gebhart/patrepeval huggingface dataset:
Quantitative gene expression analysis using Oncotype DX in ductal carcinoma in situ that is adjacent to invasive ductal carcinoma. (2009)

Abstract Abstract #2066 Background: It is common for ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC) to be observed adjacent to each other in the same tissue section. To explore the quantitative biology of DCIS, we measured ER, PR, HER2, proliferation gene expression and Recurrence Score (RS) using Oncotype DX in DCIS adjacent to IDC.&amp;#x2028; Material and Methods: Thirty cases of ER positive tumors were identified with adjacent DCIS and IDC of similar nuclear grade. Manual microdissection was performed to separate DCIS and IDC tissues from each case. Using the Oncotype DX assay, standardized quantitative expression of 16 individual cancer related genes including ER, PR and HER2 and the proliferation index (the average of the 5 proliferations genes) was measured on a scale from 0 to 15 (relative to reference genes), where a one unit increment is associated with a 2-fold change in expression. The RS was also calculated. Descriptive statistics and Pearson's R correlation coefficients were determined to compare DCIS to IDC.&amp;#x2028; Results: 27 of the 30 samples had sufficient RNA for analyses of the DCIS component (8 with low grade, 10 with intermediate grade, and 9 with high grade DCIS). The correlation coefficients for the comparison of DCIS and adjacent IDC for quantitative ER, PR, HER2, and the proliferation index was 0.78, 0.73, 0.76, and 0.83, respectively. For ER, IDC and DCIS measures were within 2 units for all 27 cases and within 1 unit for 22/27 (81%). For PR, IDC and DCIS measures were within 2 units for 25 of 27 cases and within 1 unit for 19/27 (70%). For HER2, IDC and DCIS measures were within 2 units for 26 of 27 cases and within 1 unit for 24/27 (89%). For proliferation index, IDC and DCIS measures were within 2 units for all 27 cases and within 1 unit for 26/27 (96%). There was a wide range of RS in DCIS (mean 13.9; range 0 to 56). Although for RS there was a significant correlation between DCIS and IDC (R=0.84), on average the RS was 4 units lower for DCIS.&amp;#x2028; Discussion: Quantitative RT-PCR analysis of DCIS is technically feasible and sufficient RNA for Oncotype DX analysis is obtained in 90% of cases. As has been described previously for invasive breast cancer, there is considerable expression heterogeneity in DCIS between patients. DCIS adjacent to invasive breast cancer demonstrates very similar, but not identical, quantitative biology for the genes in the assay. Further DCIS studies to evaluate Oncotype DX and recurrence rates would be of great interest. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2066.
Identification of the photosystem I antenna polypeptides in barley (1992)

The light-harvesting antenna of barley photosystem I (LHCI) was isolated from native photosystem I (PSI) complexes and fractionated into three pigment-protein subcomplexes using two consecutive rounds of green gel electrophoresis. Each complex showed a characteristic polypeptide composition and low-temperature fluorescence emission spectrum; they were designated as LHCI-730, LHCI-680A and LHCI-680B. Their four apoproteins of 21, 22, 23 and 25 kDa were purified and NH2-terminal sequences were determined; in the case of the NH2-terminally blocked 25-kDa protein, an internal sequence was obtained after cleavage with endoproteinase Lys-C. This made possible an assignment of the four proteins to the four types (I-IV) of genes coding for chlorophyll a/b proteins of PSI (cab or lha genes). The LHCI-730 complex was isolated as a heterodimer composed of the 21-kDa (LHCI type IV) and the 22-kDa (LHCI type I) polypeptides. Each LHCI-680 complex had a single apoprotein. LHCI-680A consisted of the 25-kDa (LHCI type III) and LHCI-680B of the 23-kDa (LHCI type II) polypeptides. LHCI-680B was associated with the non-pigmented PSI-E subunit, indicating that this protein may function in the binding of this antenna to the reaction centre.
Properties and Performance of Ether-Functionalized Imidazoles as Physical Solvents for CO2 Separations (2013)

Previously, we investigated 1-n-alkylimidazoles as low viscosity, low vapor pressure physical solvents for CO2/CH4 separation and noted a decrease in performance as the length of the n-alkyl chain was extended. Here, we examine imidazoles featuring oligo(ethylene glycol) substituents (“PEGn-imidazoles”) as an opportunity to improve upon the separation performance of this class of molecules. In the current work, we have characterized the density and the viscosity of PEGn-imidazoles over the temperature range 20–80 °C. PEGn-imidazoles are slightly more viscous than 1-n-alkylimidazoles but still fall below 20 cP. Ideal gas solubilities of CO2 and CH4 were measured in PEGn-imidazoles at gas partial pressures of ∼5 bar and temperatures of 25–70 °C. Solubilities of CO2 and CH4 were both found to decrease with increasing temperature, with a stronger dependence for CO2. However, better CO2/CH4 selectivity was achieved in PEGn-imidazoles at lower operating temperatures than was observed for 1-n-alkylimidazoles. Physical properties and gas separation performances were correlated with fractional free volume calculated via COSMOtherm, as well as solubility parameters. The results show trends of decreased FFV when polar ether groups comprise the substituent, and that CO2 solubility and solubility selectivity for CO2/CH4 are improved compared to their nonpolar, hydrocarbon-based analogues.
Drift-diffusion modeling of photocurrent transients in bulk heterojunction solar cells (2009)

We utilize a time-dependent drift-diffusion model incorporating electron trapping and field-dependent charge separation to explore the device physics of organic bulk-heterojunction solar cells based on blends of poly(3-hexylthiophene) (P3HT) with a red polyfluorene copolymer. The model is used to reproduce experimental photocurrent transients measured in response to a step-function excitation of light of varied intensity. The experimental photocurrent transients are characterized by (i) a fast rise of order 1 μs followed by (ii) a slow rise of order 10–100 μs that evolves into a transient peak at high intensity, (iii) a fast decay component after turn-off and (iv) a long-lived tail with magnitude that does not scale linearly with light intensity or steady-state photocurrent. The fast rise and decay components are explained by the transport of mobile carriers while the slow rise and decay components are explained by slower electron trapping and detrapping processes. The transient photocurrent peak at high intensities with subsequent decay to the steady-state value is explained by trap-mediated space-charge effects. The build-up of trapped electrons in the device produces reduction in the strength of the electric field near the transparent anode that increases the likelihood of bimolecular recombination, and lowers the overall efficiency of charge dissociation in the device. Notably the model demonstrates that a reduction in free charge generation rate by space-charge effects is as significant as bimolecular recombination in this device assuming Langevin-type bimolecular recombination. The model is also used to explore the dynamics of charge separation with an upper bound of 50 ns set for the lifetime of electron-hole pairs, and to provide an estimate of the trap density of 1.3×1022 m−3.
Oxygen and Reperfusion Damage: an Overview (1989)

The ischaemic myocardium shows a number of distinct oxygen dependent responses to reperfusion. In the case of myocardial stunning and reperfusion arrhythmias there appears to be a beneficial effect of scavenging radicals in the extracellular space. This result is supported by the finding that free radicals can be detected extracellularly after reperfusion. The source of these oxidants and site of action is as yet unclear. In contrast hypoxic myocytes shown an oxygen dependent Ca2+ uptake on reoxygenation which is not affected by externally applied antioxidants. This Ca2+ uptake may in turn lead to the cell lysis characteristic of the oxygen paradox in the perfused heart. As yet there is no compelling evidence to suggest that this aspect of reperfusion damage is due to oxidative stress. It appears more likely that mitochondrial electron transport and ion movement play a central role. In the open chested dog model of ischaemia reperfusion, in which the volume of infarcted tissue is measured, considerable evidence suggests that oxidants derived from activated neutrophils contribute to cell death. This is not however the sole mechanism for cell damage in this model since an inhibitor of mitochondrial Ca2+ uptake, ruthenium red, can improve recovery after reperfusion. We conclude that a number of mechanisms may contribute to the observed oxygen dependent dysfunctions which occur on reperfusion of ischaemic tissue.
Secretion of osteopontin by macrophages and its accumulation at tissue surfaces during wound healing in mineralized tissues: A potential requirement for macrophage adhesion and phagocytosis (1996)

Osteopontin (OPN), a noncollagenous, extracellular matrix sialoprotein found at relatively high levels in both normal and pathological mineralized tissues, is expressed by tissue-specific cells in bone, calcified cartilage, and teeth. On the other hand, a hallmark of OPN expression in pathologically mineralizing tissue, and in other soft tissues experiencing a more generalized type of necrotic injury, is the production of OPN by macrophages at the lesion site. In the present study, we have localized OPN and other noncollagenous proteins by ultrastructural colloidal-gold immunocytochemistry using a rat model in which mineralized tissue defects are surgically created in mandibular bone and teeth. The healing response was examined by immunocytochemistry and transmission electron microscopy at 10 min, 3 days and 7 days post-surgery using antibodies against OPN, bone sialoprotein, osteocalcin, bone acidic glycoprotein-75, fibronectin, and amelogenin. Whereas most of these proteins were characteristically distributed within their respective extracellular matrices as described previously, OPN was additionally observed to accumulate as a lamina limitans at surgically exposed bone and tooth surfaces, as well as at the surface of particulate, mineralized tissue debris. Intracellular labeling of the Golgi apparatus and secretory granules of macrophages at the lesion site demonstrated that OPN production by macrophages was a prominent secretory event of the inflammatory response during wound healing in mineralized tissues. Pseudopodal and lamellipodal cytoplasmic extensions of macrophages were observed in direct contact with the OPN-containing lamina limitans at these surfaces. Particulate, calcified debris internalized by macrophages also displayed a prominent surface "coating" of OPN. In conclusion, our interpretation of the present data is that OPN secreted by macrophages may serve as a macrophage adhesion protein, and where concentrated at the surface of small particulate, mineralized tissue debris, may act as an opsonin, thereby facilitating cell adhesion and phagocytosis by macrophages, a process likely mediated by integrin-binding, signal transduction, and cytoskeletal restructuring.
Identification of novel hypermethylated genes and demethylating effect of vincristine in colorectal cancer (2014)

These results suggest that these novel hypermethylated genes AKR1B1, CHST10, ELOVL4, SOX5, STK33, and ZNF304 may be potential methylation biomarkers and therapeutic targets of vincristine in CRC.
A Direct Reception System for Time Synchronization via INSAT-1 (1981)

The Indian National Satellite System INSAT-1 is being planned to be in Operation during 1982. This is a multipurpose satellite system for domestic telecommunication and meteorology with capability for nation-wide direct TV broadcasting using two S-band transponders. These transponders are also planned to carry two RN channels for the purpose of time and frequency dissemination. This paper describes in detail a complete direct reception system for time signals to be transmitted by the satellite in the band (2555–2635) MHz.
Grafting of methyl methacrylate to nitrocellulose by ceric ions (1979)

Studies were carried out on grafting of various vinyl monomers to nitrocellulose by ceric ions. It was observed that graft copolymerization occurred only with methyl methacrylate (MMA) and methyl acrylate monomer. The variables such as initiator concentration, monomer concentration, time of grafting, and nitrocellulose content on grafting of MMA are discussed. By hydrolyzing away the nitrocellulose backbone, the grafted poly(methyl methacrylate) branches were isolated and the >co peak at 1740 cm−1 in the infrared spectra of these isolated branches gave definite evidence of grafting. The molecular weight of isolated branches has been determined by viscometry. The probable mechanism of grafting may be at the α-carbon atom of primary alcohol or at a C2-C3 glycol group of the anhydro glucose unit or at the hemiacetal group of the end unit of nitrocellulose, as nitrocellulose is formed by the partial nitration of cotton cellulose.
Using elutriation to engineer bone marrow allografts. (1990)

We have used elutriation to deplete lymphocytes from the marrow allografts of 64 patients to date. The first phase I trial (1 x 10(6) lymphocytes/kg IBW) was designed to test the procedure for potential toxicities, most notably, graft failure. Study 2 (1 x 10(6) lymphocytes/kg, no CsA) was expected to reduce potential toxicity incurred from long term immunoprophylaxis while study 3 was aimed at reducing the incidence of GVHD by further reducing lymphocyte dose (5 x 10(5)/kg). Graft lymphocyte dose was based on morphologic determination and was subsequently confirmed by limiting dilution analysis and flow cytometry. Although grafts were standardized solely by lymphocyte dose, the product was more uniform than the original harvested BM with respect to other cell populations. Nearly all study I (n = 40) and study III (n = 20) patients engrafted with a median time to ANC greater than 500/ul of 19 days. Three of the 4 patients consecutively enrolled in study II failed to engraft, thus terminating the trial. While a moderate proportion of study I patients had AGVHD (44%) with attendant morbidity, only 20% of study III patients were found to have mild AGVHD (less than or equal to stage I). To date, this cohort has no organ or chronic GVHD and no GVHD-associated morbidity. Median follow-up times for patients in studies I and III are 27 and 11 months, respectively. Overall actuarial survival (n = 60) is 42% at 38 months (38% study I, 80% study III). Good prognosis study I patients experienced 45% actuarial survival versus 9% in the poor prognostic group. While lymphocyte depletion has been effective in reducing the incidence and severity of AGVHD, new strategies are needed to address the issue of disease relapse. As with other methods, lymphocyte depletion by elutriation caused an increased rate of leukemia relapse. The actuarial probability of remaining in remission for recipients of elutriated marrow containing 1 x 10(6) and 5 x 10(5) lymphocytes/kg, respectively, were 60% and 46% at 16 months. Elutriation provides a rapid, reproducible and flexible methodology for graft manipulation which has been effective in reducing the incidence and severity of AGVHD. However, if lymphocyte depletion is to fulfill its promise as a means of reducing the overall morbidity of allogeneic BMT, new strategies may be needed to address the issue of relapse. These may include changes in marrow ablative therapy and post-graft immunosuppression. Equally as important may be the ability to further manipulate accessory cells and lymphoid populations presently excluded from the graft.
Src blockade stabilizes a Flk/cadherin complex, reducing edema and tissue injury following myocardial infarction (2004)

Ischemia resulting from myocardial infarction (MI) promotes VEGF expression, leading to vascular permeability (VP) and edema, a process that we show here contributes to tissue injury throughout the ventricle. This permeability/edema can be assessed noninvasively by MRI and can be observed at the ultrastructural level as gaps between adjacent endothelial cells. Many of these gaps contain activated platelets adhering to exposed basement membrane, reducing vessel patency. Following MI, genetic or pharmacological blockade of Src preserves endothelial cell barrier function, suppressing VP and infarct volume, providing long-term improvement in cardiac function, fibrosis, and survival. To our surprise, an intravascular injection of VEGF into healthy animals, but not those deficient in Src, induced similar endothelial gaps, VP, platelet plugs, and some myocyte damage. Mechanistically, we show that quiescent blood vessels contain a complex involving Flk, VE-cadherin, and -catenin that is transiently disrupted by VEGF injection. Blockade of Src prevents disassociation of this complex with the same kinetics with which it prevents VEGF-mediated VP/edema. These findings define a molecular mechanism to account for the Src requirement in VEGF-mediated permeability and provide a basis for Src inhibition as a therapeutic option for patients with acute MI.
Intelligent selection tools (2002)

Intelligent Scissors and Intelligent Paint are complementary interactive image segmentation tools that allow a user to quickly and accurately select objects of interest. This demonstration provides a means for participants to experience the dynamic nature of these tools.
Cloning of and complementation tests with alkaline phosphatase regulatory genes (phoS and phoT) of Escherichia coli (1982)

The regulatory genes of alkaline phosphatase, phoS and phoT, of Escherichia coli were cloned on pBR322, initially as an 11.8-kilobase EcoRI fragment. A restriction map of the hybrid plasmid was established. Deletion plasmids of various sizes were constructed in vitro, and the presence of phoS and phoT genes on the cloned DNA fragments was tested by introducing the plasmids into phoS64 and phoT9 strains for complementation tests. One set complemented only phoS64 but not phoT9; the other set complemented only phoT9 but not phoS64. We conclude that phoS64 and phoT9 mutations belong to different complementation groups and probably to different cistrons. The hybrid plasmid with the 11.8-kilobase chromosomal fragment also complemented the phoT35 mutation. A smaller derivative of the hybrid plasmid was constructed in vitro which complemented phoT35 but did not complement phoS64, phoT9, or pst-2. Our results agree with the suggestion that phoT35 lies in a different complementation group from phoS, phoT, or pst-2 (Zuckier and Torriani, J. Bacteriol. 145:1249--1256, 1981). Therefore, we propose to designate phoT35 as phoU. The effect of amplification of phoS or phoT on alkaline phosphatase production was examined. It was found that multiple copies of the phoS gene borne on pBR322 repressed enzyme production even in low-phosphate medium, whether it was introduced into wild-type strains (partially repressed) or phoR (phoR68 or phoR17) strains (fully repressed), whereas the introduction of multicopy plasmids bearing the phoT gene did not affect the inducibility of the enzyme.
Crystal structure at 2.6-A resolution of human macrophage migration inhibitory factor. (1996)

Macrophage migration inhibitory factor (MIF) was the first cytokine to be described, but for 30 years its role in the immune response remained enigmatic. In recent studies, MIF has been found to be a novel pituitary hormone and the first protein identified to be released from immune cells on glucocorticoid stimulation. Once secreted, MIF counterregulates the immunosuppressive effects of steroids and thus acts as a critical component of the immune system to control both local and systemic immune responses. We report herein the x-ray crystal structure of human MIF to 2.6 angstrom resolution. The protein is a trimer of identical subunits. Each monomer contains two antiparallel alpha-helices that pack against a four-stranded beta-sheet. The monomer has an additional two beta-strands that interact with the beta-sheets of adjacent subunits to form the interface between monomers. The three beta-sheets are arranged to form a barrel containing a solvent-accessible channel that runs through the center of the protein along a molecular 3-fold axis. Electrostatic potential maps reveal that the channel has a positive potential, suggesting that it binds negatively charged molecules. The elucidated structure for MIF is unique among cytokines or hormonal mediators, and suggests that this counterregulator of glucocorticoid action participates in novel ligand-receptor interactions.
A Versatile Method for the Synthesis of Benzimidazoles from o-Nitroanilines and Aldehydes in One Step via a Reductive Cyclization (2004)

A highly efficient and versatile method for the synthesis of benzimidazoles was achieved in one step via the Na2S2O4 reduction of o-nitroanilines in the presence of aldehydes. Heating a solution of o-nitroaniline (1c) and an aldehyde in EtOH or another appropriate solvent, in the presence of aqueous or solid Na2S2O4, provided facile access to a series of 2-substituted N-H benzimidazoles 5a-m containing a wide range of functional groups not always compatible with the existing synthetic methods. This methodology has also been applied to the regioselective synthesis of N-alkyl and N-aryl benzimidazoles 6a-f via the cyclization of the corresponding N-substituted nitroanilines 13a-e, respectively. In addition, the method was applied successfully to the synthesis of other imidazole containing heterocyclic ring systems such as 1H-imidazo[4,5-b]pyridines 14a,b and 1H-imidazo[4,5-f]quinoline 15.
T cell receptor–induced phosphoinositide-3-kinase p110δ activity is required for T cell localization to antigenic tissue in mice (2008)

The establishment of T cell-mediated inflammation requires the migration of primed T lymphocytes from the blood stream and their retention in antigenic sites. While naive T lymphocyte recirculation in the lymph and blood is constitutively regulated and occurs in the absence of inflammation, the recruitment of primed T cells to nonlymphoid tissue and their retention at the site are enhanced by various inflammatory signals, including TCR engagement by antigen-displaying endothelium and resident antigen-presenting cells. In this study, we investigated whether signals downstream of TCR ligation mediated by the phosphoinositide-3-kinase (PI3K) subunit p110delta contributed to the regulation of these events. T lymphocytes from mice expressing catalytically inactive p110delta displayed normal constitutive trafficking and migratory responses to nonspecific stimuli. However, these cells lost susceptibility to TCR-induced migration and failed to localize efficiently to antigenic tissue. Importantly, we showed that antigen-induced T cell trafficking and subsequent inflammation was abrogated by selective pharmacological inhibition of PI3K p110delta activity. These observations suggest that pharmacological targeting of p110delta activity is a viable strategy for the therapy of T cell-mediated pathology.
Integration of human color vision models into high quality image compression (2000)

These Ecole polytechnique federale de Lausanne EPFL, n° 2296 (2000)Faculte des sciences et techniques de l'ingenieurInstitut de genie electrique et electroniqueLaboratoire de traitement des signaux 1Jury: Michel Benard, Sanjit Mitra, Philippe Robert, Sabine Suesstrunk Public defense: 2000-12-7 Reference doi:10.5075/epfl-thesis-2296Print copy in library catalog Record created on 2005-03-16, modified on 2016-08-08
An Overview of the Clinical Safety Profile of Atorvastatin (Lipitor), a New HMG-CoA Reductase Inhibitor (1998)

The safety profile of atorvastatin was consistent with that of all statins tested and was similar to that seen in all compounds of this class.