gebhart/patrepeval huggingface dataset:
Tumor-Driven Evolution of Immunosuppressive Networks during Malignant Progression (2006)

Tumors evolve mechanisms to escape immune control by a process called immune editing, which provides a selective pressure in the tumor microenvironment that could lead to malignant progression. A variety of tumor-derived factors contribute to the emergence of complex local and regional immunosuppressive networks, including vascular endothelial growth factor, interleukin-10, transforming growth factor-beta, prostaglandin E(2), and soluble phosphatidylserine, soluble Fas, soluble Fas ligand, and soluble MHC class I-related chain A proteins. Although deposited at the primary tumor site, these secreted factors could extend immunosuppressive effects into the local lymph nodes and the spleen, promoting invasion and metastasis. Vascular endothelial growth factors play a key role in recruiting immature myeloid cells from the bone marrow to enrich the microenvironment as tumor-associated immature dendritic cells and tumor-associated macrophages. The understanding of the immunosuppressive networks that evolve is incomplete, but several features are emerging. Accumulation of tumor-associated immature dendritic cells may cause roving dendritic cells and T cells to become suppressed by the activation of indoleamine 2,3-dioxygenase and arginase I by tumor-derived growth factors. Soluble phosphatidylserines support tumor-associated macrophages by stimulating the release of anti-inflammatory mediators that block antitumor immune responses. Soluble Fas, soluble FasL, and soluble MHC class I-related chain A proteins may help tumor cells escape cytolysis by cytotoxic T cells and natural killer cells, possibly by counterattacking immune cells and causing their death. In summary, tumor-derived factors drive the evolution of an immunosuppressive network which ultimately extends immune evasion from the primary tumor site to peripheral sites in patients with cancer.
Anti-Inflammatory Actions of Intravenous Immunoglobulin (2008)

The remarkable success story of the therapeutic application of pooled immunoglobulin G (IgG) preparations from thousands of donors, the so-called intravenous IgG (IVIG) therapy, to patients with a variety of hematological and immunological disorders began more than half a century ago. Since then, the use of this primary blood product has increased constantly, resulting in the serious danger of shortages in supply. Despite its widespread use and therapeutic success, the mechanisms of action, especially of the anti-inflammatory activity, are only beginning to be understood. In this review, we summarize the clinical use of IVIG for different diseases and discuss recent data on the molecular mechanisms that might explain how this potent drug mediates its activity in vivo.
Hierarchical Graph Matching Networks for Deep Graph Similarity Learning. (2019)

While the celebrated graph neural networks yield effective representations for individual nodes of a graph, there has been relatively less success in extending to deep graph similarity learning. Recent work has considered either global-level graph-graph interactions or low-level node-node interactions, ignoring the rich cross-level interactions (e.g., between nodes and a whole graph). In this paper, we propose a Hierarchical Graph Matching Network (HGMN) for computing the graph similarity between any pair of graph-structured objects. Our model jointly learns graph representations and a graph matching metric function for computing graph similarities in an end-to-end fashion. The proposed HGMN model consists of a node-graph matching network for effectively learning cross-level interactions between nodes of a graph and a whole graph, and a siamese graph neural network for learning global-level interactions between two graphs. Our comprehensive experiments demonstrate that HGMN consistently outperforms state-of-the-art graph matching network baselines for both classification and regression tasks.
Programmed Death Ligand 1 (PD-L1) Gene Variants Contribute to Autoimmune Addison’s Disease and Graves’ Disease Susceptibility (2009)

We confirm the role of PD-L1 variants in GD susceptibility and extend these findings to demonstrate association in two Northern European patient cohorts with AAD. PD-L1 joins the growing number of known susceptibility loci exerting modest effects in these autoimmune disorders.
Treatment of Experimental Pseudomonas Corneal Ulcers With Enoxacin, a Quinolone Antibiotic (1986)

Enoxacin is a broad-spectrum quinolone-derivative antibiotic. In a rabbit model of keratitis caused by a Pseudomonas species, enoxacin (3 mg/mL) was as effective as gentamicin sulfate (3 mg/mL) and enoxacin (10 mg/mL) in reducing viable bacterial counts in corneas after 24 hours of hourly therapy with eye drops. Bacterial counts were reduced by about 5000-fold by enoxacin treatment when compared with placebo-treated controls. Penetration studies of topical enoxacin (3 mg/mL) showed that concentrations in cornea and aqueous humor reached levels above reported minimal inhibitory concentrations when an epithelial defect was present. Further investigation of enoxacin for treatment of ocular disease is warranted.
On the achievable throughput of a multiantenna Gaussian broadcast channel (2003)

A Gaussian broadcast channel (GBC) with r single-antenna receivers and t antennas at the transmitter is considered. Both transmitter and receivers have perfect knowledge of the channel. Despite its apparent simplicity, this model is, in general, a nondegraded broadcast channel (BC), for which the capacity region is not fully known. For the two-user case, we find a special case of Marton's (1979) region that achieves optimal sum-rate (throughput). In brief, the transmitter decomposes the channel into two interference channels, where interference is caused by the other user signal. Users are successively encoded, such that encoding of the second user is based on the noncausal knowledge of the interference caused by the first user. The crosstalk parameters are optimized such that the overall throughput is maximum and, surprisingly, this is shown to be optimal over all possible strategies (not only with respect to Marton's achievable region). For the case of r>2 users, we find a somewhat simpler choice of Marton's region based on ordering and successively encoding the users. For each user i in the given ordering, the interference caused by users j>i is eliminated by zero forcing at the transmitter, while interference caused by users j<i is taken into account by coding for noncausally known interference. Under certain mild conditions, this scheme is found to be throughput-wise asymptotically optimal for both high and low signal-to-noise ratio (SNR). We conclude by providing some numerical results for the ergodic throughput of the simplified zero-forcing scheme in independent Rayleigh fading.
Identification of avidin and streptavidin binding motifs among peptides selected from a synthetic peptide library consisting solely of D‐amino acids (1995)

Peptides consisting solely of D-amino acids (D-peptides) as opposed to their L-counterparts (L-peptides) are resistant towards proteolytic degradation in the organism and may therefore be useful in future efforts to develop new stable peptide-based drugs. Using the random synthetic peptide library technique several L- and D-peptides, capable of binding to both avidin and streptavidin, were found. The L-peptides contained the previously described HPQ/M motifs, and among the D-peptides three binding motifs could be identified, of which the most frequently found one contained an N-terminal aliphatic hydrophobic amino acid (V, L or I) and an aromatic amino acid (Y or F) on the second position. At the third position in this motif several different amino acid residues were found, although N was the most frequent. Peptides representing two of the D-motifs were synthesized as well as peptides containing the HPQ/M motifs, and their binding properties were examined. Although the D-peptides were originally selected using avidin they also inhibited binding between immobilized biotin and soluble streptavidin as well as avidin. The IC50 of some of the peptides were approximately 10(5) times higher than the IC50 for biotin but some had a lower IC50 than iminobiotin. The D-peptides, which were originally selected from the library using avidin, could also inhibit the binding between streptavidin and biotin. Likewise, L-peptides selected from a library screened with streptavidin, could inhibit the binding of both streptavidin and avidin to immobilized biotin. Furthermore, the D-peptide, VFSVQSGS, as well as biotin could inhibit binding of streptavidin to an immobilized L-peptide (RYHPQSGS). This indicates that the biotin-like structure mimicked by these two seemingly very different peptides may react with the same binding sites in the streptavidin molecule.
Development of intestinal cell culture models for drug transport and metabolism studies (1996)

Cell culture models offer many advantageous features for the analysis of drug transport and drug metabolism. From a basic research perspective, these systems offer the potential for manipulating the environment or cellular properties as a means to address mechanistic questions. From a drug discovery perspective, cell culture models can be used to expedite identification of compounds with favorable pharmacokinetic properties, and to evaluate structure-absorption/metabolism relationships. In this review, we will use the intestinal epithelium as an example for discussing issues associated with the development of new cell culture models for evaluating drug metabolism. Specifically, we will discuss biological properties of the intestinal epithelium and address biological and practical consideration in the application of tumor cell lines, short-term primary cultures, stem-like cell cultures, and oncogene immortalized cells as approaches to establishing models for the intestinal epithelium.
Lipocortin I Production by Human Alveolar Macrophages (1992)

Lipocortin I, in some cells, may be a potent inhibitor of phospholipase A2 activity. These studies evaluated the relative amounts of lipocortin I in human alveolar macrophages compared with blood monocytes, using a specific polyclonal antibody and the technique of Western analysis. Lipocortin I was detected in all isolates of human alveolar macrophages and had molecular masses of 37,000 and 33,000 D. Corticosteroids increased amounts of lipocortin I in these cells in a dose-dependent manner. This effect was specific for corticosteroids as related steroids had no effect. Blood monocytes, when compared with alveolar macrophages, contained relatively small amounts of lipocortin I. We conclude that lipocortin I is present in relatively large amounts in human alveolar macrophages and that amounts of the protein can be induced by corticosteroids. We further speculate that the relative amounts of lipocortin I within monocytes/macrophages may be a marker of differentiation.
Fibroblast Growth Factor-2 (FGF-2) Induces Vascular Endothelial Growth Factor (VEGF) Expression in the Endothelial Cells of Forming Capillaries: An Autocrine Mechanism Contributing to Angiogenesis (1998)

FGF-2 and VEGF are potent angiogenesis inducers in vivo and in vitro. Here we show that FGF-2 induces VEGF expression in vascular endothelial cells through autocrine and paracrine mechanisms. Addition of recombinant FGF-2 to cultured endothelial cells or upregulation of endogenous FGF-2 results in increased VEGF expression. Neutralizing monoclonal antibody to VEGF inhibits FGF-2-induced endothelial cell proliferation. Endogenous 18-kD FGF-2 production upregulates VEGF expression through extracellular interaction with cell membrane receptors; high-Mr FGF-2 (22-24-kD) acts via intracellular mechanism(s). During angiogenesis induced by FGF-2 in the mouse cornea, the endothelial cells of forming capillaries express VEGF mRNA and protein. Systemic administration of neutralizing VEGF antibody dramatically reduces FGF-2-induced angiogenesis. Because occasional fibroblasts or other cell types present in the corneal stroma show no significant expression of VEGF mRNA, these findings demonstrate that endothelial cell-derived VEGF is an important autocrine mediator of FGF-2-induced angiogenesis. Thus, angiogenesis in vivo can be modulated by a novel mechanism that involves the autocrine action of vascular endothelial cell-derived FGF-2 and VEGF.
Growth of Haemophilus influenzae in Human Milk: Synthesis, Distribution, and Activity of IgA Protease as Determined by Study of iga+ and Mutant iga- Cells (1992)

The nonencapsulated, IgA protease-positive Haemophilus influenzae strain Rd and serogroup b clinical isolates were found to proliferate in human milk. Growth did not require supplemental X and V factors. In milk, strain Rd synthesized IgA protease, but it was completely inhibited by antibody, so secretory IgA in milk cultures remained intact. Inhibition was largely attributable to IgA1 antibodies. Rd cells also aggregated during growth in milk and showed colony size variation, whereas a protease-negative mutant of Rd (Rd225DK) aggregated less and had uniform colony size. Like differences in protease inhibition, these differences in growth pattern were mediated by secretory IgA1. Thus, milk antibody not only inhibited the extracellular protease but also interacted directly with the enzyme precursor or related antigens on growing bacterial cells. This self-protective property of milk secretory IgA may be an important immunologic attribute for the upper respiratory mucosa of the infant.
Effects of adenosine on adhesion molecule expression and cytokine production in human PBMC depend on the receptor subtype activated (2007)

Adenosine differentially regulates IL-18-induced adhesion molecule expression and cytokine production through several subtypes of its receptors.
Single-Step Assembly of Homogenous Lipid−Polymeric and Lipid−Quantum Dot Nanoparticles Enabled by Microfluidic Rapid Mixing (2010)

A key challenge in the synthesis of multicomponent nanoparticles (NPs) for therapy or diagnosis is obtaining reproducible monodisperse NPs with a minimum number of preparation steps. Here we report the use of microfluidic rapid mixing using hydrodynamic flow focusing in combination with passive mixing structures to realize the self-assembly of monodisperse lipid-polymer and lipid-quantum dot (QD) NPs in a single mixing step. These NPs are composed of a polymeric core for drug encapsulation or a QD core for imaging purposes, a hydrophilic polymeric shell, and a lipid monolayer at the interface of the core and the shell. In contrast to slow mixing of lipid and polymeric solutions, rapid mixing directly results in formation of homogeneous NPs with relatively narrow size distribution that obviates the need for subsequent thermal or mechanical agitation for homogenization. We identify rapid mixing conditions that result in formation of homogeneous NPs and show that self-assembly of polymeric core occurs independent of the lipid component, which only provides stability against aggregation over time and in the presence of high salt concentrations. Physicochemical properties of the NPs including size (35-180 nm) and zeta potential (-10 to +20 mV in PBS) are controlled by simply varying the composition and concentration of precursors. This method for preparation of hybrid NPs in a single mixing step may be useful for combinatorial synthesis of NPs with different properties for imaging and drug delivery applications.
Polydimethylsiloxane Modification of Segmented Thermoplastic Polyurethanes and Polyureas (1998)

This thesis addresses the systematic modification of poly(tetramethylene oxide) (PTMO), polyether based segmented thermoplastic polyurethane with a secondary aminoalkyl functional polydimethylsiloxane (PDMS), which was intended to improve the fire resistance of polyurethane systems. The PDMS oligomer was successfully incorporated into the polyurethane backbone via one step solution polymerization. The effect of PDMS content on thermal stability, morphology, surface composition, mechanical properties, and fire resistance of polyurethane was investigated. These polymers displayed a complex two phase morphology and composition-dependant mechanical properties. The PDMS segment microphase separated from other polyurethane segments and varying microphase separation morphologies were observed with differing PDMS content. Spherical dispersed complex phases and co-continuous phases occurred when the PDMS content was 15wt% and 55wt%, respectively. Similar thermal stability was observed for both the polyurethane control and the PDMS modified polyurethanes, but the later displayed increased char yield in air with increased PDMS concentration. Quantitative measurements of the fire resistance of the modified polyurethanes by cone calorimetry showed that the peak heat release rate of the 15wt% siloxane modified samples dropped 67wt%, compared with the polyurethane control. However, the peak heat release rate did not further change with increasing siloxane content. Excellent mechanical properties, in terms of tensile strength and elongation, were found for the modified polyurethane with 15wt% of PDMS. Higher PDMS levels did reduce tensile strength, probably because of the reduction in strain crystallizing PTMO content. The PDMS modification, which resulted in improved fire resistance and excellent mechanical properties, is attributed to the low surface energy of the PDMS segment that tended to migrate to the surface of the polymer. It could be oxidized into a partially silicate-like material upon heating in air. In addition, the syntheses of primary and secondary aminoalkyl functional PDMS based segmented polyureas are described herein. Two-phase morphology was observed for all the polyurea samples, even when the hard segment concentration was as low as 6wt%. All these polyureas formed clear transparent films that exhibited good mechanical properties even with very high PDMS content, up to 94wt%. They also demonstrated similar thermal stability, independent of the PDMS end group. However, the nature of the end group, i.e. primary or secondary aminoalkyl, had a dramatic effect on mechanical and morphological properties of these PDMS based polyureas, which was interpreted in terms of the level of hydrogen bonding.
Single-base mutational analysis of cancer and genetic diseases using membrane bound modified oligonucleotides (1991)

A convenient format for the detection of PCR amplified sequences is the hybridization of the PCR products to oligonucleotide probes which are immobilized on a solid phase. We describe a new method for site-specific attachment of such probe oligonucleotides to nylon membranes. The method is based on the formation of an amide bond between carboxyl groups present on the membranes and amino-linkers situated on the 5' end of the oligonucleotides. The covalent attachment is via a carbodiimide mediated condensation. The single, 5' end attachment of the oligonucleotides to the membrane surface leaves the probe free to interact with complementary sequences, thus increasing the hybridization efficiency relative to methods where heat or ultraviolet light is used for non-specific fixation. Using biotinylated PCR products in hybridization reactions along with a non-radioactive chemiluminescent detection system, high efficiency hybridization is obtained as well as a very good signal to noise ratio. The method has been applied successfully to the detection of RAS point mutations, cystic fibrosis deletion and point mutations and others. The sensitivity, simplicity and reproducibility of this method make it an ideal tool for the diagnosis of infectious and genetic diseases, as well as analysis of mutations in neoplasias, HLA typing and other areas.
BRL 49653 blocks the lipolytic actions of tumor necrosis factor-alpha: a potential new insulin-sensitizing mechanism for thiazolidinediones. (1998)

Thiazolidinediones (TZDs) such as BRL 49653 are a class of antidiabetic agents that are agonists for the peroxisome proliferator-activated nuclear receptor (PPAR-gamma2). In vivo, TZDs reduce circulating levels of free fatty acids (FFAs) and ameliorate insulin resistance in individuals with obesity and NIDDM. Adipocyte production of TNF-alpha is proposed to play a role in the development of insulin resistance, and because BRL 49653 has been shown to antagonize some of the effects of TNF-alpha, we examined the effects of TNF-alpha and BRL 49653 on adipocyte lipolysis. After a 24-h incubation of TNF-alpha (10 ng/ml) with 3T3-L1 adipocytes, glycerol release increased by approximately 7-fold, and FFA release increased by approximately 44-fold. BRL 49653 (10 pmol/l) reduced TNF-alpha-induced glycerol release by approximately 50% (P < 0.001) and FFA release by approximately 90% (P < 0.001). BRL 49653 also reduced glycerol release by approximately 50% in adipocytes pretreated for 24 h with TNF-alpha. Prolonged treatment (5 days) with either BRL 49653 or another PPAR-gamma2 agonist, 15-d delta-12,14-prostaglandin J2 (15-d deltaPGJ2), blocked TNF-alpha-induced glycerol release by approximately 100%. Catecholamine (isoproterenol)-stimulated lipolysis was unaffected by BRL 49653 and 15-d deltaPGJ2. BRL 49653 partially blocked the TNF-alpha-mediated reduction in protein levels of hormone-sensitive lipase and perilipin A, two proteins involved in adipocyte lipolysis. These data suggest a novel pathway that may contribute to the ability of the TZDs to reduce serum FFA and increase insulin sensitivity.
Imaging of CTLA4 Blockade–Induced Cell Replication with 18F-FLT PET in Patients with Advanced Melanoma Treated with Tremelimumab (2010)

Molecular imaging with the PET probe (18)F-FLT allows mapping and noninvasive imaging of cell proliferation in secondary lymphoid organs after CTLA4 blockade in patients with metastatic melanoma.
IN SITU GELATINOLYTIC ACTIVITY CORRELATES WITH TUMOR PROGRESSION AND PROGNOSIS IN PATIENTS WITH BLADDER CANCER (2004)

FIZ enables the direct assessment of in situ gelatinolytic activity in bladder cancer tissues. The intensity of activity appears to affect the biology of carcinoma tissues. Our results indicate a major role for MMP-2 in in situ gelatinolysis in bladder cancer.
Peripheral neural modulation of endotoxin-induced hyperventilation (1998)

Both lung vagal C-fiber afferents and peripheral chemoreceptors are involved in modulating the hyperventilation response after endotoxin challenge in rat models. Stimulation of vagal C-fiber afferents increased the respiratory rate. Conversely, the role of peripheral chemoreceptors was to restrain the hyperventilatory response and these receptors may play a protective role during endotoxemia.
Hexameric Structure and Assembly of the Interleukin-6/IL-6 α-Receptor/gp130 Complex (2003)

Interleukin-6 (IL-6) is an immunoregulatory cytokine that activates a cell-surface signaling assembly composed of IL-6, the IL-6 alpha-receptor (IL-6Ralpha), and the shared signaling receptor gp130. The 3.65 angstrom-resolution structure of the extracellular signaling complex reveals a hexameric, interlocking assembly mediated by a total of 10 symmetry-related, thermodynamically coupled interfaces. Assembly of the hexameric complex occurs sequentially: IL-6 is first engaged by IL-6Ralpha and then presented to gp130in the proper geometry to facilitate a cooperative transition into the high-affinity, signaling-competent hexamer. The quaternary structures of other IL-6/IL-12 family signaling complexes are likely constructed by means of a similar topological blueprint.