gebhart/patrepeval huggingface dataset:
A Genomic Approach to Identify Regulatory Nodes in the Transcriptional Network of Systemic Acquired Resistance in Plants (2006)

Many biological processes are controlled by intricate networks of transcriptional regulators. With the development of microarray technology, transcriptional changes can be examined at the whole-genome level. However, such analysis often lacks information on the hierarchical relationship between components of a given system. Systemic acquired resistance (SAR) is an inducible plant defense response involving a cascade of transcriptional events induced by salicylic acid through the transcription cofactor NPR1. To identify additional regulatory nodes in the SAR network, we performed microarray analysis on Arabidopsis plants expressing the NPR1-GR (glucocorticoid receptor) fusion protein. Since nuclear translocation of NPR1-GR requires dexamethasone, we were able to control NPR1-dependent transcription and identify direct transcriptional targets of NPR1. We show that NPR1 directly upregulates the expression of eight WRKY transcription factor genes. This large family of 74 transcription factors has been implicated in various defense responses, but no specific WRKY factor has been placed in the SAR network. Identification of NPR1-regulated WRKY factors allowed us to perform in-depth genetic analysis on a small number of WRKY factors and test well-defined phenotypes of single and double mutants associated with NPR1. Among these WRKY factors we found both positive and negative regulators of SAR. This genomics-directed approach unambiguously positioned five WRKY factors in the complex transcriptional regulatory network of SAR. Our work not only discovered new transcription regulatory components in the signaling network of SAR but also demonstrated that functional studies of large gene families have to take into consideration sequence similarity as well as the expression patterns of the candidates.
Lipid composition and phospholipid asymmetry of membranes from a Schwann cell line (1997)

We report the total lipid composition and phospholipid asymmetry of a plasma membrane preparation isolated from a Schwann cell line (NF1T) derived from a human neurofibroma. The specific activities of three plasma membrane markers (5'-nucleotidase, Na-K-ATPase, and CNPase) were 8-fold, 12-fold, and 16-fold higher, respectively, in the plasma membrane fraction compared to the specific activities found in the total homogenate. The specific activities of the marker enzymes of intracellular membranes in the isolated plasma membrane fraction indicated little contamination with intracellular organelles. The enrichment of cholesterol (3-fold), sphingomyelin (3-fold), and glycolipids (cerebrosides 8-fold, sulfatides 5-fold) also indicated a high degree of purity of the plasma membrane fraction. The high content of phosphatidylinositol and phosphatidylcholine (10% and 44% of total phospholipid) and the low phosphatidylserine and phosphatidylethanolamine content (3% and 14% of the total phospholipid) were also characteristic of the plasma membrane fraction derived from this cell line. The transbilayer phospholipid distribution of the plasma membrane in intact cells and in the isolated plasma membrane fraction was investigated by using phospholipase A2 (bee venom) and sphingomyelinase (S. aureus). The phospholipid asymmetry of NF1T plasma membrane followed the general features of phospholipid asymmetry in eukaryotic cells: sphingomyelin and phosphatidylcholine were preferentially located in the outer leaflet (90% and 89%, respectively) while the aminophospholipids phosphatidylethanolamine, phosphatidylserine, and phosphatidylinositol were in the inner half of the membrane (85%, 96%, and 69%, respectively). A high percentage of the total plasma membrane phosphatidylinositol (31%) was found in the outer side of the membrane indicating a decreased asymmetric distribution for this negatively charged phospholipid. The phospholipid asymmetry found in the plasma membrane vesicle fraction corroborated the phospholipid asymmetry of the intact cells, thus confirming that the plasma membrane vesicles maintained the original orientation and lipid asymmetry after homogenization and/or sonication.
Synergistic effect with Phe‐Gly‐Leu‐Met‐NH<sub>2</sub> of the C‐terminal of substance P and insulin‐like growth factor‐1 on epithelial wound healing of rabbit cornea (1999)

1. We previously reported that substance P and insulin-like growth factor-1 (IGF-1) synergistically stimulate corneal epithelial wound healing in vitro and in vivo. We wished to identify which portion of the amino acid sequence of substance P might be responsible for this synergism. 2. Corneal epithelial migration was not affected by the addition of any one of the following factors: substance P; Phe-Gly-Leu-Met-NH2 (C-terminal of substance P); Val-Gly-Leu-Met-NH2 (C-terminal of neurokinin A, neurokinin B, and kassinin); Tyr-Gly-Leu-Met-NH2 (C-terminal of physalaemin); Ile-Gly-Leu-Met-NH2 (C-terminal of eledoisin); or Gly-Leu-Met-NH2 (common C-terminal of tachykinins). 3. In the presence of IGF-1, only substance P and Phe-Gly-Leu-Met-NH2 were synergistic in stimulating corneal epithelial migration in a dose-dependent fashion. 4. The combination of Phe-Gly-Leu-Met-NH2 and IGF-1 did not affect the incorporation of [3H]-thymidine into corneal epithelial cells. 5. Treatment with Phe-Gly-Leu-Met-NH2 and IGF-1, but not with Phe-Gly-Leu-Met-NH2 or IGF-1 alone, increased attachment of corneal epithelial cells to a fibronectin matrix. 6. The levels of alpha5 and beta1 integrin were not affected by Phe-Gly-Leu-Met-NH2 or IGF-1 alone, but they were significantly increased by the combination of Phe-Gly-Leu-Met-NH2 and IGF-1. 7. Topical application of the same combination facilitated corneal epithelial wound closure in vivo. 8. These results demonstrated that Phe-Gly-Leu-Met-NH2, a sequence of 4 amino-acids of the C-terminal of substance P, is the minimum sequence necessary to produce the synergistic effects of substance P and IGF-1 on corneal epithelial wound healing.
Distribution of AAV-TK following Intracranial Convection-Enhanced Delivery into Rats (2000)

Adeno-associated virus (AAV)-based vectors are being tested in animal models as viable treatments for glioma and neurodegenerative disease and could potentially be employed to target a variety of central nervous system disorders. The relationship between dose of injected vector and its resulting distribution in brain tissue has not been previously reported nor has the most efficient method of delivery been determined. Here we report that convection-enhanced delivery (CED) of 2.5 x 10(8), 2.5 x 10(9), or 2.5 x 10(10) particles of AAV-thymidine kinase (AAV-TK) into rat brain revealed a clear dose response. In the high-dose group, a volume of 300 mm3 of brain tissue was partially transduced. Results showed that infusion pump and subcutaneous osmotic pumps were both capable of delivering vector via CED and that total particle number was the most important determining factor in obtaining efficient expression. Results further showed differences in histopathology between the delivery groups. While administration of vector using infusion pump had relatively benign effects, the use of osmotic pumps resulted in notable toxicity to the surrounding brain tissue. To determine tissue distribution of vector following intracranial delivery, PCR analysis was performed on tissues from rats that received high doses of AAV-TK. Three weeks following CED, vector could be detected in both hemispheres of the brain, spinal cord, spleen, and kidney.
Improved “Activator Trap” Method for the Isolation of Transcriptional Activation Domains from Random DNA Fragments (1996)

We have previously developed an "activator trap" method for selective isolation of activation domains from viral and cellular transcription factors. In this method, random sonicated DNA fragments were ligated next to the DNA binding domain (DBD) of the GAL4 factor in a plasmid that also contained a simian virus 40 (SV40) replication origin. A library of such random insert plasmids was transfected into a monkey cell line (CV-1-5GT), which had been stably transformed with a GAL4-inducible SV40 T-antigen gene. Chimeric GAL factors with a heterologous activation domain were harvested after selective replication in these CV-1-5GT cells. Here we report a simplification and generalization of the "activator trap" method. First, the time-consuming library construction step can be omitted by direct transfection of the sonicated DNA fragments and the linearized recipient plasmid vector into CV-1-5GT cells to obtain chimeric GAL-activation factors by in vivo ligations. Second, the dependence on CV-1-5GT cells can be bypassed by direct co-transfection of all components, including a plasmid carrying the T-antigen gene into cells other than CV-1-5GT. This latter step allows the application of the method to cultured human cells, as demonstrated with the human B-cell line BJA-B.
Development and Optimization of High-Throughput Methods To Measure<i>Plasmodium falciparum</i>-Specific Growth Inhibitory Antibodies (2006)

Antibodies that inhibit replication of Plasmodium falciparum in erythrocytes are thought to be important both in acquired immunity to malaria and as mediators of immunity generated by candidate blood-stage vaccines. However, several constraints have limited the study of these functional antibodies in population studies and vaccine trials. We report the development and optimization of high-throughput growth inhibition assays with improved sensitivity that use minimal volumes of test serum. The major inhibitory activity of serum from exposed donors was antibody mediated, but nonspecific inhibitory factors were found in untreated serum. Culture volumes could be effectively reduced to 25 microl to limit amounts of test serum or inhibitors used in assays. Performing inhibition assays over two cycles of parasite replication gave greater sensitivity than single-cycle assays, and a simple two-cycle inhibition assay was developed that yielded highly reproducible results. Determination of parasite growth by flow cytometry was most suitable for high-throughput assays using small culture volumes and was more sensitive than parasite lactate dehydrogenase assays and less prone to error and variation than microscopy. We evaluated and optimized methods to remove antimalarials and nonspecific inhibitory factors from serum that are suitable for use with small volumes of samples that are typically obtained from clinical studies. Both microdialysis and immunoglobulin purification by ammonium sulfate precipitation were effective and practical. These methods should facilitate evaluation of vaccine trials and clinical studies of immunity and are also suitable for testing drugs and other compounds for antimalarial activity.
Electrostatic fiber spinning from polymer melts. III. Electrostatic deformation of a pendant drop of polymer melt (1981)

Abstract It has been previously shown that fine jets can be drawn from polymer melts with the aid of an electric field. In an effort to understand the mechanism of jet formation, preliminary experiments have been carried out on the deformation of pendant drops of molten polymers(nylon 12 and polyethylene) subjected to an electric field. The drop deformation was measured as a function of field intensity and frequency, and the results were interpreted in terms of a theory due to Torza et al. It is shown that there is qualitative agreement between the theory and experimental observations. This permits the identification of the parameters influencing the drop deformation and leads to a qualitative picture of the mechanism of deformation.
Cloning, Sequencing, and Expression of the Genes Encoding an Isocyclomaltooligosaccharide Glucanotransferase and an α-Amylase from a<i>Bacillus circulans</i>Strain (2006)

The gene for a novel glucanotransferase, isocyclomaltooligosaccharide glucanotransferase (IgtY), involved in the synthesis of a cyclomaltopentaose cyclized by an alpha-1,6-linkage [ICG5; cyclo-{-->6)-alpha-D-Glcp-(1-->4)-alpha-D-Glcp-(1-->4)-alpha-D-Glcp-(1-->4)-alpha-D-Glcp-(1-->4)-alpha-D-Glcp-(1-->}] from starch, was cloned from the genome of B. circulans AM7. The IgtY gene, designated igtY, consisted of 2,985 bp encoding a signal peptide of 35 amino acids and a mature protein of 960 amino acids with a calculated molecular mass of 102,071 Da. The deduced amino-acid sequence showed similarities to 6-alpha-maltosyltransferase, alpha-amylase, and cyclomaltodextrin glucanotransferase. The four conserved regions common in the alpha-amylase family enzymes were also found in this enzyme, indicating that this enzyme should be assigned to this family. The DNA sequence of 8,325-bp analyzed in this study contained two open reading frames (ORFs) downstream of igtY. The first ORF, designated igtZ, formed a gene cluster, igtYZ. The amino-acid sequence deduced from igtZ exhibited no similarity to any proteins with known or unknown functions. IgtZ was expressed in Escherichia coli, and the enzyme was purified. The enzyme acted on maltooligosaccharides that have a degree of polymerization (DP) of 4 or more, amylose, and soluble starch to produce glucose and maltooligosaccharides up to DP5 by a hydrolysis reaction. The enzyme (IgtZ), which has a novel amino-acid sequence, should be assigned to alpha-amylase. It is notable that both IgtY and IgtZ have a tandem sequence similar to a carbohydrate-binding module belonging to a family 25. These two enzymes jointly acted on raw starch, and efficiently generated ICG5.
Modifiers of free radicals inhibit in vitro the oncogenic actions of x-rays, bleomycin, and the tumor promoter 12-O-tetradecanoylphorbol 13-acetate. (1983)

Using short-term cultures of hamster embryo cells, we have examined the effects of the free-radical scavenger superoxide dismutase (superoxide:superoxide oxidoreductase, EC 1.15.1.1) and the enzyme catalase (hydrogen-peroxide:hydrogenperoxide oxidoreductase, EC 1.11.1.6) on x-ray- and bleomycin-induced transformation and on the enhancement of radiogenic transformation by the tumor promoter 12-O-tetradecanoylphorbol 13-acetate (TPA). We find that superoxide dismutase inhibits (i) transformation induced by x-ray and bleomycin and (ii) promotional action of TPA in vitro. The results suggest that the oncogenic action of x-rays and bleomycin and the enhancement of oncogenic transformation by TPA are mediated in part by free radicals. The findings also suggest that superoxide dismutase can serve as an inhibitor of oncogenesis and that its actions, as seen in this in vitro system, are most predominantly on inhibiting late events in the progression of cellular transformation--those associated with promotion.
Rapid caspase‐dependent cell death in cultured human breast cancer cells induced by the polyamine analogue <i>N</i><sup>1</sup>,<i>N</i><sup>11</sup>‐diethylnorspermine (2002)

The spermine analogue N(1),N(11)-diethylnorspermine (DENSPM) efficiently depletes the cellular pools of putrescine, spermidine and spermine by down-regulating the activity of the polyamine biosynthetic enzymes and up-regulating the activity of the catabolic enzyme spermidine/ spermine N(1)-acetyltransferase (SSAT). In the breast cancer cell line L56Br-C1, treatment with 10 microm DENSPM induced SSAT activity 60 and 240-fold at 24 and 48 h after seeding, respectively, which resulted in polyamine depletion. Cell proliferation appeared to be totally inhibited and within 48 h of treatment, there was an extensive apoptotic response. Fifty percent of the cells were found in the sub-G(1) region, as determined by flow cytometry, and the presence of apoptotic nuclei was morphologically assessed by fluorescence microscopy. Caspase-3 and caspase-9 activities were significantly elevated 24 h after seeding. At 48 h after seeding, caspase-3 and caspase-9 activities were further elevated and at this time point a significant activation of caspase-8 was also found. The DENSPM-induced cell death was dependent on the activation of the caspases as it was inhibited by the general caspase inhibitor Z-Val-Ala-Asp fluoromethyl ketone. The results are discussed in the light of the L56Br-C1 cells containing mutated BRCA1 and p53, two genes involved in DNA repair.
Statistical models of music-listening sessions in social media (2010)

User experience in social media involves rich interactions with the media content and other participants in the community. In order to support such communities, it is important to understand the factors that drive the users' engagement. In this paper we show how to define statistical models of different complexity to describe patterns of song listening in an online music community. First, we adapt the LDA model to capture music taste from listening activities across users and identify both the groups of songs associated with the specific taste and the groups of listeners who share the same taste. Second, we define a graphical model that takes into account listening sessions and captures the listening moods of users in the community. Our session model leads to groups of songs and groups of listeners with similar behavior across listening sessions and enables faster inference when compared to the LDA model. Our experiments with the data from an online media site demonstrate that the session model is better in terms of the perplexity compared to two other models: the LDA-based taste model that does not incorporate cross-session information and a baseline model that does not use latent groupings of songs.
Test-retest characteristics of the Balloon Analogue Risk Task (BART). (2008)

The Balloon Analogue Risk Task (BART) is a computerized decision-making task that provides a test of behavioral risk taking. The task is increasingly used in laboratory settings and in the field with young adults and adolescents. However, there are currently no published data about the test-retest characteristics of the task when it is administered on separate days. The current paper addresses this gap. Risky behavior on the BART (adjusted average pumps) showed acceptable test-retest reliability across days (r = +.77, p < .001). The data indicate that risk behavior on the BART has adequate test-retest stability and therefore performance on the task on a single occasion is likely to be representative of an individual's performance on other occasions.
Nicotine modulates the neurotoxic effect of β-amyloid protein(25–35) in hippocampal cultures (1997)

Two major features of Alzheimer's disease (AD) are beta-amyloid protein (beta AP) deposition and a severe cholinergic deficit. An association between the two is suggested by the negative correlation found between cigarette smoking and AD. We sought to investigate this further by examining the effects of acute and chronic nicotine exposure on beta AP-induced neuronal loss in rat hippocampal cultures. Nicotine was found to attenuate the neurotoxicity of higher concentrations of beta AP(25-35), an effect which was enhanced by longer nicotine pretreatment and significantly inhibited by the nicotine receptor antagonist mecamylamine. Our results suggest that nicotine partially protects against the neurotoxic actions of beta AP(25-35) via a receptor-mediated pathway.
Myogenic stem cell function is impaired in mice lacking the <i>forkhead</i> /winged helix protein MNF (2000)

Myocyte nuclear factor (MNF) is a winged helix transcription factor that is expressed selectively in myogenic stem cells (satellite cells) of adult animals. Using a gene knockout strategy to generate a functional null allele at the Mnf locus, we observed that mice lacking MNF are viable, but severely runted. Skeletal muscles of Mnf-/- animals are atrophic, and satellite cell function is impaired. Muscle regeneration after injury is delayed and incomplete, and the normal timing of expression of cell cycle regulators and myogenic determination genes is dysregulated. Mnf mutant mice were intercrossed with mdx mice that lack dystrophin and exhibit only a subtle myopathic phenotype. In contrast, mdx mice that also lack MNF die in the first few weeks of life with a severe myopathy. Haploinsufficiency at the Mnf locus (Mnf+/-) also exacerbates the mdx phenotype to more closely resemble Duchenne's muscular dystrophy in humans. We conclude that MNF acts to regulate genes that coordinate the proliferation and differentiation of myogenic stem cells after muscle injury. Animals deficient in MNF may prove useful for evaluation of potential therapeutic interventions to promote muscle regeneration for patients having Duchenne's muscular dystrophy.
Nonlinear control experiment of RC car using internet (2005)

This paper describes the laboratory-based remote control system utilizing the Internet environment, which can be used at some specified fields. It is developed to prepare a platform for the experimental evaluation of many types of AUVs control algorithms for the autonomous or semi-autonomous approaches. As a preliminary study, using the remote control system, we have performed the tracking control experiment of a nonholonomic RC toy car, which has many unideal mechanical characteristics. Some experiment results are shown and discussed
NuRD Blocks Reprogramming of Mouse Somatic Cells into Pluripotent Stem Cells (2013)

Reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) by overexpression of a defined set of transcription factors requires epigenetic changes in pluripotency genes. Nuclear reprogramming is an inefficient process and the molecular mechanisms that reset the epigenetic state during iPSC generation are largely unknown. Here, we show that downregulation of the nucleosome remodeling and deacetylation (NuRD) complex is required for efficient reprogramming. Overexpression of Mbd3, a subunit of NuRD, inhibits induction of iPSCs by establishing heterochromatic features and silencing embryonic stem cell-specific marker genes, including Oct4 and Nanog. Depletion of Mbd3, on the other hand, improves reprogramming efficiency and facilitates the formation of pluripotent stem cells that are capable of generating viable chimeric mice, even in the absence of c-Myc or Sox2. The results establish Mbd3/NuRD as an important epigenetic regulator that restricts the expression of key pluripotency genes, suggesting that drug-induced downregulation of Mbd3/NuRD may be a powerful means to improve the efficiency and fidelity of reprogramming.
Generation, Characterization, and Deprotonation of Phenol Radical Cations (1999)

A variety of methoxy- and methyl-substituted phenol radical cations have been generated and characterized by laser flash photolysis in solution under ambient conditions. The radical cations were generated by either photosensitized electron transfer using 1,4-dicyanonaphthalene with biphenyl as a cosensitizer in acetonitrile or by direct excitation of the phenol at 266 nm. The phenol radical cations have absorption maxima between 410 and 460 nm, with the exception of the 3,5-dimethoxyphenol which absorbs at 580 nm. The assignment of the observed transients to phenol radical cations is based on their spectral similarity to matrix spectra for the same species and to the corresponding methoxybenzene radical cations, as well as their characteristic reactivity. In the presence of small amounts of water the radical cations are not detected and the phenoxyl radical is the only observed transient in the photosensitized electron transfer. For those phenols for which authentic phenoxyl spectra are not available, the identity of the radical was confirmed by its generation by hydrogen abstraction by the tert-butoxyl radical. Although several of the phenols can be photoionized in either 1:1 aqueous ethanol or in acetonitrile, this is a less general route for the formation and characterization of the phenol radical cations. The rate constants for deprotonation of the phenol radical cations by water were measured and fall within the range (0.6−6) × 108 M-1 s-1; the 2-methoxyphenol radical cation is more reactive than the 4-methoxy, consistent with a recent estimate of the pKa for these species.