gebhart/patrepeval huggingface dataset:
Microsatellites as EWS/FLI response elements in Ewing's sarcoma (2008)

The ETS gene family is frequently involved in chromosome translocations that cause human cancer, including prostate cancer, leukemia, and sarcoma. However, the mechanisms by which oncogenic ETS proteins, which are DNA-binding transcription factors, target genes necessary for tumorigenesis is not well understood. Ewing's sarcoma serves as a paradigm for the entire class of ETS-associated tumors because nearly all cases harbor recurrent chromosomal translocations involving ETS genes. The most common translocation in Ewing's sarcoma encodes the EWS/FLI oncogenic transcription factor. We used whole genome localization (ChIP-chip) to identify target genes that are directly bound by EWS/FLI. Analysis of the promoters of these genes demonstrated a significant over-representation of highly repetitive GGAA-containing elements (microsatellites). In a parallel approach, we found that EWS/FLI uses GGAA microsatellites to regulate the expression of some of its target genes including NR0B1, a gene required for Ewing's sarcoma oncogenesis. The microsatellite in the NR0B1 promoter bound EWS/FLI in vitro and in vivo and was both necessary and sufficient to confer EWS/FLI regulation to a reporter gene. Genome wide computational studies demonstrated that GGAA microsatellites were enriched close to EWS/FLI-up-regulated genes but not down-regulated genes. Mechanistic studies demonstrated that the ability of EWS/FLI to bind DNA and modulate gene expression through these repetitive elements depended on the number of consecutive GGAA motifs. These findings illustrate an unprecedented route to specificity for ETS proteins and use of microsatellites in tumorigenesis.
Generating summaries and visualization for large collections of geo-referenced photographs (2006)

We describe a framework for automatically selecting a summary set of photos from a large collection of geo-referenced photographs. Such large collections are inherently difficult to browse, and become excessively so as they grow in size, making summaries an important tool in rendering these collections accessible. Our summary algorithm is based on spa-tial patterns in photo sets, as well as textual-topical patterns and user (photographer) identity cues. The algorithm can be expanded to support social, temporal, and other factors. The summary can thus be biased by the content of the query, the user making the query, and the context in which the query is made.A modified version of our summarization algorithm serves as a basis for a new map-based visualization of large collections of geo-referenced photos, called Tag Maps. Tag Maps visualize the data by placing highly representative textual tags on relevant map locations in the viewed region, effectively providing a sense of the important concepts embodied in the collection.An initial evaluation of our implementation on a set of geo-referenced photos shows that our algorithm and visualization perform well, producing summaries and views that are highly rated by users.
Suppression of interactions in a phase-locked soliton optical memory (1993)

A perturbative and numerical analysis reveals the conditions for suppressing the interaction between adjacent phase-locked solitons in a soliton optical memory. This may permit the permanent storage of a soliton bit pattern in a diffractive or dispersive ring cavity.
REVIEW ARTICLE, Immunological Factors in the Pathogenesis and Treatment of Age-Related Macular Degeneration (2005)

Recent findings indicate that immunological factors are involved not only in the pathogenesis of age-related macular degeneration (AMD), but also in its treatment. Earlier data showing the presence of inflammatory cells in affected areas of AMD retinas support this statement. Although a possible role for autoimmunity was initially suggested, it has never reached general acceptance. Microorganisms have also been implied in the pathogenesis of AMD. Both serum antibacterial antibody levels and positive DNA tests from neovascular membranes have pointed to a possible role for Chlamydia pneumoniae in the pathogenesis of AMD. New data is providing evidence for the hypothesis that deposits between Bruch's membrane and the retinal pigment epithelium (RPE) cell layer may act as a stimulus for the local activation of the complement system. This may lead to a further growth of the deposits due to the strong chemotactic activity of certain complement activation products (such as C5a) with an influx of inflammatory cells. The buildup of cells and extracellular deposits may lead to local ischemia resulting in the activation of RPE cells. These activated RPE cells are thought to release angiogenic stimuli leading to choroidal neovascularization, which is the most serious complication of AMD. The fact that immunosuppressive drugs such as triamcinolone acetonide and anecortave acetate are capable of inhibiting choroidal neovascularization is consistent with an inflammatory component in the pathogenesis of AMD. Specific immunotherapy directed at certain cytokines or growth factors is now being investigated at both the animal and patient levels. Various clinical trials involving engineered antibodies are now being applied to block angiogenic factors such as the vascular endothelial growth factor (VEGF). An approach using gene therapy to influence angiogenesis by inducing the production of the pigment epithelium-derived factor (PEDF) was able to block neovascularization in an experimental murine model. Besides trying to block ongoing processes in AMD, retinal transplantation is now also being investigated as a treatment option. The fact that the retina is possibly an immunoprivileged tissue in combination with experimental data showing that the subretinal space is an immunoprivileged site is an indication that transplantation would not suffer from the rejection process. A larger obstacle is the question whether transplanted retinal tissue will regain its functional properties.
Synthesis of New Pyrrolo[1,2-a]quinoxaline Derivatives as Potential Inhibitors of Akt Kinase (2008)

Akt kinases are attractive targets for small molecule drug discovery because of their key role in tumor cell survival/proliferation and their overexpression/activation in many human cancers. Recent efforts in the development and biological evaluation of small molecule inhibitors of Akt have led to the identification of novel Akt kinase inhibitors, based on a quinoxaline or pyrazinone scaffold. A series of new substituted pyrrolo[1,2-a]quinoxaline derivatives, structural analogues of these active quinoxaline or pyrazinone pharmacophores, was synthesized from various substituted 2-nitroanilines or 1,2-phenylenediamine via multistep heterocyclization process. These new compounds were tested for their in vitro ability to inhibit the proliferation of the human leukemic cell lines K562, U937 and HL60, and the breast cancer cell line MCF7. Three of these human cell lines (K562, U937 and MCF7) exhibited an active phosphorylated Akt form. The most promising active pyrroloquinoxalines were found to be 1a that inhibited K562 cell line proliferation with an IC(50) of 4.5 microM, and 1h that inhibited U937 and MCF7 cell lines with IC(50) of 5 and 8 microM, respectively. These two candidates exhibited more potent activities than the reference inhibitor A6730.
Gel and buffer effects on the migration of DNA molecules in agarose. (1990)

The migration rate of linear and supercoiled DNA molecules in four brands of agarose from two different lots was compared using three buffer systems. Differences in DNA mobility were observed between brands and lots of agarose, in standard as well as in pulsed-field gel electrophoresis. A buffer-related effect on the migration of DNA molecules in agarose gels was also observed. Our results underline the need for an actual lot analysis of agarose, this extraction product varying from one preparation to another in several aspects.
Pulmonary Vascular Responses to Chronic Hypoxia Mediated by Hypoxia-inducible Factor 1 (2005)

Hypoxia-inducible factor 1 (HIF-1) is a master regulator of oxygen homeostasis that controls transcriptional responses to hypoxia. HIF-1 plays critical roles both during development and in response to physiologic and pathophysiologic stimuli in the adult. Here, the involvement of HIF-1 in lung pathophysiology will be discussed.
Mesenchymal Stem Cells Derived from CD133‐Positive Cells in Mobilized Peripheral Blood and Cord Blood: Proliferation, Oct4 Expression, and Plasticity (2005)

In this study, we used a common procedure to assess the potential of mobilized peripheral blood (MPB) and umbilical cord blood (UCB) as sources of mesenchymal stem cells (MSCs) in comparison with bone marrow (BM). We tested three methods: plastic adhesion supplemented with 5% of BM-MSC conditioned medium, unsupplemented plastic adhesion, and selection of CD133-positive cells. MSCs derived from MPB or UCB are identified by their positive expression of mesenchymal (SH2, SH3) and negative expression of hematopoietic markers (CD14, CD34, CD45, HLA-DR). We observed that the CD133-positive cell fraction contains more MSCs with high proliferative potential. Placed in appropriate conditions, these cells proved their capacity to differentiate into adipocytes, osteocytes, chondrocytes, and neuronal/glial cells. MPB- and UCB-MSCs express Oct4, a transcriptional binding factor present in undifferentiated cells with high proliferative capacity. The selection of CD133-positive cells enabled us to obtain a homogeneous population of MSCs from UCB and MPB. These sources may have a major clinical importance thanks to their easy accessibility.
Comparison of Lipid Content and Fatty Acid Composition and Their Distribution within Seeds of 5 Small Grain Species (2011)

This study was the first to document fatty acid distribution across a grain seed. Results provide 2 major reasons for improved oxidative stability of pearled grains: reduced oil content and shift of fatty acids toward more saturated and less unsaturated composition.
Adipose Tissue Engineering from Human Adult Stem Cells: Clinical Implications in Plastic and Reconstructive Surgery (2006)

These findings demonstrate that the predefined shape and dimensions of adipose tissue engineered from human mesenchymal stem cells can be maintained after in vivo implantation. These data further indicate the potential for autologous applications in reconstructive and plastic surgery procedures.
The CAG repeat within the androgen receptor gene and its relationship to prostate cancer (1997)

The length of a polymorphic CAG repeat sequence, occurring in the androgen receptor gene, is inversely correlated with transcriptional activity by the androgen receptor. Because heightened androgenic stimulation may increase risk of prostate cancer development and progression, we examined whether shorter CAG repeats in the androgen receptor gene are related to higher risk of prostate cancer. We conducted a nested case-control study of 587 newly diagnosed cases of prostate cancer detected between 1982 and 1995, and 588 controls without prostate cancer, within the Physician's Health Study. An association existed between fewer androgen receptor gene CAG repeats and higher risk of total prostate cancer [relative risk (RR) = 1.52; 95% confidence interval (CI) = 0.92-2.49; P trend = 0.04; for men with CAG repeat lengths < or = 18 relative to > or = 26 repeats]. In particular, a shorter CAG repeat sequence was associated with cancers characterized by extraprostatic extension or distant metastases (stage C or D) or high histologic grade (RR = 2.14; CI = 1.14-4.01; P trend = 0.001). This association was observed individually both for high stage (RR = 2.23) and high grade prostate cancer (RR = 1.89). Men with shorter repeats were at particularly high risk for distant metastatic and fatal prostate cancer. Variability in the CAG repeat length was not associated with low grade or low stage disease. These results demonstrate that a shorter CAG repeat sequence in the androgen receptor gene predicts higher grade and advanced stage of prostate cancer at diagnosis, and metastasis and mortality from the disease. The clinical implications of these results should be evaluated further.
The Nuclear Pool of Tetraspanin CD9 Contributes to Mitotic Processes in Human Breast Carcinoma (2014)

The discovery of a nuclear pool of CD9 has prognostic and/or therapeutic potential for patients with ductal carcinoma of the breast.
An Unprecedented Example of Pt4Ag3 Cluster Formation: Synthesis and Crystal Structure of [Pt2(dppy)4(μ3S)2Ag3(μ3S)2Pt2(dppy)4]3+ (1996)

An isosceles triangle of silver atoms is present in the novel heptanuclear heterometallic complex 1 (the structure of the core of the cation is shown on the right). In the solid state, 1 luminesces at 560 nm, which can be attributed to a metal cluster core d-s/S → Ag ligand-to-metal charge transfer, dppy = diphenylpyridin-2-ylphosphane.
Evidence for H2O2 Generation during the TiO2-Assisted Photodegradation of Dyes in Aqueous Dispersions under Visible Light Illumination (1999)

Photodegradation of a series of dyes (Rhodamine B, Orange II, Sulfo-rhodamine B, Fluorescein, Alizarin red, Squarylium cyanine, and Eosin) in the presence of TiO2 particles under air-equilibrated controlled conditions and visible light illumination led to the formation of hydrogen peroxide. Combined with chemical oxygen demand (COD) measurements and in situ adsorption of added H2O2, the results reveal that H2O2 is a perfidious intermediate species in the process of dye photodegradation. The formation rate of H2O2 depends on the rate of dye degradation. It can also be decomposed by TiO2 particles under visible light irradiation because of a TiO2/H2O2 surface complex. H2O2 was detected because its formation rate was greater than its decomposition rate; failing this, H2O2 would not be observed. Its decomposition rate depends on the amount of substrates or intermediates formed during dye degradation and adsorbed on the surface of the TiO2 particles. The greater the degradation rate of the dye or the greater the quantity of substrates or intermediates adsorbed on the TiO2 surface, the less is the depletion of H2O2 with the consequence that a large quantity of H2O2 accumulates in the solution bulk permitting its facile detection. Also, pH appears to play a beneficial role in the observation of H2O2 formed.
New Trends in Neuromodulation for the Management of Neuropathic Pain (2002)

Abstract SINCE ITS FIRST application in 1967, the methodology and technology of spinal cord stimulation for the management of chronic, intractable pain have evolved continuously. Despite these developments and improved knowledge of the effects of spinal anatomy and epidural contact configuration on paresthesia coverage, the clinical results of spinal cord stimulation—particularly the long-term effects—are still unsatisfactory in many patients. This dissatisfaction has come primarily from the failure of single-electrode configurations to provide consistent paresthesia coverage of the entire painful area. Therefore, new approaches were developed during the late 1990s that attempted to selectively cover one or more dermatomes with paresthesia as well as to provide sequential stimulation of different anatomic sites. These approaches have been applied both intraspinally and extraspinally by stimulating either the spinal nerves or the dorsal columns. To target parts of the latter, different methods have been developed and tested using either two-dimensional contact configurations or electronic field steering. These developments hold promise for improving long-term outcomes as well as increasing the number of pain conditions that can be treated with neuromodulation therapy. In this review, the history, theoretical basis, and evolution of these methodologies, as well as the ways in which they represent new trends in neuromodulation, are discussed.
Membrane glycoprotein p150,95 of human cytotoxic T cell clone is involved in conjugate formation with target cells. (1987)

The p150,95 heterodimer, one of three members of the leukocyte function associated antigen (LFA) family, is expressed by monocytes, granulocytes, NK cells, and a small percentage of lymphocytes. We now report that the p150,95 glycoprotein is expressed by some cytotoxic T cell clones and that it is involved in cell-mediated cytolysis by these clones. Two CTL clones, clone JS-93 (CD3+ CD4+ CD8-) and clone JS-102 (CD3+ CD4- CD8+) expressed high levels of p150,95 and were shown to be specifically directed against HLA-DR and HLA-A2, respectively. Immunoprecipitations followed by two-dimensional gel electrophoresis demonstrated no heterogeneity in the p150,95 molecule isolated from both clones. Furthermore, we demonstrated that monoclonal antibodies (moab) directed against p150,95 could inhibit the cytotoxic activity of both clone JS-93 and clone JS-102 (50% and 47%, respectively). Single cell assays revealed the inhibition to occur at the level of conjugate formation rather than at the level of the lethal hit. Similar results were obtained with moab directed against LFA-1 (p170,95). The capacity of the moab directed against LFA-1 and p150,95 to inhibit CTL activity and conjugate formation were additive, resulting in a similar percentage of inhibition as found with moab directed against the common beta-chain of these molecules. It is concluded that at least some CTL clones express the p150,95 antigen at their cell surface, and that this molecule, like LFA-1, acts at the level of conjugate formation between effector and target cells.
Amitotic Neuroblastoma Cells Used for Neural Implants in Monkeys (1986)

The potential utility of cultured neuroblastoma cells as donor tissue for neutral implants into the mammalian brain has been examined. Cells from a human neuroblastoma cell line, IMR-32, were labeled with [3H]thymidine and chemically rendered amitotic. These differentiated IMR-32 cells were grafted into the hippocampi of five adult African Green monkeys, and graft survival was evaluated for up to 270 days after transplantation. Autoradiographically labeled grafted cells were identified in four animals. Processes from grafted cells could be followed for distances of up to 150 micrometers into the host brain. No evidence for neoplastic growth of the transplant was found. Thus, grafted neuroblastoma cells can survive for prolonged periods in the primate brain and may serve as a practical source of donor tissue for neural implants.
UNC2025, a Potent and Orally Bioavailable MER/FLT3 Dual Inhibitor (2014)

We previously reported a potent small molecule Mer tyrosine kinase inhibitor UNC1062. However, its poor PK properties prevented further assessment in vivo. We report here the sequential modification of UNC1062 to address DMPK properties and yield a new potent and highly orally bioavailable Mer inhibitor, 11, capable of inhibiting Mer phosphorylation in vivo, following oral dosing as demonstrated by pharmaco-dynamic (PD) studies examining phospho-Mer in leukemic blasts from mouse bone marrow. Kinome profiling versus more than 300 kinases in vitro and cellular selectivity assessments demonstrate that 11 has similar subnanomolar activity against Flt3, an additional important target in acute myelogenous leukemia (AML), with pharmacologically useful selectivity versus other kinases examined.
Environmentally sensitive, SA‐dependent defense responses in the cpr22 mutant of Arabidopsis (2001)

To investigate the signaling pathways through which defense responses are activated following pathogen infection, we have isolated and characterized the cpr22 mutant. This plant carries a semidominant, conditional lethal mutation that confers constitutive expression of the pathogenesis-related (PR) genes PR-1, PR-2, PR-5 and the defensin gene PDF1.2. cpr22 plants also display spontaneous lesion formation, elevated levels of salicylic acid (SA) and heightened resistance to Peronospora parasitica Emco5. The cpr22 locus was mapped to chromosome 2, approximately 2 cM telomeric to the AthB102 marker. By analyzing the progeny of crosses between cpr22 plants and either NahG transgenic plants or npr1 mutants, all of the cpr22-associated phenotypes except PDF1.2 expression were found to be SA dependent. However, the SA signal transducer NPR1 was required only for constitutive PR-1 expression. A cross between cpr22 and ndr1-1 mutants revealed that enhanced resistance to P. parasitica is mediated by an NDR1-dependent pathway, while the other cpr22-induced defenses are not. Crosses between either coi1-1 or etr1-1 mutants further demonstrated that constitutive PDF1.2 expression is mediated by a JA- and ethylene-dependent pathway. Based on these results, the cpr22 mutation appears to induce its associated phenotypes by activating NPR1-dependent and NPR1-independent branches of the SA pathway, as well as an ethylene/JA signaling pathway. Interestingly, the SA-dependent phenotypes, but not the SA-independent phenotypes, are suppressed when cpr22 mutants are grown under high humidity.
On the evaluation of Boolean operators in the extended Boolean retrieval framework (1993)

The retrieval models based on the extended boolean retrieval framework, e.g., the fuzzy set model and the extended boolean model have been proposed in the past to provide the conventional boolean retrieval system with the document ranking facility. However, due to undesirable properties of evaluation formulas for the AND and OR operations, the former generates incorrect ranked output in certain cases and the latter suffers from the complexity of computation. There have been a variety of fuzzy operators to replace the evaluation formulas. In this paper we first investigate the behavioral aspects of the fuzzy operators and address important issues to affect retrieval effectiveness. We then define an operator class called positively compensatory operators giving high retrieval effectiveness, and present a pair of positively compensatory operators providing high retrieval efficiency as well as high retrieval effectiveness. All the claims are justified through experiments.
Isolation and mapping of Escherichia coli mutations conferring resistance to division inhibition protein DicB (1989)

Temperature-sensitive dicA mutants of Escherichia coli, dicA1(Ts), are blocked for cell division, owing to derepressed expression of a division inhibition gene, dicB. We isolated mutants which survived a high temperature in the dicA1 background and which survived induced expression of dicB carried by a high-copy-number plasmid. Most of the mutations conferred very slow growth on the cells. Two were mapped to the 90-min cluster of genes involved in translation and transcription, in or very close to gene rpoB. The majority of the other mutations were found to cause variable degrees of minicell formation and to map within or very close to the minB locus. Contrary to these mutations, the canonical min-1 mutation did not confer resistance to DicB.
The First Synthetic Application of a Monooxygenase Employing Indirect Electrochemical NADH Regeneration (2001)

In oxygen-containing media the electrochemical regeneration of NADH is easier than expected, such that the regeneration procedure can even be applied to NAD(P)H-dependent monooxygenases (see scheme).
Exonuclease III recognizes urea residues in oxidized DNA. (1985)

Escherichia coli exonuclease III was found to be associated with an activity that recognizes urea residues in DNA but not thymine glycol residues from which the urea residues were prepared. This activity was not due to a contaminating activity such as endonuclease III since urea-containing DNA was a competitive inhibitor of exonuclease III when apurinic DNA was used as a substrate and vice versa. The apparent kinetic constants for both the substrate and inhibitor were determined. Like its apurinic activity, exonuclease III activity against urea residues was endonucleolytic, nicking on the 5' side of the damage and having an optimal Mg2+ concentration between 2 and 10 mM. Also, the enzyme recognized alkali-stable damages produced in DNA by H2O2 in vitro. We suggest that it may be this activity of exonuclease III that accounts for its biological role in vivo.