gebhart/patrepeval huggingface dataset:
Characterization of argon direct-current glow discharge with a longitudinal electric field applied at ambient air (2014)

A direct-current-driven plasma jet is developed by applying a longitudinal electric field on the flowing argon at ambient air. This plasma shows a torch shape with its cross-section increased from the anode to the cathode. Comparison with its counterparts indicates that the gas flow plays a key role in variation of the plasma structure and contributes much to enlarging the plasma volume. It is also found that the circular hollow metal base promotes generation of plasma with a high-power volume density in a limited space. The optical emission spectroscopy (OES) diagnosis indicates that the plasma comprises many reactive species, such as OH, O, excited N2, and Ar metastables. Examination of the rotational and vibrational temperature indicates that the plasma is under nonequilibrium condition and the excited species OH(A (2)Σ(+)), O((5)P), and N2(C (3)Πu) are partly generated by energy transfer from argon metastables. The spatially resolved OES of plasma reveals that the negative glow, Faraday dark space, and positive column are distributed across the gas gap. The absence of the anode glow is attributed to the fact that many electrons in the vicinity of the anode follow ions into the positive column due to the ambipolar diffusion in the flowing gas.
A Syntactic Approach to Domain-Specific Automatic Question Generation (2017)

Factoid questions are questions that require short fact-based answers. Automatic generation (AQG) of factoid questions from a given text can contribute to educational activities, interactive question answering systems, search engines, and other applications. The goal of our research is to generate factoid source-question-answer triplets based on a specific domain. We propose a four-component pipeline, which obtains as input a training corpus of domain-specific documents, along with a set of declarative sentences from the same domain, and generates as output a set of factoid questions that refer to the source sentences but are slightly different from them, so that a question-answering system or a person can be asked a question that requires a deeper understanding and knowledge than a simple word-matching. Contrary to existing domain-specific AQG systems that utilize the template-based approach to question generation, we propose to transform each source sentence into a set of questions by applying a series of domain-independent rules (a syntactic-based approach). Our pipeline was evaluated in the domain of cyber security using a series of experiments on each component of the pipeline separately and on the end-to-end system. The proposed approach generated a higher percentage of acceptable questions than a prior state-of-the-art AQG system.
Decoding via cross-entropy minimization (2002)

An intuitive algorithm by Lodge et al. [1992] for iterative decoding of block codes is shown to follow from entropy optimization principles. This approach provides a novel and effective algorithm for the soft-decoding of block codes which have a product structure.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Differential involvement of the hypermethylator phenotype in hereditary and sporadic colorectal cancers with high‐frequency microsatellite instability (2001)

High-frequency microsatellite instability (MSI-H) due to defective DNA mismatch repair occurs in the majority of hereditary nonpolyposis colorectal cancers (HNPCCs) and in a subset of sporadic malignant tumors. Clinicopathologic and genotypic features of MSI-H colorectal tumors in HNPCC patients and those in sporadic cases are very similar but not identical. Correlation between the MSI phenotype and aberrant DNA methylation has been highlighted recently. A strong association between MSI and CpG island methylation has been well characterized in sporadic colorectal cancers with MSI-H but not in those of hereditary origin. To address the issue, we analyzed hereditary and sporadic colorectal cancers for aberrant DNA methylation of target genes using methylation-specific polymerase chain reaction. DNA methylation of the MLH1, CDKN2A, MGMT, THBS1, RARB, APC, and p14ARF genes was found in 0%, 23%, 10%, 3%, 73%, 53%, and 33% of 30 MSI-H cancers in HNPCC patients and in 80%, 55%, 23%, 23%, 58%, 35%, and 50% of 40 sporadic colorectal cancers with MSI-H, respectively. Cases showing methylation at three or more loci of six genes other than MLH1 were defined as CpG island methylator phenotype-positive (CIMP +), and 23% of HNPCC tumors and 53% of sporadic cancers with MSI-H were CIMP+ (P = 0.018). Differences in the extent of CpG island methylation, coupled with the differential involvement of several genes by methylation, in HNPCC tumors and sporadic MSI-H colorectal cancers may be associated with diverging developmental pathways in hereditary and sporadic cancers despite similar MSI-H phenotypes.
Mapping of punctuate hyperalgesia around a surgical incision demonstrates that ketamine is a powerful suppressor of central sensitization to pain following surgery (1997)

Low-dose i.v. infusion of ketamine during and after surgery reduces mechanical punctuate hyperalgesia surrounding the surgical incision. These results indicate that blockade of NMDA receptors prevents the central sensitization caused by nociceptive input during and after surgery.
Microfabricated reciprocating micropump for intracochlear drug delivery with integrated drug/fluid storage and electronically controlled dosing (2015)

The anatomical and pharmacological inaccessibility of the inner ear is a major challenge in drug-based treatment of auditory disorders. This also makes pharmacokinetic characterization of new drugs with systemic delivery challenging, because efficacy is coupled with how efficiently a drug can reach its target. Direct delivery of drugs to cochlear fluids bypasses pharmacokinetic barriers and helps to minimize systemic toxicity, but anatomical barriers make administration of multiple doses difficult without an automated delivery system. Such a system may be required for hair-cell regeneration treatments, which will likely require timed delivery of several drugs. To address these challenges, we have developed a micropump for controlled, automated inner-ear drug delivery with the ultimate goal of producing a long-term implantable/wearable delivery system. The current pump is designed to be used with a head mount for guinea pigs in preclinical drug characterization experiments. In this system, we have addressed several microfluidic challenges, including maintaining controlled delivery at safe, low flow rates and delivering drug without increasing the volume of fluid in the cochlea. By integrating a drug reservoir and all fluidic components into the microfluidic structure of the pump, we have made the drug delivery system robust compared to previous systems that utilized separate, tubing-connected components. In this study, we characterized the pump's unique infuse-withdraw and on-demand dosing capabilities on the bench and in guinea pig animal models. For the animal experiments, we used DNQX, a glutamate receptor antagonist, as a physiological indicator of drug delivery. DNQX suppresses compound action potentials (CAPs), so we were able to infer the distribution and spreading of the DNQX over time by measuring the changes in CAPs in response to stimuli at several characteristic frequencies.
A new miniaturized surface micromachined tunneling accelerometer (1996)

The authors have fabricated a new class of miniaturized surface micromachined tunneling accelerometers. The accelerometer structures are fabricated on the surface of a single silicon wafer and consist of a single cantilevered beam with electrostatic deflection electrodes and tunneling tip underneath. The noise level resolutions in air of 100-μm and 250-μm-long cantilever devices are 8.3×10/sup -4/ g/Hz <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> 2/ and 8.5×10/sup -5/ g/Hz <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> 2/ at 500 respectively. The devices are operated in a force rebalance feedback mode using a low noise automatic servocontrol circuit, providing a dynamic range of over 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> g. This new accelerometer technology provides devices with extremely high sensitivity, high bandwidth and wide dynamic range, in an ultracompact, low-cost package that is easily integrated with silicon control electronics.
CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences (2014)

CRISPR/Cas9 systems are a versatile tool for genome editing due to the highly efficient targeting of DNA sequences complementary to their RNA guide strands. However, it has been shown that RNA-guided Cas9 nuclease cleaves genomic DNA sequences containing mismatches to the guide strand. A better understanding of the CRISPR/Cas9 specificity is needed to minimize off-target cleavage in large mammalian genomes. Here we show that genomic sites could be cleaved by CRISPR/Cas9 systems when DNA sequences contain insertions ('DNA bulge') or deletions ('RNA bulge') compared to the RNA guide strand, and Cas9 nickases used for paired nicking can also tolerate bulges in one of the guide strands. Variants of single-guide RNAs (sgRNAs) for four endogenous loci were used as model systems, and their cleavage activities were quantified at different positions with 1- to 5-bp bulges. We further investigated 114 putative genomic off-target loci of 27 different sgRNAs and confirmed 15 off-target sites, each harboring a single-base bulge and one to three mismatches to the guide strand. Our results strongly indicate the need to perform comprehensive off-target analysis related to DNA and sgRNA bulges in addition to base mismatches, and suggest specific guidelines for reducing potential off-target cleavage.
A 32-site neural recording probe fabricated by DRIE of SOI substrates (2002)

An all-dry silicon-etch based micromachining process for neural probes was demonstrated in the manufacture of a probe with a 32-site recording electrode array. The fork-like probe shafts were formed by double-sided deep reactive ion etching (DRIE) of a silicon-on-insulator (SOI) substrate, with the buried SiO2 layer acting as an etch stop. The shafts typically had the dimensions 5 mm × 25 μm × 20 μm and ended in chisel-shaped tips with lateral taper angles of 4°. An array of Ir electrodes, each 100 μm2, and Au conductor traces were formed on top of the shafts by e-beam evaporation. An accompanying interconnect solution based on flexible printed circuitry was designed, enabling precise and flexible positioning of the probes in neural tissue. SEM studies showed sharply defined probes and probe tips. The electrical yield and function were verified in bench-top measurements in saline. The magnitude of the electrode impedance was in the 1 MΩ range at 1 kHz, which is consistent with neurophysiological recordings.
Imaging approach in radioimmunodetection. (1980)

External in vivo imaging of tumors with radioactively labeled antibodies to tumor-associated antigens requires processing to remove interfering nontarget radioactivity. Processing entails the use of simulated nontarget compounds labeled with a radionuclide physically different from that on the antibody and substraction of the simulated nontarget activity from the nontargeted antibody. A 2-fold increase of the target to nontarget radioactivity is achieved that has made possible a greater than 70% tumor detection rate.
Adeno-associated virus vector-mediated IL-10 gene delivery prevents type 1 diabetes in NOD mice (2001)

The development of spontaneous autoimmune diabetes in nonobese diabetic (NOD) mice provides for their use as a model of human type 1 diabetes. To test the feasibility of muscle-directed gene therapy to prevent type 1 diabetes, we developed recombinant adeno-associated virus (rAAV) vectors containing murine cDNAs for immunomodulatory cytokines IL-4 or IL-10. Skeletal muscle transduction of female NOD mice with IL-10, but not IL-4, completely abrogated diabetes. rAAV-IL-10 transduction attenuated the production of insulin autoantibodies, quantitatively reduced pancreatic insulitis, maintained islet insulin content, and altered splenocyte cytokine responses to mitogenic stimulation. The beneficial effects were host specific, as adoptive transfer of splenocytes from rAAV IL-10-treated animals rapidly imparted diabetes in naive hosts, and the cells contained no protective immunomodulatory capacity, as defined through adoptive cotransfer analyses. These results indicate the utility for rAAV, a vector with advantages for therapeutic gene delivery, to transfer immunoregulatory cytokines capable of preventing type 1 diabetes. In addition, these studies provide foundational support for the concept of using immunoregulatory agents delivered by rAAV to modulate a variety of disorders associated with deleterious immune responses, including allergic reactions, transplantation rejection, immunodeficiencies, and autoimmune disorders.
SP1-mediated microRNA-520d-5p suppresses tumor growth and metastasis in colorectal cancer by targeting CTHRC1. (2015)

Recent evidence suggests that miR-520 family has an important role in regulating tumorigenesis and development of various types of solid cancers. However, as one of the most common cancers in the world, there is little known about the underlying regulatory mechanisms of miR-520 in colorectal cancer (CRC). In the present study, we investigated the expression of microRNA-520d-5p (miR-520d-5p) in CRC specimens and then explored its potential role and mechanism in CRC progression. We found that miR-520d-5p was markedly down-regulated in CRC clinical specimens compared with adjacent normal tissues by real-time PCR. Dual-luciferase assays confirmed that miR-520d-5p directly targeting CTHRC1 and SP1 transactivate miR-520d-5p by binding to its upstream promoter region. The biological functional experiments showed that ectopic re-expression of miR-520d-5p suppressed CRC cell proliferation, migration and invasion, whereas the inhibition of miR-520d-5p displayed an inverse effect in vitro and in vivo. Western blot shown that miR-520d-5p abrogated the epithelial-mesenchymal transition by inactivating the phosphorylation of Erk1/2. In conclusion, our findings indicate that miR-520d-5p is significantly down-expressed and involved in CRC progression and metastasis by targeting CTHRC1 and regulated by SP1, which provide new support for miR-520d-5p maybe as a novel anti-onco molecular target for the treatment of CRC in the future.
Scanning respirometer for toxicity tests using micro-organisms (1995)

A novel respirometer is developed for microbial toxicity tests. The respirometer is based on luminescent quenching of oxygen to measure the concentration of dissolved oxygen in cell vessels and evaluate the toxicity of chemicals by monitoring the effect of toxicants on cell respiration of micro-organisms. The oxygen sensing element is ruthenium complex absorbed on the surface of silica particles followed by immobilizing on a silicone rubber film. The oxygen sensing film is coated on the inner bottom of a transparent cell vessel. A sensing device scanning under the cell vessel is used for remote monitoring of the oxygen concentration inside the cell vessels so that a large number of samples can be handled in one batch. The sensing device includes the excitation light sources and an optical cable connected to a filter and a photomultiplier tube for detecting the luminescence in the cell vessel which can then be related to the dissolved oxygen concentration inside the cell vessel. The movement of the sensing device and data acquisition are controlled by a personal computer. The toxicity of heavy metals to activated sludge, soil bacteria and E. coli were tested using the present device. The scanning respirometer provides a new alternative for fast and large scale screening and monitoring of toxicants using micro-organisms.© (1995) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
Cyclic ADP‐ribose generation by CD38 improves human hemopoietic stem cell engraftment into NOD/SCID mice (2002)

Cyclic ADP-ribose (cADPR) is a potent and universal intracellular calcium mobilizer, recently shown to behave as a new hemopoietic cytokine stimulating the in vitro proliferation of both committed and uncommitted human hemopoietic progenitors (HP). Here, we investigated the effects of cADPR on engraftment of hemopoietic stem cells (HSC) into irradiated NOD/SCID mice. Two different protocols were used: i) a 24 h in vitro priming of cord blood-derived mononuclear cells (MNC) with micromolar cADPR, followed by their infusion into irradiated mice (both primary and secondary transplants); and ii) co-infusion of MNC with CD38-transfected, cADPR-generating, irradiated murine 3T3 fibroblasts. We demonstrated a dual effect of cADPR on human HP in vivo: i) enhanced proliferation of committed progenitors, responsible for improvement of short-term engraftment; ii) expansion of HSC, with increased long-term human engraftment into secondary recipients and a significantly higher expansion factor of CD34+ progenitors in mice co-infused with MNC and CD38+ 3T3 fibroblasts. These results hold promise for the possible therapeutic use of cADPR, and of cADPR-producing stroma, to achieve long-term expansion of human HSC, that is, those HP capable of self-renewal and responsible for repopulation of the bone marrow.
Novel Tranylcypromine/Hydroxylcinnamic Acid Hybrids as Lysine-Specific Demethylase 1 Inhibitors with Potent Antitumor Activity (2015)

Novel tranylcypromine/hydroxylcinnamic acid hybrids 15a, b, and 19a-l were designed and synthesized by connecting tranylcypromine with hydroxylcinnamic acid, and their biological activities were evaluated. The in vitro assay of their inhibitory activities against lysine-specific demethylase 1 (LSD1) showed that most of the target compounds displayed high potency with IC50 values ranging from submicromolar to single-digit micromolar levels. In particular, compound 19l had robust, selective LSD1 inhibitory activity, which was obviously higher than the inhibitory activity against homologues monoamine oxidase-A (MAO-A) and MAO-B, respectively. Furthermore, the most potent compound 19l selectively inhibited cancer cell but not nontumor colon cell proliferation in vitro. In addition, compound 19l also dose-dependently increased the expression of H3K4me2 at the cellular level. Our findings suggest that tranylcypromine/hydroxylcinnamic acid hybrids as LSD1 inhibitors may hold great promise as therapeutic agents for the treatment of human cancers.
Cell Type-specific Occurrence of Caveolin-1α and -1β in the Lung Caused by Expression of Distinct mRNAs (2004)

Two isoforms of caveolin-1, alpha and beta, had been thought to be generated by alternative translation initiation of an mRNA (FL mRNA), but we showed previously that a variant mRNA (5'V mRNA) encodes the beta isoform specifically. In the present study, we demonstrated strong correlation between the expression of the caveolin-1 protein isoforms and mRNA variants in culture cells and the developing mouse lung. The alpha isoform protein and FL mRNA were expressed constantly during the lung development, whereas expression of the beta isoform protein and 5'V mRNA was negligible in the fetal lung before 17.5 days post coitum, and markedly increased simultaneously at 18.5 days post coitum, when the alveolar type I cells started to differentiate. Immunohistochemical analysis revealed the cell type-specific expression of the two isoforms; the alveolar type I cell expresses the beta isoform predominantly, while the endothelium harbors the alpha isoform chiefly. The mutually exclusive expression of caveolin-1 isoforms was verified by Western blotting of the selective plasma membrane preparation obtained from the endothelial and alveolar epithelial cells. The present result indicates that the two caveolin-1 isoforms are generated from distinct mRNAs in vivo and that their production is regulated independently at the transcriptional level. The result also suggests that the alpha and beta isoforms of caveolin-1 may have unique physiological functions.
Noninvasive Magnetic Resonance to Three-Dimensional Rotational X-Ray Registration of Vertebral Bodies for Image-Guided Spine Surgery (2004)

Noninvasive MMI registration of intraoperative 3DRX images to preoperative MR images is more accurate than point-based registration in cadaveric spine segments. It is therefore a promising technique for replacing the invasive landmark-based registration that is currently used in image-guided spine surgery.
Th1 response in Salmonella typhimurium-infected mice with a high or low rate of bacterial clearance (1997)

Previous studies have shown that the capacity to clear an attenuated strain of Salmonella typhimurium after the second week of infection varies widely among mouse strains. Bacterial clearance is mediated by CD4+ T cells and is regulated in part by the H-2 complex. The aim of the present study was to compare the patterns of cytokine mRNA expression in the spleens of C57BL/6 (H-2b) and CBA (H-2k) mice, which exhibit a low and a high rate of bacterial clearance, respectively. A transient increase in interleukin-12 (IL-12) mRNA levels was found in both mouse strains. Gamma interferon (IFN-gamma) gene expression was higher and more sustained in C57BL/6 than in CBA mice. No increase in IL-4 mRNA was detected. A transient increase in IL-10 mRNA was found in C57BL/6 mice. Separation of spleen cells into CD4+ and CD4- fractions showed that CD4+ T cells produced the bulk of IFN-gamma in both mouse strains and of IL-10 in C57BL/6 mice. Infection of H-2 congenic mice induced a higher level of IFN-gamma mRNA expression by CD4+ T cells in mice with a low rate of clearance (H-2b) than in mice with a high rate of clearance (H-2q). Treatment of infected C57BL/6 mice with anti-IFN-gamma or anti-CD4 monoclonal antibodies indicated that IFN-gamma participates in resistance in the early phase of infection, but not in bacterial clearance, and that CD4+ T cells mediate bacterial clearance during the 3rd week of infection. Taken together, these results suggest that defective bacterial clearance in H-2b mice is not linked to defective IFN-gamma production and that CD4+ T cells mediate bacterial clearance by an IFN-gamma-independent mechanism.