gebhart/patrepeval huggingface dataset:
Validity of analog free thyroxin immunoassays. (1987)

I have briefly illustrated the way in which the main features of analog methods may be readily predicted by consideration of elementary physicochemical laws. (Editorial limitations on the length of this presentation have prevented exploration of other issues such as the reasons for, and effects of, the hitherto unexplained inclusion by manufacturers of large amounts of albumin (12, 18) in kit reagents.) The main implication of our analysis is that, to conform genuinely to the principles of "unbound analog" free hormone immunoassay, an analog must bind to serum proteins to a maximal extent of approximately 10% (but preferably less) in the absence of antibody. The notion that an analog is suitable for use in this context merely if it binds to serum proteins with lower affinities than does the native hormone (6) is demonstrably fallacious. Current analog methods thus neither adhere to the principles of unbound analog free hormone assay nor do they survive classic dilution tests of free hormone assay validity. Demonstrably they do not, in a general sense, measure the free hormone in serum. They may nevertheless yield roughly "correct" values in pregnancy (and thus, arguably, possess clinical value) if the analog fortuitously distributes in an optimal manner between serum proteins, implying approximate balance between the biasing effects caused by the protein changes occurring in pregnancy. However, such methods yield incorrect estimates in all other situations in which the binding characteristics of test samples are disturbed (e.g., by the presence of binding competitors, drugs, abnormal proteins, etc. or when "unbalanced" changes in protein concentration occur), this being the fundamental cause of their diagnostic unreliability. Wilkins, Midgley, and their colleagues have consistently opposed these conclusions, although they have never (using their computer model or by other rigorous means) demonstrated them to be incorrect, nor indeed have they ever formally substantiated the physicochemical propositions on which they themselves claim the methodology rests. Furthermore, they have repeatedly misinterpreted experimental results yielded by the Amerlex kits (such as the effects thereon of serum dilution, NEFA, drugs, etc.), discreetly abandoning (and even totally reversing) their original claims (though not withdrawing them) when these appeared no longer tenable. Perhaps the most serious consequence of these events is the resulting confusion in the literature. This is of major importance in physiological research (28), but it also clearly has major implications in clinical chemistry.(ABSTRACT TRUNCATED AT 400 WORDS)
Human Umbilical Cord Blood Cells Express Neural Antigens after Transplantation into the Developing Rat Brain (2002)

Recently, our laboratory began to characterize the mononuclear cells from human umbilical cord blood (HUCB) both in vitro and in vivo. These cryopreserved human cells are available in unlimited quantities and it is believed that they may represent a source of cells with possible therapeutic and practical value. Our previous molecular and immunocytochemical studies on cultured HUCB cells revealed their ability to respond to nerve growth factor (NGF) by increased expression of neural markers typical for nervous system-derived stem cells. In addition, the DNA microarray detected downregulation of several genes associated with development of blood cell lines. To further explore the survival and phenotypic properties of HUCB cells we transplanted them into the developing rat brain, which is known to provide a conducive environment for development of neural phenotypes. Prior to transplantation, HUCB cells were either cultured with DMEM and fetal bovine serum or were exposed to retinoic acid (RA) and nerve growth factor (NGF). Neonatal pups (1 day old) received unilateral injection of cell suspension into the anterior part of subventricular zone. One month after transplantation animals were perfused, their brains cryosectioned, and immunocytochemistry was performed for identification of neural phenotypes. Our results clearly demonstrated that approximately 20% of transplanted HUCB survived (without immunosuppression) within the neonatal brain. Additionally, double-labeling with cell-type-specific markers revealed that some HUCB-derived cells (recognized by anti-human nuclei labeling) were immunopositive for glial fibrillary acidic protein (GFAP) and few donor cells expressed the neuronal marker TuJ1 (class III beta-tubulin). These findings suggest that at least some of the transplanted HUCB cells differentiated into cells with distinct glial or neuronal phenotypes after being exposed to instructive signals from the developing brain.
Toxicity of 3'-azido-3'-deoxythymidine and 9-(1,3-dihydroxy-2-propoxymethyl)guanine for normal human hematopoietic progenitor cells in vitro (1987)

The effects of 3'-azido-3'-deoxythymidine (AZT) and 9-(1,3-dihydroxy-2-propoxymethyl)guanine on myeloid and erythroid colony-forming cells were studied by clonogenic assays. Both consistently inhibited granulocyte-macrophage CFU (CFU-GM) and erythroid burst-forming units in a dose-dependent fashion. Concentrations of AZT and 9-(1,3-dihydroxy-2-propoxymethyl)guanine required for 50% inhibition of CFU-GM were, respectively, 0.9 +/- 0.1 and 2.7 +/- 0.5 microM; those required for 90% inhibition were, respectively, 34.0 +/- 2.8 and 35.7 +/- 3.6 microM. Erythroid burst-forming units were less sensitive to high concentrations of AZT than were CFU-GM.
c-JUN, JUN B, and JUN D differ in their binding affinities to AP-1 and CRE consensus sequences: effect of FOS proteins. (1991)

We have compared the binding properties of c-JUN, JUN B, and JUN D in the absence or in the presence of c-FOS, FOS B, and FRA-1 to different AP-1 and CRE-containing oligonucleotides. The results demonstrate that for a given AP-1-containing oligonucleotide the binding affinities of the different JUN proteins are always c-JUN greater than JUN D greater than JUN B. The three JUN proteins have the capacity to bind to a CRE consensus sequence with very high affinity. We have found that c-JUN, JUN B, and JUN D bind with different affinities to different oligonucleotides containing an identical AP-1 or CRE binding site, implying that the adjacent sequences influence the stability of the JUN/DNA complexes. Interestingly, an AP-1-containing oligonucleotide which binds the JUN proteins with high affinity can be converted to a CRE-containing oligonucleotide which will also bind the different JUNs very efficiently. The heterodimers formed between the different JUN and FOS proteins have an enhanced binding activity compared to the JUN:JUN homodimers. In all cases the half-lives of the JUN:FOS/DNA complexes are longer than those of the JUN:JUN/DNA complexes. The most stable complexes were obtained in the presence of FOS B, followed by FRA-1 and c-FOS.
Transfection of Corynebacterium lilium Protoplasts (1985)

A protoplast transfection system has been developed for a lysine-producing bacterium, Corynebacterium lilium, using the DNA of phage CL31. Phage CL31 is lytic and specific to C. lilium and has a genome of approximately 48 kb. The transfection procedure involves a polyethylene-glycol-mediated introduction of the DNA into lysozyme-treated cells and has a maximum efficiency of 3 X 10(4) transfectants per microgram DNA.
Antibody-Mediated Targeting of Long-Circulating (StealthR) Liposomes (1994)

Long-circulating or StealthR liposomes (S-liposomes) have a number of important properties which make them good candidates for targeting applications. These include long circulation half-lives, dose-independent pharmacokinetics and ability to move through the lymph after subcutaneous injection. A number of techniques are available for attaching antibodies to the surface of S-liposomes. S-liposomes retain their prolonged circulation times in the presence of bound antibody. In the case of liposomes containing polyethylene glycol-lipid derivatives, the ability of bound antibody to recognize its target is dependent on the molecular weight of polyethylene glycol contained in the liposomes. Antibody-mediated specific binding of S-liposomes to cells in culture could be demonstrated, as well as increased cytotoxicity in vitro of targeted S-liposomes containing anticancer drugs. Targeting of antibody-containing S-liposomes could also be demonstrated in vivo. In one therapeutic application, dramatic increases in survival rate could be demonstrated in mice bearing lung squamous cell carcinoma following treatment with doxorubicin entrapped in S-liposomes with attached monoclonal antibody.
Transaxillary Carotid Stenting: Technical Case Report (2005)

With proper patient selection and the use of ultrasound guidance during the initial puncture, the transaxillary approach is a safe and technically feasible alternative to the transfemoral approach when performing carotid stenting.
Immunotherapy of non-Hodgkin’s lymphoma with a defined ratio of CD8 + and CD4 + CD19-specific chimeric antigen receptor–modified T cells (2016)

CD19-specific chimeric antigen receptor (CAR)-modified T cells have antitumor activity in B cell malignancies, but factors that affect toxicity and efficacy have been difficult to define because of differences in lymphodepletion and heterogeneity of CAR-T cells administered to individual patients. We conducted a clinical trial in which CD19 CAR-T cells were manufactured from defined T cell subsets and administered in a 1:1 CD4(+)/CD8(+) ratio of CAR-T cells to 32 adults with relapsed and/or refractory B cell non-Hodgkin's lymphoma after cyclophosphamide (Cy)-based lymphodepletion chemotherapy with or without fludarabine (Flu). Patients who received Cy/Flu lymphodepletion had increased CAR-T cell expansion and persistence, and higher response rates [50% complete remission (CR), 72% overall response rate (ORR)] than patients who received Cy-based lymphodepletion without Flu (8% CR, 50% ORR). The CR rate in patients treated with Cy/Flu at the maximally tolerated dose was 64% (82% ORR; n = 11). Cy/Flu minimized the effects of an immune response to the murine single-chain variable fragment component of the CAR, which limited CAR-T cell expansion and clinical efficacy in patients who received Cy-based lymphodepletion without Flu. Severe cytokine release syndrome (sCRS) and grade ≥3 neurotoxicity were observed in 13 and 28% of all patients, respectively. Serum biomarkers, one day after CAR-T cell infusion, correlated with subsequent sCRS and neurotoxicity. Immunotherapy with CD19 CAR-T cells in a defined CD4(+)/CD8(+) ratio allowed identification of correlative factors for CAR-T cell expansion, persistence, and toxicity, and facilitated optimization of lymphodepletion that improved disease response and overall and progression-free survival.
Rapid and strong human CD8+ T cell responses to vaccination with peptide, IFA, and CpG oligodeoxynucleotide 7909 (2005)

The induction of potent CD8+ T cell responses by vaccines to fight microbes or tumors remains a major challenge, as many candidates for human vaccines have proved to be poorly immunogenic. Deoxycytidyl-deoxyguanosin oligodeoxynucleotides (CpG ODNs) trigger Toll-like receptor 9, resulting in dendritic cell maturation that can enhance immunogenicity of peptide-based vaccines in mice. We tested whether a synthetic ODN, CpG 7909, could improve human tumor antigen-specific CD8+ T cell responses. Eight HLA-A2+ melanoma patients received 4 monthly vaccinations of low-dose CpG 7909 mixed with melanoma antigen A (Melan-A; identical to MART-1) analog peptide and incomplete Freund's adjuvant. All patients exhibited rapid and strong antigen-specific T cell responses: the frequency of Melan-A-specific T cells reached over 3% of circulating CD8+ T cells. This was one order of magnitude higher than the frequency seen in 8 control patients treated similarly but without CpG and 1-3 orders of magnitude higher than that seen in previous studies with synthetic vaccines. The enhanced T cell populations consisted primarily of effector memory cells, which in part secreted IFN- and expressed granzyme B and perforin ex vivo. In vitro, T cell clones recognized and killed melanoma cells in an antigen-specific manner. Thus, CpG 7909 is an efficient vaccine adjuvant that promotes strong antigen-specific CD8+ T cell responses in humans.
Recovery of function in osteoarthritic chondrocytes induced by p16INK4a-specific siRNA in vitro (2004)

p16(INK4a) is instrumental in the senescence of human articular chondrocytes or OA. The reduction of p16(INK4a) by RNA interference (RNAi) contributed to the recovery of osteoarthritic chondrocytes, suggesting that p16(INK4a) may be a viable future therapeutic candidate.
Functional Characterization of an Endosome-disruptive Peptide and Its Application in Cytosolic Delivery of Immunoliposome-entrapped Proteins (2002)

Antibody-directed liposomes (immunoliposomes) are frequently used for targeted drug delivery. However, delivery of large biotherapeutic molecules (i.e. peptides, proteins, or nucleic acids) with immunoliposomes is often hampered by an inefficient cytosolic release of entrapped macromolecules after target cell binding and subsequent endocytosis of immunoliposomes. To enhance cytosolic drug delivery from immunoliposomes present inside endosomes, a pH-dependent fusogenic peptide (diINF-7) resembling the NH(2)-terminal domain of influenza virus hemagglutinin HA-2 subunit was used. Functional characterization of this dimeric peptide showed its ability to induce fusion between liposome membranes and leakage of liposome-entrapped compounds when exposed to low pH. In a second series of experiments, diINF-7 peptides were encapsulated in immunoliposomes to enhance the endosomal escape of diphtheria toxin A chain (DTA), which inhibits protein synthesis when delivered into the cytosol of target cells. Immunoliposomes targeted to the internalizing epidermal growth factor receptor on the surface of ovarian carcinoma cells (OVCAR-3) and containing encapsulated DTA did not show any cytotoxicity toward OVCAR-3 cells. Cytotoxicity was only observed when diINF-7 peptides and DTA were co-encapsulated in the immunoliposomes. Thus, diINF-7 peptides entrapped inside liposomes can greatly enhance cytosolic delivery of liposomal macromolecules by pH-dependent destabilization of endosomal membranes after cellular uptake of liposomes.
Application of the luciferin-luciferase enzyme system for determination of adenosine triphosphate (ATP) to studies on the mechanisms of herbicide action (1975)

The luciferin-luciferase enzyme system for determination of ATP is valuable for studies on the mechanisms of herbicide action. Investigations using this system have shown that certain herbicides may act by interfering with ATP production or by blocking ATP use, or by both mechanisms.
The kallikrein 14 gene is down-regulated by androgen receptor signalling and harbours genetic variation that is associated with prostate tumour aggressiveness (2012)

Kallikrein 14 (KLK14) has been proposed as a useful prognostic marker in prostate cancer, with expression reported to be associated with tumour characteristics such as higher stage and Gleason score. KLK14 tumour expression has also shown the potential to predict prostate cancer patients at risk of disease recurrence after radical prostatectomy. The KLKs are a remarkably hormone-responsive family of genes, although detailed studies of androgen regulation of KLK14 in prostate cancer have not been undertaken to date. Using in vitro studies, we have demonstrated that unlike many other prostatic KLK genes that are strictly androgen responsive, KLK14 is more broadly expressed and inversely androgen regulated in prostate cancer cells. Given these results and evidence that KLK14 may play a role in prostate cancer prognosis, we also investigated whether common genetic variants in the KLK14 locus are associated with risk and/or aggressiveness of prostate cancer in approximately 1200 prostate cancer cases and 1300 male controls. Of 41 single nucleotide polymorphisms assessed, three were associated with higher Gleason score (≥7): rs17728459 and rs4802765, both located upstream of KLK14, and rs35287116, which encodes a p.Gln33Arg substitution in the KLK14 signal peptide region. Our findings provide further support for KLK14 as a marker of prognosis in prostate cancer.
Particle swarm optimization and its application to the design of diffraction grating filters (2007)

Particle swarm optimization (PSO) is an evolutionary, easy-to-implement technique to design optical diffraction gratings. Design of reflection and transmission guided-mode resonance (GMR) grating filters using PSO is reported. The spectra of the designed filters are in good agreement with the design targets in a reasonable computation time. Also, filters are designed with a genetic algorithm (GA) and the results obtained by the GA and PSO are compared.
Immunomodulatory effects of OX40 agonists in a defined antigen challenge in cynomolgus macaques. (2015)

3086 Background: Immunomodulatory antibodies targeting specific T cell costimulatory pathways have shown great potential as cancer therapeutics. OX40 agonists can enhance T cell proliferation and survival and cause tumor regressions in mouse models. While initial evaluations of pharmacodynamic activity of these compounds in non-human primate models have relied on non-specific T cell proliferation readouts (Ki67), additional sensitive biomarkers of pharmacodynamic activity would add value in evaluating optimal dosing and timing of candidate therapeutics. Methods: In this study, we compared the in vivo activity in cynomolgus macaques of intravenously infused OX40 agonist MEDI6469 (9B12, a murine IgG1 antibody) and MEDI6383, a human OX40 ligand fusion protein consisting of a dimer of OX40L trimers held together by Fcγ domains that also agonizes the OX40 receptor. Antigen-specific responses were evaluated to respiratory syncytial virus soluble F (sF) protein, which was administered intramuscularly on the same day as OX40 agonist treatment. Ki67 proliferation was additionally measured in whole blood. Results: Enhancement of F-specific T cell responses, serum anti-F IgG responses and functional antibodies was observed in animals that received the OX40 agonists. In addition, OX40 agonism resulted in a temporal enhancement of cellular proliferation (Ki67 staining) in CD4 and CD8 T cell memory subsets, as well as in NK cells and B cells. The strongest antigen-specific and Ki67 responses were observed in response to MEDI6383, with the exception of responses observed for NK cell proliferation which were similar between MEDI6469 and MEDI6383. Conclusions: Our study indicates that antigen-specific cellular and humoral responses may be useful biomarkers of OX40 agonist activity. Additionally, our study confirms that Ki67 readouts are informative in cynomolgus macaques, which was also demonstrated in separate studies using rhesus macaques.
Expression, selection, and organellar targeting of the green fluorescent protein in Toxoplasma gondii (1998)

We have engineered a mutant version of the green fluorescent protein GFP (Cormack et al. Selected for bright fluorescence in E. coli. Gene 1996;173:33-38) for expression in the protozoan parasite Toxoplasma gondii. Although intact GFP was not expressed at any detectable level, GFP fusion proteins could be detected by fluorescence microscopy, flow cytometry (FACS), and immunoblotting. Both extracellular tachyzoites and T. gondii-infected host cells could readily be sorted by FACS, which should facilitate a variety of selection strategies. Several selectable markers were tested for their ability to produce stable green transgenic parasites. Fluorescence intensity was directly correlated with gene copy number and protein expression level. Weak selectable markers such as chloramphenicol acetyl transferase (CAT) driven by the SAG1 promoter, which yield multicopy insertions, are therefore most effective for selecting green fluorescent parasites-particularly when coupled to constructs which employ a strong promoter to drive GFP expression. Transformation vectors developed in the course of this work should be of general utility for the overexpression of heterologous transgenes in Toxoplasma. CAT-GFP fusion proteins were expressed in the parasite cytoplasm. GFP fusions to the P30 major surface antigen (linked on the same plasmid to a CAT selectable marker under control of various promoters) could be detected in dense granules within living cells, and were efficiently secreted into the parasitophorous vacuole. GFP fusions to the rhoptry protein ROP1 were targeted to rhoptries (specialized secretory organelles at the apical end of the parasite).
An anti-CD20–IL-2 immunocytokine is highly efficacious in a SCID mouse model of established human B lymphoma (2005)

We have engineered an anti-CD20-interleukin 2 (IL-2) immunocytokine (ICK) based on the Leu16 anti-CD20 antibody and have deimmunized both the variable (V) regions as well as the junction between the heavy (H) chain constant region and IL-2. Mutations were made to remove potential T-cell epitopes identified by in silico binding to major histocompatibility complex (MHC) class II molecules. The resulting immunocytokine, DI-Leu16-IL-2, retained full anti-CD20 activity as assessed by fluorescence-activated cell-sorting (FACS) analysis, and had enhanced antibody-dependent cellular cytotoxicity (ADCC) effector function relative to the DI-Leu16 antibody or control anti-CD20 antibody (rituximab). In a severe combined immunodeficient (SCID) mouse model of disseminated, residual lymphoma, anti-CD20-IL-2 immunocytokines based on Leu16 were far more effective at a dose of 0.25 mg/kg than anti-CD20 antibody given at 25/mg/kg, despite a shorter half-life of the ICK. Anti-CD20-IL-2 was also far more effective than a control ICK targeted to an antigen with greatly reduced expression on Daudi tumor cells, or various combinations of anti-CD20 antibodies and IL-2. Antitumor activity of DI-Leu16-IL-2 was shown to partially but not entirely depend on Fc receptor (R) binding, suggesting that ADCC and targeting of IL-2 both play roles in the mechanism of tumor clearance. Based on these animal models, DI-Leu16-IL-2 could offer therapeutic potential for patients with CD20 positive lymphoma. Clinical trials are currently under development.
Intercalation of Few-Layer Graphite Flakes with FeCl3: Raman Determination of Fermi Level, Layer by Layer Decoupling, and Stability (2011)

We use anhydrous ferric chloride (FeCl(3)) to intercalate graphite flakes consisting of 2-4 graphene layers and to dope graphene monolayers. The intercalant, staging, stability, and doping of the resulting intercalation compounds (ICs) are characterized by Raman scattering. The G peak of heavily doped monolayer graphene upshifts to ∼1627 cm(-1). The 2-4 layer ICs have similar upshifts, and a Lorentzian line shape for the 2D band, indicating that each layer behaves as a decoupled heavily doped monolayer. By performing Raman measurements at different excitation energies, we show that, for a given doping level, the 2D peak can be suppressed by Pauli blocking for laser energy below the doping level. Thus, multiwavelength Raman spectroscopy allows a direct measurement of the Fermi level, complementary to that derived by performing measurements at fixed excitation energy significantly higher than the doping level. This allows us to estimate a Fermi level shift of up to ∼0.9 eV. These ICs are thus ideal test-beds for the physical and chemical properties of heavily doped graphenes.