gebhart/patrepeval huggingface dataset:
Planning by Prioritized Sweeping with Small Backups (2013)

Efficient planning plays a crucial role in model-based reinforcement learning. Traditionally, the main planning operation is a full backup based on the current estimates of the successor states. Consequently, its computation time is proportional to the number of successor states. In this paper, we introduce a new planning backup that uses only the current value of a single successor state and has a computation time independent of the number of successor states. This new backup, which we call a small backup, opens the door to a new class of model-based reinforcement learning methods that exhibit much finer control over their planning process than traditional methods. We empirically demonstrate that this increased flexibility allows for more efficient planning by showing that an implementation of prioritized sweeping based on small backups achieves a substantial performance improvement over classical implementations.
Liberation from Flatland: 3D Interaction Based on the Desktop Bat (1991)

A novel device for 3D interaction is introduced, the Desktop Bat. This device is an evolutionary development of a mouse. It is like a mouse in that it is used on a desktop, but provides 5 degrees of freedom since in conjunction with translations it can be used to effect rotations about any combination of the principal axes. We discuss the requirements for 3D interaction which led to the design of the Desktop Bat, and the interaction models and software which allow it to be used as a 6 degrees of freedom input device.
Effect of C-reactive protein on platelet-activating factor-induced platelet aggregation and membrane stabilization. (1985)

C-reactive protein (CRP) is an acute phase reactant which humoral concentration rises drastically following tissue injury or inflammation. CRP of all species binds to phosphorylcholine residues. In the present studies CRP was found to inhibit platelet-activating factor-induced platelet aggregation, and to stabilize platelet membranes against the lytic effect of lysophosphatidylcholine. Inhibition of platelet aggregation by CRP is accompanied by an inhibition of arachidonic acid release from both phosphatidylcholine and phosphatidylinositol. This suggests that phospholipases are inhibited. Hydrolysis of multilamellar dipalmitoylphosphatidylcholine liposomes by purified phospholipase A2, was also inhibited by CRP. These results suggest that CRP can stabilize membranes from the detergent-like effects of lysolipids and from potentially toxic materials such as platelet-activating factor. By inhibition of phospholipases, production of inflammatory mediators would be blocked. CRP might thus act as an early protective recognition mechanism in acute inflammatory states.
Cloning and characterization of the human colipase cDNA (1990)

Pancreatic lipase hydrolyzes dietary triglycerides to monoglycerides and fatty acids. In the presence of bile salts, the activity of pancreatic lipase is markedly decreased. The activity can be restored by the addition of colipase, a low molecular weight protein secreted by the pancreas. The action of pancreatic lipase in the gut lumen is dependent upon its interaction with colipase. As a first step in elucidating the molecular events governing the interaction of lipase and colipase with each other and with fatty acids, a cDNA encoding human colipase was isolated from a lambda gt11 cDNA library with a rabbit polyclonal anti-human colipase antibody. The full-length 525 bp cDNA contained an open reading frame encoding 112 amino acids, including a 17 amino acid signal peptide. The predicted protein sequence contains 100% of the published protein sequence for human colipase determined by chemical methods, but predicts the presence of five additional NH2-terminal amino acids and four additional COOH-terminal amino acids. Comparison of the predicted protein sequence with the known sequences of colipase from other species reveals regions of extensive identity. In vitro translation of mRNA transcribed from the cDNA gave a protein of the expected molecular size that was processed by pancreatic microsomal membranes. Sequence analysis of the in vitro translation product after processing demonstrated signal peptide cleavage and the presence of a human procolipase, as exists in the pig and horse colipases. DNA blot analysis was consistent with the presence of a single gene for colipase. RNA blot analysis demonstrated tissue-specific expression of colipase mRNA in the pancreas. Thus, we report, for the first time, a cDNA for colipase.(ABSTRACT TRUNCATED AT 250 WORDS)
In vivo characterization of diatom multipartite plastid targeting signals (2002)

Plastids of diatoms and related algae are delineated by four membranes: the outermost membrane (CER) is continuous with the endoplasmic reticulum while the inner two membranes are homologous to plastid envelope membranes of vascular plants and green algae. Proteins are transported into these plastids by pre-sequences that have two recognizable domains. To characterize targeting of polypeptides within diatom cells, we generated constructs encoding green fluorecent protein (GFP) fused to leader sequences. A fusion of GFP to the pre-sequence of BiP [an endoplasmic reticulum (ER)-localized chaperone] resulted in accumulation of GFP within the ER; a construct encoding the pre-sequence of a plastid protein fused to GFP was directed into the plastids. Additional constructs demonstrated that the N-terminal region of the bipartite plastid targeting pre-sequence was necessary for transport of polypeptides to the lumen of the ER, while the C-terminal region was shown to enable the proteins to traverse the plastid double envelope membrane. Our data strongly support the hypothesis of a multi-step plastid targeting process in chromophytic algae and raises questions about the continuity of the ER and CER and the function of the latter in polypeptide trafficking.
Antibodies against Hydroxyethylstarch Produced in Rabbits by Immunization with a Protein-Hydroxyethylstarch Conjugate (1976)

Antibodies (ABS) against hydroxyethylstarch (HES) were raised in rabbits by immunization with HES-bovine serum albumin conjugate. ABS against HES were demonstrable by gel diffusion, passive hemagglutination (PH) and passive cutaneous anaphylaxis (PCA); specificity was confirmed by inhibition of PH and neutralization of PCA. No ABS against starch could be induced in comparative experiments. Non-immunogenicity of starch was attributed to its structural similarity with glycogen, widely distributed in animal species. Absence of cross-reactivity of anti-HES ABS with starch, amylopectin and glycogen and strong reactivity with 2-hydroxypropylstarch (DS = 0.65) and HES (DS = 0.7–1.2) indicate that hydroxyethyl substitution created antigenic determinants and conferred new immunochemical identity on the modified starch molecule. Anti-HES ABS represent specific analytical tools for the identification and quantitation of HES in biological material.
A Randomized, Double-Blind, Placebo-Controlled Trial of Metformin Treatment of Weight Gain Associated With Initiation of Atypical Antipsychotic Therapy in Children and Adolescents (2006)

Metformin therapy is safe and effective in abrogating weight gain, decreased insulin sensitivity, and abnormal glucose metabolism resulting from treatment of children and adolescents with atypicals.
Site-directed deletion mutagenesis using phagemid vectors and genetic selection. (1989)

Oligonucleotide-directed mutagenesis was used along with the dut and ung genetic selection method of Kunkel to introduce large site-specific deletions into cDNAs cloned into phagemid vectors. We find that large deletions can be achieved with an efficiency equal to that of single point mutations, with a very low frequency of aberrent clones. To facilitate screening of clones, E. coli strain DH5 alpha was used as the recipient host cell to genetically select for deletion mutants. Comparisons were made to deletion mutagenesis without genetic selection, and to reactions utilizing two oligonucleotide primers simultaneously. The low frequency of deletion mutants observed without genetic selection renders random screening for deletion mutant clones cumbersome. The results provide representative expectations and a useful guide for those contemplating the construction of deletion mutants.
Method of Measuring Bacillus anthracis Spores in the Presence of Copious Amounts of Bacillus thuringiensis and Bacillus cereus (2006)

A sensitive and reliable method for the detection of Bacillus anthracis (BA; Sterne strain 7702) spores in presence of large amounts of Bacillus thuringiensis (BT) and Bacillus cereus (BC) is presented based on a novel PZT-anchored piezoelectric excited millimeter-sized cantilever (PAPEMC) sensor with a sensing area of 1.5 mm2. Antibody (anti-BA) specific to BA spores was immobilized on the sensing area and exposed to various samples of BA, BT, and BC containing the same concentration of BA at 333 spores/mL, and the concentration of BT + BC was varied in concentration ratios of (BA:BT + BC) 0:1, 1:0, 1:1, 1:10, 1:100, and 1:1000. In each case, the sensor responded with an exponential decrease in resonant frequency and the steady-state frequency changes reached were 14 +/- 31 (n = 11), 2742 +/- 38 (n = 3), 3053 +/- 19 (n = 2), 2777 +/- 26 (n = 2), 2953 +/- 24 (n = 2), and 3105 +/- 27 (n = 2) Hz, respectively, in 0, 27, 45, 63, 154, and 219 min. The bound BA spores were released in each experiment, and the sensor response was nearly identical to the frequency change during attachment. These results suggest that the transport of BA spores to the antibody immobilized surface was hindered by the presence of other Bacillus species. The observed binding rate constant, based on the Langmuir kinetic model, was determined to be 0.15 min-1. A hindrance factor (alpha) is defined to describe the reduced attachment rate in the presence of BT + BC and found to increase exponentially with BT and BC concentration. The hindrance factor increased from 3.52 at 333 BT + BC spores/mL to 11.04 at 3.33 x 105 BT + BC spores/mL, suggesting that alpha is a strong function of BT and BC concentration. The significance of these results is that anti-BA functionalized PEMC sensors are highly selective to Bacillus anthracis spores and the presence of other Bacillus species, in large amounts, does not prevent binding but impedes BA transport to the sensor.
The benefits of coding over routing in a randomized setting (2003)

A novel randomized network coding approach for robust, distributed transmission and compression of information in networks is presented, and its advantages over routing-based approaches is demonstrated.
Soluble interleukin 6 (IL-6) receptor and IL-6 levels in serum and synovial fluid of patients with different arthropathies. (1997)

Unlike IL-6, sIL-6R is not produced at the site of inflammation and is not related to clinical or biological disease activity variables. Only in RA are both IL-6 and sIL-6R levels increased, suggesting that sIL-6R may reinforce the systemic effects of IL-6.
Gene expression and cellular sources of inducible nitric oxidesynthase during tumor promotion (1996)

The present studies examined the temporal sequence of inducible nitric oxide synthase (iNOS) gene expression and the cellular sources of iNOS protein and of 3-nitrotyrosine, as a marker of production of nitric oxide-derived reactive nitrogen intermediates during murine multi-stage carcinogenesis. Levels of iNOS mRNA in dorsal skin isolated from acetone-treated female Sencar mice were 2.5-fold higher than iNOS gene expression detected in cutaneous tissue isolated from Sencar mice at 1, 3, 6, 10, 16 and 22 weeks after exposure to a single topical application of 25 nmol 7,12-dimethylbenz[a]anthracene (DMBA) followed by repetitive applications of 2 microgram 17-O-tetradecanoylphorbol-13-acetate (TPA). Papillomas isolated at 16 and 22 weeks of a tumor promotion protocol also had low levels of iNOS mRNA. The diminished levels of iNOS mRNA inversely correlated with the extent of TPA-induced epidermal hyperplasia. In acetone-treated mouse skin, iNOS immunospecific antibody binding was localized to the stratum corneum and suprabasal keratinocytes. In contrast, iNOS protein was present in lower amounts and was localized to the upper-most suprabasal keratinocytes in cutaneous tissue isolated at 22 weeks following a single exposure to either 25 nmol DMBA or acetone and repetitive applications of 2 microgram TPA. At all time points examined over the 22 week time period of papilloma growth, infiltrating neutrophils within the dermis bound significant levels of anti-iNOS antibodies. The production of iNOS by neutrophils within the dermis correlated with the formation of protein nitrotyrosination within the dermal tissue, as detected by 3-nitrotyrosine-specific antibodies. The present studies indicate that NOS and reactive nitrogen intermediates, including peroxynitrite, are produced specifically by dermal neutrophils during the tumor promotion process at time points that correspond to simultaneous production of reactive oxygen intermediates. Conversely, iNOS is simultaneously down-regulated in hyperplastic epidermis and in papillomas.
High-precision optical measurements of 13 C/ 12 C isotope ratios in organic compounds at natural abundance (2009)

A continuous-flow cavity ring-down spectroscopy (CRDS) system integrating a chromatographic separation technique, a catalytic combustor, and an isotopic (13)C/(12)C optical analyzer is described for the isotopic analysis of a mixture of organic compounds. A demonstration of its potential is made for the geochemically important class of short-chain hydrocarbons. The system proved to be linear over a 3-fold injection volume dynamic range with an average precision of 0.95 per thousand and 0.67 per thousand for ethane and propane, respectively. The calibrated accuracy for methane, ethane, and propane is within 3 per thousand of the values determined using isotope ratio mass spectrometry (IRMS), which is the current method of choice for compound-specific isotope analysis. With anticipated improvements, the low-cost, portable, and easy-to-use CRDS-based instrumental setup is poised to evolve into a credible challenge to the high-cost and complex IRMS-based technique.
High‐yield anthocyanin biosynthesis in engineered Escherichia coli (2007)

Anthocyanins are red, purple, or blue plant water-soluble pigments. In the past two decades, anthocyanins have received extensive studies for their anti-oxidative, anti-inflammatory, anti-cancer, anti-obesity, anti-diabetic, and cardioprotective properties. In the present study, anthocyanin biosynthetic enzymes from different plant species were characterized and employed for pathway construction leading from inexpensive precursors such as flavanones and flavan-3-ols to anthocyanins in Escherichia coli. The recombinant E. coli cells successfully achieved milligram level production of two anthocyanins, pelargonidin 3-O-glucoside (0.98 mg/L) and cyanidin 3-O-gluside (2.07 mg/L) from their respective flavanone precursors naringenin and eriodictyol. Cyanidin 3-O-glucoside was produced at even higher yields (16.1 mg/L) from its flavan-3-ol, (+)-catechin precursor. Further studies demonstrated that availability of the glucosyl donor, UDP-glucose, was the key metabolic limitation, while product instability at normal pH was also identified as a barrier for production improvement. Therefore, various optimization strategies were employed for enhancing the homogenous synthesis of UDP-glucose in the host cells while at the same time stabilizing the final anthocyanin product. Such optimizations included culture medium pH adjustment, the creation of fusion proteins and the rational manipulation of E. coli metabolic network for improving the intracellular UDP-glucose metabolic pool. As a result, production of pelargonidin 3-O-glucoside at 78.9 mg/L and cyanidin 3-O-glucoside at 70.7 mg/L was achieved from their precursor flavan-3-ols without supplementation with extracellular UDP-glucose. These results demonstrate the efficient production of the core anthocyanins for the first time and open the possibility for their commercialization for pharmaceutical and nutraceutical applications.
Phenoxodiol inhibits growth of metastatic prostate cancer cells (2010)

These data demonstrated that Phenoxodiol promotes apoptosis, as determined by PARP-1 degradation, via mitochondrial depolarization and G1/S cell-cycle arrest thereby confirming that it is active against androgen-dependent and independent prostate cancer cells. Although a precise target for Phenoxodiol has not been identified, these data contribute to our understanding of the mechanism by which this drug promotes cell death in prostate cancer cells, and warrants the continued clinical development of Phenoxodiol as a therapeutic for the treatment of metastatic prostate cancer.
Characterization of polysilicon-gate depletion in MOS structures (1996)

This paper presents a new technique to characterize the depletion capacitance and (active) impurity concentration of gate polysilicon in MOS transistors. The method has been validated by means of 2-D simulation; experimental results obtained with state-of-the-art n-channel 0.5 micrometer transistors are presented.
Discovery of Tyrosine Kinase Inhibitors by Docking into an Inactive Kinase Conformation Generated by Molecular Dynamics (2012)

Several small molecules that bind to the inactive DFG-out conformation of tyrosine kinases (called type II inhibitors) have shown a good selectivity profile over other kinase targets. To obtain a set of DFG-out structures, we performed an explicit solvent molecular dynamics (MD) simulation of the complex of the catalytic domain of a tyrosine kinase receptor, ephrin type-A receptor 3 (EphA3), and a manually docked type II inhibitor. Automatic docking of four previously reported type II inhibitors was used to select a single snapshot from the MD trajectory for virtual screening. High-throughput docking of a pharmacophore-tailored library of 175,000 molecules resulted in about 4 million poses, which were further filtered by van der Waals efficiency and ranked according to a force-field-based energy function. Notably, around 20 % of the compounds with predicted binding energy smaller than -10 kcal mol(-1) are known type II inhibitors. Moreover, a series of 5-(piperazine-1-yl)isoquinoline derivatives was identified as a novel class of low-micromolar inhibitors of EphA3 and unphosphorylated Abelson tyrosine kinase (Abl1). The in silico predicted binding mode of the new inhibitors suggested a similar affinity to the gatekeeper mutant T315I of Abl1, which was verified in vitro by using a competition binding assay. Additional evidence for the type II binding mode was obtained by two 300 ns MD simulations of the complex between N-(3-chloro-4-(difluoromethoxy)phenyl)-2-(4-(8-nitroisoquinolin-5-yl)piperazin-1-yl)acetamide and EphA3.
[Combined activity of meliacin and foscarnet against different strains of herpes simplex virus type 1 using a three-dimensional model]. (1997)

We evaluated the in vitro antiviral activity of meliacin combined with foscarnet on the herpes simplex type 1 (HSV-1) strains F and B2006 (tk-) replication. The effective concentrations for 50% inhibition of HSV-1 (F) were 12.5 micrograms/ml for meliacin and 15.7 micrograms/ml for foscarnet, while for HSV-1 (B2006) were 3.1 micrograms/ml and 126 micrograms/ml, respectively. The data were analyzed for quantitation of synergism, additivity, and antagonism of multiple drug effect by the three-dimensional model. Some of the meliacin -foscarnet combinations synergistically inhibited HSV-1 (F) and HSV-1 (B2006) replication in vitro at concentrations that did not reduce cellular viability.
Role of Listeriolysin O in Cell-to-Cell Spread of Listeria monocytogenes (2000)

Listeria monocytogenes is a facultative intracellular bacterial pathogen that escapes from a host vacuolar compartment and grows rapidly in the cytosol. Listeriolysin O (LLO) is a secreted pore-forming protein essential for the escape of L. monocytogenes from the vacuole formed upon initial internalization. However, its role in intracellular growth and cell-to-cell spread events has not been testable by a genetic approach. In this study, purified six-His-tagged LLO (HisLLO) was noncovalently coupled to the surface of nickel-treated LLO-negative mutants. Bound LLO mediated vacuolar escape in approximately 2% of the mutants. After 5.5 h of growth, cytosolic bacteria were indistinguishable from wild-type bacteria with regard to formation of pseudopod-like extensions, here termed listeriopods, and spread to adjacent cells. However, bacteria in adjacent cells failed to multiply and were found in double-membrane vacuoles. Addition of bound LLO to mutants lacking LLO and two distinct phospholipases C (PLCs) also resulted in spread to adjacent cells, but these triple mutants became trapped in multiple-membrane vacuoles that are reminiscent of autophagocytic vacuoles. These studies show that neither LLO nor the PLCs are necessary for listeriopod formation and uptake of bacteria into neighboring cells but that LLO is required for the escape of L. monocytogenes from the double-membrane vacuole that forms upon cell-to-cell spread.
Effect of Nanoparticle Surface Charge at the Plasma Membrane and Beyond (2010)

Herein, we demonstrate that the surface charge of gold nanoparticles (AuNPs) plays a critical role in modulating membrane potential of different malignant and nonmalignant cell types and subsequent downstream intracellular events. The findings presented here describe a novel mechanism for cell-nanoparticle interactions and AuNP uptake: modulation of membrane potential and its effect on intracellular events. These studies will help understand the biology of cell-nanoparticle interactions and facilitate the engineering of nanoparticles for specific intracellular targets.