gebhart/patrepeval huggingface dataset:
Side views (2002)

We introduce Side Views, a user interface mechanism that provides on-demand, persistent, and dynamic previews of commands. Side Views are designed to explicitly support the practices and needs of expert users engaged in openended tasks. In this paper, we summarize results from field studies of expert users that motivated this work, then discuss the design of Side Views in detail. We show how Side Views' design affords their use as tools for clarifying, comparing, and contrasting commands; generating alternative visualizations; experimenting without modifying the original data (i.e., "what-if" tools); and as tools that support the serendipitous discovery of viable alternatives. We then convey lessons learned from implementing Side Views in two sample applications, a rich text editor and an image manipulation application. These contributions include a discussion of how to implement Side Views for commands with parameters, for commands that require direct user input (such as mouse strokes for a paint program), and for computationally-intensive commands.
When virtual is better than real [operating system relocation to virtual machines] (2005)

This paper argues that the operating system and applications currently running on a real machine should relocate into a virtual machine. This structure enables services to be added below the operating system and to do so without trusting or modifying the operating system or applications. To demonstrate the usefulness of this structure, we describe three services that take advantage of it: secure logging, intrusion prevention and detection, and environment migration.
Non‐ganglionic cholinergic excitatory pathways in the sympathetic supply to the feline stomach:An efferent system or afferents with excitatory axon collaterals? (1980)

Experiments were performed on chloralosed, adrenalectomized cats, paralysed with gallamine and artificially ventilated. Gastric motility was recorded by the balloon method. Efferent stimulation of the cut greater splanchnic nerve, well proximal to the celiac ganglion, could either increase or decrease gastric tone. The excitatory responses called for higher stimulation intensities than the inhibitory ones but were as a rule observed at lower frequencies only (1-4 Hz). They could be abolished by atropine but were not prevented by bilateral vagotomy, hexamethonium nor guanethidine. The latter two drugs rather reversed inhibitory responses to excitatory ones which exhibited a hyperbolic frequency-response relationship with maximal effects already at 2-4 Hz. Heating of a nerve trunk selectively activates thin afferents of the delta group and C-class. Heating of the greater splanchnic nerve caused an increase in gastric motility which, like that caused by electric stimulation, was not prevented by hexamethonium nor guanethidine; nor was it eliminated by cutting the nerve centrally, nor by vagotomy, while it was abolished by atropine. These results suggest that the excitatory gastric responses to efferent splanchnic nerve stimulation are due to antidromic activation of thin afferent fibres. Their functional significance remains obscure but their peripheral arborizations may convey 'axon reflexes' influencing gastrointestinal motility.
Immunological research using RNA interference technology (2007)

RNA interference (RNAi) is a potent method of gene silencing that has developed rapidly over the past few years as a result of its extensive importance in the study of genetics, molecular biology and physiology. RNAi technology has also recently yielded significant insight into the innate and adaptive immune systems by helping to elucidate numerous mechanisms that regulate the development, activation and function of cells that mediate immunity. In addition, because of its ability to suppress gene expression effectively, this technique may be used to regulate the immune response for clinical purposes. Nonetheless, before RNAi can be successfully administered into human patients as a medical treatment, it is necessary to overcome several major limitations of this technology, such as inefficient in vivo delivery, incomplete silencing of target genes, non-specific immune responses, and off-target effects. As novel developments and discoveries in molecular biology swiftly continue to unfold, it is likely that RNAi may soon translate into a potent form of in vivo gene silencing with profound applications to vaccination and immunotherapy. In the present review, we examine the current progress of immunological studies employing RNAi and discuss the prospects for the implementation of this technique in the clinical arena.
Effect of Xylitol on Growth of Streptococcus pneumoniae in the Presence of Fructose and Sorbitol (2001)

Xylitol is effective in preventing acute otitis media by inhibiting the growth of Streptococcus pneumoniae. To clarify this inhibition we used fructose, which is known to block similar growth inhibition observed in Streptococcus mutans. In addition, we evaluated the efficacy of sorbitol in inhibiting the growth of pneumococci, as sorbitol is widely used for indications similar to those for which xylitol is used. The addition of 5% xylitol to the growth medium resulted in marked growth inhibition, an effect which was totally eliminated in the presence of 1, 2.5, or 5% fructose but not in the presence of 1 or 5% glucose, 1% galactose, or 1% sucrose. This finding implies that xylitol-induced inhibition of pneumococcal growth is mediated via the fructose phosphotransferase system in a way similar to that in which mutans group streptococcal growth is inhibited. The addition of sorbitol at concentrations of 1, 2.5, or 5% to the growth medium did not affect the growth of pneumococci and neither inhibited nor enhanced the xylitol-induced growth impairment. Thus, it seems that xylitol is the only commercially used sugar substitute proven to have an antimicrobial effect on pneumococci.
Facile Synthesis of Ag Nanocubes of 30 to 70 nm in Edge Length with CF3COOAg as a Precursor (2010)

This paper describes a new protocol to synthesize Ag nanocubes of 30 to 70 nm in edge length with the use of CF(3)COOAg as a precursor to elemental silver. By adding a trace amount of NaSH and HCl to the polyol synthesis, Ag nanocubes were obtained with good quality, high reproducibility, and on a scale up to 0.19 g per batch for the 70 nm Ag nanocubes. The Ag nanocubes were found to grow in size at a controllable pace over the course of synthesis. The linear relationship between the edge length of the Ag nanocubes and the position of localized surface plasmon resonance (LSPR) peak provides a simple method for finely tuning and controlling the size of the Ag nanocubes by monitoring the UV/Vis spectra of the reaction at different times.
Repairing CAD models (1997)

We describe an algorithm for repairing polyhedral CAD models that have errors in their B-REP. Errors like cracks, degeneracies, duplication, holes and overlaps are usually introduced in solid models due to imprecise arithmetic, model transformations, designer errors, programming bugs, etc. Such errors often hamper further processing such as finite element analysis, radiosity computation and rapid prototyping. Our fault-repair algorithm converts an unordered collection of polygons to a shared-vertex representation to help eliminate errors. This is done by choosing, for each polygon edge, the most appropriate edge to unify it with. The two edges are then geometrically merged into one, by moving vertices. At the end of this process, each polygon edge is either coincident with another or is a boundary edge for a polygonal hole or a dangling wall and may be appropriately repaired. Finally, in order to allow user-inspection of the automatic corrections, we produce a visualization of the repair and let the user mark the corrections that conflict with the original design intent. A second iteration of the correction algorithm then produces a repair that is commensurate with the intent. This, by involving the users in a feedback loop, we are able to refine the correction to their satisfaction.
The paired box encodes a second DNA-binding domain in the paired homeo domain protein. (1991)

The homeo box, which encodes the DNA-binding homeo domain, is a DNA sequence motif present in several Drosophila developmental genes; it has been used to identify many homologous genes involved in mammalian development. The paired box is another conserved sequence motif, first identified in the paired (prd) and gooseberry (gsb) Drosophila homeo domain genes. It encodes a 128-amino-acid domain, the paired domain, which has since been found in other fly and mouse gene products, in association with the homeo domain or in its absence. We show that the paired box of the prd gene encodes a DNA-binding activity, independent of the DNA-binding activity of the Paired (Prd) homeo domain and with a different sequence specificity. The amino-terminal region of the paired domain, including one of the three predicted alpha-helices, is necessary and sufficient for binding. We investigate the binding of the Prd protein to two sites in the even-skipped promoter, which are composed of overlapping sequences bound by the homeo domain and by the paired domain. We also show that a mutation in the paired box of Prd, corresponding to the mutation in the paired box of the mouse Pax-1 gene thought to cause the undulated skeletal phenotype, destroys the ability of the Prd protein to bind to the paired domain-specific site. This supports the view that the undulated phenotype results from the inactivation of the DNA-binding activity of the paired domain of Pax-1.
Comparison of Fuzzy-Wavelet Radial Basis Function Neural Network Freeway Incident Detection Model with California Algorithm (2002)

A multiparadigm general methodology is advanced for development of reliable, efficient, and practical freeway incident detection algorithms. The performance of the new fuzzy-wavelet radial basis function neural network (RBFNN) freeway incident detection model of Adeli and Karim is evaluated and compared with the benchmark California algorithm #8 using both real and simulated data. The evaluation is based on three quantitative measures of detection rate, false alarm rate, and detection time, and the qualitative measure of algorithm portability. The new algorithm outperformed the California algorithm consistently under various scenarios. False alarms are a major hindrance to the widespread implementation of automatic freeway incident detection algorithms. The false alarm rate ranges from 0 to 0.07% for the new algorithm and from 0.53 to 3.82% for the California algorithm. The new fuzzy-wavelet RBFNN freeway incident detection model is a single-station pattern-based algorithm that is computationally efficient and requires no recalibration. The new model can be readily transferred without retraining and without any performance deterioration.
Single-Dose Vaccination of a Recombinant Parainfluenza Virus 5 Expressing NP from H5N1 Virus Provides Broad Immunity against Influenza A Viruses (2013)

Influenza viruses often evade host immunity via antigenic drift and shift despite previous influenza virus infection and/or vaccination. Vaccines that match circulating virus strains are needed for optimal protection. Development of a universal influenza virus vaccine providing broadly cross-protective immunity will be of great importance. The nucleoprotein (NP) of influenza A virus is highly conserved among all strains of influenza A viruses and has been explored as an antigen for developing a universal influenza virus vaccine. In this work, we generated a recombinant parainfluenza virus 5 (PIV5) containing NP from H5N1 (A/Vietnam/1203/2004), a highly pathogenic avian influenza (HPAI) virus, between HN and L (PIV5-NP-HN/L) and tested its efficacy. PIV5-NP-HN/L induced humoral and T cell responses in mice. A single inoculation of PIV5-NP-HN/L provided complete protection against lethal heterosubtypic H1N1 challenge and 50% protection against lethal H5N1 HPAI virus challenge. To improve efficacy, NP was inserted into different locations within the PIV5 genome. Recombinant PIV5 containing NP between F and SH (PIV5-NP-F/SH) or between SH and HN (PIV5-NP-SH/HN) provided better protection against H5N1 HPAI virus challenge than did PIV5-NP-HN/L. These results suggest that PIV5 expressing NP from H5N1 has the potential to be utilized as a universal influenza virus vaccine.
Fluid Diversion to Improve Well Stimulation (1972)

Abstract A review of diverting is made with primary emphasis on granular diverting agents, and wax-polymer diverting agents in particular. The results of laboratory tests are given. Numerous field tests are reviewed, including we!! production data. Both the laboratory and field tests production data. Both the laboratory and field tests show the wax-polymer agents to be the best of the diverting materials tested. The wax-polymer materials are also oil soluble, which will prevent formation damage. Introduction Designing treatments for the stimulation of low-productivity oil and gas wells by acidizing, hydraulic fracturing, and injecting organic solvents or surface-active chemicals is an important function of the modern petroleum engineer. These well-treating processes are well established today. However, in many cases achieved success ratios leave much to be desired. Analysis of job failures shows that all too frequently failure may be attributed to poor treating-fluid distribution. Failure to effectively divert treating fluids from thief zones results either in no treatment or poor treatment of the producing interval. Thief zones can result from any number of causes, a principal one being nonhomogeneous formations. Producing principal one being nonhomogeneous formations. Producing formations penetrated by oil and gas wells range from 3 to 3000 feet in thickness. As a rule these zones are profoundly inhomogeneous, discontinuous and variable in profoundly inhomogeneous, discontinuous and variable in permeability, sometimes from centimeter to centimeter. permeability, sometimes from centimeter to centimeter. Fluid flow surveys within wells have shown that production from and injection into permeable zones frequently occur in only 10% to 15% of the productive interval. Besides inhomogeneities, variable flow potentials can also be caused by damage to part of the formation. In view of what is known about formation and perforation damage, this is not too surprising. Productive formations, particularly sandstone formations, act essentially as filters. We know that filters become plugged with time, and we expect them to become plugged, it would appear reasonable to say that we should similarly expect formation rock to decrease in permeability as large volumes of crude oil and brine permeability as large volumes of crude oil and brine which carry solids are filtered through it into the wellbore.
Fundamental noise limits in broadband Raman amplifiers (2002)

We show that broadband discrete Raman amplifiers based on silica-germania will have a noise figure significantly greater than the quantum limit. We also present temperature measurements on a broadband distributed Raman amplifier using asymmetrically-spaced pumps.
Quantitative expression of protein markers of plasminogen activation system in prognosis of colorectal cancer (2003)

uPA and uPAR may be independent predictors of liver metastasis, patient overall survival and cancer-specific survival after resection of colorectal tumors.
Robust hash functions for digital watermarking (2002)

Digital watermarks have been proposed for authentication of both video data and still images and for integrity verification of visual multimedia. In such applications, the watermark has to depend on a secret key and on the original image. It is important that the dependence on the key be sensitive, while the dependence on the image be continuous (robust). Both requirements can be satisfied using special image digest functions that return the same bit-string for a whole class of images derived from an original image using common processing operations. It is further required that two completely different images produce completely different bit-strings. We discuss methods how such robust hash functions can be built. We also show how the hash bits has another application, the robust image digest can be used as a search index for an efficient image database search.
Atención a población en situación de desplazamiento y alternativas para la estabilización socioeconómica desde la generación de ingresos (2006)

El desplazamiento forzado se ha convertido en uno de los temas de mayor importancia y trascendencia en la última década para el gobierno nacional, los organismos internacionalesy los representantes de la sociedad civil. La violencia y el conflicto armado como focos contextuales en los que se desarrolla el desplazamiento forzado dejan entrever un fenómeno social cuyas orígenes, mucho más estructurales, contribuyen a la fragmentación progresiva de la sociedad y a su empobrecimiento continuo en medio de una transformación crítica. El presente artículo se muestra como un aporte a la comprensión de la magnitud del desplazamiento forzado en Colombia desde sus implicaciones psicosociales, políticas y económicas y las orientaciones sugeridas frente al desarrollo de las intervenciones sociales, sobre todo aquellas que pretenden estratégicamente apuntar al tan nombrado restablecimiento socioeconómico. Para ello, se pone sobre la mesa el tema de la incorporación del enfoque psicosocial para la comprensión de la problemática y un matiz necesario de toda respuesta frente a sus derechos como sociedad civil y aun estipulados en la ley.
Monoclonal murine anti‐dna antibody interacts with living mononuclear cells (1987)

A monoclonal mouse antibody, 4-B-5, that reacted with both single-stranded DNA (ssDNA) and double-stranded DNA showed direct reactivity and cell association with mouse thymocytes, as well as peripheral blood mononuclear cells. Absorption of 4-B-5 with peripheral blood mononuclear cells or with mouse thymocytes markedly reduced reactivity with both ssDNA and double-stranded DNA. However, treatment of mouse thymocytes or human T cells with DNase completely eliminated monoclonal anti-DNA reactivity with cells. The cellular reactivity was completely restored when monoclonal anti-DNA was incubated with DNase-treated cells in the presence of normal human serum. Normal human serum was found to contain 574 +/- 639 ng/ml of ssDNA. Coincubation or cell preincubation of mouse thymocytes with ssDNA produced a marked increase in 4-B-5 cell association. These findings indicate that mouse monoclonal anti-DNA can react with and can penetrate both mouse and human mononuclear cells, and that this reactivity may depend on the presence of cell membrane DNA on both types of target cells.
Efficient, high-performance algorithms for N-Best search (1990)

We present two efficient search algorithms for real-time spoken language systems. The first called the Word-Dependent N-Best algorithm is an improved algorithm for finding the top <i>N</i> sentence hypotheses. The new algorithm is shown to perform as well as the Exact Sentence-Dependent algorithm presented previously but with an order of magnitude less computation. The second algorithm is a fast match scheme for continuous speech recognition called the Forward-Backward Search. This algorithm, which is directly motivated by the Baum-Welch Forward-Backward training algorithm, has been shown to reduce the computation of a time-synchronous beam search by a factor of 40 with no additional search errors.
A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America (2010)

Although metagenomics has been previously employed for pathogen discovery, its cost and complexity have prevented its use as a practical front-line diagnostic for unknown infectious diseases. Here we demonstrate the utility of two metagenomics-based strategies, a pan-viral microarray (Virochip) and deep sequencing, for the identification and characterization of 2009 pandemic H1N1 influenza A virus. Using nasopharyngeal swabs collected during the earliest stages of the pandemic in Mexico, Canada, and the United States (n = 17), the Virochip was able to detect a novel virus most closely related to swine influenza viruses without a priori information. Deep sequencing yielded reads corresponding to 2009 H1N1 influenza in each sample (percentage of aligned sequences corresponding to 2009 H1N1 ranging from 0.0011% to 10.9%), with up to 97% coverage of the influenza genome in one sample. Detection of 2009 H1N1 by deep sequencing was possible even at titers near the limits of detection for specific RT-PCR, and the percentage of sequence reads was linearly correlated with virus titer. Deep sequencing also provided insights into the upper respiratory microbiota and host gene expression in response to 2009 H1N1 infection. An unbiased analysis combining sequence data from all 17 outbreak samples revealed that 90% of the 2009 H1N1 genome could be assembled de novo without the use of any reference sequence, including assembly of several near full-length genomic segments. These results indicate that a streamlined metagenomics detection strategy can potentially replace the multiple conventional diagnostic tests required to investigate an outbreak of a novel pathogen, and provide a blueprint for comprehensive diagnosis of unexplained acute illnesses or outbreaks in clinical and public health settings.
Molecular Minimal Residual Disease in Acute Myeloid Leukemia (2018)

Among patients with AML, the detection of molecular minimal residual disease during complete remission had significant independent prognostic value with respect to relapse and survival rates, but the detection of persistent mutations that are associated with clonal hematopoiesis did not have such prognostic value within a 4-year time frame. (Funded by the Queen Wilhelmina Fund Foundation of the Dutch Cancer Society and others.).
Type VI collagen of the intervertebral disc. Biochemical and electron-microscopic characterization of the native protein (1987)

The collagen framework of the intervertebral disc contains two major fibril-forming collagens, types I and II. Smaller amounts of other types of collagen are also present. On examination of the nature and distribution of these minor collagens within bovine disc tissue, type VI collagen was found to be unusually abundant. It accounted for about 20% of the total collagen in calf nucleus pulposus, and about 5% in the annulus fibrosus. It was discovered by serially digesting disc tissue with chondroitin ABC lyase and Streptomyces hyaluronidase that native covalent polymers of type VI collagen could be extracted. Electron micrographs of this material prepared by rotary shadowing revealed the characteristic dimensions of tetramers and double tetramers of type VI molecules, with their central rods and terminal globular domains. Molecular-sieve column chromatography on agarose under non-reducing non-denaturing conditions gave a series of protein peaks with molecular sizes equivalent to the tetramer, double tetramer and higher multimers. On SDS/polyacrylamide-gel electrophoresis after disulphide cleavage, these fractions of type VI collagen all showed a main band at Mr 140,000 and four lesser bands between Mr 180,000 and 240,000. On electrophoresis without disulphide cleavage in agarose/2.4% polyacrylamide only dimeric (six chains) and tetrameric (12 chains) forms of type VI molecules were present. The ability to extract all the type VI collagen of the tissue in 4 M-guanidinium chloride, and absence of aldehyde-mediated cross-linking residues on direct analysis, showed that, in contrast with most matrix collagens, type VI collagen does not function as a covalently cross-linked structural polymer.
A simple ultrasound approach for detection of recurrent proximal-vein thrombosis. (1993)

The serial ultrasound measurement of thrombus mass after an acute episode of DVT may allow the correct identification of patients who develop a recurrent proximal-vein thrombosis.