gebhart/patrepeval huggingface dataset:
The reactive and destabilizing disulfide bond of DsbA, a protein required for protein disulfide bond formation in vivo (1993)

The protein DsbA facilitates disulfide bond formation in the periplasm of Escherichia coli. It has only two cysteine residues that are separated in the sequence by two other residues and are shown to form a disulfide bond reversibly. Chemical modification studies demonstrate that only one of the cysteine residues has an accessible thiol group in the reduced protein. Equilibrium and kinetic characterization of thiol-disulfide exchange between DsbA and glutathione showed that the DsbA disulfide bond was 10(3)-fold more reactive than a normal protein disulfide. Similarly, the mixed disulfide between the accessible cysteine residue and glutathione was 10(4)-fold more reactive than normal. The overall equilibrium constant for DsbA disulfide bond formation from GSSG was only 8 x 10(-5) M. These properties indicate that disulfide-bonded DsbA is a potent oxidant and ideally suited for generating protein disulfide bonds. Disulfide bonds generally increase the stabilities of folded proteins, when the folded conformation reciprocally stabilizes the disulfide bonds. In contrast, the disulfide bond of DsbA was so unstable in the folded state that its stability increased by 4.5 +/- 0.1 kcal.mol-1 when the protein unfolded. This implies that the disulfide bond destabilizes the folded conformation of DsbA. This was confirmed by demonstrating that the reduced protein was 3.6 +/- 1.4 kcal.mol-1 more stable than that with the disulfide bond.
Kirsten ras Mutations in Patients With Colorectal Cancer: the Multicenter "RASCAL" Study (1998)

Ki-ras mutations are associated with increased risk of relapse and death, but some mutations are more aggressive than others.
Factors Influencing Changes in pH during Storage of PlateletConcentrates at 20-24 °C (1982)

The magnitude of the pH change during platelet concentrate storage at 20-24 °C in polyvinyl chloride containers is not determined solely by platelet count per cubic millimeter of plasma, since a wide variation in pH was observed with similar platelet concentrations. In modified platelet concentrates having lost through centrifugation 3-15% of total platelets and 61-92% of residual leukocytes, the pH was maintained at substantially higher levels than in the paired control platelet concentrates. Leukocyte levels do not appear to determine the magnitude of the pH fall. Continuous oxygen ulilization is needed if the pH is to be maintained near 7.0. However, oxygen tension per se is not the factor which influences the extent of pH change. It has been concluded that a specific platelet subpopulation comprising a small proportion of the total platelets in concentrates and having an enhanced capacity to form lactate may be responsible for a major part of the pH reduction which occurs during storage of many platelet concentrates.
Alpha 2 interferon in the prevention of N-nitroso-methyl urea induced breast cancer in rats. (1988)

Human interferons have been shown to be effective treatment for hairy cell leukaemia and are now commercially available. Their role in treatment of solid tumours has yet to be established. This study assessed the value of alpha 2 interferon (IFN) in an experimental breast cancer model. Four groups of female Sprague-Dawley rats were studied. The first received three intravenous injections (7 mg/kg) of N-nitroso-methyl urea (NMU) at weeks 0, 3 and 7. The second received the same NMU dosage regime plus IFN (100,000 IU, twice weekly for 3 weeks). A third received IFN alone and the fourth was a control group receiving three intravenous injections of normal saline. At week 16, 19 of 20 rats in the NMU alone group had developed tumours significantly more than four of 15 rats with tumour in the NMU plus IFN group (P less than 0.001). Both the mean tumour number/rat and the mean tumour weight/rat was significantly more in the NMU group than the NMU plus IFN group P less than 0.05). No rats in the IFN alone or control group developed tumour. These data suggest that IFN prevents carcinogen induced breast cancer in rats. It may have a role in the prevention and treatment of human breast cancer.
Mutant loxP vectors for selectable marker recycle and conditional knock-outs (2001)

Mutant loxP vectors have been developed for the recycle of selectable markers and conditional gene knock-out approaches. As the marker and the cDNA expression cassettes are driven by the universally active and evolutionary conserved beta-actin promoter, they can be used for the selection of stable transfectants in a wide range of cell lines.
Advances in selective wet oxidation of AlGaAs alloys (1997)

We review the chemistry, microstructure, and processing of buried oxides converted from AlGaAs layers using wet oxidation. Hydrogen is shown to have a central role in the oxidation reaction as the oxidizing agent and to reduce the intermediate predict As/sub 2/O/sub 3/ to As. The stable oxide is amorphous (Al/sub x/Ga/sub 1-x/)/sub 2/O/sub 3/ which has no defects along the oxide/semiconductor interfaces but can exhibit strain at the oxide terminus due to volume shrinkage. The influence of gas flow, gas composition, temperature, Al-content, and layer thickness on the oxidation rate are characterized to establish a reproducible process. Linear oxidation rates with Arrhenius activation energies which strongly depend upon AlAs mole fraction are found. The latter produces strong oxidation selectivity between AlGaAs layers with slightly differing Al-content. Oxidation selectivity to thickness is also shown for layer thickness <60 nm. Differences between the properties of buried oxides converted from AlGaAs and AlAs layers and the impact on selectively oxidized vertical cavity laser lifetime are reported.
Intranasal Vaccination WithSalmonella-Derived Serodominant Secreted Effector Protein B Associated With Gas-Filled Microbubbles Partially Protects Against Gut Infection in Mice (2016)

Salmonella infection is an increasingly important public health problem owing to the emergence of multidrug resistance and the lack of broadly efficient vaccines. Novel strategies of vaccination are required to induce protective immune responses at mucosal surfaces and in the circulation, to limit bacteria entry and dissemination. To this aim, intranasal anti-Salmonella vaccination with an innovative formulation composed of gas-filled microbubbles and the pathogen-derived protective protein serodominant secreted effector protein B (SseB-MB) was evaluated in a mouse infection model. Intranasal application of SseB-MB induced gut and systemic immunoglobulin A, T-helper type 17 cell (Th17), and Th1 responses, all of which are associated with natural immunity against Salmonella In vaccinated mice, a significant reduction in bacterial load was observed in intestinal tissues and the spleen after an otherwise lethal oral infection. Therefore, MB serve as an efficient carrier for nasal delivery of a Salmonella antigen that results in protection upon activation of the common mucosal immune system.
On Intra Prediction for Screen Content Video Coding (2015)

Screen content coding (SCC) is becoming increasingly important in various applications, such as desktop sharing, video conferencing, and remote education. When compared to natural camera- captured content, screen content has different characteristics, in particular sharper edges. In this paper, we propose a novel intra prediction scheme for screen content video. In the proposed scheme, bilinear interpolation in angular intra prediction in HEVC is selectively replaced by nearest-neighbor intra prediction to preserve the sharp edges in screen content video. We present three different variants of the proposed nearest neighbor prediction algorithm: two implicit methods where both the encoder, and the decoder derive whether to perform nearest neighbor prediction or not based on either (a) the sum of the absolute difference, or (b) the difference between the boundary pixels from which prediction is performed; and another variant where Rate-Distortion-Optimization (RDO) search is performed at the encoder to decide whether or not to use the nearest neighbor interpolation, and explicitly signaled to the decoder. We also discuss the various underlying trade-offs in terms of the complexity of the three variants. All the three proposed variants provide significant gains over HEVC, and simulation results show that average gains of 3.3% BD-bitrate in Intra-frame coding are achieved by the RDO variant for screen content video. To the best of our knowledge, this is the first paper that 1) points out current HEVC intra prediction scheme with bilinear interpolation does not work efficiently for screen content video and 2) uses different filters adaptively in the HEVC intra prediction interpolation.
Heparin and Heparan Sulfate Biosynthesis (2002)

Heparan sulfate is one of the most informationally rich biopolymers in Nature. Its simple sugar backbone is variously modified to different degrees depending on the cellular conditions. Thus, it matures to have an enormously complicated structure, which most likely exhibits a considerable number of unique overlapping sequences with peculiar sulfation profiles. Such sequences are recognized by specific complementary proteins, which form a huge group of "heparin-binding proteins," and the sugar sequences in turn support unique functions of the respective proteins through specific interactions. The heparan sulfate sequences are not directly encoded by genes, but are created by elaborate biosynthetic mechanisms, which ensure the generation of these indispensable sequences. In heparan sulfate biosynthesis, the tetrasaccharide sequence (GlcA-Gal-Gal-Xyl-), designated the protein linkage region, is first assembled on a specific Ser residue at the glycosaminoglycan attachment site of a core protein. A heparan sulfate chain is then polymerized on this fragment by alternate additions of GlcNAc and GlcA through the actions of glycosyltransferases with overlapping specificities encoded by the tumor suppressor EXT family genes. Then follow various modifications by N-deacetylation and N-sulfation of glucosamine, C5-epimerization of GlcA and multiple O-sulfations of the component sugars. Recent studies have achieved purification of several, and molecular cloning of most, of the enzymes responsible for these reactions. Some of these enzymes are bifunctional. The availability of cDNA probes has facilitated elucidation of the crystal structures for two of the biosynthetic enzymes, demonstration of their intracellular location, and their occurrence in complexes to achieve rapid and efficient synthesis of complex sugar sequences. Genomic structure and transcript analysis have shown the existence of multiple isoforms for most of the sulfotransferases. Many aspects of the heparan sulfate biosynthetic scheme are shared by the structural analog heparin, which is synthesized in mast cells and some other mammalian cells and is several-fold higher degree of polymerization and more extensive modification than heparan sulfate.
Modeling mass transfer in hepatocyte spheroids via cell viability, spheroid size, and hepatocellular functions (2004)

Hepatocyte aggregation into spheroids attributes to their increased activity, but in the absence of a vascular network the cells in large spheroids experience mass transfer limitations. Thus, there is a need to define the spheroid size which enables maximal cell viability and productivity. We developed a combined theoretical and experimental approach to define this optimal spheroid size. Hepatocyte spheroids were formed in alginate scaffolds having a pore diameter of 100 microm, in rotating T-flasks or spinners, to yield a maximal size of 100, 200, and 600 microm, respectively. Cell viability was found to decrease with increasing spheroid size. A mathematical model was constructed to describe the relationship between spheroid size and cell viability via the oxygen mass balance equation. This enabled the prediction of oxygen distribution profiles and distribution of viable cells in spheroids with varying size. The model describes that no oxygen limitation will take place in spheroids up to 100 microm in diameter. Spheroid size affected the specific rate of albumin secretion as well; it reached a maximal level, i.e., 60 microg/million cells/day in 100-microm diameter spheroids. This behavior was depicted in an equation relating the specific albumin secretion rate to spheroid size. The calculated results fitted with the experimental data, predicting the need for a critical number of viable hepatocytes to gain a maximal albumin secretion. Taken together, the results on mass transport in spheroids and its effects on cell viability and productivity provide a useful tool for the design of 3D scaffolds with pore diameters of 100 microm.
Sphingomyelinases and Niemann-Pick disease. (1986)

In the first part the properties of normal mammalian sphingomyelinases are reviewed: The lysosomal acid sphingomyelinase is a polymeric glycoprotein (subunit Mr between 28 000 and 70 000) which hydrolyses natural sphingomyelin, coloured and fluorescent semi-synthetic analogues (trinitrophenyl-aminolauryl-sphingomyelin and pyrenedecanoyl-sphingomyelin) and the synthetic analogue 2-N-hexadecanoylamido-nitrophenyl-phosphorylcholine. The suitability of these substrates and of synthetic fluorescent derivatives of methylumbelliferone is discussed. The effect of lipids, detergents and other effectors on the enzyme activity is also described. The neutral sphingomyelinase from brain tissue, localized in cell membranes, has a high Mr (160 000 and 600 000), is heat labile, hydrolyses sphingomyelin and its coloured and fluorescent analogues, but not 2-N-hexadecanoylamido-nitrophenyl-phosphorylcholine. A new method is available for determining enzyme activity in the intact cell through the utilization of endogenous or exogenous sphingomyelin as substrate. In the second part of the review, the classification of Niemann-Pick disease, the characteristic features of each type and the biological tools used for the diagnosis are reported. Experimental models (animal models and cellular models in culture) are reviewed with a particular attention to a new model system, Epstein-Barr virus-transformed lymphoid cell lines.
Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays (2003)

RNA binding to high-density oligonucleotide arrays has shown tantalizing differences with solution experiments. We analyze here its sequence specificity, fitting binding affinities to sequence composition in large datasets. Our results suggest that the fluorescent labels interfere with binding, causing a catch-22. To be detected, the RNA must both glow and bind: without labels it cannot be seen even if bound, while with too many it will not bind. A simple model for the binding of labeled oligonucleotides sheds light on the interplay between binding energies and labeling probability.
Simultaneous loss of expression of syndecan-1 and E-cadherin in the embryonic palate during epithelial-mesenchymal transformation (1998)

Epithelial-mesenchymal transformation (EMT) is the key mechanism for fusion and confluence of the rodent palate. During this process, medial edge epithelia (MEE) form a midline seam that subsequently transforms to mesenchymal cells. We studied syndecan-1 and E-cadherin, two molecules which have been shown to promote the epithelial phenotype, to determine their fate during palatal EMT. We found that both syndecan-1 and E-cadherin are expressed on basolateral surfaces of the MEE at day 14. Twelve hours later, when a midline seam has formed, syndecan-1 and E-cadherin are still present on its basal and lateral epithelial surfaces and they persist after the seam breaks up into epithelial islands. Then, expression of both molecules is lost simultaneously and abruptly when EMT occurs. On the contrary, previous in vitro studies of cell lines transfected with antisense cDNAs suggested that loss of syndecan-1 would lead to loss of E-cadherin or vice versa. We conclude that in vivo, synthesis of both E-cadherin and syndecan-1 is downregulated synchronously by the initiation of EMT, leading to an effective and correctly timed conversion of the epithelial cells to mesenchyme.
The Role of Artificial Organs in Restoration of Laryngeal Function (1990)

From the Departments of Otolaryngology Head and Neck Surgery, Case Western Reserve University and Saint Vincent Charity Hospital and Health Center, Artificial Organs Research, The Cleveland Clinic Foundation and The Cleveland Research Institute.
The Risk of Childhood Cancer after Neonatal Exposure to Vitamin K (1993)

We found no association between exposure to vitamin K and an increased risk of any childhood cancer or of all childhood cancers combined, although a slightly increased risk could not be ruled out. The benefits of neonatal vitamin K prophylaxis against hemorrhagic disease have been well described. Unless other evidence supporting an association between vitamin K and cancer appears, there is no reason to abandon the routine administration of vitamin K to newborns.
<italic>N</italic>-Nitrosamines in Smoke Condensate From Several Varieties of Tobacco<xref ref-type="fn" rid="FN1">1</xref><xref ref-type="fn" rid="FN2">2</xref> (1972)

N-Nitrosamines in Smoke Condensate From Several Varieties of Tobacco Get access Donald E. Johnson, Donald E. Johnson Department of Chemistry and Chemical Engineering, Southwest Research Institute, San Antonio, Texas 78284 Search for other works by this author on: Oxford Academic PubMed Google Scholar John W. Rhoades John W. Rhoades Department of Chemistry and Chemical Engineering, Southwest Research Institute, San Antonio, Texas 78284 Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 48, Issue 6, June 1972, Pages 1845–1847, https://doi.org/10.1093/jnci/48.6.1845 Published: 01 June 1972
Pharmacokinetically Guided Dose Adjustment of 5-Fluorouracil: A Rational Approach to Improving Therapeutic Outcomes (2009)

Chemotherapy dosing of the fluoropyrimidine 5-fluorouracil (5-FU) is currently based on body surface area. However, body surface area-based dosing has been associated with clinically significant pharmacokinetic variability, and as such, dosing based on body surface area may be of limited use. The clinical activity of 5-FU is modest at standard doses, and in general, dosing is limited by the safety profile, with myelosuppression and gastrointestinal toxicity being the most commonly observed side effects. Various strategies have been developed to enhance the clinical activity of 5-FU, such as biochemical modulation, alterations in scheduling of administration, and the use of oral chemotherapy. Studies that have shown an association between plasma concentration with toxicity and clinical efficacy have shown that pharmacokinetically guided dose adjustments can substantially improve the therapeutic index of 5-FU treatment. These studies have shown that only 20%-30% of patients treated with a 5-FU-based regimen have 5-FU levels that are in the appropriate therapeutic range--approximately 40%-60% of patients are underdosed and 10%-20% of patients are overdosed. To date, 5-FU drug testing has not been widely used because of the lack of a simple, fast, and inexpensive method. Recent advances in testing based on liquid chromatography-mass spectroscopy and a nanoparticle antibody-based immunoassay for 5-FU may now allow for routine monitoring of 5-FU in clinical practice. We review the data on pharmacokinetically guided dose adjustment of 5-FU and discuss the potential of this approach to advance therapeutic outcomes.
Revolutionary Times in Our Understanding of Cell Wall Biosynthesis and Remodeling in the Grasses (2009)

A major part of the daily caloric intake of human societies around the world is derived from a diverse range of foods prepared from members of the grass family, including wheat ( Triticum aestivum ), rice ( Oryza sativa ), sorghum ( Sorghum bicolor ), the millets ( Panicum miliaceum and Pennisetum
Television Receiver Design Aspects for Employing Teletext LSI (1979)

Television multiplex broadcast has caught worldwide interest as a new information media.
The role of p21ras in CD28 signal transduction: triggering of CD28 with antibodies, but not the ligand B7-1, activates p21ras. (1994)

CD28 is a 44-kD homodimer expressed on the surface of the majority of human T cells that provides an important costimulus for T cell activation. The biochemical basis of the CD28 accessory signals is poorly understood. Triggering of the T cell antigen receptor (TCR) activates the p21ras proteins. Here we show that ligation of CD28 by a monoclonal antibody (mAb) also stimulates p21ras and induces Ras-dependent events such as stimulation of the microtubule-associated protein (MAP) kinase ERK2 and hyperphosphorylation of Raf-1. One physiological ligand for CD28 is the molecule B7-1. In contrast to the effect of CD28 mAb, the present studies show that interactions between CD28 and B7-1 do not stimulate p21ras signaling pathways. Two substrates for TCR-regulated protein tyrosine kinases (PTKs) have been implicated in p21ras activation in T cells: p95vav and a 36-kD protein that associates with a complex of Grb2 and the Ras exchange protein Sos. Triggering CD28 with both antibodies and B7-1 activates cellular PTKs, and we have exploited the differences between antibodies and B7-1 for p21ras activation in an attempt to identify critical PTK-controlled events for Ras activation in T cells. The data show that antibodies against TCR or CD28 induce tyrosine phosphorylation of both Vav and p36. B7-1 also induces Vav tyrosine phosphorylation but has no apparent effect on tyrosine phosphorylation of the Grb2-associated p36 protein. The intensity of the Vav tyrosine phosphorylation is greater in B7-1 than in TCR-stimulated cells. Moreover the kinetics of Vav tyrosine phosphorylation is prolonged in the B7-1-stimulated cells. These studies show that for CD28 signaling, the activation of p21ras correlates more closely with p36 tyrosine phosphorylation than with Vav tyrosine phosphorylation. However, the experiments demonstrate that Vav is a major substrate for B7-activated PTKs and hence could be important in CD28 signal transduction pathway.
Rapid Development of T Cell Memory (2004)

Prime-boost immunization is a promising strategy for inducing and amplifying pathogen- or tumor-specific memory CD8 T cell responses. Although expansion of CD8 T cell populations following the second Ag dose is integral to the prime-boost strategy, it remains unclear when, after priming, memory T cells become competent to proliferate. In this study, we show that Ag-specific CD8 T cells with the capacity to undergo extensive expansion are already present at the peak of the primary immune response in mice. These early memory T cells represent a small fraction of the primary immune response and, at early time points, their potential to proliferate is obscured by large effector T cell populations that rapidly clear Ag upon reimmunization. With sufficient Ag boosting, however, secondary expansion of these memory cells can be induced as early as 5-7 days following primary immunization. Importantly, both early and delayed boosting result in similar levels of protective immunity to subsequent pathogen challenge. Early commitment and differentiation of memory T cells during primary immunization suggest that a short duration between priming and boosting is feasible, providing potential logistic advantages for large-scale prime-boost vaccination of human populations.