gebhart/patrepeval huggingface dataset:
Morphine promotes the growth of HIV-1 in human peripheral blood mononuclear cell cocultures (1990)

Because morphine has been shown to alter the function of human T lymphocytes and monocytes, we postulated that morphine would promote the growth of HIV-1 in these cells. To test this hypothesis, a coculture assay was used consisting of phytohemagglutinin (PHA)-activated peripheral blood mononuclear cells (PBMC) from normal donors and PBMC which had been infected with a viral isolate from an asymptomatic patient, HIV-1AT. The growth of HIV-1AT, as reflected by the concentration of p24 antigen in coculture supernatants, was markedly increased in cocultures that contained morphine. A bell-shaped dose-response curve was observed with three- to fourfold increased growth at a morphine concentration of 10(-12) M. Augmentation of HIV-1AT growth by morphine required an interaction with the PHA-activated donor PBMC. Furthermore, potentiation of HIV-1AT growth by morphine was stereospecific and was antagonized by naloxone and beta-funaltrexamine indicating involvement of an opiate receptor mechanism. These findings provide an additional explanation of how opiates could act as a cofactor in the pathogenesis of HIV-1 in intravenous drug users.
Genetically ModifiedLactococcus lactisfor Delivery of Human Interleukin-10 to Dendritic Cells (2011)

Interleukin-10 (IL-10) plays an indispensable role in mucosal tolerance by programming dendritic cells (DCs) to induce suppressor Th-cells. We have tested the modulating effect of L. lactis secreting human IL-10 (L. lactis(IL-10)) on DC function in vitro. Monocyte-derived DC incubated with L. lactis(IL-10) induced effector Th-cells that markedly suppressed the proliferation of allogenic Th-cells as compared to L. lactis. This suppressive effect was only seen when DC showed increased CD83 and CD86 expression. Furthermore, enhanced production of IL-10 was measured in both L. lactis(IL-10)-derived DC and Th-cells compared to L. lactis-derived DC and Th-cells. Neutralizing IL-10 during DC-Th-cell interaction and coculturing L. lactis(IL-10)-derived suppressor Th-cells with allogenic Th-cells in a transwell system prevented the induction of suppressor Th-cells. Only 130 pg/mL of bacterial-derived IL-10 and 40 times more exogenously added recombinant human IL-10 were needed during DC priming for the generation of suppressor Th-cells. The spatially restricted delivery of IL-10 by food-grade bacteria is a promising strategy to induce suppressor Th-cells in vivo and to treat inflammatory diseases.
Chemonucleolysis with Calpain I in Rabbits (1993)

Calpain I is a calcium-dependent cysteine proteinase that has been recently shown to degrade proteoglycan in vitro. The authors injected calpain I, which was purified from human red blood cells, into the intervertebral discs of rabbits. Roentgenograms showed disc space narrowing 1 week after the injection. Histologically, proteoglycan of the nucleus pulposus and anulus fibrosus decreased and notochordal cells in the nucleus pulposus almost disappeared. Biochemical data of the nucleus pulposus showed that the amounts of smaller proteoglycans increased 1 and 4 weeks after the injection. Eight weeks after the injection, histologic and biochemical data showed recovery compared with the data 1 week after injection. These findings show that calpain I is as potent an enzyme as chondroitinase ABC and has milder chemonucleolytic action than chymopapain. Regarding its possible clinical application, autogenous calpain I as purified from the patient's own red blood cells may have advantages over chymopapain and chondroitinase ABC in that it will prevent anaphylactic reaction.
Breast Carcinoma With Chondroid Differentiation: A Clinicopathologic Study of 21 Triple Negative (ER−, PR−, Her2/neu−) Cases (2009)

A total of 21 metaplastic breast carcinomas (MCs) with chondroid differentiation were evaluated to better establish the clinicopathological features of this variant. The tumors exhibited mainly invasive carcinoma admixed with areas of cartilaginous matrix production. An associated ductal intraepithelial neoplasia component grade 2 or 3 was observed in 43% of cases. Immunohistochemical analysis revealed a triple negative (ER-, PR-, and Her2/neu-) immunoprofile and no expression of the androgen receptor. EGFR-positivity was found in 88% of evaluated cases, consistent with the proposed basaloid phenotype for all MC. Compared with previous studies that reviewed MC with osseus and cartilaginous elements, the incidence of axillary lymph node metastasis was significantly higher in our study and 60% of positive nodes exhibited chondroid differentiation. Available follow-up data (n = 10) revealed aggressive behavior of this MC variant with frequent metastasis, including visceral involvement and local chest wall recurrence despite chemotherapy and radiation. Three patients subsequently died of metastatic disease.
Unique Gold Nanoparticle Aggregates as a Highly Active Surface-Enhanced Raman Scattering Substrate (2004)

A unique gold nanoparticle aggregate (GNA) system has been shown to be an excellent substrate for surface-enhanced Raman scattering (SERS) applications. Rhodamine 6G (R6G), a common molecule used for testing SERS activity on silver, but generally difficult to detect on gold substrates, has been found to readily bind to the GNA and exhibit strong SERS activity due to the unique surface chemistry afforded by sulfur species on the surface. This GNA system has yielded a large SERS enhancement of 107−109 in bulk solution for R6G, on par with or greater than any previously reported gold SERS substrate. SERS activity has also been successfully demonstrated for several biological molecules including adenine, l-cysteine, l-lysine, and l-histidine for the first time on a gold SERS substrate, showing the potential of this GNA as a convenient and powerful SERS substrate for biomolecular detection. In addition, the SERS spectrum of R6G on single aggregates has been measured. We have shown that the special surface properties of the GNA, in conjunction with strong near-IR absorption, make it useful for SERS analysis of a wide variety of molecules.
Modeling the Heart (2004)

Models of the heart have been developed since 1960, starting with the discovery and modeling of potassium channels. The first models of calcium balance were made in the 1980s and have now reached a high degree of physiological detail. During the 1990s, these cell models were incorporated into anatomically detailed tissue and organ models.
Formation of Isoaspartate at Two Distinct Sites during in vitro Aging of Human Growth Hormone (1989)

In vitro aging at pH 7.4, 37 degrees C causes natural sequence recombinant human growth hormone (rhGH), methionyl rhGH, and human pituitary growth hormone to become substrates for bovine brain protein carboxyl methyltransferase, an enzyme that modifies the "side chain" alpha-carboxyl group present at atypical isoaspartyl linkages. The substrate capacity of rhGH increased at a rate of 1.8 methyl-accepting sites/day/100 molecules of hormone. Reversed-phase high performance liquid chromatography (HPLC) of trypsin digests of aged rhGH revealed two altered peptides not present in digests of control rhGH. These two fragments, which had the amino acid compositions of residues 128-134 (Leu-Glu-Asp-Gly-Ser-Pro-Arg) and 146-158 (Phe-Asp-Thr-Asn-Ser-His-Asn-Asp-Asp-Ala-Leu-Leu-Lys), contained the majority of the induced methylation sites, 22 and 58%, respectively. Isoaspartate can result from deamidation of asparagine or isomerization of aspartate. Isomerization of Asp-130, the only candidate site in 128-134, was corroborated by coelution of the altered fragment with the synthetic isoaspartyl peptide upon reversed-phase HPLC. Evidence is presented that the altered 146-158 fragment is a mixture of two peptides resulting from deamidation of Asn-149 to form 70-80% isoaspartate and 20-30% aspartate at this position. The position of isoaspartate in the altered 146-158 fragment was deduced from mass spectrometry, which indicated a single deamidated asparagine; from methylation stoichiometry, which indicated only one methylation site; and from automated Edman degradation, which showed an absence of asparagine and a low yield of aspartate at position 149. These results show that isoaspartate formation from both aspartate and asparagine is a significant, and possibly the major, source of spontaneous covalent alteration of rhGH and that enzymatic carboxyl methylation provides a powerful tool for assessing this type of modification.
Exploring the basis of peptide–carbohydrate crossreactivity: Evidence for discrimination by peptides between closely related anti-carbohydrate antibodies (1997)

To investigate the molecular basis of antigenic mimicry by peptides, we studied a panel of closely related mAbs directed against the cell-wall polysaccharide of group A Streptococcus. These antibodies have restricted V-gene usage, indicating a shared mechanism of binding to a single epitope. Epitope mapping studies using synthetic fragments of the cell-wall polysaccharide supported this conclusion. All of the mAbs isolated crossreactive peptides from a panel of phage-displayed libraries, and competition studies indicated that many of the peptides bind at or near the carbohydrate binding site. Surprisingly, the peptides isolated by each mAb fell into distinct consensus-sequence groups that discriminated between the mAbs, and in general, the peptides bound only to the mAbs used for their isolation. Similar results were obtained with polyclonal antibodies directed against synthetic oligosaccharide fragments of the streptococcal cell-wall polysaccharide. Thus, the peptides appear to be specific for their isolating antibodies and are not recognized by the same mechanism as their carbohydrate counterparts.
OnTrk—The TrkB Signal Transduction Pathway Is an Increasingly Important Target in Cancer Biology (2009)

In the beginning, Trk was an oncogene. Yet Neurotrophin-Trk signaling came to preeminence in the field of neurobiology. Now it is appreciated that Trks regulate important processes in nonneuronal cells and, in addition to their impact on tumors of neural origin, may contribute to the pathogenesis of carcinomas, myelomas, and prostate and lymphoid tumors. Although mutations and rearrangements of Trk are seen only sporadically in human cancers, such as medullary thyroid carcinoma, a number of recent studies indicate that expression of TrkB contributes to tumor pathology. In neuroblastoma, TrkA expression marks good prognosis which TrkB and Brain-derived neurotrophic factor (BDNF) expression marks poor prognosis. Activation of the BDNF/TrkB signal transduction pathway also stimulates tumor cell survival and angiogenesis and contributes to resistance to cytotoxic drugs and anoikis, enabling cells to acquire many of the characteristic features required for tumorigenesis. Small molecule inhibitors, such as Cephalon's CEP-701, are in phase 1 and 2 clinical trials, and a series of AstraZeneca Trk inhibitors are poised to enter the clinic. As monotherapy, inhibitors may be effective only in tumors with activating Trk mutations. Important clinical follow-up will be the assessment of Trk inhibitors in combination with standard chemo- or radiotherapy or other signal transduction pathway inhibitors.
The ins and outs of lysophosphatidic acid signaling (2004)

Lysophosphatidic acid (LPA) is a lipid mediator with a wide variety of biological actions, particularly as an inducer of cell proliferation, migration and survival. LPA binds to specific G-protein-coupled receptors and thereby activates multiple signal transduction pathways, including those initiated by the small GTPases Ras, Rho, and Rac. LPA signaling has been implicated in such diverse processes as wound healing, brain development, vascular remodeling and tumor progression. Knowledge of precisely how and where LPA is produced has long proved elusive. Excitingly, it has recently been discovered that LPA is generated from precursors by 'autotaxin', a once enigmatic exo-phosphodiesterase implicated in tumor cell motility. Exogenous phospholipases D can also produce LPA, which may contribute to their toxicity. Here we review recent progress in our understanding of LPA bioactivity, signaling and synthesis.
<title>Quantization and multilevel halftoning of color images for near original image quality</title> (1990)

Algorithms are investigated for the printing or display of color images at near original image quality with a minimum number of output colors. Each algorithm consists of a quantizer possibly used in conjunction with haiftoning. We consider both image independent and image dependent quantizers implemented in RGB or in the uniform color space L*u*v*. The halftoning techniques that we use are multilevel extensions of error diffusion and ordered dither. Image quality resulting from use of these algorithms is measured by subjective evaluation.
On fast microscopic browsing of MPEG compressed video (2002)

In this paper we address the problem of rapid access to individual shots and frames in MPEG video. We build upon the compressed video processing framework proposed in Yeo (1996) and Yeo and Liu (1995), and propose new and fast algorithms based on an adaptive mixture of approximation techniques for extracting a spatially reduced image sequence of uniform quality from MPEG video across different frame types and also under different motion activities in the scenes. The algorithms execute faster than real-time on a Pentium personal computer. We demonstrate how the reduced images facilitate fast and convenient shot and frame-level video browsing and access, shot level editing and annotation, without the need for frequent decompression of MPEG video. We further propose methods for reducing the auxiliary data size associated with the reduced images through exploitation of spatial and temporal redundancy. The algorithms, tools for browsing and techniques for video processing presented in this paper have been used by many in IBM Research on more than 30 hours of MPEG-1 video for video browsing and analysis, and found to be indispensable.
Protection of chickens against avian influenza with nonreplicating adenovirus-vectored vaccine (2009)

Protective immunity against avian influenza (AI) virus has been elicited in chickens by single-dose in ovo or i.m. vaccination with a replication-competent adenovirus (Ad)-free human Ad vector encoding the AI virus A/Turkey/Wisconsin/68 H5 (AdTW68. H5) or the A/Chicken/New York/94 H7 (AdChNY94. H7) hemagglutinin (HA). The AdTW68.H5-vaccinated chickens were protected against both H5N1 and H5N2 highly pathogenic AI virus challenges. The AdChNY94. H7-vaccinated chickens were protected against an H7N3 highly pathogenic avian influenza virus challenge. Chickens vaccinated in ovo with AdTW68.H5 followed by posthatch i.m. vaccination with AdChNY94.H7 responded to both vaccinations, with robust antibody titers against both the H5 and H7 AI proteins. The use of a synthetic AI H5 HA gene codon optimized to match the tRNA pool found in chicken cells is more potent than the cognate H5 HA gene. Mass administration of this AI vaccine can be streamlined with available robotic in ovo injectors. In addition, Ad5-vectored vaccines can be produced rapidly and the safety margin of the nonreplicating vector is superior to that of a replicating counterpart. Furthermore, this mode of vaccination will not interfere with epidemiological surveys of natural AI infections. Finally, the demonstration that Ad-vectored vaccines can be administered repeatedly without appreciably losing potency highlights the commercial potential of this new class of vaccine in poultry.
Recalculated Nitrogen Conversion Factors for Several Soybean Protein Products (1982)

ABSTRACT Amino acid composition and micro‐Kjeldahl N contents of various soybean protein products are used for calculating N conversion factors by the Factor Method and Kjeldahl Method. Efforts were made to refine these methods and to minimize the magnitude of the discrepancies within these N conversion factors. Recalculated N conversion factors by the Factor Method ranged from 5.66–5.80, and by the Kjeldahl Method from 5.66–5.79. It is recommended that these conversion factors be used (rather than the common 6.25 factor) for converting N values to protein content in soy protein‐containing products.
Appraising the health of health risk appraisal. (1982)

Appraising the health of health risk appraisal. J E FieldingCopyRight https://doi.org/10.2105/AJPH.72.4.337 Published Online: October 07, 2011
Anomalously Soft Dynamics of Water in a Nanotube: A Revelation of Nanoscale Confinement (2004)

Quasi-one-dimensional water encapsulated inside single-walled carbon nanotubes, here referred to as nanotube water, was studied by neutron scattering. The results reveal an anomalously soft dynamics characterized by pliable hydrogen bonds, anharmonic intermolecular potentials, and large-amplitude motions in nanotube water. Molecular dynamics simulations consistently describe the observed phenomena and propose the structure of nanotube water, which comprises a square-ice sheet wrapped into a cylinder inside the carbon nanotube and interior molecules in a chainlike configuration.
Illegitimate and homologous recombination in mammalian cells: differential sensitivity to an inhibitor of poly(ADP-ribosylation) (1990)

We determined the effect of 3-methoxybenzamide (3-MB), a competitive inhibitor of poly(ADP-ribose)polymerase (E.C. 2.4.2.30), on illegitimate and extrachromosomal homologous recombination in mouse Ltk- cells. Cells were transfected with a wild type Herpes thymidine kinase (tk) gene or with two defective tk gene sequences followed by selection for tk-positive colonies. Using a wild type tk gene, colony formation required uptake, integration, and expression of the tk gene. Using defective tk genes, colony formation had the additional requirement for homologous recombination to reconstruct a functional tk gene. The presence of non-cytotoxic levels of 3-MB during and after transfection reduced the number of colonies recovered with a wild type tk gene in a dose-dependent manner, with 2 mM 3-MB causing a 10 to 20-fold reduction. 3-MB reduced the number of colonies recovered with defective tk genes only to the same extent as in transfections with a wild type gene. Treatment with 3-methoxybenzoic acid, a non-inhibitory analog of 3-MB, did not reduce the recovery of colonies in any experiment. Similar results were obtained using linear or supercoiled molecules and when defective tk genes were transfected into cells on one or two different DNA molecules. By assaying for transient expression of the tk gene, we found that 3-MB did not inhibit uptake or expression of the tk gene. We conclude that poly(ADP-ribosylation) plays a role in random integration (illegitimate recombination) of DNA but does not play an important role in extrachromosomal homologous recombination, demonstrating that these two recombination pathways in cultured mouse fibroblasts are biochemically distinct.
Human immunodeficiency virus type 1 infection alters chemokine beta peptide expression in human monocytes: implications for recruitment of leukocytes into brain and lymph nodes. (1996)

Two chemokine (chemoattractant cytokines) beta peptides, macrophage inflammatory proteins 1 alpha and 1 beta (MIP-1 alpha and MIP-1 beta), were induced in human monocyte cultures following infection with the human immunodeficiency virus type 1 (HIV-1). Induction depended on productive viral infection: not only did the kinetics of MIP-1 peptide induction closely follow those of viral replication, but monocyte cultures inoculated with heat-inactivated virus or infected in the presence of AZT failed to produce these chemokine beta peptides. In addition, HIV infection markedly altered the pattern of beta chemokine expression elicited by tumor necrosis factor (TNF), itself a potent proinflammatory cytokine upregulated during the development of AIDS. Reverse transcription (RT)-PCR and RT-in situ PCR studies on brain tissue from patients with AIDS dementia demonstrated elevated MIP-1 alpha and MIP-1 beta mRNA expression relative to comparable samples from HIV-1-infected patients without dementia. Cells expressing chemokines in HIV-1-infected brains were identified morphologically as microglia and astrocytes. As MIP-1 alpha and MIP-1 beta are potent chemoattractants for both monocytes and specific subpopulations of lymphocytes, this dysregulation of beta chemokine expression may influence the trafficking of leukocytes during HIV infection. These data, taken together, suggest a mechanism by which HIV-1-infected monocytes might recruit uninfected T cells and monocytes to sites of active viral replication or inflammation, notably the brain and lymph nodes.
In Situ Hybridization Histochemistry: A Technique for the Study of Gene Expression in Single Cells (1983)

The patterns of growth hormone and proopiomelanocortin gene expression in the rat pituitary were used to detail the application of the in situ hybridization histochemistry technique in tissue sections. Parameters affecting the efficiency and resolution of hybridization have been optimized so that this technique can be used to identify sites of peptide synthesis and to study hormonal regulation of gene expression at the single cell level.
Interallelic Class Switch Recombination Contributes Significantly to Class Switching in Mouse B Cells (2005)

Except for the expression of IgM and IgD, DNA recombination is constantly needed for the expression of other Ig classes and subclasses. The predominant path of class switch recombination (CSR) is intrachromosomal, and the looping-out and deletion model has been abundantly documented. However, switch regions also occasionally constitute convenient substrates for interchromosomal recombination, since it is noticeably the case in a number of chromosomal translocations causing oncogene deregulation in the course of lymphoma and myeloma. Although asymmetric accessibility of Ig alleles should theoretically limit its occurrence, interallelic CSR was shown to occur at low levels during IgA switching in rabbit, where the definition of allotypes within both V and C regions helped identify interchromosomally derived Ig. Thus, we wished to evaluate precisely interallelic CSR frequency in mouse B cells, by using a system in which only one allele (of b allotype) could express a functional VDJ region, whereas only interallelic CSR could restore expression of an excluded (a allotype) allele. In our study, we show that interchromosomal recombination of V(H) and Cgamma or Calpha occurs in vivo in B cells at a frequency that makes a significant contribution to physiological class switching: trans-association of V(H) and C(H) genes accounted for 7% of all alpha mRNA, and this frequency was about twice higher for the gamma3 transcripts, despite the much shorter distance between the J(H) region and the Cgamma3 gene, thus confirming that this phenomenon corresponded to site-specific switching and not to random recombination between long homologous loci.
Oligodeoxyribonucleotide Phosphorothioate Fluxes and Localization in Hematopoietic Cells (1992)

An antisense oligonucleotide phosphorothioate, previously shown to inhibit HIV-1 viral expression in chronically infected H9 cells, was fluorescently labeled to study oligonucleotide fluxes and localization within living cells. Observations based on flow cytometry and fluorescence microscopy show the following: within around 0.5-2 h, an apparent steady-state distribution of the oligonucleotide is achieved in which the intracellular oligonucleotide concentration is less than that present in the external medium; following oligonucleotide uptake and resuspension of the cells in oligonucleotide-free medium, an oligonucleotide efflux, with a time constant similar to that for uptake, is observed (although a significant fraction of the phosphorothioate remains within the cell); cellular uptake as a function of the external oligonucleotide concentration is nonlinear, being more efficient at lower concentrations (less than 2 microM); and a predominant oligonucleotide localization within the cell nucleus and perinuclear organelles is observed.