gebhart/patrepeval huggingface dataset:
Enhanced Production of Neuroprogenitors, Dopaminergic Neurons, and Identification of Target Genes by Overexpression of Sonic Hedgehog in Human Embryonic Stem Cells (2011)

Molecular and cellular signaling pathways are involved in the process of neural differentiation from human embryonic stem cells (hESC) to terminally differentiated neurons. The Sonic hedgehog (SHH) morphogen is required to direct the differentiation of hESC to several neural subtypes, for example, dopaminergic (DA) or motor neurons. However, the roles of SHH signaling and the pathway target genes that regulate the diversity of cellular responses arising from SHH activation during neurogenesis of hESC have yet to be elucidated. In this study, we report that overexpression of SHH in hESC promotes the derivation of neuroprogenitors (NP), increases proliferation of NP, and subsequently increases the yield of DA neurons. Next, gene expression changes resulting from the overexpression of SHH in hESC-derived NP were examined by genome-wide transcriptional profiling. Categorizing the differentially expressed genes according to the Gene Ontology biological processes showed that they are involved in numerous cellular processes, including neural development, NP proliferation, and neural specification. In silico GLI-binding sites analysis of the differentially expressed genes also identified a set of putative novel direct target genes of SHH in hESC-derived NP, which are involved in nervous system development. Electrophoretic mobility shift assays and promoter-luciferase assays confirmed that GLI1 binds to the promoter region and activates transcription of HEY2, a NOTCH signaling target gene. Taken together, our data provide evidence for the first time that there is cross-talk between the NOTCH and SHH signaling pathways in hESC-derived NP and also provide significant new insights into transcriptional targets in SHH-mediated neural differentiation of hESC.
Plasmonic photocatalysts: harvesting visible light with noble metal nanoparticles (2012)

The efforts to produce photocatalysts operating efficiently under visible light have led to a number of plasmonic photocatalysts, in which noble metal nanoparticles are deposited on the surface of polar semiconductor or insulator particles. In the metal-semiconductor composite photocatalysts, the noble metal nanoparticles act as a major component for harvesting visible light due to their surface plasmon resonance while the metal-semiconductor interface efficiently separates the photogenerated electrons and holes. In this article, we survey various plasmonic photocatalysts that have been prepared and characterized in recent years.
Neural Induction Intermediates Exhibit Distinct Roles of Fgf Signaling   (2010)

Formation of the neural plate is an intricate process in early mammalian embryonic development mediated by cells of the inner cell mass and involving a series of steps, including development of the epiblast. Here, we report on the creation of an embryonic stem (ES) cell-based system to isolate and identify neural induction intermediates with characteristics of epiblast cells and neural plate. We demonstrate that neural commitment requires prior differentiation of ES cells into epiblast cells that are indistinguishable from those derived from natural embryos. We also demonstrate that epiblast cells can be isolated and cultured as epiblast stem cell lines. Fgf signaling is shown to be required for the differentiation of ES cells into these epiblast cells. Fgf2, widely used for maintenance of both human ES cells and epiblast stem cells, inhibits formation of early neural cells by epiblast intermediates in a dose-dependent manner and is sufficient to promote transient self-renewal of epiblast stem cells. In contrast, Fgf8, the endogenous embryonic neural inducer, fails to promote epiblast self-renewal, but rather promotes more homogenous neural induction with transient self-renewal of early neural cells. Removal of Fgf signaling entirely from epiblast cells promotes rapid neural induction and subsequent neurogenesis. We conclude that Fgf signaling plays different roles during the differentiation of ES cells, with an initial requirement in epiblast formation and a subsequent role in self-renewal. Fgf2 and Fgf8 thus stimulate self-renewal in different cell types.
Elaeodendroside D, E, H, I and J : New Cardiac Steroids from Elaeodendron glaucum (1981)

Five new cardiac glycosides having an unusual sugar linkage, elaeodendroside D, E, H, I and J, were isolated from seeds of Elaeodendron slaucum Pegs.and their structures were assigned on the basis of chemical correlation with elaeodendroside A, respectively.An improved procedure for cleavage of a glycoside having a doubly linked sugar was applied to characterization of elaeodendroside B and C. The probable structures of these two stereoisomers were proposed.In the preceding papers we reported the isolation and structure elucidation of cardiac steroids named elaeodendroside A and elaeodendrogenin from seeds of Elaeodendronglaucum Per& ---(Cela~traceae)~ by x-ray crystallography3 and chemical m e a n ~. ~ The probable structures of elaeodendroside B and C obtained from the same plant materials were also proposed.4The present paper describes the structures of elaeodendroside D, E, H, I and J which have been isolated by the method similar 3 to that previously reported and the application of an improved procedure for cleavage of a glycoside having a doubly linked sugar to characterization of elaeodendroside B and C. Elaeodendroside D ( 6 ) was isolated as colorless prisms (from CH,Cl,-ether), mp 275 -285' ldecomp.),[ a 1 2 +30.O0 (c=0.10 in C H C ~~) .Inspection of the high resolution mass spectrum, 'H n.m.r.spectrum5 and elemental analysis permitted us to assign the structure 6 to elaeodendroside D. The structure was definitely
Delay testing for non-robust untestable circuits (2002)

Recently published results have shown that, for many circuits, only a small percentage of path delay faults is robust testable. Among the robust untestable faults, a significant percentage of them is not non-robust testable either. In this paper, we take a closer look at the properties of these non-robust untestable faults with the goal of determining whether and how these faults should be tested.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
MgcRacGAP, A New Human GTPase-activating Protein for Rac and Cdc42 Similar to Drosophila rotundRacGAP Gene Product, Is Expressed in Male Germ Cells (1998)

In a search for new partners of the activated form of Rac GTPase, we have isolated through a two-hybrid cloning procedure a human cDNA encoding a new GTPase-activating protein (GAP) for Rho family GTPases. A specific mRNA of 3.2 kilobases was detected in low abundance in many cell types and found highly expressed in testis. A protein of the predicted size 58 kDa, which we call MgcRacGAP, was detected in human testis as well as in germ cell tumor extracts by immunoblotting with antibodies specific to recombinant protein. In vitro, the GAP domain of MgcRacGAP strongly stimulates Rac1 and Cdc42 GTPase activity but is almost inactive on RhoA. N-terminal to its GAP domain, MgcRacGAP contains a cysteine-rich zinc finger-like motif characteristic of the Chimaerin family of RhoGAPs. The closest homolog of MgcRacGAP is RotundRacGAP, a product of the Drosophila rotund locus. In situ hybridization experiments in human testis demonstrate a specific expression of mgcRacGAP mRNA in spermatocytes similar to that of rotundRacGAP in Drosophila testis. Therefore, protein sequence similarity and analogous developmental and tissue specificities of gene expression support the hypothesis that RotundRacGAP and MgcRacGAP have equivalent functions in insect and mammalian germ cells. Since rotundRacGAP deletion leads to male sterility in the fruit fly, the mgcRacGAP gene may prove likewise to play a key role in mammalian male fertility.
Artificial Intelligence Used to Evaluate 23 Single-Well Surfactant-Soak Treatments (2006)

Summary Following a series of laboratory imbibition-cell experiments, field tests were conducted to determine the effectiveness of surfactant-soak treatments as a single-well enhanced-oil-recovery (EOR) technique. The tests were conducted in the dolomite interval of the Phosphoria formation. Artificial intelligence was applied to analyze the mixed test results. The analysis suggested that the gamma ray log can be used to predict results and that a minimum amount of surfactant is required to improve production.
Cultural Margins in Borges: Mimesis, Autobiography and Catastrophe (1998)

The history of commentary on the work of Jorge Luis Borges is marked by a persistent resistance, which manifests itself in the difficulty or impossibility of identifying and documenting a Borgesian system (a poetics, a grammar, a rhetoric, and also a philosophy), and likewise in the problem of delimiting a field and an application with respect to Borges' text, of assessing its standing with cultural, national and socio-political concerns. With respect to these difficulties, there are two prevailing tendencies in reading Borges: 1) the tendency to critique, devalue or even dismiss him, on the grounds of a self-evident Eurocentrism, in light of his conservative political statements or on the basis of a supposed lack of political relevance (identified in the author's refusal to provide a political context in or for his stories, and his insistence on the textuality of any and all context), and finally his silence with regard to issues of Argentine or Latin American specificity or communality (and here the devaluation consists in a deprivation: Borges is not Argentine enough); 2) from the other pole, a prevailing tendency to celebrate Borges as a writer of the universal who is - again - essentially indifferent to a particular question of origin and community (whence, it seems, his "universal" applicability and appeal). This latter assessment continues to allocate Borges' text to broadly defined categories (mystical, fantastic, escapist) while refusing, or finding itself unable, to address the specificity of Borges' subject matter, which may indeed appear to be universal in scope, but which also never ceases to return upon and re-articulate the question of a particular. In either of these common readings, Borges' text could be said to be essentially reducible to an ideal notion of translation, or a movement between the particular and the universal: as either absolutely impossible or absolutely possible, and in both cases entirely devoid of any remainder or play of difference.
An Error Analysis For Surface Orientation From Vanishing Points (1988)

There are many cases in which perspective information can be used to derive three-dimensional spatial information about objects from their two-dimensional images. There are established algorithms for estimating the direction of lines and the orientation of surfaces based on their projections onto the image plane. Given two parallel lines on a plane, their projections onto the viewing plane intersect at a vanishing point, which provides a constraint on the orientation of the plane. Two such independent constraints define a vanishing line, and thereby determine the orientation of the plane uniquely. In order to effectively recover surface orientations via lines extracted from the image, it is necessary to put bounds on the errors while applying these constraints. Our approach involves representing line directions and surface normal vectors as points on a Gaussian sphere and computing the error bounds as regions on the sphere. Multiple constraints are combined by intersecting the corresponding regions. The starting point for computing the error bounds is an estimate of the accuracy of the lines which are extracted from the image. A mathematical analysis of the imaging geometry is used to propagate these errors to vanishing points, vanishing lines, and surface orientations. In addition, constraints based on a priori knowledge can be introduced to improve the accuracy. Some experimental results are presented to illustrate this.
Plasma-Enhanced Chemical Vapor Deposition of Fluorinated Silicon Nitride (1984)

Fluorinated silicon nitride films are deposited by the plasma-reaction of SiF 4 –N 2 –H 2 gas mixture. The fluorine content in the film is ∼25 at%. Although hydrogen is incorporated in the form of N–H bonds, the bondings remain stable up to 640°C. The films have relatively high resistivity (7×10 16 Ωcm at 2 MV/cm), high breakdown strength (10 MV/cm), and low deep trap density.
Identification and localization of a tau peptide to paired helical filaments of Alzheimer disease. (1989)

Amino acid sequencing of a CNBr digest of the tau protein isolated from bovine brain revealed an amino acid sequence of 17 residues, Pro-Gly-Leu-Lys-Glu-Ser-Pro-Leu-Gln-Ile-Gly-Ala-Ala-Pro-Gly-Leu-Lys, which we call peptide I, with heterogeneity at position 11 of glycine (peptide Ia) and proline (peptide Ib); peptide I showed no homology with the previously reported cDNA-derived mouse and human tau sequences. Antisera raised to synthetic peptides corresponding to peptides Ia and Ib labeled all the bovine tau polypeptides recognized by other monoclonal and polyclonal antibodies to bovine tau. Antisera to peptide Ib did not label any mouse tau polypeptides; however, an anti-Ia antiserum labeled two of the four mouse tau polypeptides. Antisera to both peptides labeled paired helical filaments (PHF) as neurofibrillary tangles, plaque neurites, and neuropil threads in Alzheimer disease brain and PHF polypeptides on immunoblots. Immunostaining with anti-Ia antisera of PHF in tissue sections and PHF polypeptides, but not bovine tau, on immunoblots was markedly increased when pretreated with alkaline phosphatase. These studies suggest that (i) the amino acid sequences of some isoforms of tau peptide might be different from that predicted from cDNAs, (ii) a tau peptide that is absent in the predicted sequences is present in PHF in Alzheimer disease, and (iii) tau in PHF is abnormally phosphorylated.
Gain enhancement in linear and circularly polarised microstrip patch antennas using shorted metallic patches (2005)

The influence of shorted metallic patches (SMPs) in the design of linear and circularly polarised microstrip patch antennas is investigated. The SMP structure consists of square patches connected to the ground plane by shorting pins. Effects of different parameters such as the dimension, and position of the SMPs on the performance of patch antennas are studied. It is shown that the implementation of the SMP in the patch design has led to significant improvements in gain and radiation patterns. The SMPs have also been incorporated in four element circularly polarised arrays to increase the gain and improve the axial ratio and impedance bandwidths. A comparison of the experimental results with simulation data demonstrates their good agreement.
Online detection of utility cloud anomalies using metric distributions (2010)

The online detection of anomalies is a vital element of operations in data centers and in utility clouds like Amazon EC2. Given ever-increasing data center sizes coupled with the complexities of systems software, applications, and workload patterns, such anomaly detection must operate automatically, at runtime, and without the need for prior knowledge about normal or anomalous behaviors. Further, detection should function for different levels of abstraction like hardware and software, and for the multiple metrics used in cloud computing systems. This paper proposes EbAT - Entropy-based Anomaly Testing - offering novel methods that detect anomalies by analyzing for arbitrary metrics their distributions rather than individual metric thresholds. Entropy is used as a measurement that captures the degree of dispersal or concentration of such distributions, aggregating raw metric data across the cloud stack to form entropy time series. For scalability, such time series can then be combined hierarchically and across multiple cloud subsystems. Experimental results on utility cloud scenarios demonstrate the viability of the approach. EbAT outperforms threshold-based methods with on average 57.4% improvement in accuracy of anomaly detection and also does better by 59.3% on average in false alarm rate with a `near-optimum' threshold-based method.
The Specificity of Cathepsin D (1973)

Abstract Bovine spleen cathepsin D has been partially purified for studies of its specificity. Isoelectric focusing of the purest preparation obtained indicated the presence of three molecular forms having approximately the same specific activity, but differing in their isoelectric points. Gel chromatography of this preparation on Sephadex G-100 gave an apparent molecular weight of about 42,000, and its sedimentation equilibrium behavior was found to be consistent with that of a dissociating system, with an apparent molecular weight of about 43,000 for an oligomer. Polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate indicated the presence of a subunit of molecular weight about 28,000. A series of oligopeptides having a p-nitro-l-phenylalanyl-l-phenylalanyl (Phe(NO2)-Phe) unit were tested as substrates for purified cathepsin D. It was found that for substrates of the type A-Phe(NO2)-Phe-B, where the Phe(NO2)-Phe bond is the only one cleaved by the enzyme, modification of the A and B groups markedly affected the kinetic parameters. The best substrate found was Phe-Gly-His-Phe-(NO2)-Phe-Val-Leu-OMe. This substrate is cleaved by cathepsin D at pH 4 more slowly than by pepsin, but at about the same rate as by the acid proteinase of Rhizopus chinensis. The data give further evidence of the similarity in the specificity of cathepsin D to that of other known acid proteinases and underline the importance of secondary enzyme-substrate interactions, at a distance from the site of catalytic action, in determining the apparent differences among these enzymes in their cleavage of oligopeptide substrates. The availability of a suitable synthetic substrate for cathepsin D has permitted the study of the competitive inhibition of this enzyme by peptides, including pepstatin. Like other acid proteinases, cathepsin D is inhibited by active site-directed diazoketones, and it has been found that this enzyme is less susceptible to such inhibition than are pepsin and the Rhizopus proteinase. This difference in behavior may be correlated with the apparent weaker binding of small oligopeptide substrates at the active site of cathepsin D.
Improving the sensitivity of the end-cap reflectron time-of-flight mass spectrometer (2000)

A miniaturized time-of-flight (TOF) mass spectrometer utilizes an end-cap reflectron to achieve high kinetic energy focusing and improved mass resolution. However, the coaxial geometry gives rise to considerable losses in sensitivity resulting from reflected ion trajectories close to the center. These trajectories were modeled, using initial ion velocity distributions in the radial direction up to 300 m s(-1), and the portion of the active area of the detector that is utilized was evaluated experimentally using a variable diameter iris diaphragm. The sensitivity was improved by modification of the reflectron by tilting the end-cap electrode 4 degrees and redirecting the ions to a portion of the detector active area. Sensitivity was then measured as 3 fmol of the peptide substance P.
Exploring agency relationship in transport service sector by analysing traveller choice behaviour (2015)

Examining travellers’ preferences for mode choices to understand a rela-tionship between traveller and transport for New South Wales (TfNSW) from the perspective of agency theory (AT) is the main focus of this paper. This paper emphasises on latent and traditional objective attributes to as-sess the mode choice process within the agency relationship as indicated in AT as a method by which the utility of the principal (traveller) can be max-imised. It is found that the probability of car use is significantly higher than public transport due to mismatch between traveller expectations and present transport services and it indicates an existence of agency problem in this services. Finally, some arguments have been identified to minimise this problem. Thus, the contribution of this research is three-fold: firstly, the application of agency theory’s utility and implications in traveller choice behaviour; secondly, the demonstration of scale to which attributes influence traveller mode choice to shape the agency relationship within transport mode services; and finally, a pathway for the improvement of agency relationship in transport mode services.
[Variation of betaine and proline contents in wheat seedlings under salt stress]. (2005)

Glycine betaine (GB) and proline contents of leaf and root were simultaneously determined by HPLC-ESI-MS at seedling stage in the three wheat (Triticum aestivum L.) varieties (salt tolerance from high to low), SW12, Ningchun No.4 and Chinese Spring (C.S) under 5 different salt stress levels. The GB contents among SW12, Ningchun No.4 and C.S were found outstanding difference by ANOVA (P<0.01) and consistent with salt tolerance in wheat. Proline contents were not different among 3 wheat varieties in leaf, but difference was found in the root between the Ningchun No.4 and C.S (P<0.05). The result suggested GB, as one of the materials for osmotic adjustment in plant, had the closest relationship with salt tolerance and could be used as an index of salt tolerance in wheat.