gebhart/patrepeval huggingface dataset:
Restriction enzyme analysis of mouse cellular type C viral DNA: emergence of new viral sequences in spontaneous AKR/J lymphomas. (1979)

The topography of endogenous type C viral sequences in mouse cellular DNA was investigated by EcoRI nuclease restriction and application of the Southern blotting technique. The DNAs from one outbred and five inbred strains were resolved into 20-35 fragments containing viral sequences, distributed in unique, though related, patterns for each mouse strain. Different normal tissues from the same animal were indistinguishable in their DNA patterns, suggesting that tissue differentiation is not associated with gross alteration in the topography of endogenous type C virus sequences. Tumor tissues from spontaneous lymphomas of AKR/J mice were similarly analyzed. In four out of seven individual tumors we detected the emergence of one or two new virus-containing DNA fragments. The mass of these fragment varied, indicating different insertion sites of the new viral sequences. The detection of these new viral sequences suggests that each tumor was composed of descendents of only one or a few cells.
Prospects for specific immunotherapy in myasthenia gravis (1990)

Myasthenia gravis is an autoimmune disease resulting from a breakdown in T and B cell tolerance to acetylcholine receptor (AChR). Autoantibodies to AChR mediate the disease. Recent advances in experimental immunotherapy of autoimmune disease provide several possibilities for specific intervention in this well-characterized condition.
Hidden Markov model speed heuristic and iterative HMM search procedure (2010)

Our search heuristic, HMMERHEAD, significantly reduces the time needed to score a profile-HMM against large sequence databases. This search heuristic allowed us to implement an iterative profile-HMM search method, JackHMMER, which detects significantly more remote protein homologs than SAM's T2K and NCBI's PSI-BLAST.
Definition of the carbohydrate response element of the rat S14 gene. Evidence for a common factor required for carbohydrate regulation of hepatic genes. (1992)

The 5'-flanking region of the S14 gene from -4316 to +18 contains regulatory sequences responsible for activation of promoter activity in response to elevated carbohydrate metabolism in primary hepatocytes. To map these sequences, a series of constructs containing various internal deletions of the S14 5'-flanking sequence were assayed in primary hepatocytes. The region from -1601 to -1395 was found to be essential for this response. Comparison of the sequence of this S14 region to a region of the L-type pyruvate kinase gene that has been shown to mediate carbohydrate regulation (Thompson, K. S., and Towle, H. C. (1991) J. Biol. Chem. 266, 8679-8682) revealed a segment with 9 out of 10 identity. In both cases, this conserved sequence aligned with a DNase I footprint formed with hepatic nuclear extract. Oligonucleotides (approximately 30 base pairs) from either S14 or pyruvate kinase genes containing the conserved element bound to a hepatic nuclear factor(s) that gave identical complexes by mobility shift assay. Furthermore, these two oligonucleotides cross-competed for binding to the nuclear factor(s), suggesting that a common factor(s) binds to this conserved element. Reinsertion of the S14 oligonucleotide into an unresponsive S14 promoter construct restored the carbohydrate control. Moreover, this oligonucleotide could confer a glucose response when fused to a heterologous promoter. Thus, the S14 segment from -1457 to -1428 is a carbohydrate response element essential for the binding of nuclear factor(s) regulated by increased carbohydrate metabolism. This factor(s) may be common to the carbohydrate regulation of the S14 and pyruvate kinase genes.
Biodegradable Cisplatin Microspheres for Direct Brain Injection: Preparation and Characterization (1997)

The objectives of the present study were to prepare cisplatin loaded-PLGA microspheres that are suitable for direct brain injection and to characterize them in terms of their physicochemical properties, in vitro drug release, and self-removal mechanism. The microspheres were prepared by emulsification/solvent evaporation method using PLGA (50:50) as the biodegradable matrix forming polymer. The physicochemical characterization encompassed the following: surface morphology, particle size, entrapment efficiency, surface area, and density. The in vitro release and in vitro degradation studies were performed in phosphate buffer and in 10% rat brain preparation. SEM micrographs revealed that the microspheres have a rough porous surface and a smooth interior. Particle size typically ranged from 180 to 250 microns with an average of 230 T microns. Entrapment efficiency was approximately 70% and was found to be dependent on the particle size. Surface area and density ranged from 0.038 to 0.025 m2/g and from 1.44 to 1.39 g/cm3, respectively. Both were also dependent on particle size. In the in vitro release study in phosphate buffer, approximately 80% of cisplatin was released over 30 days, after which the release rate plateaued. The release profile in 10% rat brain preparation was comparable in shape to that obtained in phosphate buffer. However, the release rate was lower and the total amount released by the end of the study was only 55% of the total cisplatin content. The degradation of PLGA microspheres in phosphate buffer and in rat brain homogenate correlated well with the respective release profiles. Based on the evidence of self-removal and the sustained release of cisplatin for over a month, cisplatin-loaded PLGA microspheres may be useful for local delivery to brain tumors.
Activins, Inhibins, and Follistatins: From Endocrinology to Signaling. A Paradigm for the New Millennium (2002)

It has been 70 years since the name inhibin was used to describe a gonadal factor that negatively regulated pituitary hormone secretion. The majority of this period was required to achieve purification and definitive characterization of inhibin, an event closely followed by identification and characterization of activin and follistatin (FS). In contrast, the last 15-20 years saw a virtual explosion of information regarding the biochemistry, physiology, and biosynthesis of these proteins, as well as identification of activin receptors, and a unique mechanism for FS action-the nearly irreversible binding and neutralization of activin. Many of these discoveries have been previously summarized; therefore, this review will cover the period from the mid 1990s to present, with particular emphasis on emerging themes and recent advances. As the field has matured, recent efforts have focused more on human studies, so the endocrinology of inhibin, activin, and FS in the human is summarized first. Another area receiving significant recent attention is local actions of activin and its regulation by both FS and inhibin. Because activin and FS are produced in many tissues, we chose to focus on a few particular examples with the most extensive experimental support, the pituitary and the developing follicle, although nonreproductive actions of activin and FS are also discussed. At the cellular level, it now seems that activin acts largely as an autocrine and/or paracrine growth factor, similar to other members of the transforming growh factor beta superfamily. As we discuss in the next section, its actions are regulated extracellularly by both inhibin and FS. In the final section, intracellular mediators and modulators of activin signaling are reviewed in detail. Many of these are shared with other transforming growh factor beta superfamily members as well as unrelated molecules, and in a number of cases, their physiological relevance to activin signal propagation remains to be elucidated. Nevertheless, taken together, recent findings suggest that it may be more appropriate to consider a new paradigm for inhibin, activin, and FS in which activin signaling is regulated extracellularly by both inhibin and FS whereas a number of intracellular proteins act to modulate cellular responses to these activin signals. It is therefore the balance between activin and all of its modulators, rather than the actions of any one component, that determines the final biological outcome. As technology and model systems become more sophisticated in the next few years, it should become possible to test this concept directly to more clearly define the role of activin, inhibin, and FS in reproductive physiology.
Detailed DNA methylation profiles of the E-cadherin promoter in the NCI-60 cancer cells (2007)

E-cadherin (E-cad) is a transmembrane adhesion glycoprotein, the expression of which is often reduced in invasive or metastatic tumors. To assess E-cad's distribution among different types of cancer cells, we used bisulfite-sequencing for detailed, base-by-base measurement of CpG methylation in E-cad's promoter region in the NCI-60 cell lines. The mean methylation levels of the cell lines were distributed bimodally, with values pushed toward either the high or low end of the methylation scale. The 38 epithelial cell lines showed substantially lower (28%) mean methylation levels compared with the nonepithelial cell lines (58%). The CpG site at -143 with respect to the transcriptional start was commonly methylated at intermediate levels, even in cell lines with low overall DNA methylation. We also profiled the NCI-60 cell lines using Affymetrix U133 microarrays and found E-cad expression to be correlated with E-cad methylation at highly statistically significant levels. Above a threshold of approximately 20% to 30% mean methylation, the expression of E-cad was effectively silenced. Overall, this study provides a type of detailed analysis of methylation that can also be applied to other cancer-related genes. As has been shown in recent years, DNA methylation status can serve as a biomarker for use in choosing therapy.
Gene-Coding Assignments of Rotavirus Double-Stranded RNA Segments 10 and 11 (1981)

The gene-coding assignments for genome segments 10 and 11 of a simian virus and two human rotaviruses were determined. For those viruses having a "long" RNA gel pattern (electropherotype), segments 10 and 11 encoded proteins NS(3) and O(4), respectively. The human virus with a "short" electropherotype had the opposite assignments and also differed in (enzyme-linked immunosorbent assay) serotype from the human virus with a long electropherotype.
Significant satiety effect of bombesin in lean but not in obese subjects. (1994)

The aim of this work was to determine whether infusion of bombesin inhibits intake of a carbohydrate-rich meal in lean and obese women. A double blind study was carried out using bombesin or saline infusion. The subjects were nine lean and nine obese women of the same age. Food intake and hunger feelings were measured. During infusion of bombesin, the amount of food eaten by the lean individuals (294 +/- 55 g) was significantly less than during infusion of saline (467 +/- 69 g, P < 0.01). However, bombesin induced no significant feeding suppression in the obese women when compared to saline (431 +/- 60 vs 499 +/- 99 g). Subjective hunger feelings were significantly affected by bombesin infusion in the lean subjects only. It was concluded that bombesin infusion inhibits food intake and increases satiety in lean women, whereas obese women are less sensitive to these bombesin-induced satiety effects.
Expression ofBCR/ABLandBCL-2in myeloid progenitors leads to myeloid leukemias (2003)

Chronic myelogenous leukemia is a myeloproliferative disorder (MPD) that, over time, progresses to acute leukemia. Both processes are closely associated with the t(9;22) chromosomal translocation that creates the BCR/ABL fusion gene in hematopoietic stem cells (HSCs) and their progeny. Chronic myelogenous leukemia is therefore classified as an HSC disorder in which a clone of multipotent HSCs is likely to be malignantly transformed, although direct evidence for malignant t(9;22)+ HSCs is lacking. To test whether HSC malignancy is required, we generated hMRP8p210BCR/ABL transgenic mice in which expression of BCR/ABL is absent in HSCs and targeted exclusively to myeloid progenitors and their myelomonocytic progeny. Four of 13 BCR/ABL transgenic founders developed a chronic MPD, but only one progressed to blast crisis. To address whether additional oncogenic events are required for progression to acute disease, we crossed hMRP8p210BCR/ABL mice to apoptosis-resistant hMRP8BCL-2 mice. Of 18 double-transgenic animals, 9 developed acute myeloid leukemias that were transplantable to wild-type recipients. Taken together, these data indicate that a MPD can arise in mice without expression of BCR/ABL in HSCs and that additional mutations inhibiting programmed cell death may be critical in the transition of this disease to blast-crisis leukemia.
Modifying the chain-length selectivity of the lipase from Burkholderia cepacia KWI-56 through in vitro combinatorial mutagenesis in the substrate-binding site (2002)

The mature lipase of Burkholderia cepacia KWI-56 was synthesized in an enzymatically active form using an in vitro Escherichia coli S30 coupled transcription/translation system by expressing the mature lipase gene (rlip) in the presence of its specific activator. To investigate the substrate specificity of the lipase comprehensively, a large number of mutant lipases were constructed and analyzed in a high throughput manner by combining overlapping PCR and in vitro protein synthesis. In this paper, Phe119 and Leu167, which are located in the acyl portion of the substrate-binding pocket of the lipase of B.cepacia KWI-56, were substituted with six hydrophobic amino acid residues by the in vitro combinatorial mutagenesis. The wild-type and 35 mutant genes amplified by PCR were directly used as templates for the in vitro transcription/translation. The acyl chain-length selectivity of the in vitro expressed lipases against p-nitrophenyl butyrate, p-nitrophenyl caprylate and p-nitrophenyl palmitate, was compared by their relative hydrolysis rates. Two mutant lipases, L167V and F119A/L167M, which showed a significant shift in substrate selectivity were further expressed in vivo and refolded in vitro. It was found that L167V raised its preference for the short-chain ester, whereas F119A/L167M improved its selectivity for the long-chain ester.
Enzymatic hydrolysis of steam-pretreated lignocellulosic materials with Trichoderma atroviride enzymes produced in-house (2009)

Enzyme supernatants produced by the mutant T. atroviride TUB F-1663 on various pretreated lignocellulosic substrates have good filter paper activity values combined with high levels of beta-glucosidase activities, leading to cellulose conversion in the enzymatic hydrolysis that is as efficient as with a commercial cellulase mixture. On the other hand, in order to achieve good xylan conversion, the supernatants produced by the mutant have to be supplemented with additional beta-xylosidase activity.
Preparation of spherical encapsulation of activated carbons and their adsorption capacity of typical uremic toxins (1990)

A method has been designed for making spherical microencapsulation of activated-carbon particles for use in the removal of metabolic wastes and/or toxins from blood. This bench-scale method was able to make better uniformity in particle size, and at a higher particle production rate. The material properties such as particle size, particle porosity, electromicroscopy of surface morphology, surface hardness, and pore-size distribution were characterized in order to conclude with their adsorption capacity for specific toxin solutes. The performance characteristics of these self-prepared particle encapsulation was also evaluated against the commercially available hemoperfusion particles, e.g., Kuraray's DHP (Japan). The encapsulation particles were also coated with polyhydroxyethyl methacrylate (PHEMA) for blood compatibility purpose.
Nitric Oxide Inactivates Xanthine Dehydrogenase and Xanthine Oxidase in Interferon-γ-Stimulated Macrophages (1994)

Abstract Interferon-γ (IFN-γ) has been reported to up-regulate transcription of the xanthine dehydrogenase (XDH) gene and to regulate XDH and xanthine oxidase (XO) activity in endothelial cells and liver tissue. Macrophages are a source of XDH/XO activity at inflammatory sites and are functionally regulated by IFN-γ. We studied the effect of IFN-γ on XDH and XO in rat bone marrow macrophages, rat alveolar macrophages, and murine RAW cells. Instead of an induction of enzyme activity, XDH/XO activity was almost totally lost after incubation with 100 to 1,000 U/ml of IFN-γ for 24 h in all three cell types. The loss of cell-associated XDH/XO activity was not correlated with the appearance of XDH/XO activity in the media. In addition, the loss of XDH/XO activity could not be accounted for by transcriptional repression, since there was an increase in steady-state levels of XDH mRNA. To determine whether XDH/XO activity might be lost through nitric oxide-mediated inactivation of XDH/XO, we compared the time course and dose response for XDH/XO inactivation with that of nitric oxide production and found them similar. Treatment with the nitric oxide inhibitor N-monomethyl arginine appeared to totally block inactivation of XDH/XO by IFN-γ. We conclude that upon stimulation with IFN-γ, inducible nitric oxide in macrophages leads to post-transcriptional inhibition of XDH/XO, possibly minimizing the potential for tissue injury from XO released from macrophages into the inflammatory milieu. Inactivation of XDH may represent yet another "protective" role for nitric oxide at sites of inflammation.
Predictors of a favourable response to icodextrin in peritoneal dialysis patients with ultrafiltration failure (2005)

Icodextrin significantly augments ultrafiltration volumes in patients with refractory fluid overload. A high peritoneal membrane transporter status is the best predictor of a favourable ultrafiltration response to icodextrin.
Both-faces hindered porphyrins. Part 1. Synthesis and characterization of basket-handle porphyrins and their iron complexes (1983)

The synthesis of the ‘both-faces’ hindered porphyrins using two different methods is reported. These so-called ‘basket-handle’ porphyrins (BHP) are derived from 5,10,15,20-tetraphenylporphyrin in which two opposite phenyl groups are bridged by alkylene or arylene-p-bisalkylene chains. In addition to the desired compounds [the cross-trans-linked isomer (7)], two other isomers were obtained [adjacent-trans-linked (8) and adjacent-cis-linked (9)]. These were separated by t.l.c. on silica gel and then individually characterized. The structural assignment of the three isomers in the five series studied was based on the 1H n.m.r. spectra of the free bases and of their iron(II) complexes.
Escalas de equivalencia de consumo y deducciones por hijos en el impuesto personal sobre la renta: una aplicación al caso español (1999)

La equidad horizontal en el Impuesto Personal sobre la Renta exige graduar la carga
tributaria de las familias en funcion de su tamano y composicion. Sin embargo, en la
practica, es la renta monetaria el indicador de capacidad de pago empleado por el Impuesto,
siendo las deducciones familiares en la cuota el unico factor de correccion del coste que
supone la existencia de personas a cargo, principalmente los hijos, del sujeto pasivo. En
nuestro trabajo estimamos una escala de consumo equivalente a partir de los datos de la
Encuesta de Presupuestos Familiares 1990-91 para comparar el gasto necesario de dos
familias con distinta composicion para alcanzar el mismo nivel de bienestar. Comparado
con la renta equivalente de estas familias despues del pago del Impuesto sobre la Renta
podemos comprobar como el tratamiento que reciben las unidades familiares se aleja
notoriamente de este principio de equidad horizontal.
Asymmetric Flexible Supercapacitor Stack (2008)

Electrical double layer supercapacitor is very significant in the field of electrical energy storage which can be the solution for the current revolution in the electronic devices like mobile phones, camera flashes which needs flexible and miniaturized energy storage device with all non-aqueous components. The multiwalled carbon nanotubes (MWNTs) have been synthesized by catalytic chemical vapor deposition technique over hydrogen decrepitated Mischmetal (Mm) based AB3alloy hydride. The polymer dispersed MWNTs have been obtained by insitu polymerization and the metal oxide/MWNTs were synthesized by sol-gel method. Morphological characterizations of polymer dispersed MWNTs have been carried out using scanning electron microscopy (SEM), transmission electron microscopy (TEM and HRTEM). An assymetric double supercapacitor stack has been fabricated using polymer/MWNTs and metal oxide/MWNTs coated over flexible carbon fabric as electrodes and nafion®membrane as a solid electrolyte. Electrochemical performance of the supercapacitor stack has been investigated using cyclic voltammetry, galvanostatic charge-discharge, and electrochemical impedance spectroscopy.
The use of hapten-polysaccharide conjugates for the induction of B-cell tolerance involving IgE responses. I. Preparation, characterization and specific tolerogenic activity of penicilloy l-substituted levans affecting IgE responses in normal and sensitized mice. (1978)

Benzyl penicillin was coupled directly to the hydroxylic groups of dextrans and levans, and indirectly to the amino groups of diaminopropyl-carboxymethyl-levans. Derivatives of both types were tested for their capacity to react with anti-penicilloyl antibodies, either in vitro (immunoprecipitation and its inhibition) or in vivo (inhibition of PCA reaction). Only derivatives coupled to diaminopropyl-carboxymethyl-levans were active by both criteria. High molecular weight penicilloyl-diaminopropyl-carboxymethyl-levans were tested for their immunogenicity (IgM response) and capacity to induce tolerance in the IgE component of anti-penicilloyl responses in DBA/2 and CBAT6T6 mice. The IgM response to the levan carrier was very much depressed by penicilloyl substitution of the levan, whilst that to the penicilloyl determinants was also very poor. These derivatives induced a state of IgE antibody tolerance when given before or after the induction of an allergic response with penicilloyl-ovalbumin. A higher degree of substitution was required for the induction of tolerance after immunization. The tolerance induced was specific, since it did not affect IgE responses against ovalbumin and persisted for at least 3 months. Further challenges with penicilloyl-ovalbumin did not break the tolerant status.
Widows: perceptions, demography, residence patterns, and standard of living (2002)

The role of the widow in society can be explored from a variety of perspectives. Five of these are featured prominently in the set of articles assembled below: specification of the range of behavio...
Positioning unmanned aerial vehicles as communication relays for surveillance tasks (2009)

When unmanned aerial vehicles (UAVs) are used to survey distant targets, it is important to transmit sensor information back to a base station. As this communication often requires high uninterrupted bandwidth, the surveying UAV often needs a free line-of-sight to the base station, which can be problematic in urban or mountainous areas. Communication ranges may also be limited, especially for smaller UAVs. Though both problems can be solved through the use of relay chains consisting of one or more intermediate relay UAVs, this leads to a new problem: Where should relays be placed for optimum performance? We present two new algorithms capable of generating such relay chains, one being a dual ascent algorithm and the other a modification of the Bellman-Ford algorithm. As the priorities between the number of hops in the relay chain and the cost of the chain may vary, we calculate chains of different lengths and costs and let the ground operator choose between them. Several different formulations for edge costs are presented. In our test cases, both algorithms are substantially faster than an optimized version of the original Bellman-Ford algorithm, which is used for comparison.