gebhart/patrepeval huggingface dataset:
Geometry and Topology of Diatom Shape and Surface Morphogenesis for Use in Applications of Nanotechnology (2005)

Diatoms have attracted the interest of those involved in nanotechnology and the development of this discipline for research and practical application. These microorganisms exhibit self-assembly of silica on the micrometer scale, with parts of diatoms measuring on the nanometer scale. They exhibit a wide variety of shapes and patterns. An interest in diatom development and the geometry and topology of diatom shapes and gross patterns formed the focus of this study. Diatoms may be theoretically created on the basis of conic sections and quadratic surfaces expressed in parametric two-dimensional (2D) and three-dimensional (3D) functions (as sheets). Recreated diatom shapes, surfaces, and gross patterns based on 3D parametric equations are presented. Changes from one form to another are discussed as changes in magnitude or functional element within a given set of 3D equations for sequences that are phylogenetically or taxonomically related. Topological evolution and combinations of diatom shapes and surfaces are explored. An example shows how diatom forms depicted as 2-manifolds can be subjected to topological gluing to create a form whose surface is topologically different from the original. Topological surgery and gluing of diatoms as geometric forms may be useful in hypotheses about creating nanosubstrates and nanopatterned nanomaterials or in other applications of nanotechnology.
Changes in Proinflammatory Cytokine Activity after Menopause (2002)

There is now a large body of evidence suggesting that the decline in ovarian function with menopause is associated with spontaneous increases in proinflammatory cytokines. The cytokines that have obtained the most attention are IL-1, IL-6, and TNF-alpha. The exact mechanisms by which estrogen interferes with cytokine activity are still incompletely known but may potentially include interactions of the ER with other transcription factors, modulation of nitric oxide activity, antioxidative effects, plasma membrane actions, and changes in immune cell function. Experimental and clinical studies strongly support a link between the increased state of proinflammatory cytokine activity and postmenopausal bone loss. Preliminary evidence suggests that these changes also might be relevant to vascular homeostasis and the development of atherosclerosis. Better knowledge of the mechanisms and the time course of these interactions may open new avenues for the prevention and treatment of some of the most prevalent and important disorders in postmenopausal women.
A conserved human germline V kappa gene directly encodes rheumatoid factor light chains. (1986)

The full-length gene that encodes the light chain variable regions of an idiotypically related group of human IgM kappa rheumatoid factors (RFs) has been cloned and sequenced. The deduced amino acid sequence is identical to four separate RF proteins. These results prove that genes capable of encoding human anti-IgG autoantibody light chains without any somatic mutation are present in the kappa gene repertoire of normal people.
The Human Immunodeficiency Virus Long Terminal Repeat Is Preferentially Expressed in Langerhans Cells in Transgenic Mice (1989)

Four lines of transgenic mice containing the HIV LTR linked to the bacterial gene encoding chloramphenicol acetyltransferase (CAT) were constructed. In each line, a characteristic tissue pattern of CAT expression was observed with detectable levels present in the eye, heart, spleen, thymus, and tail. Low levels of CAT were present in circulating lymphocytes, but CAT activity in these cells could be augmented following treatment with the mitogen phytohemagglutinin (PHA). Likewise, CAT expression was present at only low levels in circulating monocytes, but higher levels of CAT were observed in macrophages grown in the presence of various cytokines (CSF-1, GM-CSF, IL-1 alpha, IL-4, and IL-2). Furthermore, Langerhans cells recovered from skin showed higher levels of CAT activity than those observed in other cells of monocyte-macrophage lineage. These results indicate that LTR-CAT expression in cells of monocyte-macrophage lineage may increase in proportion to the degree of differentiation of these cells. These animals may be useful in the study of cell-specific determinants of LTR-directed gene activity and may serve to identify exogenous cofactors that promote the progression of HIV-related disease in vivo.
Expression of Ah receptor (TCDD receptor) during human monocytic differentiation (1995)

We have previously found a high expression of human Ah receptor (TCDD receptor) mRNA in peripheral blood cells of individuals. In this paper, the expression of this gene in blood cells was first investigated in fractions of nucleated cells, revealing predominant expression of the Ah receptor gene in the monocyte fraction. Then the expression levels of AhR mRNA in various hematopoietic cell lines were examined together with those of Arnt and P450IA1. AhR was expressed at high levels in monocytoid U937, THP1, and HEL/S cells, and at moderate levels in promyelocytic HL60 cells and erythroblastic HEL cells. However, it was not detected in lymphoid cells MOLT4 (T cell) and BALL1 (B cell), nor in K562 erythroblasts. Furthermore, a specific induction of AhR during monocytic differentiation was investigated in HL60 and HEL cells. HL60 cells were induced to differentiate toward monocytes-macrophages by incubation with phorbol ester, showing a 5- to 2-fold increase of AhR mRNA. The incubation with transforming growth factor beta 1 and 1 alpha,25-dihydroxyvitamin D3 resulted in a 5- to 7-fold increase of AhR mRNA. The HEL cells also exhibited a similar elevation of AhR mRNA level, when they had differentiated toward monocyte-macrophage cells by these combined inducers, but little change in the mRNA level was observed when the cells were induced to differentiate into other cell types. Treatment of the differentiated HL60 cells with 3-methylcholanthrene, a ligand of AhR, induced the expression of the P450IA1 gene. These results indicated that expression of AhR mRNA was significantly induced during monocytic differentiation and that the differentiated cells were responsive to xenobiotics. Our results suggest that AhR may play an important role in the function of monocytes and also in the eventual activation of environmental carcinogens.
Microsatellite instability in sporadic‐colon‐cancer patients with and without liver metastases (1997)

Microsatellite instability (MSI) is intrinsic to most colorectal carcinomas (CRC) from patients with hereditary non-polyposis colorectal cancer (HNPCC), reflecting germline mutations in the mismatch-repair (MMR) genes. Its occurrence and chronological sequence of development in sporadic CRC appears less well defined. To explore the time sequence in acquisition of MSI, and the role it plays during tumor progression in sporadic CRC, we compared the incidence of MSI in tissue samples from 40 Dukes'-B and 30 Dukes'-D CRC patients with liver metastases, at 4 different microsatellite loci, representing sites on the APC, DCC and p53 genes respectively as well as the D2S123 site. Among the 30 patients with hepatic metastases, MSI was found in 9 (30%) of the primary, and 13 (43.3%) of the metastatic tumors. In comparison, among the 40 Dukes'-B CRC, MSI was found in only 8 cases (20%). CRC with MSI were more frequently located in the right colon, less frequently on the left side, and seldom in the rectum. Tumor ploidy analysis shows that 46.2% of Dukes'-D primary tumors with MSI are diploid (χ2 = 4.46, p = 0.035). With a mean follow-up time of 4.2 years for the Dukes'-B CRC, there were no recurrences in the 8 patients with MSI, whilst 6 (18.8%) relapses occurred amongst the 32 patients without MSI, average time to recurrence being 15 months. In Dukes'-D CRC, mean survival time for patients with MSI was 37 months (95% CI, 24 to 51 months), for those without MSI 26 months (95% CI, 18 to 35 months), although this was not statistically significant. Our data suggest that tumor progression may involve increased genetic instability. Int. J. Cancer 74:470–474, 1997. © 1997 Wiley-Liss, Inc.
Monoclonal antibodies against simian virus 40 T antigens: evidence for distinct sublcasses of large T antigen and for similarities among nonviral T antigens (1980)

We have isolated three clones of hybrid cells which synthesize antibodies specific for determinants on simian virus 40 (SV40) T antigens. Mouse myeloma NS1 cells were fused with spleen cells from mice that had been immunized with SV40-transformed mouse cells. Hybrid cells were selected in HAT medium and cloned in soft agar. We used an enzyme-linked immunosorbent assay for detection and quantification of mouse antibodies against SV40 T antigens. Monoclonal antibodies from 3 of the 24 clones that scored as positive in the enzyme-linked immunosorbent assay were verified by immunoprecipitation to be specific for SV40 T antigens. Two clones (7 and 412) produced antibodies that recognized denaturation-sensitive antigenic determinants unique to large T antigen. Antibodies from clone 7 appeared to have a low affinity for large T antigen. Antibodies from clone 412 had a higher affinity for large T antigen but did not recognize a subclass of large T antigen that was recognized by tumor serum. Antibodies of the third clone, clone 122, recognized a denaturation-stable antigenic determinant of the 53,000-dalton mouse nonviral T antigen in SV40-transformed cells. Antibodies from clone 122 also recognized similar (51,000- to 56,000-dalton) nonviral T antigens in SV40-transormed or lytically infected cells from five mammalian species and in four uninfected mouse lines. From these observations, we have concluded that (i) the 94,000-dalton SV40 large T antigen may exist as immunologically distinguishable subclasses, and (ii) the nonviral T antigens of five mammalian species share at least one antigenic determinant.
Targeted inhibition of T-cell factor activity promotes syndecan-2 expression and sensitization to doxorubicin in osteosarcoma cells and bone tumors in mice (2012)

Alterations of Wnt signaling appear to be involved in the pathogenesis of osteosarcoma, presenting mutations of adenomatous polyposis coli (APC) and epigenetic downregulation of Wnt inhibitory factor 1. However, the precise role of Wnt effectors in the bone cancer progression remains unclear. We previously showed that Wnt/β-catenin/T-cell factor (TCF) activation are responsible for the repression of syndecan-2, a key modulator of apoptosis and chemosensitivity in osteosarcoma cells, suggesting a role of Wnt signaling in chemoresistance. In this study, we investigated the functional relationship between syndecan-2, Wnt/β-catenin/TCF signaling and chemosensitivity in these cells. To this goal, we selected resistant osteosarcoma cells from sensitive human cell lines using repeated exposures to doxorubicin. In doxorubicin-responsive but not in doxorubicin-resistant-derived cells syndecan-2 expression was upregulated by doxorubicin treatment. Moreover, syndecan-2 overexpression restored the sensitivity to doxorubicin in resistant-derived cells. We found that syndecan-2 induction by doxorubicin is forkhead box protein O3A (Foxo3a)-dependent. Foxo3a overexpression resulted in increased syndecan-2 expression in sensitive and resistant-derived cells. Doxorubicin modulated Foxo3a binding on syndecan-2 gene promoter and induced Foxo-dependent inhibition of Wnt/TCF activity. Conversely, β-catenin/TCF activation impaired syndecan-2 induction by doxorubicin, indicating that Wnt signaling is competing with the action of the cytotoxic drug. However, β-catenin was also found to be required for Foxo3a activity. Consistently, Dickkopf 1 (DKK1) and secreted frizzled-related protein 1 (sFRP-1) altered doxorubicin action in sensitive cells, whereas inhibition of TCF activity strongly decreased cell viability and increased sensitivity to doxorubicin in sensitive and resistant cells. TCF inhibition also increased the effect of doxorubicin treatment in an orthotopic bone tumor model in mice. Altogether, these data provide evidence that the repression of syndecan-2 by Wnt/β-catenin/TCF signaling contributes to the resistance of osteosarcoma cells to doxorubicin and suggest that TCF inhibition may represent a novel therapeutic strategy in osteosarcoma.
Analysis of 15 adenovirus hexon proteins reveals the location and structure of seven hypervariable regions containing serotype-specific residues (1996)

The first full-length hexon protein DNA and deduced amino acid sequences of a subgenus D adenovirus (AV) were determined from candidate AV48 (85-0844). Comprehensive comparison of this sequence with hexon protein sequences from human subgenera A, B, C, D, F, bovine AV3, and mouse AV1 revealed seven discrete hypervariable regions (HVRs) among the 250 variable residues in loops 1 and 2. These regions differed in length between serotypes, from 2 to 38 residues, and contained > 00% of hexon serotype-specific residues among human serotypes. Alignment with the published crystal structure of AV2 established the location and structure of the type-specific regions. Five HVRs were shown to be part of linear loops on the exposed surfaces of the protein, analogous to the serotype-specific loops or "puffs" in picornavirus capsid proteins. The HVRs were supported by a common framework of conserved residues, of which 68 to 75% were hydrophobic. Unique sequences were limited to the seven HVRs, so that one or more of these regions contain the type-specific neutralization epitopes. A neutralizing AV48 hexon-specific antiserum recognized linear peptides that corresponded to six HVRs by enzyme immunoassay. Affinity-purification removal of all peptide-reactive antibodies did not significantly decrease the neutralization titer. Eluted peptide-reactive antibodies did not neutralize. Human antisera that neutralized AV48 did not recognize linear peptides. Purified trimeric native hexon inhibited neutralization, but monomeric heat-denatured hexon did not. We conclude that the AV48 neutralization epitope(s) is complex and conformational.
Inactivation of blasticidin S by Bacillus cereus. II. Isolation and characterization of a plasmid, pBSR8, from Bacillus cereus. (1988)

In a recent communication0, we described the isolation of Bacillus cereus K55-S1 as a bacterium resistant to blasticidin S (abbreviated to BS), a cytosine-containing antibiotic50 , and the bacterial conversion of the antibiotic to inactive 4-deamino-4-hydroxy blasticidin S (HO-BS) by the production of BS-deaminase. (Fig. This paper concerns the possible involvement of a plasmid in this resistant mechanism.
Immune targeting of fibroblast activation protein triggers recognition of multipotent bone marrow stromal cells and cachexia (2013)

Fibroblast activation protein (FAP) is a candidate universal target antigen because it has been reported to be selectively expressed in nearly all solid tumors by a subset of immunosuppressive tumor stromal fibroblasts. We verified that 18/18 human tumors of various histologies contained pronounced stromal elements staining strongly for FAP, and hypothesized that targeting tumor stroma with FAP-reactive T cells would inhibit tumor growth in cancer-bearing hosts. T cells genetically engineered with FAP-reactive chimeric antigen receptors (CARs) specifically degranulated and produced effector cytokines upon stimulation with FAP or FAP-expressing cell lines. However, adoptive transfer of FAP-reactive T cells into mice bearing a variety of subcutaneous tumors mediated limited antitumor effects and induced significant cachexia and lethal bone toxicities in two mouse strains. We found that FAP was robustly expressed on PDGFR-α(+), Sca-1(+) multipotent bone marrow stromal cells (BMSCs) in mice, as well as on well-characterized, clinical-grade multipotent human BMSCs. Accordingly, both mouse and human multipotent BMSCs were recognized by FAP-reactive T cells. The lethal bone toxicity and cachexia observed after cell-based immunotherapy targeting FAP cautions against its use as a universal target. Moreover, the expression of FAP by multipotent BMSCs may point toward the cellular origins of tumor stromal fibroblasts.
Intestinal GATA4 deficiency protects from diet-induced hepatic steatosis (2012)

Our results provide strong indications for a protective effect of intestinal GATA4 deficiency on the development of hepatic steatosis and fibrosis via GLP-1, thereby blocking hepatic de novo lipogenesis.
Selective recognition of pyrophosphate in water using a backbone modified cyclic peptide receptor (2006)

A cyclic peptide based receptor, bearing two dipicolylamino arms complexed to zinc(II) ions, binds pyrophosphate ions with high affinity and selectivity in aqueous solution as determined using an indicator displacement assay.
Persistence of Memory CD8 T Cells in MHC Class I-Deficient Mice (1999)

An understanding of how T cell memory is maintained is crucial for the rational design of vaccines. Memory T cells were shown to persist indefinitely in major histocompatibility complex (MHC) class I-deficient mice and retained the ability to make rapid cytokine responses upon reencounter with antigen. In addition, memory CD8 T cells, unlike naïve cells, divided without MHC-T cell receptor interactions. This "homeostatic" proliferation is likely to be important in maintaining memory T cell numbers in the periphery. Thus, after naïve CD8 T cells differentiate into memory cells, they evolve an MHC class I-independent "life-style" and do not require further stimulation with specific or cross-reactive antigen for their maintenance.
Nucleotide sequence of theCandida albicansaspartyl proteinase gene (1989)

Journal Article Nucleotide sequence of the Candida albicans aspartyl proteinase gene Get access T.J. Lott, T.J. Lott * *To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar L.S. Page, L.S. Page Search for other works by this author on: Oxford Academic PubMed Google Scholar P. Boiron, P. Boiron 2Mycology Unit, Pasteur InstituteFrance Search for other works by this author on: Oxford Academic PubMed Google Scholar J. Benson, J. Benson 1Division of Host Factors, Centers for Disease Control1600 Clifton Road, Atlanta, GA 30333, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar E. Reiss E. Reiss Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 4, 25 February 1989, Page 1779, https://doi.org/10.1093/nar/17.4.1779 Published: 25 February 1989 Article history Received: 07 December 1988 Published: 25 February 1989
Prognostic importance of measuring early clearance of leukemic cells by flow cytometry in childhood acute lymphoblastic leukemia (2002)

Early clearance of leukemic cells is a favorable prognostic indicator in childhood acute lymphoblastic leukemia (ALL). However, identification of residual leukemic cells by their morphologic features is subjective and lacks sensitivity. To improve estimates of leukemia clearance, we applied flow cytometric techniques capable of detecting 1 leukemic cell in 10,000 or more normal cells and prospectively measured residual leukemia in bone marrow samples collected on day 19 of remission-induction chemotherapy from 248 children with newly diagnosed ALL. In 134 samples (54.0%), we identified at least 0.01% leukemic cells (0.01%-< 0.1% in 51 samples [20.6%], 0.1%-< 1% in 36 [14.5%], and > or = 1% in 47 [19.0%]). Among 110 children treated within a single chemotherapy program, the 5-year mean +/- SE cumulative incidence of relapse or failure to achieve remission was 32.2% +/- 6.5% for the 59 patients with 0.01% residual leukemic cells or greater on day 19 and 6.0% +/- 3.4% for the 51 patients with less than 0.01% leukemic cells (P <.001). The prognostic value of day-19 bone marrow status defined by flow cytometry was superior to that defined by morphologic studies and remained significant after adjustment for other clinical and biologic variables. Lack of detectable leukemic cells on day 19 was more closely associated with relapse-free survival than was lack of detectable residual disease at the end of remission induction (day 46). Thus, approximately half of the children with ALL achieve profound clearance of leukemic cells after 2 to 3 weeks of remission-induction chemotherapy, and these patients have an excellent treatment outcome.
Altered angiogenesis and survival in human tumor‐derived endothelial cells (2003)

Knowledge on the functional properties of tumor-derived endothelial cells (TEC) can be relevant for the development of antiangiogenic therapeutic strategies. In the present study, we obtained and characterized endothelial cell lines from human renal carcinomas. TEC did not undergo senescence and showed constant expression of markers of endothelial activation and angiogenesis. In vitro, TEC, in contrast to normal endothelial cells, were resistant to apoptosis, proadhesive for renal carcinoma cells, and able to grow and organize in the absence of serum in persistent capillary-like structures. In vivo, TEC were able to grow in immunodeficient mice and to form vascular structures connected with the circulation. At a molecular level, gene array analysis showed an increased expression of genes involved in survival and cell adhesion compared with expression in normal microvascular endothelial cells. Moreover, expression of angiopoietin-1 and vascular endothelial growth factor (VEGF)-D and the Akt survival pathway were up-regulated. Inhibition of interaction of VEGFR-2 or VEGFR-3 with VEGF-D but not of Tie-2-angiopoietin-1 interaction with soluble receptors abrogated Akt activation and survival of TEC. These results indicate that at least some of the TEC within a tumor display abnormal characteristics in terms of survival and angiogenic properties and also indicate the presence of a functional autocrine pathway related to VEGF-D.
Switched vs. broadcast video for fiber-to-the-home systems (1990)

The potential benefits of the state of the art in fiber-based video transmission for both broadcast and switched network configurations are examined, and these designs are compared based on performance, channel capacities, compatibility, ability to provide new interactive services, and cost per subscriber. Analysis results show that the broadcast network provides the best compatibility with video delivery but lacks the flexibility to deliver the interactive services of the future, and does not tend to lower the cost per channel. The switched network provides the best flexibility but it is the least compatible with today's video usage and may be too expensive. It is found that a hybrid system, using a subset of the features of both broadcast and switched networks, can meet both near-term and future video service demands, and offers the best flexibility. This network will be capable of implementing CATV (cable television) transport services while at the same time creating a flexible switch-based platform for new interactive video services, all with a lower capital cost per channel.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Platelet adhesion and contact activation time tests on HEMA coated cellulose acetate membranes (1975)

Surface modification of cellulose acetate dialysis membranes was carried out by 60Co radiation induced graft copolymerization of the hydrogel, hydroxyethyl methacrylate (HEMA). The degree of grafting was controlled by varying the HEMA monomer concentration in the grafting solution and the radiation dose. A continuous flow platelet adhesion test was designed which allows testing under conditions more closely approximating hemodialysis than other small scale in vitro tests. Platelet adhesion on treated membranes fell substantially with increasing surface HEMA concentration. The presence of HEMA on the membrane surface did not affect the membrane activated clotting times significantly.