gebhart/patrepeval huggingface dataset:
Costimulation of T cell proliferation by a chimeric B7-2 antibody fusion protein specifically targeted to cells expressing the erbB2 proto-oncogene (1997)

T cells require at least two signals for activation and clonal expansion. The first signal conferring specificity is initiated by interaction of the T cell receptor with antigenic peptides in the context of MHC molecules. The second, costimulatory signal can be provided by cell surface molecules on APCs such as B7-1 (CD80) and B7-2 (CD86), which interact with their counter-receptors on T cells. The absence of costimulatory signals presents one possible mechanism for tumor cells to escape immune surveillance. In experimental models transfection of B7 genes into tumor cells can result in T cell-dependent tumor rejection. We have developed a novel approach to direct the costimulatory B7-2 molecule to the surface of target cells. Our approach is based on a chimeric fusion protein that consists of the extracellular domain of human B7-2 fused to a single-chain Ab domain (scFv) specific for the ErbB2 protein, a type I growth factor receptor overexpressed in a high percentage of human adenocarcinomas. This B7-2(225)-scFv(FRP5) molecule expressed in the yeast Pichia pastoris and purified from culture supernatants is functionally active and binds to B7 counter-receptors and to ErbB2. B7-2(225)-scFv(FRP5) localizes specifically to the surface of ErbB2-expressing target cells, thereby providing a costimulatory signal that results in enhanced proliferation of syngeneic T cells. Our results suggest that effective tumor vaccines for cancer immunotherapy could be created by targeting such chimeric ligands to the surface of tumor cells.
Fertilizer Placement and Tillage Effects of Nitrogen Assimilation by Wheat (1992)

Abstract Little information is available concerning tillage effects on seasonal N accumulation and their effect on wheat yield. Field studies were conducted to determine the effects of fertilizer N placement and tillage practices on the reduction and assimilation of N in winter wheat ( Triticum aestivum L.) during 1984 through 1987 on Renfrow silt loam (fine, mixed, thermic, Uderic, Paleustolls) near El Reno, OK. Fertilizer N (50 kg ha −1 ) and P (60 kg ha −1 ) including 4 kg N ha −1 and 11 kg P ha −1 , with the seed was applied in the fall. In the spring, an additional 50 to 100 kg N ha −1 as ammonium nitrate was either broadcast or placed in narrow bands on the soil surface. Nitrate reductase (NR) activity, NO 3 ‐N, and crude protein (CP) content of wheat plants were determined periodically during spring growth until anthesis, and final grain and straw yield and their CP contents were determined. The NR activity in early spring was slightly greater during early spring in plants grown under no‐till when compared to conventional till in 1985 and 1986, whereas the reverse was observed in 1987. Increased NR activity was paralleled by an increase in vegetative CP. Placement of N in a narrow band on the soil surface in the spring improved NR activity levels, but the effect of N placement had little effect on CP concentration. Grain yield followed NR activity levels and was 36% higher in no‐till in 1985, similar in 1986, but 51% lower in 1987 than conventionally tilled plots. Placement of N in narrow bands increased N‐use efficiency by increasing N reduction and assimilation; but had little effect on the yield of grain and straw in both tillage methods.
In vitro enzymatic stability of dendritic peptides (2005)

PEGylated polyamidoamine (PAMAM) dendrimers as drug carriers have been a topic of interest because of their biomedically favorable features, including minimal toxicity, reduced immunogenicity, and excellent solubility in aqueous and most organic solutions. A PEG shell on dendrimer surface may provide steric hindrance, known as stealth properties of PEG, to stabilize drug molecules to be delivered. In this article, the effects of PEG and coupling sequence of drug, PEG, and dendrimer in modulating the stability of delivered drug molecules were evaluated. N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide was chosen as a model peptide. Dendritic peptides, that is, peptide-dendrimer, peptide-PAMAM-PEG, and peptide-PEG-dendrimer, were constructed based on Starbursttrade mark G3.0 PAMAM dendrimer and characterized by (1)H-NMR spectroscopy. Hydrolysis of dendritic peptides was catalyzed by alpha-chymotrypsin in pH 7.4 PBS buffer containing 5% DMF (v/v) at room temperature. The enzymatic stability of dendritic peptides was peptide-PAMAM-PEG > peptide-PAMAM > free peptide > peptide-PEG-PAMAM. The ratio of PEG/peptide could be reduced for increasing peptide loading while maintaining the delivered peptides' relatively high enzymatic stability. The quantitative analysis of dendritic peptide/enzyme interactions provided the understandings of the molecular structure/stability relationships of dendrimer/drug for the design of an optimal PEGylated dendrimer-based drug-delivery system.
Sensitive detection of rare cancer cells in sputum and peripheral blood samples of patients with lung cancer by preproGRP-specific RT-PCR (2001)

RT-PCR-based amplification of transcripts expressed in cancer but not in normal non-neoplastic cells is increasingly used for the sensitive detection of rare disseminated or exfoliated cancer cells to improve cancer staging and early detection protocols. However, these assays are frequently hampered by false-positive test results due to low-level transcription of the marker genes in normal cells. To overcome these limitations, target transcripts have to be identified that are tightly suppressed in normal non-neoplastic tissues, whereas they should be actively transcribed in the respective cancer cells. Here, we tested RT-PCR assays for 7 neuroendocrine marker transcripts including NCAM, PGP 9.5, gastrin, gastrin receptor, synaptophysin, preprogastrin-releasing peptide (preproGRP) and GRP-receptor to detect rare exfoliated tumor cells in peripheral venous blood and sputum samples from patients with lung cancer. Among these preproGRP RT-PCR was the only assay with which illegitimate transcription in blood or sputum samples from healthy donors or patients with unrelated diseases did not interfere. However, it reproducibly detected up to 10 small-cell lung cancer cells diluted in either 10 ml blood or 5 ml sputum samples. Single blood and sputum samples were collected directly before diagnostic bronchoscopy from 175 patients suspected to have lung cancer. Twenty-six of these had small-cell lung cancer (SCLC). Thereof, 13 patients (50%) tested positive in the blood sample and 5 of 23 patients (22%) tested positive in the sputum sample. Moreover, among 92 patients with non-small-cell lung cancer (NSCLC) 25 patients (27%) had disseminated cancer cells in peripheral blood. Amplification of preproGRP transcripts from clinical samples is a sensitive and specific assay to detect disseminated or exfoliated lung cancer cells either in peripheral blood or sputum samples.
Cytotoxic and antitumor activity of a recombinant immunotoxin composed of disulfide‐stabilized anti‐TAC Fv fragment and truncated pseudomonas exotoxin (1994)

Disulfide-stabilized Fv (dsFv)-immunotoxins are recombinant immunotoxins in which the inherently unstable Fv moiety, composed of the VH-VL heterodimer, is stabilized by a disulfide bond engineered between structurally conserved framework positions of VH and VL. Anti-Tac(dsFv)-PE38KDEL is composed of such a dsFv, directed to the alpha subunit of the IL2 receptor (IL2R), and containing a truncated form of Pseudomonas exotoxin (PE38KDEL). We have found this new type of immunotoxin to be indistinguishable in its in vitro activity and specificity from its single-chain immunotoxin counterpart, anti-Tac(Fv)-PE38KDEL. We have now examined the therapeutically relevant factors, including stability, pharmacokinetics, and antitumor activity of this new disulfide-stabilized Fv-immunotoxin. We found that anti-Tac(dsFv)-PE38KDEL was specifically cytotoxic to human activated T-lymphocytes in addition to IL2R bearing cell lines. Anti-Tac(dsFv)-PE38KDEL was considerably more stable at 37 degrees C in human serum and in buffered saline than the single-chain immunotoxin, anti-Tac(Fv)-PE38KDEL. The half-life in blood was similar for both immunotoxins (approx. 20 min). The therapeutic potential of the disulfide-stabilized immunotoxin was evaluated using an animal model of immunodeficient mice bearing subcutaneous tumor xenografts of human IL2R-bearing cells. Anti-Tac(dsFv)-PE38KDEL caused complete regression of tumors with no toxic effects in mice. Because dsFv-immunotoxins are more stable and can be produced with significantly improved yields compared to scFv-immunotoxins, dsFv-immunotoxin may be more useful for therapeutic applications.
Effect of the immunomodulating agent, pentoxifylline, in the treatment of sepsis in prematurely delivered infants (1999)

Pentoxifylline significantly affects the synthesis of TNF and IL-6 as well as reduces the mortality rate in premature infants with sepsis. The dosage and schedule of drug administration in this study attenuated the severity of the clinical course of sepsis in this group of patients.
Confinement and Detection of Single Molecules in Submicrometer Channels (1997)

Detection channels with submicrometer dimensions (500−600 nm i.d.) have been produced directly on electrophoresis capillaries for confinement and detection of single molecules at room temperature. These restrictive channels markedly reduce the Brownian motion of low molecular weight analytes and allow detailed studies of single molecules in solution. With a confocal fluorescence microscope, single molecules have been observed for an extended period of ∼60 ms, which is 50−100 times longer than the bulk diffusion time. These molecules have also been manipulated by an electrokinetic force and detected on-line with high signal-to-noise ratios.
Mouse Model for Pre‐Clinical Study of Human Cancer Immunotherapy (2015)

This unit describes protocols for developing tumors in mice, including subcutaneous growth, pulmonary metastases of B16 melanoma, and spontaneous melanoma in B-Raf V600E/PTEN deletion transgenic mouse models. Two immunization methods to prevent B16 tumor growth are described using B16.GM-CSF and recombinant vaccinia virus. A therapeutic approach is also included that uses adoptive transfer of tumor antigen-specific T cells. Methods including CTL induction, isolation, testing, and genetic modification of mouse T cells for adoptive transfer by using retrovirus-expressing genes of interest are provided. Additional sections, including growing B16 melanoma, enumerating pulmonary metastases, tumor imaging technique, and use of recombinant viruses for vaccination, are discussed together with safety concerns.
Sequence-specific recognition of DNA by zinc-finger peptides derived from the transcription factor Sp1. (1992)

We have overexpressed and purified two peptide fragments of Sp1 that contain the three "zinc-finger" domains necessary for specific Sp1 DNA binding. These peptides assume a stable, folded conformation in solution in the presence of Zn2+ as shown by DNA binding assays and NMR spectroscopy. Mobility-shift assays demonstrate that the Sp1 peptides recognize a number of different Sp1 DNA binding sites (GC boxes, with the core sequence GGGCGG). The dissociation constant for a 92-amino acid peptide binding to the GGGGCGGGGC sequence (Kd approximately 10 nM) and the relative affinities for several other DNA sequences definitively demonstrate Sp1-like binding properties. The thermodynamic binding site for Sp1-Zn92 has been mapped using the primer-extension/mobility-shift assay revealing that the 5' portion of the GC box DNA sequence (GGG GCG) contributes more strongly to the total binding energy than the 3' portion (GGGC). These findings are interpreted in the context of the Sp1 amino acid sequence in comparison with the structurally characterized Zif-268/DNA complex. A model is proposed that offers a structural explanation for the ability of Sp1 to recognize a diverse array of DNA sequences in terms of the individual (and different) DNA binding properties of each of the three zinc-finger domains.
Cardiac Stem Cell and Myocyte Aging, Heart Failure, and Insulin-Like Growth Factor-1 Overexpression (2004)

To determine whether cellular aging leads to a cardiomyopathy and heart failure, markers of cellular senescence, cell death, telomerase activity, telomere integrity, and cell regeneration were measured in myocytes of aging wild-type mice (WT). These parameters were similarly studied in insulin-like growth factor-1 (IGF-1) transgenic mice (TG) because IGF-1 promotes cell growth and survival and may delay cellular aging. Importantly, the consequences of aging on cardiac stem cell (CSC) growth and senescence were evaluated. Gene products implicated in growth arrest and senescence, such as p27Kip1, p53, p16INK4a, and p19ARF, were detected in myocytes of young WT mice, and their expression increased with age. IGF-1 attenuated the levels of these proteins at all ages. Telomerase activity decreased in aging WT myocytes but increased in TG, paralleling the changes in Akt phosphorylation. Reduction in nuclear phospho-Akt and telomerase resulted in telomere shortening and uncapping in WT myocytes. Senescence and death of CSCs increased with age in WT impairing the growth and turnover of cells in the heart. DNA damage and myocyte death exceeded cell formation in old WT, leading to a decreased number of myocytes and heart failure. This did not occur in TG in which CSC-mediated myocyte regeneration compensated for the extent of cell death preventing ventricular dysfunction. IGF-1 enhanced nuclear phospho-Akt and telomerase delaying cellular aging and death. The differential response of TG mice to chronological age may result from preservation of functional CSCs undergoing myocyte commitment. In conclusion, senescence of CSCs and myocytes conditions the development of an aging myopathy.
Clinical benefit from bevacizumab (BV) in responding (R) and non-responding (NR) patients (pts) with metastatic colorectal cancer (mCRC) (2005)

3514 Background: BV, a monoclonal antibody to vascular endothelial growth factor, is a potent anti-angiogenic agent with demonstrated survival benefit when combined with irinotecan, 5-fluorouracil and leucovorin (IFL) in first-line mCRC. Because preclinical data suggest BV is primarily a cytostatic agent, we explored the clinical benefit of BV assessed by progression-free survival (PFS) and overall survival (OS) in R and NR subgroups. Methods: In the pivotal trial, 813 pts with untreated mCRC were randomized to receive IFL plus either BV or placebo. For this retrospective, exploratory analysis, pts were grouped by best response achieved (complete/partial responses [R] vs. stable/progressive disease or non-evaluable [NR]). For both R and NR subgroups, PFS and OS within these subgroups were estimated from Kaplan-Meier curves, and hazard ratios (HRs) for progression and death were estimated by Cox regression. Results: The BV and placebo arms in both the R and NR subgroups had similar baseline characteristics. Statistically significant improvements in HR for PFS and OS for BV-treated pts were observed in both subgroups (Table 1) and were consistent between the groups (interaction p-value for OS = 0.44; for PFS, 0.73). Conclusion: These analyses suggest that the magnitude of clinical benefit associated with BV treatment, as measured by HR for PFS and OS, is similar in mCRC regardless of objective tumor response. This response-independent survival benefit is a novel observation in mCRC, and has implications for endpoint selection in BV-based clinical trials and the routine clinical use of BV. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Genentech Genentech Genentech
Conformational Lability of Herpesvirus Protein VP22 (2000)

The herpesvirus protein VP22 traffics between cells, being exported from expressing cells in a non-Golgi-dependent manner and localizing in the nuclei of surrounding cells. This transport is retained in certain VP22 fusion proteins, making VP22 a candidate for use in macromolecular drug delivery. In an effort to understand the physical basis for this activity, we have initiated structural studies of VP22.C1, the C-terminal half of VP22, which possesses the full transport activity of the native protein. CD and Fourier transform infrared analyses indicate a secondary structure consisting of approximately 30% alpha-helix, 17% beta-sheet, and 51% disordered and turn structure. Unfolding studies conducted by CD, differential scanning calorimetry, and fluorescence reveal a series of discrete structural transitions in the range of 20-60 degrees C. CD and fluorescence studies of interactions between VP22.C1 and divalent cations and model polyanions indicate that Mg(2+), Zn(2+), oligonucleotides, and heparin interact with the protein, causing changes in secondary structure and thermal stability. Additionally, the interaction of VP22.C1 with model lipids was examined. Fluorescence titrations of the protein with trans-parinaric acid at various temperatures suggest the binding of one to two molecules of parinaric acid to VP22.C1 at temperatures >40 degrees C, suggesting the possibility of conformation dependent membrane interaction under physiological conditions.
Isolation and phenotypic characterization of colonic macrophages (1998)

Macrophages play an important role in the intestinal mucosal immune system. However, they are a poorly defined cell population. We therefore determined their phenotype in normal colonic mucosa. Macrophages were isolated from colonic biopsies and surgical specimens by collagenase digestion. Colonic macrophages were positively sorted by anti-CD33 magnetic beads. Flow cytometric triple fluorescence analysis was applied to study CD14, CD16, CD33, CD44, CD11b, CD11c, CD64, HLA-DR, CD80, CD86 and CD3/CD19 expression. CD33 was evaluated as a positive marker for intestinal macrophages. CD33+ cells isolated from normal colonic mucosa showed co-expression of the established intracellular macrophage marker CD68 in FACS analysis. CD33+ cells were capable of phagocytosis. Isolation of this cell population by magnetic anti-CD33 beads and culture resulted in a 4.2-40-fold increase in IL-1beta and 4.5-44-fold increase in tumour necrosis factor-alpha (TNF-alpha) secretion compared with unsorted lamina propria mononuclear cells (LPMC). Of the CD33+ cells, 90.9 +/- 6.9% (mean +/- s.d.) were CD44+. However, macrophages from colonic mucosa showed only a low expression of CD14 (10.5 +/- 3.8%), CD16 (10.1 +/- 3.9%), HLA-DR (27.3 +/- 9.2%), CD11b (17.4 +/- 6.8%), CD11c (17.8 +/- 10.4%). Furthermore, expression of CD80 (9.2 +/- 4.2%) and CD86 (15.1 +/- 7.3%) was low, suggesting a low ability of normal intestinal macrophages to activate T cells and T cell-mediated immune responses. We conclude that CD33 is useful for the isolation and flow cytometric characterization of colonic macrophages. These cells exhibit a single phenotype in normal mucosa (CD33++, CD44++, CD14-, CD16-, CD11b-, CD11c-, HLA-DRlow, CD80-, CD86-) lacking lipopolysaccharide (LPS) receptor and costimulatory molecules.
A phase 1/2, open-label dose-escalation study of liposomal irinotecan (nal-IRI) plus 5- fluorouracil/leucovorin (5-FU/LV) and oxaliplatin (OX) in patients with previously untreated metastatic pancreatic cancer (mPAC). (2018)

4111 Background: nal-IRI+5-FU/LV is effective for patients with mPAC after disease progression following gemcitabine-based therapy. The current study (NCT02551991) is a phase 1/2, open-label trial to assess the safety, tolerability, and dose-limiting toxicities (DLT) of nal-IRI+5-FU/LV+OX (NAPOX) for the first-line treatment of patients with mPAC and to determine Phase 3 dosing. Methods: NAPOX is being evaluated in patients ≥18 yrs with previously untreated mPAC, with an ECOG performance status ≤1 and adequate organ function. Three of 4 dose-escalation cohorts of NAPOX, dosed on day 1 and 15, have been initiated. Safety and tolerability are the primary endpoints of this study, with assessment of exploratory efficacy signals. Results: As of 10 Nov 2017, 24 patients (Cohort A: n = 7; Cohort B: n = 7; Cohort C: n = 10) have received ≥1 dose of NAPOX (median age: 66.0 yrs, range: 44–78 yrs). Five patients reported ≥1 DLT (Cohort A: n = 2/7; Cohort B: n = 1/7; Cohort C: n = 2/10). The most frequent treatment-emergent adverse events (TEAEs) were gastrointestinal (GI) disorders (Cohort A: 71%; Cohort B: 71%; Cohort C: 60%). Grade 3 or 4 TEAEs were GI disorders (Cohort A; 43%; Cohort B: 14%; Cohort C: 50%) and neutropenia (Cohort A: 43%; Cohort B: 29%; Cohort C: 40%). The best overall response was partial response (PR) in 6/24 patients (Cohort B: n = 3/7; Cohort C: n = 3/10). In Cohort B (the lowest and most tolerable cohort), n = 5/7 patients reached disease control (PR or stable disease > 16 weeks), with n = 4/7 patients were treated for ≥24 weeks. Conclusions: Initial analysis suggests a well-tolerated dose and promising antitumor clinical activity of NAPOX. Dose escalation and expansion is ongoing. Clinical trial information: NCT02551991. Dose Current Patients Grade 3/4 TEAEs Cohort nal-IRI (mg/m2) 5-FU/LV (mg/m2) Oxaliplatin (mg/m2) Dosed (n) Ongoing (n) Neutropenia (n) Diarrhea (n) Vomiting (n) Nausea (n) A 80 2,400 / 400 60 7 0 3 3 1 0 B 60 2,400 / 400 60 7 2 2 1 0 0 C 60 2,400 / 400 85 10 3 4 3 3 2 D* 65 2,400 / 400 70 - - - - - - * Cohort not yet initiated
Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome (2001)

Following transcription and splicing, each mRNA of a mammalian cell passes into the cytoplasm where its fate is in the hands of a complex network of ribonucleoproteins (mRNPs). The success or failure of a gene to be expressed depends on the performance of this mRNP infrastructure. The entry, gating, processing, and transit of each mRNA through an mRNP network helps determine the composition of a cell's proteome. The machinery that regulates storage, turnover, and translational activation of mRNAs is not well understood, in part, because of the heterogeneous nature of mRNPs. Recently, subsets of cellular mRNAs clustered as members of mRNP complexes have been identified by using antibodies reactive with RNA-binding proteins, including ELAV/Hu, eIF-4E, and poly(A)-binding proteins. Cytoplasmic ELAV/Hu proteins are involved in the stability and translation of early response gene (ERG) transcripts and are expressed predominately in neurons. mRNAs recovered from ELAV/Hu mRNP complexes were found to have similar sequence elements, suggesting a common structural linkage among them. This approach opens the possibility of identifying transcripts physically clustered in vivo that may have similar fates or functions. Moreover, the proteins encoded by physically organized mRNAs may participate in the same biological process or structural outcome, not unlike operons and their polycistronic mRNAs do in prokaryotic organisms. Our goal is to understand the organization and flow of genetic information on an integrative systems level by analyzing the collective properties of proteins and mRNAs associated with mRNPs in vivo.
InGaN/GaN/AlGaN-Based Laser Diodes with Modulation-Doped Strained-Layer Superlattices (1997)

InGaN multi-quantum-well-structure laser diodes with Al 0.14 Ga 0.86 N/GaN modulation doped strained-layer superlattice cladding layers grown on an epitaxially laterally overgrown GaN substrate were demonstrated to have an estimated lifetime of more than 10000 h under continuous-wave operation at 20° C. Under operation at a high temperature of 50° C, the lifetime was longer than 1000 h. With the operating current increasing to above the threshold, a self-pulsation with a high frequency of 3.5 GHz was observed. The carrier lifetime was estimated to be 1.8 ns from the pulsed modulation of the LDs.