gebhart/patrepeval huggingface dataset:
A synthetic peptide derived from the sequence of a type I collagen receptor inhibits type I collagen-mediated platelet aggregation. (1997)

A synthetic peptide-1, an 18 amino acid residue peptide derived from a hydrophilic domain of a cloned platelet type I collagen receptor, was used to study the role of the receptor on types I and III collagen-induced platelet aggregation and the release of ATP. The peptide inhibits the type I, but not the type III, collagen-induced platelet aggregation and the release of ATP in a dose-dependent manner. The [125I]peptide-1 specifically binds to type I collagen-coated microtiter wells in a dose-dependent manner (with Kd = 10 nM). The binding of [125I]peptide-1 can be inhibited by an excess of unlabeled peptide-1 suggesting that the binding is specific. The labeled peptide-1 does not bind to type III collagen-coated microtiter wells. Results from an enzyme-linked immunosorbent assay show that the peptide reacts with the poly- and monoclonal antibodies raised against the purified platelet type I collagen receptor (Mr 65 kD). The peptide also inhibits the adhesion of platelets on type I collagen matrix and rabbit aortic segments in a dose-dependent manner. These results suggest that the reactive site of the platelet receptor for type I collagen resides in this portion of the molecule.
Doxil Synergizes with Cancer Immunotherapies to Enhance Antitumor Responses in Syngeneic Mouse Models (2015)

Based on the previously described roles of doxorubicin in immunogenic cell death, both doxorubicin and liposomal doxorubicin (Doxil) were evaluated for their ability to boost the antitumor response of different cancer immunotherapies including checkpoint blockers (anti-PD-L1, PD-1, and CTLA-4 mAbs) and TNF receptor agonists (OX40 and GITR ligand fusion proteins) in syngeneic mouse models. In a preventative CT26 mouse tumor model, both doxorubicin and Doxil synergized with anti-PD-1 and CTLA-4 mAbs. Doxil was active when CT26 tumors were grown in immunocompetent mice but not immunocompromised mice, demonstrating that Doxil activity is increased in the presence of a functional immune system. Using established tumors and maximally efficacious doses of Doxil and cancer immunotherapies in either CT26 or MCA205 tumor models, combination groups produced strong synergistic antitumor effects, a larger percentage of complete responders, and increased survival. In vivo pharmacodynamic studies showed that Doxil treatment decreased the percentage of tumor-infiltrating regulatory T cells and, in combination with anti-PD-L1, increased the percentage of tumor-infiltrating CD8(+) T cells. In the tumor, Doxil administration increased CD80 expression on mature dendritic cells. CD80 expression was also increased on both monocytic and granulocytic myeloid cells, suggesting that Doxil may induce these tumor-infiltrating cells to elicit a costimulatory phenotype capable of activating an antitumor T-cell response. These results uncover a novel role for Doxil in immunomodulation and support the use of Doxil in combination with checkpoint blockade or TNFR agonists to increase response rates and antitumor activity.
Silicon Nanowire‐Based Devices for Gas-Phase Sensing (2013)

Since their introduction in 2001, SiNW-based sensor devices have attracted considerable interest as a general platform for ultra-sensitive, electrical detection of biological and chemical species. Most studies focus on detecting, sensing and monitoring analytes in aqueous solution, but the number of studies on sensing gases and vapors using SiNW-based devices is increasing. This review gives an overview of selected research papers related to the application of electrical SiNW-based devices in the gas phase that have been reported over the past 10 years. Special attention is given to surface modification strategies and the sensing principles involved. In addition, future steps and technological challenges in this field are addressed.
Interleukin-8 is produced in neoplastic and infectious diseases of the human central nervous system. (1992)

The presence of interleukin-8 (IL-8), a leukocyte chemotactic factor, was examined in primary and metastatic central nervous system tumors and in nonneoplastic acute meningoencephalitides. In vitro: (a) 11 of 12 glioblastoma cell lines constitutively expressed IL-8 mRNA; (b) 5 of 6 of these cell lines secreted IL-8 protein as detected by enzyme-linked immunosorbent assay and a glucosaminidase release bioassay; and (c) IL-1 beta or tumor necrosis factor was able to augment both IL-8 mRNA steady state levels and protein secretion of all cell lines tested except IN-319. IL-8 was also found in vivo. (a) IL-8 poly A+ mRNA was detected in 2 of 2 low grade astrocytomas, 1 of 2 anaplastic astrocytomas, and 6 of 6 glioblastomas. (b) IL-8 protein was present in the cyst fluid of 1 of 4 low grade astrocytomas, 1 anaplastic astrocytoma, 2 of 2 glioblastomas, 1 oligodendroglioma grade III, and one central nervous system cervical carcinoma metastasis. (c) The cerebrospinal fluid of 3 of 4 metastatic lymphomas, 2 of 16 glioblastomas, 1 of 2 low grade astrocytomas, but none of 3 anaplastic astrocytomas and none of 9 meningiomas contained IL-8. The presence of IL-8 was not restricted to central nervous system tumors as 2 of 2 bacterial meningitis and 5 of 5 acute viral meningitis patients contained considerable IL-8 levels in the cerebrospinal fluid. (d) Immunohistochemical analysis showed IL-8 immunoreactivity in perivascular tumor cells in 11 of 15 glioblastoma sections. These data suggest that IL-8 secretion could be a key factor involved in the determination of the lymphoid infiltrates observed in brain tumors and the development of cerebrospinal fluid pleocytosis in meningoencephalitides.
Patterned nanoporous gold as an effective SERS template (2011)

We demonstrate large area two-dimensional arrays of patterned nanoporous gold for use as easy-to-fabricate, cost-effective, and stable surface enhanced Raman scattering (SERS) templates. Using a simple one-step direct imprinting process, subwavelength nanoporous gold (NPG) gratings are defined by densifying appropriate regions of a NPG film. Both the densified NPG and the two-dimensional grating pattern are shown to contribute to the SERS enhancement. The resulting substrates exhibit uniform SERS enhancement factors of at least 10(7) for a monolayer of adsorbed benzenethiol molecules.
Differential expression of peroxisome proliferator-activated receptors (PPARs): tissue distribution of PPAR-alpha, -beta, and -gamma in the adult rat. (1996)

Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear hormone receptor superfamily that can be activated by various xenobiotics and natural fatty acids. These transcription factors primarily regulate genes involved in lipid metabolism and also play a role in adipocyte differentiation. We present the expression patterns of the PPAR subtypes in the adult rat, determined by in situ hybridization using specific probes for PPAR-alpha, -beta and -gamma, and by immunohistochemistry using a polyclonal antibody that recognizes the three rat PPAR subtypes. In numerous cell types from either ectodermal, mesodermal, or endodermal origin, PPARs are coexpressed, with relative levels varying between them from one cell type to the other. PPAR-alpha is highly expressed in hepatocytes, cardiomyocytes, enterocytes, and the proximal tubule cells of kidney. PPAR-beta is expressed ubiquitously and often at higher levels than PPAR-alpha and -gamma. PPAR-gamma is expressed predominantly in adipose tissue and the immune system. Our results suggest new potential directions to investigate the functions of the different PPAR subtypes.
Analysis of the measurement precision of arterial lumen and wall areas using high-resolution MRI (2000)

High-resolution MRI may be used to monitor the progression of human carotid atherosclerosis by measuring the lumen and wall area changes over time. The purpose of this study was to analyze the precision of quantitative measurements of lumen and wall areas. Two independent MR scans near the carotid bifurcation were conducted on eight patients within 2 weeks. The error of lumen area measurement was 6. 2%, 9.2%, and 9.7% for T(1), proton density, and T(2)-weighted images, respectively, and the error of wall area measurement was 10. 8%, 10.9%, and 12.0%. The precision of area measurement correlates strongly with image quality.
Regulation of hypoxia-inducible factor 1α is mediated by an O 2 -dependent degradation domain via the ubiquitin-proteasome pathway (1998)

Hypoxia induces a group of physiologically important genes such as erythropoietin and vascular endothelial growth factor. These genes are transcriptionally up-regulated by hypoxia-inducible factor 1 (HIF-1), a global regulator that belongs to the basic helix-loop-helix PAS family. Although HIF-1 is a heterodimer composed of alpha and beta subunits, its activity is primarily determined by hypoxia-induced stabilization of HIF-1alpha, which is otherwise rapidly degraded in oxygenated cells. We report the identification of an oxygen-dependent degradation (ODD) domain within HIF-1alpha that controls its degradation by the ubiquitin-proteasome pathway. The ODD domain consists of approximately 200 amino acid residues, located in the central region of HIF-1alpha. Because portions of the domain independently confer degradation of HIF-1alpha, deletion of this entire region is required to give rise to a stable HIF-1alpha, capable of heterodimerization, DNA-binding, and transactivation in the absence of hypoxic signaling. Conversely, the ODD domain alone confers oxygen-dependent instability when fused to a stable protein, Gal4. Hence, the ODD domain plays a pivotal role for regulating HIF-1 activity and thereby may provide a means of controlling gene expression by changes in oxygen tension.
Oncostatin M is a novel inhibitor of TGF-β1-induced matricellular protein expression (2011)

Matricellular proteins in the kidney have been associated with the development of tubulointerstitial fibrogenesis and the progression of renal disease. This study investigated potential antifibrotic effects of the cytokine oncostatin M (OSM) in human proximal tubule cells (PTC), particularly with regard to inhibition of profibrotic events initiated by TGF-β1. In human PTC, OSM diminished transforming growth factor (TGF)-β1-induced expression of the transcriptional epithelial-mesenchymal transition mediator FoxC2. Furthermore, exposure to OSM attenuated basal and TGF-β1-induced expression of the matricellular proteins SPARC, TSP-1, TNC, and CTGF regardless of the sequence of ligand administration. OSM was shown to result in rapid and sustained phosphorylation of both Stat1 and Stat3 and also in transient phosphorylation of Smad2/3 in contrast to TGF-β1, which demonstrated a gradually building phosphorylation of Smad2/3 and a brief phosphorylation of Smad1/5/8. Utilizing receptor-blocking molecules, we found the inhibitory effect of OSM on TGF-β1-induced CTGF mRNA expression occurs independently of Smad2/3 signaling and present evidence that this effect may be partially driven by OSM receptor-mediated Stat1 and/or Stat3 signaling pathways, thereby providing a mechanism whereby OSM can contribute to tubulointerstitial protection.
Pretreatment Serum Levels of Cytokines and Cytokine Receptors in Patients with Non-Small Cell Lung Cancer, and Correlations with Clinicopathological Features and Prognosis (2006)

Increased pretreatment serum M-CSF level is a significant independent predictor of poor survival in patients with NSCLC.
Two-dimensional Cell Manipulation Technology An Artificial Neural Circuit Based on Surface Microphotoprocessing (1992)

The precise regional control of cell adhesion and growth on a substrate may create two-dimensional tissue formation, as in a neural network. To prepare a neural circuit, micropositioning of neural cells and guidance of extending axons in a given region are required. In general, the adhesion of neural cells and their axonal extension are mediated by adhesive proteins found in the extracellular matrix. This paper describes a novel surface photoprocessing that enables the creation and guidance of regionally selective cell adhesion, leading to a neural network. The non-adherent region was created by chemical fixation of a photoreactive hydrophilic co-polymer of azidostyrene and N, N-dimethylacrylamide on a hydrophobic substrate. Ultraviolet irradiation with the use of a photomask placed on a substrate hydrophilically modified the irradiated regions, which was evident in ESCA and contact angle measurements. The addition of a collagen buffer solution resulted in collagen adsorption only on the non-irradiated hydrophobic portions. Seeded neuroblastoma cells adhered only on collagen-adsorbed pathways 130 microns in width. One day after seeding, nerve growth factor was added to the culture medium, resulting in cell differentiation from growth to axonal extension. The axons grew along the collagen-adsorbed pathways. Sooner or later, cells were interconnected with extended axons, which was clearly visible microscopically. Further culturing completed the honeycomb-like patterning, as designed. The surface processing developed here can manipulate fundamental cellular behavior, leading to two-dimensional patterned tissue, which may provide information on the morphogenesis of the neural network and neurotransmission.
Twelve aberrant strains of Staphylococcus aureus subsp. aureus from clinical specimens (1993)

A new biovar of Staphylococcus aureus subsp. aureus was isolated from human clinical specimens and described on the basis of studies of 12 isolates that were compared with 11 standard reference strains. Both DNA hybridization experiments and numerical taxonomy analysis demonstrated that these strains were strictly related to S. aureus subsp. aureus; however, they were significantly different from the latter. The atypical strains belonging to the new biovar can be distinguished from typical S. aureus subsp. aureus strains by their alpha-chymotrypsin, alpha-glucosidase, beta-N-acetylglucosaminidase, lipase (C-14), and leucine arylamidase enzymatic activities and novobiocin resistance. Thus, the combination of alpha-glucosidase and beta-N-acetyl-glucosaminidase is more useful for distinguishing these S. aureus strains from the other, typical ones.
Powers of ten thousand (1994)

How would you interactively browse a very large display space, for example, a street map of the entire United States? The traditional solution is zoom and pan. But each time a zoom-in operation takes place, the context from which it came is visually lost. Sequential applications of the zoom-in and zoom-out operations may become tedious. This paper proposes an alternative technique, the macroscope, based on zooming and planning in multiple translucent layers. A macroscope display should comfortably permit browsing continuously on a single image, or set of images in multiple resolutions, on a scale of at least 1 to 10,000.
Lipid coated chitosan microparticles as protein carriers (2011)

Abstract In this study, a novel protein‐loaded and lipid‐coated drug carrier system for pulmonary application was developed. In a first step, spherically shaped chitosan particles were produced by spray‐drying. The produced particles showed sizes between 2 μm and 3.5 µm and zeta potentials ranged between 1.4 mV and 37.9 mV. Due to the positive charge of the particles, they could easily be loaded with the model protein drug Bovine Serum Albumine (BSA) via electrostatic interaction. In a final step, the prepared BSA loaded chitosan microparticles were coated with a lipid layer to improve drug delivery via the pulmonary and nasal route. This lipid‐based surface modification changed the physico‐chemical characteristics of the drug carrier systems. While unmodified chitosan particles showed a fast burst release of the protein, the lipid coated particles released the protein over a time period of 2 days. In Conclusion, the lipid‐coated particles show characteristics which make them a promising vehicle for pulmonary administration of proteins. (© 2011 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Clinical relevance of urokinase plasminogen activator, its receptor, and its inhibitor in patients with renal cell carcinoma (1996)

BACKGROUND Urokinase plasminogen activator (u-PA) plays a key role in the metastatic process by promoting plasmin mediated tissue degradation. Metastatic cell invasion requires localized proteolysis, which may be directed by u-PA receptor. The binding of u-PA and PAI-1 to the u-PA-receptor may cause internalization of the trimeric complex into the cell and activate a tyrosine-kinase. In a prospective study the u-PA, u-PA-R, and PAI-1 content in patients with renal cell carcinoma (RCC) and benign renal tissue were correlated with traditional prognostic factors such as the TNM staging, histologic grading, ploidy, and the clinical outcome of the patients. METHODS One hundred fifty-two patients who underwent transperitoneal tumor nephrectomy for RCC were followed up for a mean of 23.9 months. u-PA, u-PA-R, and PAI-1 from the tumor tissue and corresponding benign renal tissue were quantified from detergent extracted tissue samples (1% Trinton-X-100 in triethanolamine-buffered saline) and measured with an enzyme-linked immunoadsorbent assay. RESULTS PAI-1 significantly correlated with the prevalence of distant metastasis (M0: 10.04 vs. M1 23.79, P = 0.02) and the development of new metastases postoperatively (M0: 10.85 vs. M1 27.36, P = 0.001). A cut-off level of 12 ng/mg protein for PAI-1 selected a group of patients at high risk for relapse. Forty-one patients had PAI-1 > 12 ng/mg with 6 relapses compared with 55 patients with PAI-1 < 12 ng/mg with 1 relapse during the follow-up. Content of μ-PA correlated with the development of distant metastases (log rank 4.32, P = 0.037). A cut-off value of 0.84 ng/mg selected 2 groups: a group at high risk for metastasizing (u-PA > 0.84, n = 11 with 9 events and a group at low risk (u-PA < 0.84 with 94 patients and 5 events). Applying a cut-off value of 0.85 for u-PA-R 2 groups could be discriminated: 31 patients had no relapse with u-PA-R < 0.85 and 18 had 3 recurrences with u-PA-R > 0.85 g/ml. CONCLUSIONS U-PA, u-PA-R, and PAI-1 are strong and independent prognostic factors for predicting early relapse for RCC. Especially with PAI-1, a high and low risk group for disease free survival can be discriminated. Cancer 1996;78:487-92.
Gap junction proteins in the light-damaged albino rat. (2014)

The results suggest that connexins are regulated differently in the retina than in the choroid in response to photoreceptor damage. Changes in connexins, including Cx36, Cx43, and Cx45, may contribute to the damage process. Specifically, Cx43 was associated with inflammatory damage. Therefore, connexins may be candidate targets for treatment for ameliorating disease progression.
Horizon Lines in the Wild (2016)

The horizon line is an important contextual attribute for a wide variety of image understanding tasks. As such, many methods have been proposed to estimate its location from a single image. These methods typically require the image to contain specific cues, such as vanishing points, coplanar circles, and regular textures, thus limiting their real-world applicability. We introduce a large, realistic evaluation dataset, Horizon Lines in the Wild (HLW), containing natural images with labeled horizon lines. Using this dataset, we investigate the application of convolutional neural networks for directly estimating the horizon line, without requiring any explicit geometric constraints or other special cues. An extensive evaluation shows that using our CNNs, either in isolation or in conjunction with a previous geometric approach, we achieve state-of-the-art results on the challenging HLW dataset and two existing benchmark datasets.
Neoadjuvant chemotherapy for ovarian cancer. (2005)

Primary debulking surgery by a gynecologic oncologist remains the standard of care in advanced ovarian cancer. Optimal debulking surgery should be defined as no residual tumor load. In retrospective analyses, neoadjuvant chemotherapy followed by interval debulking surgery does not seem to worsen prognosis compared to primary debulking surgery followed by chemotherapy. However, we will have to wait for the results of future randomized trials to know whether neoadjuvant chemotherapy followed by interval debulking surgery is as good as primary debulking surgery in stage IIIC and IV patients. Interval debulking is defined as an operation performed after a short course of induction chemotherapy. Based on the randomized European Organization for Research and Treatment of Cancer-Gynecological Cancer Group (EORTC-GCG) trial, interval debulking by an experienced surgeon improves survival in some patients who did not undergo optimal primary debulking surgery. Based on Gynecologic Oncology Group (GOG) 152 data, interval debulking surgery does not seem to be indicated in patients who underwent primarily a maximal surgical effort by a gynecologic oncologist. Open laparoscopy is probably the most valuable tool for evaluating the operability primarily or at the time of interval debulking surgery.
Single-Cell in Situ RNA Analysis With Switchable Fluorescent Oligonucleotides (2018)

Comprehensive RNA analyses in individual cells in their native spatial contexts promise to transform our understanding of normal physiology and disease pathogenesis. Here we report a single-cell <i>in situ</i> RNA analysis approach using switchable fluorescent oligonucleotides (SFO). In this method, transcripts are first hybridized by pre-decoding oligonucleotides. These oligonucleotides subsequently recruit SFO to stain their corresponding RNA targets. After fluorescence imaging, all the SFO in the whole specimen are simultaneously removed by DNA strand displacement reactions. Through continuous cycles of target staining, fluorescence imaging, and SFO removal, a large number of different transcripts can be identified by unique fluorophore sequences and visualized at the optical resolution. To demonstrate the feasibility of this approach, we show that the hybridized SFO can be efficiently stripped by strand displacement reactions within 30 min. We also demonstrate that this SFO removal process maintains the integrity of the RNA targets and the pre-decoding oligonucleotides, and keeps them hybridized. Applying this approach, we show that transcripts can be restained in at least eight hybridization cycles with high analysis accuracy, which theoretically would enable the whole transcriptome to be quantified at the single molecule sensitivity in individual cells. This <i>in situ</i> RNA analysis technology will have wide applications in systems biology, molecular diagnosis, and targeted therapies.