gebhart/patrepeval huggingface dataset:
Thiazolidinedione Effects on Glucocorticoid Receptor-Mediated Gene Transcription and Differentiation in Osteoblastic Cells (1999)

The glucocorticoid receptor (GR) and peroxisome proliferator-activated receptors (PPARs) play important roles in the differentiation of mesenchymal cells. Glucocorticoids acting via the GR promote osteoblastic differentiation of bone marrow stromal cells, whereas PPAR ligands induce these cells to become adipocytes. To explore potential interactions between PPAR and GR pathways in osteoblasts, we studied the interaction between PPAR subtype-selective ligands and dexamethasone (DEX) in a murine calvaria-derived osteoblastic cell line (MB 1.8) that expresses endogenous GR and PPARs. In ligand-dependent transcription assays, the PPARgamma-selective ligand TZD [(5-(4-N-methyl-N(2-pyridyl)amino)ethoxy)benzyl)thiazolidine-2,4-dione], a thiazolidinedione antidiabetic, enhanced the effect of DEX to stimulate transcription of a glucocorticoid-inducible reporter gene (mouse mammary tumor virus-luciferase). No effect was seen with PPARalpha- or hNUC1/PPARdelta-selective ligands. The GR antagonist RU-486 inhibited the DEX and TZD responses, suggesting that the effects were mediated through endogenous GR. TZD also enhanced glucocorticoid-mediated transcription in SaOS-2/B10 human osteosarcomatous cells, but not in CV-1 cells, even though both cell lines were transfected with GR plasmid and expressed significant levels of endogenous PPARgamma messenger RNA. In MB 1.8 cells, TZD decreased alkaline phosphatase activity and the expression of osteoblast-associated genes while it up-regulated the adipocyte fatty acid-binding protein. DEX counteracted the effects of TZD on alkaline phosphatase enzyme activity and osteoblastic gene expression, but enhanced the actions of TZD on adipocyte fatty acid-binding protein. Interestingly, TZD inhibited in vitro bone nodule formation and mineralization, and DEX counteracted this effect. Thus, depending on the promoter context, TZD and DEX can oppose or enhance each other's actions on gene transcription. Collectively, these results point to a complex interaction between PPAR and GR signaling pathways that regulates the effects of TZD and DEX on osteoblastic differentiation. The mechanism of this interaction is still under investigation, but might involve PPAR -dependent and -independent pathways. As thiazolidinediones represent an important new class of drugs, our findings also raise the need for further studies in bone.
Stimulation of cell migration by overexpression of focal adhesion kinase and its association with Src and Fyn (1996)

Cellular interactions with the extracellular matrix proteins play important roles in a variety of biological processes. Recent studies suggest that integrin-mediated cell-matrix interaction can transduce biochemical signals across the plasma membrane to regulate cellular functions such as proliferation, differentiation and migration. These studies have implicated a critical role of focal adhesion kinase (FAK) in integrin-mediated signal transduction pathways. We report here that overexpression of FAK in CHO cells increased their migration on fibronectin. A mutation of the major autophosphorylation site Y397 in FAK abolished its ability to stimulate cell migration, while phosphorylation of Y397 in a kinase-defective FAK by endogenous FAK led to increased migration. We also find that the wild-type and the kinase-defective FAK were associated with Src and Fyn in CHO cells whereas the F397 mutant was not. These results directly demonstrate a functional role for FAK in integrin signaling leading to cell migration. They also provide evidence for the functional significance of FAK/Src complex formation in vivo.
ELK1 is up-regulated by androgen in bladder cancer cells and promotes tumor progression (2015)

Little is known about biological significance of ELK1, a transcriptional factor that activates downstream targets including c-fos proto-oncogene, in bladder cancer. Recent preclinical evidence also suggests the involvement of androgen receptor (AR) signaling in bladder cancer progression. In this study, we aim to investigate the functions of ELK1 in bladder cancer growth and their regulation by AR signals. Immunohistochemistry in bladder tumor specimens showed that the levels of phospho-ELK1 (p-ELK1) expression were significantly elevated in urothelial neoplasms, compared with non-neoplastic urothelium tissues, and were also correlated with AR positivity. Patients with p-ELK1-positive non-muscle-invasive and muscle-invasive tumors had significantly higher risks for tumor recurrence and progression, respectively. In AR-positive bladder cancer cell lines, dihydrotestosterone treatment increased ELK1 expression (mRNA, protein) and its nuclear translocation, ELK1 transcriptional activity, and c-fos expression, which was restored by an anti-androgen hydroxyflutamide. ELK1 silencing via short hairpin RNA (shRNA) resulted in decreases in cell viability/colony formation, and cell migration/invasion as well as an increase in apoptosis. Importantly, ELK1 appears to require activated AR to regulate bladder cancer cell proliferation, but not cell migration. Androgen also failed to significantly induce AR transactivation in ELK1-knockdown cells. In accordance with our in vitro findings, ELK1-shRNA expression considerably retarded tumor formation as well as its growth in xenograft-bearing male mice. Our results suggest that ELK1 plays an important role in bladder tumorigenesis and cancer progression, which is further induced by AR activation. Accordingly, ELK1 inhibition, together with AR inactivation, has the potential of being a therapeutic approach for bladder cancer.
Mechanisms of Inhibitory and Regulatory Effects of Methylenedioxyphenyl Compounds on Cytochrome P450-Dependent Drug Oxidation (2000)

Cytochrome P450 (CYP) enzymes catalyse the oxidative conversion of drugs and other lipophilic compounds to hydrophilic metabolites. Thus, CYPs play a dominant role in the elimination of drugs from the body. Inhibitory interactions occur when drugs compete for oxidation by specific CYPs whereas certain drugs increase the capacity for oxidative biotransformation by inducing the synthesis of new CYPs. Methylenedioxyphenyl (MDP) compounds have been widely employed as commercially important pesticide synergists and a number of derivatives are found in oils and spices. MDP compounds are of considerable toxicological significance because of their capacity to inhibit and induce CYP enzymes in mammals; some derivatives produce neurotoxic and hepatotoxic effects. Although there are relatively few therapeutic agents of present clinical importance that possess the MDP structural feature, the synthesis and preclinical evaluation of such agents appears to be increasing. In the context of the existing literature surrounding MDP compounds it is noteworthy that these potential drugs also elicit significant modulatory effects on CYP activities in rat and human liver. These developments indicate the importance of understanding the chemical mechanisms by which MDPs interact with CYPs. Thus, the presence of the MDP structure may undermine the potential clinical value of new drugs.
Biosynthesis of a Highly Stable Coiled-Coil Protein Containing Hexafluoroleucine in an Engineered Bacterial Host (2001)

Incorporation of nonnatural amino acid residues allows engineering&#13;\nof proteins with novel chemical functionality and unusual&#13;\nphysical properties. We have shown recently that coiled-coil&#13;\nproteins prepared in vivo can be stabilized significantly by&#13;\nreplacement of leucine by trifluoroleucine (1). In the same series&#13;\nof experiments, however, we were unsuccessful in our attempts&#13;\nto incorporate the more highly fluorinated analogue hexafluoroleucine&#13;\n(2). We report here that modification of the leucyl-tRNA&#13;\nsynthetase (LeuRS) activity of the host allows efficient incorporation&#13;\nof 2 into recombinant proteins prepared in Escherichia coli.&#13;\nFurthermore, the coiled-coil protein used to demonstrate incorporation&#13;\nof 2 exhibits enhanced stability in comparison to the&#13;\nsame protein enriched in 1, possibly due to the increased&#13;\nhydrophobic character of the additional trifluoromethyl group in&#13;\nthe protein core.
A continuous density neural tree network word spotting system (2002)

A new classifier is described that combines the discriminatory ability of the neural tree network (NTN) with the Gaussian mixture model to create a continuous density neural tree network (CDNTN). The CDNTN is used within a hidden Markov model (HMM), along with a nonparametric state duration model to construct a continuous word spotting system for real time applications. The new word spotting system does not use a general background model, allowing construction of independent models whose performance is independent of the number of models in the recognition system, supporting a direct parallel implementation. Although HMM word spotting systems are shown to provide good performance when sufficient training data is available, for applications where background speech data is not available or only a limited numbers of training tokens are available, the CDNTN word spotting system is shown to out perform comparable HMM systems.
Increased Angiogenesis and Expression of Vascular Endothelial Growth Factor during Scarless Repair (2005)

Vascular endothelial growth factor (VEGF) is a dimeric heparin-binding glycoprotein that is a potent endothelial cell-specific mitogen with increased expression during adult cutaneous wound healing. VEGF activity is mediated by two receptors, VEGFR-1 (Flt-1) and VEGFR-2 (Flk-1/KDR), which are expressed primarily in vascular endothelial cells. Initiation of profibrotic cytokine expression likely coordinates the transition from scarless healing to scar formation in fetal wounds. Angiogenesis is an important component of the scarring repair process, but the function of VEGF and degree of angiogenesis during scarless repair has not been investigated. We hypothesize that VEGF and its receptors are differentially expressed in scarless compared with scarring fetal wounds because VEGF is implicated in angiogenesis during skin development and adult wound healing. Excisional wounds were created on fetal rats at gestational ages 16.5 days (E16) and 18.5 days (E18) (term = 21.5 days). Wounds were harvested at 24 and 72 hours (n = 12 wounds per time point). Nonwounded fetal skin (E17, E19, and E21) was used as control. Reduced-cycle, specific-primer, reverse-transcriptase polymerase chain reaction was performed to determine the expression of VEGF and its receptors, VEGFR-1 and VEGFR-2. Wounds at 72 hours and fetal skin controls were examined under high-power microscopy for blood vessel counts. Unpaired two-tailed t test was used (p < 0.05 was considered significant). VEGF expression increased 2.4-fold (p < 0.001) during normal skin development from E17 to E19. In scarless wounds (E16), VEGF expression increased 2.8-fold (p < 0.02) at 72 hours. No increased expression occurred in the scarring wounds (E18). VEGFR-1 and VEGFR-2 expression increased over 2-fold during normal skin development from E17 to E21. However, each was down-regulated 30 to 50 percent in scarless (E16) and scarring (E18) wounds. There is a 2-fold increase in mean vessel counts per high-power field in scarless (E16) wounds at 72 hours compared with age-matched control skin (p < 0.02) and a 1.7-fold increase in mean vessel count in scarring fetal wounds (E18) compared with age-matched control skin (p < 0.05). There is no difference in the total number of vessels found in scarless versus scarring wounds or between 19.5-day versus 21.5-day fetal skin. VEGF and its receptors, VEGFR-1 and VEGFR-2, increase expression during skin development and dermal differentiation. VEGF expression quickly elevates during scarless compared with scarring repair, which likely contributes to the more rapid scarless fetal repair rate. Similar numbers of new ves-sels are formed during scarless and scarring fetal repair.
Role of CFTR in Airway Disease (1999)

Role of CFTR in Airway Disease. Physiol. Rev. 79, Suppl.: S215-S255, 1999. - Cystic fibrosis (CF) is caused by mutations in the gene encoding the CF transmembrane conductance regulator (CFTR), which accounts for the cAMP-regulated chloride conductance of airway epithelial cells. Lung disease is the chief cause of morbidity and mortality in CF patients. This review focuses on mechanisms whereby the deletion or impairment of CFTR chloride channel function produces lung disease. It examines the major themes of the channel hypothesis of CF, which involve impaired regulation of airway surface fluid volume or composition. Available evidence indicates that the effect of CFTR deletion alters physiological functions of both surface and submucosal gland epithelia. At the airway surface, deletion of CFTR causes hyperabsorption of sodium chloride and a reduction in the periciliary salt and water content, which impairs mucociliary clearance. In submucosal glands, loss of CFTR-mediated salt and water secretion compromises the clearance of mucins and a variety of defense substances onto the airway surface. Impaired mucociliary clearance, together with CFTR-related changes in the airway surface microenvironment, leads to a progressive cycle of infection, inflammation, and declining lung function. Here, we provide the details of this pathophysiological cascade in the hope that its understanding will promote the development of new therapies for CF.
The ???Fistula VAC,??? a Technique for Management of Enterocutaneous Fistulae Arising within the Open Abdomen: Report of 5 Cases (2006)

Application of the fistula-VAC should be considered a useful option in treating patients with intestinal fistulae in open abdominal wounds.
Improved access to computers for the visually handicapped: new prospects and principles (1994)

Discusses the future of computer access products for people with a visual handicap. The existing special computer access solutions are briefly reviewed. Their limitations are examined in terms of a human-computer interaction, and the technical origins of these limitations are analyzed. New technologies are explored and their potential for significantly improving the human-computer interface are reviewed. Finally, principles for the future development of nonvisual human-computer interfaces are proposed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A numerical study of microparticle acoustophoresis driven by acoustic radiation forces and streaming-induced drag forces (2012)

We present a numerical study of the transient acoustophoretic motion of microparticles suspended in a liquid-filled microchannel and driven by the acoustic forces arising from an imposed standing ultrasound wave: the acoustic radiation force from the scattering of sound waves on the particles and the Stokes drag force from the induced acoustic streaming flow. These forces are calculated numerically in two steps. First, the thermoacoustic equations are solved to first order in the imposed ultrasound field taking into account the micrometer-thin but crucial thermoviscous boundary layer near the rigid walls. Second, the products of the resulting first-order fields are used as source terms in the time-averaged second-order equations, from which the net acoustic forces acting on the particles are determined. The resulting acoustophoretic particle velocities are quantified for experimentally relevant parameters using a numerical particle-tracking scheme. The model shows the transition in the acoustophoretic particle motion from being dominated by streaming-induced drag to being dominated by radiation forces as a function of particle size, channel geometry, and material properties.
Diagnostic and Prognostic Value of K39 Recombinant Antigen in Indian Leishmaniasis (1995)

The recombinant product (rK39) of the 39 amino acid repeats encoded by a kinesin-like gene of visceral Leishmania spp. was further evaluated by enzyme-linked immunosorbent assay (ELISA) for its diagnostic potential in Indian kala-azar (VL) and post kala-azar dermal leishmaniasis (PKDL). Anti-rK39 antibodies were highly positive in 20 symptomatic cases, including 6 resistant to single or double chemotherapy, but became negligible or absent in 9 recently cured patients. Endpoint titration of samples from the 20 active cases showed that the anti-rK39 IgG titers fell within a wide range of 10(-2) to > 10(-6), and that their mean was > 1 order of magnitude higher than in VL reported previously. The anti-rK39 IgG titers were correlated with parasite burden found in the patients and remained undiminished in those refractory to chemotherapy. These results indicate that: (1) the K39 epitope is conserved in Indian strains of Leishmania donovani, (2) the extremely high levels of K39 antibodies in both VL and PKDL suggest the application of rK39 for sensitive and specific serodiagnosis, and (3) rK39 ELISA is also valuable for prognostic evaluation of both diseases.
Response of Factor VIII and IX-Deficient Blood to Wild Type and High Membrane Affinity Mutant Factor VIIa in an In Vitro Whole Blood Clotting Assay: Possible Correlation to Clinical Outcome (2002)

A modified form of the activated whole blood clotting time was used to evaluate response of blood from hemophilia patients to factor VIIa. Repeated assays of individuals over a one-year period showed consistency for each individual and significant difference between individuals. Four hemophilia patients with inhibitors gave low response to factor VIIa in the assay and were characterized as low or moderate clinical responders to factor VIIa therapy. Another four patients with moderate to good clinical responsiveness to factor VIIa therapy showed a strong response to factor VIIa in the assay. A factor VIIa mutant with enhanced membrane affinity showed 10- to 13-fold higher activity than wild type factor VIIa. The results may justify larger studies to determine the utility of this assay for evaluation of patient responsiveness and to set factor VIIa therapy levels.
Phagocyte responses to degradable polymers (2007)

Although many biodegradable polymers, such as poly-L-lactic acid and poly-L-glycolic acid, are preferentially composed of biological residues normally present in the human body, implants made of these materials often trigger inflammatory and fibrotic responses. Unfortunately, the mechanisms involved in degradable material-mediated tissue responses remain largely unknown. Using animal implantation and cell culture system models, we found a strong correlation between the rate of material degradation and the degree of inflammatory response to material implants. Furthermore, we have identified that both water-soluble and water-insoluble degradation products are potent triggers of phagocyte activation, including at the least, superoxide production. These results support a new concept that slow degradation may improve the biocompatibility of degradable drug-releasing particles and tissue engineering scaffolds.
WT1 Gene Expression in Human Testicular Germ-Cell Tumors. (1999)

The Wilms' tumor 1 gene (WT1) is a tumor suppressor gene whose alterations are linked to the genesis of Wilms¹ tumor. The gene is expressed in the urogenital organs and plays a key role in their development. Recent studies have shown that the WT1 gene product acts as a growth promoter of human leukemic cells. Because WT1 has been reported to be important in testicular development, we have investigated WT1 messenger RNA (mRNA) expression in testicular germ-cell tumors. Quantitative reverse transcription­polymerase chain reaction (RT-PCR) was used to examine the levels of WT1 mRNA in 34 patients with testicular germ-cell tumor, including 25 low-stage and 9 high-stage tumors. There were 23 seminomas and 11 nonseminomas. The WT1 mRNA was highly expressed in 6 of 9 high-stage lesions (67%) but only 5 of 25 low-stage cases (20%). A significant correlation was observed between the extent of WT1 mRNA expression and tumor stage (P = 0.017). There was no significant difference in WT1 mRNA expression between seminomas and nonseminomatous tumors. These results suggest that WT1 may be causal for the progression of testicular germ-cell tumors.
Human monocyte-derived macrophages bind low-density-lipoprotein-proteoglycan complexes by a receptor different from the low-density-lipoprotein receptor (1993)

We have shown recently that lipoprotein-proteoglycan complexes isolated from human atherosclerotic lesions stimulated cholesteryl ester synthesis in human monocyte-derived macrophages [Vijayagopal, Srinivasan, Radhakrishnamurthy and Berenson (1992) Arterioscler. Thromb. 12, 237-249]. The present study was conducted to determine the mechanism of cellular uptake of the complexes. A chondroitin sulphate-dermatan sulphate proteoglycan was isolated from normal human aorta and complexed to 125I-labelled human low-density lipoprotein (LDL). The binding and degradation of 125I-LDL-proteoglycan complex were then studied in human monocyte-derived macrophages. The specific binding and degradation of the complex showed saturability and concentration-dependency. The Kd for binding was 1.5 x 10(-8) M, which was greater than that reported for LDL in monocyte-derived macrophages. Binding of the complex was not subject to down-regulation. Chloroquine inhibited degradation of the complex and the resultant stimulation of cholesteryl ester synthesis. Limited treatment of macrophages with proteolytic enzymes abolished binding and degradation of the complex significantly. Macrophages bound 125I-methyl-LDL-proteoglycan complex to the same extent as 125I-LDL-proteoglycan complex. Excess LDL and proteoglycan did not compete against the binding of the complex; however, excess acetyl-LDL competed for 61% of the binding. Likewise, excess LDL-proteoglycan complex inhibited the binding of 125I-acetyl-LDL by 64%. Polyinosinic acid and cytochalasin D inhibited the binding of 125I-LDL-proteoglycan complex by 60% and 36% respectively. Compared with that of acetyl-LDL, the degradation of LDL-proteoglycan complex was retarded in human macrophages. The results indicate that the uptake of LDL-proteoglycan complex in human monocyte-derived macrophages is not mediated through binding to the LDL receptor; but occurs predominantly via the scavenger receptor, with phagocytosis playing a minor role in the process.
Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution (2015)

Our systematic, high-resolution survey of lncRNA localization reveals aspects of lncRNAs that are similar to mRNAs, such as cell-to-cell variability, but also several distinct properties. These characteristics may correspond to particular functional roles. Our study also provides a quantitative description of lncRNAs at the single-cell level and a universally applicable framework for future study and validation of lncRNAs.
Large-Scale Synthesis of Monodisperse Nanorods of Se/Te Alloys Through a Homogeneous Nucleation and Solution Growth Process (2001)

Uniform single-crystalline nanorods of Se/Te alloys—for example, the Se0.5Te0.5 crystals (934±48 nm × 223±10 nm) shown in the Figure—are reported to have been directly grown from aqueous solutions through a homogeneous nucleation process that involves no physical template, thus facilitating large-scale synthesis.