gebhart/patrepeval huggingface dataset:
Successor Features for Transfer in Reinforcement Learning (2019)

Transfer in reinforcement learning refers to the notion that generalization should occur not only within a task but also across tasks. Our focus is on transfer where the reward functions vary across tasks while the environment's dynamics remain the same. The method we propose rests on two key ideas: "successor features," a value function representation that decouples the dynamics of the environment from the rewards, and "generalized policy improvement," a generalization of dynamic programming's policy improvement step that considers a set of policies rather than a single one. Put together, the two ideas lead to an approach that integrates seamlessly within the reinforcement learning framework and allows transfer to take place between tasks without any restriction. The proposed method also provides performance guarantees for the transferred policy even before any learning has taken place. We derive two theorems that set our approach in firm theoretical ground and present experiments that show that it successfully promotes transfer in practice.
Glutamate Dehydrogenase Reaction as a Source of Glutamic Acid in Synaptosomes (1991)

The role of the glutamate dehydrogenase reaction as a pathway of glutamate synthesis was studied by incubating synaptosomes with 5 mM 15NH4Cl and then utilizing gas chromatography-mass spectrometry to measure isotopic enrichment in glutamate and aspartate. The rate of formation of [15N]glutamate and [15N]aspartate from 5 mM 15NH4Cl was approximately 0.2 nmol/min/mg of protein, a value much less than flux through glutaminase (4.8 nmol/min/mg of protein) but greater than flux through glutamine synthetase (0.045 nmol/min/mg of protein). Addition of 1 mM 2-oxoglutarate to the medium did not affect the rate of [15N]glutamate formation. O2 consumption and lactate formation were increased in the presence of 5 mM NH3, whereas the intrasynaptosomal concentrations of glutamate and aspartate were unaffected. Treatment of synaptosomes with veratridine stimulated reductive amination of 2-oxoglutarate during the early time points. The production of ([15N]glutamate + [15N]aspartate) was enhanced about twofold in the presence of 5 mM beta-(+/-)-2-aminobicyclo [2.2.1]heptane-2-carboxylic acid, a known effector of glutamate dehydrogenase. Supplementation of the incubation medium with a mixture of unlabelled amino acids at concentrations similar to those present in the extracellular fluid of the brain had little effect on the intrasynaptosomal [glutamate] and [aspartate]. However, the enrichment in these amino acids was consistently greater in the presence of supplementary amino acids, which appeared to stimulate modestly the reductive amination of 2-oxoglutarate. It is concluded: (a) compared with the phosphate-dependent glutaminase reaction, reductive amination is a relatively minor pathway of synaptosomal glutamate synthesis in both the basal state and during depolarization; (b) NH3 toxicity, at least in synaptosomes, is not referable to energy failure caused by a depletion of 2-oxoglutarate in the glutamate dehydrogenase reaction; and (c) transamination is not a major mechanism of glutamate nitrogen production in nerve endings.
EFFECT OF EXPERIMENTAL VARIATION OF TEMPERATURE ON SERUM TRIGLYCERIDES IN UROMASTYX HARDWICKII (2012)

Background: The study has been performed on Uromastyx hardwickii, a local lacertilian species. This male Poikilotherm vertebrate mainly inhabits the arid regions of the Indo-Pakistan subcontinent. The objective of this study was to see whether artificially created high temperature in winter can increase triglycerides level in this species, as it is normally seen in summers. Material and Methods: This study was conducted in Oct 2005 and Jan 2006 in Physiology Lab, University of Health Sciences, Lahore. Male Uromastyx hardwickii (n=20) were kept for this study carried out in autumn and winter within 48 hours of their arrival in the laboratory. Blood samples were collected by anterior abdominal venepuncture from conscious animals using a heparinised syringe and serum Triglyceride was measured by GPO-PAP method (Human, Weisbaden, Germany). Results: Mean serum Triacylglycerol levels were found to be significantly higher in summer and with an increase in temperature observed during winter and autumn season. Conclusion: There is significant increase in serum triglycerides in Uromastyx hardwickii on artificial increase in temperature even during winter season.
Ligation of CTLA-4 to the TCR inhibits T cell activation and directs differentiation into Foxp3+ regulatory T cells (72.2) (2012)

Abstract ABSTRACT Crosslinking of ligand-engaged cytotoxic T lymphocyte antigen-4 (CTLA-4) to the T cell receptor (TCR) during the early phase of T cell activation attenuates TCR signaling, leading to T cell inhibition. To promote this event, a bispecific fusion protein comprising a mutant mouse CD80 (CD80w88a) and lymphocyte activation antigen-3 (LAG-3) was engineered to concurrently engage CTLA-4 and crosslink it to the TCR. Crosslinking is expected to attain via ligation of CTLA-4 first to MHC II and then indirectly to the TCR, generating a CTLA-4-MHC II-TCR tri-molecular complex that forms between T cells and antigen-presenting cells (APCs) during T cell activation. Treating T cells with this bispecific fusion protein inhibited T cell activation. In addition, it induced the production of IL-10 and TGF- β and attenuated AKT and mTOR signaling. Intriguingly, treatment with the bispecific fusion protein also directed early T cell differentiation into Foxp3+ regulatory T cells (Tregs). This process was dependent on the endogenous production of TGF- β. Thus, bispecific fusion proteins that engage CTLA-4 and co-ligate it to the TCR during the early phase of T cell activation can negatively regulate the T cell response. Bispecific biologics with such dual functions may therefore represent a novel class of therapeutics for immune modulation. The findings presented here also reveal a potential new role for CTLA-4 in Treg differentiation.
Seismic wavelet estimation: a frequency domain solution to a geophysical noisy input-output problem (1998)

In seismic reflection prospecting for oil and gas a key step is the ability to estimate the seismic wavelet (impulse response) traveling through the Earth. Such estimation enables filters to be designed to deblur the recorded seismic time series and allows the integration of "downhole" and surface seismic data for seismic interpretation purposes. An appropriate model for the seismic time series is a noisy-input/noisy-output linear model. The authors tackle the estimation of the impulse response in the frequency domain by estimating its frequency response function. They use a novel approach where multiple coherence analysis is applied to the replicated observed output series to estimate the output signal-to-noise ratio (SNR) at each frequency. This, combined with an estimate of the ordinary coherence between observed input and observed output, and with the spectrum of the observed input and cross-spectrum of the observed input and output, enables estimation of the frequency response function. The methodology is seen to work well on real and synthetic data.
The native structure of the activated Raf protein kinase is a membrane-bound multi-subunit complex. (1994)

Raf is a mitogen-stimulated protein kinase that functions as a component of the signaling cascade that leads to the stimulation of mitogen-activated protein kinase. Here we show that the native structure of Raf is a large multi-subunit protein complex with an apparent mass of 300-500 kDa that interacts with Ras and the mitogen-activated protein kinase kinase Mek. Analysis of the structure of the Raf complex demonstrates that it contains a single Raf protein kinase together with the molecular chaperones hsp90 and p50. The Raf-hsp90-p50 complex was observed in starved cells and in cells activated with serum or phorbol ester. Thus, changes in complex formation with hsp90 and p50 are not required for activation of the Raf protein kinase. However, Raf activation caused by Ras was associated with the translocation of the cytoplasmic Raf-hsp90-p50 complex to the cell membrane. Significantly, it is only the membrane-bound complex that exhibits increased protein kinase activity. Thus, the Ras-activated Raf protein kinase functions as a membrane-bound multi-subunit complex.
Cyanophycin Production in a Phycoerythrin-Containing Marine <i>Synechococcus</i> Strain of Unusual Phylogenetic Affinity (2002)

Thirty-two strains of phycoerythrin-containing marine picocyanobacteria were screened for the capacity to produce cyanophycin, a nitrogen storage compound synthesized by some, but not all, cyanobacteria. We found that one of these strains, Synechococcus sp. strain G2.1 from the Arabian Sea, was able to synthesize cyanophycin. The cyanophycin extracted from the cells was composed of roughly equimolar amounts of arginine and aspartate (29 and 35 mol%, respectively), as well as a small amount of glutamate (15 mol%). Phylogenetic analysis, based on partial 16S ribosomal DNA (rDNA) sequence data, showed that Synechococcus sp. strain G2.1 formed a well-supported clade with several strains of filamentous cyanobacteria. It was not closely related to several other well-studied marine picocyanobacteria, including Synechococcus strains PCC7002, WH7805, and WH8018 and Prochlorococcus sp. strain MIT9312. This is the first report of cyanophycin production in a phycoerythrin-containing strain of marine or halotolerant Synechococcus, and its discovery highlights the diversity of this ecologically important functional group.
CAG repeat polymorphisms in KCNN3 (HSKCa3) and PPP2R2B show no association or linkage to schizophrenia (2002)

The purpose of this study was to determine whether genetic linkage or association could be observed between schizophrenia (SZ) and the CAG repeat polymorphisms within the genes KCNN3 (known previously as hSKCa3) and PPP2R2B (linked to Spino-Cerebellar Atrophy 12) in the Xhosa population in South Africa. Neither locus has been studied previously in African populations. The polymorphisms were genotyped in 589 individuals to form samples for Transmission Disequilibrium Test (TDT) analysis (176 unrelated probands, 145 with both parents and 30 with one parent genotyped), linkage analysis (49 families with 54 independent affected sib pairs [ASPs]), and case-control analyses (67 familial cases with a first-degree SZ relative, 101 sporadic cases with no affected first- or second-degree relative, and 90 control cases). No significant differences were found among familial cases, sporadic cases and controls in allele sizes (Kruskal-Wallis tests) or the numbers of alleles with sizes above and below the mean size for each polymorphism. Allele size was not correlated with age of onset (Spearman correlation). No significant evidence for association was observed using TDT analyses for all triads and separately for the familial triads. No significant evidence for linkage was observed for either locus with affected sib pair analysis using the possible triangle method or with Non-Parametric Linkage (NPL) analysis of the multiplex families. In conclusion, no significant evidence for linkage or association with SZ was observed for either polymorphism in this population.
Classified Vector Quantization of Images (1986)

Vector quantization (VQ) provides many attractive features for image coding with high compression ratios. However, initial studies of image coding with VQ have revealed several difficulties, most notably edge degradation and high computational complexity. We address these two problems and propose a new coding method, classified vector quantization (CVQ), which is based on a composite source model. Blocks with distinct perceptual features, such as edges, are generated from different subsources, i.e., belong to different classes. In CVQ, a classifier determines the class for each block, and the block is then coded with a vector quantizer designed specifically for that class. We obtain better perceptual quality with significantly lower complexity with CVQ when compared to ordinary VQ. We demonstrate with CVQ visual quality which is comparable to that produced by existing coders of similar complexity, for rates in the range 0.6-1.0 bits/pixel.
Nucleofection and Primary Culture of Embryonic Mouse Hippocampal and Cortical Neurons (2011)

Hippocampal and cortical neurons have been used extensively to study central nervous system (CNS) neuronal polarization, axon/dendrite outgrowth, and synapse formation and function. An advantage of culturing these neurons is that they readily polarize, forming distinctive axons and dendrites, on a two dimensional substrate at very low densities. This property has made them extremely useful for determining many aspects of neuronal development. Furthermore, by providing glial conditioning for these neurons they will continue to develop, forming functional synaptic connections and surviving for several months in culture. In this protocol we outline a technique to dissect, culture and transfect embryonic mouse hippocampal and cortical neurons. Transfection is accomplished by electroporating DNA into the neurons before plating via nucleofection. This protocol has the advantage of expressing fluorescently-tagged fusion proteins early in development (~4-8 hrs after plating) to study the dynamics and function of proteins during polarization, axon outgrowth and branching. We have also discovered that this single transfection before plating maintains fluorescently-tagged fusion protein expression at levels appropriate for imaging throughout the lifetime of the neuron (>2 months in culture). Thus, this methodology is useful for studying protein localization and function throughout CNS development with little or no disruption of neuronal function.
Nanochemistry aspects of titania in dye-sensitized solar cells (2009)

We analyze the main nanochemistry factors affecting photovoltaic performance in TiO2 employed as wide bandgap semiconductor in dye-sensitized solar cells (DSCs). What is the best morphology of the oxide? Which processes yield the required structures? Finally, putting the discussion in the context of the rapid evolution of photovoltaic technologies, we argue that new titania nanostructures will form the basic component of second-generation solar modules based on dye solar cells.
Characterizing and Optimizing Qubit Coherence Based on SQUID Geometry (2020)

The dominant source of decoherence in contemporary frequency-tunable superconducting qubits is $1/f$ flux noise. To understand its origin and find ways to minimize its impact, we systematically study flux noise amplitudes in more than 50 flux qubits with varied superconducting quantum interference device (SQUID) geometry parameters and compare our results to a microscopic model of magnetic spin defects located at the interfaces surrounding the SQUID loops. Our data are in agreement with an extension of the previously proposed model, based on numerical simulations of the current distribution in the investigated SQUIDs. Our results and detailed model provide a guide for minimizing the flux noise susceptibility in future circuits.
Fluoroethylenepropylene ferroelectret films with cross-tunnel structure for piezoelectric transducers and micro energy harvesters (2014)

Layered fluoroethylenepropylene (FEP) ferroelectret films with cross-tunnel structure were fabricated from sheets of FEP films by template-patterning followed by a fusion-bonding process and contact charging. The typical piezoelectric d33 coefficients, measured by a quasi-static method of samples not annealed, are in the range of 1000–3700 pC/N. The resonance behavior of the samples is analyzed by dielectric spectroscopy which also yields Young's modulus. Microphones built with such films exhibit a somewhat decreasing frequency response up to 1 kHz, an increase of the responses due to diffraction effects at higher frequencies, and eventually a peak probably due to a thickness resonance at about 40 kHz. Annealing at 125 °C indicates that the sensitivity stabilizes at about 40% of the original value. From this data, stable dynamic d33 coefficients of up to 300 pC/N can be calculated. A micro energy harvesting generator utilizing these films and based on the excitation of thickness vibrations is also described. With an active area of 4.3 cm2 and a seismic mass of 69.5 g, power up to 0.5 μW referred to an acceleration of 1 g can be generated at a frequency of 120 Hz.
The Fatty Acid-binding Protein, aP2, Coordinates Macrophage Cholesterol Trafficking and Inflammatory Activity (2005)

Fatty acid-binding proteins are cytosolic fatty acid chaperones, and the adipocyte isoform, aP2, plays an important role in obesity and glucose metabolism. Recently, this protein has been detected in macrophages where it strongly contributes to the development of atherosclerosis. Here, we investigated the role of aP2 in macrophage biology and the molecular mechanisms underlying its actions. We demonstrate that aP2-deficient macrophages display defects in cholesterol accumulation and alterations in pro-inflammatory responsiveness. Deficiency of aP2 alters the lipid composition in macrophages and enhances peroxisome proliferator-activated receptor gamma activity, leading to elevated CD36 expression and enhanced uptake of modified low density lipoprotein. The increased peroxisome proliferator-activated receptor gamma activity in aP2-deficient macrophages is also accompanied by a significant stimulation of the liver X receptor alpha-ATP-binding cassette transporter A1-mediated cholesterol efflux pathway. In parallel, aP2-deficient macrophages display reduced IkappaB kinase and NF-kappaB activity, resulting in suppression of inflammatory function including reduced cyclooxygenase-2 and inducible nitric-oxide synthase expression and impaired production of inflammatory cytokines. Our results demonstrate that aP2 regulates two central molecular pathways to coordinate macrophage cholesterol trafficking and inflammatory activity.
A Two-Point Modulation Technique for CMOS Power Amplifier in Polar Transmitter Architecture (2008)

A two-point modulation technique is presented that improves the performance of nonlinear power amplifiers (PAs) in polar transmitters. In this scheme, the output amplitude modulation is performed by controlling the current of the PA. The current control technique enables the PA to provide wideband amplitude modulation, as well as high power control dynamic range. In addition, the supply voltage of the PA is adjusted based on the output power level. The voltage supply adjustment substantially improves the effective power efficiency of the PA. The voltage supply control is performed using a second-order sigma-delta dc-dc converter, which presents an efficiency of over 95% in its operational range. The PA operates at 900 MHz with maximum output power of 27.8 dBm and power efficiency of 34% at maximum output power. The proposed PA achieves 62-dB power control dynamic range with amplitude modulation bandwidth of over 17.1 MHz. The circuits are fabricated in a CMOS 0.18 mum process with a 3.3-V power supply.
DNA substrate requirements for stable joint molecule formation by the RecA and single-stranded DNA-binding proteins of Escherichia coli (1991)

In reactions between linear single-stranded DNAs (ssDNAs) and circular double-stranded DNAs (dsDNAs), stable joint molecule formation promoted by the recA protein (RecA) requires negative superhelicity, a homologous end, and an RecA-ssDNA complex. Linear ssDNAs with 3'-end homology react more efficiently than linear ssDNAs with 5'-end homology. This 3'-end preference is explained by the finding that 3'-ends are more effectively coated by RecA than 5'-ends, as judged by exonuclease VII protection, and are thus more reactive. The ability of linear ssDNAs with 5'-end homology to react is improved by the presence of low concentrations of exonuclease VII. In reactions between ssDNAs and linear dsDNAs with end homology, stable joint molecule formation occurs more efficiently when the homology is at the 3'-end rather than at the 5'-end of the complementary strand. In addition, linear dsDNAs with homology at the 3'-end of the complementary strand react more efficiently with linear ssDNAs with 3'-end homology than with linear ssDNAs with 5'-end homology. The ability of linear ssDNAs with 5'-end homology to react, in the absence of single-stranded DNA-binding protein, is improved by adding 33-46 nucleotides of heterologous sequence to the 5'-end of the linear ssDNA. The poor reactivity of linear ssDNAs with 5'-end homology is explained by a lack of RecA at the 5'-ends of linear ssDNAs, which is a consequence of the polar association and dissociation of RecA.
Effect of cyclic bis(3â²â5â²)diguanylic acid and its analogs on bacterial biofilm formation (2009)

Cyclic bis(3'-5')diguanylic acid (cyclic-di-GMP) functions as a second messenger in diverse species of bacteria to trigger wide-ranging physiological changes. We measured cyclic-di-GMP and its structural analogs such as cyclic bis(3'-5')guanylic/adenylic acid (cyclic-GpAp), cyclic bis(3'-5')guanylic/inosinic acid (cyclic-GpIp) and monophosphorothioic acid of cyclic-di-GMP (cyclic-GpGps) for effects on the biofilm formation of Staphylococcus aureus and Pseudomonas aeruginosa. We constructed a knockout mutant of SA0701, which is a GGDEF motif protein relevant to diguanylate cyclase from S. aureus 2507. We confirmed that the biofilm formation of this mutant (MS2507 Delta SA0701) was reduced. Cyclic-di-GMP corresponding to physiological intracellular levels given in the culture recovered the biofilm formation of MS2507 Delta SA0701, whereas its analogs did not, indicating that unlike a previous suggestion, cyclic-di-GMP was involved in the positive regulation of the biofilm formation of S. aureus and its action was structurally specific. At a high concentration (200 microM), cyclic-di-GMP and its analogs showed suppression effects on the biofilm formation of S. aureus and P. aeruginosa, and according to the quantification study using costat analysis, the suppression potential was in the order of cyclic-di-GMP, cyclic-GpGps, cyclic-GpAp and cyclic-GpIp, suggesting that the suppression effect was not strictly specific and the change of base structure quantitatively affected the suppression activity.
Discrete rotation for directional orthogonal wavelet packets (2002)

We propose a simple and new way of defining the directional wavelet packets basis. This new decomposition is based on a discrete rotation. To avoid information loss or modification (in order to keep the orthogonality property) we use a new one-to-one discrete rotation. This rotation is based on three discrete shear transformations. This new oriented basis does not divide the 2D Fourier plane into square regions. Instead of horizontal and vertical favourite directions, our directional scheme treats different arbitrary directions.