gebhart/patrepeval huggingface dataset:
Activation of SoxR-Dependent Transcription in Pseudomonas aeruginosa (2004)

The SoxR protein of Escherichia coli responds to redox signals by activating the transcription of soxS, which encodes another transcription activator that directly stimulates oxidative stress genes. In contrast, Pseudomonas aeruginosa has an open reading frame (ORF) encoding a putative protein homologous to E. coli SoxR, but not to SoxS. Instead of a soxS homolog, ORFs encoding an unknown hypothetical protein and soxR are arranged divergently with their 5' ends separated by a 78 bp region containing a sequence homologous to the SoxR-binding soxS promoter. In this study, we report the overproduction and purification of SoxR from P. aeruginosa to investigate the mechanism of gene activation by SoxR. The spectroscopic properties of the purified SoxR protein indicate that it contains a redox active iron-sulfur [2Fe-2S] cluster. Redox titration of the SoxR protein revealed a midpoint potential of -290 mV. The SoxR protein specifically binds a fragment of the SoxS promoter-like region in a concentration-dependent fashion, as shown by both gel mobility shift and fluorescence polarization assays. The purified SoxR stimulates the in vitro transcription of the gene encoding the hypothetical protein in P. aeruginosa. This activity was lost following reduction of the SoxR [2Fe-2S] clusters. The levels of mRNA in the hypothetical protein increased in paraquat-treated cells. These results indicate that P. aeruginosa SoxR is a direct transcriptional activator of the hypothetical protein, and suggest that SoxR proteins may play multiple regulatory roles as a transcription factor in addition to its protective role in oxidative stress.
Jalview Version 2—a multiple sequence alignment editor and analysis workbench (2009)

The Jalview 2 Desktop application and JalviewLite applet are made freely available under the GPL, and can be downloaded from www.jalview.org.
Defect Etch for <100> Silicon Evaluation (1979)

The Secco etch, with ultrasonic agitation, is widely used to determine dislocation densities in <100> Si. Experiments have shown that under certain conditions, the cavitation of the ultrasonics can generate anomalous defect etch pits. A new defect etch formulation was developed for evaluating <100> Si ingot material which does not require ultrasonic agitation. It consists of . The etching time compared to Secco etch with ultrasonics is reduced by one‐half in developing etch pits of equivalent size. This composition is useful for revealing dislocations in 0.6–15 Ωcm n‐ and p‐type silicon. In addition, dislocation etch pits are readily developed in more heavily doped <100> Si crystals using a mixture of.
Analytic explanation of spatial resolution related to bandwidth and detector aperture size in thermoacoustic or photoacoustic reconstruction (2003)

An analytic explanation of the spatial resolution in thermoacoustic or photoacoustic reconstruction is presented. Three types of specific recording geometries, including spherical, planar, and cylindrical surface, as well as other general cases, are investigated. Analytic expressions of the point-spread functions (PSF's), as a function of the bandwidth of the measurement system and the finite size of the detector aperture, are derived based on rigorous reconstruction formulas. The analyses clearly reveal that the dependence of the PSF's on the bandwidth of all recording geometries shares the same space-invariant expression while the dependence on the aperture size of the detector differs. The bandwidth affects both axial and lateral resolutions; in contrast, the detector aperture blurs the lateral resolution greatly but the axial resolution only slightly.
Stimulated mobilization of monocyte Mac-1 and p150,95 adhesion proteins from an intracellular vesicular compartment to the cell surface. (1987)

Monocytes were stimulated to increase their cell surface quantity of leukocyte adhesion proteins p150,95 and Mac-1 by the chemoattractant formyl-methionyl-leucyl-phenylalanine, or other mediators such as platelet-derived growth factor, tumor necrosis factor, C5a, and leukotriene B4. Dose-response curves indicated variations in the sensitivity of monocytes and granulocytes to these mediators. These increases were independent of protein synthesis and half-maximal at 2 min. Human alveolar and murine peritoneal macrophages, cells that had previously diapedised, could not be induced to upregulate Mac-1 or p150,95. Detergent permeabilization studies in monocytes indicated that these proteins were stored in internal latent pools, which were reduced upon stimulation. Electron microscopy utilizing rabbit antiserum against p150,95 revealed these proteins on the plasma membrane, and in intracellular vesicles and peroxidase negative granules. Together with other functional studies, these findings suggest that the mobilization of Mac-1 and p150,95 from an intracellular compartment to the plasma membrane regulates the monocyte's ability to adhere and diapedese.
Traffic Jam: A Compendium of Human Diseases that Affect Intracellular Transport Processes (2000)

As sequencing of the human genome nears completion, the genes that cause many human diseases are being identified and functionally described. This has revealed that many human diseases are due to defects of intracellular trafficking. This 'Toolbox' catalogs and briefly describes these diseases.
Antimelanoma monoclonal antibody-ricin A chain immunoconjugate (XMMME-001-RTA) plus cyclophosphamide in the treatment of metastatic malignant melanoma: results of a phase II trial. (1990)

Prior studies with the XMMME-001-RTA immunoconjugate composed of an antimelanoma monoclonal antibody and ricin A chain demonstrated some antitumor activity. However, almost all patients studied developed human antimurine antibodies and antiricin antibodies. In an effort to abrogate these host anti-immunotoxin immune responses and thus enhance antitumor activity, we treated 20 patients with the immunoconjugate plus a single dose of intravenous cyclophosphamide. An overall response rate of 20% was observed-predominantly in pulmonary and soft tissue nodules. There was no diminution in antibody responses against either the murine antibody or the ricin moiety. Further studies to elucidate the role of cyclophosphamide in monoclonal antibody therapy are planned.
La concreción del delito antecedente en el blanqueo de capitales (1) (2015)

El presente trabajo de investigacion refiere a la controvertida determinacion y concrecion de la actividad delictiva antecedente, fuente originaria de los bienes, como elemento objetivo del delito de blanqueo de capitales, asi como su debida acreditacion y el tipo de prueba que sirve a su evidencia, todo ello en el marco del tipo penal contenido en el art. 301 del CP y las posiciones jurisprudenciales mas significativas que lo desarrollan.
Aberrant expression of the gastric mucin MUC6 in human pulmonary adenocarcinoma xenografts (2005)

Certain pulmonary adenocarcinomas show gastrointestinal differentiation with the expression of various mucins. The CDX homeobox gene, an intestine-specific transcription factor, is related to gastric carcinogenesis with MUC2 and MUC6 expression. The intestinal mucin MUC2 is expressed in the normal lung, while the gastric mucin MUC6 is not. Previously, we have reported that the expressions of MUC2 and MUC6 were related to a poor prognosis in small adenocarcinomas of the lung. We estimated the expressions of the mucin (MUC2 and MUC6) and CDX (CDX1 and CDX2) to examine how CDX relates to the gastrointestinal mucin production in the pulmonary adenocarcinoma. Thirty-nine human non-small cell lung cancer (NSCLC) xenografts were examined (13 adenocarcinoma, 18 squamous cell carcinoma and 8 large cell carcinoma). Significant expression of the MUC6 gene was observed in 7 out of 39 (17.9%) NSCLC xenografts. The expressions of the MUC6 genes were noted in 6 out of 13 (46.2%) adenocarcinoma xenografts, but only in 1 of 18 (0.06%) squamous cell carcinoma xenografts. The adenocarcinoma xenografts significantly showed higher expression of the MUC6 gene than squamous cell carcinoma xenografts (t-test, p=0.0343). Four adenocarcinoma-xenografts co-expressed both the MUC2 and MUC6 genes, and the residual 2 adenocarcinoma-xenografts expressed only the MUC6 gene. One MUC6 overexpressing squamous cell carcinoma focally contained an adenocarcinoma component. The expression patterns of the gastrointestinal mucins were analogous to gastric cancer. The cellular morphology of these carcinoma xenografts was of the gastric cancer type. The proteins of the MUC2 and MUC6 were immunohistochemically confirmed in the xenografts. The expression of the MUC6 gene was significantly correlated with the expressions of the CDX1 and CDX2 genes in the xenografts (Fisher's test, p<0.0001 and p=0.0005, respectively), while there was no significant association between the expression of the MUC2 and CDX genes. These results suggest that the expression of CDX molecules in the pulmonary carcinogenesis pathway relates to gastric cancerous features of aberrant MUC6 expression.
The structure and function of the glucagon‐like peptide‐1 receptor and its ligands (2011)

Glucagon-like peptide-1(7-36)amide (GLP-1) is a 30-residue peptide hormone released from intestinal L cells following nutrient consumption. It potentiates the glucose-induced secretion of insulin from pancreatic beta cells, increases insulin expression, inhibits beta-cell apoptosis, promotes beta-cell neogenesis, reduces glucagon secretion, delays gastric emptying, promotes satiety and increases peripheral glucose disposal. These multiple effects have generated a great deal of interest in the discovery of long-lasting agonists of the GLP-1 receptor (GLP-1R) in order to treat type 2 diabetes. This review article summarizes the literature regarding the discovery of GLP-1 and its physiological functions. The structure, function and sequence-activity relationships of the hormone and its natural analogue exendin-4 (Ex4) are reviewed in detail. The current knowledge of the structure of GLP-1R, a Family B GPCR, is summarized and discussed, before its known interactions with the principle peptide ligands are described and summarized. Finally, progress in discovering non-peptide ligands of GLP-1R is reviewed. GLP-1 is clearly an important hormone linking nutrient consumption with blood sugar control, and therefore knowledge of its structure, function and mechanism of action is of great importance.
Interaction between Phosphatidylserine and the Phosphatidylserine Receptor Inhibits Immune Responses In Vivo (2005)

Phosphatidylserine (PS) on apoptotic cells promotes their uptake and induces anti-inflammatory responses in phagocytes, including TGF-beta release. Little is known regarding the effects of PS on adaptive immune responses. We therefore investigated the effects of PS-containing liposomes on immune responses in mice in vivo. PS liposomes specifically inhibited responses to Ags as determined by decreased draining lymph node tissue mass, with reduced numbers of total leukocytes and Ag-specific CD4(+) T cells. There was also a decrease in formation and size of germinal centers in spleen and lymph nodes, accompanied by decreased levels of Ag-specific IgG in blood. Many of these effects were mimicked by an agonistic Ab-specific for the PS receptor. TGF-beta appears to play a critical role in this inhibition, as the inhibitory effects of PS were reversed by in vivo administration of anti-TGF-beta Ab. PS-containing liposomes did not appear to directly inhibit dendritic cell maturation in vitro in response to a variety of stimuli, nor did it prevent their migration to regional lymph nodes in vivo, suggesting that the inhibitory effects may have resulted from complicated interactions between tissue cells and dendritic cells, subsequently inhibiting their ability to productively activate T lymphocytes.
Correlation between the anticellular and DNA fragmenting activities of tumor necrosis factor. (1988)

The treatment of cells sensitive to the anticellular effect of tumor necrosis factor (TNF) with TNF results in a degradation of their cellular DNA into DNA fragments that are multiples of 200 base pairs. TNF treatment of cells resistant to the anticellular effect of TNF, but bearing receptors for TNF, fails to result in any DNA fragmentation. Incubation conditions, such as temperature, the presence of metabolic inhibitors or amino acid deprivation, that modulate the effectiveness of TNF or affect the rate at which TNF exerts its anticellular effect have a similar effect on the ability of the TNF to generate DNA fragments. Thus the TNF-mediated DNA fragmentation and the rate at which it occurs correlates with the rate at which cells respond to the anticellular effect of TNF and, as such, might serve as a marker for the responsiveness of cells to TNF.
Remote, Long-Pathlength Cell for High-Sensitivity Raman Spectroscopy (1987)

Fiber optics were used to interface a Raman spectrometer to a long (1 m) sample tube, with the objective being increased sensitivity. Internal reflection of the laser light and the Raman scatter within the sample tube permitted a long solution length to be sampled, increasing the Raman sensitivity by factors of 30–50 over conventional capillary tube sampling systems. In addition, the sample was subjected to much lower power densities than with systems employing a focused beam, thus minimizing radiation damage. Detection limits of 10 −9 to 10 −8 M were achieved for resonance Raman scatterers, and normal Raman scatterers could be detected at the 1 × 10 −5 M level.
Influence of acetylsalicylic acid on antibody-dependent cellular cytotoxicity (ADCC) of peritoneal macrophages. (1993)

Very recent evidence indicates that, in addition to its already known analgesic, anti-inflammatory, antipyretic, and platelet-aggregation-inhibiting properties, acetylsalicylic acid (ASA) exerts a positive influence on the immune system. Therefore, its action on murine peritoneal macrophages was investigated in the present study. Various ASA concentrations (50-200 micrograms/ml) failed to have any stimulating or inhibiting effect on antibody-dependent cellular cytotoxicity (ADCC) and on the binding capacity of macrophages from various levels of activation against SW 707 tumor cells. Furthermore, no time dependence of the stimulation was observed over a period of up to 48 hrs. These results suggest that the reported positive effect of ASA on the immune system, manifested by increased production of interleukins and interferon, is due to an interaction of macrophages and lymphocytes and not to a direct increase in macrophage activity.
Glucocorticoid regulation of genes in the amiloride-sensitive sodium transport pathway by semicircular canal duct epithelium of neonatal rat (2005)

The lumen of the inner ear has an unusually low concentration of endolymphatic Na+, which is important for transduction processes. We have recently shown that glucocorticoid receptors (GR) stimulate absorption of Na+ by semicircular canal duct (SCCD) epithelia. In the present study, we sought to determine the presence of genes involved in the control of the amiloride-sensitive Na+ transport pathway in rat SCCD epithelia and whether their level of expression was regulated by glucocorticoids using quantitative real-time RT-PCR. Transcripts were present for alpha-, beta-, and gamma-subunits of the epithelial sodium channel (ENaC); the alpha1-, alpha3-, beta1-, and beta3-isoforms of Na+-K+-ATPase; inwardly rectifying potassium channels [IC50 of short circuit current (Isc) for Ba2+: 210 microM] Kir2.1, Kir2.2, Kir2.3, Kir2.4, Kir3.1, Kir3.3, Kir4.1, Kir4.2, Kir5.1, and Kir7.1; sulfonyl urea receptor 1 (SUR1); GR; mineralocorticoid receptor (MR); 11beta-hydroxysteroid dehydrogenase (11beta-HSD) types 1 and 2; serum- and glucocorticoid-regulated kinase 1 (Sgk1); and neural precursor cell-expressed developmentally downregulated 4-2 (Nedd4-2). On the other hand, transcripts for the alpha4-subunit of Na+-K+-ATPase, Kir1.1, Kir3.2, Kir3.4, Kir6.1, Kir6.2, and SUR2 were found to be absent, and Isc was not inhibited by glibenclamide. Dexamethasone (100 nM for 24 h) not only upregulated the transcript expression of alpha-ENaC (approximately 4-fold), beta2-subunit (approximately 2-fold) and beta3-subunit (approximately 8-fold) of Na+-K+-ATPase, Kir2.1 (approximately 5-fold), Kir2.2 (approximately 9-fold), Kir2.4 (approximately 3-fold), Kir3.1 (approximately 3- fold), Kir3.3 (approximately 2-fold), Kir4.2 (approximately 3-fold), Kir7.1 (approximately 2-fold), Sgk1 (approximately 4-fold), and Nedd4-2 (approximately 2-fold) but also downregulated GR (approximately 3-fold) and 11beta-HSD1 (approximately 2-fold). Expression of GR and 11beta-HSD1 was higher than MR and 11beta-HSD2 in the absence of dexamethasone. Dexamethasone altered transcript expression levels (alpha-ENaC and Sgk1) by activation of GR but not MR. Proteins were present for the alpha-, beta-, and gamma-subunits of ENaC and Sgk1, and expression of alpha- and gamma-ENaC was upregulated by dexamethasone. These findings are consistent with the genomic stimulation by glucocorticoids of Na+ absorption by SCCD and provide an understanding of the therapeutic action of glucocorticoids in the treatment of Meniere's disease.
Mild detergent treatment of Candida tropicalis reveals a NADPH‐dependent reductase in the crude membrane fraction, which enables the production of pure bicyclic exo‐alcohol (2004)

This study demonstrated the occurrence of a NADPH-dependent exo-alcohol reductase in the crude membrane fraction of Candida tropicalis. Cytosolic endo-alcohol reductase activity could be separated from the membrane-bound exo-alcohol activity by means of detergent treatment, enabling the preparation of pure exo-alcohol via the enzymatic conversion of the bicyclic diketone, bicyclo[2.2.2]octane-2,6-dione. The exo-alcohol reductase is, to our knowledge, the first membrane-bound NADPH-dependent reductase accepting a xenobiotic carbonyl substrate that was not a steroid. When C. tropicalis was grown on D-sorbitol, a two-fold increase in the exo-reductase activity was observed as compared to when grown on glucose. An in silico comparison at the protein level between putative xenobiotic carbonyl reductases in Candida albicans, C. tropicalis and Saccharomyces cerevisiae was performed to explain why Candida species are often encountered when screening yeasts for novel stereoselective reduction properties. C. albicans contained more reductases with the potential to reduce xenobiotic carbonyl compounds than did S. cerevisiae. C. tropicalis had many membrane-bound reductases (predicted with the bioinformatics program, TMHMM), some of which had no counterpart in the two other organisms. The exo-reductase is suspected to be either a beta-hydroxysteroid dehydrogenase or a polyol dehydrogenase from either the short chain dehydrogenase family or the dihydroflavonol reductase family.
RPC investigation using finely spaced 2-D strip readout (2007)

RPCs are in use for many high energy physics applications where there is no need for fine spatial resolution. However, there are applications such as digital calorimetry where the dimension of the induced charge at pick-up pads is of interest. Such calorimetry is proposed for eg, Particle flow calorimetrey at the ILC. While there are both experiments and calculations which address this to some extent, we have been able to read out a single gap RPC using fine pitch laser etched two-dimensional strip readout as used in GEM tracking. This measurement was made in the Fermilab test beam in conjunction with the GEM tracking test for the STAR upgrade. We discuss both data and electrostatic simulations of the signal from a single gap glass RPC.
Dynamic Eco-Driving for Signalized Arterial Corridors and Its Indirect Network-Wide Energy/Emissions Benefits (2012)

There are various strategies being considered to reduce fuel consumption and emissions from the transportation sector. From the transportation operations perspective, one strategy that has gained interest worldwide is eco-driving. Eco-driving typically consists of changing a person's driving behavior based on providing general advice to the driver, such as accelerating slowly, driving smoothly, and reducing high speeds. More advanced dynamic eco-driving provides real-time advice to drivers based on changing traffic and infrastructure conditions for even greater fuel and emission savings. The concept of dynamic eco-driving takes advantage of real-time traffic sensing and infrastructure information, which can then be communicated to a vehicle with a goal of reducing fuel consumption and emissions. This article considers dynamic eco-driving in an arterial corridor with traffic control signals, where signal phase and timing (SPaT) information of traffic lights is provided to the vehicle as it drives down the corridor. The vehicle can then adjust its velocity while traveling through the corridor with the goal of minimizing fuel consumption and emissions. A dynamic eco-driving velocity planning methodology has been developed and is described herein. This algorithm has then been extensively tested in simulation, showing individual vehicle fuel consumption and CO2 reductions of around 10–15%, depending on corridor parameters including traffic volume, traffic speed, and other factors. This 10–15% improvement is realized directly by the vehicle that is equipped with this dynamic eco-driving technology and can be accomplished with very little time loss. We have also carried out an extensive analysis of the entire traffic stream under different traffic volumes and different penetration rates of the dynamic eco-driving technology. It is found that there are also significant indirect network-wide energy and emissions benefits on the overall traffic, even at low penetration rates of the technology-equipped vehicles. Based on the simulation results, the maximum fuel saving and emission reduction occur during medium traffic volumes (corresponding to traffic volume of 300 vehicles/hr/link) and with low penetration rates (5%, 10%, and 20%). Under these conditions, the total traffic energy/emissions savings typically triple what is saved from the technology-equipped vehicles alone (e.g., total 4% savings compared to 1.3% savings). This is due primarily to the eco-driving velocity planning affecting nonequipped vehicles that follow behind.
Diblock Copolymer Thin Films on Heterogeneous Striped Surfaces: Commensurate, Incommensurate and Inverted Lamellae (1998)

We study a symmetric melt $\mathrm{AB}$ diblock copolymer thin film which is placed on a periodically striped $\mathrm{CD}$ surface. Because of different surface energies each stripe has a different preference for each of the blocks. There is thus a competition between the preferred bulk lamellar spacing, ${L}_{b}$, and the width of the stripes, $\ensuremath{\lambda}$. This system is similar to the Frenkel-Kontorowa model of solid state physics. We consider the case ${L}_{b}\ensuremath{\ge}\ensuremath{\lambda}$, and assume perpendicular alignment. The periodic striped surface will induce lamellae with unequal spacings. We also show that the striped potential can induce inverted bilayers, i.e., an $AB,AB$ pattern rather than the more usual $AB,BA$.