gebhart/patrepeval huggingface dataset:
Platelet-derived growth factor and its receptors in human glioma tissue: expression of messenger RNA and protein suggests the presence of autocrine and paracrine loops. (1992)

The expression of platelet-derived growth factor (PDGF) and its receptors was analyzed in 14 gliomas of various degrees of malignancy and compared with three gliosis cases by in situ hybridization and immunohistochemistry techniques. Expression of both PDGF A- and B-chains was higher in glioblastomas than in astrocytomas. The PDGF A-chain mRNA was predominantly found in cell-rich areas in glioblastomas. The cognate PDGF-alpha receptor (PDGFR-alpha) mRNA was heterogeneously distributed in gliomas of all grades, and PDGFR-alpha expression was higher in gliomas than in gliosis. Within some glioblastomas probed with PDGFR-alpha complementary RNA, cells heavily loaded with grains were intermingled with others containing low or moderate signals. The heavily labeled cells were often found in the vicinity of proliferating capillaries. Immunostaining with an anti-PDGF antibody and an affinity-purified antiserum against the PDGFR-alpha showed strong staining of most tumor cells with both antibodies in glioblastoma. In addition, the PDGFR-alpha antibodies yielded a strong staining of scattered cells, and the anti-PDGF antibody yielded staining of a few cells within the astrocytoma. Furthermore, high levels of the PDGF-beta receptor (PDGFR-beta) and PDGF B-chain mRNA as well as the beta receptor protein were found in hyperplastic capillaries. These results suggest the presence of autocrine and paracrine loops in glioma, activating the PDGFR-alpha in glioma cells and the PDGFR-beta in endothelial cells.
Intense vascular sprouting from rat femoral vein induced by prostaglandins E1 and E2 (1994)

The formation of new capillaries from the rat femoral vein was specifically explored to assess whether venous vessels of this caliber may participate in the process of angiogenesis. Prostaglandins of the E series (PGE1 and PGE2) were administered into the soft connective tissue surrounding the rat femoral vessels as angiogenic inducers. In these conditions, between 2 and 7 days, a great number of new capillaries were observed in the media of the femoral vein, arising from the endothelial cells (EC) in the intima. The events of the capillary growth from the femoral vein included EC activation, local degradation of the basal membrane followed by migration and proliferation of EC, solid sprout formation with posterior canalization, development of a new basal membrane, and appearance of pericytes around the new capillary. Although numerous vascular buds were also observed arising from the small venules and capillaries in the periadventitial tissues, they were separated at first from those in the media of the femoral vein by the venous adventitia. Later, connections were observed between both newly formed microcirculations. The present study shows the capacity of PGE1 and PGE2 in the extravascular position of inducing capillary sprouting from veins. Furthermore, the observations provide greater evidence that vessels with characteristics similar to those of the rat femoral vein may contribute to angiogenesis, on occasion with an intense neovascularization. This fact may be of interest for the establishment of a functional circulation after angiogenesis by anastomoses of the new capillaries with those arising from pre-existing vessels of greater caliber than the venules.
Fatty Acid-responsive Control of mRNA Stability (1996)

The Saccharomyces cerevisiae OLE1 gene encodes the Delta-9 fatty acid desaturase, a highly regulated integral membrane enzyme involved in the formation of unsaturated fatty acids from saturated acyl-coenzyme A precursors. The mRNA levels of the OLE1 gene are regulated by at least two independent control systems that respond to nutrient fatty acids. One involves the unsaturated fatty acid repression of OLE1 transcription; the second, described in this report, involves unsaturated fatty acid-responsive changes in the half-life of the OLE1 mRNA. Measurements of OLE1 mRNA half-life indicate that it is a moderately stable species (t1/2 = 10 +/- 1.5 min) in cells grown in medium without exogenous fatty acids. Its half-life is drastically reduced (t1/2 < 2.5 min), in a time-dependent manner, following the addition of unsaturated fatty acids to the growth medium. Saturated fatty acids that have previously been shown to increase activation of OLE1 transcription do not regulate its mRNA stability. Inhibition of translation, by the addition of cycloheximide, slows the nucleolytic degradation of the OLE1 mRNA and blocks the unsaturated fatty acid-triggered reduction in its half-life. This suggests an intimate link between the two processes of mRNA decay and protein synthesis. A chimeric mRNA, produced by replacing the upstream activation and fatty acid-regulated regions of the OLE1 promoter with the GAL1 promoter sequences is destabilized by exogenous unsaturated fatty acids. A similar chimera under GAL1 control that replaces the OLE1 mRNA 5'-untranslated region with GAL1 sequences is not regulated by unsaturated fatty acids. These results suggest that the 5'-untranslated region of the OLE1 mRNA contains sequence elements required for fatty acid-triggered destabilization. Disruption of the XRN1 gene, which encodes a 5' --> 3'-exoribonuclease, results in an approximate 4-fold increase in OLE1 mRNA half-life in the absence of fatty acids. Its half-life is reduced when those cells are exposed to unsaturated fatty acids, indicating that the 5'-exoribonuclease encoded by the XRN1 gene is required for the rapid degradation of the OLE1 transcript but is not required for fatty acid-induced destabilization.
Chemically Functionalized Water Soluble Single-Walled Carbon Nanotubes Modulate Neurite Outgrowth (2005)

We report the use of chemically-functionalized water soluble single-walled carbon nanotube (SWNT) graft copolymers for modulation of outgrowth of neuronal processes. The graft copolymers were prepared by the functionalization of SWNTs with poly-m-aminobenzene sulphonic acid and polyethylene glycol. When added to the culturing medium, these functionalized water soluble SWNTs were able to increase the length of various neuronal processes.
Comparison of Cellular Binding and Uptake of Antisense Phosphodiester, Phosphorothioate, and Mixed Phosphorothioate and Methylphosphonate Oligonucleotides (1993)

The effects of phosphorothioate (S-oligonucleotide) or terminal phosphorothioate-phosphodiester (S-O-oligonucleotides) or methylphosphonate-phosphodiester (MP-O-oligonucleotides) modifications on mouse spleen cell surface binding, uptake, and degradation were studied using fluorescein (FITC)-conjugated oligonucleotides. S-oligonucleotides had the highest cell binding and uptake, followed by S-O-, O-, and MP-O-oligonucleotides. Competition studies indicated that S-oligonucleotides have an increased affinity for cell membrane oligonucleotide binding sites, because they could completely block O-oligonucleotide binding at a molar ratio of just 0.1. Uptake of all oligonucleotides was higher in B cells than T cells and was increased by stimulation with the B-cell mitogen, lipopolysaccharide. Although our cells had been purified using conventional techniques to eliminate dead cells, there remained about 5% of cells that were dead or dying, as determined by flow cytometry using propidium iodide staining. Of note, oligonucleotide association with dead cells was approximately 50-fold greater than that with living cells. Confocal microscopy confirmed that the oligonucleotides in living cells were intracellular, and indicated little nuclear uptake by 4 h. While extensive degradation of intracellular O-oligonucleotides was apparent by 4 h, there was no detectable degradation of S-, S-O, or MP-O-oligonucleotides.
Fetal liver hematopoietic stem cell niches associate with portal vessels (2015)

Whereas the cellular basis of the hematopoietic stem cell (HSC) niche in the bone marrow has been characterized, the nature of the fetal liver niche is not yet elucidated. We show that Nestin(+)NG2(+) pericytes associate with portal vessels, forming a niche promoting HSC expansion. Nestin(+)NG2(+) cells and HSCs scale during development with the fractal branching patterns of portal vessels, tributaries of the umbilical vein. After closure of the umbilical inlet at birth, portal vessels undergo a transition from Neuropilin-1(+)Ephrin-B2(+) artery to EphB4(+) vein phenotype, associated with a loss of periportal Nestin(+)NG2(+) cells and emigration of HSCs away from portal vessels. These data support a model in which HSCs are titrated against a periportal vascular niche with a fractal-like organization enabled by placental circulation.
Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers (2021)

PD-1 blockade unleashes CD8 T cells<sup>1</sup>, including those specific for mutation-associated neoantigens (MANA), but factors in the tumour microenvironment can inhibit these T cell responses. Single-cell transcriptomics have revealed global T cell dysfunction programs in tumour-infiltrating lymphocytes (TIL). However, the majority of TIL do not recognize tumour antigens<sup>2</sup>, and little is known about transcriptional programs of MANA-specific TIL. Here, we identify MANA-specific T cell clones using the MANA functional expansion of specific T cells assay<sup>3</sup> in neoadjuvant anti-PD-1-treated non-small cell lung cancers (NSCLC). We use their T cell receptors as a 'barcode' to track and analyse their transcriptional programs in the tumour microenvironment using coupled single-cell RNA sequencing and T cell receptor sequencing. We find both MANA- and virus-specific clones in TIL, regardless of response, and MANA-, influenza- and Epstein-Barr virus-specific TIL each have unique transcriptional programs. Despite exposure to cognate antigen, MANA-specific TIL express an incompletely activated cytolytic program. MANA-specific CD8 T cells have hallmark transcriptional programs of tissue-resident memory (TRM) cells, but low levels of interleukin-7 receptor (IL-7R) and are functionally less responsive to interleukin-7 (IL-7) compared with influenza-specific TRM cells. Compared with those from responding tumours, MANA-specific clones from non-responding tumours express T cell receptors with markedly lower ligand-dependent signalling, are largely confined to HOBIT<sup>high</sup> TRM subsets, and coordinately upregulate checkpoints, killer inhibitory receptors and inhibitors of T cell activation. These findings provide important insights for overcoming resistance to PD-1 blockade.
Feature Extraction with Convolutional Neural Networks for Handwritten Word Recognition (2013)

In this paper, we show that learning features with convolutional neural networks is better than using hand-crafted features for handwritten word recognition. We consider two kinds of systems: a grapheme based segmentation and a sliding window segmentation. In both cases, the combination of a convolutional neural network with a HMM outperform a state-of-the art HMM system based on explicit feature extraction. The experiments are conducted on the Rimes database. The systems obtained with the two kinds of segmentation are complementary: when they are combined, they outperform the systems in isolation. The system based on grapheme segmentation yields lower recognition rate but is very fast, which is suitable for specific applications such as document classification.
Restoration of Physiologically Responsive Low-Density Lipoprotein Receptor-Mediated Endocytosis in Genetically Deficient Induced Pluripotent Stem Cells (2015)

Acquiring sufficient amounts of high-quality cells remains an impediment to cell-based therapies. Induced pluripotent stem cells (iPSC) may be an unparalleled source, but autologous iPSC likely retain deficiencies requiring correction. We present a strategy for restoring physiological function in genetically deficient iPSC utilizing the low-density lipoprotein receptor (LDLR) deficiency Familial Hypercholesterolemia (FH) as our model. FH fibroblasts were reprogrammed into iPSC using synthetic modified mRNA. FH-iPSC exhibited pluripotency and differentiated toward a hepatic lineage. To restore LDLR endocytosis, FH-iPSC were transfected with a 31 kb plasmid (pEHZ-LDLR-LDLR) containing a wild-type LDLR (FH-iPSC-LDLR) controlled by 10 kb of upstream genomic DNA as well as Epstein-Barr sequences (EBNA1 and oriP) for episomal retention and replication. After six months of selective culture, pEHZ-LDLR-LDLR was recovered from FH-iPSC-LDLR and transfected into Ldlr-deficient CHO-a7 cells, which then exhibited feedback-controlled LDLR-mediated endocytosis. To quantify endocytosis, FH-iPSC ± LDLR were differentiated into mesenchymal cells (MC), pretreated with excess free sterols, Lovastatin, or ethanol (control), and exposed to DiI-LDL. FH-MC-LDLR demonstrated a physiological response, with virtually no DiI-LDL internalization with excess sterols and an ~2-fold increase in DiI-LDL internalization by Lovastatin compared to FH-MC. These findings demonstrate the feasibility of functionalizing genetically deficient iPSC using episomal plasmids to deliver physiologically responsive transgenes.
Human Umbilical Cord Blood–Derived CD133+ Cells Enhance Function and Repair of the Infarcted Myocardium (2005)

The use of adult stem cells for myocardial tissue repair might be limited in elderly and sick people because their cells are depleted and exhausted. The present study was conducted to explore the potential of human umbilical cord blood (UCB) CD133+ progenitor cells for myocardial tissue repair in a model of extensive myocardial infarction (MI). CD133+ progenitor cells were isolated from newborn UCB. Cells (1.2-2 x 10(6)) or saline (control) was infused intravenously 7 days after permanent coronary artery ligation in athymic nude rats. Left ventricular (LV) function was assessed before and 1 month after infusion by echocardiography. Tracking of human cells was performed by fluorescent in situ hybridization for human X and Y chromosomes or by immunostaining for HLA-DR or HLA-ABC. One month after delivery, LV fractional shortening improved by 42 +/- 17% in cell-treated hearts and decreased by 39 +/- 10% in controls (p = .001). Anterior wall thickness decreased significantly in controls but not in treated hearts. Microscopic examination revealed that the UCB cells were able to migrate, colonize, and survive in the infarcted myocardium. Human cells were identified near vessel walls and LV cavity and were occasionally incorporated into endothelial cells in six of nine cell-treated animals but not in controls. Scar tissue from cell-treated animals was significantly populated with autologous myofibroblasts as indicated by colocalization of HLA-DR and alpha-smooth muscle actin staining. In conclusion, the present work suggests that, after MI, intravenous delivery of human UCB-derived CD133+ cells can produce functional recovery by preventing scar thinning and LV systolic dilatation.
Gene therapy strategies in glaucoma and application for steroid-induced hypertension (2011)

Gene therapy of the eye has a high potential of becoming the preferred treatment of a number of eye diseases. Because of its easy accessibility, all the tissues of the eye can be reached and genetically manipulated with nowadays standard gene delivery technologies. Gene therapy offers the possibility to do both, correct a genetic defect by replacing the mutated or missing gene and that of using genes as drugs. Gene drugs would be more specific and would have a longer duration of action and less toxicity than conventional drugs. Examples of both applications are beginning to emerge. Using gene replacement, vision has been restored in several patients of Leber congenital amaurosis (Maguire et al., 2009). Some gene drugs, such as siRNA, are currently in clinical trials to silence angiogenic factors in macular degeneration (Campa and Harding, 2011). In this manuscript we first give a short overview of the basics of gene therapy in the eye and then review the ongoing preclinical studies in our laboratory for the gene-drug treatment of steroid-induced ocular hypertension.
A model-based approach to correcting spectral irradiance data using an upward-looking airborne sensor (CASI ILS) (2001)

A number of aircraft sensors have the facility to measure spectral downwelling irradiance using a sensor mounted on the roof of the aircraft, but these data are rarely used for atmospheric correction. Part of the problem is that the attitude of the airborne platform is always changing during flight, even in stable conditions, so that direct use of data from an incident light sensor (ILS) can introduce errors into atmospheric correction methods. The continual motion of the ILS is used here to advantage, as a means to fit a sky radiance distribution model developed by Brunger and Hooper (1993) to data from the Itres Instruments CASI ILS. The inclination of the ILS sensor, due to changing aircraft attitude, is considered as\nthe slope plane in the model. The selected model coefficients correspond to parameterised atmospheric conditions and represent atmospheric transmission and the proportion of direct:diffuse flux. The method was used to correct CASI ILS data acquired over a site in southern England. Comparison with spectral irradiance measured simultaneously on the ground shows that the method reduced the variability of the ILS data and also compensated for the effect of different flight directions. The sky radiance distribution at sensor level is also calculated by\nthe model, and shows the characteristics of the sky conditions at the time of each flight.
Visually-guided adaptive robot (ViGuAR) (2011)

A neural modeling platform known as Cog ex Machina <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> (Cog) developed in the context of the DARPA SyNAPSE <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> program offers a computational environment that promises, in a foreseeable future, the creation of adaptive whole-brain systems subserving complex behavioral functions in virtual and robotic agents. Cog is designed to operate on low-powered, extremely storage-dense memristive hardware <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> that would support massively-parallel, scalable computations. We report an adaptive robotic agent, ViGuAR <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> , that we developed as a neural model implemented on the Cog platform. The neuromorphic architecture of the ViGuAR brain is designed to support visually-guided navigation and learning, which in combination with the path-planning, memory-driven navigation agent - MoNETA <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> - also developed at the Neuromorphics Lab at Boston University, should effectively account for a wide range of key features in rodents' navigational behavior.
Chromoatographic Methods for the Insolation of, and Refolding of Proteins forms, Escherichia coli Inclusion Bodies (2002)

Chromoatographic Methods for the Insolation of, and Refolding of Proteins forms, Escherichia coli Inclusion Bodies
Two-channel optical filtering of 1 Gbit/s signal with DBR filter (1991)

Distributed Bragg reflector (DBR) lasers have been used as tunable, narrow-band, amplifying optical filters and as tunable oscillators in two-channel, system experiments. A bit error rate of 10-9 with −25dBm input power has been measured at 1 Gbit/s signal rate.
Combinatorial diffusion assay used to identify topically active melanocyte-stimulating hormone receptor antagonists. (1995)

alpha-Melanocyte-stimulating hormone (alpha-MSH) is implicated in pigmentation, central nervous system and immune system functions, growth, mitogenesis, and melanoma. Evaluation of these roles has been hindered by the lack of alpha-MSH antagonists. A combinatorial chemistry-based diffusion assay is used to find random tripeptides that antagonize normal frog and human melanoma MSH receptors and to identify pharmacological groups responsible for receptor interaction. The alpha-MSH antagonist D-Trp-Arg-Leu-NH2 is used to demonstrate directly the contribution of MSH to normal skin tone in frogs following injection or topical application.
Luminescence and photophysics of cadmium sulfide semiconductor clusters: the nature of the emitting electronic state (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLuminescence and photophysics of cadmium sulfide semiconductor clusters: the nature of the emitting electronic stateN. Chestnoy, T. D. Harris, R. Hull, and L. E. BrusCite this: J. Phys. Chem. 1986, 90, 15, 3393–3399Publication Date (Print):July 1, 1986Publication History Published online1 May 2002Published inissue 1 July 1986https://pubs.acs.org/doi/10.1021/j100406a018https://doi.org/10.1021/j100406a018research-articleACS PublicationsRequest reuse permissionsArticle Views3107Altmetric-Citations653LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Upregulating promoter polymorphisms of RANTES relate to atopic dermatitis (2006)

It has been reported that a functional polymorphism in the promoter of the RANTES gene (-403G/A) is associated with atopic dermatitis in a German population. Although there are several reports on the association of RANTES promoter polymorphisms (-403G/A and -28C/G) with asthma, the association of these polymorphisms with atopic dermatitis has not yet been confirmed in other populations. We therefore aimed to test whether the RANTES promoter polymorphisms relate to atopic dermatitis in a well-defined Japanese population. We conducted an association study of upregulating promoter polymorphisms of RANTES (-403G/A and -28C/G) in 389 patients with atopic dermatitis and 177 healthy control subjects. There was a significant association between the upregulating variant of RANTES -28G and atopic dermatitis, while -403A variant showed a significant association with atopic dermatitis with high IgE productivity. These results support a role for RANTES promoter polymorphisms in susceptibility to atopic dermatitis.