gebhart/patrepeval huggingface dataset:
A simple rule-based part of speech tagger (1992)

Automatic part of speech tagging is an area of natural language processing where statistical techniques have been more successful than rule-based methods. In this paper, we present a simple rule-based part of speech tagger which automatically acquires its rules and tags with accuracy comparable to stochastic taggers. The rule-based tagger has many advantages over these taggers, including: a vast reduction in stored information required, the perspicuity of a small set of meaningful rules, ease of finding and implementing improvements to the tagger, and better portability from one tag set, corpus genre or language to another. Perhaps the biggest contribution of this work is in demonstrating that the stochastic method is not the only viable method for part of speech tagging. The fact that a simple rule-based tagger that automatically learns its rules can perform so well should offer encouragement for researchers to further explore rule-based tagging, searching for a better and more expressive set of rule templates and other variations on the simple but effective theme described below.
[Development of single-tube multiplex real-time PCR for simultaneous detection of novel influenza A H1N1 and human seasonal influenza A H1N1 and H3N2 virus]. (2010)

In this study, we established a rapid and sensitive multiplex Real-time reverse transcription polymerase chain reaction (mrtRT-PCR) to simultaneously detect the novel human influenza A H1N1 virus, human seasonal influenza A H1N1 and H3N2. This assay had three pairs of primer to target the conserved regions of the HA gene for each of the HA types including novel H1N1, seasonal H1N1 and seasonal H3N2, and one pair of primer designed to detect the internal control-RnaseP gene. This assay was performed in one-step in one tube. To validate the specificity of the multiplex Real-time RT-PCR assay, different human influenza virus including human seasonal influenza A H1N1 and H3N2, human influenza B and reference A/California/07/2009 (H1N1) sw1 was tested. To evaluate the sensitivity of the assay, serial dilutions of RNA from in vitro transcription of the novel human influenza A H1N1 HA gene was tested. Finally this assay was evaluated with clinical samples from 54 fever patients diagnosed with novel influenza A H1N1 or seasonal H1/H3 or HB infection either by real-time PCR recommended by the WHO or HI assay by the National Influenza Center. Our results showed that the assay could achieve a sensitivity of 20 RNA copies of novel influenza A H1N1 with high specificity and could detect potential mixed co-infection. In conclusion, this multiplex real-time RT-PCR assay combines both rapidity and sensitivity for not only detecting the novel human influenza A H1N1 virus, but also monitoring the human seasonal influenza A H1N1 and H3N2 simultaneously.
Electrophoretic and serological characterization of the lipopolysaccharides of Legionella pneumophila (1986)

Lipopolysaccharide (LPS) is a major constituent of the outer membrane of gram-negative bacteria. We used sodium dodecyl sulfate-polyacrylamide gel electrophoresis of proteinase-K-digested cell lysates to provide preliminary data on the LPS chemotypes for 20 strains of Legionella pneumophila (serogroups 1 to 8). The profiles of all strains except Chicago 2 (serogroup 6) were similar in the number, spacing, and size distribution of the bands visualized on silver-stained gels and were indicative of smooth LPS. However, compared with the bands from Salmonella minnesota smooth LPS, their banding pattern was much tighter, with three to four legionella bands for every salmonella band. The proteinase K digest of Chicago 2 was unique in that only two widely separated silver-stained bands were seen. LPS profiles of 10 serogroup 1 strains were identical, and the profile of Knoxville 1 was not altered by extensive in vitro passage. We used immunoblotting to investigate the serological specificities of the LPSs. When a rabbit antiserum prepared against a serogroup 1 strain was used to probe nitrocellulose sheets that bound LPS from strains belonging to eight different serogroups, it recognized only the LPS from the homologous serogroup. Similar results were observed with serogroup 2, 4, and 6 antisera. Our data indicate that L. pneumophila has a smooth-type LPS with an unusual banding pattern and that it is a serogroup-specific antigen.
Prediction of software reliability: a comparison between regression and neural network non-parametric models (2002)

In this paper, neural networks have been proposed as an alternative technique to build software reliability growth models. A feedforward neural network was used to predict the number of faults initially resident in a program at the beginning of a test/debug process. To evaluate the predictive capability of the developed model, data sets from various projects were used. A comparison between regression parametric models and neural network models is provided.
Emerging Role of Nanomaterials in Circulating Tumor Cell Isolation and Analysis (2014)

Circulating tumor cells (CTCs) are low frequency cells found in the bloodstream after having been shed from a primary tumor. These cells are research targets because of the information they may potentially provide about both an individual cancer as well as the mechanisms through which cancer spreads in the process of metastasis. Established technologies exist for CTC isolation, but the recent progress and future of this field lie in nanomaterials. In this review, we provide perspective into historical CTC capture as well as current research being conducted, emphasizing the significance of the materials being used to fabricate these devices. The modern investigation into CTCs initially featured techniques that have since been commercialized. A major innovation in the field was the development of a microfluidic capture device, first fabricated in silicon and followed up with glass and thermopolymer devices. We then specifically highlight the technologies incorporating magnetic nanoparticles, carbon nanotubes, nanowires, nanopillars, nanofibers, and nanoroughened surfaces, graphene oxide and their fabrication methods. The nanoscale provides a new set of tools that has the potential to overcome current limitations associated with CTC capture and analysis. We believe the current trajectory of the field is in the direction of nanomaterials, allowing the improvements necessary to further CTC research.
A fast algorithm for gamma evaluation in 3D (2007)

The gamma-evaluation method is a tool by which dose distributions can be compared in a quantitative manner combining dose-difference and distance-to-agreement criteria. Since its introduction, the gamma evaluation has been used in many studies and is on the verge of becoming the preferred dose distribution comparison method, particularly for intensity-modulated radiation therapy (IMRT) verification. One major disadvantage, however, is its long computation time, which especially applies to the comparison of three-dimensional (3D) dose distributions. We present a fast algorithm for a full 3D gamma evaluation at high resolution. Both the reference and evaluated dose distributions are first resampled on the same grid. For each point of the reference dose distribution, the algorithm searches for the best point of agreement according to the gamma method in the evaluated dose distribution, which can be done at a subvoxel resolution. Speed, computer memory efficiency, and high spatial resolution are achieved by searching around each reference point with increasing distance in a sphere, which has a radius of a chosen maximum search distance and is interpolated "on-the-fly" at a chosen sample step size. The smaller the sample step size and the larger the differences between the dose distributions, the longer the gamma evaluation takes. With decreasing sample step size, statistical measures of the 3D gamma distribution converge. Two clinical examples were investigated using 3% of the prescribed dose as dose-difference and 0.3 cm as distance-to-agreement criteria. For 0.2 cm grid spacing, the change in gamma indices was negligible below a sample step size of 0.02 cm. Comparing the full 3D gamma evaluation and slice-by-slice 2D gamma evaluations ("2.5D") for these clinical examples, the gamma indices improved by searching in full 3D space, with the average gamma index decreasing by at least 8%.
Prognosis in carcinoma of the urinary bladder based upon tissue blood group abh and Thomsen-Friedenreich antigen status and karyotype of the initial tumor. (1983)

Several markers of initial bladder carcinomas described recently may be clinically significant predictors of biological behavior of future recurrences. Comparison of the marker systems and assessment of the value of using multiple markers have been difficult, because the various markers have been studied in different patients. In this study, we compared four markers [chromosome mode, marker chromosomes, and expression of the ABH "blood group" antigens and the Thomsen-Friedenreich antigen (using immunoperoxidase or lectin immunoperoxidase methods)] in 39 patients presenting initially with low-stage bladder carcinoma and followed 3 to 11 years or until deep muscle invasion occurred. Each of the markers was significantly related to subsequent recurrences with deep muscle invasion, and each marker system was able to identify those patients with a very low risk of subsequent invasion. For detection of a subpopulation of patients with Grade II carcinomas who were at high risk for development of subsequent invasion, combinations of markers, especially hyperdiploidy and abnormal expression of the Thomsen-Friedenreich antigen, were significantly more effective than any single marker system.
Electron source brightness and degeneracy from Fresnel fringes in field emission point projection microscopy (1994)

Fresnel edge fringes observed in a lensless point projection field-emission electron microscope operating at 90 eV have been studied and found to be formally equivalent to the fringes observed in transmission electron microscopy (TEM) under weak scattering conditions at the edge of an opaque object. The tip-to-spectrum distance z1 plays the role of the objective lens defocus setting Δf in conventional TEM. The image magnification, effective source size, transverse coherence width, instrumental resolution, and source brightness are all obtained from an analysis of the fringe spacings and intensity. The quantum mechanical upper limit on source brightness, as well as relationships among beam brightness, coherence parameters, and degeneracy, are discussed, and the degeneracy measured from experimental Fresnel fringes.
The Min DNA inversion enzyme of plasmid p15B of Escherichia coli 15T−: a new member of the Din family of site‐specific recombinases (1990)

Plasmid p15B is a bacteriophage P1-related resident of Escherichia coli 15T-. Both genomes contain a segment in which DNA inversion occurs, although this part of their genomes is not identical. This DNA segment of p15B was cloned in a multicopy vector plasmid. Like its parent, the resulting plasmid, pAW800, undergoes complex multiple DNA inversions: this DNA inversion system is therefore called Min. The min gene, which codes for the p15B Min DNA invertase, can complement the P1 cin recombinase gene. The Min inversion system is thus a new member of the Din family of site-specific recombinases to which Cin belongs. The DNA sequence of the min gene revealed that Min is most closely related to the Pin recombinase of the e14 defective viral element on the E. coli K12 chromosome. Like other members of the Din family, the min gene contains a recombinational enhancer element which stimulates site-specific DNA inversion 300-fold.
Photo-Generation of Linearly Polymerized Liquid Crystal Aligning Layers Comprising Novel, Integrated Optically Patterned Retarders and Color Filters (1995)

For the first time photo cross-linking of linearly polymerizable polymers (LPPs) is shown to induce uniaxial planar alignment in adjacent liquid crystal polymer (LCP)-layers on single substrates. Ways and novel materials allowing integration of LPP-aligning layers with optical retarders in patterned, hybrid LPP-LCP-configurations with freely adjustable optical axes are presented. The novel multifunctional, anisotropic photopolymer configurations are shown to render in-situ optical retarders and polarization interference filters for black-white and color liquid crystal displays (LCDs) feasible. The molecular mechanisms inducing the anisotropic film properties and their thermal and optical stabilities are outlined. The photo-patternable, high resolution hybrid configurations are shown to exhibit excellent thermal and light stability.
Spontaneous Repair of Superficial Defects in Articular Cartilage in a Fetal Lamb Model* (1998)

A fetal lamb model was developed to investigate the capacity of fetal articular cartilage for repair after the creation of a superficial defect. Superficial defects, 100 micrometers deep, were made in the articular cartilage of the trochlear groove in the distal aspect of the femur in eighteen fetal lambs that were halfway through the 145-day gestational period; the contralateral limb was used as a sham control. The wounds were allowed to heal in utero for three, seven, fourteen, twenty-one, or twenty-eight days. Seven days after the injury, the defects were filled with a hypocellular matrix, which stained lightly with safranin O. At twenty-eight days, the staining of the matrix was similar to that of the sham controls and the chondrocyte density and the architectural arrangement of the cell layers had been restored. An inflammatory response was not elicited, and no fibrous scar tissue was observed.
Targeted Radiofrequency Therapy for Training Induced Muscle Fatigue - Effective or Not? (2016)

Background:&nbsp;Training induced muscle fatigue (hereinafter also referred as TIMF) is leading to unwanted consequences among sportsmen and actively sporting people such as decreased muscle strength and additional painful discomfort and mobility issues. The knowledge about the mechanisms of influencing the fatigue induced processes in muscle tissue is not comprehensive. The conventional manual techniques, cold patches and conventional physiotherapy have some effect in improving these conditions, however, finding effective methods to influence these consequences appears beneficial in sports medicine. Such method could be Radiofrequency therapy up to 0.5 MHz, known as Targeted Radiofrequency Therapy (hereinafter also referred as TR-Therapy). Aim of this self-controlled study is to evaluate the effect of the TR-Therapy for over-exertion management including the effect on decreased muscle strength, limited range ofmotion and possible painful discomfort.Materials:&nbsp;7 healthy and actively sporting participants underwent through 2 stages (Active stage – including overexertion of the forearm flexors and subsequent TR-Therapy session; and Control stage - including overexertion of the forearm flexors and subsequent resting period). Data for muscle strength in kg, active Range of Motion (ROM) in (º) and Pain and discomfort perception by 10 point Visual Analog Scale (VAS) were obtained and evaluated.Results:&nbsp;31% increase in the muscle strength during the active stage was observed and respectively 12% during the control stage, with level of significance p&lt;0.05. ROM and pain and discomfort perception data did not show statistically significant results (p&gt;0.05).Conclusions:&nbsp;The results of this study suggest TR-Therapy as effective solution for muscle strength restoration after TIMF.
Affine 3-D reconstruction from two projective images of independently translating planes (2002)

Consider two views of a multi-body scene consisting of k planar bodies moving in pure translation one relative to the other. We show that the fundamental matrices, one per body, live in a 3-dimensional subspace, which when represented as a step-3 extensor is the common transversal on the collection of extensors defined by the homograph matrices H/sub 1/,...,H/sub k/ of the moving planes. We show that as much as five bodies are necessary for recovering the common transversal from the homograph matrices, from which we show how to recover the fundamental matrices and the affine calibration between the two cameras.
Erythromycin series. XII. Antibacterial in vitro evaluation of 10-dihydro-10-deoxo-11-azaerythromycin A: Synthesis and structure-activity relationship of its acyl derivatives. (1987)

Antibacterial in vitro evaluation of 10-dihydro-10-deoxo-11-azaerythromycin A (5), the new 15-membered semi-synthetic macrolide antibiotic with nitrogen as additional atom in the aglycone ring of erythromycin A (1), was reported. Although amine (5) and its 13,14-cyclic carbonate (14) were less active than 1 against erythromycin-sensitive Staphylococcus aureus strains they showed advantageous properties against Gram-negative test organisms and clinical isolates. Also, a large number of acyl derivatives of 5 were synthesized and evaluated. N-11 monoacyl compounds exhibited 2 to 50 times lower in vitro antibacterial efficacy than the parent amine (5).
Review: Semiconductor Piezoresistance for Microsystems (2009)

Piezoresistive sensors are among the earliest micromachined silicon devices. The need for smaller, less expensive, higher performance sensors helped drive early micromachining technology, a precursor to microsystems or microelectromechanical systems (MEMS). The effect of stress on doped silicon and germanium has been known since the work of Smith at Bell Laboratories in 1954. Since then, researchers have extensively reported on microscale, piezoresistive strain gauges, pressure sensors, accelerometers, and cantilever force/displacement sensors, including many commercially successful devices. In this paper, we review the history of piezoresistance, its physics and related fabrication techniques. We also discuss electrical noise in piezoresistors, device examples and design considerations, and alternative materials. This paper provides a comprehensive overview of integrated piezoresistor technology with an introduction to the physics of piezoresistivity, process and material selection and design guidance useful to researchers and device engineers.
Handbook of Animal Models in Transplantation Research (2024)

Handbook of Animal Models in Transplantation Research is a new surgical handbook that provides detailed information concerning the transplantation of a variety of tissues in experimental animals. The text provides a practical guide for experienced investigators to develop new surgical transplantation models for application in a laboratory setting. Each chapter gives consistent descriptions of the anatomical considerations, the surgical model, and potential applications of the procedure. The organ systems covered include the heart and/or lung, liver, small bowel, kidneys, and bone marrow. The species selected for representation of each experimental model is based upon the usefulness and frequency of the model for studies in transplantation research. This book is important for all experimental surgeons, transplantation biologists, and students of surgical research.
Splicing of many human genes involves sites embedded within introns (2015)

The conventional model for splicing involves excision of each intron in one piece; we demonstrate this inaccurately describes splicing in many human genes. First, after switching on transcription of SAMD4A, a gene with a 134 kb-long first intron, splicing joins the 3' end of exon 1 to successive points within intron 1 well before the acceptor site at exon 2 is made. Second, genome-wide analysis shows that >60% of active genes yield products generated by such intermediate intron splicing. These products are present at ∼15% the levels of primary transcripts, are encoded by conserved sequences similar to those found at canonical acceptors, and marked by distinctive structural and epigenetic features. Finally, using targeted genome editing, we demonstrate that inhibiting the formation of these splicing intermediates affects efficient exon-exon splicing. These findings greatly expand the functional and regulatory complexity of the human transcriptome.
Epigenetic variation in Arabidopsis disease resistance (2002)

Plant pathogen resistance is mediated by a large repertoire of resistance (R) genes, which are often clustered in the genome and show a high degree of genetic variation. Here, we show that an Arabidopsis thaliana R-gene cluster is also subject to epigenetic variation. We describe a heritable but metastable epigenetic variant bal that overexpresses the R-like gene At4g16890 from a gene cluster on Chromosome 4. The bal variant and Arabidopsis transgenics overexpressing the At4g16890 gene are dwarfed and constitutively activate the salicylic acid (SA)-dependent defense response pathway. Overexpression of a related R-like gene also occurs in the ssi1 (suppressor of SA insensitivity 1) background, suggesting that ssi1 is mechanistically related to bal.
Trophic factors for cardiac myocytes. (1990)

During early neonatal myocardial growth, cardiac myocytes undergo a terminal differentiation stage after which cellular proliferation no longer occurs. Subsequent growth occurs by means of enlargement/hypertrophy of the existing cells. In an effort to dissect the molecular mechanisms underlying myocardial hypertrophy, a cell culture model of cardiac hypertrophy was developed in our laboratory. In this model, neonatal rat heart muscle cells respond to alpha 1-adrenergic receptor stimulation with an increase in cell size, total protein and the cellular contents of several messenger (m)RNA encoding fetal/neonatal contractile protein isoforms, and also that encoding the proto-oncogene c-myc. Similar changes in gene expression are seen in pressure-load hypertrophy in vivo. Recent observations on the production of peptide growth factors by the myocardium suggest an additional role of cell-cell interaction in cardiac growth and development. Some of the growth factors which have been found in normal myocardium include platelet-derived growth factor B chain, fibroblast growth factor (both acidic and basic), transforming growth factor beta, insulin-like growth factor-1 and insulin-like growth factor-2, and nerve growth factor. We recently identified a heparin-binding growth factor produced by cardiac non-myocytes in culture, which acts in a dose-dependent fashion to produce hypertrophy of cardiac muscle cells in culture. Preliminary work suggests that this is dissimilar from previously identified growth factors. Furthermore, the quantitative response of the cardiac myocytes to our growth factor exceeds that seen for other factors. Further work is necessary to ascertain how these factors and the alpha 1-adrenergic system interact to produce the different clinical forms of myocardial hypertrophy.