gebhart/patrepeval huggingface dataset:
Prostaglandin E2 mediates sensory nerve regulation of bone homeostasis (2019)

Whether sensory nerve can sense bone density or metabolic activity to control bone homeostasis is unknown. Here we found prostaglandin E2 (PGE2) secreted by osteoblastic cells activates PGE2 receptor 4 (EP4) in sensory nerves to regulate bone formation by inhibiting sympathetic activity through the central nervous system. PGE2 secreted by osteoblasts increases when bone density decreases as demonstrated in osteoporotic animal models. Ablation of sensory nerves erodes the skeletal integrity. Specifically, knockout of the EP4 gene in the sensory nerves or cyclooxygenase-2 (COX2) in the osteoblastic cells significantly reduces bone volume in adult mice. Sympathetic tone is increased in sensory denervation models, and propranolol, a β2-adrenergic antagonist, rescues bone loss. Furthermore, injection of SW033291, a small molecule to increase PGE2 level locally, significantly boostes bone formation, whereas the effect is obstructed in EP4 knockout mice. Thus, we show that PGE2 mediates sensory nerve to control bone homeostasis and promote regeneration.
Expression Profiling of t(12;22) Positive Clear Cell Sarcoma of Soft Tissue Cell Lines Reveals Characteristic Up-Regulation of Potential New Marker Genes Including ERBB3 (2004)

Clear cell sarcoma of soft tissue (CCSST), also known as malignant melanoma of soft parts, represents a rare lesion of the musculoskeletal system usually affecting adolescents and young adults. CCSST is typified by a chromosomal t(12;22)(q13;q12) translocation resulting in a fusion between the Ewing sarcoma gene (EWSR1) and activating transcription factor 1 (ATF1), of which the activity in nontransformed cells is regulated by cyclic AMP. Our aim was to identify critical differentially expressed genes in CCSST tumor cells in comparison with other solid tumors affecting children and young adults to better understand signaling pathways regulating specific features of the development and progression of this tumor entity. We applied Affymetrix Human Genome U95Av2 oligonucleotide microarrays representing approximately 12,000 genes to generate the expression profiles of the CCSST cell lines GG-62, DTC-1, KAO, MST2, MST3, and Su-CC-S1 in comparison with 8 neuroblastoma, 7 Ewing tumor, and 6 osteosarcoma cell lines. Subsequent hierarchical clustering of microarray data clearly separated all four of the tumor types from each other and identified differentially expressed transcripts, which are characteristically up-regulated in CCSST. Statistical analysis revealed a group of 331 probe sets, representing approximately 300 significant (P < 0.001) differentially regulated genes, which clearly discriminated between the CCSST and other tumor samples. Besides genes that were already known to be highly expressed in CCSST, like S100A11 (S100 protein) or MITF (microphthalmia-associated transcription factor), this group shows an obvious portion of genes that are involved in cyclic AMP response or regulation, in pigmentation processes, or in neuronal structure and signaling. Comparison with other expression profile analyses on neuroectodermal childhood tumors confirms the high robustness of this strategy to characterize tumor entities based on their gene expression. We found the avian erythroblastic leukemia viral oncogene homologue 3 (ERBB3) to be one of the most dramatically up-regulated genes in CCSST. Quantitative real-time PCR and Northern blot analysis verified the mRNA abundance and confirmed the absence of the inhibitory transcript variant of this gene. The protein product of the member of the epidermal growth factor receptor family ERBB3 could be shown to be highly present in all of the CCSST cell lines investigated, as well as in 18 of 20 primary tumor biopsies. In conclusion, our data demonstrate new aspects of the phenotype and the biological behavior of CCSST and reveal ERBB3 to be a useful diagnostic marker.
Measuring Expectations About College Adjustment (1992)

Research on an instrument designed to measure matriculating students' expectations or level of confidence regarding their capacity for adjusting to college shows the instrument to be reliable and predictably related to a variety of pre- and postmatriculation self-report data and real-life behaviors. Uses of the instrument in high school as well as college are considered.
A new objective metric to predict image quality using deep neural networks (2018)

Quality assessment of images is of key importance for mulmedia applications. In this paper we present a new full reference objective metric to predict the quality of images using deep neural networks. The network makes use of both the color as well as frequency information extracted from reference and distorted images. Our method comprises of extracting a number of equal sized random patches from the reference image and the corresponding patches from the distorted image, then feeding the patches themselves as well as their 3-scale wavelet transform coefficients as input to a neural network. The architecture of the network consists of four branches, with the first three generating frequency features and the fourth extracting color features. Feature extraction is carried out using 12 to 15 convolutional layers and one pooling layer, while two fully connected layers are used for regression. The overall image quality is computed as a weighted sum of patch scores, where local weights are also learned by the network using two additional fully connected layers. The network was trained using TID2013 and tested on TID2013, CSIQ and LIVE image databases. Our results show high correlations with subjective test scores, are generalizable for certain types of distortions and are competitive with respect to the state-of-the-art methods.
Hepatocyte Growth Factor Stimulates Proliferation of Respiratory Epithelial Cells during Postpneumonectomy Compensatory Lung Growth in Mice (2002)

Although it is known that the lung undergoes compensatory growth after pulmonary resection, mechanisms by which lung cells exhibit compensatory proliferation are not well defined. We investigated the involvement of hepatocyte growth factor (HGF) in postpneumonectomy compensatory lung regeneration in mice, because HGF has mitogenic and morphogenic actions on lung epithelial cells. Following left pneumonectomy, alveolar and airway epithelial cells underwent compensatory DNA synthesis, reaching maximal levels 5 d after the surgery. Before changes in DNA synthesis in lung epithelial cells, expression of HGF mRNA and protein levels in the remaining lung, liver, and kidney were changed in response to left pneumonectomy, and these changes were associated with postoperative increases in plasma HGF levels. c-Met/HGF receptor expression was localized predominantly in alveolar type II and airway epithelial cells, whereas c-Met/HGF receptor mRNA expressions were transiently upregulated before the peak in lung DNA synthesis. Neutralization of endogenous HGF by an antibody in pneumonectomized mice suppressed the compensatory DNA synthesis in lung epithelial cells, whereas administration of recombinant HGF to pneumonectomized mice stimulated DNA synthesis in lung epithelial cells. These results strongly suggest that HGF has a role as a pulmotrophic factor in postpneumonectomy compensatory lung regeneration.
Cofilin peptide homologs interfere with immunological synapse formation and T cell activation (2004)

The formation of supramolecular activation clusters within the immunological synapse, crucial for sustained signaling and T lymphocyte activation, requires costimulation-dependent reorganization of the actin cytoskeleton. Here we have identified the actin-remodeling protein cofilin as a key player in this process. Cell-permeable peptides that block costimulation-induced cofilin/F-actin interactions in untransformed human T lymphocytes impair receptor capping and immunological synapse formation at the interface between T cells and antigen-presenting cells. As a consequence, T cell activation, as measured by cytokine production and proliferation, is inhibited.
Transforming growth factor-beta 1 mediates mast cell chemotaxis. (1994)

It remains unknown which factor(s) control mast cell recruitment in chronic immune reactions. Although TGF-beta has been shown to function as a potent chemotactic factor for monocytes, fibroblasts, and neutrophils, its effect on mast cells has not been previously determined. In this study, TGF-beta 1 was shown to cause directed migration of cultured mouse mast cells at femtomolar concentrations, with a maximal chemotactic response observed at 25 fM. Moreover, chemotaxis to TGF-beta was also seen using freshly isolated rat peritoneal mast cells. Addition of neutralizing Ab to TGF-beta abrogated its chemotactic activity for both freshly isolated rat peritoneal mast cells and cultured mouse mast cells, whereas an irrelevant species-matched control Ab had no effect. Checkerboard analysis confirmed the mast cell chemotactic activity after exposure to concentration gradients of TGF-beta. Mast cells were observed to undergo rapid and extensive shape changes on exposure to TGF-beta, assuming a polarized morphology in preparation for migration. Other known mast cell chemoattractants including laminin, c-kit ligand, and IL-3 were found to be considerably less potent on a molar basis in inducing directed migration. Affinity cross-linking studies identified TGF-beta binding proteins with M(r) at 70 and 288 kDa, consistent with types I and III TGF-beta receptors on the mast cells. In summary, TGF-beta is the most potent chemoattractant described for mast cells and conceivably relevant, because pathologic processes mediated by TGF-beta are often associated with mast cell accumulation.
Polyurethane Elastomer Biostability (1995)

Polyurethanes have unique mechanical and biologic properties that make them ideal for many implantable devices. They are subject to some in vivo degradation mechanisms, however. Polyester polyurethanes are subject to hydrolytic degradation and are no longer used in long-term implanted devices. Polyether polyurethanes, while hydrolytically stable, are subject to oxidative degradation in several forms, including environmental stress cracking and metal ion oxidation. Mineralization is also known to occur. A new polycarbonate polyurethane has superior biostability in early in vivo qualification tests compared to the polyether polyurethanes, including no evidence of hydrolysis, ESC or MIO.
Reactive Astrocytosis from Excitotoxic Injury in Hippocampal Organ Culture Parallels that Seen in Vivo (1997)

Reactive astrocytes influence not only the severity of brain injury, but also the capacity of brain to reshape itself with learning. Mechanisms responsible for astrogliosis remain unknown but might be best studied in vitro, where improved access and visualization permit application of modern molecular and cellular techniques. We have begun to explore whether gliosis might be studied in hippocampal organotypic cultures (HOTCs), where potential cell-to-cell interactions are preserved and the advantages of an in vitro preparation are still realized. Following HOTC exposure to N-methyl-D-aspartate (NMDA), dose-dependent changes occurred in the optical density (OD) values for the astrocytic immunohistochemical [immunostaining (IS)] markers glial fibrillary acidic protein (GFAP) and vimentin. Exposure of HOTCs to NMDA (10 microM) caused selective death in the CA1 hippocampal region and the dentate gyrus. It also significantly increased GFAP IS and vimentin IS OD values in these regions. Increased GFAP IS and vimentin IS OD values were also seen in CA3, a hippocampal region that displayed no cell death. Light microscopic examination revealed hypertrophied GFAP and vimentin IS cells, characteristic of reactive astrocytes. Cellular proliferation, as assessed by proliferating cell nuclear antigen IS, was also significantly increased in all three of these hippocampal regions. In contrast, exposure of HOTCs to a noninjurious level of NMDA (1 microM) caused only minor changes in GFAP IS and vimentin IS OD values but a significantly reduced cellular proliferation in all HOTC regions. These results show that reactive astrocytosis from excitotoxic injury of HOTC parallels changes seen in vivo after global ischemia. Furthermore, since resting astroglia within HOTCs are also similar to their counterparts in vivo, HOTCs may be used to examine mechanisms by which these cells are transformed into reactive species within tissue that resembles intact brain.
Conversion of Xylose to Furfural Using Lewis and Brønsted Acid Catalysts in Aqueous Media (2012)

The role of molecular structure on pentose dehydration to furfural has been examined using HCl as a Brønsted acid catalyst in a single phase aqueous media. It is shown that xylulose dehydration results in a much higher furfural yield than xylose dehydration under similar reaction conditions. Furthermore, a cascade of reactions for the efficient conversion of xylose to furfural in a single pot reactor is presented whereby a Lewis acid, CrCl3, is used to isomerize xylose to xylulose, and a Brønsted acid, HCl, is employed to dehydrate xylulose to furfural. Using the combination of Lewis and Brønsted acids, a furfural yield of ∼39% is achieved compared to ∼29% using HCl alone, at a moderate reaction temperature (∼418 K) in a single aqueous phase, with an associated decrease in the residence time by a factor of 5. With this combined catalyst functionalities, a much higher yield (76%) to furfural can be obtained in a biphasic system at low temperatures and short times. Aside from increasing performance, our results indicate that the combined Lewis and Brønsted acids change the pathway for the conversion of xylose to furfural compared to carrying out the reaction in Brønsted acids alone.
Analysis of a cDNA clone expressing a human autoimmune antigen: full-length sequence of the U2 small nuclear RNA-associated B" antigen. (1987)

A U2 small nuclear RNA-associated protein, designated B'', was recently identified as the target antigen for autoimmune sera from certain patients with systemic lupus erythematosus and other rheumatic diseases. Such antibodies enabled us to isolate cDNA clone lambda HB''-1 from a phage lambda gt11 expression library. This clone appeared to code for the B'' protein as established by in vitro translation of hybrid-selected mRNA. The identity of clone lambda HB''-1 was further confirmed by partial peptide mapping and analysis of the reactivity of the recombinant antigen with monospecific and monoclonal antibodies. Analysis of the nucleotide sequence of the 1015-base-pair cDNA insert of clone lambda HB''-1 revealed a large open reading frame of 800 nucleotides containing the coding sequence for a polypeptide of 25,457 daltons. In vitro transcription of the lambda HB''-1 cDNA insert and subsequent translation resulted in a protein product with the molecular size of the B'' protein. These data demonstrate that clone lambda HB''-1 contains the complete coding sequence of this antigen. The deduced polypeptide sequence contains three very hydrophilic regions that might constitute RNA binding sites and/or antigenic determinants. These findings might have implications both for the understanding of the pathogenesis of rheumatic diseases as well as for the elucidation of the biological function of autoimmune antigens.
Coxsackie‐and‐adenovirus receptor mRNA expression in human heart failure (2003)

Abstract Background Adenoviral vectors are widely used as gene‐transfer vehicles in experimental and clinical studies. Since virus incorporation and transfection efficacy depend to a large extent on the concentration of the coxsackie‐and‐adenovirus (CAR) receptor on target cells the aim of this study was to quantify the CAR‐receptor concentration in various human cardiomyopathies. Methods After RNA isolation from myocardial biopsies obtained during surgical procedures, cDNA was generated by reverse transcription. The relative RNA content was analyzed by quantitative PCR using glyceraldehydes‐3‐phosphate dehydrogenase (GAPDH) as a standard reference. The cardiomyopathies (CM) analyzed were categorized according to their etiology in dilated CM (DCM, n = 28), ischemic CM (ICM, n = 52), CM in mitral valve disease (MVCM, n = 32) and aortic valve disease (AVCM, n = 32). Data were related to non‐cardiomyopathic tissue from donor hearts (non‐CM, n = 64). Results Compared with non‐CM hearts DCM showed a 34‐fold (±5.4) increase in CAR mRNA concentration, in ICM CAR mRNA was elevated by a factor of 12 (±4.3), in MVCM by 27 (±7) and AVCM by factor 47 (±9.3) (ANOVA p &lt; 0.001). Compared with the expression in rat hearts CAR levels were found to be similar to those in human ICM. Conclusions These results show that cardiomyopathies associated with heart failure transcribe substantially higher levels – on average by a factor of 30 – of CAR‐mRNA than non‐failing control hearts. Myocardial gene transfer using adenoviral vectors should therefore be facilitated in human cardiomyopathies and may present a promising approach for therapeutic interventions. Copyright © 2003 John Wiley &amp; Sons, Ltd.
Characterization of a novel fusion geneEML4-NTRK3in a case of recurrent congenital fibrosarcoma (2015)

Abstract We describe the clinical course of a recurrent case of congenital fibrosarcoma diagnosed in a 9-mo-old boy with a history of hemimelia. Following complete surgical resection of the primary tumor, the patient subsequently presented with bulky bilateral pulmonary metastases 6 mo following surgery. Molecular characterization of the tumor revealed the absence of the prototypical ETV6-NTRK3 translocation. However, tumor characterization incorporating cytogenetic, array comparative genomic hybridization, and RNA sequencing analyses, revealed a somatic t(2;15)(2p21;15q25) translocation resulting in the novel fusion of EML4 with NTRK3 . Cloning and expression of EML4-NTRK3 in murine fibroblast NIH 3T3 cells revealed a potent tumorigenic phenotype as assessed in vitro and in vivo. These results demonstrate that multiple fusion partners targeting NTRK3 can contribute to the development of congenital fibrosarcoma.
Isolation of cDNA for a human granulocyte-macrophage colony-stimulating factor by functional expression in mammalian cells. (1985)

A cDNA sequence coding for a human granulocyte-macrophage colony-stimulating factor has been isolated from cDNA libraries prepared from mRNA derived from concanavalin A-activated human T-cell clones. The libraries constructed in the pcD vector system were screened by transfecting COS-7 monkey cells with DNA pools to express the products encoded by full-length cDNA inserts. By assaying the cell supernatants, we identified clones encoding a factor that stimulates the formation of granulocyte and macrophage colonies from human progenitor cells. These results demonstrate that identification of full-length cDNAs for many colony-stimulating factors may be achieved entirely on the basis of detecting the functional polypeptide produced in mammalian cells.
The synthesis of XTT: A new tetrazolium reagent that is bioreducible to a water‐soluble formazan (1988)

Abstract A new tetrazolium salt, XTT, has been synthesized. XTT is reduced by a considerable variety of cell lines to a water‐soluble formazan. XTT appears to merit further investigation as a reagent for broader application to cell culture assay systems.
Stable Encapsulation of Air in Mesoporous Silica Nanoparticles: Fluorocarbon‐Free Nanoscale Ultrasound Contrast Agents (2016)

While gas-filled micrometer-sized ultrasound contrast agents vastly improve signal-to-noise ratios, microbubbles have short circulation lifetimes and poor extravasation from the blood. Previously reported fluorocarbon-based nanoscale contrast agents are more stable but their contrast is generally lower owing to their size and dispersity. The contrast agents reported here are composed of silica nanoparticles of ≈100 nm diameter that are filled with ≈3 nm columnar mesopores. Functionalization of the silica surface with octyl groups and resuspension with Pluronic F127 create particles with pores that remain filled with air but are stable in buffer and serum. Administration of high intensity focused ultrasound (HIFU) allows sensitive imaging of the silica nanoparticles down to 10(10) particles mL(-1) , with continuous imaging for at least 20 min. Control experiments with different silica particles supported the hypothesis that entrapped air could be pulled into bubble nuclei, which can then in turn act as acoustic scatterers. This process results in very little hemolysis in whole blood, indicating potential for nontoxic blood pool imaging. Finally, the particles are lyophilized and reconstituted or stored in PBS (phosphate-buffered saline, at least for four months) with no loss in contrast, indicating stability to storage and reformulation.
GDNF: a Potent Survival Factor for Motoneurons Present in Peripheral Nerve and Muscle (1994)

For survival, embryonic motoneurons in vertebrates depend on as yet undefined neurotrophic factors present in the limb bud. Members of the neurotrophin family are currently the best candidates for such neurotrophic factors, but inactivation of their receptor genes leads to only partial loss of motoneurons, which suggests that other factors are involved. Glial cell line-derived neurotrophic factor (GDNF), originally identified as a trophic factor specific for dopaminergic neurons, was found to be 75-fold more potent than the neurotrophins in supporting the survival of purified embryonic rat motoneurons in culture. GDNF messenger RNA was found in the immediate vicinity of motoneurons during the period of cell death in development. In vivo, GDNF rescues and prevents the atrophy of facial motoneurons that have been deprived of target-derived survival factors by axotomy. GDNF may therefore be a physiological trophic factor for spinal motoneurons. Its potency and specificity in vitro and in vivo also make it a good candidate for treatment of motoneuron disease.
Wall-associated kinase 1 (WAK1) is crosslinked in endomembranes, and transport to the cell surface requires correct cell-wall synthesis (2006)

The Arabidopsis thaliana wall-associated kinases (WAKs) bind to pectin with an extracellular domain and also contain a cytoplasmic protein kinase domain. WAKs are required for cell elongation and modulate sugar metabolism. This work shows that in leaf protoplasts a WAK1-GFP fusion protein accumulates in a cytoplasmic compartment that contains pectin. The WAK compartment contains markers for the Golgi, the site of pectin synthesis. The migration of WAK1-GFP to the cell surface is far slower than that of a cell surface receptor not associated with the cell wall, is influenced by the presence of fucose side chains on one or more unidentified molecules that might include pectin, and is dependent upon cellulose synthesis on the plasma membrane. WAK is crosslinked into a detergent-insoluble complex within the cytoplasmic compartment before it appears on the cell surface, and this is independent of fucose modification or cellulose synthesis. Thus, the assembly and crosslinking of WAKs may begin at an early stage within a cytoplasmic compartment rather than in the cell wall itself, and is coordinated with synthesis of surface cellulose.
HighSpeed TCP for Large Congestion Windows (2002)

This document proposes HighSpeed TCP, a modification to TCP&amp;apos;s congestion control mechanism for use with TCP connections with large congestion windows. The congestion control mechanisms of the current Standard TCP constrains the congestion windows that can be achieved by TCP in realistic environments. For example, for a Standard TCP connection with 1500-byte packets and a 100 ms round-trip time, achieving a steady-state throughput of 10 Gbps would require an average congestion window of 83,333 segments, and a packet drop rate of at most one congestion event every 5,000,000,000 packets (or equivalently, at most one congestion event every 1 2/3 hours). This is widely acknowledged as an unrealistic constraint. To address this limitation of TCP, this document proposes HighSpeed TCP, and solicits experimentation and feedback from the wider community.