gebhart/patrepeval huggingface dataset:
Synthesis and regiospecificity in methylation of pyrido[1,2‐a]pyrazinium‐1‐ and 3‐olates and pyrido[1,2‐b]pyridazinium‐2‐ and 4‐olates (1990)

Abstract New methods have been developed for the synthesis of pyrido[1,2‐ a ]pyrazinium‐1‐ and 3‐olates 5a‐f, 9 and 1‐thiolate 24 as well as of pyrido[1,2‐ b ]pyridazinium‐4‐ and 2‐olates 14, 20 . The methylation of these new compounds was studied by soft and hard methylating agents. Depending on the nature of the reagent used, the pyrido[1,2‐ a ]pyrazinium‐1‐olates 5a‐f gave NMe 22a‐f and/or OMe 23a‐f products, whereas the 3‐olate 9 and both the 4‐ and 2‐pyridazinium‐olates 14, 20 afforded solely OMe compounds 10, 15, 21 . A selectivity rule for methylation is proposed.
Harvest, yield, and scalable tolerant systems (2003)

The cost of reconciling consistency and state management with high availability is highly magnified by the unprecedented scale and robustness requirements of today's Internet applications. We propose two strategies for improving overall availability using simple mechanisms that scale over large applications whose output behavior tolerates graceful degradation. We characterize this degradation in terms of harvest and yield, and map it directly onto engineering mechanisms that enhance availability by improving fault isolation, and in some cases also simplify programming. By collecting examples of related techniques in the literature and illustrating the surprising range of applications that can benefit from these approaches, we hope to motivate a broader research program in this area.
Comparative sequence specificities of human 72- and 92-kDa gelatinases (type IV collagenases) and PUMP (matrilysin) (1993)

The sequence specificities of human 72-kDa fibroblast gelatinase (type IV collagenase), human 92-kDa neutrophil gelatinase (type IV collagenase), and putative metalloproteinase (PUMP or matrilysin) have been examined by measuring the rate of hydrolysis of over 50 synthetic oligopeptides covering the P4 through P4' subsites of the substrate. The peptides investigated in this paper were those employed in our previous study which systematically examined the sequence specificity of human fibroblast and neutrophil collagenases [Netzel-Arnett et al. (1991) J. Biol. Chem. 266, 6747]. The initial rate of hydrolysis of the P1-P1' bond of each peptide has been measured under first-order conditions ([S0] << KM), and kcat/KM values have been calculated from the initial rates. The specificities of these five metalloproteinases are similar, but distinct, with the largest differences occurring at subsites P1, P1', and P3'. The specificities of the two gelatinases are the most similar to each other. They tolerate only small amino acids such as Gly and Ala in subsite P1. In contrast, larger residues such as Met, Pro, Gln, and Glu are also accommodated well by PUMP. All five enzymes prefer hydrophobic, aliphatic residues in subsite P1'. PUMP exhibits a stronger preference for Leu in this subsite than is shown by the other enzymes. The P3' subsite specificities of the gelatinases and collagenases are very similar but different from those of PUMP which particularly prefers Met in this position. The specificity data from this study allow the design of optimized substrates and selective inhibitors for these metalloproteinases.
"Why Can't I Just Start with a Map?" - Case Histories for Integrated Asset Management (2004)

Abstract Data sharing is an integral component of strategies to support critical decisions during the life of field value chain. Petroleum organizations face major challenges in the integration of legacy database systems to support an effective methodology for maximizing asset value. Case histories are presented that show effective integration of data, information, and knowledge in the asset value chain.
Expression of Antibody Fab Fragments and Whole Immunoglobulin in Mammalian Cells (2003)

The technologies described in this volume enable the isolation of recombi- nant antibodies (Abs) from libraries of variable regions (Fvs) or Fabs displayed on the surface of filamentous phage by fusion to a structural protein ( -7). Production of selected Abs in sufficient quantity for further evaluation often requires the transfer of their coding sequences to vectors specfiically designed for expression in eukaryotic cells. For Fab and/or immunoglobulin G (IgG) expression, these systems either employ separate plasmids for the heavy-chain (HC) and light-chain (LC) sequences or a single plasmid in which both HC and LC cassettes are expressed.
Ricin A-chain containing immunotoxins directed against different epitopes on the CD2 molecule differ in their ability to kill normal and malignant T cells. (1988)

Immunoconjugates consisting of mAb covalently coupled to plant or bacterial toxins or to cytotoxic drugs have provided novel experimental reagents for the treatment of malignancies and autoimmune diseases. In this report, we analyzed the efficacy of three ricin A chain-containing immunotoxins (IT-A) which recognize different epitopes on the CD2 molecule (E rosette receptor) on human T cells. Although all IT-A had similar binding avidities and A-chain activities, one (RFT11-A) was 100-1000-fold more effective in killing normal and malignant T cells than the others (35.1-A, 9.6-A). Immunoprecipitation experiments confirmed that all IT-A bound to the CD2 molecule. However, cross-blocking experiments, differential proteolysis with trypsin, and T cell co-activation experiments showed that the less effective IT-A, 35.1-A and 9.6-A, bound to an epitope far from the cell membrane (region I), whereas the more effective IT-A, RFT11-A bound to an epitope closer to the membrane (region II). Using cellular RIA and immunoelectron microscopy, it was shown that both RFT11-A and 35.1-A were rapidly internalized by T cells, but that their intracellular fates differed. The more toxic IT-A, RFT11-A, was retained for longer periods of time inside the cells and was more slowly degraded than the less effective IT-A, 35.1-A, which was rapidly transported to lysosomes, digested, and expelled. These results demonstrate that different IT-A targeting the same surface molecule can differ markedly in potency, and that the epitope recognized by an IT-A may have a significant impact on the ability of the IT-A to insert into cell membranes, translocate to the cytosol, and kill cells.
Human immunodeficiency virus type 1 infection of the nervous system: Pathogenetic mechanisms (1993)

Human immunodeficiency virus type 1 (HIV-1) infection of the central nervous system is associated with characteristic virological, clinical, and neuropathological findings in adults and children. Productive infection in the brain and spinal cord occurs in blood-derived macrophages, resident microglia, and multinucleated giant cells. Previous work implicated indirect mechanisms for neurotoxicity by HIV-1 gene products or by factors secreted from HIV-1--infected macrophages. However, this cannot explain the paradox between the small numbers of infected cells and the widespread tissue pathology. Based on recent studies from our laboratories, we suggest that HIV-1--infected macrophages can initiate neurotoxicity, which is then amplified through cell-to-cell interactions with astrocytes. Macrophage-astrocyte interactions produce cytokines tumor necrosis factor-alpha and interleukin-1 beta and arachidonic metabolites that cause astroglial proliferation and neuronal injury. Inevitably, the astrogliosis serves to amplify these cellular processes while brain infection maintains itself in macrophage and microglia and possibly in astrocytes (by restricted infection). These findings, taken together, provide fresh insights into how low numbers of productively infected cells could elicit progressive and devastating neurological impairment during HIV-1 disease, and suggest therapeutic strategies to interrupt the pathological process.
Formation and Hydrolysis of Cyclic ADP-Ribose Catalyzed by Lymphocyte Antigen CD38 (1993)

CD38 is a 42-kilodalton glycoprotein expressed extensively on B and T lymphocytes. CD38 exhibits a structural homology to Aplysia adenosine diphosphate (ADP)-ribosyl cyclase. This enzyme catalyzes the synthesis of cyclic ADP-ribose (cADPR), a metabolite of nicotinamide adenine dinucleotide (NAD+) with calcium-mobilizing activity. A complementary DNA encoding the extracellular domain of murine CD38 was constructed and expressed, and the resultant recombinant soluble CD38 was purified to homogeneity. Soluble CD38 catalyzed the formation and hydrolysis of cADPR when added to NAD+. Purified cADPR augmented the proliferative response of activated murine B cells, potentially implicating the enzymatic activity of CD38 in lymphocyte function.
Separation of CO2 from Flue Gas: A Review (2005)

Abstract:As a result of human activity, approximately 7 Gt of carbon are emitted to the earth's atmosphere each year. A large portion of this carbon is in the form of gaseous CO2, and approximately 30% of this CO2 comes from fossil fuel power plants. In addition to rising levels of atmospheric CO2, the earth's temperature is increasing. Since CO2 can act as a trap for heat (similar to the glass in a greenhouse), reduction of CO2 emissions is an important area of research. Separation and sequestration of CO2 are near-term goals for emissions reduction. Better fuel efficiency (in power production, transportation, and other areas) can be considered a mid-term goal. An acceptable long-term goal for reducing emissions is using alternate power sources such as nuclear, solar, and wind power. Because separation and sequestration are short-term goals, they are critical and challenging steps for researchers. Methods that are reviewed in this paper include absorption using solvents or solid sorbents, pressure- and temperature-swing adsorption using various solid sorbents, cryogenic distillation, membranes, and several novel and emerging technologies. Upon completion of this review, it was concluded that the most promising current method for CO2 separation is liquid absorption using monoethanolamine (MEA). While this method is currently most promising, the development of ceramic and metallic membranes for membrane diffusion should produce membranes significantly more efficient at separation than liquid absorption. The other methods investigated in this report are either too new for comparison or appear unlikely to experience significant changes to make them desirable for implementation.
Electrochemical activation of CO2in ionic liquid (BMIMBF4): synthesis of organic carbonates under mild conditions (2007)

A new electrochemical procedure for electrosynthesis of organic carbonates from CO2 and alcohols has been established in CO2-saturated room temperature ionic liquid BMIMBF4 solution, followed by addition of an alkylating agent. The synthesis was carried out under mild (PCO2 =1.0 atm, T = 55 °C) and safe conditions. The use of volatile and toxic solvents and catalysts as well as of any additional supporting electrolytes has been avoided. The influence of temperature, cathode material, working potential, alcohol concentration and the charge passed on the reaction using methanol (1a) as the model compound was examined. The ionic liquid used for the reaction was recyclable. The obtained results showed that the primary and secondary alcohols were converted in good yields, whereas tertiary alcohol and phenol were unreactive.
A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity (2011)

Sequence-specific nucleases represent valuable tools for precision genome engineering. Traditionally, zinc-finger nucleases (ZFNs) and meganucleases have been used to specifically edit complex genomes. Recently, the DNA binding domains of transcription activator-like effectors (TALEs) from the bacterial pathogen Xanthomonas have been harnessed to direct nuclease domains to desired genomic loci. In this study, we tested a panel of truncation variants based on the TALE protein AvrBs4 to identify TALE nucleases (TALENs) with high DNA cleavage activity. The most favorable parameters for efficient DNA cleavage were determined in vitro and in cellular reporter assays. TALENs were designed to disrupt an EGFP marker gene and the human loci CCR5 and IL2RG. Gene editing was achieved in up to 45% of transfected cells. A side-by-side comparison with ZFNs showed similar gene disruption activities by TALENs but significantly reduced nuclease-associated cytotoxicities. Moreover, the CCR5-specific TALEN revealed only minimal off-target activity at the CCR2 locus as compared to the corresponding ZFN, suggesting that the TALEN platform enables the design of nucleases with single-nucleotide specificity. The combination of high nuclease activity with reduced cytotoxicity and the simple design process marks TALENs as a key technology platform for targeted modifications of complex genomes.
Ultrahigh-resolution plastic graded-index fused image plates (2000)

Fiber-optic imaging systems such as the medical endoscope, the boroscope, the fused-image faceplate, and the image conduit are now made from glass step-index (SI) fibers, and the image resolution of the SI fiber-optic imaging systems is limited to ~5 microm. Ultrahigh-resolution fiber-optic fused-image plates with fiber diameter sizes of 5 and 2.8 microm were fabricated with plastic graded-index (GRIN) fibers. The measured image resolutions of the 5-microm SI and GRIN-based guides were comparable, and the resolution of the plastic GRIN image guides improved as the fiber diameter was reduced from 5 to 2.8 microm.
Linear and nonlinear analysis of human dynamic cerebral autoregulation (1999)

The linear dynamic relationship between systemic arterial blood pressure (ABP) and cerebral blood flow velocity (CBFV) was studied by time- and frequency-domain analysis methods. A nonlinear moving-average approach was also implemented using Volterra-Wiener kernels. In 47 normal subjects, ABP was measured with Finapres and CBFV was recorded with Doppler ultrasound in both middle cerebral arteries at rest in the supine position and also during ABP drops induced by the sudden deflation of thigh cuffs. Impulse response functions estimated by Fourier transfer function analysis, a second-order mathematical model proposed by Tiecks, and the linear kernel of the Volterra-Wiener moving-average representation provided reconstructed velocity model responses, for the same segment of data, with significant correlations to CBFV recordings corresponding to r = 0.52 +/- 0.19, 0.53 +/- 0.16, and 0.67 +/- 0.12 (mean +/- SD), respectively. The correlation coefficient for the linear plus quadratic kernels was 0.82 +/- 0.08, significantly superior to that for the linear models (P < 10(-6)). The supine linear impulse responses were also used to predict the velocity transient of a different baseline segment of data and of the thigh cuff velocity response with significant correlations. In both cases, the three linear methods provided equivalent model performances, but the correlation coefficient for the nonlinear model dropped to 0.26 +/- 0.25 for the baseline test set of data and to 0.21 +/- 0.42 for the thigh cuff data. Whereas it is possible to model dynamic cerebral autoregulation in humans with different linear methods, in the supine position a second-order nonlinear component contributes significantly to improve model accuracy for the same segment of data used to estimate model parameters, but it cannot be automatically extended to represent the nonlinear component of velocity responses of different segments of data or transient changes induced by the thigh cuff test.
Repeat sequences in the Bordetella pertussis adenylate cyclase toxin can be recognized as alternative carboxy‐proximal secretion signals by the Escherichia coliα‐haemolysin translocator (1993)

The 1706-residue adenylate cyclase toxin (CyaA) of Bordetella pertussis is an RTX protein with extensive carboxy-proximal glycine and aspartate-rich repeats. CyaA does not have a cleavable amino-terminal signal peptide and can be secreted across both bacterial membranes of the Escherichia coli cell envelope by the alpha-haemolysin (HlyA) translocator (HlyBD/TolC). We performed deletion mapping of secretion signals recognized in CyaA by this heterologous translocator. Truncated proteins with N-terminal and internal deletions were secreted at levels up to 10 times higher than intact CyaA and similar to HlyA. A secretion signal recognized by HlyBD/TolC was found within the last 74 residues of CyaA. However, secretion of CyaA was reduced but not abolished upon deletion of the last 75 or 217 residues, indicating that at least two additional secretion signals recognized by HlyBD/TolC are within CyaA. One of them was localized to the repeat sequence between residues Asp-1587 to Ile-1631. Interestingly, a conserved 'acidic' motif (Glu/Asp)-(X)11-Asp-(X)3/5-(Glu/Asp)-(X)14-Asp was found in the C-terminal sequences of HlyA, CyaA and the two secreted CyaA derivatives. We speculate that the presence and spacing of acidic residues may be an important feature of secretion signals recognized by the haemolysin translocator.
The palm tree Copernicia cerifera (carnaúba) as an ecotope of Rhodnius nasutus in rural areas of the State of Piauí Northeastern Brazil (1986)

The C. cerifera palm tree (carnaúba) is widely distributed in the Northeastem Brazil, including the State of Piauí. This investigation revealed that R. nasutus is the ortly triatomine species captured on that palm tree, in five different localities. 78% of palm trees were infested with triatomines, and 4.0% were infected with flagellates morphologically and biologically indistinguishable from Trypanosoma cruzi. Birds, rodents and marsupials were found as major blood meai sources for R. nasutus.
Testing of a Field Dielectric Soil Moisture Meter (1981)

Abstract The functional relationship between dielectric constant and soil content has been applied to the development of a dielectric soil water moisture meter based on converter capacitance-frequency. A measured capacitance forms part of the tuning capacitance of an oscillator and causes a definite frequency deviation. A cylindrical probe fitted with an oscillator is used to measure the electrical field. The author has determined the basic characteristics of the instrument—center of sensitivity, radius of the electrical field, and influence of soil properties, particularly changes in bulk density, chemical composition, and temperature. The device is applicable for either continuous use, with the probe permanently built in to the soil layer, or use with the probe sliding inside an access tube, in which case the vertical distribution of soil moisture is measured. Field calibration of the meter is required.
Identification of the Catalytic Nucleophile of Endoglucanase I from Fusarium oxysporum by Mass Spectrometry (1997)

The endoglucanase EG I from Fusarium oxysporum catalyzes the hydrolysis of cellulose via a double-displacement mechanism involving the formation and hydrolysis of a glycosyl-enzyme intermediate. Treatment of EG I with 2',4'-dinitrophenyl-2-deoxy-2-fluoro-beta-D-cellobioside results in the time-dependent inactivation of the enzyme (k(i) = 1.36 min(-1), Ki = 0.88 mM) via trapping of a covalent 2-deoxy-2-fluorocellobiosyl-enzyme intermediate. This intermediate is, however, catalytically competent undergoing transglycosylation, thus reactivation, in the presence of D-cellobiose. Analysis of a peptic digest of the inactivated enzyme by HPLC/ESMS/MS in the neutral loss mode allowed identification of a 2-fluorocellobiosyl-labeled peptide containing Glu197. This was confirmed by comparative mapping studies and subsequent Edman degradation analysis. This residue is completely conserved in glycosidase family 7, to which EG I belongs, consistent with its key role as the catalytic nucleophile.
Functional dissection of a sugar‐repressed α‐amylase gene (RAmy1A) promoter in rice embryos (1998)

The gibberellin-inducible rice alpha-amylase gene, RAmy1 A, was demonstrated to be sugar repressed in rice embryos and functional dissection of the promoter of RAmy1 A in relation of its sugar-modulated expression was performed. Gibberellin-response cis-elements of GARE (TAACAAA) and pyrimidine box (CCTTTT) were partially involved in the sugar repression.
Pluripotent Protective Effects of Carnosine, a Naturally Occurring Dipeptidea (1998)

Carnosine is a naturally occurring dipeptide (beta-alanyl-L-histidine) found in brain, innervated tissues, and the lens at concentrations up to 20 mM in humans. In 1994 it was shown that carnosine could delay senescence of cultured human fibroblasts. Evidence will be presented to suggest that carnosine, in addition to antioxidant and oxygen free-radical scavenging activities, also reacts with deleterious aldehydes to protect susceptible macromolecules. Our studies show that, in vitro, carnosine inhibits nonenzymic glycosylation and cross-linking of proteins induced by reactive aldehydes (aldose and ketose sugars, certain triose glycolytic intermediates and malondialdehyde (MDA), a lipid peroxidation product). Additionally we show that carnosine inhibits formation of MDA-induced protein-associated advanced glycosylation end products (AGEs) and formation of DNA-protein cross-links induced by acetaldehyde and formaldehyde. At the cellular level 20 mM carnosine protected cultured human fibroblasts and lymphocytes, CHO cells, and cultured rat brain endothelial cells against the toxic effects of formaldehyde, acetaldehyde and MDA, and AGEs formed by a lysine/deoxyribose mixture. Interestingly, carnosine protected cultured rat brain endothelial cells against amyloid peptide toxicity. We propose that carnosine (which is remarkably nontoxic) or related structures should be explored for possible intervention in pathologies that involve deleterious aldehydes, for example, secondary diabetic complications, inflammatory phenomena, alcoholic liver disease, and possibly Alzheimer's disease.
Designing immunocytokines: genetically engineered fusion proteins for targeted immune therapy (2001)

The use of antibodies and antibody-based therapeutic agents has accelerated in the last ten years through the combined technological advances in hybridoma technology and genetic engineering. In fact, molecular biological approaches have now been applied to the antibody engineering field in ways that both enhance the hybridoma approach, e.g., through the generation of transgenic mice capable of expressing human immunoglobulins and, in some cases, by replacing the use of animals altogether. The latter approaches involve the use of phage display or in vitro molecular evolution technologies that use antigen binding selection coupled with linked gene sequence identification to isolate binding proteins and their coding sequences from enormously complex mixtures of randomly generated molecules.
Double Positive CD4CD8 αβ T Cells: A New Tumor-Reactive Population in Human Melanomas (2010)

In conclusion, we can postulate that, according to their broad tumor reactivity and to their original cytokine profile, the tumor associated DP T cells could participate in immune responses to tumors in vivo. Therefore, the presence of these cells and their role will be crucial to address in cancer patients, especially in the context of immunotherapies.
Intraperitoneal radioimmunotherapy of ovarian cancer with lutetium-177-CC49. (1996)

Intraperitoneal radioimmunotherapy with 177Lu-CC49 is well tolerated and appears to have antitumor activity against chemotherapy-resistant ovarian cancer in the peritoneal cavity.