gebhart/patrepeval huggingface dataset:
Wrapper generation for Web accessible data sources (1998)

There is an increase in the number of data sources that can be queried across the WWW. Such sources typically support HTML forms-based interfaces and search engines query collections of suitably indexed data. The data is displayed via a browser: One drawback to these sources is that there is no standard programming interface suitable for applications to submit queries. Second, the output (answer to a query) is not well structured. Structured objects have to be extracted from the HTML documents which contain irrelevant data and which may be volatile. Third, domain knowledge about the data source is also embedded in HTML documents and must be extracted. To solve these problems, we present technology to define and (automatically) generate wrappers for Web accessible sources. Our contributions are as follows: (1) Defining a wrapper interface to specify the capability of Web accessible data sources. (2) Developing a wrapper generation toolkit of graphical interfaces and specification languages to specify the capability of sources and the functionality of the wrapper (3) Developing the technology to automatically generate a wrapper appropriate to the Web accessible source, from the specifications.
A cosmid for selecting genes by complementation in Aspergillus nidulans : Selection of the developmentally regulated yA locus (1985)

We constructed a 9.9-kilobase cloning vector, designated pKBY2, for isolating genes by complementation of mutations in Aspergillus nidulans. pKBY2 contains the bacteriophage lambda cos site, to permit in vitro assembly of phage particles; a bacterial origin of replication and genes for resistance to ampicillin and chloramphenicol, to permit propagation in Escherichia coli; the A. nidulans trpC(+) gene, to permit selection in Aspergillus; and a unique BamHI restriction site, to permit insertion of DNA fragments produced by digestion with restriction endonucleases BamHI, BglII, Mbo I, or Sau3A. We used this cosmid to form a quasirandom recombinant DNA library containing 35- to 40-kilobase DNA fragments from a wild-type strain of A. nidulans. DNA from this library transformed a yellow-spored (yA(-)) pabaA(-)trpC(-)Aspergillus strain (FGSC237) to trpC(+) at frequencies of approximately 10 transformants per mug of DNA. Three of approximately 1000 trpC(+)pabaA(-) colonies obtained were putative yA(+) transformants, because they produced wild-type (green) spores. DNA from each of the green-spored transformants contained pKBY2 sequences and DNA from two transformants transduced E. coli to ampicillin resistance following treatment in vitro with a lambda packaging extract. The cosmids recovered in E. coli had similar restriction patterns and both yielded trpC(+) transformants of A. nidulans FGSC237, 85% of which produced green spores. Several lines of evidence indicate that the recovered cosmids contain a wild-type copy of the yA gene.
Time interval of increased risk for Clostridium difficile infection after exposure to antibiotics (2011)

Antibiotic use increases the risk for CDI during therapy and in the period of 3 months after cessation of antibiotic therapy. The highest risk for CDI was found during and in the first month after antibiotic use. Our study will aid clinicians to identify high-risk patients.
Measurement of Superoxide Dismutase-like Activity of Natural Antioxidants (1995)

The superoxide dismutase (SOD)-like activity of natural antioxidants was evaluated by measuring the inhibition of pyrogallol autoxidation that is catalyzed by the superoxide radical. Among 22 water-soluble antioxidants tested, L-ascrobic acid, L-ascorbic acid 6-palmitate, glutathione (reduced form), (+)-catechin, and (-)-epicatechin showed effective SOD-like activity. To analyze lipophilic antioxidants, an optically clear organic system composed of diethyl ether, surfactant (dioctyl sulfosuccinate, AOT) and water, called reverse micelles, was developed. The optimum concentrations of AOT, water and pyrogallol for determining SOD-like activity were found to be 50 mM, 1.3 M, and 40 mM, respectively. After proving that pyrogallol autoxidation was mediated by the superoxide anion in that system, the SOD-like activity of 24 lipophilic antioxidants was measured. Cinnamon oil, gamma-oryzanol, extract of rosemary leaf, L-alpha-lecithin, and L-alpha-cephalin exhibited activity, although the activity of some antioxidants could not be measured because of the intense color or low solubility.
One-bit Time Reversal for WLAN Applications (2006)

Time reversal (TR) is a technique that can achieve remarkable temporal focusing (delay spread reduction) and spatial focusing (low spatial interference) in the context of wideband multiple/ single input-single output systems. In this paper, we investigate a simpli ed form of time-reversal, referred to as one-bit time reversal. The ef ciency of this technique has already been demonstrated for ultrasound applications. We apply it to radio waves and demonstrate that it can preserve the spatial focusing properties of TR, while requiring much simpler transmit Iters. However, it does not have as good temporal focusing properties as pure TR.
Charge Detection Mass Spectrometry with Almost Perfect Charge Accuracy (2015)

Charge detection mass spectrometry (CDMS) is a single-particle technique where the masses of individual ions are determined from simultaneous measurement of each ion’s mass-to-charge ratio (m/z) and charge. CDMS has many desirable features: it has no upper mass limit, no mass discrimination, and it can analyze complex mixtures. However, the charge is measured directly, and the poor accuracy of the charge measurement has severely limited the mass resolution achievable with CDMS. Since the charge is quantized, it needs to be measured with sufficient accuracy to assign each ion to its correct charge state. This goal has now been largely achieved. By reducing the pressure to extend the trapping time and by implementing a novel analysis method that improves the signal-to-noise ratio and compensates for imperfections in the charge measurement, the uncertainty has been reduced to less than 0.20 e rmsd (root-mean-square deviation). With this unprecedented precision peaks due to different charge states are resolved in the charge spectrum. Further improvement can be achieved by quantizing the charge (rounding the measured charge to the nearest integer) and culling ions with measured charges midway between the integral values. After ions with charges more than one standard deviation from the mean are culled, the fraction of ions assigned to the wrong charge state is estimated to be 6.4 × 10–5 (i.e., less than 1 in 15 000). Since almost all remaining ions are assigned to their correct charge state, the uncertainty in the mass is now almost entirely limited by the uncertainty in the m/z measurement.
Three-dimensional integration technology and integrated systems (2009)

A three-dimensional (3-D) integration technology based on the wafer-to-wafer bonding using through silicon vias (TSV's) has been developed for the fabrication of new 3-D LSIs. A 3-D image sensor chip, 3-D shared memory chip, 3-D artificial retina chip and 3-D microprocessor test chip have been fabricated by using this technology. In addition, we have proposed a new reconfigurable parallel image processing system. To achieve this system, we have proposed a new 3-D integration technology based on multichip-to-wafer bonding called a super-chip integration. Many chips are simultaneously aligned and bonded onto lower chips using a self-assembly technique in a super-chip integration.
Adhesion promotion and corrosion prevention using thin anisotropic coatings (1991)

Using sol-gel technology, thin organic/ceramic (ceramer) coatings have been applied to metal surfaces to enhance such surface properties as adhesion promotion and corrosion prevention. Isotropic coatings have been found to be effective in certain applications such as corrosion prevention, but the formation of anisotropic (functionally gradient) coatings permits greater flexibility over the resulting properties. Isotropic coatings derived from tetraethoxysilane, for example, have been found to effectively inhibit corrosion while being only 100-1000 A thick. These coatings do not, however, promote adhesion. Thin coatings made from traditional silane adhesion promoters alone are unable to prevent corrosion of metallic substrates. Using monomers with appropriate reactivities permits the single-step synthesis of anisotropic coatings that can both promote adhesion and prevent corrosion. These types of anisotropic coatings allow the physical and chemical properties of a coating to be varied as a function of the distance from the substrate and confer properties to the substrate that would not be possible from a single isotropic coating. The principle behind the construction of these anisotropic coatings is general enough that it can be used in many applications where microengineering of surface structures is important.
Identification of mRNAs associated with programmed cell death in immature thymocytes. (1991)

Programmed cell death is an essential cellular process that occurs in epithelial turnover, neural development, and regulation of cell populations of the immune system. Thymocytes undergo programmed cell death in response to several inductive stimuli, including exposure to glucocorticoids or radiation. This program can be blocked by inhibitors of RNA or protein synthesis; this implies that new proteins are required to execute the death programs. To search for possible death-associated mRNAs, we directionally cloned cDNA representing mRNA from control and dexamethasone-treated thymocytes. These libraries were used to produce ample amounts of DNA and RNA used in subtractive hybridization for the removal of sequences present in both control and induced cells. The remaining unhybridized sequences were selectively amplified by polymerase chain reaction and cloned to produce a library enriched for sequences expressed in death-induced cells. From this library we isolated cDNAs of death-associated mRNAs. One of these mRNAs, RP-8, appears within 1 h after exposure to gamma radiation, and a second mRNA, RP-2, is observed within 2 h. Both of these mRNAs accumulate during a period when a reference mRNA, actin, is declining. RP-2 and RP-8 are no longer detectable after 6 h postinduction, when apoptosis and mRNA degradation are evident in the culture. Sequence analysis of RP-8 cDNA indicates the presence of a zinc finger domain suggestive of a possible DNA regulatory role for the RP-8 protein. cDNA sequence results on RP-2 classify the corresponding protein as an integral membrane protein. We conclude that RP-2 and RP-8 are death-associated mRNAs that should be functionally evaluated in the context of the death process. As previously suggested, it may be that a family of "death genes" is activated by various stimuli depending on the type of cell, in a manner somewhat analogous to the induction of heat shock (stress) protein genes.
Kinetics of high‐pressure removal of hydrogen sulfide using calcium oxide powder (2000)

Abstract Sulfidation reaction of CaO at high pressure (up to 2 MPa) and high temperature (up to 900°C) to remove H 2 S in a coal‐fired gasifier was studied in a high‐pressure and temperature differential‐bed flow‐through reactor. Experimental conditions selected are typical for pressurized gasifiers. Effects of total pressure, H 2 S partial pressure, reaction temperature, fuel gas composition, and CaO surface area on the extent of sulfur capture and sorbent conversions were determined. The gasifier pressure affected the in‐situ calcination of calcium carbonate particles through reduction in available surface area and pore volume of CaO formed, thus limiting the sulfidation conversion. Time‐resolved conversion data of CaO sulfidation were analyzed using a modified grain model. The model incorporates external and internal diffusion, surface reaction, product layer diffusion, and the structural changes of the sulfiding CaO particle. The activation energy for the reaction was 37 kcal/mol. The estimated product layer diffusivity was 8×10 −15 m 2 /s at 800°C with an associated activation energy of 38.4 kcal/mol—typical of solid state diffusion of ionic species through the product layer. The extent of conversion increased with increasing initial surface area and porosity of CaO particles. The high‐pressure sulfidation reaction data for CaO will be useful in understanding and optimizing the in‐gasifier H 2 S capture using calcium‐based sorbents.
Acetylcholine receptor-inducing activity stimulates expression of the epsilon-subunit gene of the muscle acetylcholine receptor. (1991)

Motor neurons regulate the transcription of acetylcholine receptor subunit genes in postsynaptic muscle fibers both through muscle electrical activity produced by motor neuron acetylcholine release and by mechanisms independent of such transmitter release. Factors secreted by the motor neuron may mediate activity-independent regulation, including the postnatal switch from alpha 2 beta gamma delta (embryonic type) to alpha 2 beta epsilon delta (adult type) receptors. We have investigated the effect of putative trophic factors, agents affecting second-messenger systems, and muscle activity on the levels of acetylcholine receptor subunit mRNAs in primary mouse muscle cultures. We found that ARIA (acetylcholine receptor-inducing activity), a 42-kDa glycoprotein purified on the basis of its ability to increase the synthesis of acetylcholine receptors in chick myotubes, increases epsilon-subunit mRNA levels up to 10-fold. In addition, ARIA stimulated alpha-, gamma-, and delta-subunit mRNA levels 2-fold but had no effect on the expression of the beta-subunit gene. These effects of ARIA were independent of muscle activity, and they were not mimicked by calcitonin gene-related peptide nor by thyroxine, forskolin, phorbol 12-myristate 13-acetate, the calcium ionophore A23187, basic fibroblast growth factor, or transforming growth factor beta. Based on these data, we suggest that ARIA may act at the mammalian neuromuscular junction to induce adult-type acetylcholine receptors.
TRANSPLANTATION IN MINIATURE SWINE (1976)

Three strains of miniature swine, each homozygous for a different allele of the major histocompatibility locus (MHC), have been developed by a selective breeding scheme based on tissue typing of the offspring of each generation. Prior to breeding, the original parents were reciprocally immunized by skin grafts and lymphocyte injections to produce lymphocytotoxic antisera. These antisera were then used to assess the MHC genotype of the offspring by an analysis based on selective absorption of cytotoxicity. Offspring inheriting the same serologically determined genotype were then bred sequentially. Subsequent mixed lymphocyte cultures showed a pattern of reactivity consistent with the serological genotyping, further confirming the homology between the MHC of these miniature swine and those of man and mouse. In addition to their usefulness as a model for large animal surgical transplantation, these animals provide an abundant homozygous source of histocompatibility antigens and of antihistocompatibility antisera for use in chemical characterization of products of the MHC.
Analysis of Survival Data (2018)

This monograph contains many ideas on the analysis of survival data to present a comprehensive account of the field. The value of survival analysis is not confined to medical statistics, where the benefit of the analysis of data on such factors as life expectancy and duration of periods of freedom from symptoms of a disease as related to a treatment applied individual histories and so on, is obvious. The techniques also find important applications in industrial life testing and a range of subjects from physics to econometrics. In the eleven chapters of the book the methods and applications of are discussed and illustrated by examples.
Gene Expression Profiling of the Effects of Castration and Estrogen Treatment in the Rat Uterus (2003)

The development and functions of female reproductive tissues are regulated by the actions of two major sex steroid hormones, estrogen and progesterone. To investigate estrogen-dependent gene expression in the rat uterus, we studied the effect of ovariectomy with or without estrogen treatment on the uterine expression of 3000 genes using cDNA microarrays. Many genes were regulated by either treatment, but only few were reciprocally regulated by these contrasting treatments. The present study confirms previous findings and identifies several genes with expressions not previously known to be influenced by estrogen. These genes include follistatin-related protein, Thy-1 glycoprotein, alpha-fodrin, CD24, immediate early response 5, insulin-like growth factor-binding protein 2, growth response protein CL-6 (INSIG-1), ladinin1, class I major histocompatibility complex heavy chain, lactadherin, ezrin, and Fas-activated serine/threonine kinase. Because of their function as regulators of proliferation and apoptosis, CD24, insulin-like growth factor-binding protein 2, and Fas/Fas ligand were examined further by immunohistochemical expression and tissue localization analysis. Our analysis confirms a contrasting regulation of these gene products by ovariectomy and estrogen treatment. The present study identifies novel mediators of estrogen actions in the uterus and provides genome-wide expression data from which novel hypotheses regarding uterine function can be generated.
A Timestepping Scheme for Coupled Reservoir Flow and Geomechanics on Nonmatching Grids (2005)

Abstract This paper presents numerical techniques for coupled simulations with different time scales and space discretizations for reservoir flow and geomechanics. We use an explicitly coupled approach together with an iterative coupling to increase stability and reduce time discretization error. An error indicator is proposed to determine when displacement must be updated and whether the explicit or iterative coupling technique is required. Under this setting, one geomechanics calculation is performed for several reservoir flow steps. For time steps without geomechanics updates linear extrapolated pore volume is used for porous flow calculations. The resulting algorithm is computationally more efficient than the iterative coupling, and it is more stable and accurate than the loosely coupled technique. In the event that different meshes are used for the reservoir flow and geomechanics models, special treatments are required for the integration of the coupling terms over each element. To avoid complex 3D grid intersection calculations we propose to divide an element into a number of subelements and apply the midpoint integration rule over each subelement. Numerical results are presented to demonstrate the efficiency and accuracy of the proposed method for coupled simulations with different time and space discretizations.
Lung Delivery Studies Using siRNA Conjugated to TAT(48−60) and Penetratin Reveal Peptide Induced Reduction in Gene Expression and Induction of Innate Immunity (2007)

The therapeutic application of siRNA shows promise as an alternative approach to small-molecule inhibitors for the treatment of human disease. However, the major obstacle to its use has been the difficulty in delivering these large anionic molecules in vivo. In this study, we have investigated whether siRNA-mediated knockdown of p38 MAP kinase mRNA in mouse lung is influenced by conjugation to the nonviral delivery vector cholesterol and the cell penetrating peptides (CPP) TAT(48-60) and penetratin. Initial studies in the mouse fibroblast L929 cell line showed that siRNA conjugated to cholesterol, TAT(48-60), and penetratin, but not siRNA alone, achieved a limited reduction of p38 MAP kinase mRNA expression. Intratracheal administration of siRNA resulted in localization within macrophages and scattered epithelial cells and produced a 30-45% knockdown of p38 MAP kinase mRNA at 6 h. As with increasing doses of siRNA, conjugation to cholesterol improved upon the duration but not the magnitude of mRNA knockdown, while penetratin and TAT(48-60) had no effect. Importantly, administration of the penetratin or TAT(48-60) peptides alone caused significant reduction in p38 MAP kinase mRNA expression, while the penetratin-siRNA conjugate activated the innate immune response. Overall, these studies suggest that conjugation to cholesterol may extend but not increase siRNA-mediated p38 MAP kinase mRNA knockdown in the lung. Furthermore, the use of CPP may be limited due to as yet uncharacterized effects upon gene expression and a potential for immune activation.
Digital watermarking through CDMA channels using spread spectrum techniques (2002)

In image transmission systems using spread spectrum (SS) techniques, the main problem is how to transmit an image whose information is huge, efficiently. We have already proposed a color image communication system through code division multiple access (CDMA) channels with spreading sequences of variable-period to transmit YIQ signals. We propose a digital watermarking system where YIQ signal channels and the embedded watermark image channel are separately used. Such a system has two advantages: (1) interception on communications network is prevented; and (2) the copyright of rightful owner of digital images is protected.
Generation and purification of CD8+ melan-A-specific cytotoxic T lymphocytes for adoptive transfer in tumor immunotherapy. (2000)

Tumor antigens that might serve as potential targets for adoptive T-cell therapy have been defined in different tumor entities, especially in malignant melanoma. To generate conditions to induce primary T-cell responses against different HLA-A*0201-restricted melanoma peptides and to allow further expansion of peptide-specific T cells for adoptive transfer, CD8+-purified T cells from healthy donors were stimulated with Melan-A-pulsed autologous dendritic cells. Dendritic cells were generated in vitro from monocytes with granulocyte macrophage colony-stimulating factor, interleukin-4, and transforming growth factor-beta1. After 3-4 weekly stimulation cycles with Melan-A-pulsed DCs, we were able to induce a strong peptide-specific CTL response in vitro. MHC-peptide tetramer staining revealed a frequency of up to 3.5% CD8+/Melan-A+ T cells. Additional antigen-independent expansion with anti-CD3/anti-CD28 monoclonal antibodies together with interleukin-2 gave rise to 600-fold expansion of CD8+ CTLs that maintained Melan-A specificity and were able to efficiently lyse Melan-A-expressing melanoma cells. To enrich antigen-specific T cells in vitro, we used a recently established technology for analysis and sorting of live cells according to secreted cytokines. In the present study, we demonstrated that Melan-A-specific T cells can be purified by magnetic separation according to secreted IFN-gamma. These cells revealed a very potent monospecific CTL response, even at low E:T ratios, against Melan-A-pulsed and Melan-A-expressing target cells. Altogether, our study demonstrated that we have developed an efficient method for generating large numbers of peptide-specific T cells in vitro that may be used for adoptive T-cell transfer in tumor immunotherapy.
Prognostic Significance of Tumor Necrosis Factor–Related Apoptosis-Inducing Ligand and Its Receptors in Adjuvantly Treated Stage III Colon Cancer Patients (2006)

High DR4 expression is associated with worse disease-free and overall survival in stage III adjuvant-treated colon cancer patients. Evaluation of DR4 expression in stage III colon cancer patients may identify a subset requiring more aggressive adjuvant treatment.