gebhart/patrepeval huggingface dataset:
Hepatocellular Carcinoma Cells and Their Fibrotic Microenvironment Modulate Bone Marrow-Derived Mesenchymal Stromal Cell Migration <i>in Vitro</i> and <i>in Vivo</i> (2011)

Hepatocellular carcinoma (HCC) is the fifth most common cancer and the third cause of cancer-related death. Fibrogenesis is an active process characterized by the production of several proinflammatory cytokines, chemokines and growth factors. It involves the activation of hepatic stellate cells (HSCs) which accumulate at the site of injury and are the main source of the extracellular matrix deposits. There are no curative treatments for advanced HCC, thus, new therapies are urgently needed. Mesenchymal stromal cells (MSCs) have the ability to migrate to sites of injury or to remodeling tissues after in vivo administration; however, in several cancer models they demonstrated limited efficacy to eradicate experimental tumors partially due to poor engraftment. Thus, the aim of this work was to analyze the capacity of human MSCs (hMSCs) to migrate and anchor to HCC tumors. We observed that HCC and HSCs, but not nontumoral stroma, produce factors that induce hMSC migration in vitro. Conditioned media (CM) generated from established HCC cell lines were found to induce higher levels of hMSC migration than CM derived from fresh patient tumor samples. In addition, after exposure to CM from HCC cells or HSCs, hMSCs demonstrated adhesion and invasion capability to endothelial cells, type IV collagen and fibrinogen. Consistently, these cells were found to increase metalloproteinase-2 activity. In vivo studies with subcutaneous and orthotopic HCC models indicated that intravenously infused hMSCs migrated to lungs, spleen and liver. Seven days post-hMSC infusion cells were located also in the tumor in both models, but the signal intensity was significantly higher in orthotopic than in subcutaneous model. Interestingly, when orthotopic HCC tumors where established in noncirrhotic or cirrhotic livers, the amount of hMSCs localized in the liver was higher in comparison with healthy animals. A very low signal was found in lungs and spleens, indicating that liver tumors are able to recruit them at high efficiency. Taken together our results indicate that HCC and HSC cells produce factors that efficiently induce hMSC migration toward tumor microenvironment in vitro and in vivo and make MSCs candidates for cell-based therapeutic strategies to hepatocellular carcinoma associated with fibrosis.
Gantt Chart visualization for MPI and Apache multi-dimensional trace files (2003)

Trace visualization is a way to understand the behavior of an application on computer systems. In this paper we describe the design and implementation of a Gantt Chart visualization tool for visualizing multi-dimensional trace files, particularly traces from Message Passing Interface (MPI) programs and Apache servers. An MPI tracing library is developed for MPI programs, and an Apache server plug-in is developed to generate Web traces. Since the amount of trace data may be large, utilities are provided to convert and merge multiple event trace files into one scalable, self-defining interval file for visualization. The interval format facilitates the development of multiple time-space diagrams for visualization tools. For MPI traces, each record also includes an instruction address for source code association, which provides a way to display the source code and pin-point the line that generates the event.
Penetration problems in rock mechanics (1973)

A REVIEW IS PRESENTED OF THE FUNDAMENTAL ASPECTS OF THE MECHANICAL PENETRATION OF ROCK BY TOOLS. PART I DEALS WITH THE PENETRATION OF ELASTIC-BRITTLE ROCK AND PART II IS CONCERNED WITH THE PENETRATION OF DUCTILE ROCK. /AUTHOR/
Timing of the appearance of ubiquitinated histones in developing new macronuclei of <i>Tetrahymena thermophila</i> (1991)

Vegetative cells of the ciliated protozoan Tetrahymena thermophila contain a transcriptionally active macronucleus and a transcriptionally inert micronucleus. During vegetative growth, macronuclear histones H2A and H2B and micronuclear H2A are ubiquitinated. Despite differences in function, macro- and micro-nuclei are related. During conjugation (the sexual phase of the life cycle in Tetrahymena), postzygotic division products of micronuclei give rise to new micro- and macro-nuclei. Using an anti-ubiquitin antibody in Western blotting experiments, we determined the levels of ubiquitinated histones in new macro- and micro-nuclei at various times during conjugation. Very soon after the second postzygotic division (approximately 8 h) when new macronuclei begin to synthesize RNA, ubiquitinated H2B and polyubiquitinated H2A are present. At this time micronuclei have only low levels of ubiquitinated H2A. During later stages of conjugation (15 h), the level of polyubiquitinated H2A decreases, while ubiquitinated H2B increases in developing new macronuclei, attaining levels of ubiquitinated H2B approaching that of parental macronuclei. Ubiquitinated histones are not detectable in the 15-h micronuclei. These results show that ubiquitination of H2B coincides with the transformation of an inert germinal nucleus into that of a transcriptionally active somatic nucleus, suggesting that ubiquitinated H2B has a role in maintaining the transcriptionally active chromatin state.Key words: histone ubiquitination, Tetrahymena thermophila, chromatin, transcription.
Retroreflecting multipass cell for Raman scattering (1977)

A retroreflecting multipass cell consisting of two lenses and both on-axis and off-axis retroreflecting mirror assemblies has been constructed and tested. A gain in Raman scattered signal intensity of 20 has been attained in a focal volume 1.1 mm x 0.3 mm x 0.3 mm. A system employing off-axis paraboloids should provide somewhat higher gain and a diffraction limited focal volume. These systems are applicable to Raman diagnostics of various gas dynamic processes, including flame gases, or the characterization of the gas mixing process in gas-dynamic or chemical laser nozzle arrays.
A Generic Framework for Recommendations Based on User Data Aggregation (2016)

The next generation intelligent devices need to grow and evolve with the user. Mobile user framework solution allows us to move towards this goal. In this paper, we describe a service framework that captures user's interest and intent which is mined through latent analysis of content. Applications using such a framework can provide adaptive and customized services to the user. We provide details of four demonstrator applications that use this framework, utilizing user interest and intent information to provision targeted advertisements, recommend products and songs. We provide details of our evaluation with subjective and objective analysis of the system.
Generation of high rapamycin producing strain via rational metabolic pathway‐based mutagenesis and further titer improvement with fed‐batch bioprocess optimization (2010)

Rapamycin is a triene macrolide antibiotic produced by Streptomyces hygroscopicus. Besides its wide application as an effective immunosuppressive agent, other important bioactivities have made rapamycin a potential drug lead for novel pharmaceutical development. However, the low titer of rapamycin in the original producer strain limits further industrialization efforts and restricts its use for other applications. Predicated on knowledge of the metabolic pathways related to rapamycin biosynthesis in S. hygroscopicus, we have rationally designed approaches to generate a rapamycin high producer strain of S. hygroscopicus HD-04-S. These have included alleviation of glucose repression, improved tolerance towards lysine and shikimic acid, and auxotrophy of tryptophan and phenylalanine through the application of stepwise UV mutagenesis. The resultant strain produced rapamycin at 450 mg/L in the shake flask scale. These fermentations were further scaled up in 120 and 20,000 L fermentors, respectively, at the pilot plant. Selected fermentation factors including agitation speed, pH, and on-line supplementation were systematically evaluated. A fed-batch strategy was established to maximize rapamycin production. With these efforts, an optimized fermentation process in the larger scale fermentor was developed. The final titer of rapamycin was 812 mg/L in the 120 L fermentor and 783 mg/L in the 20,000 L fermentor. This work highlights a high rapamycin producing strain derived by mutagenesis and subsequent screening, fermentation optimization of which has now made it feasible to produce rapamycin on an industrial scale by fermentation. The strategies developed here should also be applicable to titer improvement of other important microbial natural products on an industrial scale.
Analogs of propranolol. Synthesis of 3‐alkylamino‐1‐(3‐benzo[<i>b</i>]thienyloxy)‐2‐propanols (1980)

Abstract The synthesis by two alternative routes of 1‐(3‐benzo[ b ]thienyloxy)‐3‐isopropylamino‐2‐propanol hydrochloride ( 1a HCl), a thiophenic isoster of Propranolol, and related compounds, is reported. The protecting and enolizing properties of the 2‐methoxycarbonyl group on benzo[ b ]thiophene‐3‐one, along with its facile removal, are utilized in the first route. In the second one, conversion of 3‐bromobenzo[ b ]thiophene in 1‐(3‐benzo[ b ]thienyloxy)‐2,3‐ o ‐isopropylidenepropane is the key step. On the other hand, hydrolysis of 1‐(3‐benzo[ b ]furanyloxy)‐2,3‐ o ‐isopropylidenepropane to the corresponding diol, in order to obtain a furanic isoster of Propranolol (17a ), was unsuccessful.
Sodium‐Dependent Proline Uptake in the Rat Hippocampal Formation: Association with Ipsilateral‐Commissural Projections of CA3 Pyramidal (1987)

Na+-dependent uptake of L-[3H]proline was measured in a crude synaptosomal preparation from the entire rat hippocampal formation or from isolated hippocampal regions. Among hippocampal regions, Na+-dependent proline uptake was significantly greater in areas CA1 and CA2-CA3-CA4 than in the fascia dentata, whereas there was no marked regional difference in the distribution of Na+-dependent gamma-[14C]aminobutyric acid ([14C]GABA) uptake. A bilateral kainic acid lesion, which destroyed most of the CA3 hippocampal pyramidal cells, reduced Na+-dependent proline uptake by an average of 41% in area CA1 and 52% in area CA2-CA3-CA4, without affecting the Na+-dependent uptake of GABA. In the fascia dentata, neither proline nor GABA uptake was significantly altered. Kinetic studies suggested that hippocampal synaptosomes take up proline by both a high-affinity (KT = 6.7 microM) and a low-affinity (KT = 290 microM) Na+-dependent process, whereas L-[14C]glutamate is taken up predominantly by a high-affinity (KT = 6.1 microM) process. A bilateral kainic acid lesion reduced the Vmax of high-affinity proline uptake by an average of 72%, the Vmax of low-affinity proline uptake by 44%, and the Vmax of high affinity glutamate uptake by 43%, without significantly changing the affinity of the transport carriers for substrate. Ipsilateral-commissural projections of CA3 hippocampal pyramidal cells appear to possess nearly as great a capacity for taking up proline as for taking up glutamate, a probable transmitter of these pathways. Therefore proline may play an important role in transmission at synapses made by the CA3-derived Schaffer collateral, commissural, and ipsilateral associational fibers.
Lactational competence and involution of the mouse mammary gland require plasminogen (2000)

Urokinase-type plasminogen activator expression is induced in the mouse mammary gland during development and post-lactational involution. We now show that primiparous plasminogen-deficient (Plg(-/-)) mice have seriously compromised mammary gland development and involution. All mammary glands were underdeveloped and one-quarter of the mice failed to lactate. Although the glands from lactating Plg(-/-) mice were initially smaller, they failed to involute after weaning, and in most cases they failed to support a second litter. Alveolar regression was markedly reduced and a fibrotic stroma accumulated in Plg(-/-) mice. Nevertheless, urokinase and matrix metalloproteinases (MMPs) were upregulated normally in involuting glands of Plg(-/-) mice, and fibrin did not accumulate in the glands. Heterozygous Plg(+/-) mice exhibited haploinsufficiency, with a definite, but less severe mammary phenotype. These data demonstrate a critical, dose-dependent requirement for Plg in lactational differentiation and mammary gland remodeling during involution.
Depletion of L3MBTL1 promotes the erythroid differentiation of human hematopoietic progenitor cells: possible role in 20q− polycythemia vera (2010)

L3MBTL1, the human homolog of the Drosophila L(3)MBT polycomb group tumor suppressor gene, is located on chromosome 20q12, within the common deleted region identified in patients with 20q deletion-associated polycythemia vera, myelodysplastic syndrome, and acute myeloid leukemia. L3MBTL1 is expressed within hematopoietic CD34(+) cells; thus, it may contribute to the pathogenesis of these disorders. To define its role in hematopoiesis, we knocked down L3MBTL1 expression in primary hematopoietic stem/progenitor (ie, CD34(+)) cells isolated from human cord blood (using short hairpin RNAs) and observed an enhanced commitment to and acceleration of erythroid differentiation. Consistent with this effect, overexpression of L3MBTL1 in primary hematopoietic CD34(+) cells as well as in 20q- cell lines restricted erythroid differentiation. Furthermore, L3MBTL1 levels decrease during hemin-induced erythroid differentiation or erythropoietin exposure, suggesting a specific role for L3MBTL1 down-regulation in enforcing cell fate decisions toward the erythroid lineage. Indeed, L3MBTL1 knockdown enhanced the sensitivity of hematopoietic stem/progenitor cells to erythropoietin (Epo), with increased Epo-induced phosphorylation of STAT5, AKT, and MAPK as well as detectable phosphorylation in the absence of Epo. Our data suggest that haploinsufficiency of L3MBTL1 contributes to some (20q-) myeloproliferative neoplasms, especially polycythemia vera, by promoting erythroid differentiation.
Enhancing Tumor Targeting and Apoptosis Using Noncovalent Antibody Homodimers (2002)

A rare type of antibody that spontaneously binds to each self (homodimerizes) has been described. This self-binding (autophilic) antibody provides stronger protection against bacterial infection than a non self-binding antibody with identical specificity and affinity due to increase of polymeric avidity. A peptide derived from the self-binding domain of the autophilic antibody was crosslinked to the Fc carbohydrate of two monoclonal antibodies specific for the B-cell receptor (BCR) of a murine and a human B-cell tumor. Peptide-crosslinked antibodies bind to themselves on solid phase ELISA as homodimer and establish in solution a monomer-dimer equilibrium. Autophilic antibodies bind to their respective tumor target cells with increased efficiency as determined by FACS analysis. They also induce twice the amount of apoptosis of target tumor cells than the control antibodies. Furthermore, the modified antibodies inhibit tumor growth in culture more efficiently than the control antibodies. Criss-cross protocols in FACS, apoptosis, and growth inhibition indicate the specificity of targeting the BCR with autophilic antitumor antibodies. The chemical approach of increasing the binding of antibodies without creating chemically crosslinked dimers mimics naturally occurring autophilic antibodies and represents a simple and attractive alternative to chemical dimerizing and antibody engineering techniques for improving their antitumor effect. Furthermore, these results provide a guide to incorporate the self-binding peptide into the structure of antibodies using modeling and molecular crafting techniques.
Tiled++: An Enhanced Tiled Hi-Res Display Wall (2009)

In recent years, high-resolution displays have become increasingly important to decision makers and scientists because large screens combined with a high pixel count facilitate content rich, simultaneous display of computer-generated imagery and high-definition video data from multiple sources. Tiled displays are attractive due to their extended screen real estate, scalability, and low cost. LCD panels are usually preferred over projectors because of their superior resolution. One of the drawbacks of LCD-based tiled displays is the fact that users sometimes get distracted by the screens' bezels, which cause discontinuities in rendered images, animations, or videos. Most conventional solutions either ignore the bezels and display all pixels, causing objects to become distorted, or eliminate the pixels that would normally fall under the bezels, causing pixels to be missing in the display of static images. In animations, the missing pixels will eventually reappear when the object moves, providing an experience that is similar to looking through a French window. In this paper, we present a new scalable approach that leads neither to discontinuities nor to significant loss of information. By projecting onto the bezels, we demonstrate that a combination of LCD-based tiled displays and projection significantly reduces the bezel problem. Our technique eliminates ambiguities that commonly occur on tiled displays in the fields of information visualization, visual data analysis, human-computer interaction, and scientific data display. It improves the usability of multimonitor systems by virtually eliminating the bezels. We describe a setup and provide results from an evaluation experiment conducted on a 3 x 3 and on a 10 x 5 tiled display wall.
Determination of Petroleum Hydrocarbons in Soil: Sfe Versus Soxhlet and Water Effect on Recovery (1995)

Abstract In an interlaboratory study to determine the concentration of petroleum hydrocarbons (PHCs) in an above ground bioreactor at a refinery site in Montreal we found that the EPA Method # 418.1 for the analysis of semivolatile hydrocarbons gave concentrations up two fold higher than expected. The silica mixing step used to clean-up the crude Soxhlet extract and the inclusion of chlorobenzene or benzene in the composition of the IR quantitative standard were later implicated as major sources of bias in the Method. In another comparative study we have determined water effect on the recovery of PHCs from wood preserving soil using the Soxhlet EPA Method # 3450 (with Freon-113) and the SFE Method # 3560 (with CO2). In the Soxhlet method water did not seem to affect the recovery of PHCs since variations in PHC concentrations did not exceed RSD values, i. e., ± 2% to ± 8%. While in SFE, an optimal extraction efficiency occurred when the water content in the soil was around the 20% limit, similar to what has been described in the EPA Method # 3560. In the case of a bioslurry both SFE and Soxhlet showed that water removal enhanced the recovery of PHCs, i. e., a reduction in the water content by a factor of two resulted in an increase in the recovery of PHCs by roughly a factor of two.
Effect of Adsorption in Barrier Separation (1958)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEffect of Adsorption in Barrier SeparationKarl. Kammermeyer and Darrell D. WyrickCite this: Ind. Eng. Chem. 1958, 50, 9, 1309–1310Publication Date (Print):September 1, 1958Publication History Published online1 May 2002Published inissue 1 September 1958https://pubs.acs.org/doi/10.1021/ie50585a043https://doi.org/10.1021/ie50585a043research-articleACS PublicationsRequest reuse permissionsArticle Views96Altmetric-Citations13LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Selecting Refining and Evaluating Properties for Program Analysis (2003)

This research proposes and evaluates techniques for selectingpredicates for conditional program propertiesÂthatis, implications such as p ) q whose consequent must betrue whenever the predicate is true. Conditional propertiesare prevalent in recursive data structures, which behave differentlyin their base and recursive cases, in programs thatcontain branches, in programs that fail only on some inputs,and in many other situations. The experimental context ofthe research is dynamic detection of likely program invariants,but the ideas are applicable to other domains.Trying every possible predicate for conditional propertiesis computationally infeasible and yields too many undesirableproperties. This paper compares four policies forselecting predicates: procedure return analysis, code conditionals,clustering, and random selection. It also showshow to improve predicates via iterated analysis. An experimentalevaluation demonstrates that the techniques improveperformance on two tasks: statically proving the absence ofrun-time errors with a theorem-prover, and separating faultyfrom correct executions of erroneous programs.
INTERNAL SURFACE REVERSE PHASE LIQUID CHROMATOGRAPHY (1985)

Prior to this work, it was not possible to analyze serum drugs with reverse phase high performance liquid chromatography (HPLC) by injection of the serum sample directly onto the column. The serum proteins interact with and accumulate on the support, resulting in a rapid degeneration of column performance. In most laboratories, therefore, the proteins are removed before injection by time consuming sample preparation procedures. The goal of this research was to develop a reverse phase liquid chromatography support requiring no sample pretreatment. The novel support, termed the Internal Surface Reverse Phase (ISRP) packing is similar to ordinary liquid chromatography supports, except that the hydrophobic partitioning layer is confined to the internal surface of the chromatography particles, only. The external surface contains a hydrophilic, protein non-adsorptive layer. The pore sizes of the support are small, preventing the large serum proteins from reaching the internal hydrophobic surface. When a serum containing drugs is injected onto the ISRP support, the serum proteins, unretained by the external surface, elute in the interstitial void volume. The hydrophobic drugs partition with the internal phase and elute similarly to conventional reverse phase chromatography. The ISRP support was produced by first attaching hydrophilic glycerylpropyl silane to silica particles. Hydrophobic peptide moieties were then covalently bonded to the hydrophilic surface resulting in a hydrophobic layer attached to both the external and internal surfaces. The external hydrophobic groups were then cleaved off by carboxypeptidase A, leaving the outside of the particles hydrophilic again. Carboxypeptidase is too large to enter the pores, allowing the internal surface to remain hydrophobic. Additional synthetic methods utilizing chymotrypsin as the cleavage reagent are described within the thesis. Some application of the ISRP support are demonstrated. For example, the drug phenytoin was isolated from serum proteins with a large particle ISRP precolumn and quantitated by a conventional ODS HPLC column connected in-line with the precolumn. Furthermore, anticonvulsant drugs in human serum were resolved from each other and the serum proteins with a high performance ISRP analytical column.