gebhart/patrepeval huggingface dataset:
Polymorphic extracellular glucoamylase genes and their evolutionary origin in the yeast Saccharomyces diastaticus (1985)

DNA coding for extracellular glucoamylase genes STA1 and STA3 was isolated from DNA libraries of two Saccharomyces diastaticus strains, each carrying STA1 or STA3. Cells transformed with a plasmid carrying either the STA1 or STA3 gene secreted glucoamylases having the same enzymatic and immunological properties and the same electrophoretic mobilities in acrylamide gel electrophoresis as those of authentic glucoamylases. Southern blot analysis of genomic DNA from S. diastaticus and a glucoamylase-non-secreting yeast, Saccharomyces cerevisiae, revealed that the STA1 and STA3 loci of S. diastaticus showed a high degree of homology, and that both yeast species (S. diastaticus and S. cerevisiae) contained DNA segments highly homologous to those of the extracellular glucoamylase genes. Restriction maps of the homologous DNA segments suggested that the extracellular glucoamylase genes of S. diastaticus may have arisen from recombination among the resident DNA segments in S. cerevisiae.
Maleation of linear low‐density polyethylene by reactive processing (1992)

Abstract The reaction of maleic anhydride (MAH) with molten 2 MI poly(ethylene‐ co ‐butene‐1) (LLDPE) at 160°C in the presence of peroxyesters ( t 1/2 < 10 s) as catalysts resulted in the formation of a mixture of cross‐linked and trichlorobenzene‐soluble LLDPE‐ g ‐MAH. The soluble fraction constituted more than 50% of the mixture and had an MI of 0.0 and an MAH content ranging from 0.3 to 1.8 wt %. The presence of tri(nonylphenyl) phosphite (TNPP) in the LLDPE–MAH– t ‐butyl peroctoate ( t BPO) reaction at 160°C increased the MI of the soluble product to 0.7–2. The amount of soluble polymer increased at higher TNPP concentrations while its MAH content ranged from 0.05 to 0.54 wt %, with most contents in the 0.2–0.3 wt % range. The color development that usually occurs in polyolefin–MAH reactions was reduced by the presence of TNPP. However, the reaction of TNPP with the peroxide and from the thermal decomposition thereof reduced the availability of the excited species necessary for the appendage of MAH units onto the polyofin.
Recovering shape and spatially-varying surface reflectance under unknown illumination (2016)

We present a novel integrated approach for estimating both spatially-varying surface reflectance and detailed geometry from a video of a rotating object under unknown static illumination. Key to our method is the decoupling of the recovery of normal and surface reflectance from the estimation of surface geometry. We define an apparent normal field with corresponding reflectance for each point (including those not on the object's surface) that best explain the observations. We observe that the object's surface goes through points where the apparent normal field and corresponding reflectance exhibit a high degree of consistency with the observations. However, estimating the apparent normal field requires knowledge of the unknown incident lighting. We therefore formulate the recovery of shape, surface reflectance, and incident lighting, as an iterative process that alternates between estimating shape and lighting, and simultaneously recovers surface reflectance at each step. To recover the shape, we first form an initial surface that passes through locations with consistent apparent temporal traces, followed by a refinement that maximizes the consistency of the surface normals with the underlying apparent normal field. To recover the lighting, we rely on appearance-from-motion using the recovered geometry from the previous step. We demonstrate our integrated framework on a variety of synthetic and real test cases exhibiting a wide variety of materials and shape.
Perceptual Framework For A Modern Left-Turn Collision Warning System (2009)

Most of the collision warning systems currently available in the automotive market are mainly designed to warn against imminent rear-end and lane-changing collisions. No collision warning system is commercially available to warn against imminent turning collisions at intersections, especially for left-turn collisions when a driver attempts to make a left-turn at either a signalized or non-signalized intersection, conflicting with the path of other approaching vehicles traveling on the opposite-direction traffic stream. One of the major factors that lead to left-turn collisions is the human error and misjudgment of the driver of the turning vehicle when perceiving the speed and acceleration of other vehicles traveling on the opposite-direction traffic stream; therefore, using a properly-designed collision warning system will likely reduce, or even eliminate, this type of collisions by reducing human error. This paper introduces perceptual framework for a proposed collision warning system that can detect imminent left-turn collisions at intersections. The system utilizes a commercially-available detection sensor (either a radar sensor or a laser detector) to detect approaching vehicles traveling on the opposite-direction traffic stream and calculate their speeds and acceleration rates to estimate the time-tocollision and compare that time to the time required for the turning vehicle to clear the intersection. When calculating the time required for the turning vehicle to clear the intersection, consideration is given to the perception-reaction time of the driver of the turning vehicle, which is the time required by the driver to perceive the message given by the warning system and react to it by engaging the throttle. A regression model was developed to estimate perception-reaction time based on age and gender of the driver of the host vehicle. Desired acceleration rate selected by the driver of the turning vehicle, when making the left-turn movement, is another human factor that is considered by the system. Another regression model was developed to estimate the acceleration rate selected by the driver of the turning vehicle based on driver-s age and gender as well as on the location and speed of the nearest approaching vehicle along with the maximum acceleration rate provided by the mechanical characteristics of the turning vehicle. By comparing time-to-collision with the time required for the turning vehicle to clear the intersection, the system displays a message to the driver of the turning vehicle when departure is safe. An application example is provided to illustrate the logic algorithm of the proposed system.
Calibrating OPC models using asymmetric structures (2006)

Good OPC model calibration structures should be representative of and span the dimensions and layout forms that will be found in the product on which the model will be applied. If model fitting is done using edge placement (EPE) methods, only symmetric structures can be used and this constrains the model fitter to a classic but limited set of calibration structures. The most critical features, such as those from a bit cell tend to be asymmetric. While asymmetric structures have typically been used for model verification, using them in model calibration structures provides more degrees of freedom for the calibration test structures to capture two dimensional behavior. This produces more robust, accurate models which yield better quality corrections on wafer. During process development models are re-calibrated as the process is adjusted and optimized. In some cases particularly important critical configurations can be added to the calibration set to insure maximum accuracy on those features. As these configurations are extracted from real designs, they are rarely symmetric. This paper describes how by using a CD-based rather than an edge-placement based modeling approach, OPC models can be created from asymmetric, more product-like type structures, and demonstrates how this can allow better predictability on other verification structures. The paper will also review the two types of model forms commonly used (Constant and Variable Threshold models) and compare their performance while using asymmetric calibration structures.
Methods of reduced-complexity overlapped block motion compensation (2002)

Overlapped block motion compensation (OBMC) can significantly improve upon the prediction performance of conventional block motion compensation, though at the cost of increased decoder computational complexity. This paper analyzes the complexity costs of OBMC, and offers several modifications to OBMC that significantly reduce its decoder complexity while retaining most of the OBMC performance gain.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Synthesis of the First C3 Ribosylated Imidazo[1,2-<i>a</i>]pyridine C-Nucleoside by Enantioselective Construction of the Ribose Moiety (1998)

The metabolic instability of the glycosidic linkage in 2,5,6-trichloro-1-(β-d-ribofuranosyl)benzimidazole prompted us to synthesize the structurally related C-nucleoside 2,6,7-trichloro-3-(β-d-ribofuranosyl)imidazo[1,2-a]pyridine. Synthesis of this first C3-ribofuranosylimidazo[1,2-a]pyridine was accomplished by developing a modification of existing iodocyclization methodology for obtaining a 1‘,4‘-syn furanosyl precursor, without an extensive protection scheme. This 1‘,4‘-syn precursor was elaborated into the desired ribofuranosyl C-nucleoside. X-ray crystallography was used to unambiguously determine structure and absolute stereochemistry of this C-nucleoside.
Biomass and Phosphorus Uptake Responses of Maize to Phosphorus Application in Three Acid Soils from Southern Cameroon (2008)

Abstract A phosphorus (P) greenhouse experiment was carried out with maize (Zea Mays L.) using surface horizons of three contrasted acid soils from southern Cameroon. The objectives were (i) to assess causal factors of maize differential growth and P uptake and (ii) to explore plant–soil interactions in acid soils under increasing P supply. Shoot and root dry‐matter yield and P uptake were significantly influenced by soil type and P rate (P<0.000), but the interaction was not significant. Soil properties that significantly (P<0.05) influenced maize growth variables were available P, soil pH, exchangeable bases [calcium (Ca), magnesium (Mg)], and exchangeable aluminium (Al). Data ordination through principal‐component analysis highlighted a four‐component model that accounted for 88.1% of total system variance (TSV) and summarized plant reaction in acid soil condition. The first component, associated with 36.1% of TSV, pointed at increasing root–shoot ratio with increasing soil acidity and exchangeable Al. The second component (24.6% of TSV) highlighted soil labile P pool increase as a function of P rate. The third and fourth components reflected nitrogen (N) accumulation in soils and soil texture variability, respectively. Keywords: Acid soilmaize growthP fertilizationsoil propertiessouth Cameroon
In vitro permeation of diclofenac sodium from novel microemulsion formulations through rabbit skin (2005)

Abstract In order to increase topical penetration of the nonsteroidal anti‐inflammatory drug, diclofenac sodium, new microemulsion formulations were prepared to increase drug solubility and in vitro penetration of the drug. The influence of dimethyl sulfoxide and propylene glycol were also investigated as enhancers on the in vitro penetration of diclofenac sodium using Franz diffusion cells using excised dorsal rabbit skin. Factorial randomized design was performed to analyze the results of in vitro permeation studies. Microemulsions prepared with isopropyl alcohol were superior to those prepared with propanol. Enhancers had different effects depending on the formulation. Propylene glycol was superior to dimethyl sulfoxide when incorporated into isopropyl alcohol microemulsion, whereas dimethyl sulfoxide was superior to propylene glycol in propanol microemulsions. There were no observable histopathological differences between the skin of the control group and the treated groups at the light microscope level due to swelling of the skin tissue. The present study shows that microemulsion formulations containing isopropyl alcohol as co‐surfactant and propylene glycol as enhancer represent a promising approach for a topical vehicle for diclofenac sodium. Drug Dev. Res. 65:17–25, 2005. © 2005 Wiley‐Liss, Inc.
Minimum residual methods for cloth simulation (2014)

This paper presents a new method for cloth simulation which improves the position based dynamics method, first popularized for games by Jakobsen. We are replacing the widely used iterative relaxation techniques (Jacobi and Gauss-Seidel) with conjugate gradient like methods (Minimum Residual and Conjugate Residuals) and show that they have better convergence and stability properties. They are also as easy to parallelize as Jacobi and can be optimized to faster versions, well suited for real-time applications. We tested our method on multi-core processors and obtained considerable speedups while maintaining iteration count and accuracy.
Activation of PPARγ by curcumin inhibits Moser cell growth and mediates suppression of gene expression of cyclin D1 and EGFR (2004)

Colorectal cancer is a leading cause of cancer-related morbidity and mortality in the United States. Curcumin, the yellow pigment in turmeric, possesses inhibitory effects on growth of a variety of tumor cells by reducing cell proliferation and inducing apoptosis. Effects of the peroxisome proliferator-activated receptor-gamma (PPARgamma) on stimulating cell differentiation and on inducing cell cycle arrest have attracted attention from the perspective of treatment and prevention of cancer. The aim of this study was to elucidate the mechanisms by which curcumin inhibits colon cancer cell growth. In the present report, we observed that curcumin, in a dose-dependent manner, inhibited the growth of Moser cells, a human colon cancer-derived cell line, and stimulated the trans-activating activity of PPARgamma. Further studies demonstrated that activation of PPARgamma was required for curcumin to inhibit Moser cell growth. Activation of PPARgamma mediated curcumin suppression of the expression of cyclin D1, a critical protein in the cell cycle, in Moser cells. In addition, curcumin blocked EGF signaling by inhibiting EGF receptor (EGFR) tyrosine phosphorylation and suppressing the gene expression of EGFR mediated by activation of PPARgamma. In addition to curcumin reduction of the level of phosphorylated PPARgamma, inhibition of cyclin D1 expression played a major and significant role in curcumin stimulation of PPARgamma activity in Moser cells. Taken together, our results demonstrated for the first time that curcumin activation of PPARgamma inhibited Moser cell growth and mediated the suppression of the gene expression of cyclin D1 and EGFR. These results provided a novel insight into the roles and mechanisms of curcumin in inhibition of colon cancer cell growth and potential therapeutic strategies for treatment of colon cancer.
Defective synthesis of envelope proteins by temperature-sensitive mutants representing complementation groups B and D of respiratory syncytial virus (1991)

The phenotypes of two complementing temperature-sensitive (ts) mutants of respiratory syncytial (RS) virus indicate that the mutational lesions involve the attachment (G) and matrix (M) proteins of the viral envelope. Synthesis of the G protein was affected in cells infected with mutant tsA2 (complementation group B); the p50 precursor of the G protein was synthesized normally, but further maturation to the fully glycosylated form was defective at 39 degrees C. A non-ts alteration in the efficiency of cleavage of the F0 precursor to the F1 and F2 subunits of the fusion protein was also observed in tsA2-infected cells, which is consistent with the aberrant non-syncytial plaque morphology induced by tsA2 in certain cells. In cells infected with mutant tsN1 (complementation group D) the M protein disappeared from the soluble cytoplasmic fraction soon after synthesis at 39 degrees C and had a slightly decreased electrophoretic mobility. The M protein of non-ts revertants was stable at 39 degrees C, which links the defect in M protein stability with the tsN1 phenotype. However, the aberrant mobility phenotype remained, suggesting pseudoreversion. These results assign two of the eight complementation groups of ts mutants of RS virus.
Modified Nucleosides. II.<sup>1</sup>Economical Synthesis of 2′,3′-Dideoxycytidine (1992)

Abstract An economical two pot synthesis of 2′,3′-dideoxycytidine (2) from N4-acetyl-cytidine (4) has been developed. The key feature of this sequence is the in situ reductive elimination of a mixture of 1-(3-bromo-3-deoxy-2,5-di-O-acetyl-β-D-xylofuranosyl)-N4-acetylcytosine (5) and 1-(2-bromo-3-deoxy-3,5-di-O-acetyl-β-D-arabinofuranosyl)-N4-acetylcytosine (6) and subsequent hydrogenation of the resultant olefin over palladised charcoal.
Solution Structure of an Intramolecular Pyrimidine−Purine−Pyrimidine Triplex Containing an RNA Third Strand (1998)

We have used two-dimensional NMR spectroscopy to study an intramolecular pyrimidine−purine−pyrimidine triplex composed of a Watson−Crick paired DNA duplex and an RNA third strand connected by two hexakis(ethylene glycol) linkers. The solution structure of the triplex was calculated using restrained molecular dynamics and relaxation matrix refinement. The overall helical structure of the Watson−Crick duplex part of the triplex more closely resembles B-DNA than A-DNA. Thus, binding of a third-strand RNA in the major groove does not cause a structural transition toward A-DNA. Both the spectroscopic data and the calculated structures show a narrowing of the minor groove relative to an all-DNA triplex of the same sequence. The sugar puckers of the DNA residues are mostly C2‘-endo while the RNA third strand residues show only partial C3‘-endo character.
Distribution of voltage-gated sodium channel ?-subunit and ?-subunit mRNAs in human hippocampal formation, cortex, and cerebellum (2000)

The distribution of mRNAs encoding voltage-gated sodium channel alpha subunits (I, II, III, and VI) and beta subunits (beta1 and beta2) was studied in selected regions of the human brain by Northern blot and in situ hybridisation experiments. Northern blot analysis showed that all regions studied exhibited heterogenous expression of sodium channel transcripts. In situ hybridisation experiments confirmed these findings and revealed a predominantly neuronal distribution. In the parahippocampal gyrus, subtypes II and VI and the beta-subunit mRNAs exhibited robust expression in the granule cells of the dentate gyrus and pyramidal cell layer of the hippocampus. Subtypes I and III showed moderate expression in granule cells and low expression in the pyramidal cell layer. Distinct expression patterns were also observed in the cortical layers of the middle frontal gyrus and in the entorhinal cortex. In particular, all subtypes exhibited higher levels of expression in cortical layers III, V, and VI compared with layers I and II. All subtypes were expressed in the granular layer of the cerebellum, whereas specific expression of subtypes I, VI, beta1, and beta2 mRNAs was observed in Purkinje cells. Subtypes I, VI, and beta1 mRNAs were expressed, at varying levels, in the pyramidal cells of the deep cerebellar nuclei. These data indicate that, as in rat, human brain sodium channel mRNAs have a distinct regional distribution, with individual cell types expressing different compliments of sodium channels. The differential distribution of sodium channel subtypes suggest that they have distinct roles that are likely to be of paramount importance in maintaining the functional heterogeneity of central nervous system neurons.
House dust exposure mediates gut microbiome <i>Lactobacillus</i> enrichment and airway immune defense against allergens and virus infection (2013)

Exposure to dogs in early infancy has been shown to reduce the risk of childhood allergic disease development, and dog ownership is associated with a distinct house dust microbial exposure. Here, we demonstrate, using murine models, that exposure of mice to dog-associated house dust protects against ovalbumin or cockroach allergen-mediated airway pathology. Protected animals exhibited significant reduction in the total number of airway T cells, down-regulation of Th2-related airway responses, as well as mucin secretion. Following dog-associated dust exposure, the cecal microbiome of protected animals was extensively restructured with significant enrichment of, amongst others, Lactobacillus johnsonii. Supplementation of wild-type animals with L. johnsonii protected them against both airway allergen challenge or infection with respiratory syncytial virus. L. johnsonii-mediated protection was associated with significant reductions in the total number and proportion of activated CD11c(+)/CD11b(+) and CD11c(+)/CD8(+) cells, as well as significantly reduced airway Th2 cytokine expression. Our results reveal that exposure to dog-associated household dust results in protection against airway allergen challenge and a distinct gastrointestinal microbiome composition. Moreover, the study identifies L. johnsonii as a pivotal species within the gastrointestinal tract capable of influencing adaptive immunity at remote mucosal surfaces in a manner that is protective against a variety of respiratory insults.
N-Type Bismuth Telluride Nanocomposite Materials Optimization for Thermoelectric Generators in Wearable Applications (2019)

Thermoelectric materials could play a crucial role in the future of wearable electronic devices. They can continuously generate electricity from body heat. For efficient operation in wearable systems, in addition to a high thermoelectric figure of merit, <i>zT</i>, the thermoelectric material must have low thermal conductivity and a high Seebeck coefficient. In this study, we successfully synthesized high-performance nanocomposites of n-type Bi<sub>2</sub>Te<sub>2.7</sub>Se<sub>0.3</sub>, optimized especially for body heat harvesting and power generation applications. Different techniques such as dopant optimization, glass inclusion, microwave radiation in a single mode microwave cavity, and sintering conditions were used to optimize the temperature-dependent thermoelectric properties of Bi<sub>2</sub>Te<sub>2.7</sub>Se<sub>0.3</sub>. The effects of these techniques were studied and compared with each other. A room temperature thermal conductivity as low as 0.65 W/mK and high Seebeck coefficient of -297 μV/K were obtained for a wearable application, while maintaining a high thermoelectric figure of merit, <i>zT</i>, of 0.87 and an average <i>zT</i> of 0.82 over the entire temperature range of 25 °C to 225 °C, which makes the material appropriate for a variety of power generation applications.