gebhart/patrepeval huggingface dataset:
Two sesquiterpene synthases are responsible for the complex mixture of sesquiterpenes emitted from Arabidopsis flowers (2005)

Despite the fact that Arabidopsis is largely self-pollinating, its flowers emit a complex mixture of terpene volatiles consisting predominantly of a large group of over 20 sesquiterpenes. Here we report that only two terpene synthases, encoded by the florally expressed genes At5g23960 and At5g44630, are responsible for the formation of virtually all sesquiterpenes found in the Arabidopsis floral volatile blend. Two independent mutant lines with T-DNA insertions in the previously identified At5g23960 gene lacked the emission of three sesquiterpenes, including the main sesquiterpene volatile (E)-beta-caryophyllene, confirming the previous in vitro functional assignment for this gene. Flowers of a mutant line carrying a T-DNA insertion in gene At5g44630 emitted these three sesquiterpenes, but did not emit any of the remaining sesquiterpene volatiles. An At5g44630 cDNA was expressed in Escherichia coli and the produced protein catalyzed the conversion of farnesyl diphosphate into over 15 sesquiterpenes in similar proportions to those found in the floral volatile blend. At5g23960 and At5g44630 promoter-beta-glucuronidase (GUS) fusion experiments demonstrated that both genes are expressed in several parts of the Arabidopsis flower, with strong At5g23960 promoter-GUS activity in the stigma and strong expression of At5g44630 in intrafloral nectaries. Given the previously reported antimicrobial activity of terpenes, their production in stigmas and nectaries may serve to inhibit microbial infection at these vulnerable sites. A survey of 37 Arabidopsis thaliana ecotypes revealed quantitative, but almost no qualitative, variations of floral monoterpene and sesquiterpene emissions suggesting that floral terpene volatiles must play some significant role in the life of the Arabidopsis plant.
<title>Thermal properties of state of the art novolak-diazonaphtoquinone systems: differences between bulk and film properties</title> (1993)

As demonstrated by both thermal analysis (DSC) and thermal flow experiments, the latest resists for advanced i-line lithography exhibit improved thermal properties. Emphasis is placed upon experimental details to obtain reliable and meaningful data. In addition to the results of these experiments, the high glass transition temperatures (T<SUB>g</SUB>) measured, equal or superior to the recommended soft-bake conditions, raise new questions concerning the formation and properties of the resist film. The T<SUB>g</SUB> of the film is shown to be different from that of the bulk material and to depend on the bake conditions. The DSC results are confirmed by thermal flow experiments and a good correlation is obtained between the two methods. The consequences induced by the use of high T<SUB>g</SUB> materials on other steps in the lithographic process, namely standing wave reduction and plasma durability, are also discussed.
Development of Autoimmunity in IL-14α-Transgenic Mice (2006)

Multiple genetic loci contribute to the development of systemic lupus erythematosus (SLE). In murine models for SLE, various genes on chromosome four have been implicated. IL-14 is a cytokine originally identified as a B cell growth factor. The il14 gene is located on chromosome 4. IL-14alpha is a cytokine encoded by the plus strand of the IL-14 gene using exons 3-10. The expression of IL-14alpha is increased in (NZB x NZW)F1 mice. In this study, we produced IL-14alpha-transgenic mice to study the role of IL-14alpha in the development of autoimmunity. At age 3-9 mo, IL-14alpha-transgenic mice demonstrate increased numbers of B1 cells in the peritoneum, increased serum IgM, IgG, and IgG 2a and show enhanced responses to T-dependent and T-independent Ags compared with littermate controls. At age 9-17 mo, IL-14alpha-transgenic mice develop autoantibodies, sialadenitis, as in Sjögren's syndrome, and immune complex-mediated nephritis, as in World Health Organization class II SLE nephritis. Between the ages 14-18 mo, 95% of IL-14alpha-transgenic mice developed CD5+ B cell lymphomas, consistent with the lymphomas seen in elderly patients with Sjögren's syndrome and SLE. These data support a role for IL-14alpha in the development of both autoimmunity and lymphomagenesis. These studies may provide a genetic link between these often related disorders.
Distributed regression (2004)

We present distributed regression, an efficient and general framework for in-network modeling of sensor data. In this framework, the nodes of the sensor network collaborate to optimally fit a global function to each of their local measurements. The algorithm is based upon kernel linear regression, where the model takes the form of a weighted sum of local basis functions; this provides an expressive yet tractable class of models for sensor network data. Rather than transmitting data to one another or outside the network, nodes communicate constraints on the model parameters, drastically reducing the communication required. After the algorithm is run, each node can answer queries for its local region, or the nodes can efficiently transmit the parameters of the model to a user outside the network. We present an evaluation of the algorithm based upon data from a 48-node sensor network deployment at the Intel Research - Berkeley Lab, demonstrating that our distributed algorithm converges to the optimal solution at a fast rate and is very robust to packet losses.
Mapping Patterns of CpG Island Methylation in Normal and Neoplastic Cells Implicates Both Upstream and Downstream Regions inde Novo Methylation (1997)

Promoter region CpG island methylation is associated with tumor suppressor gene silencing in neoplasia. GenBank sequence analyses revealed that a number of CpG islands are juxtaposed to multiple Alu repeats, which have been proposed as "de novo methylation centers." These islands also contain multiple Sp1 elements located upstream and downstream of transcription start, which have been shown to protect CpG islands from methylation. We mapped the methylation patterns of the E-cadherin (E-cad) and von Hippel-Lindau (VHL) tumor suppressor gene CpG island regions in normal and neoplastic cells. Although unmethylated in normal tissue, these islands were embedded between densely methylated flanking regions containing multiple Alu repeats. These methylated flanks were segregated from the unmethylated, island CpG sites by Sp1-rich boundary regions. Finally, in human fibroblasts overexpressing DNA methyltransferase, de novo methylation of the E-cad CpG island initially involved sequences at both ends of the island and the adjacent, flanking regions and progressed with time to encompass the entire CpG island region. Together, these data suggest that boundaries exist at both ends of a CpG island to maintain the unmethylated state in normal tissue and that these boundaries may be progressively overridden, eliciting the de novo methylation associated with tumor suppressor gene silencing in neoplasia.
T helper type 1/T helper type 2 cytokines and T cell death: preventive effect of interleukin 12 on activation-induced and CD95 (FAS/APO-1)-mediated apoptosis of CD4+ T cells from human immunodeficiency virus-infected persons. (1995)

Human immunodeficiency virus (HIV) infection leads to a progressive loss of CD4+ T helper (Th) type 1 cell-mediated immunity that is associated with defective in vitro CD4+ T cell proliferation and abnormal T cell death by apoptosis in response to T cell receptor (TCR) stimulation. Quantification of interleukin (IL)-2, interferon gamma, IL-4, IL-5, and IL-10 secretion by immunoassays, and of interferon gamma, IL-4 and IL-10 messenger RNA expression by competitive reverse transcriptase polymerase chain reaction after in vitro stimulation of the TCR revealed a similar Th1 cytokine profile in T cells from HIV-infected persons and from controls. These data indicated that the loss of CD4+ Th1 cell function in HIV-infected persons is not related to a Th1 to Th2 cytokine switch as previously proposed, but to a process of activation-induced death of CD4+ Th1 cells. Despite the absence of elevated levels of Th2 cytokines, apoptosis of CD4+ T cells, but not of CD8+ T cells, was prevented in vitro by antibodies to IL-10 or IL-4, two Th2 cytokines that downregulate Th1 cell responses, or by the addition of recombinant IL-12, a cytokine that upregulates Th1 functions. TCR-induced apoptosis of T cell hybridomas and preactivated T cells has been shown to involve the CD95 (Fas/Apo-1) molecule. CD4+ and CD8+ T cells from HIV-infected persons expressed high levels of the CD95 molecule, and, in contrast to T cells from controls, were highly sensitive to antibody-mediated CD95 ligation, which induced apoptosis in a percentage of T cells similar to that induced by TCR stimulation. As TCR-induced apoptosis, CD95-mediated apoptosis of CD4+ T cells, but not of CD8+ T cells, was prevented by the addition of recombinant IL-12. Together, these findings suggest that apoptosis of CD4+ T cells from HIV-infected persons involves an abnormal sensitivity to CD95 ligation, and to TCR stimulation in the presence of normal levels of Th2 cytokines. The preventive effect of IL-12 on both mechanisms has potential implications for the design of immunotherapy strategies aimed at the upregulation of CD4+ Th1 cell functions in AIDS.
Tense and Aspect Error Correction for ESL Learners Using Global Context (2012)

As the number of learners of English is constantly growing, automatic error correction of ESL learners ’ writing is an increasingly active area of research. However, most research has mainly focused on errors concerning articles and prepositions even though tense/aspect errors are also important. One of the main reasons why tense/aspect error correction is difficult is that the choice of tense/aspect is highly dependent on global context. Previous research on grammatical error correction typically uses pointwise prediction that performs classification on each word independently, and thus fails to capture the information of neighboring labels. In order to take global information into account, we regard the task as sequence labeling: each verb phrase in a document is labeled with tense/aspect depending on surrounding labels. Our experiments show that the global context makes a moderate contribution to tense/aspect error correction. 1
Investigations of bulk dynamic threshold-voltage MOSFET with 65 GHz "normal-mode" f/sub t/ and 220 GHz "over-drive mode" f/sub t/ for RF applications (2002)

The RF properties of bulk dynamic threshold-voltage MOSFET (B-DTMOS) with deep n-well isolation was investigated both under the normal DTMOS mode and two newly-proposed DTMOS operation modes: moderate (0.6 V 0.85 V) modes. While f/sub t/ can be improved to 65 GHz at 12.5 mA with 1.5 V V/sub ds/ bias under normal mode DTMOS operation, a high f/sub t/ of 220 GHz with good linearity and stability is achieved under over-drive operation mode.
Diffusion of Hydrogen and Deuterium in Fused Quartz (1962)

A mass spectrometer was used to record the transfer of hydrogen and deuterium through hollow, thinwalled cylinders of fused quartz over the temperature range of 300–1000°C. Steady-state gas permeation measurements resulted in permeability values which agree well with the literature; however, results of transient experiments which provide a direct means of measuring diffusion coefficients did not agree with so-called ``normal'' diffusion. The deviation from normal diffusion increases with increasing temperature. Measurements were made of the temperature variation in the rate of release of deuterium from fused quartz resulting from replacement by dissolved hydrogen. A chemical exchange between the diffusing molecules (H2 or D2) and one or more species of trapped gas within the fused quartz is thought to be the principal cause of the nondiffusion-like character of the high-temperature gas transport. Activation energies were calculated for the permeability (H2:8.88 kcal/mole. D2:9.05 kcal/mole), diffusion (H2:10.37 kcal/mole D2:10.52 kcal/mole), and chemical exchange (15.5 kcal/mole) mechanisms. Experimental solubilities were compared with the so-called normal solubilities (Sn=permeability/diffusion coefficient) and were found to exceed the normal to a greater extent with increasing temperature.
Allergenicity of alum‐precipitated grass pollen extracts with different RAST activity (1987)

The biological potency of therapeutic allergen extracts is fundamentally important in terms of maximal security of immunotherapy, especially when changing batches. As regards pyridine-extracted alum-precipitated allergen preparations, the potency is commercially controlled by the RAST technique. In the present study, titrated intradermal tests were performed in thirty-three adult grass-pollen rhinitis patients with three ten-fold dilutions of two batches of Allpyral 5-grass mix with different RAST activity. The difference in potency was estimated as the horizontal distance at the midpoint of the two dose-response curves after performing linear regression on the log-dose/log-weal area response, and as the concentration of each batch eliciting a weal equal to the histamine HC1 0.1 mg/ml reference. The difference in potency as estimated by RAST was a factor 5.0 vs a factor 8.3 and 7.2 (median) estimated by the horizontal distance and histamine-equivalent reaction, respectively. Considering the biological variation, the RAST-estimated difference in potency is in the same order as that found by skin test. It is, therefore, concluded that the routine control of new production batches by RAST is acceptable with the use of standardized reference sera as regards alum-precipitated grass pollen allergen extracts.
Autophagy as a Regulated Pathway of Cellular Degradation (2000)

Macroautophagy is a dynamic process involving the rearrangement of subcellular membranes to sequester cytoplasm and organelles for delivery to the lysosome or vacuole where the sequestered cargo is degraded and recycled. This process takes place in all eukaryotic cells. It is highly regulated through the action of various kinases, phosphatases, and guanosine triphosphatases (GTPases). The core protein machinery that is necessary to drive formation and consumption of intermediates in the macroautophagy pathway includes a ubiquitin-like protein conjugation system and a protein complex that directs membrane docking and fusion at the lysosome or vacuole. Macroautophagy plays an important role in developmental processes, human disease, and cellular response to nutrient deprivation.
Synchronization of Cortical Activity and its Putative Role in Information Processing and Learning (1993)

Macrophage polarization refers to how macrophages have been activated at a given point in space and time. Polarization is not fixed, as macrophages are sufficiently plastic to integrate multiple signals, such as those from microbes, damaged tissues, and ...Read More
First trimester urinary placental growth factor and development of pre‐eclampsia (2009)

The development of pre-eclampsia is not preceded by altered urinary PlGF concentration in the first trimester of pregnancy.
Effects of S-nitroso-glutathione in the human forearm circulation: evidence for selective inhibition of platelet activation (1994)

These results show that GSNO is more effective as an inhibitor of platelet activation than as a vasodilator, suggesting that it is possible to achieve selective antiplatelet and potentially antithrombotic effects with NO donors.
C3a and C3b Activation Products of the Third Component of Complement (C3) Are Critical for Normal Liver Recovery after Toxic Injury (2004)

Although the complement system has been implicated in liver regeneration after toxic injury and partial hepatectomy, the mechanism or mechanisms through which it participates in these processes remains ill-defined. In this study, we demonstrate that complement activation products (C3a, C3b/iC3b) are generated in the serum of experimental mice after CCl(4) injection and that complement activation is required for normal liver regeneration. Decomplementation by cobra venom factor resulted in impaired entry of hepatocytes into S phase of the cell cycle. In addition, livers from C3-deficient (C3(-/-)) mice showed similarly impaired proliferation of hepatocytes, along with delayed kinetics of both hepatocyte hyperplasia and removal of injured liver parenchyma. Restoration of hepatocyte proliferative capabilities of C3(-/-) mice through C3a reconstitution, as well as the impaired regeneration of C3a receptor-deficient mice, demonstrated that C3a promotes liver cell proliferation via the C3a receptor. These findings, together with data showing two waves of complement activation, indicate that C3 activation is a pivotal mechanism for liver regeneration after CCl(4) injury, which fulfills multiple roles; C3a generated early after toxin injection is relevant during the priming of hepatocytes, whereas C3 activation at later times after CCl(4) treatment contributes to the clearance of injured tissue.
RAFT polymerization of fatty acid containing monomers: controlled synthesis of polymers from renewable resources (2013)

The incorporation of bio-renewable resources such as fatty acids into the polymer chain allows tailoring the properties of products, for their widespread applications. A series of methacrylate monomers with side-chain fatty acids (FAMA) were synthesized by esterification of 2-hydroxyethyl methacrylate (HEMA) and fatty acids, such as caprylic, capric, lauric, mysritic, palmitic and stearic acid. Consequent polymerization of FAMAs via reversible addition-fragmentation chain transfer (RAFT) gave side-chain fatty acid-containing well-defined polymers (PFAMA) with targeted molecular weights, narrow molecular weight distribution and precise chain-end functionality. The PFAMAs were subsequently used as macro-chain transfer agents (macro-CTA) for the polymerization of 2-(2-methoxyethoxy)ethyl methacrylate (MEO2MA) to obtain block copolymers. Homopolymers with fatty acid pendants display crystalline behaviour depending on the chain length of the fatty acids, evidenced by differential scanning calorimetry (DSC), polarized optical microscopy, small-angle X-ray scattering (SAXS) and wide-angle X-ray scattering (WAXS) techniques.
Chemical nature of the light emitter of the Aequorea green fluorescent protein (1996)

The jellyfish Aequorea victoria possesses in the margin of its umbrella a green fluorescent protein (GFP, 27 kDa) that serves as the ultimate light emitter in the bioluminescence reaction of the animal. The protein is made up of 238 amino acid residues in a single polypeptide chain and produces a greenish fluorescence (lambda max = 508 nm) when irradiated with long ultraviolet light. The fluorescence is due to the presence of a chromophore consisting of an imidazolone ring, formed by a post-translational modification of the tripeptide -Ser65-Tyr66-Gly67-. GFP has been used extensively as a reporter protein for monitoring gene expression in eukaryotic and prokaryotic cells, but relatively little is known about the chemical mechanism by which fluorescence is produced. To obtain a better understanding of this problem, we studied a peptide fragment of GFP bearing the chromophore and a synthetic model compound of the chromophore. The results indicate that the GFP chromophore consists of an imidazolone ring structure and that the light emitter is the singlet excited state of the phenolate anion of the chromophore. Further, the light emission is highly dependent on the microenvironment around the chromophore and that inhibition of isomerization of the exo-methylene double bond of the chromophore accounts for its efficient light emission.
A delayed-early gene activated by fibroblast growth factor-1 encodes a protein related to aldose reductase. (1994)

The addition of polypeptide mitogens to quiescent cell lines induces the expression of various gene products, some of which are likely to perform functions critical for cell cycle progression, DNA synthesis, and mitosis. We have used a differential display approach to identify fibroblast growth factor (FGF)-1-inducible genes in NIH-3T3 cells. One of these genes, termed FGF-regulated (FR)-1, encodes a 316-amino acid protein with approximately 82% amino acid sequence identity to an abundant protein expressed in mouse vas deferens and approximately 70% identity to human aldose reductase. The function of the vas deferens protein is unknown; however, aldose reductase is an NADPH-dependent monomeric oxidoreductase implicated in the pathogenesis of diabetic complications. FGF-1 induction of FR-1 mRNA expression is first detectable at 4 h after mitogen addition and is dependent on de novo RNA and protein synthesis. FGF-2 or phorbol ester treatment can also increase FR-1 mRNA levels; in contrast, whole blood serum or individual growth factors present in serum have only minimal effects on FR-1 mRNA expression. FR-1 mRNA is detectable in a number of mouse tissues but is most abundant in newborn liver and in adult intestine, ovary, and testis. These results raise the possibility that aldose reductase-related proteins may play a role in FGF-1- and FGF-2-stimulated mitogenesis.
Functional expression of bacteriorhodopsin in oocytes allows direct measurement of voltage dependence of light induced H+ pumping (1995)

We report on the first successful expression of the light driven H + pump, bacteriorhodopsin, into the plasma membrane of oocytes from Xenopus laevis . The light induced photocurrents which reflect the pumping of H + by BR were analysed under voltage clamp conditions. At least 100 active BR molecules per μm 2 were expressed in the plasma membrane so that both the voltage clamp and giant patch clamp method could be applied. We show that H + pumping by BR is modulated by the membrane potential, i.e. the pump current shows strong voltage dependence in the range measured between −165 mV to +60 mV.
Using the RDP Classifier to Predict Taxonomic Novelty and Reduce the Search Space for Finding Novel Organisms (2012)

We conclude that selecting a read-length appropriate RDP bootstrap score can significantly reduce the search space for identifying novel genera and higher levels in taxonomy. In addition, having a well-represented database significantly improves performance while having genera that are "highly" similar does not make a significant improvement. On a real dataset from an Amazon Terra Preta soil sample, we show that the detector can predict (or correlates to) whether novel sequences will be assigned to new taxa when the RDP database "doubles" in the future.