gebhart/patrepeval huggingface dataset:
Transcriptional regulation of the estrogen-inducible pS2 breast cancer marker gene by the ERR family of orphan nuclear receptors. (2001)

The estrogen-receptor-related receptors (ERRs) alpha, beta, and gamma are orphan nuclear hormone receptors that share significant homology with the estrogen receptors (ERs) but are not activated by natural estrogens. In contrast, the ERRs display constitutive transcriptional activity in the absence of exogenously added ligand. However, the ERRs bind to the estrogen response element and to the extended half-sites of which a subset can also be recognized by ERalpha, suggesting that ERRs and ERs may control overlapping regulatory pathways. To test this hypothesis, we explored the possibility that ERRs could regulate the expression of the estrogen-inducible pS2 gene, a human breast cancer prognostic marker. Transfection studies show that all of the ERR isoforms can activate the pS2 promoter in a variety of cell types, including breast cancer cell lines. Surprisingly, sequence analysis combined with mutational studies revealed that, in addition to the well-characterized estrogen response element, the presence of a functional extended half-site within the pS2 promoter is also required for complete response to both ER and ERR pathways. We show that ERR transcriptional activity on the pS2 promoter is considerably enhanced in the presence of all three members of the steroid receptor coactivator family but is completely abolished on treatment with the synthetic estrogen diethylstilbestrol, a recently described inhibitor of ERR function. Finally, we demonstrate that ERRalpha is the major isoform expressed in human breast cancer cell lines and that diethylstilbestrol can inhibit the growth of both ER-positive and -negative cell lines. Taken together, these results demonstrate that estrogen-inducible genes such as pS2 can be ERR targets and suggest that pharmacological modulation of ERRalpha activity may have therapeutic value in the treatment of breast cancer.
Functional roles of fibroblast growth factor receptors (FGFRs) signaling in human cancers (2013)

The fibroblast growth factor receptors (FGFRs) regulate important biological processes including cell proliferation and differentiation during development and tissue repair. Over the past decades, numerous pathological conditions and developmental syndromes have emerged as a consequence of deregulation in the FGFRs signaling network. This review aims to provide an overview of FGFR family, their complex signaling pathways in tumorigenesis, and the current development and application of therapeutics targeting the FGFRs signaling for treatment of refractory human cancers.
Bimonthly Leucovorin, Infusion 5-Fluorouracil, Hydroxyurea, and Irinotecan (FOLFIRI-2) for Pretreated Metastatic Colorectal Cancer (2003)

Irinotecan has shown activity in advanced colorectal cancer resistant to leucovorin and fluorouracil. Preclinical experiments on cell cultures and human tumor xenografts indicated potential synergy when combining irinotecan and fluorouracil. We designed a new regimen combining leucovorin, fluorouracil, irinotecan, and hydroxyurea (FOLFIRI-2) and conducted a phase II study to establish its efficacy and tolerance in advanced colorectal cancer refractory to fluorouracil and oxaliplatin. Treatment was repeated every 2 weeks and consisted of leucovorin 400 mg/m2 on day 1, immediately followed by 46 hours of continuous infusion of fluorouracil 2,000 mg/m2, irinotecan 180 mg/m2 on day 3, and hydroxyurea 1,500 mg the day before leucovorin, and on days 1 and 2. Treatment was continued until progression or limiting toxicity. Twenty-nine heavily pretreated patients entered the study. Five patients achieved an objective response (17%), and 12 obtained stabilization of disease or minor response (52%). Five patients failed to continue treatment (17%) because of toxicity or worsening condition. From the start of FOLFIRI-2 treatment, median progression-free survival was 4.1 months and median survival was 9.7 months. Grade III/IV National Cancer Institute-Common Toxicity Criteria toxicities were nausea 17%, diarrhea 31%, mucositis 14%, neutropenia 52%, and febrile neutropenia 14%. FOLFIRI-2 achieved a good rate of response and stabilization in heavily pretreated patients despite significant toxicity.
Evaluation of arylmethylaminopropanediols by a novel in vitro pharmacodynamic assay: correlation with antitumor activity in vivo. (1990)

The pharmacodynamics of a new series of antitumor DNA intercalators, known as arylmethylaminopropanediols (AMAPs), has been evaluated in vitro against adherent (MCF-7 human breast cancer) and nonadherent (P388 murine leukemia) cell lines. Previous work had shown that the in vitro antitumor activity of the model AMAP crisnatol was a function of exposure (Cn x T), rather than concentration alone. A unique exposure parameter, the minimum C x T, was proposed as an end point for antitumor activity in cell culture. Comparison of crisnatol to several established agents by the minimum C x T versus the standard concentration producing 10% survival indicated that these end points were not equivalent. The current work examined the validity of the pharmacodynamic approach using AMAP isomers from three different ring systems that were known to exhibit a spectrum of activity against the P388 tumor in vivo. The results indicated that antiproliferative, but not cytotoxic, activity of AMAPs in the pharmacodynamic assay correlated with their differential activity in vivo, expressed as percentage of increase in life span. In contrast, the concentration producing 10% survival either at 1 h or after continuous exposure did not show a similar correlation. The pharmacodynamic assay also revealed that certain AMAPs, while equipotent by concentration alone, required significantly less time and therefore less overall exposure for efficacy. Finally, the activity of AMAP isomers in P388 cells differed from that in MCF-7 cells, which may indicate AMAP selectivity for certain tumor types. Since AMAP action was a function of exposure, drug effects on cellular targets could likewise depend on exposure rather than concentration. These findings emphasize the importance of relating drug mechanisms to the pharmacodynamics of anticancer agents.
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE (2008)

Finding and characterizing mRNAs, their transcription start sites (TSS), and their associated promoters is a major focus in post-genome biology. Mammalian cells have at least 5-10 magnitudes more TSS than previously believed, and deeper sequencing is necessary to detect all active promoters in a given tissue. Here, we present a new method for high-throughput sequencing of 5' cDNA tags-DeepCAGE: merging the Cap Analysis of Gene Expression method with ultra-high-throughput sequence technology. We apply DeepCAGE to characterize 1.4 million sequenced TSS from mouse hippocampus and reveal a wealth of novel core promoters that are preferentially used in hippocampus: This is the most comprehensive promoter data set for any tissue to date. Using these data, we present evidence indicating a key role for the Arnt2 transcription factor in hippocampus gene regulation. DeepCAGE can also detect promoters used only in a small subset of cells within the complex tissue.
Prospects for the therapeutic use of human monoclonal antibodies. (1986)

Despite much recent progress, human monoclonal antibodies (HuMAbs) are currently more difficult to generate than conventional rodent monoclonals. Clinical trials using rodent monoclonals suggest that they can be given safely, but that the human antimouse immune response can limit their efficacy. We review the human monoclonals that have been generated to date, and explore the clinical uses that will be made of these reagents in the near future.
Semi-supervised learning with graphs (2005)

In traditional machine learning approaches to classification, one uses only a labeled set to train the classifier. Labeled instances however are often difficult, expensive, or time consuming to obtain, as they require the efforts of experienced human annotators. Meanwhile unlabeled data may be relatively easy to collect, but there has been few ways to use them. Semi-supervised learning addresses this problem by using large amount of unlabeled data, together with the labeled data, to build better classifiers. Because semi-supervised learning requires less human effort and gives higher accuracy, it is of great interest both in theory and in practice. We present a series of novel semi-supervised learning approaches arising from a graph representation, where labeled and unlabeled instances are represented as vertices, and edges encode the similarity between instances. They address the following questions: How to use unlabeled data? (label propagation); What is the probabilistic interpretation? (Gaussian fields and harmonic functions); What if
Western equine encephalitis virus is a recombinant virus. (1988)

The alphaviruses are a group of 26 mosquito-borne viruses that cause a variety of human diseases. Many of the New World alphaviruses cause encephalitis, whereas the Old World viruses more typically cause fever, rash, and arthralgia. The genome is a single-stranded nonsegmented RNA molecule of + polarity; it is about 11,700 nucleotides in length. Several alphavirus genomes have been sequenced in whole or in part, and these sequences demonstrate that alpha-viruses have descended from a common ancestor by divergent evolution. We have now obtained the sequence of the 3'-terminal 4288 nucleotides of the RNA of the New World Alphavirus western equine encephalitis virus (WEEV). Comparisons of the nucleotide and amino acid sequences of WEEV with those of other alphaviruses clearly show that WEEV is recombinant. The sequences of the capsid protein and of the (untranslated) 3'-terminal 80 nucleotides of WEEV are closely related to the corresponding sequences of the New World Alphavirus eastern equine encephalitis virus (EEEV), whereas the sequences of glycoproteins E2 and E1 of WEEV are more closely related to those of an Old World virus, Sindbis virus. Thus, WEEV appears to have arisen by recombination between an EEEV-like virus and a Sindbis-like virus to give rise to a new virus with the encephalogenic properties of EEEV but the antigenic specificity of Sindbis virus. There has been speculation that recombination might play an important role in the evolution of RNA viruses. The current finding that a widespread and successful RNA virus is recombinant provides support for such an hypothesis.
Remote control of tumour-targeted Salmonella enterica serovar Typhimurium by the use of l-arabinose as inducer of bacterial gene expression in vivo (2007)

We have used Salmonella enterica serovar Typhimurium (S. typhimurium) which are able to colonize tumours besides spleen and liver. Bacteria were equipped with constructs encoding green fluorescent protein or luciferase as reporters under control of the promoter PBAD that is inducible with L-arabinose. Reporter genes could be induced in culture but also when the bacteria resided within the mouse macrophages J774A.1. More important, strong expression of reporters by the bacteria could be detected in mice after administration of L-arabinose. This was especially pronounced in bacteria colonizing tumours. Histology demonstrated that the bacteria had accumulated in and close to necrotic areas of tumours. Bacterial gene induction was observed in both regions. PBAD is tightly controlled also in vivo because gene E of bacteriophage PhiX174 could be introduced as inducible suicide gene. The possibility to deliberately induce genes in bacterial carriers within the host should render them extremely powerful tools for tumour therapy.
A sunflower helianthinin gene upstream sequence ensemble contains an enhancer and sites of nuclear protein interaction. (1989)

Genes encoding helianthinin, the major seed protein in sunflower, are highly regulated. We have identified putative cis-acting and trans-acting elements that may function in the control of helianthinin expression. A 404-base pair DNA fragment on the sunflower helianthinin gene HaG3D, located 322 base pairs from the transcriptional start site, enhanced beta-glucuronidase expression in transgenic tobacco embryos. Sequences within this fragment were found to bind nuclear proteins present in both sunflower embryo and hypocotyl nuclear extracts. The binding site was localized by phenanthroline-copper ion footprinting experiments to A/T-rich sequences located from -705 to -654. Binding competition experiments revealed that these sunflower proteins also bind to upstream promoter sequences from another helianthinin gene (HaG3A) and two other plant embryo-specific genes, carrot DcG3 and French bean phaseolin. However, sequences of the cauliflower mosaic virus 35S promoter/enhancer complex failed to compete for its binding. Phenanthroline-copper ion footprinting experiments showed that the binding sites for the sunflower proteins in HaG3A (-1463 to -1514 and -702 to -653) and in phaseolin (-671 to -627) are also very A/T-rich, have similar sizes, and are located at similar distances from their respective promoters.
The molecular chaperone concept. (1989)

Molecular chaperones are a ubiquitous family of proteins whose proposed role is to mediate the folding and assembly of other proteins into oligomeric structures. The essential function of molecular chaperones is to prevent the formation of incorrect structures which may result from the transient exposure of charged or hydrophobic surfaces normally involved in interactions between or within polypeptide chains. Such transient exposure may occur during the synthesis of polypeptides, the unfolding and refolding that occurs during their transport across membranes, the association of polypeptides made in one subcellular compartment with those made in another, changes in protein-protein interactions during the normal functioning of a complex, and recovery from stresses such as heat shock. Three classes of molecular chaperone are discussed: the nucleoplasmins, the BiP group, and the chaperonins.
EVALUATION OF RECOMBINANT HUMAN SOLUBLE DIMERIC TUMOR NECROSIS FACTOR RECEPTOR FOR PREVENTION OF OKT3-ASSOCIATED ACUTE CLINICAL SYNDROME1,2 (1996)

Tumor necrosis factor alpha (TNFa) has been shown to be the primary cytokine responsible for the OKT3-induced acute clinical syndrome (OKT3-ACS). Recombinant human soluble tumor necrosis factor receptor (TNFR:Fc) is a dimer of the p80 TNF receptor, which binds both TNFa and lymphotoxin (LT). Renal allograft recipients undergoing OKT3 therapy for steroid-resistant rejection were randomized to receive OKT3 alone or in combination with TNFR:Fc to determine its safety and efficacy in decreasing the severity of OKT3-ACS and in restoring renal function. Six of 12 patients were given TNFR:Fc prior to each of the first two injections of OKT3. All patients were monitored for manifestations of OKT3-ACS and changes in renal function. In addition, serial serum samples were assayed for TNFa and TNFR:Fc levels (ELISA) and TNFa bioactivity (L929). No adverse side effects were identified in patients receiving TNFR:Fc. Patients treated with TNFR:Fc had significantly fewer symptoms by day 2 of OKT3, and had a lower overall incidence of chills and arthralgias. Renal dysfunction reversed within 24 hr in the TNFR:Fc-treated group in contrast to the 48-72-hr delay in the control group. Antigenic TNFa levels increased in the control group from < 10 pg/ml pre OKT3 to a mean peak level of 30 +/- 13 pg/ml on day 1 and decreased to pretreatment levels by day 2. TNFR:Fc-treated patients had a mean peak TNFa level of 235 +/- 135 pg/ml, suggesting a carrier effect of TNFR:Fc. In contrast, bioactivity was barely detectable (mean 20 +/- 14 pg/ml) in the day 1 samples from TNFR:Fc-treated patients, whereas significant bioactivity (peak mean 60 +/- 35 pg/ml) was detected in sera from control patients. TNF receptor levels reached 600 ng/ml in treated patients and remained elevated for up to 18 days confirming the long half-life of TNFR:Fc. This phase 1 trial demonstrates that TNFR:Fc is well tolerated and may limit the severity of OKT3-ACS. The most significant observation was a more rapid improvement in renal function in the TNFR:Fc-treated patients. The absence of TNFa bioactivity indicates that TNFR:Fc functions as a TNF antagonist. Further evaluation of higher doses of TNFR:Fc in OKT3-treated patients is currently in progress.
Declaring War on the Environment: The Failure of International Environmental Treaties During the Persian Gulf War (1992)

was the most environmentally damaging war in history).Official
Association between Risk Factors for Vascular Dementia and Adiponectin (2014)

Vascular dementia is caused by various factors, including increased age, diabetes, hypertension, atherosclerosis, and stroke. Adiponectin is an adipokine secreted by adipose tissue. Adiponectin is widely known as a regulating factor related to cardiovascular disease and diabetes. Adiponectin plasma levels decrease with age. Decreased adiponectin increases the risk of cardiovascular disease and diabetes. Adiponectin improves hypertension and atherosclerosis by acting as a vasodilator and antiatherogenic factor. Moreover, adiponectin is involved in cognitive dysfunction via modulation of insulin signal transduction in the brain. Case-control studies demonstrate the association between low adiponectin and increased risk of stroke, hypertension, and diabetes. This review summarizes the recent findings on the association between risk factors for vascular dementia and adiponectin. To emphasize this relationship, we will discuss the importance of research regarding the role of adiponectin in vascular dementia.
User learning and performance with marking menus (1994)

A marking menu is designed to allow a user to perform a menu selection by either popping-up a radial (or pie) menu, or by making a straight mark in the direction of the desired menu item without popping-up the menu. Previous evaluations in laboratory settings have shown the potential of marking menus. This paper reports on a case study of user behavior with marking menus in a real work situation.
Applications of universal context modeling to lossless compression of gray-scale images (1996)

Inspired by theoretical results on universal modeling, a general framework for sequential modeling of gray-scale images is proposed and applied to lossless compression. The model is based on stochastic complexity considerations and is implemented with a tree structure. It is efficiently estimated by a modification of the universal algorithm context. Several variants of the algorithm are described. The sequential, lossless compression schemes obtained when the context modeler is used with an arithmetic coder are tested with a representative set of gray-scale images. The compression ratios are compared with those obtained with state-of-the-art algorithms available in the literature, with the results of the comparison consistently favoring the proposed approach.
Quantitative Comparison of the Efficacy of Various Compounds in Lowering Intracellular Cholesterol Levels in Niemann-Pick Type C Fibroblasts (2012)

Niemann-Pick Type C disease (NPC) is a lethal, autosomal recessive disorder caused by mutations in the NPC1 and NPC2 cholesterol transport proteins. NPC's hallmark symptoms include an accumulation of unesterified cholesterol and other lipids in the late endosomal and lysosomal cellular compartments, causing progressive neurodegeneration and death. Although the age of onset may vary in those affected, NPC most often manifests in juveniles, and is usually fatal before adolescence. In this study, we investigated the effects of various drugs, many of which modify the epigenetic control of NPC1/NPC2 gene expression, in lowering the otherwise harmful elevated intracellular cholesterol levels in NPC cells. Our studies utilized a previously described image analysis technique, which allowed us to make quantitative comparisons of the efficacy of these drugs in lowering cholesterol levels in a common NPC1 mutant model. Of the drugs analyzed, several that have been previously studied (vorinostat, panobinostat, and β-cyclodextrin) significantly lowered the relative amount of unesterified cellular cholesterol, consistent with earlier observations. In addition, a novel potential treatment, rapamycin, likewise alleviated the NPC phenotype. We also studied combinations of effective compounds with β-cyclodextrin; the addition of β-cyclodextrin significantly enhanced the cholesterol-lowering activity of vorinostat and panobinostat, but had mixed effects with rapamycin. Collectively, these results may provide a basis for the eventual development of improved NPC therapies.
Intensity-Modulated Radiation Therapy, Proton Therapy, or Conformal Radiation Therapy and Morbidity and Disease Control in Localized Prostate Cancer (2012)

Among patients with nonmetastatic prostate cancer, the use of IMRT compared with conformal radiation therapy was associated with less gastrointestinal morbidity and fewer hip fractures but more erectile dysfunction; IMRT compared with proton therapy was associated with less gastrointestinal morbidity.
Internetworking: integrating IP/ATM LAN/WAN security (1996)

Computer and network security is a complex problem that is not solely restricted to classified computer systems and networks. Accelerating trends in networking and the emphasis on open interoperable networks has left many unclassified systems vulnerable to a wide variety of attacks. Computer and network professionals must understand the scope of security, recognize the need for security even in unclassified systems, and then take appropriate action to protect their systems. Transmission of static passwords in plaintext over the Internet is one of the most widely publicized network vulnerabilities. Cue-time password mechanisms (such as S-Key) or other secure network access mechanisms (such as Kerberos) have been recommended to improve access security for computer systems connected to the Internet. This thesis examines many of the issues that must be addressed when assessing the need for computer and network security. This work provides the results of a site security survey for the unclassified IP/ATM LAN in the Systems Technology Lab (STL) at the Naval Postgraduate School (NPS). These results highlight new security vulnerabilities and strengths that occur when standard Internet Protocol (P) local-area networks (LANs) are internetworked with Asynchronous Transfer Mode (ATM) wide-area networks (WANs). Finally, we examine the feasibility of using the Kerberos authentication protocol for remote plaintext password protection and provide recommendations for additional work
The Ancient Drug Salicylate Directly Activates AMP-Activated Protein Kinase (2012)

Salicylate, a plant product, has been in medicinal use since ancient times. More recently, it has been replaced by synthetic derivatives such as aspirin and salsalate, both of which are rapidly broken down to salicylate in vivo. At concentrations reached in plasma after administration of salsalate or of aspirin at high doses, salicylate activates adenosine monophosphate-activated protein kinase (AMPK), a central regulator of cell growth and metabolism. Salicylate binds at the same site as the synthetic activator A-769662 to cause allosteric activation and inhibition of dephosphorylation of the activating phosphorylation site, threonine-172. In AMPK knockout mice, effects of salicylate to increase fat utilization and to lower plasma fatty acids in vivo were lost. Our results suggest that AMPK activation could explain some beneficial effects of salsalate and aspirin in humans.