gebhart/patrepeval huggingface dataset:
Grafting BSA onto Poly[(L‐lactide)‐co‐carbonate] Microspheres by Click Chemistry (2008)

Model protein bovine serum albumin (BSA) was covalently grafted onto poly[(L-lactide)-co-carbonate] microsphere surfaces by "click chemistry." The grafting was confirmed by confocal laser scanning microscopy and X-ray photoelectron spectroscopy. The maximum amount of surface-grafted BSA was 45 mg x g(-1). The secondary structure of the grafted BSA was analyzed by FTIR and the results demonstrated that the grafting did not affect protein structure. This strategy can also be used on microspheres prepared from poly(L-lactide)/poly[(L-lactide)-co-carbonate] blend materials.
Codon usage bias from tRNA's point of view: Redundancy, specialization, and efficient decoding for translation optimization (2004)

The selection-mutation-drift theory of codon usage plays a major role in the theory of molecular evolution by explaining the co-evolution of codon usage bias and tRNA content in the framework of translation optimization. Because most studies have focused only on codon usage, we analyzed the tRNA gene pool of 102 bacterial species. We show that as minimal generation times get shorter, the genomes contain more tRNA genes, but fewer anticodon species. Surprisingly, despite the wide G+C variation of bacterial genomes these anticodons are the same in most genomes. This suggests an optimization of the translation machinery to use a small subset of optimal codons and anticodons in fast-growing bacteria and in highly expressed genes. As a result, the overrepresented codons in highly expressed genes tend to be the same in very different genomes to match the same most-frequent anticodons. This is particularly important in fast-growing bacteria, which have higher codon usage bias in these genes. Three models were tested to understand the choice of codons recognized by the same anticodons, all providing significant fit, but under different classes of genes and genomes. Thus, co-evolution of tRNA gene composition and codon usage bias in genomes seen from tRNA's point of view agrees with the selection-mutation-drift theory. However, it suggests a much more universal trend in the evolution of anticodon and codon choice than previously thought. It also provides new evidence that a selective force for the optimization of the translation machinery is the maximization of growth.
Preferential Heterodimer Formation by Isolated Leucine Zippers from Fos and Jun (1989)

The products of the nuclear oncogenes fos and jun are known to form heterodimers that bind to DNA and modulate transcription. Both proteins contain a leucine zipper that is important for heterodimer formation. Peptides corresponding to these leucine zippers were synthesized. When mixed, these peptides preferentially form heterodimers over homodimers by at least 1000-fold. Both homodimers and the heterodimer are parallel alpha helices. The leucine zipper regions from Fos and Jun therefore correspond to autonomous helical dimerization sites that are likely to be short coiled coils, and these regions are sufficient to determine the specificity of interaction between Fos and Jun. The Fos leucine zipper forms a relatively unstable homodimer. Instability of homodimers provides a thermodynamic driving force for preferential heterodimer formation.
Weight-Based, Low-Dose Pediatric Whole-Body PET/CT Protocols (2009)

Low-dose PET/CT protocols for 11 patient weight categories were developed. The proposed protocols offer an initial set of acquisition parameters for pediatric PET/CT. The use of multiple categories allows for the continued refinement of dose-reduction parameters to minimize dose while maintaining image quality across the range of pediatric patient sizes.
An Adaptive Coding Technique For PAPR Reduction (2007)

In this work, we present an adaptive technique to reduce high peak-to-average power ratio in coded orthogonal frequency division multiplexing. High peak-to-average power ratio has been a primary hurdle for the use of orthogonal frequency division multiplexing in low cost applications. Our coding approach for reduction of peak-to-average power ratio combines the error correction capability of the channel encoder and achieves peak-to-average power ratio reduction in the OFDM system. Our technique is easily implemented in terms of encoding as well as decoding. We develop analytical analysis of the maximum peak-to-average power ratio reduction achievable by this method. We consider the effect on bit error rate based on general analysis of antipodal signals.
In Situ RT-PCR and Hybridization Techniques (2003)

In situ polymerase chain reaction (PCR) is a very powerful tool, which enhances our ability to detect minute quantities of a rare, single copy number, target nucleic acid sequences in freshly frozen or paraffin-embedded intact cells or tissue sections (1–10). In 1986, the introduction of PCR methods opened new horizons and revolutionized research in all areas of molecular biology (11,12). Dr. Hasse and his coworkers in 1990 used multiple primers and successfully amplified the target nucleic acid sequences in intact cells by combining a traditional in situ hybridization protocol with a powerful PCR technology (13).
Molecular Determinants of AHPN (CD437)-Induced Growth Arrest and Apoptosis in Human Lung Cancer Cell Lines (1998)

6-[3-(1-Adamantyl)-4-hydroxyphenyl]-2-naphthalene carboxylic acid (AHPN or CD437), originally identified as a retinoic acid receptor gamma-selective retinoid, was previously shown to induce growth inhibition and apoptosis in human breast cancer cells. In this study, we investigated the role of AHPN/CD437 and its mechanism of action in human lung cancer cell lines. Our results demonstrated that AHPN/CD437 effectively inhibited lung cancer cell growth by inducing G0/G1 arrest and apoptosis, a process that is accompanied by rapid induction of c-Jun, nur77, and p21(WAF1/CIP1). In addition, we found that expression of p53 and Bcl-2 was differentially regulated by AHPN/CD437 in different lung cancer cell lines and may play a role in regulating AHPN/CD437-induced apoptotic process. On constitutive expression of the c-JunAla(63,73) protein, a dominant-negative inhibitor of c-Jun, in A549 cells, nur77 expression and apoptosis induction by AHPN/CD437 were impaired, whereas p21(WAF1/CIP1) induction and G0/G1 arrest were not affected. Furthermore, overexpression of antisense nur77 RNA in A549 and H460 lung cancer cell lines largely inhibited AHPN/CD437-induced apoptosis. Thus, expression of c-Jun and nur77 plays a critical role in AHPN/CD437-induced apoptosis. Together, our results reveal a novel pathway for retinoid-induced apoptosis and suggest that AHPN/CD437 or analogs may have a better therapeutic efficacy against lung cancer.
What you should know about simulation and derivatives (2008)

Abstract Derivatives (or gradients) are important for both sensitivity analysis and optimization, and in simulation models, these can often be estimated efficiently using various methods other than brute‐force finite differences. This article briefly summarizes the main approaches and discusses areas in which the approaches can most fruitfully be applied: queueing, inventory, and finance. In finance, the focus is on derivatives of another sort. © 2008 Wiley Periodicals, Inc. Naval Research Logistics, 2008
A self-powered, one-step chip for rapid, quantitative and multiplexed detection of proteins from pinpricks of whole blood (2010)

We describe an automated, self-powered chip based on lateral flow immunoassay for rapid, quantitative, and multiplex protein detection from pinpricks of whole blood. The device incorporates on-chip purification of blood plasma by employing inertial forces to focus blood cells away from the assay surface, where plasma proteins are captured and detected on antibody "barcode" arrays. Power is supplied from the capillary action of a piece of adsorbent paper, and sequentially drives, over a 40 minute period, the four steps required to capture serum proteins and then develop a multiplex immunoassay. An 11 protein panel is assayed from whole blood, with high sensitivity and high reproducibility. This inexpensive, self-contained, and easy to operate chip provides a useful platform for point-of-care diagnoses, particularly in resource-limited settings.
Kinetics of phenolic polymerization catalyzed by peroxidase in organic media (1995)

Phenolic polymerization was carried out by enzymatic catalysis in organic media, and its kinetics was studied by using high-pressure liquid chromatography (HPLC). Phenols and aromatic amines with electron-withdrawing groups could hardly be polymerized by HRP catalysis, but phenols and aromatic amines with electron-donating groups could easily be polymerized. The reaction rate of either the para-substituted substrate or meta-substituted substrate was higher than that of ortho-substituted substrate. When ortho-position of hydroxy group of phenols was occupied by an electron-donating group and if another electron-donating group occupied para-position of hydroxy group, the reaction rate increased. Horseradish peroxidase and lactoperoxidase could easily catalyze the polymerization, but chloroperoxidase and laccase failed to yield polymers. Metallic ions such as Mn(2+), Fe(2+), or Fe(3+), and Cu(2+) could poison horseradish peroxidase to various extents, but ions such as Co(2+), Cd(2+), Zn(2+), and K(+) were not found to inhibit the reaction. (c) 1995 John Wiley & Sons, Inc.
Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases (2013)

RNA-guided endonucleases (RGENs), derived from the prokaryotic adaptive immune system known as CRISPR/Cas, enable targeted genome engineering in cells and organisms. RGENs are ribonucleoproteins that consist of guide RNA and Cas9, a protein component originated from Streptococcus pyogenes. These enzymes cleave chromosomal DNA, whose sequence is complementary, to guide RNA in a targeted manner, producing site-specific DNA double-strand breaks (DSBs), the repair of which gives rise to targeted genome modifications. Despite broad interest in RGEN-mediated genome editing, these nucleases are limited by off-target mutations and unwanted chromosomal translocations associated with off-target DNA cleavages. Here, we show that off-target effects of RGENs can be reduced below the detection limits of deep sequencing by choosing unique target sequences in the genome and modifying both guide RNA and Cas9. We found that both the composition and structure of guide RNA can affect RGEN activities in cells to reduce off-target effects. RGENs efficiently discriminated on-target sites from off-target sites that differ by two bases. Furthermore, exome sequencing analysis showed that no off-target mutations were induced by two RGENs in four clonal populations of mutant cells. In addition, paired Cas9 nickases, composed of D10A Cas9 and guide RNA, which generate two single-strand breaks (SSBs) or nicks on different DNA strands, were highly specific in human cells, avoiding off-target mutations without sacrificing genome-editing efficiency. Interestingly, paired nickases induced chromosomal deletions in a targeted manner without causing unwanted translocations. Our results highlight the importance of choosing unique target sequences and optimizing guide RNA and Cas9 to avoid or reduce RGEN-induced off-target mutations.
Synthesis of blood-group substances. Part 11. Synthesis of the trisaccharide O-α-D-galactopyranosyl-(1 → 3)-O-β-D-galactopyranosyl-(1 → 4)-2-acetamido-2-deoxy-D-glucopyranose (1981)

Reaction of 2,3,4,6-tetra-O-acetyl-α-D-galactopyranosyl bromide with benzyl 2-acetamido-3,6-di-O-benzyl-2-deoxy-α-D-glucopyranoside in 1,2-dichloroethane in the presence of mercuric bromide and molecular sieves (4 Å) provided after O-deacetylation crystalline benzyl 2-acetamido-3,6-di-O-benzyl-2-deoxy-4-O-(β-D-galacto pyranosyl)-α-D-glucopyranoside. Acetonation followed by benzylation and mild acid hydrolysis provided crystaline benzyl 2-acetamido-4-O-(2,6-di-O-benzyl-β-D-galactopyranosyl)-3,6-di-O-benzyl-2-deoxy-α-D-glucopyranoside. Reaction of this diol with 1-O-(N-methyl) acetimidyl-2,3,4,6-tetra-O-benzyl-β-D-galactopyranose in nitromethane in the presence of toluene-p-sulphonic acid regiospecifically gave the derivative (15). The title trisaccharide was obtained after catalytic hydrogenolysis. The alcohol benzyl 2-acetamido-4-O-(2,3,6-tri-O-benzyl-β-D-galactopyranosyl)-3,6-di-O-benzyl-2-deoxy-α-D-glucopyranoside was found to be unreactive under the same conditions.
Suppression of Murine Endotoxin Response by E5531, a Novel Synthetic Lipid A Antagonist (1998)

As a consequence of blood-borne bacterial sepsis, endotoxin or lipopolysaccharide (LPS) from the cell walls of gram-negative bacteria can trigger an acute inflammatory response, leading to a series of pathological events and often resulting in death. To block this inflammatory response to endotoxin, a novel lipid A analogue, E5531, was designed and synthesized as an LPS antagonist, and its biological properties were examined in vitro and in vivo. In murine peritoneal macrophages, E5531 inhibited the release of tumor necrosis factor alpha (TNF-alpha) by Escherichia coli LPS with a 50% inhibitory concentration (IC50) of 2.2 nM, while E5531 elicited no significant increases in TNF-alpha on its own. In support of a mechanism consistent with antagonism of binding to a cell surface receptor for LPS, E5531 inhibited equilibrium binding of radioiodinated LPS ([125I]2-(r-azidosalicylamido)-1, 3'-dithiopropionate-LPS) to mouse macrophages with an IC50 of 0.50 microM. E5531 inhibited LPS-induced increases in TNF-alpha in vivo when it was coinjected with LPS into C57BL/6 mice primed with Mycobacterium bovis bacillus Calmette-Guérin (BCG). In this model, the efficacy of E5531 was inversely correlated to the LPS challenge dose, consistent with a competitive antagonist-like mechanism of action. Blockade of the inflammatory response by E5531 could further be demonstrated in other in vivo models: E5531 protected BCG-primed mice from LPS-induced lethality in a dose-dependent manner and suppressed LPS-induced hepatic injury in Propionibacterium acnes-primed or galactosamine-sensitized mice. These results argue that the novel synthetic lipid A analogue E5531 can antagonize the action of LPS in in vitro and suppress the pathological effects of LPS in vivo in mice.
Dependence on doping type (p/n) of the water vapor oxidation of high-gap AlxGa1−xAs (1992)

The oxidation (H2O vapor+N2 carrier gas, 425–525 °C) of high-gap AlxGa1−xAs of different doping types (p and n) is characterized by oxide depth measurements utilizing scanning electron microscopy. The conductivity type is found to affect significantly the oxidation rate, with p-type samples oxidizing more rapidly than n-type samples. Classical oxidation theory is employed to explain these phenomena which are related to the position of the Fermi level in the samples.
A New Connected-Component Labeling Algorithm (2015)

This paper presents a new connected component labeling algorithm. The proposed algorithm scans image lines every three lines and processes pixels three by three. When processing the current three pixels, we also utilize the information obtained before to reduce the repeated work for checking pixels in the mask. Experimental results demonstrated that our method is more efficient than the fastest conventional labeling algorithm.
Thrombospondin-1 limits ischemic tissue survival by inhibiting nitric oxide–mediated vascular smooth muscle relaxation (2006)

The nitric oxide (NO)/cGMP pathway, by relaxing vascular smooth muscle cells, is a major physiologic regulator of tissue perfusion. We now identify thrombospondin-1 as a potent antagonist of NO for regulating F-actin assembly and myosin light chain phosphorylation in vascular smooth muscle cells. Thrombospondin-1 prevents NO-mediated relaxation of precontracted vascular smooth muscle cells in a collagen matrix. Functional magnetic resonance imaging demonstrated that an NO-mediated increase in skeletal muscle perfusion was enhanced in thrombospondin-1-null relative to wild-type mice, implicating endogenous thrombospondin-1 as a physiologic antagonist of NO-mediated vasodilation. Using a random myocutaneous flap model for ischemic injury, tissue survival was significantly enhanced in thrombospondin-1-null mice. Improved flap survival correlated with increased recovery of oxygen levels in the ischemic tissue of thrombospondin-1-null mice as measured by electron paramagnetic resonance oximetry. These findings demonstrate an important antagonistic relation between NO/cGMP signaling and thrombospondin-1 in vascular smooth muscle cells to regulate vascular tone and tissue perfusion.
Ovicidal and Adulticidal Effects of Eugenia caryophyllata Bud and Leaf Oil Compounds on Pediculus capitis (2003)

The toxicity of Eugenia caryophyllata bud and leaf oil-derived compounds (acetyleugenol, beta-caryophyllene, eugenol, alpha-humulene, and methyl salicylate) and congeners of eugenol (isoeugenol and methyleugenol) against eggs and females of Pediculus capitis was examined using direct contact application and fumigation methods and compared with those of the widely used delta-phenothrin and pyrethrum. In a filter paper diffusion bioassay with female P. capitis, the pediculicidal activity of the Eugenia bud and leaf oils was comparable to those of delta-phenothrin and pyrethrum on the basis of LT(50) values at 0.25 mg/cm(2). At 0.25 mg/cm(2), the compound most toxic to female P. capitis was eugenol followed by methyl salicylate. Acetyleugenol, beta-caryophyllene, alpha-humulene, isoeugenol, and methyleugenol were not effective. Eugenol at 0.25 mg/cm(2) was as potent as delta-phenothrin and pyrethrum but was slightly less effective than the pyrethroids at 0.125 mg/cm(2). Against P. capitis eggs, methyl salicylate and eugenol were highly effective at 0.25 and 1.0 mg/cm(2), respectively, whereas little or no activity at 5 mg/cm(2) was observed with the other test compounds as well as with delta-phenothrin and pyrethrum. In fumigation tests with female P. capitis at 0.25 mg/cm(2), eugenol and methyl salicylate were more effective in closed cups than in open ones, indicating that the effect of the compounds was largely due to action in the vapor phase. Neither delta-phenothrin nor pyrethrum exhibited fumigant toxicity. The Eugenia bud and leaf essential oils, particularly eugenol and methyl salicylate, merit further study as potential P. capitis control agents or lead compounds.
Dietary intake and cell membrane levels of long-chain n-3 polyunsaturated fatty acids and the risk of primary cardiac arrest (1995)

<h3>Objective.</h3> —To assess whether the dietary intake of long-chain n-3 polyunsaturated fatty acids from seafood, assessed both directly and indirectly through a biomarker, is associated with a reduced risk of primary cardiac arrest. <h3>Design.</h3> —Population-based case-control study. <h3>Setting.</h3> —Seattle and suburban King County, Washington. <h3>Participants</h3> —A total of 334 case patients with primary cardiac arrest, aged 25 to 74 years, attended by paramedics during 1988 to 1994 and 493 population-based control cases and controls, matched for age and sex, randomly identified from the community. All cases and controls were free of prior clinical heart disease, major comorbidity, and use of fish oil supplements. <h3>Measures of Exposure.</h3> —Spouses of case patients and control subjects were interviewed to quantify dietary n-3 polyunsaturated fatty acid intake from seafood during the prior month and other clinical characteristics. Blood specimens from 82 cases (collected in the field) and 108 controls were analyzed to determine red blood cell membrane fatty acid composition, a biomarker of dietary n-3 polyunsaturated fatty acid intake. <h3>Results.</h3> —Compared with no dietary intake of eicosapentaenoic acid (C<sub>20:5n-3</sub>) and docosahexaenoic acid (C<sub>22:6n-3</sub>), an intake of 5.5 g of n-3 fatty acids per month (the mean of the third quartile and the equivalent of one fatty fish meal per week) was associated with a 50% reduction in the risk of primary cardiac arrest (odds ratio [OR], 0.5; 95% confidence interval [CI], 0.4 to 0.8), after adjustment for potential confounding factors. Compared with a red blood cell membrane n-3 polyunsaturated fatty acid level of 3.3% of total fatty acids (the mean of the lowest quartile), a red blood cell n-3 polyunsaturated fatty acid level of 5.0% of total fatty acids (the mean of the third quartile) was associated with a 70% reduction in the risk of primary cardiac arrest (OR, 0.3; 95% CI, 0.2 to 0.6). <h3>Conclusion.</h3> —Dietary intake of n-3 polyunsaturated fatty acids from seafood is associated with a reduced risk of primary cardiac arrest. (<i>JAMA</i>. 1995;274:1363-1367)
Protection of Normal Proliferating Cells Against Chemotherapy by Staurosporine-Mediated, Selective, and Reversible G1 Arrest (2000)

Breast cancer cells with defective checkpoints regulated by the pRb pathway can be targeted specifically with chemotherapeutic agents, following staurosporine-mediated, selective and reversible G(0)/G(1) arrest in normal cells.
Glycophosphatidylinositol-anchored protein deficiency as a marker of mutator phenotypes in cancer. (2001)

Phosphatidylinositol glycan-A (PIGA) is a gene that encodes an element required for the first step in glycosylphosphatidylinositol (GPI) anchor assembly. Because PIGA is X-located, a single mutation is sufficient to abolish cell surface GPI-anchored protein expression. In this study, we investigated whether mutation of the PIGA gene could be exploited to identify mutator (Mut) phenotypes in cancer. We examined eight Mut colon cancer lines and four non-Mut colon cancers as controls. In every case, flow cytometric analyses of cells sorted for low fluorescence after staining for GPI-linked CD59 and CD55 revealed negative peaks in the Mut lines but not in the controls. Single cell cloning of purged and sorted GPI-anchor- HCT116 cells and sequencing of the PIGA gene in each clone uniformly showed mutations. Pretreatment of the Mut lines with anti-CD55 or anti-CD59 antibodies and complement or with the GPI-anchor-reactive bacterial toxin aerolysin enriched for the GPI-anchor- populations. Expansion of purged GPI-anchor+ cells in the Mut lines and analyses using aerolysin in conjunction with flow cytometry yielded PIGA gene mutation frequencies of 10(-5) to 10(-4), values similar to the mutation frequencies of the hprt gene. This novel approach allows for the detection of as yet undescribed repair or replication defects and in addition to its considerably greater ease of use than existing techniques and in principle would not require the production of cell lines.
Entropy Driven Multi-Photon Frequency Up-Conversion (2013)

We experimentally demonstrate a fundamentally new, entropy driven photon up-conversion mechanism, where 10.6µ photons are tenfold up-converted to 1µ with efficiency of 10%. This work opens novel ways of converting thermal-radiation to electricity.
Physical Factors Influencing Pleasant Touch during Tactile Exploration (2013)

Characteristics of the frictional force fluctuations and of the net friction taking place during scanning can reliably be correlated with the pleasantness sensation of surfaces.
Performance evaluation of minimum average correlation energy filters (1991)

A new SDF type correlation filter referred to as the minimum average correlation energy (MACE) filter has been recently described in the literature. In this paper, we experimentally address the distortion tolerance and noise properties of this filter. The MACE filter has attractive properties that include: easily detectable peaks, distortion invariance, simplified training set selection, solutions to input bias effects, performance in noise and real background clutter, and less clutter with its reduced number of training set images. Each of these properties is investigated in detail in this paper.