gebhart/patrepeval huggingface dataset:
Autonomous planning for mobile manipulation services based on multi-level robot skills (2009)

General purpose service robots are expected to deal with many different tasks in unknown environments. The number of possible tasks and changing situations prevent developers from writing control programs for all tasks and possible situations. Complex robot tasks are thus accomplished by sequential execution of less complex robot actions that are triggered and configured by a task planner. The question of the appropriate abstraction level of robot actions is still being researched and not discussed conclusively. In this paper, we address the problem of atomicity of robot actions and provide some key properties that have to be considered while designing plan-based robot control systems. Based on these properties, we define and implement atomic skills of different abstraction level for the service robot TASER. The HTN planner JShop2 is used to complete the plan-based control architecture which is evaluated in a set of experiments.
Unexpected Catalyzed CC Bond Cleavage by Molecular Oxygen Promoted by a Thiyl Radical (2001)

Olefin oxidation with molecular oxygen, promoted by a transition metal catalyst and a thiophenol, involved C=C bond cleavage into the corresponding carbonyl derivatives. This new reaction proceeds under one atmosphere of oxygen, at room temperature, in the presence of an excess of thiophenol and a catalyst such as MnL(2) 3a or VClL(2) 3c. It was applied to aromatic and aliphatic olefins, as well as to functionalized or unfunctionalized acyclic compounds, providing the corresponding ketones and aldehydes in up to 98% yield. The synthetic interest of this catalytic oxidation was illustrated by a one-step preparation of the fragrance (-)-4-acetyl-1-methylcyclohexene 7e in 73% isolated yield. The C=C bond cleavage probably results from a catalyzed decomposition of the beta-hydroperoxysulfide intermediate 12 that is formed by the radical addition of thiophenol to the olefin in the presence of oxygen. Although an excess of the thiophenol was used, it was transformed into the disulfide which could then be reduced without purification in 83% overall yield, thereby allowing for recycling. In addition, the C=C bond cleavage under oxygen could be promoted by catalytic quantities of the thiyl radical, generated by photolysis of the disulfide; thus, in the presence of 0.1 equiv of bis(4-chlorophenyl) disulfide 4b and 5% of the manganese complex 3a, trans-methylstilbene 1b gave, under radiation, benzaldehyde 6a and acetophenone 7a in up to 95% yield. This new reaction offers an alternative to the classical C=C bond cleavage procedures, and further developments in the fields of bioinorganic and environmental chemistry are likely.
Mechanical stress analysis of an LDD MOSFET structure (1996)

This paper presents a mechanical stress study of the LDD MOSFET structure. The stresses are successively evaluated through the forming steps and topological modifications are proposed in order to minimize the residual substrate stress. The analysis is based on a two dimensional finite element method. It includes the cumulative effects from the thermal oxidation, the thermal cycles and the intrinsic stresses, allowing the estimation of the evolution of the stress field during the manufacturing. A nonlinear viscoelastic approach is used to model the nitride, thermal and deposited oxides rheological behaviors. For those oxides, a complete calibration of the mechanical properties is proposed.
Dedifferentiated fat cells: A cell source for regenerative medicine (2015)

The identification of an ideal cell source for tissue regeneration remains a challenge in the stem cell field. The ability of progeny cells to differentiate into other cell types is important for the processes of tissue reconstruction and tissue engineering and has clinical, biochemical or molecular implications. The adaptation of stem cells from adipose tissue for use in regenerative medicine has created a new role for adipocytes. Mature adipocytes can easily be isolated from adipose cell suspensions and allowed to dedifferentiate into lipid-free multipotent cells, referred to as dedifferentiated fat (DFAT) cells. Compared to other adult stem cells, the DFAT cells have unique advantages in their abundance, ease of isolation and homogeneity. Under proper condition in vitro and in vivo, the DFAT cells have exhibited adipogenic, osteogenic, chondrogenic, cardiomyogenc, angiogenic, myogenic, and neurogenic potentials. In this review, we first discuss the phenomena of dedifferentiation and transdifferentiation of cells, and then dedifferentiation of adipocytes in particular. Understanding the dedifferentiation process itself may contribute to our knowledge of normal growth processes, as well as mechanisms of disease. Second, we highlight new developments in DFAT cell culture and summarize the current understanding of DFAT cell properties. The unique features of DFAT cells are promising for clinical applications such as tissue regeneration.
Cometabolism of Chlorinated Solvents by Nitrifying Bacteria: Kinetics, Substrate Interactions, Toxicity Effects, and Bacterial Response (1999)

Pure cultures of ammonia-oxidizing bacteria, Nitrosomonas europaea, were exposed to trichloroethylene (TCE), 1,1-dichloroethylene (1,1-DCE), chloroform (CF), 1,2-dichloroethane (1,2-DCA), or carbon tetrachloride (CT), in the presence of ammonia, in a quasi-steady-state bioreactor. Estimates of enzyme kinetics constants, solvent inactivation constants, and culture recovery constants were obtained by simultaneously fitting three model curves to experimental data using nonlinear optimization techniques and an enzyme kinetics model, referred to as the inhibition, inactivation, and recovery (IIR) model, that accounts for inhibition of ammonia oxidation by the solvent, enzyme inactivation by solvent product toxicity, and respondent synthesis of new enzyme (recovery). Results showed relative enzyme affinities for ammonia monooxygenase (AMO) of 1,1-DCE approximately TCE > CT > NH(3) > CF > 1,2-DCA. Relative maximum specific substrate transformation rates were NH(3) > 1,2-DCA > CF > TCE approximately 1,1-DCE > CT (=0). The TCE, CF, and 1,1-DCE inactivated the cells, with 1,1-DCE being about three times more potent than TCE or CF. Under the conditions of these experiments, inactivating injuries caused by TCE and 1,1-DCE appeared limited primarily to the AMO enzyme, but injuries caused by CF appeared to be more generalized. The CT was not oxidized by N. europaea while 1,2-DCA was oxidized quite readily and showed no inactivation effects. Recovery capabilities were demonstrated with all solvents except CF. A method for estimating protein yield, the relationship between the transformation capacity model and the IIR model, and a condition necessary for sustainable cometabolic treatment of inactivating substrates are presented. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 54: 520-534, 1997.
Mechanically Induced Catalytic Amplification Reaction for Readout of Receptor‐Mediated Cellular Forces (2016)

Mechanics play a fundamental role in cell biology, but detecting piconewton (pN) forces is challenging because of a lack of accessible and high throughput assays. A mechanically induced catalytic amplification reaction (MCR) for readout of receptor-mediated forces in cells is described. Mechanically labile DNA duplexes presenting ligands are surface immobilized such that specific receptor forces denature the duplex and thus expose a blocked primer. Amplification of primers is achieved using an isothermal polymerization reaction and quantified by fluorescence readout. As a proof of concept, the assay was used to test the activity of a mechanomodulatory drug and integrin adhesion receptor antibodies. To the best of our knowledge, this is the first example of a catalytic reaction triggered in response to molecular piconewton forces. The MCR may transform the field of mechanobiology by providing a new facile tool to detect receptor specific mechanics with the convenience of the polymerase chain reaction (PCR).
Neuronal rescue with transforming growth factor-β1 after hypoxic-ischaemic brain injury (1994)

Transforming growth factor-beta 1 (TGF-beta 1) mRNA is induced from 5 h to 3 days following hypoxic-ischaemic brain injury. Cell death also develops during this time suggesting that extracellular accumulation of this peptide may be involved in the processes that regulate cell loss. We examined the effect of rhTGF-beta 1 (0,2.5, 10,50 ng) injected into the cerebral lateral ventricle of rats 2 h after severe hypoxic-ischaemic brain injury. Histological outcome and B4-isolectin histochemistry were assessed 5 and 2 days, respectively following hypoxia. Treatment with 10 ng TGF-beta 1 reduced the microglia reaction (p < 0.05), the magnitude of neuronal loss (p < 0.01) and the area of cortical infarction (p < 0.05). Exogenous TGF-beta 1 given soon after hypoxic-ischaemic brain injury may have therapeutic potential and act by inhibiting the microglial reaction.
Stochastic models for the<i>Trojan Y-Chromosome</i>eradication strategy of an invasive species (2015)

The Trojan Y-Chromosome (TYC) strategy, an autocidal genetic biocontrol method, has been proposed to eliminate invasive alien species. In this work, we develop a Markov jump process model for this strategy, and we verify that there is a positive probability for wild-type females going extinct within a finite time. Moreover, when sex-reversed Trojan females are introduced at a constant population size, we formulate a stochastic differential equation (SDE) model as an approximation to the proposed Markov jump process model. Using the SDE model, we investigate the probability distribution and expectation of the extinction time of wild-type females by solving Kolmogorov equations associated with these statistics. The results indicate how the probability distribution and expectation of the extinction time are shaped by the initial conditions and the model parameters.
Cytotoxicity of rhein, the active metabolite of sennoside laxatives, is reduced by multidrug resistance-associated protein 1 (2002)

Anthranoid laxatives, belonging to the anthraquinones as do anthracyclines, possibly increase colorectal cancer risk. Anthracyclines interfere with topoisomerase II, intercalate DNA and are substrates for P-glycoprotein and multidrug resistance-associated protein 1. P-glycoprotein and multidrug resistance-associated protein 1 protect colonic epithelial cells against xenobiotics. The aim of this study was to analyse the interference of anthranoids with these natural defence mechanisms and the direct cytotoxicity of anthranoids in cancer cell lines expressing these mechanisms in varying combinations. A cytotoxicity profile of rhein, aloe emodin and danthron was established in related cell lines exhibiting different levels of topoisomerases, multidrug resistance-associated protein 1 and P-glycoprotein. Interaction of rhein with multidrug resistance-associated protein 1 was studied by carboxy fluorescein efflux and direct cytotoxicity by apoptosis induction. Rhein was less cytotoxic in the multidrug resistance-associated protein 1 overexpressing GLC4/ADR cell line compared to GLC4. Multidrug resistance-associated protein 1 inhibition with MK571 increased rhein cytotoxicity. Carboxy fluorescein efflux was blocked by rhein. No P-glycoprotein dependent rhein efflux was observed, nor was topoisomerase II responsible for reduced toxicity. Rhein induced apoptosis but did not intercalate DNA. Aloe emodin and danthron were no substrates for MDR mechanisms. Rhein is a substrate for multidrug resistance-associated protein 1 and induces apoptosis. It could therefore render the colonic epithelium sensitive to cytotoxic agents, apart from being toxic in itself.
Inhibitory Effects of Triterpenes and Flavonoids on the Enzymatic Activity of Hyaluronic Acid‐Splitting Enzymes (2006)

The effect of triterpenes and flavonoids on the activity of several hyaluronic acid-splitting enzymes was investigated. Studies showed that the inhibitory effect of the triterpenes glycyrrhizin and glycyrrhetinic acid is dependent on the source of hyaluronate lyase. Hyaluronate lyase from Streptococcus agalactiae (Hyal B) and recombinant hyaluronate lyase from Streptococcus agalactiae (rHyal B) demonstrated strongest inhibition. In contrast, hyaluronate lyases from Streptomyces hyalurolyticus (Hyal S), Streptococcus equisimilis (Hyal C) and hyaluronidase from bovine testis (Dase) showed only reduced inhibition action. A non-competitive dead end inhibition with Ki=3.1+/-1.8x10(-6) mol/mL and Kii=6.7+/-2.4x10(-6) mol/mL was found for glycyrrhizin on recombinant hyaluronate lyase from Streptococcus agalactiae. The inhibitory effect of flavonoids on Hyal B, rHyal B and Dase was determined depending on the number of hydroxyl groups and side chain substituents in the molecule. Flavonoids with many hydroxyl groups inhibited hyaluronate lyase stronger than those with only a few. Native hyaluronate lyase (Hyal B) showed a more extensive inhibition than the recombinant protein (rHyal B). Accordingly, the inhibition by triterpenes and flavonoids is presumably specific for each hyaluronic acid (HA)-splitting enzyme.
The Reaction of Chymotrypsin with 2,3-Butanedione Trimer (1975)

A method for the preparation of the trimer of 2,3-butanedione has been developed; The reaction of this trimer with chymotrypsin A alpha was examined in the presence or absence of light. Under conditions of exclusion of light, modification of one to two arginine residues and of a similar number of lysine residues could be achieved without any loss of enzymatic activity. The trimer facilitated a rapid photoinactivation of the enzyme with little or no modification of the above amino acid residues. Such photoinactivation was not found to react with proflavine and diiosopropylfluorophosphate to an extent greater than that expected on the basis of residual activity presentmproflavine protected the enzyme from the trimer promoted photoinactivation.
Neuromorphic algorithms on clusters of PlayStation 3s (2010)

There is a significant interest in the research community to develop large scale, high performance implementations of neuromorphic models. These have the potential to provide significantly stronger information processing capabilities than current computing algorithms. In this paper we present the implementation of five neuromorphic models on a 50 TeraFLOPS 336 node Playstation 3 cluster at the Air Force Research Laboratory. The five models examined span two classes of neuromorphic algorithms: hierarchical Bayesian and spiking neural networks. Our results indicate that the models scale well on this cluster and can emulate between 108 to 1010 neurons. In particular, our study indicates that a cluster of Playstation 3s can provide an economical, yet powerful, platform for simulating large scale neuromorphic models.
MicroPheno: Predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples (2018)

Motivation: Microbial communities play important roles in the function and maintenance of various biosystems, ranging from the human body to the environment. A major challenge in microbiome research is the classification of microbial communities of different environments or host phenotypes. The most common and cost-effective approach for such studies to date is 16S rRNA gene sequencing. Recent falls in sequencing costs have increased the demand for simple, efficient, and accurate methods for rapid detection or diagnosis with proved applications in medicine, agriculture, and forensic science. We describe a reference- and alignment-free approach for predicting environments and host phenotypes from 16S rRNA gene sequencing based on k-mer representations that benefits from a bootstrapping framework for investigating the sufficiency of shallow sub-samples. Deep learning methods as well as classical approaches were explored for predicting environments and host phenotypes. Results: k-mer distribution of shallow sub-samples outperformed the computationally costly Operational Taxonomic Unit (OTU) features in the tasks of body-site identification and Crohn's disease prediction. Aside from being more accurate, using k-mer features in shallow sub-samples allows (i) skipping computationally costly sequence alignments required in OTU-picking, and (ii) provided a proof of concept for the sufficiency of shallow and short-length 16S rRNA sequencing for phenotype prediction. In addition, k-mer features predicted representative 16S rRNA gene sequences of 18 ecological environments, and 5 organismal environments with high macro-F1 scores of 0.88 and 0.87. For large datasets, deep learning outperformed classical methods such as Random Forest and SVM. Availability: The software and datasets are available at https://llp.berkeley.edu/micropheno.
Nuclear Substitution Derivatives of Isonicotinic Acid (1958)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNuclear Substitution Derivatives of Isonicotinic AcidH. HERBERT FOX and J. T. GIBASCite this: J. Org. Chem. 1958, 23, 1, 64–66Publication Date (Print):January 1, 1958Publication History Published online1 May 2002Published inissue 1 January 1958https://pubs.acs.org/doi/10.1021/jo01095a019https://doi.org/10.1021/jo01095a019research-articleACS PublicationsRequest reuse permissionsArticle Views337Altmetric-Citations11LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Myeloperoxidase binds to low‐density lipoprotein: potential implications for atherosclerosis (2000)

Myeloperoxidase (MPO), an abundant heme enzyme released by activated phagocytes, catalyzes the formation of a number of reactive species that can modify low-density lipoprotein (LDL) to a form that converts macrophages into lipid-laden or 'foam' cells, the hallmark of atherosclerotic lesions. Since MPO has been shown to bind to a number of different cell types, we investigated binding of MPO to LDL. Using the precipitation reagents phosphotungstate or isopropanol, MPO co-precipitated with LDL, retaining its catalytic activity. The association of MPO with LDL was confirmed using native gel electrophoresis. MPO was also found to co-precipitate with apolipoprotein B-100-containing lipoproteins in whole plasma. No precipitation of MPO was observed in lipoprotein-deficient plasma, and there was a dose-dependent increase in precipitation following addition of LDL to lipoprotein-deficient plasma. Binding of MPO to LDL could potentially enhance site-directed oxidation of the lipoprotein and limit scavenging of reactive oxygen species by antioxidants.
Effect of Sleep Position on Sleep Apnea Severity (1984)

Thirty male patients evaluated sequentially for sleep apnea syndrome by all-night clinical polysomnography were compared for apnea plus hypopnea index (A + HI) during the time in the side versus time in the back sleep posture. For 24 subjects of this sample, who occupied both major body positions during the evaluation night, the apnea index was found to be twice as high during the time spent sleeping on their backs as it was when they slept in the side position. This difference is reliable and inversely related to obesity. Five patients meeting diagnostic criteria for sleep apnea on an all-night basis fell within normal limits while in the side sleep position. This suggests sleep position adjustment may be a viable treatment for some nonobese sleep apnea patients.
Downlink Interference Alignment (2011)

We develop an interference alignment (IA) technique for a downlink cellular system. In the uplink, IA schemes need channel-state-information exchange across base-stations of different cells, but our downlink IA technique requires feedback only within a cell. As a result, the proposed scheme can be implemented with a few changes to an existing cellular system where the feedback mechanism (within a cell) is already being considered for supporting multi-user MIMO. Not only is our proposed scheme implementable with little effort, it can in fact provide substantial gain especially when interference from a dominant interferer is significantly stronger than the remaining interference: it is shown that in the two-isolated cell layout, our scheme provides four-fold gain in throughput performance over a standard multi-user MIMO technique. We also show through simulations that our technique provides respectable gain under a more realistic scenario: it gives approximately 28% gain for a 19 hexagonal wrap-around-cell layout. Furthermore, we show that our scheme has the potential to provide substantial gain for macro-pico cellular networks where pico-users can be significantly interfered with by the nearby macro-BS.
Acetylcholine receptor-reactive T and B cells in myasthenia gravis and controls. (1991)

Myasthenia gravis (MG) is strongly associated with antibodies to acetylcholine receptor (AChR), whereas the extent of T cell involvement is not settled. The number of cells secreting interferon-gamma (IFN-gamma) in response to AChR during 48 h culture of blood mononuclear cells (PBL) may reflect AChR-reactive T cells. Using an immunospot assay, we detected such cells in 23 of 30 patients with MG at a mean number of 1 per 33.333 PBL. AChR-reactive T cells were also found in patients with other neurological diseases (OND) and in healthy subjects but at lower frequencies and numbers. The T cell response to purified protein derivative and to PHA, and also to two major myelin proteins (basic protein and proteolipid protein) did not differ between MG and the two control groups, underlining the specificity of an augmented T cell reactivity to AChR in MG. Evaluation of the B cell response by enumerating anti-AChR IgG antibody secreting cells revealed such cells in 27 of 28 patients with MG at a mean value of 1 per 14,085 PBL. Cells secreting anti-AChR antibodies of the IgA and IgM isotypes were also detected in MG, but less frequently, at lower numbers, and only in conjunction with IgG antibody secreting cells. Anti-AChR antibody secreting cells were also found among patient with OND and in healthy controls, but at lower frequencies and numbers. These data confirm that AChR is a major target for autoimmune response in MG.
Normally-Off Thin-Film Silicon Heterojunction Field-Effect Transistors and Application to Complementary Circuits (2014)

A thin blocking structure is incorporated in the gate-stack of heterojunction field-effect transistor (HJFET) devices to substantially suppress the gate current when the gate heterojunction is forward-biased. As a result, normally-OFF HJFET devices with MOSFET-like characteristics are obtained. The HJFET devices are comprised of gate, source, and drain regions formed by plasma-enhanced chemical vapor deposition on thin-film crystalline Si substrates at temperatures below 200°C. The ON/OFF ratios larger than 106, operation voltages as low as 1 V, and subthreshold slopes of ~85 mV/decade are demonstrated. The HJFET devices can be integrated with MOSFET devices fabricated on the same crystalline Si substrates to form complementary circuits.