gebhart/patrepeval huggingface dataset:
Rituximab plus CHOP (R-CHOP) overcomes bcl-2--associated resistance to chemotherapy in elderly patients with diffuse large B-cell lymphoma (DLBCL) (2003)

In diffuse large B-cell lymphoma (DLBCL), the combination of rituximab and CHOP (cyclophosphamide, doxorubicine, vincristine, prednisone; R-CHOP) has been shown to be more effective than CHOP for the treatment of elderly patients. Bcl-2 protein expression has been associated with poor prognosis in patients with DLBCL. To establish whether or not rituximab reduces bcl-2-associated treatment failure, we studied bcl-2 protein expression and clinical outcome in patients included in the Groupe d'Etude des Lymphomes de l'Adulte LNH-98-5 trial. Patients between 60 and 80 years of age were randomized to receive 8 cycles of either CHOP or R-CHOP every 3 weeks. Of the 399 patients included, 292 with histologically proven DLBCL had material available for bcl-2 study. Tumors were considered positive when at least 50% of tumor cells expressed bcl-2 protein. There were 193 (66%) bcl-2+ patients and 99 (34%) bcl-2- patients. The response rates for R-CHOP and CHOP were, respectively, 78% and 60% (P =.01) in bcl-2+ patients and 76% and 73% (P =.7) in bcl-2- patients. At a median of 2 years of follow-up, R-CHOP was significantly associated with a better overall survival than CHOP in bcl-2+ patients (67% +/- 9% versus 48% +/- 11%, P =.004). In bcl-2- patients there was no statistically significant difference (72% +/- 12% versus 67% +/- 14%, P =.6). In addition, R-CHOP was associated with significantly better event-free survival than CHOP in bcl-2+ patients (58% +/- 10% versus 32% +/- 10%, P <.001) but not in bcl-2- patients (60% +/- 13% versus 40% +/- 15%, P =.13). Multivariate analysis confirmed the significant benefit for survival and event-free survival of R-CHOP in bcl-2+ patients. These results suggest that rituximab is able to prevent chemotherapy failure in patients with bcl-2 protein overexpression.
Polybenzimidazoles containing anthracene photodimer (1982)

Abstract Polybenzimidazoles that contained anthracene photodimer were prepared. The molecular weights of the polymers prepared by the photopolymerization of bis‐anthrylbenzimidazoles were limited by the precipitation of the resulting polymers from the reaction organic solvents. Higher molecular weight polymers were obtained by the photopolymerization of bis‐anthryl‐Schiff's bases, followed by the oxidation of the resulting polymers. These polymers were soluble in acidic solvents such as formic and sulfuric acids but were insoluble in organic solvents.
The protein tyrosine kinase ZAP-70 can associate with the SH2 domain of proto-Vav. (1994)

Stimulation of the T cell antigen receptor (TCR) leads to tyrosine phosphorylation of a number of cellular proteins, including the vav proto-oncogene product. We now report the detection of several phosphotyrosine proteins (80, 74, and 70 kDa) from TCR-stimulated T cells that bind to the Src homology 2 (SH2) domain of proto-Vav (Vav-SH2) and co-immunoprecipitate with the proto-Vav product. Their binding to Vav-SH2 differs from that observed with SH2 domains from other proteins. None of the Vav-SH2-associated phosphoproteins bind to either of the Src homology 3 (SH3) domains of proto-Vav or to mutant Vav-SH2 proteins. The association of the phosphoproteins with Vav-SH2 requires induction of tyrosine phosphorylation of cellular proteins since proteins from lysates of herbimycin A-treated TCR-activated T cells fail to associate with Vav-SH2. Among the proteins from T cells that co-immunoprecipitate with the proto-Vav product and bind to its SH2 domain, specific antibodies identified the 70-kDa tyrosine phosphoprotein as ZAP-70, a protein tyrosine kinase (PTK) involved in TCR signal transduction. Binding of this PTK to Vav-SH2 is inhibited by a ZAP-70-specific synthetic tyrosine phosphopeptide. We suggest that ZAP-70 may function as a PTK for proto-Vav.
Expression of Bovine 17α-Hydroxylase Cytochrome P-450 cDNA in Nonsteroidogenic (COS 1) Cells (1986)

Cortisol production requires the activity of only 17 alpha-hydroxylase, whereas the formation of sex steroids requires both 17 alpha-hydroxylase and 17,20-lyase activities. Studies in reconstituted enzyme systems have suggested that a single steroid hydroxylase, 17 alpha-hydroxylase cytochrome P-450 (P-450(17) alpha), catalyzes both activities. By expression of bovine adrenocortical P-450(17 alpha) in COS 1 (transformed monkey kidney) cells, which normally contain no detectable P-450(17) alpha, it has now been established in situ that a single polypeptide chain does catalyze both the 17 alpha-hydroxylase and the 17,20-lyase reactions. This heterologous system supports 17 alpha-hydroxylation of pregnenolone and progesterone with equal efficiency, but catalyzes about five times as much 17,20-lyase activity when 17 alpha-hydroxypregnenolone is the substrate than when 17 alpha-hydroxyprogesterone is the substrate. For these activities to be observed in COS 1 cells, newly synthesized apocytochrome P-450(17) alpha must bind heme and insert into the endoplasmic reticulum such that endogenous cytochrome P-450 reductase can support hydroxylation. Thus, COS 1 cells are a useful system for expression and study of various forms of cytochrome P-450.
Model Wellbore Evaluation of Diverter Effectiveness Confirmed by Field Results (1996)

Abstract Effective diversion is critical to successful stimulation of long-interval, high-rate wells. Once near-wellbore damage has been removed in one portion of the completion interval, steps must be taken to divert stimulation fluids to intervals that remain damaged. Viscous fluid diverters, such as gels, foams, and emulsions, have all been used with success in field applications. These three diverter types were compared in the Westport Technology Center wellbore model. Foams and emulsions were found to provide more effective diversion than gel. Based on the laboratory results, foam diversion was used during stimulation of injection wells at Shell Offshore Inc.'s Bullwinkle platform. Comparison of diverted and undiverted treatments quantifies the benefits to be gained from effective diversion and demonstrates that wellbore model studies correlate well with field results.
Soy Isoflavones in Conjunction With Radiation Therapy in Patients With Prostate Cancer (2010)

Soy isoflavones sensitize prostate cancer cells to radiation therapy by inhibiting cell survival pathways activated by radiation. At the same time, soy isoflavones have significant antioxidant and anti-inflammatory activity, which may help prevent the side effects of radiation. Therefore, we hypothesized that soy isoflavones could be useful when given in conjunction with curative radiation therapy in patients with localized prostate cancer. In addition to enhancing the efficacy of radiation therapy, soy isoflavones could prevent the adverse effects of radiation. We conducted a pilot study to investigate the effects of soy isoflavone supplementation on acute and subacute toxicity (≤6 mo) of external beam radiation therapy in patients with localized prostate cancer. Forty-two patients with prostate cancer were randomly assigned to receive 200 mg soy isoflavone (Group 1) or placebo (Group 2) daily for 6 mo beginning with the first day of radiation therapy, which was administered in 1.8 to 2.5 Gy fractions for a total of 73.8 to 77.5 Gy. Adverse effects of radiation therapy on bladder, bowel, and sexual function were assessed by a self-administered quality of life questionnaire at 3 and 6 mo. Only 26 and 27 patients returned completed questionnaires at 3 and 6 mo, respectively. At each time point, urinary, bowel, and sexual adverse symptoms induced by radiation therapy were decreased in the soy isoflavone group compared to placebo group. At 3 mo, soy-treated patients had less urinary incontinence, less urgency, and better erectile function as compared to the placebo group. At 6 mo, the symptoms in soy-treated patients were further improved as compared to the placebo group. These patients had less dripping/leakage of urine (7.7% in Group 1 vs. 28.4% in Group 2), less rectal cramping/diarrhea (7.7% vs. 21.4%), and less pain with bowel movements (0% vs. 14.8%) than placebo-treated patients. There was also a higher overall ability to have erections (77% vs. 57.1%). The results suggest that soy isoflavones taken in conjunction with radiation therapy could reduce the urinary, intestinal, and sexual adverse effects in patients with prostate cancer.
Genetic Abnormalities and Microsatellite Instability in Colorectal Cancer (1998)

Our purpose was to investigate different genetic abnormalities, such as K-ras mutations, p53 alterations, and c-myc RNA overexpression, as well as microsatellite instability in 63 colorectal tumors obtained from patients that had undergone surgery. K-ras point mutations were analyzed by PCR-RFLP technique, followed by sequencing; p53 protein accumulation by immunohistochemistry; p53 gene mutations in exons 5-9 were studied by the SSCP and sequencing techniques, and c-myc overexpression by Northern blot. Microsatellite instability was performed at chromosomes 2p, 3p, and 11p by a PCR-based technique. Our data indicate a trend toward a poorer prognosis in patients who had K-ras transversions; besides, we have obtained a prevalence of c-myc RNA overexpression and p53 exon 7 mutations in the latest stages of tumor progression. In conclusion, our findings suggest that the recognition of molecular abnormalities might be used in colorectal cancer as a prognostic indicator or to determine the metastatic potential of colorectal adenocarcinomas.
CpG-DNA-induced IFN-alpha production involves p38 MAPK-dependent STAT1 phosphorylation in human plasmacytoid dendritic cell precursors. (2002)

Human plasmacytoid or CD4(+)CD11c(-) type 2 dendritic cell precursors (PDC) were identified as natural type I interferon (IFN)-producing cells in response to viral and bacterial infection. They represent effector cells of innate immunity and link it to the distinct adaptive immunity by differentiating into mature DC. It has been reported that oligodeoxyribonucleotides containing unmethylated CpG motifs (CpG DNA) stimulate PDC to produce IFN-alpha, but the molecular mechanisms involved remain unknown. We found that CpG-DNA-induced IFN-alpha production in PDC was completely impaired by the inhibitor of the p38 mitogen-activated protein kinase (MAPK) pathway. Expression of IFN regulatory factor (IRF)-7 was enhanced by CpG-DNA treatment, which was preceded by the phosphorylation of signal transducer and activator of transcription (STAT)1 on Tyr-701, as well as its enhanced phosphorylation on Ser-727. All of these events were also suppressed by the p38 MAPK inhibitor. STAT1, STAT2, and IRF-9, components of IFN-stimulated gene factor 3 (ISGF3), were recognized in the nuclear fraction of CpG-DNA-treated cells. Neither anti-IFN-alpha/beta antibodies (Ab) nor anti-IFNAR Ab suppressed STAT1 phosphorylation, enhancement of IRF-7 expression, or IFN-alpha production in the early phase of the culture. These results suggest that CpG DNA induces p38 MAPK-dependent phosphorylation of STAT1 in a manner independent of IFN-alpha/beta, which may cause ISGF3 formation to increase the transcription of the IRF-7 gene, thereby leading to IFN-alpha production in human PDC.
Totally relaxed Ge<i>x</i>Si1−<i>x</i> layers with low threading dislocation densities grown on Si substrates (1991)

We have grown compositionally graded GexSi1−x layers on Si at 900 °C with both molecular beam epitaxy and rapid thermal chemical vapor deposition techniques. Triple-crystal x-ray diffraction reveals that for 0.10&amp;lt;x&amp;lt;0.53, the layers are totally relaxed. GexSi1−x cap layers grown on these graded layers are threading-dislocation-free when examined with conventional plan-view and cross-sectional transmission electron microscopy. Electron beam induced current images were used to count the low threading dislocation densities, which were 4×105±5×104 cm−2 and 3×106±2×106 cm−2 Eq. 2×106 cm−2 for x=0.23 and x=0.50, respectively. Photoluminescence spectra from the cap layers are identical to photoluminescence from bulk GexSi1−x.
Hemoglobinase Activity of the Lysine Gingipain Protease (Kgp) of Porphyromonas gingivalis W83 (1999)

Porphyromonas gingivalis, an important periodontal disease pathogen, forms black-pigmented colonies on blood agar. Pigmentation is believed to result from accumulation of iron protoporphyrin IX (FePPIX) derived from erythrocytic hemoglobin. The Lys-X (Lys-gingipain) and Arg-X (Arg-gingipain) cysteine proteases of P. gingivalis bind and degrade erythrocytes. We have observed that mutations abolishing activity of the Lys-X-specific cysteine protease, Kgp, resulted in loss of black pigmentation of P. gingivalis W83. Because the hemagglutinating and hemolytic potentials of mutant strains were reduced but not eliminated, we hypothesized that this protease played a role in acquisition of FePPIX from hemoglobin. In contrast to Arg-gingipain, Lys-gingipain was not inhibited by hemin, suggesting that this protease played a role near the cell surface where high concentrations of hemin confer the black pigmentation. Human hemoglobin contains 11 Lys residues in the alpha chain and 10 Lys residues in the beta chain. In contrast, there are only three Arg residues in each of the alpha and beta chains. These observations are consistent with human hemoglobin being a preferred substrate for Lys-gingipain but not Arg-gingipain. The ability of the Lys-gingipain to cleave human hemoglobin at Lys residues was confirmed by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry of hemoglobin fragments resulting from digestion with the purified protease. We were able to detect several of the predicted hemoglobin fragments rendered by digestion with purified Lys-gingipain. Thus, we postulate that the Lys-gingipain of P. gingivalis is a hemoglobinase which plays a role in heme and iron uptake by effecting the accumulation of FePPIX on the bacterial cell surface.
Using Mass Spectrometry to Characterize Self‐Assembled Monolayers Presenting Peptides, Proteins, and Carbohydrates (2002)

Peptide and carbohydrate biochips can be assayed with MALDI mass spectrometry. Self-assembled monolayers (SAMs) that are modified with ligands provide a platform for identifying selective protein–ligand and enzyme–substrate interactions. MALDI provides a rapid and sensitive method for detection and avoids the need to label protein analytes with fluorescent or radioactive tags. The picture shows the mass spectrum of a SAM presenting a carbohydrate.
Effect of Surfactants on Hydrate Formation Kinetics (1993)

ABSTRACT In this paper we investigate experimentally the effect of surfactants on the formation kinetics of methane hydrate. The compounds tested include: anionic, cationic and nonionic surfactants. Experimental results indicate that surfactants (at concentrations levels near their CMC) do not influence the thermodynamics, however, they have a strong influence on the kinetics of gas dissolution in the water phase as well as on the overall rate of hydrate formation. In addition, the formed hydrate particles in the presence of the various surfactants exhibit diverse agglomeration characteristics. This work is part of an overall effort to develop the technology required for the safe operation of offshore oil and gas transportation pipelines without inhibitors.
Loss of myostatin attenuates severity of muscular dystrophy in <i>mdx</i> mice (2002)

Myostatin, a transforming growth factor-beta family member, is a negative regulator of skeletal muscle growth. To explore the therapeutic potential of targeting myostatin in settings of muscle degeneration, we crossed myostatin null mutant mice with mdx mice, a model for Duchenne and Becker muscular dystrophy. Mdx mice lacking myostatin were stronger and more muscular than their mdx counterparts. Diaphragm muscle showed less fibrosis and fatty remodeling, suggesting improved muscle regeneration.
Ensemble Tracking (2005)

We consider tracking as a binary classification problem, where an ensemble of weak classifiers is trained online to distinguish between the object and the background. The ensemble of weak classifiers is combined into a strong classifier using AdaBoost. The strong classifier is then used to label pixels in the next frame as either belonging to the object or the background, giving a confidence map. The peak of the map, and hence the new position of the object, is found using mean shift. Temporal coherence is maintained by updating the ensemble with new weak classifiers that are trained online during tracking. We show a realization of this method and demonstrate it on several video sequences.
Cytocompatibility of UV and visible light photoinitiating systems on cultured NIH/3T3 fibroblasts in vitro (2000)

This work investigates the cytocompatibility of several photoinitiating systems for potential cell encapsulation applications. Both UV and visible light initiating schemes were examined. The UV photoinitiators included 2,2-dimethoxy-2-phenylacetophenone (Irgacure 651), 1-hydroxycyclohexyl phenyl ketone (Irgacure 184), 2-methyl-1-[4-(methylthio) phenyl]-2-(4-morpholinyl)-1-propanone (Irgacure 907), and 2-hydroxy-1-[4-(hydroxyethoxy)phenyl]-2-methyl-1-propanone (Darocur 2959). The visible light initiating systems included camphorquinone (CQ) with ethyl 4-N,N-dimethylaminobenzoate (4EDMAB) and triethanolamine (TEA) and the photosensitizer isopropyl thioxanthone. A cultured fibroblast cell line, NIH/3T3, was exposed to the photoinitiators at varying concentrations from 0.01% (w/w) to 0.1% (w/w) with and without the presence of initiating light. The results demonstrated that at low photoinitiator concentrations (< or = 0.01% (w/w)), all of the initiator molecules were cytocompatible with the exception of CQ, Irgacure 651, and 4EDMAB which had a relative survival approximately 50% lower than a control. In the presence of low intensity initiating light (approximately 6 mWcm(-2) of 365 nm UV light and approximately 60 mWcm(-2) of 470-490 nm visible light) and initiating radicals, Darocur 2959 at concentrations < or = 0.05% (w/w) and CQ at concentrations < or = 0.01% (w/w) were the most promising cytocompatible UV and visible light initiating systems, respectively. To demonstrate the potential use of cytocompatible photoinitiating systems in cell encapsulation applications, chondrocytes were encapsulated in a photocrosslinked hydrogel using 0.05% (w/w) Darocur 2959 (cytocompatible) and 0.01% (w/w) Irgacure 651 (cyto-incompatible). After photopolymerizing for 10 minutes with approximately 8 mWcm(-2) of 365 nm light, nearly all the chondrocytes survived the process with Darocur 2959 while very few of the chondrocytes survived the process with Irgacure 651.
Characterisation of decay of frequency induced potentiation and post-extrasystolic potentiation (1990)

P1 was interpreted as the expression of accumulation of activator in an internal release store; P3 was interpreted as a manifestation of negative feedback control of activator entry by the released activator itself, and the slow recovery to P4 as due to the slow lengthening of action potential duration and/or recovery from accumulation of an intracellular metabolite or ion.
Regulatory T cell epitopes (Tregitopes) in IgG induce tolerance in vivo and lack immunogenicity per se (2013)

Tregitopes are a set of epitopes, derived from IgG, that bind to MHCII, activate nTregs, and promote tolerance. We have now confirmed that coadministration of Tregitopes with a range of proteins (autoantigens and nominal antigens, such as OVA) in vitro and in vivo leads to suppression of T cell and antibody responses to the test antigens. In this study, we demonstrate that Tregitopes are not immunogenic in vivo even when emulsified with strong adjuvants, such as IFA or CFA. Moreover, in vivo administration of Tregitopes with IFA or CFA does not induce Th1 or Th2 cytokine expression under restimulation conditions in vitro. We investigated tolerance induction by codelivering Tregitopes with OVA using B cells. When B cells were pulsed with OVA plus Tregitopes and transferred into naïve mice, we found that cellular and humoral immune responses to the OVA were suppressed. As a result of their ability to induce Tregs and the absence of immunogenicity in the context of strong adjuvants, Tregitopes might be considered a novel immunomodulatory approach for the suppression of immune responses to protein therapeutics (such as FVIII and mAb), as well as for treatment of autoimmune diseases.
You say ITAM and I say ITIM, let's call the whole thing off: the ambiguity of immunoreceptor signalling (2006)

Paradigms of protein tyrosine kinase (PTK)-mediated immunoreceptor signalling have developed largely from studies of molecules containing immunoreceptor tyrosine-based activation motifs (ITAM) and immunoreceptor tyrosine-based inhibition motifs (ITIM). In some circumstances, ITAM can mediate inhibition and ITIM can propagate activation signals. In addition to classical immune cells, some ITAM- and ITIM-encoding proteins are more widely expressed and are crucial to the development of haemopoietic cells, like osteoclasts and natural killer cells, as well as tissues such as bone and brain. Closer analysis of activating proteins reveals that some potentially encode ITIM within an ITAM. These 'closet' ITIM could, under conditions of partial ITAM phosphorylation, mediate inhibitory signalling.
Molecular Divergence of Lysozymes and α-Lactalbumin (1997)

The vast number of proteins that sustain the currently living organisms have been generated from a relatively small number of ancestral genes that has involved a variety of processes. Lysozyme is an ancient protein whose origin goes back an estimated 400 to 600 million years. This protein was originally a bacteriolytic defensive agent and has been adapted to serve a digestive function on at least two occasions, separated by nearly 40 million years. The origins of the related goose type and T4 phage lysozyme that are distinct from the more common C type are obscure. They share no discernable amino acid sequence identity and yet they possess common secondary and tertiary structures. Lysozyme C gene also gave rise, after gene duplication 300 to 400 million years ago, to a gene that currently codes for alpha-lactalbumin, a protein expressed only in the lactating mammary gland of all but a few species of mammals. It is required for the synthesis of lactose, the sugar secreted in milk. alpha-Lactalbumin shares only 40% identity in amino acid sequence with lysozyme C, but it has a closer spatial structure and gene organization. Although structurally similar, functionally they are quite distinct. Specific amino acid substitutions in alpha-lactalbumin account for the loss of the enzyme activity of lysozyme and the acquisition of the features necessary for its role in lactose synthesis. Evolutionary implications are as yet unclear but are being unraveled in many laboratories.
Study and Demonstration of Sleep and Adaptive Link Rate Control Mechanisms for Energy Efficient 10G-EPON (2010)

This paper describes sleep and adaptive link rate (ALR) control functions to reduce the power consumption of optical network units (ONUs) in 10 Gb∕s Ethernet passive optical network (10G-EPON) systems. A hybrid mechanism that includes both sleep and ALR control functions is proposed with a view to further improving the power-saving performance. The sleep control function switches the ONU mode, i.e., active or sleep, depending on the presence or absence of traffic. The ALR control function switches the downlink rates between an optical line terminal (OLT) and an ONU, i.e., 1 Gb∕s or 10 Gb∕s, depending on the quantity of traffic. The proposed hybrid mechanism offers effective power management of ONUs on the basis of the traffic conditions. The proposed hybrid mechanism is validated by a numerical simulation and an experiment.