gebhart/patrepeval huggingface dataset:
Multiproduct High-Resolution Monoclonal Antibody Charge Variant Separations by pH Gradient Ion-Exchange Chromatography (2009)

In the biotechnology industry, ion-exchange chromatography is widely used for profiling the charge heterogeneity of proteins, including monoclonal antibodies. Ionic strength based ion exchange separations, while having excellent resolving power and robustness, are product specific and time-consuming to develop. In the present work, a pH gradient based separation using a cation exchange column is described and shown to be a multiproduct charge sensitive separation method for monoclonal antibodies. Simple mixtures of defined buffer components were used to generate the pH-gradients that separate closely related antibody species. The form of the pH gradient was controlled and optimized by the pump as well as the buffer composition if necessary. During this work, the buffer compositions for the separation were optimized in parallel for several MAbs. The data shows that the multiproduct method is optimal for all of the MAbs studied. Operational aspects of the separation such as column chemistry, column length, and sample matrix indicate a very robust method. The pH gradient ion-exchange method is demonstrated to have significant resolving power and peak capacities far in excess of what we would expect for ionic strength elution ion-exchange. Data obtained demonstrates that the separation is relatively insensitive to column length. Direct analysis (no buffer exchange) of samples in matrixes consistent with in-process manufacturing pools is demonstrated. Such a capability is extremely useful for the high throughput evaluation of in-process and final product samples.
Reduced expression of NFAT-associated genes in UCB versus adult CD4+ T lymphocytes during primary stimulation (2003)

The cellular and molecular mechanisms underlying the blunted allo-responsiveness of umbilical cord blood (UCB) T cells have not been fully elucidated. Protein expression of NFATc2 (nuclear factor of activated T cells c2), a critical transcription factor necessary for up-regulation of multiple cytokines known to amplify T-cell allogeneic responses, is reduced in UCB T cells. Affymetrix oligonucleotide microarrays were used to compare gene expression of primary purified CD4+ UCB T cells to adult peripheral blood CD4+ T cells (AB) at baseline, 6, and 16 hours of primary stimulation. NFAT-regulated genes exhibited lower expression in UCB CD4+ T cells including the following: granulocyte-macrophage colony-stimulating factor (GM-CSF), interferon-gamma (IFN-gamma), tumor necrosis factor-alpha (TNF-alpha), interleukin 3 (IL-3), IL-4, IL-5, IL-13, IL-2 receptor alpha (IL-2Ralpha; CD25), CD40L, and macrophage inflammatory protein 1 alpha (MIP-1alpha). Transcription factors involved in the NFAT pathway including C/EBPbeta, JunB, and Fosl1 (Fra-1), as well as Th1- and Th2-related transcription factors STAT4 (signal transducers and activators of transcription 4), T-bet, and c-maf showed reduced expression in UCB compared with AB during primary stimulation. Reduced cytokine, chemokine, and receptor expression was also found in UCB. Gene array data were confirmed using RNase protection assays, flow cytometry, and quantitative multiplexed cytokine measurements. Reduced global expression of NFAT-associated genes, as well as cytokines and chemokines, in UCB CD4+ T cells may contribute to the decreased graft-versus-host disease (GVHD) observed after UCB transplantation.
Polymorphisms in angiogenesis related genes predict clinical outcome in patients (pts) with metastatic colorectal cancer (mCRC) treated with first line 5-FU or capecitabine in combination with oxaliplatin and bevacizumab (FOLFOX/BV or XELOX/BV) (2007)

10576 Background: The inhibition of angiogenesis is central to the mechanism of action of BV, a monoclonal antibody to vascular endothelial growth factor (VEGF). We evaluated functionally significant polymorphisms of genes involved in the angiogenesis/VEGF pathway as potential molecular predictors of clinical outcome in pts with mCRC who received BV as part of their frontline therapy. These genes included: VEGF, VEGF receptor 2 (KDR), neuropilin 1 (NRP 1), Interleukin (IL) 6 and 8, IL receptor 1 and 2 (CXCR 1, CXCR 2) adrenomedullin (AM), leptin, fibroblast growth factor receptor 4 (FGFR4), tissue factor (TF), matrix metalloproteinases (MMP 2,7,9), epidermal growth factor receptor (EGFR), aryl hydrocarbon receptor nuclear translocator (ARNT), and nuclear factor kappa b (NFkb). Methods: PCR-RFLP assays were performed on genomic DNA extracted from the blood of 30 pts with mCRC treated with first-line FOLFOX/BV or XELOX/BV at USC. Results: the cohort consisted of 21 males and 9 females with a median age of 56 years (range: 29–81). 20 pts received XELOX/BV as part of an on-going phase II study, 10 pts received FOLFOX/BV. Radiologic response was evaluable in 27/30 pts: 2/27 (7%) complete response (CR), 14/27 (52%) partial response (PR), and 10/27 (37%) stable disease (SD) and 1/28 (4%) progressive disease. At a median follow-up of 19.4 months, 16/30 pts progressed with a median progression free survival (PFS) of 11.8 months. Pts homozygous A/A at the leptin 5'UTR region had a higher probability of response than pts with the G/A or G/G genotypes (p=0.03, Fisher's exact test). Pts with one or more G allele (G/G or A/G) at locus -181 in the promoter region of MMP7 had a higher probability of response than pts with the AA genotype (p=0.014, Fisher's exact test). There were statistically significant associations between genomic polymorphisms of KDR, CXCR2, MMP7 and PFS (&lt;0.05, Log-rank test). Conclusions: This pilot study demonstrated, in a preliminary fashion, the potential predictive and prognostic value of several genomic polymorphisms in pts with mCRC treated with FOLFOX/BV or XELOX/BV. No significant financial relationships to disclose.
Neurotrophin-based strategies for neuroprotection (2005)

Neurotrophins activate a number of signaling pathways relevant to neuroprotection; however, their poor pharmacological properties and their pleiotropic effects resulting from interaction with the p75(NTR)-Trk-sortilin three-receptor signaling system limit therapeutic application. While local application of neurotrophin proteins addresses some of the pharmacological challenges, selective targeting of neurotrophin receptors might allow for more selective application of neurotrophin receptor signaling modulation. Recent studies have supported the feasibility of developing non-peptidyl small molecules that mimic specific domains of neurotrophins and modulate signaling of specific neurotrophin receptors. The expression of p75(NTR) by populations of neurons most vulnerable in Alzheimer's disease and the linkage of p75(NTR) signaling to aberrant signaling mechanisms occurring in this disorder, point to potential applications for p75(NTR)-based small molecule strategies. Small molecules targeted to p75(NTR) in the settings of neurodegenerative disease and other forms of neural injury might serve to inhibit death signaling, block proNGF-mediated degenerative signaling and minimize deleterious effects promoted by pharmacologically upregulated Trk signaling.
Studies on Preparation and Absolute Bioavailability of a Self-Emulsifying System Containing Puerarin (2007)

The purpose of the study was to develop an optimum formulation of self-emulsifying drug delivery systems (SEDDS) containing puerarin and to evaluate its absolute bioavailability. Using oleic acid as oil, Tween-80 as surfactant and propylene glycol as cosurfactant, a series of mixtures comprising oleic acid, propylene glycol and Tween 80 were prepared and their self-emulsifying properties were studied. Pseudo-ternary phase diagrams were constructed to identify the efficient self-emulsification region and particle sizes of the resultant emulsions were determined using a laser diffraction sizer. From these studies, an optimized formulation consisting of oil (17.5%), Tween-80 (34.5%) and cosurfactant (34.5%) was selected and its absolute bioavailability in beagle dogs after oral administration was about 24.8%. The data suggest the use of SEDDS to provide a potential way of puerarin administered orally.
A Layered Vegetation Model for GPR Full-Wave Inversion (2015)

The vegetation cover strongly affects microwave remote sensing backscattered signals and makes difficulties in retrieving the surface soil water content (SWC). In this paper, we developed a vegetation cover model for full-wave inversion of ground-penetrating radar (GPR) data assuming multiple layers with effective electrical properties. Measurements were performed in laboratory conditions over spelt wheat grown in a sandy soil. A stepped-frequency continuous-wave (SFCW) GPR system was set up using a vector network analyzer and a horn antenna operating in 1-4 GHz range in far-field conditions with different incidence angles and both VV and HH polarizations. In order to control the sand surface water content, a water table was fixed at 20 cm depth and 6 time-domain reflectometry (TDR) probes were horizontally placed at 2 and 20 cm depth. Measurements were performed and recorded hourly for about 1 month and the canopy height was measured daily. The effective electromagnetic properties of the vegetation layer were modeled using a complex refractive index model (CRIM) combined with a single Debye relaxation model. A scattering loss parameter was included in the electromagnetic full-wave GPR model for the vegetation layer. The proposed method was also applied in a ~7 ha agricultural field with a vegetation canopy height of ~27 cm (spring wheat). The laboratory measurements resulted in a strong link between the vegetation scattering losses parameter and canopy height (generally, the biomass structure), which cannot be retrieved directly from the GPR measurements. Applying this vegetation model to the GPR full-wave inversion led to a significant correction on GPR-derived SWC values from the field measurements.
ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers (2010)

We describe the methodology, parametrization, and application of a conformational search method, called ConfGen, designed to efficiently generate bioactive conformers. We define efficiency as the ability to generate a bioactive conformation within a small total number of conformations using a reasonable amount of computer time. The method combines physics-based force field calculations with empirically derived heuristics designed to achieve efficient searching and prioritization of the ligand's conformational space. While many parameter settings are supported, four modes spanning a range of speed and quality trades-offs are defined and characterized. The validation set used to test the method is composed of ligands from 667 crystal structures covering a broad array of target and ligand classes. With the fastest mode, ConfGen uses an average of 0.5 s per ligand and generates only 14.3 conformers per ligand, at least one of which lies within 2.0 A root-mean-squared deviation of the crystal structure for 96% of the ligands. The most computationally intensive mode raises this recovery rate to 99%, while taking 8 s per ligand. Combining multiple search modes to "fill-in" holes in the conformation space or energy minimizing using an all-atom force field each lead to improvements in the recovery rates at higher resolutions. Overall, ConfGen is at least as good as competing programs at high resolution and demonstrates higher efficiency at resolutions sufficient for many downstream applications, such as pharmacophore modeling.
Prognostic significance of plasma osteopontin levels in patients with chronic stable angina (2006)

Baseline levels of OPN are an independent predictor of future adverse cardiac events in patients with CSA and may be useful for risk stratification.
Monoclonal antibody analysis of p53 expression in normal and transformed cells (1986)

The cellular phosphoprotein p53 binds tightly and specifically to simian virus 40 T antigen and the 58,000-molecular-weight adenovirus E1b protein. Many human and murine tumor cell lines contain elevated levels of the p53 protein even in the absence of these associated viral proteins. Recently the cloned p53 gene, linked to strong viral promoters, has been shown to complement activated ras genes in transformation of primary rodent cell cultures. Overexpression of the p53 gene alone rescues some primary rodent cell cultures from senescence. We isolated three new monoclonal antibodies to the p53 protein, designated PAb242, PAb246, and PAb248, and mapped the epitopes they recognized on p53 in comparison with other previously isolated antibodies. At least five sterically separate epitopes were defined on murine p53. One of the antibodies, PAb246, recognizes an epitope on p53 that is unstable in the absence of bound simian virus 40 T antigen. This effect is demonstrable in vivo and in newly developed in vitro assays of T-p53 complex formation. Using the panel of anti-p53 antibodies and sensitive immunocytochemical methods, we found that p53 has a predominantly nuclear location in established but not transformed cells as well as in the vast majority of transformed cell lines. Several monoclonal antibodies to p53 showed cross-reactions with non-p53 components in immunocytochemical staining.
Will Multiple Coreceptors Need To Be Targeted by Inhibitors of Human Immunodeficiency Virus Type 1 Entry? (1999)

Despite being able to use the Bonzo coreceptor as efficiently as CCR5 in transfected cells, pediatric human immunodeficiency virus type 1 isolate P6 was unable to replicate in peripheral blood mononuclear cells (PBMC) lacking the CCR5 receptor. Furthermore, its replication in wild-type PBMC was completely inhibited by inhibitors of CCR5-mediated entry. Similarly, maternal isolate M6 could use CCR5, CXCR4, Bonzo, and other coreceptors in transfected cells but was completely sensitive to inhibitors of CCR5- and CXCR4-mediated entry when grown in PBMC. The ability of these viruses to use coreceptors in addition to CCR5 and CXCR4 in vitro was, therefore, irrelevant to their drug sensitivity in primary cells. We argue that CCR5 and CXCR4 should remain the primary targets for antiviral drug development, pending strong evidence to the contrary.
A wide range of human cancers express interleukin 4 (IL4) receptors that can be targeted with chimeric toxin composed of IL4 and Pseudomonas exotoxin (1993)

A chimeric toxin has been constructed by fusion of a gene encoding human interleukin 4 (hIL4) to a gene encoding a mutant form of Pseudomonas exotoxin A (PE) which cannot bind to its receptors (PE4E). The chimeric gene was expressed in Escherichia coli where large amounts of the chimeric toxin, hIL4-PE4E, was produced. Purified hIL4-PE4E was very cytotoxic to cancer cell lines of both hematopoietic and solid tumor origin. In the HUT 102 T cell leukemia and Daudi B cell lymphoma cell lines, protein synthesis was inhibited by 50% (ID50) at a hIL4-PE4E concentration of 2 and 7 ng/ml (25 and 86 pM, respectively). hIL4-PE4E was also very cytotoxic to cell lines derived from carcinomas of the colon, breast, stomach, liver, adrenals, and prostate, as well as melanoma and epidermoid carcinoma, indicating that hIL4 receptors are widely expressed on human malignancies. We also found that human phytohemagglutinin-activated peripheral blood lymphocytes were extremely sensitive to hIL4-PE4E with an ID50 of 0.2 ng/ml (2.5 pM). The cytotoxic action of hIL4-PE4E was specific because it was blocked by an excess of hIL4 and not of human interleukin 2. In addition, hIL4-PE4ED553, an enzymatically inactive form of the chimeric toxin, was not cytotoxic. These results suggest that the hIL4 receptor may be a target for therapy in malignant and immunologic disorders using hIL4 chimeric toxin.
C9orf72 ablation causes immune dysregulation characterized by leukocyte expansion, autoantibody production and glomerulonephropathy in mice (2016)

The expansion of a hexanucleotide (GGGGCC) repeat in C9ORF72 is the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Both the function of C9ORF72 and the mechanism by which the repeat expansion drives neuropathology are unknown. To examine whether C9ORF72 haploinsufficiency induces neurological disease, we created a C9orf72-deficient mouse line. Null mice developed a robust immune phenotype characterized by myeloid expansion, T cell activation, and increased plasma cells. Mice also presented with elevated autoantibodies and evidence of immune-mediated glomerulonephropathy. Collectively, our data suggest that C9orf72 regulates immune homeostasis and an autoimmune response reminiscent of systemic lupus erythematosus (SLE) occurs in its absence. We further imply that haploinsufficiency is unlikely to be the causative factor in C9ALS/FTD pathology.
The role of satellites in the Information Superhighway (2002)

Universal access to the Information Superhighway infrastructure is a major principle advanced by the Canadian government to guide the development and implementation of the infrastructure. The ultimate aim of this information revolution is to ensure that everyone will have access to information, anytime, anywhere, at reasonable cost. To this end, satellites are uniquely qualified to ensure universal access to the infrastructure, for the cost of wiring every home, office, hospital, library, and school in many areas not currently served by terrestrial digital networks would be prohibitive. In addition, satellite communications is at a crucial juncture, in that new advanced satellite system designs will dramatically change the cost-structure of satellite communications, making it affordable to residential users. An advanced satcom concept is introduced which could provide a very large user base with small, easy-to-install, low-cost, high-rate terminals, while meeting the high performance requirements associated with wideband multimedia applications.
Platelet-derived growth factor BB induces functional vascular anastomoses in vivo. (1995)

Neovascularization that generates collateral blood flow can limit the extent of tissue damage after acute ischemia caused by occlusion of the primary blood supply. The neovascular response stimulated by the BB homodimeric form of recombinant platelet-derived growth factor (PDGF-BB) was evaluated for its capacity to protect tissue from necrosis in a rat skin flap model of acutely induced ischemia. Complete survival of the tissue ensued, when the original nutritive blood supply was occluded, as early as 5 days after local PDGF-BB application, and the presence of a patent vasculature was evident compared to control flaps. To further evaluate the vascular regenerative response, PDGF-BB was injected into the muscle/connective tissue bed between the separated ends of a divided femoral artery in rats. A patent new vessel that functionally reconnected the ends of the divided artery within the original 3- to 4-mm gap was regenerated 3 weeks later in all PDGF-BB-treated limbs. In contrast, none of the paired control limbs, which received vehicle with an inactive variant of PDGF-BB, had vessel regrowth (P < 0.001). The absence of a sustained inflammatory response and granulation tissue suggests locally delivered PDGF-BB may directly stimulate the angiogenic phenotype in endothelial cells. These findings indicate that PDGF-BB can generate functional new blood vessels and nonsurgically anastomose severed vessels in vivo. This study supports the possibility of a therapeutic modality for the salvage of ischemic tissue through exogenous cytokine-induced vascular reconnection.
Majorana Fermion Induced Resonant Andreev Reflection (2009)

We describe experimental signatures of Majorana fermion edge states, which form at the interface between a superconductor and the surface of a topological insulator. If a lead couples to the Majorana fermions through electron tunneling, the Majorana fermions induce resonant Andreev reflections from the lead to the grounded superconductor. The linear tunneling conductance is 0 (2e(2)/h) if there is an even (odd) number of vortices in the superconductor. Similar resonance occurs for tunneling into the zero mode in the vortex core. We also study the current and noise of a two-lead device.
Gene Therapy Strategy for Long-Term Myocardial Protection Using Adeno-Associated Virus-Mediated Delivery of Heme Oxygenase Gene (2002)

This study documents the beneficial therapeutic effect of rAAV-mediated transfer, before myocardial injury, of a cytoprotective gene that confers long-term myocardial protection from ischemia/reperfusion injury. Our data suggest that this novel "pre-event" gene transfer approach may provide sustained tissue protection from future repeated episodes of injury and may be beneficial as preventive therapy for patients with or at risk of developing coronary ischemic events.
Setting Up a PCR Laboratory (2003)

1. Introduction One of the most important attributes of the polymerase chain reaction (PCR) is its exquisite sensitivity. However, this high sensitivity has also given PCR its main weakness, namely, its tendency to produce false-positive results due to exogenous contamination (1,2). Contamination avoidance is therefore the single most important consideration when setting up a PCR laboratory, especially one concerned with generating diagnostic information. In many situations, precautions which are normally taken in the handling of microbiological materials are equally applicable to PCR-related procedures.
In vitro and in vivo targeting of radiolabeled monovalent and divalent haptens with dual specificity monoclonal antibody conjugates: enhanced divalent hapten affinity for cell-bound antibody conjugate. (1989)

A method of pretargeted immunolocalization of a mouse cell subset, using dual specificity monoclonal antibody conjugates and labeled divalent haptens, is described. Conjugates were prepared by coupling F(ab')2 fragments of an antibody specific for the allelic mouse B cell antigen Lyb8.2, to Fab' fragments of an anti-2,4-dinitrophenyl antibody. Divalent and monovalent haptens were obtained by coupling dinitrophenyl to peptides or to diethylene-triamine-pentaacetic acid. In vitro, divalent haptens bind with higher affinity to mouse spleen lymphocyte-bound than to excess soluble conjugate (affinity enhancement). In vivo, localization of 125I- or 111In-labeled divalent haptens in mouse spleen is much higher than that of the monovalent analogs. Thus, using divalent haptens, a new kind of specificity to target cells was achieved, suggesting that affinity enhancement may improve target to background ratios in radioimmunoscintigraphy.