gebhart/patrepeval huggingface dataset:
Light-Response Quantitative Trait Loci Identified with Composite Interval and eXtreme Array Mapping in Arabidopsis thalianaSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY394847 and AY466496. (2004)

Genetic analysis of natural variation in ecotypes of Arabidopsis thaliana can facilitate the discovery of new genes or of allelic variants of previously identified genes controlling physiological processes in plants. We mapped quantitative trait loci (QTL) for light response in recombinant inbred lines (RILs) derived from the Columbia and Kashmir accessions via two methods: composite interval mapping and eXtreme array mapping (XAM). After measuring seedling hypocotyl lengths in blue, red, far-red, and white light, and in darkness, eight QTL were identified by composite interval mapping and five localized near photoreceptor loci. Two QTL in blue light were associated with CRY1 and CRY2, two in red light were near PHYB and PHYC, and one in far-red light localized near PHYA. The RED2 and RED5 QTL were verified in segregating lines. XAM was tested for the identification of QTL in red light with pools of RILs selected for extreme phenotypes. Thousands of single feature polymorphisms detected by differential DNA hybridized to high-density oligo-nucleotide arrays were used to estimate allele frequency differences between the pools. The RED2 QTL was identified clearly; differences exceeded a threshold of significance determined by simulations. The sensitivities of XAM to population type and size and genetic models were also determined by simulation analysis.
Ventral mesodermal patterning in Xenopus embryos: Expression patterns and activities of BMP‐2 and BMP‐4 (1995)

We provide a comparative analysis of the expression patterns and ventral mesoderm-inducing properties of Xenopus BMP-2 and BMP-4. Transcripts for BMP-2 and BMP-4 are maternally stored in eggs, and zygotic expression of these genes is uniform in the ectoderm and mesoderm in late blastulae. During gastrulation, BMP-2 is expressed at a low level throughout the ectoderm and marginal zone, but at early neurula stages a patch of dorso-anterior cells displays enhanced expression. In contrast, BMP-4 transcripts are restricted to the ventrolateral marginal zone during gastrulation, and in late gastrula and early neurula BMP-4 is expressed in the epidermis but not the neural plate. At post-neurula stages, BMP-2 and BMP-4 transcripts are associated with a variety of mesodermal structures, including the pharyngeal pouches, heart, blood island, and blastopore. At tailbud stages, BMP-2 and BMP-4 are expressed in neural tissues including the neural tube and brain. In mesoderm induction assays, BMP-2 and BMP-4 induce Xhox3, an early ventral-posterior mesoderm marker, and larval alpha Tl globin, a marker for red blood cells. Induction of red blood cells in response to BMP-4 was demonstrated by staining with a hemoglobin-specific reagent. Little is known about factors that induce hematopoietic lineages in vertebrates, and these results provide evidence linking BMP activity and blood differentiation. Globin induction by BMP-2 and BMP-4 is blocked by co-expression of a dominant-negative activin receptor, suggesting that either endogenous activin signals are required for BMP-mediated induction, or that the truncated activin receptor interferes with signaling by BMP receptors. In assays on marginal zone explants, we demonstrate that BMP-4 respecifies dorsal mesoderm to form ventral mesoderm, consistent with its ability to induce blood and to ventralize embryos. BMP-2, however, does not display such activity. The findings extend and support evidence that BMP-2 and BMP-4 function in ventral mesoderm induction and patterning in Xenopus. Our data furthermore highlight the multiple functions these factors fulfill during early vertebrate embryogenesis.
Homoharringtonine, omacetaxine mepesuccinate, and chronic myeloid leukemia circa 2009 (2009)

Homoharringtonine (HHT) is a natural alkaloid that is obtained from various Cephalotaxus species. The mechanism of action by which HHT exerts its antitumor activity is through inhibition of protein synthesis and promotion of apoptosis. In the 1990s, HHT proved to be significantly active as salvage therapy for patients with chronic myeloid leukemia (CML) after failure on interferon-alpha therapy. However, the remarkable success of imatinib mesylate in the treatment of CML relegated HHT to oblivion. The development of omacetaxine mepesuccinate, a subcutaneously bioavailable semisynthetic form of HHT, and its activity in imatinib-resistant CML has established this agent for the second time as a valuable option in the management of this disease. Preliminary results appear to support the use of this agent for patients who have imatinib-resistant CML, including those who carry the tyrosine kinase inhibitor-insensitive mutation that exchanges the amino acids threonine and isoleucine at position 315 (the T315I mutation). In this article, the authors discuss the current data on omacetaxine and the prospects of this agent to be integrated into the state-of-the-art treatment algorithms for CML.
Mechanisms of cell signaling by the scavenger receptor CD36: implications in atherosclerosis and thrombosis. (2010)

CD36 is a multifunctional membrane receptor present on mononuclear phagocytes, platelets, and other cells that serves as a scavenger receptor for oxidized phospholipids, apoptotic cells and certain microbial pathogens. On macrophages, CD36 interaction with oxidized LDL (oxLDL) triggers a signaling response that is pro-inflammatory and pro-atherogenic. The signaling pathway involves activation of src-family kinases, MAP kinases, and Vav family guanine nucleotide exchange factors and results in ligand internalization, foam cell formation and inhibition of migration. On platelets, CD36 interaction with oxLDL and cell-derived microparticles transduces intracellular signals that render them more reactive to low concentrations of classical agonists. In vitro studies and in vivo experiments in CD36 null mice have revealed an important mechanistic role for CD36 in atherosclerosis and thrombosis. Identification of the precise CD36 signaling pathways in specific cells elicited in response to specific ligands may yield novel targets for drug development in athero-thrombotic disorders.
Postfabrication wavelength trimming of fiber Bragg gratings written in H/sub 2/-loaded fibers (2001)

A postfabrication technique for writing fiber Bragg gratings in H/sub 2/-loaded fiber with precise wavelength control is reported. The grating wavelength is highly stable and less than a 0.01-nm shift was observed after storing at room temperature for two months. This technique allows 1 nm of wavelength trimming and significantly enhances the grating thermal stability.
Roles of conserved and allelic regions of the major merozoite surface protein (gp195) in immunity against Plasmodium falciparum (1992)

The Plasmodium falciparum major merozoite surface protein gp195 is a candidate antigen for a vaccine against human malaria. The significance of allelism and polymorphism in vaccine-induced immunity to gp195 was investigated in this study. Rabbits were immunized with each of two allelic forms of gp195 that were affinity purified from the FUP and FVO parasite isolates. gp195-specific antibodies raised against one allelic form of gp195 cross-reacted extensively with the gp195 of the heterologous allele in enzyme-linked immunosorbent assays (ELISAs) and immunofluorescence assays. Competitive binding ELISAs with homologous and heterologous gp195s confirmed that a majority of the anti-gp195 antibodies produced against either allelic protein were cross-reactive. Moreover, the biological activities of the gp195 antibody responses were also highly cross-reactive, since anti-gp195 sera inhibited the in vitro growth of the homologous and heterologous parasites with equal efficiency. The degree of cross-reactivity with strain-specific and allele-specific determinants of gp195 in the ELISA was low. These results suggest that the immunological cross-reactivity between the two gp195 proteins is due to recognition of conserved determinants. They also suggest that a gp195-based vaccine may be effective against blood-stage infection with a diverse array of parasite isolates.
Natural Image Retrieval with Sketches (2005)

In this paper, we present a method to retrieve natural images by sketch query. To measure the similarity between the sketch and an image, relevant regions are first located in that image through a multi-resolution search, and a normalized local shape similarity is proposed for image retrieval. Efficiency and other implementation issues are discussed. Experimental results show that it is an effective approach for content-based image retrieval
ChemInform Abstract: A Convenient Preparation of Monosubstituted N,N′‐di(Boc)‐Protected Guanidines. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Alginate type and RGD density control myoblast phenotype (2002)

Alginates are being increasingly used for cell encapsulation and tissue engineering applications; however, these materials cannot specifically interact with mammalian cells. We have covalently modified alginates of varying monomeric ratio with RGD-containing cell adhesion ligands using carbodiimide chemistry to initiate cell adhesion to these polymers. We hypothesized that we could control the function of cells adherent to RGD-modified alginate hydrogels by varying alginate polymer type and cell adhesion ligand density, and we have addressed this possibility by studying the proliferation and differentiation of C2C12 skeletal myoblasts adherent to these materials. RGD density on alginates of varying monomeric ratio could be controlled over several orders of magnitude, creating a range of surface densities from 1-100 fmol/cm(2). Myoblast adhesion to these materials was specific to the RGD ligand, because adhesion could be competed away with soluble RGD in a dose-dependent manner. Myoblast proliferation and differentiation could be regulated by varying the alginate monomeric ratio and the density of RGD ligands at the substrate surface, and specific combinations of alginate type and RGD density were required to obtain efficient myoblast differentiation on these materials.
Hematologic and immunologic effects of the systemic administration of recombinant interleukin-2 after autologous bone marrow transplantation (1990)

T cells from allogeneic bone marrow grafts are responsible for a graft versus leukemia effect. Use of recombinant Interleukin-2 (rIL-2) after autologous bone marrow transplantation (BMT) may enhance immune function and hopefully reproduce the allogeneic reaction. We report here the hematologic and immunologic changes observed in the first 10 patients of a phase 1 trial studying the infusion of IL-2 after autologous BMT. All patients had high-risk malignancies and received 6 days of a constant infusion of IL-2 (Eurocetus, Amsterdam, The Netherlands) at dose of 3 x 10(6) Cetus Units/m2/d, 79 +/- 12 days after autologous BMT. Clinical toxicities involving cutaneous, cholestatic, gastrointestinal, and hemodynamic effects occurred during IL-2 treatment but reversed in all cases. Completion of treatment was 91% of the scheduled dose of IL-2. Hematologic toxicity was moderate and transient with no graft failure. Increases in eosinophil and lymphocyte counts were significant (P less than .05). Stimulation of the immune system was intense and prolonged, manifested by increase numbers of CD3+, CD3+DR+, CD3+ CD25+ lymphocytes, and natural killer (NK) cells (all P less than .01), and increase of Lymphokine-activated killers (LAK) and NK activities (P less than .01 and P less than .05). This study establishes the feasibility of a 6-day administration of rIL-2 after autologous BMT leading to a major immune activation 2.5 months after BMT.
Use of preferentially replicating bacteria for the treatment of cancer (2000)

About 40 years ago, the observation was made that conditions within experimental animal tumors could favor the preferential replication of bacteria.
Multiagent Learning and Adaptation in an Information Filtering Market (1996)

This paper presents an adaptive model for multiagent coordination based on the metaphor of economic markets. This model has been used to develop SIGMA, a system for filtering Usenet netnews which is able to cope with the non-stationary and partially observable nature of the information filtering task at hand. SIGMA integrates a number of different learning and adaptation techniques, including reinforcement learning, bidding price adjustment, and relevance feedback. Aspects of these are discussed below. Introduction With the widespread availability of electronically stored information in such environments as the World Wide Web (WWW), it is becoming increasingly important to use automatic methods for filtering such information (Belkin and Croft 1992). Traditional off-line approaches to information filtering (IF) consist of building database indices upon which traditional search and retrieval algorithms are subsequently applied. Because of the need to manipulate vast numbers of heterogen...
Chiroptical Molecular Switches (2001)

Introduction Switching of Enantiomers Overcrowded Alkenes Axially Chiral Cycloalkanones Switching of Diastereoisomers Overcrowded Alkenes Diarylethenes Other Diastereoselective Switches Multifunctional Chiral Switches Gated Photoisomerization Dual-mode Photoswitching of Luminescence Chiral Molecular Recognition Unidirectional Rotary Motion Switching of Macromolecules and Supramolecular Organization Photochromic Polymers Reversible Gel Formation Switching of Liquid Crystalline Phases Conclusions
Stability and plasticity of wild‐type and Pax5‐deficient precursor B cells (2002)

In Pax5-deficient mice, B cell development is blocked at the pre-BI cell stage. Like wild-type, Pax5-/- pre-BI cells can be grown long-term in vitro in the presence of stromal cells and IL-7. However, unlike their wild-type in vitro-grown counterparts, Pax5-/- pre-BI cells possess an extraordinary developmental plasticity showing hematopoietic stem cell features such as multipotency and self renewing capacity. Here we review and discuss this in vitro and in vivo plasticity of Pax5-/- pre-BI cells.
Antiphospholipid syndrome associated with immunotherapy for patients with melanoma (1995)

The high incidence of therapy-induced elevated APA concentrations suggests that these should be carefully monitored in all patients receiving immunotherapy with alpha-interferon.
An Immunologic Model for Rapid Vaccine Assessment — A Clinical Trial in a Test Tube (2009)

While the duration and size of human clinical trials may be difficult to reduce, there are several parameters in pre-clinical vaccine development that may be possible to further optimise. By increasing the accuracy of the models used for pre-clinical vaccine testing, it should be possible to increase the probability that any particular vaccine candidate will be successful in human trials. In addition, an improved model will allow the collection of increasingly more-informative data in pre-clinical tests, thus aiding the rational design and formulation of candidates entered into clinical evaluation. An acceleration and increase in sophistication of pre-clinical vaccine development will thus require the advent of more physiologically-accurate models of the human immune system, coupled with substantial advances in the mechanistic understanding of vaccine efficacy, achieved by using this model. We believe the best viable option available is to use human cells and/or tissues in a functional in vitro model of human physiology. Not only will this more accurately model human diseases, it will also eliminate any ethical, moral and scientific issues involved with use of live humans and animals. An in vitro model, termed "MIMIC" (Modular IMmune In vitro Construct), was designed and developed to reflect the human immune system in a well-based format. The MIMIC System is a laboratory-based methodology that replicates the human immune system response. It is highly automated, and can be used to simulate a clinical trial for a diverse population, without putting human subjects at risk. The MIMIC System uses the circulating immune cells of individual donors to recapitulate each individual human immune response by maintaining the autonomy of the donor. Thus, an in vitro test system has been created that is functionally equivalent to the donor's own immune system and is designed to respond in a similar manner to the in vivo response.
shRNA targeting HDGF suppressed cell growth and invasion of squamous cell lung cancer (2009)

Hepatoma-derived growth factor (HDGF), a nuclear protein with both mitogenic and angiogenic activity, has been reported to be mainly involved in tumorigenesis and the progression of non-small cell lung cancer. In this study, the HDGF expression was knocked down by specific-shRNA with lentivirus expression vector targeting HDGF in lung squamous cell carcinoma 520 cells. HDGF knocked down by shRNA suppressed the cell proliferation significantly both in vitro and in vivo as indicated by MTT, plate clone and transplanted tumor model assays. In addition, the knocked-down expression of HDGF also inhibited cell migration and invasion as shown in transwell and Boyden experiments. We concluded that HDGF acts as an oncogene participating in the pathogenesis of squamous cell lung cancer, and HDGF may be a key therapeutic target for non-small cell lung cancer.
Regulation of platelet heparanase during inflammation: Role of pH and proteinases (1998)

Heparan sulfate is rapidly degraded by an endoglycosidase (heparanase) secreted by activated platelets. Since the cleavage and release of heparan sulfate would profoundly alter the local physiology of the endothelium, platelet heparanase activity should be tightly regulated. Consistent with this hypothesis, platelet heparanase was found to degrade endothelial cell heparan sulfate at pH 6.0 but not at pH 7.4, even though 25% of maximum activity was detected at pH 7.4. Loss of heparanase activity occurred rapidly (t1/2 is approximately equal to 20 min) and reversibly at physiologic pH but did not occur at acidic pH (<7.0). Inactivation of heparanase at pH 7.4 did not affect heparin binding and was reversed by 0.5 M NaCl or by heparan sulfate but not by chondroitin sulfate, suggesting inactive heparanase could be tethered on cell surfaces and the function regulated by heparan sulfate. Heparanase was gradually inactivated by trypsin and urokinase (t1/2 = 5 h) but resisted cleavage by leukocyte cathepsin G, leukocyte elastase, plasmin, and thrombin. These findings are consistent with a model in which platelet heparanase is active at the low pH of inflammation but inactive under physiologic conditions preventing inadvertent cleavage of heparan sulfate and loss of physiologic functions of endothelial cells.
The prognostic value of plasma soluble urokinase plasminogen activator receptor (suPAR) levels in stage III ovarian cancer patients. (2004)

The level of the urokinase plasminogen activator receptor (uPAR) is elevated in tumor tissue from several forms of cancer. uPAR is shed from the cell surface and the soluble form, soluble urokinase plasminogen activator receptor (suPAR), has been detected in several body fluids. High plasma levels of suPAR in patients with colorectal cancer and high serum levels of suPAR in patients with recurrent metastatic breast cancer have been associated with poor prognosis. In patients with ovarian cancer (OC) it has been shown that the level of suPAR is very high in ascites and cystic fluid and that high serum levels of suPAR were associated with shorter survival of the patients. We evaluated suPAR preoperatively in plasma from primary OC stage III patients and tested for association with prognosis. The prognostic significance of suPAR was also compared to two biochemical markers; cancer antigen 125 (CA125) and tetranectin (TN). No significant differences were found between patients who died of OC compared to patients still alive regarding median plasma suPAR levels (p=0.62) and median serum CA125 levels (p=0.26). In contrast, a significant difference was found between dead and alive OC patients for the median serum TN level (p<0.0001). Dividing the patients into two groups, corresponding to preoperative plasma suPAR levels below or equal to 2.0 ng/ml and higher than 2.0 ng/ml, no significant difference in survival was found between the two groups (p=0.49). When different cut-off levels of plasma suPAR were considered (2.74 ng/ml, 3.25 ng/ml and 4.18 ng/ml), no significant differences in survival could be detected (p=0.58, p=0.68 and p=0.05). Multivariate Cox regression analysis showed that the only independent prognostic factors were radicality after primary surgery (RH=5.34; 95% CI, 2.34-12.20; p<0.0001) and preoperative serum TN (RH=0.69, 95% CI, 0.57-0.82; p<0.0001), whereas plasma suPAR (4.18 ng/ml), age, histological type of tumour and serum CA 125 had no independent prognostic value. In conclusion, preoperative plasma suPAR level was of no prognostic value in this cohort of Danish stage III OC patients.
Dual stream input for pointing and scrolling (1997)

To find ways to improve users' performance of tasks that involve both scrolling and pointing, we studied three dual-stream input methods, with one stream for pointing and one for scrolling. The results showed that a mouse augmented with a tracking wheel did not outperform the conventional single stream mouse. Two other methods, a mouse with an isometric rate-control joystick and a two handed system significantly improved users' performance.
Compehensive two‐dimensional gas chromatography (GC×GC) and its applicability to the characterization of complex (petrochemical) mixtures (1997)

Abstract In general, petrochemical products contain only a limited number of chemical classes of compounds (sample dimensionality). The enormous number of individual components within these classes, however, soon puts limitations upon a single chromatographic technique when it comes to adequate characterization of these products. Comprehensive two‐dimensional gas chromatography (GC×GC) clearly opens the possibility of estimating the composition of hydrocarbon mixtures in a far more detailed fashion than hitherto possible. Although the emphasis of papers of GCxGC thus far almost exclusively applies to the unsurpassed peak‐capacity, in the oil industry there is a need for characterization, rather than for analyzing all the individual compounds. In principle a GCxGC system can provide an almost perfect match between its intrinsic properties and the dimensionality of oil samples. To establish the applicability of GCxGC towards petrochemical analytical challenges, a commercially aavailable prototype instrument was subjected to an exhaustive characterization of a typical hydrocarbon precess stream and a fast characterization of a light gas oil. Although there are no fundamental limitations towards the quantitative aspects of a GCxGC system, this paper confines itself to qualitative results only. Quantitative aspects of GCxGC will be published in a forthcoming paper.
The Design, Production, and Validation of an Anti-HIV Type 1 Ribozyme (2003)

The development of acquired immunodeficiency syndrome (AIDS) generally takes of the order of ten years with no effective therapy currently available (,). HIV, the causative agent, exhibits tropism for CD4+ T-lymphocytes, the primary targets for HIV infection in vivo. Infection of these cells with HIV results in their selective loss resulting in a progressive and irreversible destruction of the immune system. Viral replication is found at all stages of the disease (,) with an immune response evident, namely antibodies to env and p24 as well as HIV specific cytotoxic T-lymphocytes ().