gebhart/patrepeval huggingface dataset:
Planning and Execution of Straight Line Manipulator Trajectories (1979)

Recently developed manipulator control languages typically specify motions as sequences of points through which a tool affixed to the end of the manipulator is to pass. The effectiveness of such motion specification formalisms is greatly increased if the tool moves in a straight line between the user-specified points. This paper describes two methods for achieving such straight line motions. The first method is a refinement of one developed in 1974 by R. Paul. Intermediate points are interpolated along the Cartesian straight line path at regular intervals during the motion, and the manipulator's kinematic equations are solved to produce the corresponding intermediate joint parameter values. The path interpolation functions developed here offer several advantages, including less computational cost and improved motion characteristics. The second method uses a motion planning phase to precompute enough intermediate points so that the manipulator may be driven by interpolation of joint parameter values while keeping the tool on an approximately straight line path. This technique allows a substantial reduction in real time computation and permits problems arising from degenerate joint alignments to be handled more easily. The planning is done by an efficient recursive algorithm which generates only enough intermediate points to guarantee that the tool's deviation from a straight line path stays within prespecified error bounds.
Reduction of established spontaneous mammary carcinoma metastases following immunotherapy with major histocompatibility complex class II and B7.1 cell-based tumor vaccines. (1998)

For many cancer patients, removal of primary tumor is curative; however, if metastatic lesions exist and are not responsive to treatment, survival is limited. Although immunotherapy is actively being tested in animal models against primary tumors and experimental metastases (i.v. induced), very few studies have examined immunotherapy of spontaneous, established metastatic disease. The shortage of such studies can be attributed to the paucity of adequate animal models and to the concern that multiple metastatic lesions may be more resistant to immunotherapy than a localized primary tumor. Here, we use the BALB/c-derived mouse mammary carcinoma, 4T1, and show that this tumor very closely models human breast cancer in its immunogenicity, metastatic properties, and growth characteristics. Therapy studies demonstrate that treatment of mice with established primary and metastatic disease with MHC class II and B7.1-transfected tumor cells reduces or eliminates established spontaneous metastases but has no impact on primary tumor growth. These studies indicate that cell-based vaccines targeting the activation of CD4+ and CD8+ T cells may be effective agents for the treatment of malignancies, such as breast cancer, where the primary tumor is curable by conventional methods, but metastatic lesions remain refractile to current treatment modalities.
Complement C3a receptors in the pituitary gland: a novel pathway by which an innate immune molecule releases hormones involved in the control of inflammation (2003)

Two-way communication exists between the endocrine and immune systems using molecules such as hormones and cytokines. Here we describe a new pathway by which C3a, a complement-derived cytokine, stimulates anterior pituitary hormone release and activates the hypothalamic-pituitary-adrenal axis, a reflex central to the stress response and to the control of inflammation. We show that C3a receptors are expressed in pituitary hormone secreting and non-hormone secreting (folliculostellate) cells and that both C3a and C3adesArg (a non-inflammatory metabolite) stimulate pituitary cell cultures to release prolactin, growth hormone, and adrenocorticotropin. Serum levels of these hormones, together with adrenal corticosterone, increase dose dependently with recombinant C3a and C3adesArg administration in vivo. Pertussis toxin blocks the response to C3a but not C3adesArg, which indicates the presence of two receptors, only one of which is coupled to Galphai-proteins. We propose that the complement innate immune molecules (cytokines) modulate tissue-specific and systemic inflammatory responses through communication with the endocrine pituitary gland.
Performance of MEMS inertial sensors (2002)

Advanced microfabrication techniques have produced small, low-cost silicon inertial sensors of high performance, ruggedness, and inherent symmetry. When integrated with Applications Specific Integrated Circuits (ASIC's), the sensors fit in a 3 cm per side flat pack and operate from a single 5 Vdc supply. They have been evaluated in automotive anti-skid and traction control systems, and in guided munitions. Multi-Chip Module (MCM) versions instruments enable guided munitions to improve the accuracy of the Navy 5"/54 gun platform. These sensors are fabricated using a dissolved wafer process that features single crystal silicon anodically bonded to a glass substrate, resulting in a sensor die size approximately 1 mm. Uncompensated bias and scale factor performance of 0.5/spl deg//s and 1.0% for the gyroscope, and 30 mg and 0.5% for the accelerometer are nominally demonstrated over the temperature range of -40/spl deg/C to +85/spl deg/C. Stability over smaller temperature ranges of 0.5/spl deg/C has surpassed 10/spl deg//hr(0.003/spl deg//s) in overnight (6 hour) tests, while the companion accelerometer nominally demonstrates sub milli-g performance. Angle random walk of 0.25/spl deg///spl radic/h is typical for the gyros with best to date performance of 0.05/spl deg///spl radic/h observed, while the accelerometers provide velocity random walk of 5 cm/s//spl radic/h. When compensated for performance across the temperature range of -40/spl deg/C to +85/spl deg/C, instrument scale factor performance surpasses 200 ppm stability, and bias uncertainty is less than 50/spl deg//hr and 1 mg for the gyro and accelerometer respectively. The robustness of these demonstrated in the ability to survive air guns tests in excess of 60000 g. This paper discusses measured and performance, with the principal focus on recent gyro and accelerometer instrument test results. Associated electronics, controls, and applications issues are also addressed.
Mammalian Peroxiredoxin Isoforms Can Reduce Hydrogen Peroxide Generated in Response to Growth Factors and Tumor Necrosis Factor-α (1998)

Mammalian tissues express three immunologically distinct peroxiredoxin (Prx) proteins (Prx I, II, and III), which are the products of distinct genes. With the use of recombinant proteins Prx I, II, and III, all have now been shown to possess peroxidase activity and to rely on Trx as a source of reducing equivalents for the reduction of H2O2. Prx I and II are cytosolic proteins, whereas Prx III is localized in mitochondria. Transient overexpression of Prx I or II in cultured cells showed that they were able to eliminate the intracellular H2O2 generated in response to growth factors. Moreover, the activation of nuclear factor kappaB (NFkappaB) induced by extracellularly added H2O2 or tumor necrosis factor-alpha was blocked by overproduction of Prx II. These results suggest that, together with glutathione peroxidase and catalase, Prx enzymes likely play an important role in eliminating peroxides generated during metabolism. In addition, Prx I and II might participate in the signaling cascades of growth factors and tumor necrosis factor-alpha by regulating the intracellular concentration of H2O2.
Interleukin 2 (IL-2)-induced tyrosine phosphorylation of IL-2 receptor p75. (1990)

We have recently established a mAb named TU11 mAb specific for the p75 subunit of human IL-2 receptor (IL-2R). The present study using TU11 mAb demonstrates the IL-2-induced phosphorylation of IL-2Rp75 on tyrosine residues in IL-2-dependent T cells. The tyrosine phosphorylation is mediated by the high affinity IL-2R, correlates with the IL-2-induced cell growth, and rapidly increases during the first 5 min of IL-2 stimulation. Phosphorylation of serine and threonine residues of IL-2Rp75 is also detected, but its IL-2 dependency is not significant during at least the first 5 min. These results suggest some roles of a tyrosine kinase associated with IL-2Rp75 in the IL-2-induced signal-transducing pathway.
3-Substituted adenines. In vitro enzyme inhibition and antiviral activity (1979)

The direct alkylation of adenine at the 3 position has been extended to produce series of 3-alkyl-, 3-allyl-, and 3-(substituted benzyl)adenines. When these compounds were tested for enzyme inhibition and antiviral activity in vitro, 3-n-pentyladenine was found to be the most active compound in inhibiting the enzyme dopamine-beta-hydroxylase, and 3-(2-bromobenzyl)adenine showed the most striking inhibition of multiplication of Vaccinia virus and of Herpes simplex virus in tissue culture.
Principles, protocols, and architecture (1995)

This reference has now been divided into two volumes to reflect the most recent changes in the field. Volume 1 provides a broad, conceptual introduction to the TCP/IP internetworking protocols and the connected TCP/IP Internet. It reviews network hardware, including wide area national backbones ARPANET and NSFNET, and local area technologies Ethernet and token rings. Addresses binding (ARP) and the IP concepts of connectionless datagram delivery, error detection and control, multicasting, and routing are covered. In addition, Comer compares the ISO 7-layer reference model to the TCP/IP 5-layer model in his discussion of protocol layering.
Functions and Regulation of RNA Editing by ADAR Deaminases (2010)

One type of RNA editing converts adenosines to inosines (A-->I editing) in double-stranded RNA (dsRNA) substrates. A-->I RNA editing is mediated by adenosine deaminase acting on RNA (ADAR) enzymes. A-->I RNA editing of protein-coding sequences of a limited number of mammalian genes results in recoding and subsequent alterations of their functions. However, A-->I RNA editing most frequently targets repetitive RNA sequences located within introns and 5' and 3' untranslated regions (UTRs). Although the biological significance of noncoding RNA editing remains largely unknown, several possibilities, including its role in the control of endogenous short interfering RNAs (esiRNAs), have been proposed. Furthermore, recent studies have revealed that the biogenesis and functions of certain microRNAs (miRNAs) are regulated by the editing of their precursors. Here, I review the recent findings that indicate new functions for A-->I editing in the regulation of noncoding RNAs and for interactions between RNA editing and RNA interference mechanisms.
Mediation of Serum Resistance in Salmonella typhimurium by an 11-Kilodalton Polypeptide Encoded by the Cryptic Plasmid (1987)

A cosmid bank of the DNA (including cryptic plasmid DNA) of a virulent strain of Salmonella typhimurium was prepared in Escherichia coli K12, and clones that contained cryptic plasmid DNA were detected by probing. Two such clones expressed a new outer membrane protein of 11 kilodaltons (kDa) and were serum resistant (E. coli K12 is serum sensitive). The gene encoding the 11-kDa protein was subcloned in a 2.1-kilobase fragment and shown to mediate serum resistance in both E. coli K12 and a cryptic plasmid-free (serum-sensitive) strain of S. typhimurium. The cryptic plasmid-free S. typhimurium strain did not express normal lipopolysaccharide, but introduction of the 11-kDa protein gene into the strain rendered the strain serum resistant without restoration of normal lipopolysaccharide synthesis. The 11-kDa protein gene was not sufficient to restore either macrophage resistance or virulence to a cryptic plasmid-free strain of S. typhimurium.
Secure software attestation for military telesurgical robot systems (2010)

Telesurgical robot systems (TRS) are often deployed in unattended environments such as battlefields or rural areas. Therefore, adversaries can easily access the devices, compromise the system, and install their own malware. If the integrity and health of the system software and configuration files are not verified before their usage, the safety and lives of the injured soldiers and patients may be in danger. Many existing software attestation mechanisms depend on the calculation delay to distinguish a correct memory image from a compromised system. We cannot directly apply this technique to transcontinental TRS when we consider the long transmission delay between the verifier and the prover. In this paper, we propose a software attestation mechanism that can distinguish between these two kinds of delay. A secure communication protocol among the verifier, telesurgical robot, and secure token of the remote medical personnel is designed. The safety of the approach is analyzed and its overhead is evaluated.
Free Radicals Generated during the Glycation Reaction of Amino Acids by Methylglyoxal (1995)

The formation of alpha-dicarbonyl compounds seems to be an important step for cross-linking proteins in the glycation or Maillard reaction. To elucidate the mechanism for the cross-linking reaction, we studied the reaction between a three-carbon alpha-dicarbonyl compound, methylglyoxal, and amino acids. Our results showed that this reaction generated yellow fluorescent products as formed in some glycated proteins. In addition, three types of free radical species were also produced, and their structures were determined by EPR spectroscopy. These free radicals are 1) the cross-linked radical cation, 2) the methylglyoxal radical anion as the counterion, and 3) the superoxide radical anion produced only in the presence of oxygen. The generation of the cross-linked radical cations and the methylglyoxal radical anions does not require metal ions or oxygens. These results indicate that dicarbonyl compounds cross-link free amino groups of protein by forming Schiff bases, which donate electrons directly to dicarbonyl compounds to form the cross-linked radical cations and the methylglyoxal radical anions. Oxygen can accept an electron from the radical anion to generate a superoxide radical anion, which can initiate damaging chain reactions. Time course studies suggest that the cross-linked radical cation is a precursor of yellow fluorescent glycation end products.
AKR1C Isoforms Represent a Novel Cellular Target for Jasmonates alongside Their Mitochondrial-Mediated Effects (2009)

Members of the aldo-keto reductase (AKR) superfamily, particularly the AKR1C subfamily, are emerging as important mediators of the pathology of cancer. Agents that inhibit these enzymes may provide novel agents for either the chemoprevention or treatment of diverse malignancies. Recently, jasmonates, a family of plant stress hormones that bear a structural resemblance to prostaglandins, have been shown to elicit anticancer activities both in vitro and in vivo. In this study, we show that jasmonic acid (JA) and methyl jasmonate (MeJ) are capable of inhibiting all four human AKR1C isoforms. Although JA is the more potent inhibitor of recombinant AKR1C proteins, including the in vitro prostaglandin F synthase activity of AKR1C3, MeJ displayed greater potency in cellular systems that was, at least in part, due to increased cellular uptake of MeJ. Moreover, using the acute myelogenous leukemia cell lines HL-60 and KG1a, we found that although both jasmonates were able to induce high levels of reactive oxygen species in a dose-dependent fashion, only MeJ was able to induce high levels of mitochondrial superoxide (MSO), possibly as an epiphenomenon of mitochondrial damage. There was a strong correlation observed between MSO formation at 24 hours and reduced cellularity at day 5. In conclusion, we have identified AKR1C isoforms as a novel target of jasmonates in cancer cells and provide further evidence of the promise of these compounds, or derivatives thereof, as adjunctive therapies in the treatment of cancer.
Induced DNA demethylation by targeting Ten-Eleven Translocation 2 to the human ICAM-1 promoter (2013)

Increasing evidence indicates that active DNA demethylation is involved in several processes in mammals, resulting in developmental stage-specificity and cell lineage-specificity. The recently discovered Ten-Eleven Translocation (TET) dioxygenases are accepted to be involved in DNA demethylation by initiating 5-mC oxidation. Aberrant DNA methylation profiles are associated with many diseases. For example in cancer, hypermethylation results in silencing of tumor suppressor genes. Such silenced genes can be re-expressed by epigenetic drugs, but this approach has genome-wide effects. In this study, fusions of designer DNA binding domains to TET dioxygenase family members (TET1, -2 or -3) were engineered to target epigenetically silenced genes (ICAM-1, EpCAM). The effects on targeted CpGs' methylation and on expression levels of the target genes were assessed. The results indicated demethylation of targeted CpG sites in both promoters for targeted TET2 and to a lesser extent for TET1, but not for TET3. Interestingly, we observed re-activation of transcription of ICAM-1. Thus, our work suggests that we provided a mechanism to induce targeted DNA demethylation, which facilitates re-activation of expression of the target genes. Furthermore, this Epigenetic Editing approach is a powerful tool to investigate functions of epigenetic writers and erasers and to elucidate consequences of epigenetic marks.
Spectrum of Chemically Induced Mutations From a Large-Scale Reverse-Genetic Screen in Arabidopsis (2003)

Chemical mutagenesis has been the workhorse of traditional genetics, but it has not been possible to determine underlying rates or distributions of mutations from phenotypic screens. However, reverse-genetic screens can be used to provide an unbiased ascertainment of mutation statistics. Here we report a comprehensive analysis of approximately 1900 ethyl methanesulfonate (EMS)-induced mutations in 192 Arabidopsis thaliana target genes from a large-scale TILLING reverse-genetic project, about two orders of magnitude larger than previous such efforts. From this large data set, we are able to draw strong inferences about the occurrence and randomness of chemically induced mutations. We provide evidence that we have detected the large majority of mutations in the regions screened and confirm the robustness of the high-throughput TILLING method; therefore, any deviations from randomness can be attributed to selectional or mutational biases. Overall, we detect twice as many heterozygotes as homozygotes, as expected; however, for mutations that are predicted to truncate an encoded protein, we detect a ratio of 3.6:1, indicating selection against homozygous deleterious mutations. As expected for alkylation of guanine by EMS, >99% of mutations are G/C-to-A/T transitions. A nearest-neighbor bias around the mutated base pair suggests that mismatch repair counteracts alkylation damage.
Water‐Responsive Shape Memory Polyurethane Block Copolymer Modified with Polyhedral Oligomeric Silsesquioxane (2006)

Nanostructured polyurethane block copolymers with shape memory were synthesized by using polyhedral oligomeric silsesquioxane (POSS) molecules and poly(ethylene glycol) (PEG), which acted as the hydrophobic and hydrophilic groups, respectively. The hard segment domains appeared to be dominantly governed by POSS molecules according to X‐ray diffraction and Fourier transform‐infrared (FT‐IR) measurements. As the POSS content increased, the phase separation between hard and soft segments gradually developed, followed by the crystallization of POSS molecules, and the melting temperature and heat of fusion for POSS crystals increased. The water‐responsive shape memory behavior which resulted from the dissolution of soft segments was demonstrated at 30°C. More than 70% shape recovery was achieved in the water‐responsive shape recovery test, which depended on the POSS content.
Extraction of indicative summary sentences from imaged documents (2002)

A system for selecting sentences from an imaged document for presentation as part of a document summary is presented. The extracts are identified without the use of optical character recognition. The sentences are selected based on a set of discrete features characterizing the words within a sentence and the location of the sentence within the imaged document. Each sentence is scored based on the values of the discrete features using a statistically based classifier. The imaged document is processed to identify the word locations, the reading order of words, and the location of sentence and paragraph boundaries in the text. The words are grouped into equivalence classes to mimic the terms in a text document. A sample extract for a technical document is shown, and evaluation against a set of abstracts created by a professional abstracting company is given. These results are compared with text-based abstracts.
A synthetic Escherichia coli predator–prey ecosystem (2008)

We have constructed a synthetic ecosystem consisting of two Escherichia coli populations, which communicate bi-directionally through quorum sensing and regulate each other's gene expression and survival via engineered gene circuits. Our synthetic ecosystem resembles canonical predator-prey systems in terms of logic and dynamics. The predator cells kill the prey by inducing expression of a killer protein in the prey, while the prey rescue the predators by eliciting expression of an antidote protein in the predator. Extinction, coexistence and oscillatory dynamics of the predator and prey populations are possible depending on the operating conditions as experimentally validated by long-term culturing of the system in microchemostats. A simple mathematical model is developed to capture these system dynamics. Coherent interplay between experiments and mathematical analysis enables exploration of the dynamics of interacting populations in a predictable manner.
The Beneficial Interaction Between Enalapril and Danazol in Normal Rat (2002)

Danazol, a weekly androgenic, heterocyclic compound with anabolic properties, is used primarily in the treatment of endometriosis and other gynecological complaints. Effects of co-administration of enalapril, an angiotensin converting enzyme inhibitor (ACE inhibitor) with danazol on some biochemical parameters in rats were studied. Treatment of rats with danazol (200mglkg i.p) for 15 days induced a significant elevation of serum aspartate transaminase activity (AST, EC: 2.6.1.1), triglycerides (TG) and induced a significant decrease in serum cholesterol. However, enalapril treatment (20mglkg i.p) for 15 days caused a significant elevation of serum alanine transaminase activity (ALT, EC: 2.6.1.2). Co-administration of danazol and enalapril significantly lowered the elevated levels of serum transaminases enzyme activities and serum TG. It could be concluded that long term treatment with enalapril might be beneficial in patients danazol in clinical situations through protection against undesirable side effects.
Plasma MicroRNAs as Sensitive and Specific Biomarkers of Tissue Injury (2009)

These results demonstrate that tissue-specific miRNAs may serve as diagnostically sensitive plasma biomarkers of tissue injury.
Development and Application of Expressed Protein Ligation (2001)

Expressed protein ligation (EPL) is a protein semi-synthesis approach that allows synthetic and recombinant polypeptides to be chemoselectively and regioselectively joined together via a peptide bond. The approach makes the primary structure of proteins accessible to the tools of synthetic organic chemistry and thus provides expanded opportunities in the area of protein engineering. The development and application of this process will be discussed.