gebhart/patrepeval huggingface dataset:
RINSE: The Real-Time Immersive Network Simulation Environment for Network Security Exercises (2005)

The RINSE simulator is being developed to support large-scale network security preparedness and training exercises, involving hundreds of players and a modeled network composed of hundreds of LANs. The simulator must be able to present a realistic rendering of network behavior as attacks are launched and players diagnose events and try counter measures to keep network services operating. We describe the architecture and function of RINSE and outline how techniques like multiresolution traffic modeling and new routing simulation methods are used to address the scalability challenges of this application. We also describe in more detail new work on CPU/memory models necessary for the exercise scenarios and a latency absorption technique that help when extending the range of client tools usable by the players.
Game theory with economic applications (1993)

This text looks at game theory and its uses as a tool to enable people to make strategic decisions. The second edition emphasises the practical aspects of game theory. The text is divided into five parts allowing the logical selection of material based on teaching needs.
Synthesis and Morphology of Molecular Brushes with Polyacrylonitrile Block Copolymer Side Chains and Their Conversion into Nanostructured Carbons (2007)

Densely grafted brushes with polyacrylonitrile (PAN) di- (AB) and triblock (ABC) copolymer side chains were synthesized first time by ATRP using the “grafting from” technique. Tapping-mode atomic force microscopy showed that these brushes displayed wormlike shapes on mica surface. A necklacelike structure was observed for brushes with poly(n-butyl acrylate)-b-polyacrylonitrile-b-poly(tert-butyl acrylate) triblock copolymer side chains. After conversion of poly(tert-butyl acrylate) side chains to poly(acrylic acid), they were cross-linked with diamine to fix the extended 3-dimensional structure. Such shell-cross-linked molecular brushes showed improved stability during transferring from solution to flat substrates and have been successfully converted into nanostructured carbons through pyrolysis. The pyrolyzed materials exhibited characteristics of partially graphitic carbon.
Toward Integrated Scene Text Reading (2013)

The growth in digital camera usage combined with a worldly abundance of text has translated to a rich new era for a classic problem of pattern recognition, reading. While traditional document processing often faces challenges such as unusual fonts, noise, and unconstrained lexicons, scene text reading amplifies these challenges and introduces new ones such as motion blur, curved layouts, perspective projection, and occlusion among others. Reading scene text is a complex problem involving many details that must be handled effectively for robust, accurate results. In this work, we describe and evaluate a reading system that combines several pieces, using probabilistic methods for coarsely binarizing a given text region, identifying baselines, and jointly performing word and character segmentation during the recognition process. By using scene context to recognize several words together in a line of text, our system gives state-of-the-art performance on three difficult benchmark data sets.
The L7/L12 ribosomal domain of the ribosome: structural and functional studies (1997)

The L7/L12 protein forms a functionally important domain in the ribosome. This domain is involved in interaction with translation factors during protein biosynthesis. The tertiary and quaternary structure of the L7/L12 protein was established as a result of intensive studies in solution and in the ribosome. The conformational changes of L7/L12, the elongation factors Tu and G and other ribosomal proteins were traced by different experimental techniques. These changes occur upon interaction of the ribosome with the elongation factors and depend on GTP hydrolysis in accordance with the functional states of the ribosome.
Reversible Logic Circuits Made of DNA (2011)

We report reversible logic circuits made of DNA. The circuits are based on an AND gate that is designed to be thermodynamically and kinetically reversible and to respond nonlinearly to the concentrations of its input molecules. The circuits continuously recompute their outputs, allowing them to respond to changing inputs. They are robust to imperfections in their inputs.
Stress reduction in tungsten films using nanostructured compliant layers (2004)

The residual stress in thin films is a major limiting factor for obtaining high quality films. We present a strategy for stress reduction in sputter deposited films by using a nanostructured compliant layer obtained by the oblique angle deposition technique, sandwiched between the film and the substrate. The technique is all in situ, does not require any lithography steps, and the nanostructured layer is made from the same material as the deposited thin film. By using this approach we were able to reduce stress values by approximately one order of magnitude in sputter deposited tungsten films. These lower stress thin films also exhibit stronger adhesion to the substrate, which retards delamination buckling. This technique allows the growth of much thicker films and has enhanced structural stability. A model is developed to explain the stress relief mechanism and the stronger adhesion associated with the presence of the nanostructured compliant layer.
Expression of bone sialoprotein, a bone matrix protein, in human breast cancer. (1994)

Microcalcifications are often associated with human mammary lesions, particularly with breast carcinomas. To date, the molecular mechanism that leads to the deposition of hydroxyapatite in the mammary tissue has not been elucidated. Bone sialoprotein (BSP) is a glycoprotein the expression of which coincides with the appearance of the first hydroxyapatite crystals during bone development. In this study, we report the observation that BSP, a bone matrix protein, is expressed in human mammary cancer cells. Using an immunoperoxidase technique, we studied the expression of BSP in 79 breast lesions, including 28 benign and 51 malignant specimens. Two polyclonal antibodies, one directed against intact human BSP and the other against a synthetic peptide of BSP (residues 277-294), were used and gave identical results. Normal mammary glands expressed undetectable or barely detectable amounts of BSP, and the majority of the benign lesions examined were generally unstained (0) or weakly stained (1+). Most of the breast carcinoma specimens (around 87%) showed a significant increase (P = 0.0001) in BSP expression. Breast carcinomas with microcalcifications had the highest immunoreactivity (2+ or 3+) to BSP antibodies. This is the first demonstration that BSP expression is significantly increased in breast cancer. Expression of BSP by breast cancer cells could play a major role in the deposition of microcalcifications and in the preferred bone homing of breast cancer cells.
A High-Performance Neural Prosthesis Incorporating Discrete State Selection With Hidden Markov Models (2016)

Communication neural prostheses aim to restore efficient communication to people with motor neurological injury or disease by decoding neural activity into control signals. These control signals are both analog (e.g., the velocity of a computer mouse) and discrete (e.g., clicking an icon with a computer mouse) in nature. Effective, high-performing, and intuitive-to-use communication prostheses should be capable of decoding both analog and discrete state variables seamlessly. However, to date, the highest-performing autonomous communication prostheses rely on precise analog decoding and typically do not incorporate high-performance discrete decoding. In this report, we incorporated a hidden Markov model (HMM) into an intracortical communication prosthesis to enable accurate and fast discrete state decoding in parallel with analog decoding. In closed-loop experiments with nonhuman primates implanted with multielectrode arrays, we demonstrate that incorporating an HMM into a neural prosthesis can increase state-of-the-art achieved bitrate by 13.9% and 4.2% in two monkeys ( ). We found that the transition model of the HMM is critical to achieving this performance increase. Further, we found that using an HMM resulted in the highest achieved peak performance we have ever observed for these monkeys, achieving peak bitrates of 6.5, 5.7, and 4.7 bps in Monkeys J, R, and L, respectively. Finally, we found that this neural prosthesis was robustly controllable for the duration of entire experimental sessions. These results demonstrate that high-performance discrete decoding can be beneficially combined with analog decoding to achieve new state-of-the-art levels of performance.
Convenient and Effective Method for Removing Fibrinogen from Serum Specimens before Protein Electrophoresis (2003)

Ethanol, 100 mL/L, can selectively precipitate fibrinogen without significantly interfering with the immunoglobulins. The precipitation process can be completed in 15 min at 0-4 degrees C and can avoid the need to obtain another blood sample.
Robust Positioning Algorithms for Distributed Ad-Hoc Wireless Sensor Networks (2002)

A distributed algorithm for determining the positions of nodes in an ad-hoc, wireless sensor network is explained in detail. Details regarding the implementation of such an algorithm are also discussed. In a 400 node network in which the nodes are randomly placed within a 100x100 square, the algorithm is shown to achieve average position errors of less than 33% of a node&amp;apos;s radio range in the presence of 5% range measurement error when at least 5% of the nodes are anchor nodes (with known position) and the average connectivity of a node is greater than 7 nodes. It is shown that the algorithm performs well in networks in which nodes are connected to at least 7 one-hop neighbors on average and where average range errors are less than 40%.
Applications for green fluorescent protein (GFP) in the study of hostpathogen interactions (1996)

The green fluorescent protein (GFP) from Aequorea victoria is a novel fluorescent marker that has potential use in the study of bacterial pathogenicity. To explore some of the potential applications of GFP to the study of host-parasite interactions, we constructed two GFP expression vectors suitable for different facultative intracellular bacterial pathogens. The first expression vector was tested in the enteric pathogens, Salmonella typhimurium and Yersinia pseudotuberculosis, and the second vector tested in Mycobacterium marinum (Mm). Both expression vectors were found to be stable and to direct high levels of GFP synthesis. Standard epifluorescence microscopy was used to detect all three bacterial pathogenic species during the early and late stages of infection of live mammalian cells. Mm expressing gfp was also visualized in infected animal tissues. gfp expression did not adversely affect bacterial survival, nor did it compromise entry into mammalian cells or their survival within macrophages. In addition, all three gfp-expressing bacterial pathogens could be detected and sorted in a flow cytometer, either alone or in association with epithelial cells or macrophages. Therefore, GFP not only provides a convenient tool to image pathogenic bacteria, but allows the quantitative measurement of bacterial association with mammalian cells.
Effect of chemical and heat inactivation on the antigenicity and immunogenicity of Vibrio cholerae (1982)

The effects of heat and chemical inactivation on the antigenicity and immunogenicity of Vibrio cholerae 1418 in rabbits were studied. V. cholerae 1418 was inactivated with heat and chemical inactivants (phenol or Formalin) alone or in combination. Enzyme-linked immunoassay systems employing whole cells of V. cholerae 1418, lipopolysaccharide, or flagella as immobilized antigens were used to measure the antibody response (immunoglobulins G and M) after parenteral immunization of rabbits with various inactivated whole-cell preparations. The "classical" whole-cell vaccine, produced by phenol treatment, was found to be a comparatively poor immunogen. When Formalin was used instead of phenol, the antibody response to all three enzyme-linked immunosorbent assay antigens was greatly increased. Immunoglobulin G titers to intact V. cholerae cells were as much as 100-fold higher in rabbits immunized with the Formalin-inactivated preparation as compared to the classical phenol-inactivated vaccine. Furthermore, antibody produced against the Formalin-inactivated preparation was capable of recognizing antigenic determinants expressed on the cell surface of several heterologous strains of V. cholerae. These results indicate that the antigenicity and immunogenicity of V. cholerae are greatly affected by the inactivation conditions employed for vaccine production and that Formalin is much superior to phenol as an inactivant under the conditions employed in the present study.
CB2 cannabinoid receptor mediation of antinociception (2006)

Management of acute pain remains a significant clinical problem. In preclinical studies, CB2 cannabinoid receptor-selective agonists inhibit nociception without producing central nervous system side effects. The CB2 receptor-selective agonist AM1241 produces antinociceptive effects that are antagonized by CB2, but not CB1, receptor-selective antagonists, suggesting that activation of CB2 receptors results in antinociception. However, it has not been possible to definitively demonstrate that these effects are mediated by CB2 receptors, because we have lacked the pharmacological tools to confirm the in vivo receptor selectivity of the antagonists used. Further, recent evidence for cannabinoid-like receptors beyond CB1 and CB2 raises the possibility that AM1241 exerts its antinociceptive effects at uncharacterized CB2-like receptors that are also inhibited by AM630. The experiments reported here further test the hypothesis that CB2 receptor activation inhibits nociception. They evaluated the antinociceptive actions of AM1241 and the less-selective CB2 receptor agonist WIN55,212-2 in wild-type (CB2+/+) mice and in mice with genetic disruption of the CB2 receptor (CB2-/- mice). AM1241 inhibited thermal nociception in CB2+/+ mice, but had no effect in CB2-/- littermates. WIN55,212-2 produced equivalent antinociception in CB1+/+ and CB1-/- mice, while its antinociceptive effects were reduced in CB2-/- compared to CB2+/+ mice. The effects of morphine were not altered in CB2-/- compared to CB2+/+ mice. These data strongly suggest that AM1241 produces antinociception in vivo by activating CB2 cannabinoid receptors. Further, they confirm the potential therapeutic relevance of CB2 cannabinoid receptors for the treatment of acute pain.
Vitamin E analog, alpha-tocopherol ether-linked acetic acid analog, alone and in combination with celecoxib, reduces multiplicity of ultraviolet-induced skin cancers in mice (2008)

The goals of this study were to determine whether alpha-tocopherol ether-linked acetic acid analog (alpha-TEA), a novel vitamin E analog, and celecoxib, alone or in combination, when administered as a late intervention can reduce the ultraviolet-induced nonmelanoma skin-tumor burden of established tumors, prevent additional tumors from developing, and prevent tumor recurrence once treatments are stopped. Hairless SKH-1 female mice were ultraviolet-irradiated for 24 weeks, divided into treatment groups so that each group had approximately 5.8 tumors/mouse, and then treated with 72 mug of liposome-formulated alpha-TEA by aerosol inhalation, 500 p.p.m. celecoxib in AIN-76 A diet, or a combination of alpha-TEA and celecoxib for 4 weeks. At the end of 4 weeks of treatment, each treatment group was subdivided, with one subgroup continuing to receive treatment and with treatment being stopped in the other. Skin-tumor development was monitored visually throughout the study and by histologic evaluation at the end. After 4 weeks of treatment, all treatments showed statistically significant reductions in tumor number when compared with controls. After termination of treatment, only alpha-TEA prevented a significant increase in tumor recurrence; however, continuous combination treatment resulted in the lowest total number of tumors. In conclusion alpha-TEA is an effective late-stage chemopreventive agent for nonmelanoma skin cancer that exhibits lasting benefits.
Characterization of Polystyrene-block-poly(acrylic acid) Micelles (2005)

Thesis (S.B.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 2005.
Microglial Activation in Perinatal Rabbit Brain Induced by Intrauterine Inflammation: Detection with 11C-(R)-PK11195 and Small-Animal PET (2007)

Intrauterine inflammation leads to activation of microglial cells that may be responsible for the development of brain injury and white matter damage in the perinatal period. PET with the tracer (11)C-(R)-PK11195 can be used as a noninvasive, sensitive tool for determining the presence and progress of neuroinflammation due to perinatal insults in newborns.
Opiate Analgesia (1991)

It is generally accepted that systemically administered opiates produce analgesia through an action in the central nervous system. Indeed, mu, delta, and appa opiate receptors and receptor-selective opioid peptides, although widely distributed in the central nervous system, are concentrated in several sites that have been implicated in the regulation of nociceptive messages. The analgesia produced by the microinjection of opioids at these sites is hypothesized to result from activation of a descending antinociceptive pathway, which originates in the midbrain periaqueductal gray matter and inhibits the transmission of nociceptive messages at the level of the spinal cord.1 Injection of opiates at . . .
A Pan-H1 Anti-Hemagglutinin Monoclonal Antibody with Potent Broad-Spectrum Efficacy<i>In Vivo</i> (2012)

Seasonal epidemics caused by antigenic variations in influenza A virus remain a public health concern and an economic burden. The isolation and characterization of broadly neutralizing anti-hemagglutinin monoclonal antibodies (MAb) have highlighted the presence of highly conserved epitopes in divergent influenza A viruses. Here, we describe the generation and characterization of a mouse monoclonal antibody designed to target the conserved regions of the hemagglutinin of influenza A H1 viruses, a subtype that has caused pandemics in the human population in both the 20th and 21st centuries. By sequentially immunizing mice with plasmid DNA encoding the hemagglutinin of antigenically different H1 influenza A viruses (A/South Carolina/1/1918, A/USSR/92/1977, and A/California/4/2009), we isolated and identified MAb 6F12. Similar to other broadly neutralizing MAb previously described, MAb 6F12 has no hemagglutination inhibition activity against influenza A viruses and targets the stalk region of hemagglutinins. As designed, it has neutralizing activity against a divergent panel of H1 viruses in vitro, representing 79 years of antigenic drift. Most notably, MAb 6F12 prevented gross weight loss against divergent H1 viruses in passive transfer experiments in mice, both in pre- and postexposure prophylaxis regimens. The broad but specific activity of MAb 6F12 highlights the potent efficacy of monoclonal antibodies directed against a single subtype of influenza A virus.
Tissue antioxidants and postmenopausal breast cancer: the European Community Multicentre Study on Antioxidants, Myocardial Infarction, and Cancer of the Breast (EURAMIC). (1996)

Antioxidants may protect against free radical mediated carcinogenesis. Epidemiological studies have not confirmed this hypothesis for breast cancer, possibly because of methodological limitations. Time-integrated exposure of alpha-tocopherol and beta-carotene in adipose tissue, and selenium in toenails was investigated in a case-control study among postmenopausal women, ages 50-74 years, from five European countries. The study group comprised 347 incident breast cancer cases and 374 controls. Mean antioxidant levels, adjusted for age and center, did not significantly differ for alpha-tocopherol (cases were 4.5% higher than controls), beta-carotene (3.0% lower), or selenium (1.8% lower). Odds ratios for highest versus lowest tertiles of exposure, adjusted for potential confounders, were 1.15 (95% confidence interval, 0.75-1.77), 0.74 (0.45-1.23), and 0.96 (0.63-1.47), respectively, without evidence for a decreasing trend. No statistically significant interactions were observed. Moreover, a provisional antioxidant score, indicating whether concentrations were above the median for zero, one, two, or all three antioxidants, yielded odds ratios of 1.00 (reference; all below median), 1.58, 1.58, and 1.21, respectively (chi2 for association = 4.00; P = 0.26). These results do not support the hypothesis that antioxidants are important determinants of this hormone-related malignancy among postmenopausal women.
Enhancing the recognition of tumour associated antigens. (1994)

Activated CD8+ T cells (TCD8+) can directly recognize malignant cells because processed fragments of tumour associated antigens (TAA), 8-10 amino acids in length and complexed with MHC class I molecules, are displayed on tumour cell surfaces. Tumour cells have been genetically modified in a variety of ways in efforts to enhance the immune recognition of TAA. An alternative strategy is the expression of TAA in recombinant or synthetic form. This has been made possible by the recent cloning of TAA recognized by TCD8+. In this communication we review recent work in our own laboratory on the expression of TAA as synthetic peptide, by "naked" plasmid DNA injected intramuscularly or transdermally, and by recombinant viruses including vaccinia (rVV), fowlpox (rFV) and adenovirus (rAd). The expression of TAA in recombinant and synthetic forms allows increased control over the quantity, location, and kinetics of TAA presentation and can result in powerful, specific, anti-tumour immune responses.
Characterization of three fimbrial genes, sefABC, of Salmonella enteritidis (1993)

Salmonella enteritidis produces thin, filamentous fimbriae designated SEF14. A 3.9-kb region of a 5.3-kb fragment encoding genes responsible for SEF14 biosynthesis was sequenced and found to contain three genes, sefABC. sefA encoded a novel fimbrin, the structural subunit of SEF14 fimbriae. sefB and sefC encoded proteins homologous to Escherichia coli and Klebsiella pneumoniae fimbrial periplasmic chaperone proteins and fimbrial outer membrane proteins, respectively, and are the first such genes to be characterized from Salmonella spp. in vitro expression directed by the 5.3-kb DNA fragment identified SefA, SefB, and SefC as approximately 14,000-, 28,000-, and 90,000-M(r) proteins, respectively, which correlated with their predicted amino acid sequences. sefB and sefC were not expressed in the absence of sefA. Primer extension analysis of sefABC revealed two major transcription start sites located upstream of sefA. Transcription of sefBC also initiated from the sefA promoter region. Secondary-structure analysis of the mRNA transcript for sefABC predicted the formation of two stable stem-loop structures in the intercistronic region between sefA and sefB indicative of differential regulation of SefA, SefB, and SefC translation. E. coli cells carrying the 5.3-kb DNA fragment of S. enteritidis DNA were unable to assemble distinguishable SEF14 fimbriae; however, immunogold-labelled SEF14 fimbriae were displayed on E. coli clones containing a 44-kb DNA fragment which encompassed the 5.3-kb region. Therefore, sefABC genes make up part of a complex sef operon responsible for the expression and assembly of SEF14 fimbriae.