequency of interest, this will reveal distortion of the injected CS101 test signal.In addition to the injected signal quality verification, we also evaluated an effective just-before-test verification for CS101 testing to detect issues with the test setup and employed AC power frequency filter solutions and to examine the influence of power frequency feedback to the amplifier before a test.
Glucose-transporter-type-I-gene amplification correlates with Sialyl-Lewis-X synthesis and proliferation in lung cancer (1997)

Increased glucose transport is a common characteristic of most tumors. To examine the role of elevated glucose uptake in lung cancer, we performed PCR amplification of 2 facilitative glucose transporter genes (GLUT1 and GLUT3) and immunohistochemical staining for GLUT1, proliferating cell nuclear antigen (PCNA), and sialyl Lewis x (sLe(x)) on tumor specimens from 327 patients with lung cancer who underwent surgical resection from 1980 to 1993. To evaluate the relationship between GLUT, alpha-2,3-sialyltransferase (ST), and alpha-1,3-fucosyltransferase (Fuc-T) genes, PCR amplification of the ST3N and Fuc-TVII also was performed. Amplification of GLUT1 was significantly greater than that of GLUT3. GLUT1 and GLUT3 amplification correlated with PCNA staining (p < 0.01). In addition, GLUT1 amplification correlated with the grading of sLe(x) staining as well as with the grading of GLUT1 staining (p < .03, p < 0.01). GLUT1 was co-amplified with ST3N and Fuc-TVII genes, which are involved in the synthesis of sLe(x) (p < 0.01). The survival of patients whose tumors showed GLUT1 amplification was significantly shorter than that of patients whose tumors did not (p < 0.01). In a multivariate analysis of survival, GLUT1 remained a statistically significant prognostic factor. Our results suggest that GLUT1 amplification may participate in sLe(x) synthesis as well as in proliferation, and may be of prognostic value in lung cancer.
Design of Low-Power Structural FIR Filter Using Data-Driven Clock Gating and Multibit Flip-Flops (2020)

Optimization for power is one of the most important design objectives in modern digital signal processing (DSP) applications. The digital finite duration impulse response (FIR) filter is considered to be one of the most essential components of DSP, and consequently a number of extensive works had been carried out by researchers on the power optimization of the filters. Data-driven clock gating (DDCG) and multibit flip-flops (MBFFs) are two low-power design methods that are used and often treated separately. The combination of these methods into a single algorithm enables further power saving of the FIR filter. The experimental results show that the proposed FIR filter achieves 25% and 22% power consumption reduction compared to that using the conventional design.
The enzymic deacylation of phospholipids and galactolipids in plants. Purification and properties of a lipolytic acyl-hydrolase from potato tubers (1971)

An enzyme preparation that catalyses the deacylation of mono- and di-acyl phospholipids, galactosyl diglycerides, mono- and di-glycerides has been partially purified from potato tubers. The preparation also hydrolyses methyl and p-nitrophenyl esters and acts preferentially on esters of long-chain fatty acids. Triglycerides, wax esters and sterol esters are not hydrolysed. The same enzyme preparation catalyses acyl transfer reactions in the presence of alcohols and also catalyses the synthesis of wax esters from long-chain alcohols and free fatty acids. Gel filtration, DEAE-cellulose chromatography and free-flow electrophoresis failed to achieve any separation of the acyl-hydrolase activities towards different classes of acyl lipids (phosphatidylcholine, monogalactosyl diglyceride, mono-olein, methyl palmitate and p-nitrophenyl palmitate) or any separation of these activities from a major protein component. For each class of lipid the acyl-hydrolase activity was subject to substrate inhibition, was inhibited by relatively high concentrations of di-isopropyl phosphorofluoridate and the pH responses were changed by Triton X-100. The hydrolysis of phosphatidylcholine was stimulated 30-40-fold by Triton X-100. The specific activities of the potato enzyme with galactolipids were at least 70 times higher than those reported for a homogeneous galactolipase enzyme purified from runner bean leaves. The possibility that a single lipolytic acyl-hydrolase enzyme is responsible for the deacylation of several classes of acyl lipid is discussed.
Catalysis by metallic nanoparticles in aqueous solution: model reactions (2012)

Catalysis by metallic nanoparticles is certainly among the most intensely studied problems in modern nanoscience. However, reliable tests for catalytic performance of such nanoparticles are often poorly defined, which makes comparison and benchmarking rather difficult. We tackle in this tutorial review a subset of well-studied reactions that take place in aqueous phase and for which a comprehensive kinetic analysis is available. Two of these catalytic model reactions are under consideration here, namely the reduction of (i) p-nitrophenol and (ii) hexacyanoferrate (iii), both by borohydride ions. Both reactions take place at the surface of noble metal nanoparticles at room temperature and can be accurately monitored by UV-vis spectroscopy. Moreover, the total surface area of the nanoparticles in solution can be known with high precision and thus can be directly used for the kinetic analysis. Hence, these model reactions represent cases of heterogeneous catalysis that can be modelled with the accuracy typically available for homogeneous catalysis. Both model reactions allow us to discuss a number of important concepts and questions, namely the dependence of catalytic activity on the size of the nanoparticles, electrochemistry of nanoparticles, surface restructuring, the use of carrier systems and the role of diffusion control.
RevDedup: A Reverse Deduplication Storage System Optimized for Reads to\n Latest Backups (2013)

Scaling up the backup storage for an ever-increasing volume of virtual\nmachine (VM) images is a critical issue in virtualization environments. While\ndeduplication is known to effectively eliminate duplicates for VM image\nstorage, it also introduces fragmentation that will degrade read performance.\nWe propose RevDedup, a deduplication system that optimizes reads to latest VM\nimage backups using an idea called reverse deduplication. In contrast with\nconventional deduplication that removes duplicates from new data, RevDedup\nremoves duplicates from old data, thereby shifting fragmentation to old data\nwhile keeping the layout of new data as sequential as possible. We evaluate our\nRevDedup prototype using microbenchmark and real-world workloads. For a 12-week\nspan of real-world VM images from 160 users, RevDedup achieves high\ndeduplication efficiency with around 97% of saving, and high backup and read\nthroughput on the order of 1GB/s. RevDedup also incurs small metadata overhead\nin backup/read operations.\n
Birefringent Fresnel zone plates in silica fabricated by femtosecond laser machining (2002)

We demonstrate maskless, single-step fabrication of strongly birefringent Fresnel zone plates by focusing of femtosecond laser pulses deep within silica substrates. The process allows us to produce alternate zone rings directly by inducing a local refractive-index modification of the order of n~10(-2) . The embedded zone plates shown in this Letter exhibit efficiencies that vary by as much as a factor of ~6 for orthogonal polarizations. Focal lengths of primary and secondary foci are shown to compare well with theory.
Integrating technology to improve medication administration (2011)

By integrating two stand-alone technologies, i.v. interoperability was implemented to improve medication administration. Medication errors were reduced, nursing workflow was simplified, and pharmacists became involved in checking infusion rates of i.v. medications.
Analytic 3D image reconstruction using all detected events (1989)

The authors present the results of testing an algorithm for three-dimensional image reconstruction that uses all gamma-ray coincidence events detected by a PET (positron emission tomography) volume imaging scanner. By using two iterations of an analytic filter-backprojection method, the algorithm is not constrained by the requirement of a spatially invariant detector point spread function, which limits normal analytic techniques. Removing this constraint allows the incorporation of all detected events, regardless of orientation, which improves the statistical quality of the final reconstructed image.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Succinate causes pathological cardiomyocyte hypertrophy through GPR91 activation (2014)

These results show for the first time that succinate plays an important role in cardiomyocyte hypertrophy through GPR91 activation, and extend our understanding of how ischemia can induce hypertrophic cardiomyopathy.
Photo-vibrational sensing of trace chemicals and explosives by long-distance differential laser Doppler vibrometer (2017)

Photoacoustic/photothermal spectroscopy is an established technique for trace detection of chemicals and explosives. Normally high-sensitive microphone or PZT sensor is used to detect the signal in photoacoustic cell. In recent years, laser Doppler vibrometer (LDV) is proposed to remote-sense photoacoustic signal on various substrates. It is a highsensitivity sensor with a displacement resolution of <10pm. In this research, the photoacoustic effect of various chemicals and explosives is excited by a quantum cascade laser (QCL) at their absorbance peak. A home-developed differential LDV at 1550nm wavelength is applied to detect the vibration signal at 100m. A differential configuration is applied to minimize the environment factors, such as environment noise and vibration, air turbulence, etc. and increase the detection sensitivity. The photo-vibrational signal of chemicals and explosives on different substrates are detected. The results show the potential of the proposed technique on detection of trace chemicals and explosives at long standoff distance.
Pyrrolidine-5,5-<i>trans</i>-lactams. 5. Pharmacokinetic Optimization of Inhibitors of Hepatitis C Virus NS3/4A Protease (2003)

[reaction: see text] In this, the second of two Letters, the optimization of the pyrrolidine-5,5-trans-lactam template (exemplified by 1a) as a mechanism-based inhibitor of hepatitis C NS3/4A protease is described. "Right Box" analysis of cassette dosing screening pharmacokinetic data was used to rapidly categorize the compounds. GW0014 (compound 4d) emerged as the compound displaying an optimal balance of biochemical and replicon potency, along with low i.v. clearance in the dog.
Echocardiographic measurement of right ventricular volume. (1984)

The volume of the right ventricle can be determined angiographically from its projections in two mutually perpendicular planes. Echocardiographic techniques for measuring right ventricular volume, however, have been more difficult and less successful. In this study, a method was developed for calculating right ventricular volume from two intersecting cross-sectional echocardiographic views: the apical four-chamber and subcostal right ventricular outflow tract views. First, the areas and lengths of casts of 12 human right ventricles obtained at autopsy were directly measured in the chosen views. Actual cast volumes correlated best with a formula giving volume as 2/3 times the area in one view times the long axis in the other view. The degree of correlation was similarly high for calculations involving the area derived from either view and the length of the roughly orthogonal section. This relationship for right ventricular volume was then confirmed with two-dimensional echocardiographic images of hollow latex molds made from the casts (r = .95, p less than .0001). The significance of these findings is discussed in relation to angiographic results and models of the right ventricle.
A complete monolithic 10-bit D/A converter (1973)

This paper will describe a monolithic 10-bit plus sign D/A converter incorporating all of the necessary circuit functions including voltage reference and internally-compensated high-speed output op amp. Circuit features accuracy, speed and flexibility.
Nanoengineered Colloidal Inks for 3D Bioprinting (2017)

Nanoengineered hydrogels offer the potential to design shear-thinning bioinks for three-dimensional (3D) bioprinting. Here, we have synthesized colloidal bioinks composed of disk-shaped two-dimensional (2D) nanosilicates (Laponite) and poly(ethylene glycol) (PEG). The addition of Laponite reinforces the PEG network and increases viscosity, storage modulus, and network stability. PEG-Laponite hydrogels display shear-thinning and self-recovery characteristics due to rapid internal phase rearrangement. As a result, a range of complex patterns can be printed using PEG-Laponite bioinks. The 3D bioprinted structure has similar mechanical properties compared to the as-casted structure. In addition, encapsulated cells within the PEG-Laponite bioink show high viability after bioprinting. Overall, this study introduces a new class of PEG-Laponite colloidal inks for bioprinting and cell delivery.
Computing Clear Day Solar Radiation Spectra for the Terrestrial Ecological Environment (1971)

Clear sky (cloud—free) horizontal plane terrestrial solar radiation spectral fluxes can be computed for any time of day and year, geographic location (latitude and longitude), and elevation upon inputing the optical properties of the atmosphere and reflecting properties of the underlying surface. Consideration is given to the problem of diffuse terrestrial radiation spectra for non—sea level elevations and where the terrestrial atmosphere cannot be regarded as being purely a Rayleigh atmosphere. Computation of terrestrial spectra for "large" zenith angles (Z > or = 72 degrees) is considered along with a discussion of irradiation patterns peculiar to polar zones (i.e., long days and nights). Selected results from the integration of these concepts into a computer program include the computation of total diffuse—to—direct flux ratios for radiation from a Rayleigh atmosphere at any solar zenith angle and selected elevations with typical mean ground albedos. Comparisons of integrated energy predictions with measurements in the literature agree favorably.
[Severe poisoning by 4-aminopyridine in a body builder]. (1995)

A 22-year-old man was admitted to hospital with severe, accidental intoxication with 4-aminopyridine, a medicine which increases the acetylcholine concentration in the synapses and has a limited application in the treatment of some neurological diseases. The patient acted on the assumption of body-building capacities of this 'amino'. Apart from the previously documented symptoms of intoxication such as an epileptic attack and confusion, he showed cardiac arrhythmias, conduction disorders and severe hypertension. The serum concentration of 4-aminopyridine was 335 mg/l, while the therapeutic level is 25-75 mg/l.
The value of geophysics to the oil industry (1974-present) (1989)

The general population has never really understood the link between earth science and petroleum products. Or perhaps they have understood it better than many earth scientists. They see only a vague association between petroleum products and the subsurface origin of these products. So, instead of lamenting the decline in the value of geoscience to society, let us look at the value of earth scientists to that important subset of society: the owners and managers of US oil-and-gas companies.
Protective effect of saffron (Crocus sativus L.) aqueous extract against genetic damage induced by anti-tumor agents in mice (2006)

The genotoxic potential of anti-tumor drugs limits their efficacy in the treatment of cancers. Since ancient times, saffron (dried stigmas of Crocus sativus L.) has been used as a spice and medicinal herb. Saffron is a rich source of carotenoids and is known for its anti-cancer and anti-tumor properties. The present study was designed to ascertain the chemoprotective potential of saffron against the genotoxicity of three well-known anti-tumor drugs-cisplatin (CIS), cyclophosphamide (CPH) and mitomycin-C (MMC)--using comet assay. Three doses of saffron (20, 40 and 80 mg/kg b.w.) were orally administered to mice for five consecutive days prior to the administration of anti-tumor drugs under investigation. Pre-treatment with saffron significantly inhibited anti-tumor drugs induced cellular DNA damage (strand breaks) as revealed by decreased comet tail length, tail moment and percent DNA in the tail. These findings, together with our previous results, suggest a potential role for saffron as an anti-genotoxic, anti-oxidant and chemopreventive agent and could be used as an adjuvant in chemotherapeutic applications.