gebhart/patrepeval huggingface dataset:
Messenger RNA-based Vaccines With Dual Activity Induce Balanced TLR-7 Dependent Adaptive Immune Responses and Provide Antitumor Activity (2010)

In Brief Direct vaccination with messenger RNA (mRNA) molecules encoding tumor-associated antigens is a novel and promising approach in cancer immunotherapy. The main advantage of using mRNA for vaccination is that the same molecule not only provides an antigen source for adaptive immunity, but can simultaneously bind to pattern recognition receptors, thus stimulating innate immunity. However, achieving both features remains challenging, as the complexation of mRNA required for immune-stimulating activity may inhibit its translatability. In this study, we present a new and more effective vaccine design: a two-component mRNA-based tumor vaccine that supports both: antigen expression and immune stimulation, mediated by Toll like receptor 7 (TLR7). The two-component mRNA vaccines, containing free and protamine-complexed mRNA, induce balanced adaptive immune responses providing humoral as well as T cell mediated immunity. This balanced immune response is based on the induction of antigen-specific CD4+ T helper cells and cytotoxic CD8+ T cells. Once activated, these CD4+ and CD8+ T cells secrete a wide set of cytokines, which drive a TH1 response. Immunization with the two-component vaccines induces sustained memory responses, mediated by antigen-specific memory T cells. Moreover, treatment of mice with the two-component mRNA vaccine mediates a strong antitumor response against OVA-expressing tumor cells, not only in a prophylactic but also in a therapeutic setting. In conclusion, two-component mRNA vaccines with self-adjuvanting activity induce balanced adaptive immune responses and mediate sustained antitumor activity. Supplemental Digital Content is available for this article. Direct URL citations appear in the printed text and are provided in the HTML and PDF versions of this article on the Journal's website, www.immunotherapy-journal.com.
Meniscal repair using fibrin sealant and endothelial cell growth factor (1992)

The effect of fibrin sealant and endothelial cell growth factor on the healing of defects of the avascular portion of canine menisci was investigated in 30 menisci of 15 adult mongrel dogs. The defects were treated in one of three ways: Group 1, the defect was left empty; Group 2, the defect was filled with fibrin sealant; and Group 3, the defect was filled with fibrin sealant and endothelial cell growth factor. The healing process was evaluated macroscopically and histologically at intervals of 1, 2, 6, 12, and 24 weeks. The average percentage of each defect that was filled with connective tissue was 5% in Group 1, 76.6% in Group 2, and 89.4% in Group 3. In the early phase of this repair, the extrinsic pannus-like tissue that contained many capillary vessels extended from the meniscosynovial junction into the defect. Subsequently, organized fibrous connective tissue was formed, which had changed to cartilaginous tissue at 12 to 24 weeks. The combination of fibrin sealant and endothelial cell growth factor enhanced the neovascularization and formation of granulation tissue, which accounted for the increased healing level in the avascular portion of the meniscus.
Aryl-Fluoride Reductive Elimination from Pd(II):  Feasibility Assessment from Theory and Experiment (2007)

DFT methods were used to elucidate features of coordination environment of Pd(II) that could enable Ar-F reductive elimination as an elementary C-F bond-forming reaction potentially amenable to integration into catalytic cycles for synthesis of organofluorine compounds with benign stoichiometric sources of F(-). Three-coordinate T-shaped geometry of Pd(II)Ar(F)L (L = NHC, PR(3)) was shown to offer kinetics and thermodynamics of Ar-F elimination largely compatible with synthetic applications, whereas coordination of strong fourth ligands to Pd or association of hydrogen bond donors with F each caused pronounced stabilization of Pd(II) reactant and increased activation barrier beyond the practical range. Decreasing donor ability of L promotes elimination kinetics via increasing driving force and para-substituents on Ar exert a sizable SNAr-type TS effect. Synthesis and characterization of the novel [Pd(C(6)H(4)-4-NO(2))ArL(mu-F)](2) (L = P(o-Tolyl)(3), 17; P(t-Bu)(3), 18) revealed stability of the fluoride-bridged dimer forms of the requisite Pd(II)Ar(F)L as the key remaining obstacle to Ar-F reductive elimination in practice. Interligand steric repulsion with P(t-Bu)(3) served to destabilize dimer 18 by 20 kcal/mol, estimated with DFT relative to PMe(3) analog, yet was insufficient to enable formation of greater than trace quantities of Ar-F; C-H activation of P(t-Bu)(3) followed by isobutylene elimination was the major degradation pathway of 18 while Ar/F- scrambling and Ar-Ar reductive elimination dominated thermal decomposition of 17. However, use of Buchwald's L = P(C(6)H(4)-2-Trip)(t-Bu)(2) provided the additional steric pressure on the [PdArL(mu-F)](2) core needed to enable formation of aryl-fluoride net reductive elimination product in quantifiable yields (10%) in reactions with both 17 and 18 at 60 degrees over 22 h.
Developmental and environmental regulation of tissue‐ and cell‐specific expression for a pea protein farnesyltransferase gene in transgenic plants (1997)

Farnesylation mediates membrane targeting and in vivo activities of several key regulatory proteins such as Ras and Ras-related GTPases and protein kinases in yeast and mammals, and is implicated in cell cycle control and abscisic acid (ABA) signaling in plants. In this study, the developmental expression of a pea protein farnesyltransferase (FTase) gene was examined using transgenic expression of the beta-glucuronidase (GUS) gene fused to a 3.2 kb 5' upstream sequence of the gene encoding the pea FTase beta subunit. Coordinate expression of the GUS transgene and endogenous tobacco FTase beta subunit gene in tobacco cell lines suggests that the 3.2 kb region contains the key FTase promoter elements. In transgenic tobacco plants, GUS expression is most prominent in meristematic tissues such as root tips, lateral root primordia and the shoot apex, supporting a role for FTase in the control of the cell cycle in plants. GUS activity was also detected in mature embryos and imbibed embryos, in accordance with a role for FTase in ABA signaling that modulates seed dormancy and germination. In addition, GUS activity was detected in regions that border two organs, e.g. junctions between stems and leaf petioles, cotyledons and hypocotyls, roots and hypocotyls, and primary and secondary roots. GUS is expressed in phloem complexes that are adjacent to actively growing tissues such as young leaves, roots of light-grown seedlings, and hypocotyls of dark-grown seedlings. Both light and sugar (e.g. sucrose) treatments repressed GUS expression in dark-grown seedlings. These expression patterns suggest a potential involvement of FTase in the regulation of nutrient allocation into actively growing tissues.
Chiral Silver Amide-Catalyzed Enantioselective [3 + 2] Cycloaddition of α-Aminophosphonates with Olefins (2010)

The first catalytic asymmetric [3 + 2] cycloadditions of Schiff bases of alpha-aminophosphonates with olefins have been developed. Chiral silver amide complexes bearing (R)-DTBM-SEGPHOS worked well as catalysts for the first time, and proline phosphonic analogues were obtained in high yields with excellent exo- and enantioselectivities.
Cyclic nucleotide-independent protein kinase from rat liver. Purification and characterization of a multifunctional protein kinase. (1985)

A rat liver cAMP-independent protein kinase that phosphorylates peptide b of ATP-citrate lyase (Ramakrishna, S., Pucci, D. L., and Benjamin, W. B. (1983) J. Biol. Chem. 258, 4950-4956) has been purified to apparent homogeneity. The molecular weight, determined by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate, sucrose density gradient, and by gel filtration, was found to be 36,000. This protein kinase phosphorylates in vitro ATP-citrate lyase, acetyl-CoA carboxylase, and glycogen synthase and does not phosphorylate phosphorylase, phosphorylase kinase, histone, phosvitin, and casein. It has Fa (activity factor) activity stimulating the ATP X Mg-dependent phosphatase and is therefore named a multifunctional protein kinase. This kinase differs from glycogen synthase kinase-3 with regard to substrate specificity, kinetic parameters, and physicochemical properties.
Scaling up the accuracy of Naive-Bayes classifiers: a decision-tree hybrid (1996)

Naive-Bayes induction algorithms were previously shown to be surprisingly accurate on many classification tasks even when the conditional independence assumption on which they are based is violated. However, most studies were done on small databases. We show that in some larger databases, the accuracy of Naive-Bayes does not scale up as well as decision trees. We then propose a new algorithm, NBTree, which induces a hybrid of decision-tree classifiers and Naive-Bayes classifiers: the decision-tree nodes contain univariate splits as regular decision-trees, but the leaves contain Naive-Bayesian classifiers. The approach retains the interpretability of Naive-Bayes and decision trees, while resulting in classifiers that frequently outperform both constituents, especially in the larger databases tested.
The Influence of Serum-Free Culture Conditions on Skeletal Muscle Differentiation in a Tissue-Engineered Model (2008)

The influence of differentiation medium (DM) components on C2C12 murine myoblast differentiation has only been studied in monolayer cultures. Serum-free formulations have been applied that omit the use of sera with unknown composition. The goal of the present study was to compare the influence of serum-free media on C2C12 differentiation in 3-dimensional tissue-engineered muscle constructs. Myoblast proliferation and differentiation in media containing Ultroser G (DMU), insulin-like growth factor (IGF)-I (DMI), or both (DMUI) were compared with those induced by more-traditional media containing horse serum (HS) or horse serum and IGF-I (HSI). Effects of the applied media were assessed from gross construct morphology, total protein content, creatine kinase activity, and tissue viability. Addition of IGF-I (HSI) to the standard DM (HS) improved myoblast differentiation in muscle constructs. Even better results were obtained using DMU and DMUI culture conditions. DMI could not induce differentiation or maintain cell viability. Serum-free culture medium supplemented with DMU or DMUI accelerates and improves myoblast differentiation in engineered muscle tissue better than the gold standard HS.
Ultra-Wideband Multilayer Substrate Integrated Folded Waveguides (2006)

A substrate integrated folded waveguide is shown that remains monomode from 2.6 GHz to 11 GHz covering the entire Federal communications commission's allocated ultra-wideband spectrum of 3.1 GHz to 10.6 GHz. Furthermore, the structure is only 8.5 mm wide. Measured results are given that verify the operation of the guide
Aspartate Aminotransferase of Escherichia coli: Nucleotide Sequence of the aspC Gene1 (1985)

The nucleotide sequence of the aspartate aminotransferase [EC 2.6.1.1] structural gene, aspC, of Escherichia coli K-12 was determined. The coding region of the aspC gene contained 1,188 nucleotide residues and encoded 396 amino acid residues. The amino acid sequence deduced from the nucleotide sequence agreed perfectly with that of the protein recently determined for the aspartate aminotransferase of E. coli B (Kondo, K., Wakabayashi, S., Yagi, T., & Kagamiyama, H. (1984) Biochem. Biophys. Res. Commun. 122, 62-67).
Two proteins with reverse transcriptase activities associated with hepatitis B virus-like particles (1988)

Recent studies suggest that hepatitis B virus (HBV), despite being a DNA virus, replicates via an RNA intermediate (R. H. Miller, P. L. Marion, and S. W. Robinson, Virology 139:64-72, 1984; J. Summers and W. S. Mason, Cell 29:403-415, 1982). The HBV life cycle is therefore a permuted version of the RNA retroviral life cycle. Sequence homology between retroviral reverse transcriptase and the putative HBV polymerase gene product suggests the presence of an HBV reverse transcriptase (H. Toh, H. Hajashida, and T. Miyata, Nature (London) 305:827-829, 1983). As yet, there has been no direct evidence that reverse transcriptase activity is present in the viral particle. We used activity gel analysis to detect the in situ catalytic activities of DNA polymerases after sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Our studies demonstrated that HBV-like particles secreted by a differentiated human hepatoma cell line transfected with genomic HBV DNA contain two major polymerase activities which migrate as approximately 90- and approximately 70-kilodalton (kDa) proteins. This demonstrated, for the first time, that HBV-like particles contain a novel DNA polymerase-reverse transcriptase activity. Furthermore, we propose that the 70-kDa reverse transcriptase may be produced by proteolytic self-cleavage of the 90-kDa precursor protein.
Measurement of Rayleigh backscattering at 1.55 mu m with 32 mu m spatial resolution (1992)

Rayleigh backscattering at a wavelength of 1.55 mu m is measured in standard single-mode fiber with a spatial resolution of 32 mu m and a dynamic range of over 30 dB. A minimum reflection sensitivity of -148 dB is the best reported to date using optical low-coherence reflectometry.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Site-specific processing of Ras and Rap1 Switch I by a MARTX toxin effector domain (2015)

Ras (Rat sarcoma) protein is a central regulator of cell growth and proliferation. Mutations in the RAS gene are known to occur in human cancers and have been shown to contribute to carcinogenesis. In this study, we show that the multifunctional-autoprocessing repeats-in-toxin (MARTX) toxin-effector domain DUF5(Vv) from Vibrio vulnificus to be a site-specific endopeptidase that cleaves within the Switch 1 region of Ras and Rap1. DUF5(Vv) processing of Ras, which occurs both biochemically and in mammalian cell culture, inactivates ERK1/2, thereby inhibiting cell proliferation. The ability to cleave Ras and Rap1 is shared by DUF5(Vv) homologues found in other bacteria. In addition, DUF5(Vv )can cleave all Ras isoforms and KRas with mutations commonly implicated in malignancies. Therefore, we speculate that this new family of Ras/Rap1-specific endopeptidases (RRSPs) has potential to inactivate both wild-type and mutant Ras proteins expressed in malignancies.
Learning Hidden Markov Model Structure for Information Extraction (2018)

Statistical machine learning techniques, while well proven in fields such as speech recognition, are just beginning to be applied to the information extraction domain. We explore the use of hidden Markov models for information extraction tasks, specifically focusing on how to learn model structure from data and how to make the best use of labeled and unlabeled data. We show that a manually-constructed model that contains multiple states per extraction field outperforms a model with one state per field, and discuss strategies for learning the model structure automatically from data. We also demonstrate that the use of distantly-labeled data to set model parameters provides a significant improvement in extraction accuracy. Our models are applied to the task of extracting important fields from the headers of computer science research papers, and achieve an extraction accuracy of 90.1%. Introduction Hidden Markov modeling is a powerful statistical machine learning technique that is just b...
Studies of Sex Attractant of Banded Cucumber Beetle (1964)

A natural sex attractant Produced by females of the banded cucumber beetle, Diabrotica balteata LeConte, usually by the time they were 10 days old, lured males of this species from distances as far 49 feet. Unmated females remained attractive to males for as long as 79 days. Most females ceased to be attractive after 1 mating and none were attractive after 2 matings. The attractant was extracted from female abdomens with alcohol. Extracts of the heads and thoraces and of filter paper on which females had crawled gave negative results. Male behavioral responses are described.
A Low-Power Driving Scheme for a-Si:H Active-Matrix Organic Light-Emitting Diode Displays (2005)

This paper describes a low-power driving scheme along with a pixel circuit based on hydrogenated amorphous silicon (a-Si:H) technology for active matrix organic light emitting diode (AMOLED) displays. The driving scheme can provide different current levels for the OLED while compensating for long-term (and gradual) instabilities caused by material defect metastability which will make it amenable for use in AMOLED displays. Moreover, since the threshold voltage is known in this method, it can be used to compensate for the time-dependent errors of the charge injection and clock feed-through effects. Therefore, the error for a 3V shift in the VT of T1 is almost zero. More importantly, it has low power consumption because the line capacitance is charged just one time during the programming cycle. For example, the total power consumption of a QVGA array (240*320) is expected to be less than 1.5W.
Digital Image Processing for Camera Application in Mobile Devices Using Artificial Neural Networks (2012)

This paper utilizes artificial neural networks based image processing techniques for low capacity and resource constrained devices like mobile phones for camera applications. The system is trained to develop the operating matrix, called the function matrix, by using artificial neural network theory, from a sample input and output image matrix. This is done when the system is in idle mode. After having obtained the function matrix, it can be very conveniently operated upon any other input image matrix by simple multiplication to obtain the desired modification in the input image in real time. Computer simulation results are provided to prove the concept. Keywords: image processing, artificial neural networks, mobile devices, camera application
Dimethylbiguanide Inhibits Cell Respiration via an Indirect Effect Targeted on the Respiratory Chain Complex I (2000)

We report here a new mitochondrial regulation occurring only in intact cells. We have investigated the effects of dimethylbiguanide on isolated rat hepatocytes, permeabilized hepatocytes, and isolated liver mitochondria. Addition of dimethylbiguanide decreased oxygen consumption and mitochondrial membrane potential only in intact cells but not in permeabilized hepatocytes or isolated mitochondria. Permeabilized hepatocytes after dimethylbiguanide exposure and mitochondria isolated from dimethylbiguanide pretreated livers or animals were characterized by a significant inhibition of oxygen consumption with complex I substrates (glutamate and malate) but not with complex II (succinate) or complex IV (N,N,N',N'-tetramethyl-1, 4-phenylenediamine dihydrochloride (TMPD)/ascorbate) substrates. Studies using functionally isolated complex I obtained from mitochondria isolated from dimethylbiguanide-pretreated livers or rats further confirmed that dimethylbiguanide action was located on the respiratory chain complex I. The dimethylbiguanide effect was temperature-dependent, oxygen consumption decreasing by 50, 20, and 0% at 37, 25, and 15 degrees C, respectively. This effect was not affected by insulin-signaling pathway inhibitors, nitric oxide precursor or inhibitors, oxygen radical scavengers, ceramide synthesis inhibitors, or chelation of intra- or extracellular Ca(2+). Because it is established that dimethylbiguanide is not metabolized, these results suggest the existence of a new cell-signaling pathway targeted to the respiratory chain complex I with a persistent effect after cessation of the signaling process.
A density-based algorithm for discovering clusters in large spatial Databases with Noise (1996)

Clustering algorithms are attractive for the task of class iden-tification in spatial databases. However, the application to large spatial databases rises the following requirements for clustering algorithms: minimal requirements of domain knowledge to determine the input parameters, discovery of clusters with arbitrary shape and good efficiency on large da-tabases. The well-known clustering algorithms offer no solu-tion to the combination of these requirements. In this paper, we present the new clustering algorithm DBSCAN relying on a density-based notion of clusters which is designed to dis-cover clusters of arbitrary shape. DBSCAN requires only one input parameter and supports the user in determining an ap-propriate value for it. We performed an experimental evalua-tion of the effectiveness and efficiency of DBSCAN using synthetic data and real data of the SEQUOIA 2000 bench-mark. The results of our experiments demonstrate that (1) DBSCAN is significantly more effective in discovering clus-ters of arbitrary shape than the well-known algorithm CLAR-ANS, and that (2) DBSCAN outperforms CLARANS by factor of more than 100 in terms of efficiency.
Suppression of transcription factor PDX-1/IPF1/STF-1/IDX-1 causes no decrease in insulin mRNA in MIN6 cells. (1997)

The insulin gene transcription factor PDX-1/IPF1/STF-1/ IDX-1 plays a key role in directing beta cell-specific gene expressions. Recently, impairment of PDX-1 expression or activity has been observed in beta cell-derived HIT cells cultured under high glucose concentrations, and this has been suggested as a possible cause of the decrease in insulin gene transcription. To investigate the pathophysiological significance of PDX-1 as a determinant of the rate of insulin gene transcription, we suppressed its expression in beta cell-derived MIN6 cells using an antisense oligodeoxynucleotide (ODN) and searched for possible changes in the beta cell-specific gene expression. Treatment of MIN6 cells with an 18-mer phosphorothioate ODN complementary to a sequence starting at the translation initiation codon of PDX-1 caused a potent, concentration-dependent reduction in PDX-1 expression; addition of 2 microM antisense ODN could reduce PDX-1 expression to 14+/-4% of the control. There was also a decrease in its DNA binding to the insulin gene A element. Despite such suppression of PDX-1, Northern blot analysis revealed no decrease in the amount of insulin mRNA in the MIN6 cells. Similarly, no changes were detected in the transcription of the glucokinase or islet amyloid polypeptide gene, for which PDX-1 was shown to function as a transcription factor. Thus, our findings dispute the physiological significance of PDX-1 in determining the rate of insulin gene transcription. This means that other components constituting the transcription-controlling machinery need to be evaluated in order to understand the molecular basis of impaired insulin biosynthesis such as that observed due to glucose toxicity.
A Sheep Model for the Study of Biofilms in Rhinosinusitis (2007)

The demonstration of bacterial biofilms in this animal model of sinusitis further supports the hypotheses that biofilms may play a role in the pathogenesis of this condition. There is an obvious discrepancy in the sensitivity and specificity of biofilm detection using the three modalities mentioned. CSLM appears to be the most objective technique. The inherent flaws, sampling error, and subjectivity involved in SEM and TEM make these less reliable in documenting biofilm existence.