gebhart/patrepeval huggingface dataset:
Genotypic predictors of human immunodeficiency virus type 1 drug resistance (2006)

Understanding the genetic basis of HIV-1 drug resistance is essential to developing new antiretroviral drugs and optimizing the use of existing drugs. This understanding, however, is hampered by the large numbers of mutation patterns associated with cross-resistance within each antiretroviral drug class. We used five statistical learning methods (decision trees, neural networks, support vector regression, least-squares regression, and least angle regression) to relate HIV-1 protease and reverse transcriptase mutations to in vitro susceptibility to 16 antiretroviral drugs. Learning methods were trained and tested on a public data set of genotype-phenotype correlations by 5-fold cross-validation. For each learning method, four mutation sets were used as input features: a complete set of all mutations in > or =2 sequences in the data set, the 30 most common data set mutations, an expert panel mutation set, and a set of nonpolymorphic treatment-selected mutations from a public database linking protease and reverse transcriptase sequences to antiretroviral drug exposure. The nonpolymorphic treatment-selected mutations led to the best predictions: 80.1% accuracy at classifying sequences as susceptible, low/intermediate resistant, or highly resistant. Least angle regression predicted susceptibility significantly better than other methods when using the complete set of mutations. The three regression methods provided consistent estimates of the quantitative effect of mutations on drug susceptibility, identifying nearly all previously reported genotype-phenotype associations and providing strong statistical support for many new associations. Mutation regression coefficients showed that, within a drug class, cross-resistance patterns differ for different mutation subsets and that cross-resistance has been underestimated.
Simultaneous Giant Pulses from Five Ruby Laser Oscillators (1966)

A laser system using bleachable-filter Q-switching has enabled us to obtain simultaneous ``giant pulses'' from five ruby laser oscillators. The beams from the different oscillators were found to be phase-locked; the beam divergence was limited by the initial ruby quality. Two other systems for obtaining simultaneous giant pulses were investigated. One involved using the giant pulse from one oscillator to switch the bleachable cells in other oscillators; the other consisted of feeding the giant pulse from one oscillator into a branching chain of amplifiers. These latter systems proved less desirable for expansion to a large number of laser rods.
Epidemiology of HIV Infection and AIDS in the United States (1988)

By the end of 1987, nearly 50,000 cases of acquired immunodeficiency syndrome (AIDS) had been reported since 1981, 20,745 in the past year alone. Black and Hispanic adults and children have reported rates 3 to 12 times as high as whites. This can be largely attributed to higher reported rates in black and Hispanic intravenous (IV) drug abusers, their sex partners, and infants. In 1986, reported AIDS deaths increased adult male and female mortality in the United States by an estimated 0.7 and 0.07%, respectively, with much greater increases in selected age groups or areas of the country. The greatest variation in infection with the human immunodeficiency virus (HIV) (0 to 70%) has been found in surveys of IV drug abusers, while surveys of homosexual men reveal infection rates of 20 to 50%. Infection with HIV ranged from 0 to 2.6% in limited sexually transmitted disease clinic surveys of heterosexual men and women without a history of IV drug abuse or known sexual contact with persons at increased risk. The modes of HIV transmission are now well understood, but a large amount of biologic variability in efficiency of transmission remains to be explained. The period between initial infection with HIV and the development of AIDS is variable, but the risk for disease progression increases with duration of infection.
APPLICATION OF SHELLAC IN POLYMERS (1986)

Abstract Lac is the only known natural resin of animal origin. It is the secretion of a tiny insect known as Kerriar lacca (formally called Laceifer lacca). The lac-forming tiny insect grows on some types of trees, mostly abundant in tropical countries, including India. The secretion of the lac insect hardens in air and forms a covering on the body of the insect. This covering or the nest forms a continuous incrustation on the branches of the host trees. Lac is collected by scraping the incrustation from the branches of the trees.
Species specificity in the blood cholesterol‐lowering effect of YM‐16638 (1996)

1. The compound YM-16638, [[5-[[3-(4-acetyl-3-hydroxy-2-propylphenoxy)propyl] thio]-1,3,4-thiadiazol-2-yl]thio] acetic acid was developed in a series of in vitro and in vivo studies as a leukotriene D4 receptor antagonist. 2. In a clinical trial as a leukotriene antagonist drug, this compound was found to have a potent serum cholesterol lowering effect in normolipidaemic healthy male volunteers. 3. In the present study, we investigated the serum cholesterol lower effect of this compound in various species of experimental animals. 4. Administration of YM-16638 did not cause a significant decrease in serum total cholesterol (TC) in mice (up to 200 mg kg-1, body weight per day for 28 days), rats (200 mg kg-1 for 15 days) or rabbits (90 mg kg-1 for 18 days). In hamsters, administration of YM-16638 orally or by peritoneal injection at 50 mg kg-1 or more daily for 7 days caused a significant decrease in serum TC and the rate of body weight gain. In monkeys, serum TC did not change in YM-16638-administered squirrel monkeys (50 mg kg-1 daily for 3 weeks), but a significant decrease in serum TC was observed in cynomolgus monkeys (33% decrease at 30 mg kg-1 for 4 weeks) and rhesus monkeys (27% decrease at 30 mg kg-1 for 3 weeks) without any serious decrease in body weight. These results were consistent with those in a phase I study with human subjects. In contrast, serum alanine aminotransferase (ALT) level decreased in all animals after YM-16638 treatment. 5. From these results, we conclude that YM-16638 has a potent hypocholesterolaemic effect, but that this effect if species-specific and is only recognized clearly in human subjects and old-world monkeys.
Conserved Motif of CDK5RAP2 Mediates Its Localization to Centrosomes and the Golgi Complex (2010)

As the primary microtubule-organizing centers, centrosomes require gamma-tubulin for microtubule nucleation and organization. Located in close vicinity to centrosomes, the Golgi complex is another microtubule-organizing organelle in interphase cells. CDK5RAP2 is a gamma-tubulin complex-binding protein and functions in gamma-tubulin attachment to centrosomes. In this study, we find that CDK5RAP2 localizes to the Golgi complex in an ATP- and centrosome-dependent manner and associates with Golgi membranes independently of microtubules. CDK5RAP2 contains a centrosome-targeting domain with its core region highly homologous to the Motif 2 (CM2) of centrosomin, a functionally related protein in Drosophila. This sequence, referred to as the CM2-like motif, is also conserved in related proteins in chicken and zebrafish. Therefore, CDK5RAP2 may undertake a conserved mechanism for centrosomal localization. Using a mutational approach, we demonstrate that the CM2-like motif plays a crucial role in the centrosomal and Golgi localization of CDK5RAP2. Furthermore, the CM2-like motif is essential for the association of the centrosome-targeting domain to pericentrin and AKAP450. The binding with pericentrin is required for the centrosomal and Golgi localization of CDK5RAP2, whereas the binding with AKAP450 is required for the Golgi localization. Although the CM2-like motif possesses the activity of Ca(2+)-independent calmodulin binding, binding of calmodulin to this sequence is dispensable for centrosomal and Golgi association. Altogether, CDK5RAP2 may represent a novel mechanism for centrosomal and Golgi localization.
Refractive indices of laser nanocrystalline ceramics based on Y3Al5O12 (2003)

Refractive indices of the nanocrystalline Y3Al5O12 ceramic and a garnet single crystal of the same composition have been measured. In the visible and near IR range (0.4–1.064 μm), the prism method was used; in the medium IR range (2–6.2 μm), the interference method with the use of thin plates was applied. The refractive indices of these crystalline materials are practically the same over the entire spectral range studied and are described by the approximate formula proposed earlier for a single crystal. The parameters of the continuos-wave lasing in the nanocrystalline Y3Al5O12 ceramic doped with Nd3+ and Yb3+ ions measured recently are presented.
On the quality of service of failure detectors (2002)

We study the quality of service (QoS) of failure detectors. By QoS, we mean a specification that quantifies: (1) how fast the failure detector detects actual failures and (2) how well it avoids false detections. We first propose a set of QoS metrics to specify failure detectors for systems with probabilistic behaviors, i.e., for systems where message delays and message losses follow some probability distributions. We then give a new failure detector algorithm and analyze its QoS in terms of the proposed metrics. We show that, among a large class of failure detectors, the new algorithm is optimal with respect to some of these QoS metrics. Given a set of failure detector QoS requirements, we show how to compute the parameters of our algorithm so that it satisfies these requirements and we show how this can be done even if the probabilistic behavior of the system is not known. We then present some simulation results that show that the new failure detector algorithm provides a better QoS than an algorithm that is commonly used in practice. Finally, we suggest some ways to make our failure detector adaptive to changes in the probabilistic behavior of the network.
Film redistribution layer technology (2002)

This paper describes the design and process for an advanced card technology capable of achieving wiring densities of the order of 500-1000 in/sq. inch. It's unique features consist of using a photosensitive dielectric (PSD) redistribution layer to produce very small (2-4.0 mil) blind vias, as well as utilizing PCB signal and power planes for global interconnect of fine grid surface mount components (QFPs, SMA, and ICs). The process consists of subtractive etched power cores and/or additively plated signal cores. The subcomposite is completed using conventional PCB processing. The redistribution layer is added sequentially by coating and/or laminating a photosensitive dielectric and photoprocessing the blind vias. The circuitization of the redistribution layer is completed by a full additive plating process and/or electro pattern plating. A solder mask is applied, and Eutectic Solder is electroplated over the surface for component assembly. A key element of the technology that will allow the escape of high I/O components with a dense interconnecting grid (8.0-20.0 mils/200-500 microns), is the utilization of the signal and power planes in the subcomposite structure.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Interlayer nanoparticles of copper, nickel, and silver in Bi2Te3 (2009)

According to electronic micropictures and results of roentgen diffractometry (RD) in the Bi2Te3 metal system, nanodimensional fragments are formed in the van der Waals slot Te(1)-Te(1). These structural vacuum nanoreactors are filled not only with metal nanoparticles (Cu, Ni, and Ag) but also with formed semiconductor nanofragments and fractal surfaces on their basis. They are formed upon adhesion of diffusing atoms according to a mechanism specific to the known solid fractal structures. Their analysis based on the physical concept of fractals formed upon deposition of atoms in unlimited volume on crystal faces is carried out.
Soil greenhouse gas emissions from afforested organic soil croplands and cutaway peatlands (2024)

The effects of land-use and land-use change on soil greenhouse gas (GHG) fluxes are of concern due to Kyoto Protocol requirements. To quantify the soil GHG-fluxes of afforested organic soils in Finland, chamber measurements of soil CO 2 , CH 4 and N 2 O fluxes were made during the years 2002 to 2005 on twelve organic soil cropland and six cutaway peatland sites afforested 9 to 35 years ago. The annual soil CO 2 effluxes were statistically modelled using soil temperature as the driving variable and the annual CH 4 and N 2 O fluxes were estimated using the average fluxes during the measurement period. Soil CO 2 effluxes on afforested organic soil croplands varied from 207 to 539 g CO 2 -C m -2 a -1 and on cutaway peatlands from 276 to 479 g CO 2 -C m -2 a -1 . Both the afforested organic soil cropland and cutaway peatland sites acted mainly as small sinks for CH 4 ; the annual flux ranged from 0.32 to 0.61 g CH 4 -C m -2 . Afforested organic croplands emitted more N 2 O (from 0.1 to over 3.0 g N 2 O-N m -2 a -1 ) than cutaway peatland sites (from 0.01 to 0.48 g N 2 O-N m -2 a -1 ). Due to the decrease in soil CO 2 efflux, and no change in CH 4 and N 2 O fluxes, afforestation of organic croplands appears to decrease the greenhouse impact of these lands.
Nano-Sized Hollow Bump Array Generated by Single Femtosecond Laser Pulse (2003)

The generation of a nano-sized hollow bump array of gold thin film by uniformly spaced melting and inflation of the film induced by a single shot of four interfering fs laser beams is reported. The shape changed from a bump, to a bead on bump, to a standing bead on a hole, and finally to a hole, with the increase in fs laser fluence. The bump height, diameter, and shape as functions of laser fluence are shown. Moreover, the basic shape of the bump changed upon changing the number of interfering beams.
Study and discrimination of human cervical tissue images through multifractal analysis (2013)

We report here a study of confocal microscope images to classify cervical precancers by a multifractal analysis. This study is performed using an inverted confocal microscope with laser scanning fluorescence imaging. The periodic structure of collagen present in the stromal region of cervical tissue gets disordered with progress in grade of dysplasia. This disorder is investigated through the β-exponent of a Discrete Fourier Transform (DFT) of the confocal images, enabling us to discriminate between the lowest and highest grades of dysplasia in human cervical tissue sections. The Holder exponent from 2D images further classifies various grades of dysplasia from normal tissue sections though Gd3 and Gd1 are indistinguishable. DFT however, clearly distinguishes Gd3 from Gd1. In addition to stromal images, epithelial images were also investigated for better classification. The cellular density of epithelium increases with depth for various grades of dysplasia and is not uniform. The Holder exponent, which measures multifractality, is higher for dysplastic tissue sections than for normal ones because of the above morphological differences. Extraction of subtle fluctuations from optical images through multifractal studies promise to be a powerful diagnostic technique.
Oxygen Uptake after Major Abdominal Surgery (1991)

To examine the effect of an alpha-2 agonist, clonidine, on oxygen uptake and on the incidence of postoperative shivering, 28 patients presenting for major abdominal surgery were randomly assigned in a double-blind manner to one of two groups. Intraoperatively, 14 patients received 5 micrograms.kg-1 clonidine infused over 3 h (clonidine group), and 14 patients received placebo (placebo group). Oxygen uptake was measured continuously over the first 3 postoperative hours with a mass spectrometer system. Circulatory variables, esophageal temperature, and skin temperature were measured over the first 6 postoperative hours. Heart rate, mean arterial pressure, rate pressure product, and norepinephrine concentration were decreased in the clonidine group (P less than 2 x 10(-4)). There were no differences among groups in the incidence of shivering and in the rate of increase of esophageal temperature. By contrast, oxygen uptake was lower in the clonidine group (P = 4 x 10(-4)). This contrasting pattern may be secondary to a reduction in the intensity of mean muscular tremor in the clonidine group.
Glycochenodeoxycholate-induced lethal hepatocellular injury in rat hepatocytes. Role of ATP depletion and cytosolic free calcium. (1993)

Chenodeoxycholate is toxic to hepatocytes, and accumulation of chenodeoxycholate in the liver during cholestasis may potentiate hepatocellular injury. However, the mechanism of hepatocellular injury by chenodeoxycholate remains obscure. Our aim was to determine the mechanism of cytotoxicity by chenodeoxycholate in rat hepatocytes. At a concentration of 250 microM, glycochenodeoxycholate was more toxic than either chenodeoxycholate or taurochenodeoxycholate. Cellular ATP was 86% depleted within 30 min after addition of glycochenodeoxycholate. Fructose, a glycolytic substrate, maintained ATP concentrations at 50% of the initial value and protected against glycochenodeoxycholate cytotoxicity. ATP depletion in the absence of a glycolytic substrate suggested impairment of mitochondrial function. Indeed, glycochenodeoxycholate inhibited state 3 respiration in digitonin-permeabilized cells in a dose-dependent manner. After ATP depletion, a sustained rise in cytosolic free calcium (Cai2+) was observed. Removal of extracellular Ca2+ abolished the rise in Cai2+, decreased cellular proteolysis, and protected against cell killing by glycochenodeoxycholate. The results suggest that glycochenodeoxycholate cytotoxicity results from ATP depletion followed by a subsequent rise in Cai2+. The rise in Cai2+ leads to an increase in calcium-dependent degradative proteolysis and, ultimately, cell death. We conclude that glycochenodeoxycholate causes a bioenergetic form of lethal cell injury dependent on ATP depletion analogous to the lethal cell injury of anoxia.
Development of New Products and High Value Added Biopolymer from Softwoods by Chemical Modification - Quantitative Variation of Water-soluble Extracts from Coniferous Barks for Tannin-based Adhesives - (1996)

Extracts from bark have been studied with a view to producing water-proof wood adhesives. Lately many softwoods, such as radiata pine from New Zealand and larch from Siberia, Russia, have been imported and utilized, and their residual barks would be expecting as potential raw materials for something useful chemicals. The great effort toward utilization of bark extractives as a chemical feedstock has been made on a worldwide level. However few report has been done for the utilization of tree bark extractives in Korea. Hot-water extracts were prepared from barks of Japanese larch(Larix leptolepis). Siberian larch(Larix gmelinii) and Radiata pine(Pinus radiata). The effect of various factors, such as particle size, liquor ratio, extraction temperature, and reaction time, on the extractive yields was discussed. Particle sizes affected the hot-water extractives: the finer the particle size, the higher extractives and extract efficiency. Higher temperature and higher liquor ratio were more effective. Extractives from Japanese larch were relatively less than those from Siberian larch and Radiata pine barks. Formaldehyde precipitates was the highest in extractives of Radiata pine barks. It could be concluded that Siberian larch bark was the best raw material for tannin adhesives, because its extractive yield was higher than those of the other barks.
Chemopreventive Effect of a Xanthine Oxidase Inhibitor, 1′‐Acetoxychavicol Acetate, on Rat Oral Carcinogenesis (1996)

The effect of a xanthine oxidase inhibitor, 1'-acetoxychavicol acetate (ACA), on 4-nitroquinoline 1-oxide (4-NQO)-induced oral carcinogenesis was investigated in male F344 rats. All rats except those in the ACA-alone and untreated groups were given 4-NQO (20 ppm) In the drinking water for 8 weeks to induce oral cancer. Starting 1 week before the 4-NQO exposure, animals were fed diet containing 100 ppm or 500 ppm ACA for 10 weeks, followed by the basal diet without ACA for 22 weeks. Other groups were fed the diet containing ACA at 100 ppm or 500 ppm for 22 weeks, starting 1 week after the cessation of 4-NQO exposure. The remaining groups consisted of rats given 500 ppm ACA alone or untreated rats. At the termination of the experiment (32 weeks), the incidences of tongue neoplasms and preneoplastic lesions, polyamine levels in the tongue tissue, and cell proliferation activity estimated in terms of 5-bromodeoxyuridine (BrdU)-labeling index and by morphometric analysis of silver-stained nucleolar organizer regions' protein (AgNORs) were compared among the groups. Feeding of ACA at the two doses during initiation or postinitiation significantly decreased the development of tongue carcinoma (93-100% reduction, P < 0.001) and preneoplasia (43-50% reduction for hyperplasia and 34-48% reduction for dysplasia, P < 0.05). There were no such lesions in rats fed ACA alone or those in the untreated control group. The number of AgNORs per cell nucleus was significantly decreased by feeding of ACA at a high dose (500 ppm) (29% inhibition, P < 0.05). The BrdU-labeling index was also reduced by dietary administration of ACA (23-32% inhibition, P < 0.01). In addition, ACA feeding reduced tongue polyamine levels (35-40% inhibition, P < 0.05). These results indicate that ACA inhibited rat oral carcinogenesis, and such inhibition might be related to suppression of cell proliferation in the oral mucosa by the xanthine oxidase inhibitor.
Computer simulation of oxygen precipitation in CZ-silicon during rapid thermal anneals (1990)

A new computer model for the simulation of oxygen precipitation in conventional as well as rapid thermal anneals is presented. The kinetic part of the model combines chemical rate equations and a Fokker-Planck equation. This allows for an adequate description of both small and larger precipitate sizes. The model cran be fitted to experimental data reported by Hawkins and Lavine [1] concerning reduction of interstitial oxygen after a 950°C/1h - 1200°C/10h annealing cycle. If the annealing cycle is preceded by a short therma1 pulse (1200°C/2s)) retardation of oxygen precipitation is observed experimentally. In our simulations this can be explained by t he dissolution of small precipitates, which have formed during crystal growth.