gebhart/patrepeval huggingface dataset:
Identification of the increased expression of monocyte chemoattractant protein-1, cathepsin S, UPIX-1, and other genes in dystrophin-deficient mouse muscles by suppression subtractive hybridization (2000)

The lack of dystrophin results in muscular dystrophy characterized by degeneration, inflammation, and partial regeneration of skeletal muscles. The fate of these muscles may be determined by the extent of adaptation to the defect and the efficiency of regeneration that is affected by inflammatory cells. We have used suppression subtractive hybridization and quantitative Northern blot analysis to identify differentially expressed genes. Increased expression of murine monocyte chemoattractant protein-1 (JE/MCP-1), cathepsin S, UPIX-1, nmb, cathepsin B, and lysozyme M mRNAs were identified in 2-month-old mdx mouse leg muscles. UPIX-1 is a novel gene. Although it was not expressed in control muscles, it was expressed in control brain, heart, and spleen. JE/MCP-1 and cathepsin S proteins in mdx muscles, as well as JE/MCP-1 protein in the serum of mdx mice were also detected. JE/MCP-1 may be responsible for attraction of inflammatory cells, and cathepsin S, a potent elastolytic protease, may contribute to the remodeling of the extracellular matrix that is required for the migration of these cells to the injured muscles.
Applied weed science (1985)

1. Characteristics, Biology, and Importance of Weeds. 2. The Plant System. 3. The Soil System. 4. Methods of Weed Control. 5. Introduction to Herbicides. 6. Plant-Herbicide Interactions. 7. Soil-Herbicide Interactions. 8. Herbicide Resistance. 9. Herbicide Groups with Significant Foliar Use: Translocated Herbicides Showing Initial Symptoms on New Growth. 10. Herbicide Groups with Significant Foliar Use: Translocated Herbicides Showing Initial Symptoms on Old Growth. 11. Herbicide Groups with Significant Foliar Use: Nontranslocated Herbicides Showing Initial Localized Injury. 12. Herbicide Groups Applied Almost Exclusively to the Soil. 13. Weed Life Cycles and Management. 14. Weed Management Situations. 15. Aquatic Plant Management. 16. Herbicide Formulations and Packaging, Carriers, Spray Additives, and Tank Mixes. 17. Herbicide Application. 18.Tillage Equipment. 19.Troubleshooting. 20. Weed Control in an Age of Rapidly Changing Technology. Appendix A. Weed Identification Guides. Appendix B. Collecting Plants for Identification. Appendix C. Conversion Factors Useful in Field Plot Work. Appendix D. Weed Science Journals, Proceedings, and Societies. Glossary. Literature Cited. Index.
ChemInform Abstract: N‐Heterocyclic Carbene Copper Catalyzed Carboxylation of C—B and C—H Bonds with Carbon Dioxide (2012)

Abstract Review: 44 refs.
Shuse: Multi-Host Account Administration (1996)

At the beginning of 1995, College urgently needed an organized way of administering a large number of user accounts spread across multiple Unix systems. With 6000+ accounts on a network that had recently undergone dramatic and ill-coordinated growth, the situation was already nearly unmanageable; with the user population forecast to double in autumn, disaster loomed. NIS served reasonably well for the simple task of distributing password files, but maintaining the master copy was proving problematic, creating directories and configuration files for new users was a very ad-hoc process, and there was no obvious place to record assorted supplementary information.

The response was to create a new software package, dubbed Shuse for Sheridan user management. A central daemon maintains the user database, which is in a fully extensible text- based format. Rather than use a commercial database package, the daemon simply keeps the entire database in its (virtual) memory, and the master copy on disk is optimized for rapid updates rather than efficient access. (RAM is cheaper than database packages nowadays.) Update requests go to the central daemon; it invokes auxiliary processes on other hosts as necessary to create, destroy, and move user files.

Shuse is written essentially entirely in Expect, an extended variant of Tcl. Inter-host communication is done by using Expect's process-control primitives to fire up telnet processes; bulk data transfer is done via NFS. About 100 lines of C code, in three small auxiliary programs, provide services that are not present in Expect. A not-accidental byproduct of this approach is near- automatic portability and correct functioning even in a heterogeneous network.

Shuse is in operational use, currently administering over 20,000 user accounts (the forecasts were low). Various problems were encountered along the way, some easily solved and some requiring considerable unforeseen effort. The use of Expect has been a clear success, performance problems were easily resolved, and the central-daemon approach has worked well.
Antigen-induced cytokine and chemokine release test for tuberculosis infection using adsorption of stimulated whole blood on filter paper and multiplex analysis (2012)

Applying blood on filter paper after incubation makes in vitro stimulation tests feasible in locations where heat and electricity is unavailable.
DISSIMILATION OF GLUCOSE BY<i>BACILLUS SUBTILIS</i>(FORD'S STRAIN) (1945)

Ford's strain of Bacillus subtilis (N.C.T.C. 2586) dissimilated glucose mainly to 2,3-butanediol and glycerol under anaerobic conditions at pH 6.2 to 6.8. For each 100 moles of glucose fermented, 57 moles of 2,3-butanediol, 40 moles of glycerol, 20 moles of lactic acid, 13 moles of ethanol, and 5 moles of formic acid were produced. Aerobic conditions favoured formation of 2,3-butanediol and acetoin, oxidation of the substrate, and formation of acetic and butyric acids, but greatly depressed the amount of glycerol and lactic acid formed. In alkaline media (pH 7.5), acids were formed at the expense of the diol and glycerol.
High-power 1.5-μm tapered-gain-region lasers (1998)

Semiconductor lasers with tapered gain regions are well suited for applications requiring high output powers and good spatial mode quality. In this paper, the development of 1.5-micrometer InGaAsP/InP quantum well (QW) material suitable for this type of device will be discussed and initial results on high-power tapered lasers fabricated in this material presented. Several different 1.5-micrometer QW laser structures grown by metalorganic chemical vapor deposition are being evaluated. Structures containing three compressively strained QWs have shown transparency current densities J<SUB>T</SUB> as low as 170 A/cm<SUP>2</SUP> and net gains of approximately equal 40 cm<SUP>-1</SUP> at less than 800 A/cm<SUP>2</SUP>. With 5QWs, these parameters were J<SUB>T</SUB> approximately equals 275 A/cm<SUP>2</SUP> and net gain approximately 40 cm<SUP>-1</SUP> at 600 A/cm<SUP>2</SUP>, respectively. Self-focusing at high current densities and high intensity input into the taper section has been identified as a fundamental problem in these devices that has to be dealt with. Tapered devices with a 0.6-mm-long single-mode gain section coupled to a 1.4-mm-long tapered region fabricated in 5QW material have shown CW output powers of greater than 1.0 W at 3.8 A. Approximately 80% of the 1 W is in the near- diffraction-limited central lobe of the far field-pattern.
Meta-Model-based Estimation of Optimal System Variants with MATLAB/Simulink (2012)

The idea that the efficient usage of all necessary production resources has not only an ecological importance but is also an overwhelming economical competitive factor becomes accepted since the 1980s. Modeling and simulation with integrated parameter optimization is used routinely to improve process performance. In engineering a well known environment for this task is the MATLAB/Simulink programming system. Using this or similar, established techniques only model parameter of a single model structure is optimized. Model structure is considered to be fixed as the relationships between model elements are defined during model development. Until now no tools and methods are known which can optimize product design and production processes utilizing all existing degrees of freedom. As process performance is optimized it may be necessary to redesign the model structure. The redesign is normally carried out manually by an analyst but not automatically by the optimization method. This suboptimal combination of automatic parameter optimization and manual structure changes leads to a time consuming and error-prone optimization task. The system theoretical approach of the System Entity Structure/Model Base framework (SES/MB) is able to define alternative model structures and parameter sets in a single meta-model, called System Entity Structure (SES). Moreover, atomic models are stored in a model base (MB). Using both, SES and MB, it is possible to generate modular, hierarchical models with different structures and parameters. Evolutionary Algorithms are a subtopic of Artificial Intelligence that are involved in combinatorial optimization problems. These algorithms are based on ideas inspired by biological evolution. They often perform well for many problem types because they do not make assumptions about the problem specific search space. The research reported in this paper details an approach providing optimization through automatic reconfiguration of both: model structure and model parameters.
Effect of Metal Ions in Organic Synthesis; XVII. Mild, Easy, and High-Yield Conversion of Aldoximes into Nitriles under Copper(II) Acetate-Catalysis (1983)

Conversion des oximes d'octanal, decanal, cinnamaldehyde, benzenepropanal et benzaldehyde en les nitriles correspondants
Starfish Saponins. 55. Isolation, Structure Elucidation, and Biological Activity of the Steroid Oligoglycosides from an Antarctic Starfish of the Family<i>Asteriidae</i> (1998)

This paper reports an analysis of the chemical constituents from an Antarctic starfish of the family Asteriidae. Different steroid glycoside types are represented among its constituents, including the five hexaglycoside steroidal sulfates ("asterosaponins") asteriidosides A-E (1-5), differing in their oligosaccharide chain, and the two nonsulfated diglycosides asteriidoside F (6) and G (7), in which 6 is the 26-methyl analogue of 7. Also present are the two sulfated diglycosides asteriidoside H (8) and I (9) and one sulfated monoglycoside asteriidoside L (10). Eight of the compounds were tested against human nonsmall-cell lung carcinoma cells (NSCLC-L16) and found to be moderately cytotoxic.
Robust Self-Calibration and Fundamental Matrix Estimation in 3D Computer Vision (2013)

The recent advances in the field of computer vision have brought many of the laboratory algorithms into the realm of industry. However, one problem that still remains open in the field of 3D vision is the problem of noise. The challenging problem of 3D structure recovery from images is highly sensitive to the presence of input data that are contaminated by errors that do not conform to ideal assumptions. Tackling the problem of extreme data, or outliers has led to many robust methods in the field that are able to handle moderate levels of outliers and still provide accurate outputs. However, this problem remains open, especially for higher noise levels and so it has been the goal of this thesis to address the issue of robustness with respect to two central problems in 3D computer vision. The two problems are highly related and they have been presented together within a Structure from Motion (SfM) context. The first, is the problem of robustly estimating the fundamental matrix from images whose correspondences contain high outlier levels. Even though this area has been extensively studied, two algorithms have been proposed that significantly speed up the computation of the fundamental matrix and achieve accurate results in scenarios containing more than 50% outliers. The presented algorithms rely on ideas from the field of robust statistics in order to develop guided sampling techniques that rely on information inferred from residual analysis. The second, problem addressed in this thesis is the robust estimation of camera intrinsic parameters from fundamental matrices, or self-calibration. Self-calibration algorithms are notoriously unreliable for general cases and it is shown that the existing methods are highly sensitive to noise. In spite of this, robustness in self-calibration has received little attention in the literature. Through experimental results, it is shown that it is essential for a real-world self-calibration algorithm to be robust. In order to introduce robustness to the existing methods, three robust algorithms have been proposed that utilize existing constraints for self-calibration from the fundamental matrix. However, the resulting algorithms are less affected by noise than existing algorithms based on these constraints. This is an important milestone since self-calibration offers many possibilities by providing estimates of camera parameters without requiring access to the image acquisition device. The proposed algorithms rely on perturbation theory, guided sampling methods and a robust root finding method for systems of higher order polynomials. By adding robustness to self-calibration it is hoped that this idea is one step closer to being a practical method of camera calibration rather than merely a theoretical possibility.
Parallel Coordinates as Tool of Exploratory Data Analysis (2009)

The huge amount of multidimensional data everyday becomes bigger and more complex. For these reasons, data analysis of multivariate data becomes very difficult. In this paper, we present a visualization technique for multidimensional data sets named Parallel Coordinates as a technique for exploratory data analysis. The paper describes the technique and its applications. We present several examples of technique successful application as a tool for visual data analysis of the multivariate data.
Control of drug-resistant epilepsy after head injury with intravenous nimodipine. (1994)

The present report describes a young child who developed generalized epileptic seizures in the course of severe head injury. The start of epileptic seizures was associated with the occurrence of acute hyponatremia and hypoosmolality due to excessive Desmopressine administration. The seizures resistant to conventional therapy resolved completely with intravenous nimodipine infusion.
Sequence analysis and protein import studies of an outer chloroplast envelope polypeptide. (1990)

A chloroplast outer envelope membrane protein was cloned and sequenced and from the sequence it was possible to deduce a polypeptide of 6.7 kDa. It has only one membrane-spanning region; the C terminus extends into the cytosol, whereas the N terminus is exposed to the space between the two envelope membranes. The protein was synthesized in an in vitro transcription-translation system to study its routing into isolated chloroplasts. The import studies revealed that the 6.7-kDa protein followed a different and heretofore undescribed translocation pathway in the respect that (i) it does not have a cleavable transit sequence, (ii) it does not require ATP hydrolysis for import, and (iii) protease-sensitive components that are responsible for recognition of precursor proteins destined for the inside of the chloroplasts are not involved in routing the 6.7-kDa polypeptide to the outer chloroplast envelope.
Intracavity-Pumped 2.1-μm Ho3+: YAG Laser (1992)

An intracavity pumping scheme is used to pump the 2.1-μm Ho3+:YAG laser. Separate Tm3+:YAG and Ho3+:YAG crystals are placed within a single laser cavity. The Tm3+:YAG crystal is pumped by a Ti:sapphire laser at 785nm, and the resulting 2.0-μm Tm3+ laser emission pumps the Ho3+.YAG crystal. The slope efficiency of the 2.1-μm Ho3+:YAG laser output is 42% of the absorbed 785-nm pump power.
Autotaxin induces lung epithelial cell migration through lysoPLD activity-dependent and -independent pathways (2011)

Lung cell migration is a crucial step for re-epithelialization that in turn is essential for remodelling and repair after lung injury. In the present paper we hypothesize that secreted ATX (autotaxin), which exhibits lysoPLD (lysophospholipase D) activity, stimulates lung epithelial cell migration through LPA (lysophosphatidic acid) generation-dependent and -independent pathways. Release of endogenous ATX protein and activity was detected in lung epithelial cell culture medium. ATX with V5 tag overexpressed conditional medium had higher LPA levels compared with control medium and stimulated cell migration through G(αi)-coupled LPA receptors, cytoskeleton rearrangement, phosphorylation of PKC (protein kinase C) δ and cortactin at the leading edge of migrating cells. Inhibition of PKCδ attenuated ATX-V5 overexpressed conditional medium-mediated phosphorylation of cortactin. In addition, a recombinant ATX mutant, lacking lysoPLD activity, or heat-inactived ATX also induced lung epithelial cell migration. Extracelluar ATX bound to the LPA receptor and integrin β4 complex on A549 cell surface. Finally, intratracheal administration of LPS (lipopolysaccharide) into the mouse airway induced ATX release and LPA production in BAL (bronchoalveolar lavage) fluid. These results suggested a significant role for ATX in lung epithelial cell migration and remodelling through its ability to induce LPA production-mediated phosphorylation of PKCδ and cortactin. In addition we also demonstrated association of ATX with the epithelial cell-surface LPA receptor and integrin β4.
Smart Cards - Present and Future 1 (2000)

Smart cards have been utilized excessively during the last couple of decades. In recent years though, a new generation of smart cards evolved: programmable smart cards. In this paper the authors give an overview of the current state of the technology and compare the cards on the market. They will also examine the trends of development, thus extrapolating their experiences about the present to the future. They also compare the predicted smart card to the ideal one, and try to describe the theoretical and practical boundaries that separate these two.
Genome-wide association study to identify chromosomal regions associated with antibody response to Mycobacterium avium subspecies paratuberculosis in milk of Dutch Holstein-Friesians (2012)

Heritability of susceptibility to Johne's disease in cattle has been shown to vary from 0.041 to 0.159. Although the presence of genetic variation involved in susceptibility to Johne's disease has been demonstrated, the understanding of genes contributing to the genetic variance is far from complete. The objective of this study was to contribute to further understanding of genetic variation involved in susceptibility to Johne's disease by identifying associated chromosomal regions using a genome-wide association approach. Log-transformed ELISA test results of 265,290 individual Holstein-Friesian cows from 3,927 herds from the Netherlands were analyzed to obtain sire estimated breeding values for Mycobacterium avium subspecies paratuberculosis (MAP)-specific antibody response in milk using a sire-maternal grandsire model with fixed effects for parity, year of birth, lactation stage, and herd; a covariate for milk yield on test day; and random effects for sire, maternal grandsire, and error. For 192 sires with estimated breeding values with a minimum reliability of 70%, single nucleotide polymorphism (SNP) typing was conducted by a multiple SNP analysis with a random polygenic effect fitting 37,869 SNP simultaneously. Five SNP associated with MAP-specific antibody response in milk were identified distributed over 4 chromosomal regions (chromosome 4, 15, 18, and 28). Thirteen putative SNP associated with MAP-specific antibody response in milk were identified distributed over 10 chromosomes (chromosome 4, 14, 16, 18, 19, 20, 21, 26, 27, and 29). This knowledge contributes to the current understanding of genetic variation involved in Johne's disease susceptibility and facilitates control of Johne's disease and improvement of health status by breeding.
Environmental Whole-Genome Amplification to Access Microbial Diversity in Contaminated Sediments (2005)

Low-biomass samples from nitrate and heavy metal contaminated soils yield DNA amounts that have limited use for direct, native analysis and screening. Multiple displacement amplification (MDA) using ?29 DNA polymerase was used to amplify whole genomes from environmental, contaminated, subsurface sediments. By first amplifying the genomic DNA (gDNA), biodiversity analysis and gDNA library construction of microbes found in contaminated soils were made possible. The MDA method was validated by analyzing amplified genome coverage from approximately five Escherichia coli cells, resulting in 99.2 percent genome coverage. The method was further validated by confirming overall representative species coverage and also an amplification bias when amplifying from a mix of eight known bacterial strains. We extracted DNA from samples with extremely low cell densities from a U.S. Department of Energy contaminated site. After amplification, small subunit rRNA analysis revealed relatively even distribution of species across several major phyla. Clone libraries were constructed from the amplified gDNA, and a small subset of clones was used for shotgun sequencing. BLAST analysis of the library clone sequences showed that 64.9 percent of the sequences had significant similarities to known proteins, and ''clusters of orthologous groups'' (COG) analysis revealed that more than half of the sequences from each library contained sequence similarity to known proteins. The libraries can be readily screened for native genes or any target of interest. Whole-genome amplification of metagenomic DNA from very minute microbial sources, while introducing an amplification bias, will allow access to genomic information that was not previously accessible.
Electron interference: mystery and reality (2002)

Interference of electron waves has developed from a fascinating phenomenon in basic physics to a key method for the highly sophisticated investigation of both electric and magnetic structures in solid-state materials. After more than 20 years of development, electron holography in the transmission electron microscope is now a very powerful technique for the analysis of micro-fields down to atomic dimensions. The applications extend from highly sensitive measurements in semiconductor technology to the quantitative characterization of atomic structures.
Envelope glycoprotein gp120 of human immunodeficiency virus type 1 alters ion transport in astrocytes: implications for AIDS dementia complex. (1994)

Infection by human immunodeficiency virus type 1 (HIV-1) is often complicated by a variety of neurological abnormalities. The most common clinical syndrome, termed acquired immunodeficiency syndrome (AIDS) dementia complex, presents as a subcortical dementia with cognitive, motor, and behavioral disturbances and is unique to HIV-1 infection. The pathogenesis of this syndrome is poorly understood but is believed to involve interactions among virally infected macrophages/microglia, astrocytes, and neurons. In this study, we show that exposure of primary rat and human astrocytes to heat-activated HIV-1 virions, or to eukaryotically expressed HIV-1 and HIV-2 envelope glycoproteins (gp120) stimulates amiloride-sensitive Na+/H+ antiport, potassium conductance, and glutamate efflux. These effects are blocked specifically by amiloride, an inhibitor of Na+/H+ antiport and by the selective removal of gp120 with immobilized monoclonal antibody. As a result of modulation of astrocytic function by gp120, the ensuing neuronal depolarization and glutamate exposure could activate both voltage-gated and N-methyl-D-aspartate-regulated Ca2+ channels, leading to increases in intraneuronal Ca2+ and neuronal death. These findings implicate the astrocyte directly in the pathogenesis of AIDS dementia complex.