gebhart/patrepeval huggingface dataset:
Virus-Like Display of a Neo-Self Antigen Reverses B Cell Anergy in a B Cell Receptor Transgenic Mouse Model (2008)

The ability to distinguish between self and foreign Ags is a central feature of immune recognition. For B cells, however, immune tolerance is not absolute, and factors that include Ag valency, the availability of T help, and polyclonal B cell stimuli can influence the induction of autoantibody responses. Here, we evaluated whether multivalent virus-like particle (VLP)-based immunogens could induce autoantibody responses in well-characterized transgenic (Tg) mice that express a soluble form of hen egg lysozyme (HEL) and in which B cell tolerance to HEL is maintained by anergy. Immunization with multivalent VLP-arrayed HEL, but not a trivalent form of HEL, induced high-titer Ab responses against HEL in both soluble HEL Tg mice and double Tg mice that also express a monoclonal HEL-specific BCR. Induction of autoantibodies against HEL was not dependent on coadministration of strong adjuvants, such as CFA. In contrast to previous data showing the T-independent induction of Abs to foreign epitopes on VLPs, the ability of HEL-conjugated VLPs to induce anti-HEL Abs in tolerant mice was dependent on the presence of CD4(+) Th cells, and could be enhanced by the presence of pre-existing cognate T cells. In in vitro studies, VLP-conjugated HEL was more potent than trivalent HEL in up-regulating surface activation markers on purified anergic B cells. Moreover, immunization with VLP-HEL reversed B cell anergy in vivo in an adoptive transfer model. Thus, Ag multivalency and T help cooperate to reverse B cell anergy, a major mechanism of B cell tolerance.
Arabidopsis Transcriptome Profiling Indicates That Multiple Regulatory Pathways Are Activated during Cold Acclimation in Addition to the CBF Cold Response Pathway[W] (2002)

Many plants, including Arabidopsis, increase in freezing tolerance in response to low, nonfreezing temperatures, a phenomenon known as cold acclimation. Previous studies established that cold acclimation involves rapid expression of the CBF transcriptional activators (also known as DREB1 proteins) in response to low temperature followed by induction of the CBF regulon (CBF-targeted genes), which contributes to an increase in freezing tolerance. Here, we present the results of transcriptome-profiling experiments indicating the existence of multiple low-temperature regulatory pathways in addition to the CBF cold response pathway. The transcript levels of approximately 8000 genes were determined at multiple times after plants were transferred from warm to cold temperature and in warm-grown plants that constitutively expressed CBF1, CBF2, or CBF3. A total of 306 genes were identified as being cold responsive, with transcripts for 218 genes increasing and those for 88 genes decreasing threefold or more at one or more time points during the 7-day experiment. These results indicate that extensive downregulation of gene expression occurs during cold acclimation. Of the cold-responsive genes, 48 encode known or putative transcription factors. Two of these, RAP2.1 and RAP2.6, were activated by CBF expression and thus presumably control subregulons of the CBF regulon. Transcriptome comparisons indicated that only 12% of the cold-responsive genes are certain members of the CBF regulon. Moreover, at least 28% of the cold-responsive genes were not regulated by the CBF transcription factors, including 15 encoding known or putative transcription factors, indicating that these cold-responsive genes are members of different low-temperature regulons. Significantly, CBF expression at warm temperatures repressed the expression of eight genes that also were downregulated by low temperature, indicating that in addition to gene induction, gene repression is likely to play an integral role in cold acclimation.
Prevention of hypotension during propofol induction: a comparison of preloading with 3.5% polymers of degraded gelatin (Haemaccel) and intravenous ephedrine. (2008)

The present study compared the efficacy of preloading with colloid "Haemaccel" with vasoconstrictor (intravenous ephedrine sulphate) in preventing hypotension during propofol induction. This prospective, randomized study included 120 patients of Amercan Society of Anaesthesiologists (ASA) physical status I and II ageing 21 to 50 years of both gender coming for routine surgery. Patients were randomly allocated into three groups with 40 patients in each. Group A (control) did not receive any study medication, group B received Haemaccel (10 ml/kg intravenously over 10-15 minutes) and group C received injection ephedrine (0.2 mg/kg iv) prior to induction of anaesthesia. Propofol (2.5 mg/kg iv) was used for induction of anaesthesia. Heart rate and blood pressure were recorded before induction (baseline) and then every minute for 5 minutes after administering propofol. Anaesthesia was continued with standard technique thereafter. Hypotension was defined as fall in systolic blood pressure more than 20% from the basal value. The incidence of hypotension in Haemaccel (23.1%) or ephedrine group (22.5%) was significantly less than the control group (67.5%, P<0.01). We conclude that though preloading with colloid (Haemaccel) or prior injection of sympathomimetic (ephedrine) are not fully efficacious in preventing hypotension caused by propofol induction, both decrease the incidence in significant number of patients with heart rate less than baseline value in the colloid group.
[Glutathione S transferases-pi]. (1994)

It has been known that many drug resistant factors including p-glycoprotein related to anticancer drug resistance. It is assumed that Glutathione s-transferase (GST) is one of the resistant factors. In this present study, we examined the relationship between GST (especially GST-pi) and drug resistance, and also possibility of overcoming of drug resistance for GST-pi related drug resistance. We studied whether GST-pi directly related to anticancer drug resistance by transfection of GST-pi antisense cDNA into human colonic cancer cell line (M 7609). By transfection, cytosolic GST-pi concentrations decreased and sensitivity for adriamycin increased. It was confirmed that GST-pi directly related to some anticancer drug resistance including adriamycin. Moreover, we also have found that ketoprofen, which is an inhibitor of GST-pi activity, increased Adriamycin sensitivity. That is, partial overcoming of drug resistance was obtained. In future, it will be expected that GST-pi inhibitors etc are tried for overcoming of drug resistance.
Quantitation of protein kinase C by immunoblot—expression in different cell lines and response to phorbol esters (1987)

Antisera have been raised against human protein kinase C and also against a synthetic peptide based on the sequence of the bovine brain enzyme (LLNQEE-GEYYNVPIPE). These antibodies react with protein kinase C from a number of species (human, murine, rat, rabbit, bovine), indicating substantial conservation of epitopes. These antisera have been used to quantitate directly protein kinase C by immunoblot analysis. We show here that there is a strict correlation between the levels of immunoreactive polypeptide and extractable calcium- and phospholipid-dependent kinase activity for various cell lines. Treatment of murine, rat, and human cells with phorbol dibutyrate was found to deplete levels of immunoreactive protein kinase C severely. A detailed study of the time course of this depletion in Swiss 3T3 cells shows that it follows precisely the loss of extractable activity. On exposure to 400 nM phorbol 12,13-dibutyrate protein kinase C was essentially undetectable by 40 hours; the half-life of this down-regulation was 6.7 hours. This data thus demonstrate that the loss of immunoreactive protein kinase C and of extractable calcium- and phospholipid-dependent kinase activity precisely parallels the phorbol ester induced down-regulation of binding and responsiveness in Swiss 3T3 cells.
Development of a digital microfluidic lab-on-a-chip for automated immunoassay with magnetically responsive beads (2007)

The emerging paradigm of lab-on-a-chip powered by microfluidics is expected to revolutionize miniaturization, automation and integration in the point-of-care centers which require quick, efficient and reproducible results. Furthermore, high throughput requirement from the life sciences laboratories have made the development of lab-on-a-chip a major area of research over the past few years. Immunoassays, which are routinely used to determine the concentrations of various analytes in life sciences laboratories, are one of the most important laboratory tests that require efficient automation and integration. These are different from other laboratory tests in the clinical laboratories such as colorimetric tests because they involve formation of antibody-antigen complexes to generate a signal that can be measured. The immunoassays also involve the application of magnetically responsive beads to increase the surface area for the reactions thereby enhance the signal. Although miniaturization was started in the early 1990's there are no commercial devices that perform immunoassays involving magnetic beads. None of the state-of-the art commercial microfluidic technologies, which are based on continuous flow in etched microchannel, have been able to fully deliver the promised benefits of microfluidics. This is primarily due to their incompatability with common sample matrices and architectural inflexibility. Furthermore, the transport of the magnetic beads in microchannels is a difficult task in continuous mode of operation as magnetic susceptibility of the beads is rather weak and because of demagnetization of the particles. In this thesis, a droplet-based microfluidic lab-on-a-chip based on electrowetting actuation is developed to perform immunoassays using magnetic beads on human physiological samples. Biocompatibility of the electrowetting system is established by demonstrating repeatable and rapid transport of human physiological fluids such as whole blood, serum, proteins such as bovine serum albumin, antibodies for insulin and interleukin-6 and enzymatic reagents such as horseradish peroxidase (HRP), alkaline phosphatase (ALP). Various magnetic configurations for efficient attraction of the magnetic beads that assist in the washing are developed. Several parameters involved in washing magnetic beads are studied and the buffer for resuspending the beads, magnetic strength to attract the magnetic beads and concentration of beads to be used were established. An efficient protocol for washing magnetic beads on chip was developed with a bead retention efficiency of almost 100%. A complete magnetic immunoassay is performed on chip for Insulin and Interleukin-6. The least concentration of Insulin and IL-6 detectable on chip is 0.24 pg/μL and 4 fg/μL respectively. Standard curves are developed for both the analytes over a range of concentrations. The repeatability of the assays is established by performing the assay on different samples on different days and the standard error is shown to be less than 3%. Magnetic immunoassays…
ICDAR 2011 Robust Reading Competition - Challenge 1: Reading Text in Born-Digital Images (Web and Email) (2011)

This paper presents the results of the first Challenge of ICDAR 2011 Robust Reading Competition. Challenge 1 is focused on the extraction of text from born-digital images, specifically from images found in Web pages and emails. The challenge was organized in terms of three tasks that look at different stages of the process: text localization, text segmentation and word recognition. In this paper we present the results of the challenge for all three tasks, and make an open call for continuous participation outside the context of ICDAR 2011.
Endothelial vascular cell adhesion molecule 1 expression is suppressed by melanoma and carcinoma. (1995)

Vascular cell adhesion molecule 1 (VCAM-1) mediates extravasation of circulating leukocytes into inflamed tissues, and presumably, plays a role in the immigration of cytotoxic effector lymphocytes into tumor metastases. Since metastases are rarely cleared by blood-borne cells from the immune system, we asked whether the tumor may escape host defense by interfering with the mechanism of effector cell extravasation. Here we show that in mice and humans, VCAM-1 expression is repressed on tumor-infiltrating vascular endothelial cells in the lungs. On lung blood vessels distant from the tumor, VCAM-1 is constitutively expressed. When melanoma and endothelioma cells were cultured on either side of a Nucleopore membrane, the expression of VCAM-1 on the endothelioma cells was inhibited and VCAM-1 gene transcription was suppressed. We propose that the downregulation of VCAM-1 is a mechanism by which vascularized melanoma and carcinoma avoid invasion by cytotoxic cells of the immune system.
Thiazolidinedione‐Based PI3Kα Inhibitors: An Analysis of Biochemical and Virtual Screening Methods (2011)

A series of synthesized and commercially available compounds were assessed against PI3Kα for in vitro inhibitory activity and the results compared to binding calculated in silico. Using published crystal structures of PI3Kγ and PI3Kδ co-crystallized with inhibitors as a template, docking was able to identify the majority of potent inhibitors from a decoy set of 1000 compounds. On the other hand, PI3Kα in the apo-form, modeled by induced fit docking, or built as a homology model gave only poor results. A PI3Kα homology model derived from a ligand-bound PI3Kδ crystal structure was developed that has a good ability to identify active compounds. The docking results identified binding poses for active compounds that differ from those identified to date and can contribute to our understanding of structure-activity relationships for PI3K inhibitors.
Genetic and molecular approaches to improve nutritional value of Brassica napus L. seed (2008)

Oilseed rape (Brassica napus L.) is a major oil crop that also supplies proteins for the feed industry. In order to reduce total cost production, the objective is to increase oil yield while reducing crop inputs (especially nitrogen and pesticides). Concomitantly, it is necessary to anticipate specific uses (e.g., fatty acid composition) and to ensure the valorisation of the by-products (rapeseed meal). By the past, improvement of seed quality focused on fatty acid balance and low seed glucosinolate content. Current goals include the breeding of yellow-seeded rapeseed lines with high content of seed oil. The use of molecular tools and the exploitation of Arabidopsis knowledge will be presented and discussed.
Subtraction hybridization identifies a transformation progression-associated gene PEG -3 with sequence homology to a growth arrest and DNA damage-inducible gene (1997)

Cancer is a progressive multigenic disorder characterized by defined changes in the transformed phenotype that culminates in metastatic disease. Determining the molecular basis of progression should lead to new opportunities for improved diagnostic and therapeutic modalities. Through the use of subtraction hybridization, a gene associated with transformation progression in virus- and oncogene-transformed rat embryo cells, progression elevated gene-3 (PEG-3), has been cloned. PEG-3 shares significant nucleotide and amino acid sequence homology with the hamster growth arrest and DNA damage-inducible gene gadd34 and a homologous murine gene, MyD116, that is induced during induction of terminal differentiation by interleukin-6 in murine myeloid leukemia cells. PEG-3 expression is elevated in rodent cells displaying a progressed-transformed phenotype and in rodent cells transformed by various oncogenes, including Ha-ras, v-src, mutant type 5 adenovirus (Ad5), and human papilloma virus type 18. The PEG-3 gene is transcriptionally activated in rodent cells, as is gadd34 and MyD116, after treatment with DNA damaging agents, including methyl methanesulfonate and gamma-irradiation. In contrast, only PEG-3 is transcriptionally active in rodent cells displaying a progressed phenotype. Although transfection of PEG-3 into normal and Ad5-transformed cells only marginally suppresses colony formation, stable overexpression of PEG-3 in Ad5-transformed rat embryo cells elicits the progression phenotype. These results indicate that PEG-3 is a new member of the gadd and MyD gene family with similar yet distinct properties and this gene may directly contribute to the transformation progression phenotype. Moreover, these studies support the hypothesis that constitutive expression of a DNA damage response may mediate cancer progression.
An eye movement tracking type head mounted display for virtual reality system: evaluation experiments of a prototype system (2002)

This paper describes a head mounted display (HMD) system which can present realistic visual images of the environment. There are several types of commercial HMDs for virtual reality systems. One of the problems of their systems is that the screen size is small in order to keep the image resolution high. Therefore, the screen frame and displayed images overlap and impair the sense of reality. In order to improve it, namely to present a wider view angle and higher resolution image, a new type of HMD is proposed. The idea is based on superimposing small, high resolution images on wide, low resolution images. The high resolution images are presented only near the center of human retina, according to the motion of eyeball detected. In this paper, the structure of the proto-type display system is explained, and the presentation method of the high resolution image using the prototype system is considered. Also, some evaluation experiments are introduced to demonstrate the effectiveness of the proposed idea.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Attenuation of human immunodeficiency virus type 1 cytopathic effect by a mutation affecting the transmembrane envelope glycoprotein (1991)

The cytopathic effects of human immunodeficiency virus type 1 (HIV-1) infection are specific for cells that express the CD4 viral receptor and consist of syncytium formation and single-cell lysis. Here we report that a mutation (517A) affecting the amino terminus of the HIV-1 gp41 transmembrane envelope glycoprotein resulted in a virus that was markedly less cytopathic than was wild-type HIV-1. In systems in which cell-to-cell transmission of HIV-1 occurred, the replication ability of the 517A virus was comparable with that of the wild-type virus. Even though the levels of viral protein expression, virion production, and interaction of the envelope glycoproteins with CD4 were similar for the 517A and wild-type viruses, both syncytium formation and single-cell lysis were attenuated for the 517A mutant virus. These results demonstrate that an envelope glycoprotein region important for mediating post-receptor binding events in cell membrane fusion is important for the induction of cytopathic effects by HIV-1. These results also indicate that levels of HIV-1 viral proteins or viral particles produced in infected cells are in themselves not sufficient to induce cytopathic effects.
Transient foreign gene expression in chloroplasts of cultured tobacco cells after biolistic delivery of chloroplast vectors. (1990)

Expression of chloramphenicol acetyltransferase (cat) by suitable vectors in chloroplasts of cultured tobacco cells, delivered by high-velocity microprojectiles, is reported here. Several chloroplast expression vectors containing bacterial cat genes, placed under the control of either psbA promoter region from pea (pHD series) or rbcL promoter region from maize (pAC series) have been used in this study. In addition, chloroplast expression vectors containing replicon fragments from pea, tobacco, or maize chloroplast DNA have also been tested for efficiency and duration of cat expression in chloroplasts of tobacco cells. Cultured NT1 tobacco cells collected on filter papers were bombarded with tungsten particles coated with pUC118 (negative control), 35S-CAT (nuclear expression vector), pHD312 (repliconless chloroplast expression vector), and pHD407, pACp18, and pACp19 (chloroplast expression vectors with replicon). Sonic extracts of cells bombarded with pUC118 showed no detectable cat activity in the autoradiograms. Nuclear expression of cat reached two-thirds of the maximal 48 hr after bombardment and the maximal at 72 hr. Cells bombarded with chloroplast expression vectors showed a low level of expression until 48 hr of incubation. A dramatic increase in the expression of cat was observed 24 hr after the addition of fresh medium to cultured cells in samples bombarded with pHD407; the repliconless vector pHD312 showed about 50% of this maximal activity. The expression of nuclear cat and the repliconless chloroplast vector decreased after 72 hr, but a high level of chloroplast cat expression was maintained in cells bombarded with pHD407. Organelle-specific expression of cat in appropriate compartments was checked by introducing various plasmid constructions into tobacco protoplasts by electroporation. Although the nuclear expression vector 35S-CAT showed expression of cat, no activity was observed with any chloroplast vectors.
Nonlinear polarization evolution in passively modelocked fiber lasers (1995)

Single-mode fibers typically contain two eigenmodes with the same light intensity distribution, but with orthogonal polarization states. In perfectly isotropic fibers these modes are degenerate and have the same propagation constants. Hence isotropic fibers are polarization maintaining, i.e. the output polarization state is the same as the input polarization state. However, this statement is not generally valid in the presence of nonlinearities. Though an isotropic fiber is still polarization maintaining for linearly and circularly polarized light independent of the light intensity, an elliptical polarization state will rotate as a function of power.
Tree-Based Pursuit: Algorithm and Properties (2006)

This paper proposes a tree-based pursuit algorithm that efficiently trades off complexity and approximation performance for overcomplete signal expansions. Finding the sparsest representation of a signal using a redundant dictionary is, in general, an NP-hard problem. Even suboptimal algorithms such as Matching Pursuit remain highly complex. We propose a structuring strategy that can be applied to any redundant set of functions, and which basically groups similar atoms together. A measure of similarity based on coherence allows for representing a highly redundant subdictionary of atoms by a unique element, called molecule. When the clustering is applied recursively on atoms and then on molecules, it naturally leads to the creation of a tree structure. We then present a new pursuit algorithm that uses the structure created by clustering as a decision tree. This tree-based algorithm offers important complexity reduction with respect to Matching Pursuit, as it prunes important parts of the dictionary when traversing the tree. Recent results on incoherent dictionaries are extended to molecules, while the true highly redundant nature of the dictionary stays hidden by the tree structure. We then derive recovery conditions on the structured dictionary, under which tree-based pursuit is guaranteed to converge. Experimental results finally show that the gain in complexity offered by tree-based pursuit does in general not have a high penalty on the approximation performance. They show that the dimensionality of the problem is reduced thanks to the tree construction, without significant loss of information