gebhart/patrepeval huggingface dataset:
Effects of Growth Factors and Growth Factor-Extracellular Matrix Interactions on Mouse Trophoblast Outgrowth in Vitro1 (1993)

A variety of cell types at the blastocyst implantation site produce growth factors that could play important role(s) in the implantation process. Recent evidence indicates that decidual cells and/or embryos produce transforming growth factor-alpha (TGF-alpha), epidermal growth factor (EGF), platelet-derived growth factor (PDGF), fibroblast growth factor (FGF), and colony-stimulating factor (CSF-1). Furthermore, receptors for EGF, PDGF, and CSF-1 have been detected on embryonic and trophoblastic cells. The purpose of this study was to investigate the effects of these growth factors and possibly growth factor-extracellular matrix interactions on mouse blastocyst attachment and trophoblast outgrowth in vitro. Various dilutions of the growth factors TGF-alpha, EGF, PDGF, FGF, and CSF-1 were added to cultures of 5-day-old hatched blastocysts in fibronectin-coated plastic wells. Blastocysts were scored for attachment, trophoblast outgrowth, and surface area at 24, 48, and 72 h. Each of these growth factors significantly enhanced trophoblast outgrowth, and a cocktail containing all of the growth factors had a significantly stronger effect. PDGF and FGF, but no other growth factors, also enhanced trophoblast outgrowth following pulsatile incubation with the fibronectin matrix coating of the culture wells, indicating that interactions between these growth factors and extracellular matrix elements could influence implantation. This study suggests that various growth factors may play an important role in the implantation process, that synergistic effects may be obtained by combinations of growth factors, and that interactions between certain growth factors and extracellular matrix elements may be significant.(ABSTRACT TRUNCATED AT 250 WORDS)
Genetic basis for necrotizing enterocolitis - risk factors and their relations to genetic polymorphisms (2006)

Necrotizing enterocolitis (NEC) is a common, life-threatening neonatal gastrointestinal disease; it affects approximately 11% of extremely premature neonates. The etiology of NEC is multifactorial. Risk factors may roughly be grouped into four main categories: prematurity; transient ischemia of the intestine; local/systemic inflammation predisposing the bowel to injury, and therapeutic interventions. Recent studies have shown that carrier state of genetic polymorphisms may be associated with perinatal morbidity, including NEC. In perinatal disorders, the significance of genetic variants of cytokines, the renin-angiotensin-aldosterone system, and surfactant proteins have been investigated most widely. Positive findings indicate the implication of genetic polymorphisms of proinflammatory cytokines in premature birth; angiotensin converting enzyme in perinatal adaptation and angiotensin type 1 receptor in the closure of ductus arteriosus; surfactant proteins A and B in respiratory distress syndrome; interleukin (IL)-6 in sepsis, and IL-4-receptor alpha chain and IL-18 in NEC. This review provides an insight into the genetics of NEC and summarizes genetic data in light of pathologic processes leading to NEC.
Introduction of Single Base Substitutions at Homologous Chromosomal Sequences by Adeno-associated Virus Vectors (2001)

Adeno-associated virus (AAV) vectors can modify homologous chromosomal sequences at high rates. This gene targeting transduction pathway is distinct from the integrating and episomal pathways used in gene addition approaches. In previous studies, AAV vectors were used to introduce small insertion and deletion mutations at homologous chromosomal loci. Here we show that AAV-mediated gene targeting can also be used to introduce all possible types of single base substitution mutations at the endogenous single-copy hypoxanthine phosphoribosyl transferase locus. Southern blot and sequence analysis showed that the point mutations were introduced with high fidelity. We also show that AAV vectors can repair chromosomal alkaline phosphatase genes containing point mutations. Our results suggest that AAV vectors can be used to introduce single base substitutions at high frequencies in normal human cells, including the correction of point mutations responsible for genetic diseases.
N-cadherin Gene Expression in Prostate Carcinoma Is Modulated by Integrin-Dependent Nuclear Translocation of Twist1 (2006)

The gain of N-cadherin expression in carcinomas has been shown to be important in the regulation of cell migration, invasion, and survival. Here, we show that N-cadherin mRNA expression in PC-3 prostate carcinoma cells is dependent on beta(1) integrin-mediated cell adhesion to fibronectin and the basic helix-loop-helix transcription factor Twist1. Depletion of Twist1 mRNA by small interfering RNA resulted in decreased expression of both Twist1 and N-cadherin and the inhibition of cell migration. Whereas Twist1 gene expression was independent of beta(1) integrin-mediated adhesion, Twist1 protein failed to accumulate in the nuclei of cells cultured in anchorage-independent conditions. The increased nuclear accumulation of Twist1 following cell attachment was suppressed by treatment with an inhibitor of Rho kinase or a beta(1) integrin neutralizing antibody. The effect of Twist1 on induction of N-cadherin mRNA required an E-box cis-element located within the first intron (+2,627) of the N-cadherin gene. These data raise the possibility that integrin-mediated adhesion to interstitial matrix proteins during metastasis differentially regulates the nuclear/cytoplasmic translocation and DNA binding of Twist1, activating N-cadherin transcription.
Thermodynamics of DNA Hybridization on Gold Nanoparticles (2005)

Dynamic light scattering is used as a sensitive probe of hybridization on DNA-functionalized colloidal gold nanoparticles. When a target DNA strand possesses an 8 base "dangling end", duplex formation on the surface of the nanoparticles leads to an increase in hydrodynamic radius. Duplex melting is manifested in a drop in hydrodynamic radius with increasing temperature, and the concentration dependence of the melting temperature provides a measure of the thermodynamics of binding. The hybridization thermodynamics are found to be significantly lower at higher hybridization densities than those previously reported for initial hybridization events. The pronounced deviation from Langmuir adsorption behavior is greater for longer duplexes, and it is, therefore, consistent with electrostatic repulsion between densely packed oligonucleotides. The results have implications for sensing and DNA-directed nanoparticle assembly.
Cooperation of the proapoptotic receptor agonist rhApo2L/TRAIL with the CD20 antibody rituximab against non-Hodgkin lymphoma xenografts (2007)

Recombinant human rhApo2L/TRAIL selectively stimulates apoptosis in various cancer cells through its receptors DR4 and DR5, and is currently in clinical trials. Preclinical studies have established antitumor activity of rhApo2L/TRAIL in models of epithelial cancers; however, efficacy in non-Hodgkin lymphoma (NHL) models is not well studied. Of 7 NHL cell lines tested in vitro, rhApo2L/TRAIL stimulated apoptosis in BJAB, Ramos RA1, and DoHH-2 cells. Rituximab, a CD20 antibody used to treat certain types of NHL, augmented rhApo2L/TRAIL-induced caspase activation in Ramos RA1 and DoHH2 but not BJAB or SC-1 cells, through modulation of intrinsic rather than extrinsic apoptosis signaling. In vivo, rhApo2L/TRAIL and rituximab cooperated to attenuate or reverse growth of tumor xenografts of all 4 of these cell lines. Depletion of natural killer (NK) cells or serum complement substantially reduced combined efficacy against Ramos RA1 tumors, suggesting involvement of antibody-dependent cell- and complement-mediated cytotoxicity. Both agents exhibited greater activity against disseminated than subcutaneous BJAB xenografts, and worked together to inhibit or abolish disseminated tumors and increase survival. Moreover, rhApo2L/TRAIL helped circumvent acquired rituximab resistance of a Ramos variant. These findings provide a strong rationale for clinical investigation of rhApo2L/TRAIL in combination with rituximab as a novel strategy for NHL therapy.
Reducing Latency on the Internet using "Component-Based Download" and "File-Segment Transfer Protocol". (2000)

This thesis examines the Component-Based Download (hereinafter referred to as "CBD") and the Component-Based Download File-Segment Transfer Protocol (hereinafter referred to as "CBD-FSTP") to combat the latency due to the slow performance of the current file transfer protocols. In particular, we focus on accelerating the download of large files (e.g.: video) from the Internet. This can be achieved by the following two methods: (1) Defining a distributed server mechanism for transferring data known as CBD; and (2) Integrating a new distributed file transfer protocol known as CBD-FSTP More efficient utilization of bandwidth can be obtained by using these two methods. This will lead to a higher throughput and thus a reduced latency. The trade off will be higher processing overhead and network utilization that are no longer major drawbacks because of the emergence of fast computers with increasing processing power and the expansion of fiber optic Gigabit links. According to the data gathered throughout extensive measurements, CBD can speed up the process of downloading large-size files up to 3 times faster compared to conventional methods. The CBD-FSTP can also improve the latency by additional 30% compared to the FSTP method, which is another fast newly-developed file transfer protocol. Results show that CBD-FSTP can be 7 times faster than the File Transfer Protocol (hereinafter referred as "FTP").
Gene therapy of scarring: a lesson learned from fetal scarless wound healing (2001)

Cutaneous wounding in adult humans and higher vertebrate animals results in scar formation. In contrast, both human and animal fetuses, at early gestational ages, exhibit skin wound healing without scarring. This distinction suggests that the repair of adult wounds by skin regeneration, rather than by fibrosis, may be achieved if adult wounds can be modified to mimic the healing process of fetal wounds. The development of gene therapy offers the possibility to specifically enhance or block the gene expression of cytokines and extracellular molecules, and thus convert adult wound healing into a healing process more similar to tissue regeneration. This article reviews the characteristics of fetal wound repair focusing on cytokine profiles and the inflammatory response to dermal injury. Also included are new developments in gene transfer techniques as well as their application in wound healing. Finally, the authors propose possible strategies of wound gene therapy, to reduce wound scarring and to promote tissue regeneration.
Production of PGE2 and H2O2 from Alveolar Macrophage Stimulated by Silica (1994)

Background The pathogenesis of silicosis has been focused on the interaction between alveolar macrophages and silica particle. Although fibrosis in silicosis has been studied extensively, the mechanism is still not fully understood. There is increasing evidence that monokines and arachidonic acid metabolites produced by macrophage are involved in pathogenesis of silicosis. Recently, it was reported that prostaglandin E2 produced from macrophage counteracts the stimulatory effects of other monokines on fibroblast proliferation or collagen production. Until now, it was remained uncertain by which mechanism silica particle may activate alveolar macrophage to an enhanced release of prostaglandin E2. Methods In order to investigate the relationship between the activity of alveolar macrophage and the production of PGE2 from activated alveolar macrophage, the authors measured hydrogen peroxide and PGE2 from alveolar macrophages activated by silica in vitro and from alveolar macrophages in the silicotic nodules from rat. Experimental silicosis was induced by intratracheal infusion of silica(SiO2) suspended in saline (50 mg/ml) in Sprague-Dawley rats. Results 1) The silicotic nodules with fibrosis were seen from the sections of rat lung at 60 days after intratracheal injection with 50 mg aqueous suspension of silica. 2) In vitro, silica caused the dose dependent increase of hydrogen peroxide(p<0.05) and PGE2(p>0.05) release from alveolar macrophages. Alveolar macrophages from rats with silicotic nodules released more hydrogen peroxide and PGE2 than those of control group(p<0.05). Conclusion These results suggest that silica particle could activate macrophage directly and enhanced the release of PGE2 and hydrogen peroxide from the alveolar macrophage.
Oral Administration of Recombinant Cholera Toxin Subunit B Inhibits IL-12-Mediated Murine Experimental (Trinitrobenzene Sulfonic Acid) Colitis (2001)

Trinitrobenzene sulfonic acid (TNBS)-induced colitis is an IL-12-driven, Th1 T cell-mediated colitis that resembles human Crohn's disease. In the present study, we showed initially that the oral administration of recombinant subunit B of cholera toxin (rCT-B) at the time of TNBS-induced colitis by intrarectal TNBS instillation inhibits the development of colitis or, at later time when TNBS-induced colitis is well established, brings about resolution of the colitis. Dose-response studies showed that a majority of mice (68%) treated with rCT-B at a dose of 100 microg (times four daily doses) exhibited complete inhibition of the development of colitis, whereas a minority (30%) treated with rCT-B at a dose of 10 microg (times four daily doses) exhibited complete inhibition; in both cases, however, the remaining mice exhibited some reduction in the severity of inflammation. In further studies, we showed that rCT-B administration is accompanied by prevention/reversal of increased IFN-gamma secretion (the hallmark of a Th1 response) without at the same time causing an increase in IL-4 secretion. This decreased IFN-gamma secretion was not associated with the up-regulation of the secretion of counterregulatory cytokines (IL-10 or TGF-beta), but was associated with a marked inhibition of IL-12 secretion, i.e., the secretion of the cytokine driving the Th1 response. Finally, we showed that rCT-B administration results in increased apoptosis of lamina propria cells, an effect previously shown to be indicative of IL-12 deprivation. From these studies, rCT-B emerges as a powerful inhibitor of Th1 T cell-driven inflammation that can conceivably be applied to the treatment of Crohn's disease.
Vigabatrin in Childhood Epilepsy (1991)

Sixty-six children with various types of severe drug-resistant epilepsy were entered into a long-term, dose-rising study of vigabatrin after a 4-week run-in placebo period. All the children were receiving one to three other antiepileptic drugs, the doses of which were not changed during the 6-month dose titration phase. Following the introduction of vigabatrin, 11 patients became seizure free, and 28 responded with a greater than 50% reduction in seizure frequency. The following types of epilepsy responded favorably in order of decreasing efficacy: cryptogenic and symptomatic partial epilepsy, other symptomatic generalized epilepsy, and Lennox-Gastaut syndrome. However, three of nine patients with myoclonic epilepsy showed an increase in seizure frequency. Optimal responses were found with vigabatrin doses of 40 to 80 mg/kg/day, although no significant adverse effects were noted with doses of higher than 100 mg/kg/day. Thirty-eight responders continued on vigabatrin, 19 of whom have been treated for more than 1 year, with generally good efficacy. As a result of discontinuing concomitant antiepileptics, six patients are on monotherapy with vigabatrin, four of whom are seizure free. Vigabatrin tolerability was good, with 39 of 66 children reporting no adverse effects. Hyperkinesia was reported in 17 patients (26%), and two had to drop out of the study. All these patients had a history of hyperkinesia or mental retardation. In patients in whom vigabatrin dose was reduced because of hyperkinesia, a dose increase could later be instituted without recurrence of symptoms. There was no change in neurologic examination and no drug-related abnormalities in clinical laboratory data.(ABSTRACT TRUNCATED AT 250 WORDS)
Insights into Dengue Virus Genome Replication (2010)

Since many antiviral drugs are designed to interfere with viral genome replication, understanding this step in the viral replicative cycle has gained importance in recent years. Replication for many RNA viruses occurs in cellular compartments mainly originated from the production and reorganization of virus-induced membranes. Dengue virus translates, replicates and assembles new viral particles within virus-induced membranes from endoplasmic reticulum. In these compartments, all of the components required for replication are recruited, making the process efficient. In addition, membranes protect replication complexes from RNAases and proteases, and ultimately make them less visible to cellular defense sensors. Although several aspects in dengue virus replication are known, many others are yet to be understood. This article aims to summarize the advances in the understanding of dengue virus genome replication, highlighting the cis as well as trans elements that may have key roles in this process.
Constitutional Isomers of Dendrimer-like Star Polymers:  Design, Synthesis, and Conformational and Structural Properties (2000)

The design, synthesis, and solution properties of six constitutional isomers of dendrimer-like star polymers is described. Each of the polymers have comparable molecular weights (∼80 000), narrow polydispersities (<1.19) and an identical number of branching junctures (45) and surface hydroxyl functionalities (48). The only difference in the six isomers is the placement of the branching junctures. The polymers are constructed from high molecular weight poly(ε-caprolactone) with branching junctures derived from 2,2‘-bis(hydroxylmethyl) propionic acid (bis-MPA) emanating from a central core. The use of various generations of dendritic initiators and dendrons coupled with the ring-opening polymerization of ε-caprolactones allowed a modular approach to the dendrimer-like star polymer isomers. The most pronounced effects on the physical properties/morphology and hydrodynamic volume was for those polymers in which the branching was distributed throughout the sample in a dendrimer-like fashion. The versatility of this approach has provided the possibility of understanding the relationship between architecture and physical properties. Dynamic light scattering and small-angle X-ray scattering techniques were used to determine the hydrodynamic radius Rh and radius of gyration Rg respectively. The relationship between Rg and molecular weight was indicative of a compact starlike structure, and did not show advanced bias toward either the dense core or dense shell models. The radial density distribution of the isomers was therefore modeled according to a many arm star polymer, and good agreement was found with experimental measures of Rh/Rg.
Polyamine biogenesis in the rat mammary gland during pregnancy and lactation (1972)

Polyamines and RNA accumulate in the rat mammary gland during pregnancy, but the major increases occur after parturition. Therefore the major increases occur after the gland has obtained its maximal complement of epithelial cells. During lactation, the spermidine concentration rises above 5mm and RNA content in the lactating mammary gland reaches a value 16 times that of the unstimulated mammary gland. The ratio of spermidine/spermine, an increase of which initially signals an elevation in biosynthetic activity, is near 1 in the normal mammary gland and is greater than 10 in the lactating mammary gland. Putrescine concentration is very low during the entire course of mammary-gland development, with the exception of early pregnancy. The low putrescine concentration probably reflects the very rapid conversion of putrescine into spermidine. Both ornithine decarboxylase, the enzyme that synthesizes putrescine, and putrescine-stimulated S-adenosyl-l-methionine decarboxylase, the enzyme that synthesizes spermidine, increase in activity during middle and late pregnancy; during lactation, both enzyme activities are elevated until the 21st day of lactation, and then decline. These declines are concomitant with involution. Also, it was found that the amount of ribonuclease activity in the mammary gland was very high during lactation, almost double that in the gland during pregnancy.
Inhibitory Effects of Novel AP-1 Decoy Oligodeoxynucleotides on Vascular Smooth Muscle Cell Proliferation In Vitro and Neointimal Formation In Vivo (2002)

Excessive proliferation of vascular smooth muscle cells (VSMCs) and neointimal formation are critical steps in the pathogenesis of atherosclerosis and restenosis after percutaneous transluminal angioplasty. In this study, we investigated the hypothesis that the activator protein-1 (AP-1) plays an important role in neointimal formation after vascular injury. A circular dumbbell AP-1 decoy oligodeoxynucleotide (CDODN) was developed as a novel therapeutic strategy for restenosis after angioplasty. This CDODN was more stable than the conventional phosphorothioate linear decoy ODN (PSODN) and maintained structural integrity on exposure to exonuclease III or serum. Transfection with AP-1 decoy ODNs strongly inhibited VSMC proliferation and migration, as well as glucose- and serum-induced expression of PCNA and cyclin A genes. Administration of AP-1 decoy ODNs in vivo using the hemagglutinating virus of Japan (HVJ)-liposome method virtually abolished neointimal formation after balloon injury to the rat carotid artery. Compared with PSODN, CDODN was more effective in inhibiting the proliferation of VSMCs in vitro and neointimal formation in vivo. Our results collectively indicate that AP-1 activation is crucial for the mediation of VSMC proliferation in response to vascular injury. Moreover, the use of stable CDODN specific for AP-1 activity in combination with the highly effective HVJ-liposome method provides a novel potential therapeutic strategy for the prevention of restenosis after angioplasty in humans.
Kalman filters and neural-network schemes for sensor validation in flight control systems (1998)

Detection, identification, and accommodation of sensor failures can be a challenging task for complex dynamic systems. This paper presents the comparison of two different approaches for the task of sensor failure detection, identification, and accommodation in a flight control system assumed to be without physical redundancy in the sensory capabilities. The first approach is based on the use of a set of online learning neural networks; the second approach is based on the use of a bank of Kalman filters. The objective is to evaluate the robustness of both schemes; the comparison is performed through testing of the schemes for several types of failures presenting different level of complexity in terms of detectability. The required computational effort for both schemes is also evaluated. For each of these failure types this comparison is performed at nominal conditions, that is with the system model and its noise perfectly modeled (with the Kalman filter scheme performing at nominal conditions), and at conditions, where discrepancies occur for the modeling of the system as well as the system and measurement noises. While the Kalman-filter-based scheme takes advantage of its robustness capabilities, the neural-network-based scheme, starting from a random numerical architecture, relies on the learning accumulated either online or from off-line simulations. The study reveals that online learning neural architectures have potential for online estimation purposes in a sensor validation scheme, particularly in the case of poorly modeled dynamics.