gebhart/patrepeval huggingface dataset:
T-cell dysfunctions in hu-PBL-SCID mice infected with human immunodeficiency virus (HIV) shortly after reconstitution: in vivo effects of HIV on highly activated human immune cells (1996)

The state of activation of the immune system may be an important factor which renders a host more receptive to human immunodeficiency virus (HIV) and more vulnerable to its effects. To explore this issue with a practical in vivo model, we developed a modified protocol of HIV infection in hu-PBL-SCID mice. First, we assessed the time course of activation of human peripheral blood lymphocytes (hu-PBL) in the peritoneal cavity of SCID mice. At 2 to 24 h after the intraperitoneal injection into SCID mice, there was a clear-cut increase in the percentage of hu-PBL expressing early activation markers (CD69), concomitant with the release of soluble intercellular adhesion molecule-1 (sICAM-1) and the soluble interleukin-2 receptor (sIL-2R) and with the accumulation of mRNAs for a number of human cytokines. At 2 weeks, virtually all of the hu-PBL expressed the memory phenotype (CD45RO) and HLA-DR antigens as well. Cells collected from the SCID mouse peritoneum at 2 and 24 h after transplantation were fully susceptible to in vitro infection with HIV type 1 (HIV-1) in the absence of either IL-2 or mitogens. The injection of HIV into hu-PBL-SCID mice at 2 h after reconstitution resulted in a generalized and productive HIV infection of the xenochimeras. This early HIV-1 infection resulted in a dramatic depletion of human CD4+ cells and in decreased levels of sICAM-1 (in the peritoneal lavage fluid) as well as of sIL-2R and immunoglobulins M and A (in the serum). Enzyme-linked immunosorbent assay and/or reverse transcriptase PCR analysis showed higher levels of IL-4, IL-5, and IL-10 in the HIV-infected animals than in control hu-PBL-SCID mice, while gamma interferon levels in the two groups were comparable. When we compared the current model of HIV-1 infection at 2 weeks after the intraperitoneal injection of the hu-PBL in the SCID mice with the model described here, we found that the majority of immune dysfunctions induced in the 2-h infection of the xenochimeras are not inducible in the 2-week infection. This supports the concept that the state of activation of human cells at the moment of the in vivo infection with HIV-1 is a crucial factor in determining the immune derangement observed in AIDS patients. These results show that some immunological dysfunctions induced by HIV infection in AIDS patients can be mimicked in this xenochimeric model. Thus, the hu-PBL-SCID mouse model may be useful in exploring, in vivo, the relevance of hu-PBL activation and differentiation in HIV-1 infection and for testing therapeutic intervention directed towards either the virus or the immune system.
Antagonism of chemotherapy-induced cytotoxicity for human breast cancer cells by antiestrogens. (1989)

In a prior National Surgical Adjuvant Breast and Bowel Project (NSABP) adjuvant study, the addition of the antiestrogen tamoxifen to chemotherapy with melphalan and fluorouracil adversely affected survival in several patient subsets, suggesting an antagonistic drug interaction. To investigate this possibility, we studied the interaction of tamoxifen and other antiestrogens with several cytotoxic drugs in cultured human breast cancer cell lines. Clinically relevant concentrations of tamoxifen and melphalan reduced colony survival of estrogen receptor (ER)-positive breast cancer cells when used alone in a colony-forming assay. However, pretreatment of cells with tamoxifen followed by exposure to melphalan resulted in antagonism, with more colonies surviving treatment with the combination than with melphalan alone. Identical effects were seen using several other triphenylethelene antiestrogens. An antagonistic interaction was observed even with a brief preincubation with tamoxifen that had no effect on cell proliferation, indicating that antagonism was not due to tamoxifen's known cell kinetic effects. Tamoxifen even antagonized melphalan cytotoxicity in ER-negative breast cancer cells and in cultured liver cells. An additive drug interaction occurred when melphalan was combined with pharmacologic concentrations of estradiol or medroxyprogesterone acetate, but antagonism was also observed with dexamethasone. Tamoxifen also antagonized the cytotoxicity of fluorouracil in these cells. However, an additive interaction occurred when the antiestrogen was combined with doxorubicin or 4-hydroxy-cyclophosphamide, an alkylating agent that is transported into the cell by a different carrier-mediated mechanism than melphalan. To avoid potential antagonism in the clinic, combinations of tamoxifen with melphalan and/or fluorouracil should be avoided.
Characterization of the human CSK locus. (1993)

The CSK-gene encodes an intracellular protein-tyrosine kinase (PTK). In contrast to members of the src-family, an autophosphorylation site corresponding to Tyr416, as well as the equivalent of the regulatory Tyr527 in p60c-src are missing in the amino acid sequence deduced from the gene. CSK phosphorylates other members of the src-family of tyrosine kinases at their regulatory carboxy-terminus. By regulating the activity of these kinases, CSK may play an important role in cell growth and development. Here we describe the structure of the human CSK gene. The entire coding region spans a genomic distance of only 4.9 kb. It encompasses 12 exons ranging between 66 and 220 bp in size. The introns between coding exons vary between 76 and 920 bp in length. An exon coding for the 5'-untranslated region of CSK is separated from the first coding exon by an intron of more than 6400 bp. Based on comparisons of sequence homologies within the catalytic domains, the intracellular PTKs are divided into the src-family, the fes/fer- and the abl/arg-group. The genomic structure of four members of the SRC-family revealed nearly identical exon/intron boundaries within the catalytic domain of this family. They differ from those described for FES. Comparing the genomic structure of CSK with the exon/intron organisation of both, it is obvious that the exon/intron boundaries are in common either with those of the SRC-type or the FES boundaries. This intermediate exon/intron structure of CSK between FES and the SRC-family agrees with the position of CSK in a phylogenetic tree based on sequence homology within the kinase domain.
Association of ABCB1 polymorphisms with the efficacy of ondansetron for postoperative nausea and vomiting (2010)

We investigated whether the 2677G>T/A and 3435C>T polymorphisms of adenosine triphosphate-binding cassette subfamily B member 1 (ABCB1) affect the efficacy of ondansetron to prevent postoperative nausea and vomiting. One hundred and ninety-eight patients undergoing general anaesthesia were enrolled. Thirty minutes before the end of surgery, 0.1 mg.kg⁻¹ ondansetron was administered intravenously. The incidence of postoperative nausea and vomiting was compared between genotypes in the 2677G>T/A and 3435C>T polymorphisms of ABCB1. The incidence of postoperative nausea and vomiting was lower in patients with the 2677TT genotype (TT vs Non-TT = 25.9% vs 53.0%, p = 0.01) and 3435TT genotype (CC + CT vs TT = 52.6% vs 21.7%, p = 0.01) during the first 2 h after surgery. There were no significant differences in the incidence of postoperative nausea and vomiting between the different genotype groupings during period between 2 and 24 h after surgery. In conclusion, ABCB1 genotypes may be a clinical predictor of responsiveness for ondansetron.
Inhibition of T cell responses to alloantigens and polyclonal mitogens by Ly-5 antisera. (1984)

The effects of Ly-5 alloantisera on the generation of cytotoxic T cells (CTL), on the effector phase of CTL killing, and on polyclonal mitogenesis were studied. Ly-5 antisera added at the beginning of mixed lymphocyte culture (MLC) suppressed the production of CTL in an allele-specific manner. Neither Ly-5.1 nor Ly-5.2 antisera inhibited the generation of cytotoxic effectors by Ly-5.1/Ly-5.2 heterozygous spleen cells; however, a combination of Ly-5.1 and Ly-5.2 antisera markedly suppressed the appearance of Ly-5 heterozygous CTL. Similarly, Ly-5 antisera inhibited the effector phase of CTL killing in an allele-specific manner. In addition, Ly-5 alloantisera specifically blocked concanavalin A and oxidative mitogenesis of splenocytes carrying the appropriate Ly-5 alloantigen. The results are discussed in light of a possible functional role of Ly-5 molecules in immune processes.
ErbB Signaling Regulates Lineage Determination of Developing Pancreatic Islet Cells in Embryonic Organ Culture (2002)

The neuregulin (NRG)/epidermal growth factor (EGF) family of growth factors consists of several ligands that specifically activate four erbB receptor-tyrosine kinases, namely erbB-1 (EGF-R), erbB-2 (neu), erbB-3, and erbB-4. We have previously shown that islet morphogenesis is impaired and beta-cell differentiation delayed in mice lacking functional EGF-R [EGF-R (-/-)]. The present study aims to clarify which erbB ligands are important for islet development. Pancreatic expression of EGF, TGF-alpha, heparin-binding EGF, betacellulin (BTC), and NRG-4 was detected as early as embryonic d 13 (E13). Effects of these ligands were studied in E12.5 pancreatic explant cultures grown for 5 d ex vivo. None of the growth factors affected the ratio of endocrine to exocrine cells. However, significant effects within the endocrine cell populations were induced by EGF, BTC, and NRG-4. beta-Cell development was augmented by BTC, whereas the development of somatostatin-expressing delta-cells was stimulated by NRG-4. Both ligands decreased the numbers of glucagon-containing alpha-cells. The effect of BTC was abolished in the EGF-R (-/-) mice. A soluble erbB-4 binding fusion protein totally inhibited the effects of NRG-4 but not of BTC. Neutralization of endogenous NRG-4 activity in the model system effectively inhibited delta-cell development, indicating that this erbB4-ligand is an essential factor for delineation of the somatostatin-producing delta-cells. Our results suggest that ligands of the EGF-R/erbB-1 and erbB-4 receptors regulate the lineage determination of islet cells during pancreatic development. BTC, acting through EGF-R/erbB-1, is important for the differentiation of beta-cells. This could be applied in the targeted differentiation of stem cells into insulin-producing cells.
Structural Basis for Distinct Binding Properties of the Human Galectins to Thomsen-Friedenreich Antigen (2011)

The Thomsen-Friedenreich (TF or T) antigen, Galβ1-3GalNAcα1-O-Ser/Thr, is the core 1 structure of O-linked mucin type glycans appearing in tumor-associated glycosylation. The TF antigen occurs in about 90% of human cancer cells and is a potential ligand for the human endogenous galectins. It has been reported that human galectin-1 (Gal-1) and galectin-3 (Gal-3) can perform their cancer-related functions via specifically recognizing TF antigen. However, the detailed binding properties have not been clarified and structurally characterized. In this work, first we identified the distinct TF-binding abilities of Gal-1 and Gal-3. The affinity to TF antigen for Gal-3 is two orders of magnitude higher than that for Gal-1. The structures of Gal-3 carbohydrate recognition domain (CRD) complexed with TF antigen and derivatives, TFN and GM1, were then determined. These structures show a unique Glu-water-Arg-water motif-based mode as previously observed in the mushroom galectin AAL. The observation demonstrates that this recognition mode is commonly adopted by TF-binding galectins, either as endogenous or exogenous ones. The detailed structural comparisons between Gal-1 and Gal-3 CRD and mutagenesis experiments reveal that a pentad residue motif ((51)AHGDA(55)) at the loop (g1-L4) connecting β-strands 4 and 5 of Gal-1 produces a serious steric hindrance for TF binding. This motif is the main structural basis for Gal-1 with the low affinity to TF antigen. These findings provide the intrinsic structural elements for regulating the TF-binding activity of Gal-1 in some special conditions and also show certain target and approach for mediating some tumor-related bioactivities of human galectins.
A new antitumor antibiotic, FR900840. III. Antitumor activity against experimental tumors. (1989)

FR900840 [2S)-2-amino-2-carboxyethyl (3R)-2-diazo-3-hydroxybutyrate), a new antibiotic with antitumor activity was isolated from the fermentation broth of Streptomyces sp. No. 8727. Its antitumor activity was examined in three mouse tumor systems and ten human tumor systems. FR900840 had no clear effect on mouse ascitic tumors, P388 and L1210, and the B16 melanoma line, but had prominent antitumor effects on several human solid tumors. Its antitumor activity against A549 human lung adenocarcinoma was stronger than those of vinblastine, doxorubicin and cisplatin. These results suggest that FR900840 may become a useful prototype antitumor drug.
Interaction of human recombination proteins Rad51 and Rad54 (1997)

The cDNA for human protein HsRad54, which is a structural homolog of Saccharomyces cerevisiae recombination/repair protein Rad54, was cloned and expressed in Escherichia coli. As demonstrated by analysis in vitro and in vivo, HsRad54 protein interacts with human Rad51 recombinase. The interaction is mediated by the N-terminal domain of HsRad54 protein, which interacts with both free and DNA-bound HsRad51 protein.
Diagnostic and therapeutic endoscopy (2005)

Within the gastrointestinal tract, there is no shorter segment with a higher cancer incidence than the gastro-esophageal junction. Flexible endoscopy is the mainstay for diagnosis of early and advanced esophageal adenocarcinoma, for the treatment of early lesions, and also for the palliation of advanced cancer. New developments in endoscopy aim to improve the diagnosis and treatment of esophageal cancer. These include high resolution and magnification endoscopy in combination with chromendoscopy, and techniques based on modulation of the features of light bundles, such as narrow band imaging, fluorescence endoscopy, and elastic scattering spectroscopy. The value of these techniques for the surveillance of distal esophageal neoplasia needs further study. Furthermore, new methods of tissue sampling and evaluation are being studied to augment identification and staging of patients at risk for cancer. Finally, newer instruments may decrease patient burden during endoscopy, making screening and surveillance more acceptable from a patient's perspective. This review discusses the new developments in flexible endoscopy for diagnosis and therapy of early and advanced and advanced esophageal adenocarcinoma.
The absorption spectra of halogens and inter-halogen compounds in solution in carbon tetrachloride (1929)

Abstract When two solutions are mixed the absorption spectrum of the new solution will be the mean of those of the separate solutions provided that no chemical interaction occures. The mere fact of a departure from additivity does not, however, necessarily denote the formation of true chemical compounds. The solute or solutes may undergo solvation, loosely bound aggregates may occur, and even when marked deviations from the simple law of mixtures are observed it is rarely possible to prove the quantitative formation of a given chemical compound from spectroscopic data alone. The above considerations apply with some force to the problem of the absorption spectra of halogens and inter-halogen compounds in an inert solvent. The three elements show perfectly characteristic absorption bands, they are known to interact with the formation of some quite stable compounds, some relatively stable compounds, and some apparently very unstable compounds.
Analysis of counter-pumped small-signal fibre Ramanamplifiers (1997)

Analytic expressions for the small-signal optical gain and noise figure of a counter-pumped fibre Raman amplifier are presented, for unequal signal and pump loss coefficients. The author also presents analytic approximations for the gain limitations imposed by double Rayleigh scattering.
Nonsurgical placement of arterial endoprostheses: a new technique using nitinol wire. (1983)

A new type of endovascular prosthesis has been developed using a unique metal alloy (nitinol) with a heat-sensitive memory. Nitinol wire coil grafts were straightened in ice water and passed into the canine aorta via catheter, where they reformed into their original shapes. Follow-up aortograms demonstrated long-term patency with minimal thrombus formation. Nitinol endovascular coil grafts may eventually be used in the nonsurgical treatment of several forms of vascular disease.
Software Source Code Correlation (2006)

The degree of correlation between the source codes of different software programs is important for uncovering plagiarism, trade secret theft, copyright infringement, and patent infringement. Other uses include locating open source code within a proprietary program and determining common authorship of different programs. Measurement of source code correlation is an important factor in any punitive determination of rights infringement. Existing measures of source code correlation tend to focus on only one or two types of correlation. This paper presents a theoretical basis for a measure of source code correlation predicated on various uses and requirements. The paper also describes a software tool that uses multiple algorithms to determine this correlation measure. At the conclusion the paper compares the results produced by this tool against results produced by other tools when examining a controlled set of correlated source code files and finds that the new tool is more accurate than other tools in determining all types of source code correlation
Microscale production of hybridomas by hypo-osmolar electrofusion. (1992)

We have developed and tested a novel electrofusion chamber, the adjustable plate microchamber, that permits the successful electrofusion and production of hybridomas in a hanging droplet from as few as 1,000 B lymphocytes. Cell suspension volumes of 10 microliters may be used without excessive difficulty in aseptically recovering fused cells. With a modification of the hypo-osmolar electrofusion protocol with this microchamber, fusion efficiencies of the order of 10(-3) may be attained. These efficiencies are comparable to those attained with standard hardware and much higher numbers of input B lymphocytes. This technology should permit high efficiency hybridoma production using a variety of hitherto inaccessible B lymphocyte populations such as B cells isolated from human organ biopsies.
Poly(A)-Specific Ribonuclease Mediates 3′-End Trimming of Argonaute2-Cleaved Precursor MicroRNAs (2013)

MicroRNAs (miRNAs) are typically generated as ~22-nucleotide double-stranded RNAs via the processing of precursor hairpins by the ribonuclease III enzyme Dicer, after which they are loaded into Argonaute (Ago) proteins to form an RNA-induced silencing complex (RISC). However, the biogenesis of miR-451, an erythropoietic miRNA conserved in vertebrates, occurs independently of Dicer and instead requires cleavage of the 3' arm of the pre-miR-451 precursor hairpin by Ago2. The 3' end of the Ago2-cleaved pre-miR-451 intermediate is then trimmed to the mature length by an unknown nuclease. Here, using a classical chromatographic approach, we identified poly(A)-specific ribonuclease (PARN) as the enzyme responsible for the 3'-5' exonucleolytic trimming of Ago2-cleaved pre-miR-451. Surprisingly, our data show that trimming of Ago2-cleaved precursor miRNAs is not essential for target silencing, indicating that RISC is functional with miRNAs longer than the mature length. Our findings define the maturation step in the miRNA biogenesis pathway that depends on Ago2-mediated cleavage.
Nano-microparticles as immune adjuvants: correlating particle sizes and the resultant immune responses (2010)

The development of novel immune adjuvants is emerging as a significant area of vaccine delivery based on the continued necessity to amplify immune responses to a wide array of new antigens that are poorly immunogenic. This article specifically focuses on the application of nanoparticles and microparticles as vaccine adjuvants. Many investigators are in agreement that the size of the particles is crucial to their adjuvant activities. However, reports on correlating the size of particle-based adjuvants and the resultant immune responses have been conflicting, with investigators on both sides of the fence with impressive data in support of the effectiveness of particles with small sizes (submicron) over those with larger sizes (micron) and vice versa, while other investigators reported data that showed submicron- and micron-sized particles are effective to the same degree as immune adjuvants. We have generated a list of biological, immunological and, more importantly, vaccine formulation parameters that may have contributed to the inconsistency from different studies and made recommendations on future studies attempting to correlate the size of particulate adjuvants and the immune responses induced. The information gathered could lead to strategies to optimize the performance of nano-microparticles as immune adjuvants.
Density Mapping in Poly(Ethylene Terephthalate) Using a Fiber-Coupled Raman Microprobe and Partial Least-Squares Calibration (1996)

Partial least-squares (PLS) analysis has been used to calibrate Raman microprobe spectra of poly(ethylene terephthalate) films in terms of density, in order to give insight into changes in crystallinity through the film thickness. The microprobe utilizes a static multiplexed holographic grating to obtain the entire Raman spectrum (-1600-4000 cm- 1 ) in a “single-shot” at ∼ 5-cm −1 resolution. Because there are no moving parts, frequency registration and repeatability are excellent and ideally suited for multivariate calibration. In addition, the high spectral throughput allows the whole spectrum to be collected in a few seconds with high signal-to-noise ratio. With this equipment, cross-validated calibration precisions as low as - 0.0021 g cm −3 were achieved. In this work we considered two ways of removing fluorescence backgrounds prior to carrying out multivariate calibration. The first involved manually fitting a baseline using a polynomial curve and subtracting it. The second approach simply takes the second derivative of the spectrum to attenuate the low-frequency components (i.e., the curved baseline). It was found that either pretreatment gave good calibration precision provided that the resultant spectra were intensity-normalized to correct for variations in laser power, sample alignment, and so on. Surprisingly, it was found that the best precision was obtained by grouping the spectral resolution elements into blocks of eight data points, thereby improving the signal-to-noise but effectively degrading the spectral resolution by a factor of three. This was especially important for the derivative spectra. Alternatively, Savitsky-Golay smoothing of the second derivative data was applied to the same effect but also at the expense of degrading spectral resolution. The implication of this work is that instruments intended for multivariate calibration applications could perhaps be designed to work at rather lower spectral resolutions (but higher signal-to-noise) than might otherwise be considered.