gebhart/patrepeval huggingface dataset:
Electrochemical Reduction of Benzoic Acid and Substituted Benzoic Acids in Some Room Temperature Ionic Liquids (2008)

Using cyclic voltammetry, the electrochemical reduction of benzoic acid (BZA) has been studied at Pt and Au microelectrodes (10 and 2 μm diameter) in six room temperature ionic liquids (RTILs), namely [C2mim][NTf2], [C4mim][NTf2], [C4mpyrr][NTf2], [C4mim][BF4], [C4mim][NO3], and [C4mim][PF6] (where [Cnmim]+ = 1-alkyl-3-methylimidazolium, [NTf2]− = bis(trifluoromethylsulfonyl)imide, [C4mpyrr]+ = N-butyl-N-methylpyrrolidinium, [BF4]− = tetrafluoroborate, [NO3]− = nitrate, and [PF6]− = hexafluorophosphate). In all cases, a main reduction peak was observed, assigned to the reduction of BZA in a CE mechanism, where dissociation of the acid takes place before electron transfer to the dissociated proton. One anodic peak was observed on the reverse sweep, assigned to the oxidation of adsorbed hydrogen, and a reductive “prepeak” (assigned to the reduction of protons forming adsorbed hydrogen, H•(ads)) was observed before the main reduction peak. On extending the cathodic window, an electrochemically reversible peak was observed in [C4mpyrr][NTf2] and [C4mim][BF4], assigned to the reduction of the radical anion of BZA forming the dianion (C6H5•C(O−)2), thought to be stable in RTIL media. The voltammetry of 4-methoxy, 4-chloro, 4-bromo and 4-dialkylamino substituted BZAs yielded a main reduction peak, with two anodic peaks on the reverse sweep, (assigned to the oxidation of adsorbed hydrogen H•(ads) and the oxidation of C6H5CO2− to form (C6H5)• and CO2). At more negative potentials, the electrochemically reversible radical anion reduction peak was also observed. Potential-step chronoamperometry revealed diffusion coefficients of ca. 2 × 10−11 m2 s−1 for all BZA derivatives studied in [C4mpyrr][NTf2], with a slight tendency to decrease with increasing size of substituent. The solubilities of the substituted BZAs were much lower than that of the nonsubstituted form. In addition, the oxidation of 4-dimethylamino- and 4-diethylaminobenzoic acid yielded a sharp anodic peak, suggesting the possible formation of substituted polyaniline on the Pt electrode surface.
Bone-marrow transplantation in a patient with the Wiskott-Aldrich syndrome (1969)

Abstract A 2-year-old boy with the Wiskott-Aldrich syndrome has been treated by bone-marrow transplantation. An initial attempt to transplantation without extensive preparation of the recipient failed. Subsequently the recipient was prepared with a 4-day course of cyclophosphamide followed by bone-marrow transplantation from a sister identical at HL-A— the major histocompatibility locus in man. 6 weeks after transplantation the patient is chimaric and has shown no evidence of graft-versus-host disease.
Glucose-induced protein kinase C activity regulates arachidonic acid release and eicosanoid production by cultured glomerular mesangial cells. (1993)

Changes in glomerular eicosanoid production have been implicated in the development of diabetes-induced glomerular hyperfiltration and glomerular mesangial cells (GMC) are major eicosanoid-producing cells within the glomerulus. However, the mechanism for the effect of diabetes mellitus on glomerular mesangial eicosanoid production is unknown. The present study therefore examined whether elevated glucose concentrations activate protein kinase C (PKC) in GMC and whether this PKC activation mediates an effect of elevated glucose concentrations to increase the release of arachidonic acid and eicosanoid production by GMC. The percentage of [3H]arachidonic acid release per 30 min by preloaded GMC monolayers was significantly increased after 3-h exposure to high glucose (20 mM) medium (177% vs control medium) and this increase was sustained after 24-h exposure to high glucose concentrations. 3-h and 24-h exposure to high glucose medium also increased PGE2, 6-keto-PGF1 alpha, and thromboxane (TXB2) production by GMC. High glucose medium (20 mM) increased PKC activity in GMC at 3 and 24 h (168% vs control). In contrast, osmotic control media containing either L-glucose or mannitol did not increase arachidonic acid release, eicosanoid production, or PKC activity in GMC. Inhibiting glucose-induced PKC activation with either H-7 (50 microM) or staurosporine (1 microM) prevented glucose-induced increases in arachidonic acid release and eicosanoid production by GMC. These data demonstrate that elevated extracellular glucose concentrations directly increase the release of endogenous arachidonic acid and eicosanoids by GMC via mechanisms dependent on glucose-induced PKC activation.
Intracellular Macromolecular Mobility Measured by Fluorescence Recovery after Photobleaching with Confocal Laser Scanning Microscopes (2004)

Fluorescence recovery after photobleaching (FRAP) is a widely used tool for estimating mobility parameters of fluorescently tagged molecules in cells. Despite the widespread use of confocal laser scanning microscopes (CLSMs) to perform photobleaching experiments, quantitative data analysis has been limited by lack of appropriate practical models. Here, we present a new approximate FRAP model for use on any standard CLSM. The main novelty of the method is that it takes into account diffusion of highly mobile molecules during the bleach phase. In fact, we show that by the time the first postbleach image is acquired in a CLSM a significant fluorescence recovery of fast-moving molecules has already taken place. The model was tested by generating simulated FRAP recovery curves for a wide range of diffusion coefficients and immobile fractions. The method was further validated by an experimental determination of the diffusion coefficient of fluorescent dextrans and green fluorescent protein. The new FRAP method was used to compare the mobility rates of fluorescent dextrans of 20, 40, 70, and 500 kDa in aqueous solution and in the nucleus of living HeLa cells. Diffusion coefficients were lower in the nucleoplasm, particularly for higher molecular weight dextrans. This is most likely caused by a sterical hindrance effect imposed by nuclear components. Decreasing the temperature from 37 to 22 degrees C reduces the dextran diffusion rates by approximately 30% in aqueous solution but has little effect on mobility in the nucleoplasm. This suggests that spatial constraints to diffusion of dextrans inside the nucleus are insensitive to temperature.
Binding of Clostridium botulinum type C neurotoxin to different neuroblastoma cell lines (1989)

Binding of type C neurotoxin (C1 toxin) from Clostridium botulinum (strain Stockholm) to neuroblastoma cell lines was studied by using biotinylated anti-toxin antibody and avidin-biotinylated peroxidase complex. The neurotoxin bound with high efficiency to mouse neuroblastoma (NS-20Y and NIE-115) cells and to hybridomas of rat glioblastoma and mouse neuroblastoma (NG108-C15) cells. The toxin bound little to human neuroblastoma, rat astrocytoma, and nonneural cell lines. Binding of the neurotoxin to NG108-C15 cells was inhibited by gangliosides (GT1b and GM1) and by monoclonal antibodies (CA-12 and C-9), although inhibition was not complete. Sequential preincubation of C1 toxin with GT1b and CA-12 caused complete inhibition. A Scatchard plot of binding of 125I-labeled C1 toxin to NG108-C15 cells showed a hyperbolic curve. Monoclonal antibody CA-12 but not C-9 neutralized the lethal activity of the toxin toward mice. Only C-9 clearly inhibited toxin binding to GT1b. These results suggest that NG108-C15 cells have at least two kinds of receptors for C1 toxin. From the results of binding tests with neuraminidase-, pronase-, and trypsin-treated NG108-C15 cells, the chemical nature of the high-affinity site was presumed to be a glycoprotein containing sialic acid. GT1b may have an important role in low-affinity sites.
Differential expression of lymphoid and myeloid markers on differentiating hematopoietic stem cells in normal and tumor-bearing adult human liver (2000)

The presence and phenotype of lineage-committed hematopoietic progenitors in the normal adult human liver (AHL) were investigated and compared with the profiles of differentiating hematopoietic precursor populations detected in liver bearing metastases of colonic origin. Levels of hematopoietic stem cells (HSCs) (CD34(+)CD45(+)) detected in hepatic mononuclear cell (HMNC) populations were increased 6-fold when compared with matched peripheral blood samples. In normal liver, less than 5% of HSCs expressed the myeloid-associated antigen, CD33, whereas considerable proportions expressed lymphoid-associated markers (T cell, 33.39%; B cell, 17.39%; and natural killer [NK] cell, 37.17%). Significant increases were observed in the relative proportions of hepatic HSCs coexpressing CD33 (20.53%; P =.001), and the T-cell marker (CD7, 58. 13%; P =.02) in tumor-bearing liver compared with normal liver. HSCs with B-cell progenitor phenotype (CD19(+)) were significantly decreased in tumor-bearing liver (0.06%; P =.02). Despite these differences, the activation status of hematopoiesis, as measured by the coexpression of the differentiation and activation markers, CD38 and CD45RA, did not differ significantly between normal and tumor-bearing liver. These results indicate that the normal AHL harbors lineage-committed hematopoietic progenitors, and the vast majority of these progenitors express lymphoid-associated antigens with changes occurring in both the myeloid and lymphoid compartments of the hepatic hematopoietic pathway on tumor challenge. While tumor-bearing livers are enriched for intrahepatic myeloid precursors and T-cell progenitor cells, further studies are required to establish the origin and in situ development potential of hepatic HSCs in the adult human and their role in tumor immunity.
Surface properties and biocompatibility of cellulose acetates (2012)

Abstract The article describes some properties of cellulose acetates (CAs) with different substitution degrees. The hydrophilic/hydrophobic properties, morphological aspects, and interface properties with red blood cells and platelets are affected by the substitution degree, synthesis conditions, history of the formed films from solutions in acetone/water nonsolvent/nonsolvent mixtures, and low pressure plasma treatment. The results obtained are useful in biomedical applications, including evaluation of bacterial adhesion onto surfaces, or utilization of CA for semipermeable membranes. © 2012 Wiley Periodicals, Inc. J Appl Polym Sci, 2012
Hydrogen sulfide induces the synthesis of proinflammatory cytokines in human monocyte cell line U937 via the ERK-NF-κB pathway (2007)

Hydrogen sulfide (H2S) is now considered an endogenous, gaseous mediator, which has been demonstrated to be involved in many inflammatory states. However, the mechanism of its proinflammatory function remains unknown. In the present study, we used IFN-gamma-primed human monocytic cell line U937 to investigate the effects of H2S in vitro on monocytes. We found that treatment with the H2S donor, sodium hydrosulfide, led to significant increases in the mRNA expression and protein production of TNF-alpha, IL-1beta, and IL-6 in U937 cells. H2S-triggered monocyte activation was confirmed further by the up-regulation of CD11b expression on the cell surface. We also observed that H2S could induce a rapid degradation of IkappaBalpha and subsequent activation of NF-kappaB p65, and this effect was attenuated by Bay 11-7082, a specific inhibitor of NF-kappaB. Furthermore, pretreatment of cells with Bay 11-7082 substantially inhibited the secretion of TNF-alpha, IL-1beta, and IL-6 induced by H2S. We also found that H2S stimulated the phosphorylation and activation of ERK1/2, but not of p38 MAPK and JNK, and pretreatment with PD98059, a selective MEK1 antagonist, could inhibit H2S-induced NF-kappaB activation markedly. Together, our findings suggest for the first time that H2S stimulates the activation of human monocytes with the generation of proinflammatory cytokines, and this response is, at least partially, through the ERK-NF-kappaB signaling pathway.
Next steps in near-duplicate detection for eRulemaking (2006)

Large volume public comment campaigns and web portals that encourage the public to customize form letters produce many near-duplicate documents, which increases processing and storage costs, but is rarely a serious problem. A more serious concern is that form letter customizations can include substantive issues that agencies are likely to overlook. The identification of exact- and near-duplicate texts, and recognition of unique text within near-duplicate documents, is an important component of data cleaning and integration processes for eRulemaking.This paper presents DURIAN (DUplicate Removal In lArge collectioN), a refinement of a prior near-duplicate detection algorithm DURIAN uses a traditional bag-of-words document representation, document attributes ("metadata"), and document content structure to identify form letters and their edited copies in public comment collections. Experimental results demonstrate that DURIAN is about as effective as human assessors. The paper concludes by discussing challenges to moving near-duplicate detection into operational rulemaking environments.
Microfabricating Conjugated Polymer Actuators (2000)

Conjugated polymer actuators can be operated in aqueous media, which makes them attractive for laboratories-on-a-chip and applications under physiological conditions. One of the most stable conjugated polymers under these conditions is polypyrrole, which can be patterned by means of standard photolithography. Polypyrrole-gold bilayer actuators that bend out of the plane of the wafer have been microfabricated in our laboratory. These can be used to move and position other microcomponents. Here we review the current status of these microactuators, outlining the methods used to fabricate them. We describe the devices that have been demonstrated as well as some potential future applications.
Automatic detection of dining plates in digital video (2010)

An efficient approach to detect and localize dining plates in images and videos based on human vision is reported in this paper. Rapid processing is achieved by using random checkpoints on edges only, simulating the knowledge based target search in biological visual systems. A new grouping algorithm based on convexity is presented for a top-down segmentation of candidate objects. Our experiments demonstrate the effectiveness of the new approach.
Superhydrophobic Functionalized Graphene Aerogels (2011)

Carbon-based nanomaterials such as carbon nanotubes and graphene are excellent candidates for superhydrophobic surfaces because of their intrinsically high surface area and nonpolar carbon structure. This paper demonstrates that graphene aerogels with a silane surface modification can provide superhydrophobicity. Graphene aerogels of various concentrations were synthesized and the receding contact angle of a water droplet was measured. It is shown that graphene aerogels are hydrophobic and become superhydrophobic following the application of a fluorinated surfactant. The aerogels produced for this experiment outperform previous carbon nanomaterials in creating superhydrophobic surfaces and offer a more scalable synthetic procedure for production.
Blockade of Chemokine Activity by a Soluble Chemokine Binding Protein from Vaccinia Virus (1998)

Abstract Chemokines direct migration of immune cells into sites of inflammation and infection. Chemokine receptors are seven-transmembrane domain proteins that, in contrast to other cytokine receptors, cannot be easily engineered as soluble chemokine inhibitors. Poxviruses encode several soluble cytokine receptors to evade immune surveillance, providing new strategies for immune modulation. Here we show that vaccinia virus and other orthopoxviruses (cowpox and camelpox) express a secreted 35-kDa chemokine binding protein (vCKBP) with no sequence similarity to known cellular chemokine receptors. The vCKBP binds CC, but not CXC or C, chemokines with high affinity (Kd = 0.1–15 nM for different CC chemokines), blocks the interaction of chemokines with cellular receptors, and inhibits chemokine-induced elevation of intracellular calcium levels and cell migration in vitro, thus representing a soluble inhibitor that binds and sequesters chemokines. The potential of vCKBP as a therapeutic agent in vivo was illustrated in a guinea pig skin model by the blockade of eotaxin-induced eosinophil infiltration, a feature of allergic inflammatory reactions. Furthermore, vCKBP may enable the rational design of antagonists to neutralize pathogens that use chemokine receptors to initiate infection, such as HIV or the malarial parasite.
Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method (2005)

Making the SMM method publicly available enables bioinformaticians and experimental biologists to easily access it, to compare its performance to other prediction methods, and to extend it to other applications.
Posttraumatic stress disorder: diagnostic and epidemiological perspectives. (2009)

We reviewed epidemiological findings for the diagnosis of posttraumatic stress disorder (PTSD) and its core diagnostic features, focusing on whether epidemiology has been helpful in clarifying some of the critical diagnostic issues relevant to the revision of the Diagnostic and Statistical Manual of Mental Disorders and the International Statistical Classification of Diseases. Though epidemiology has provided increasingly rich data and knowledge regarding prevalence and incidence, patterns of onset and course, comorbidity, and risk factors for traumatic experiences and posttraumatic stress, little systematic research has been performed specifically addressing such critical diagnostic issues. Particularly, unresolved concerns remain regarding the definition of trauma, duration and impairment/distress criteria, the distinctiveness of the PTSD-syndrome, and even the position of PTSD in the classification system of mental disorders. A further exploitation of the existing data, and an improvement of existing epidemiological methods, strategies, and assessments are likely to substantially contribute to the clarification of unresolved diagnostic issues.
Nuclear magnetic resonance imaging of the liver: initial experience (1982)

Nuclear magnetic resonance (NMR) scans of the liver were obtained in 12 normal volunteers and 32 patients using a whole-body machine developed by Thorn-EMI Ltd., and the results were compared with x-ray computed tomography (CT). Two types of NMR scan, saturation-recovery and inversion-recovery, were performed in order to obtain values for the spin-lattice relaxation time, T1. Although the saturation-recovery scans show little soft-tissue detail, the inversion-recovery scans demonstrated the interlobar fissure, hepatic veins, portal veins, bile ducts, and gallbladder. In comparison with CT (Siemens Somatom 2), both types of NMR scan showed some blurring due to respiratory movement but much less linear artifact across the liver from the air-fluid interface in the stomach. Focal disease within the liver was demonstrated by both CT and NMR, although an area of focal atrophy and another of hepatic infarction were only recognized with NMR. In diffuse disease the pattern varied. In steatosis CT was virtually diagnostic, while NMR showed no specific features. In hemochromatosis, hepatitis, eight cases of cirrhosis, and one of Wilson disease, both techniques showed abnormalities of varying specificity. In two cases of cirrhosis and one of primary biliary cirrhosis, only the NMR scan was abnormal. Nuclear magnetic resonance images are now sufficiently anatomically detailed to permit serious comparisons with technically advanced computed tomography. The information revealed is fundamentally different and can be expected to have some diagnostic utility.
Potential of Machine-Vision Light Microscopy in Toxicologic Pathology (1994)

Major developments in machine-vision light microscopy and in reagent chemistry have led to a renaissance and revolution in the use of the light microscope in biology, biotechnology, and medicine. The potential use of this technology in the field of toxicologic pathology is discussed. It is suggested that a combination of investigating living cells and tissues and fixed samples using the new technologies will lead to understanding mechanisms of toxicity. Examples of the use of the methods in basic cell biology and medicine are presented.
High-temperature alkali vapor cells with antirelaxation surface coatings (2009)

Antirelaxation surface coatings allow long spin relaxation times in alkali-metal cells without buffer gas, enabling faster diffusion of the alkali atoms throughout the cell and giving larger signals due to narrower optical linewidths. Effective coatings were previously unavailable for operation at temperatures above 80 °C. We demonstrate that octadecyltrichlorosilane (OTS) can allow potassium or rubidium atoms to experience hundreds of collisions with the cell surface before depolarizing, and that an OTS coating remains effective up to about 170 °C for both potassium and rubidium. We consider the experimental concerns of operating without buffer gas and with minimal quenching gas at high vapor density, studying the stricter need for effective quenching of excited atoms and deriving the optical rotation signal shape for atoms with resolved hyperfine structure in the spin-temperature regime. As an example of a high-temperature application of antirelaxation coated alkali vapor cells, we operate a spin-exchange relaxation-free atomic magnetometer with sensitivity of 6 fT/Hz and magnetic linewidth as narrow as 2 Hz.
Widespread CXCR4 Activation in Astrocytomas Revealed by Phospho-CXCR4-Specific Antibodies (2005)

The chemokine receptor CXCR4 is expressed in many cancers where it may regulate tumor cell growth and migration. The role of CXCR4 in cancer will depend on it being in an activated, signaling state. To better define the significance of CXCR4 expression in cancer, we developed an antibody that can distinguish CXCR4 phosphorylated on serine 339, a residue previously identified as a site for ligand-induced phosphorylation. With this antibody, we investigated the mechanisms of CXCR4 phosphorylation and evaluated the phosphorylation status of CXCR4 in human astrocytomas. In vitro, phosphorylation of serine 339 occurred in response to CXCL12 or epidermal growth factor (EGF) treatment and was increased by protein kinase C activation. In all grades of astrocytomas, CXCR4 was expressed in tumor cells and some endothelial cells, whereas CXCL12 was present in endothelial cells and infiltrating microglia. We found that CXCR4 phosphorylated on serine 339 was present in tumor cells and vascular endothelial cells in all grades of astrocytoma. These data indicate that CXCR4 is expressed and activated in astrocytomas and that phosphorylation of CXCR4 can occur through ligand activation or transactivation via the EGF receptor. These studies extend the potential roles of CXCR4 in cancer to include functions associated with benign (grade 1) tumors. The ability to distinguish phosphorylated CXCR4 will be invaluable for the continued analysis of the role of CXCR4 in cancer and the development of CXCR4 antagonist therapy for patients suffering with primary tumors of the brain and other sites.